Genome annotation with prokka

Now that we have some extra information about our bins, we can continue to analyse the high-quality bins. The final CheckM results will give you a good overview of the bins with low contamination and high completeness and show the bin's lowest taxonomic rank. Pick a bin that you think is interesting to study further. Alternatively, you may also make a loop to annotate multiple bins.

With this selected bin(s), we are going to do genome annotation. Whole-genome annotation is the process of identifying features of interest in a set of genomic DNA sequences and labelling them with useful information. Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.

[DO:] make a directory for the prokka output:

mkdir data/annotation

[DO:] read the prokka help page Remember to look for the usage line.

prokka -h

Option h is ambiguous (help, hmms)
Name:
  Prokka 1.13 by Torsten Seemann <torsten.seemann@gmail.com>
Synopsis:
  rapid bacterial genome annotation
Usage:
  prokka [options] <contigs.fasta>
General:
  --help            This help
  --version         Print version and exit
  --docs            Show full manual/documentation
  --citation        Print citation for referencing Prokka
  --quiet           No screen output (default OFF)
  --debug           Debug mode: keep all temporary files (default OFF)
Setup:
  --listdb          List all configured databases
  --setupdb         Index all installed databases
  --cleandb         Remove all database indices
  --depends         List all software dependencies
Outputs:
  --outdir [X]      Output folder [auto] (default '')
  --force           Force overwriting existing output folder (default OFF)
  --prefix [X]      Filename output prefix [auto] (default '')
  --addgenes        Add 'gene' features for each 'CDS' feature (default OFF)
  --addmrna         Add 'mRNA' features for each 'CDS' feature (default OFF)
  --locustag [X]    Locus tag prefix [auto] (default '')
  --increment [N]   Locus tag counter increment (default '1')
  --gffver [N]      GFF version (default '3')
  --compliant       Force Genbank/ENA/DDJB compliance: --addgenes --mincontiglen 200 --centre XXX (default OFF)
  --centre [X]      Sequencing centre ID. (default '')
  --accver [N]      Version to put in Genbank file (default '1')
Organism details:
  --genus [X]       Genus name (default 'Genus')
  --species [X]     Species name (default 'species')
  --strain [X]      Strain name (default 'strain')
  --plasmid [X]     Plasmid name or identifier (default '')
Annotations:
  --kingdom [X]     Annotation mode: Archaea|Bacteria|Mitochondria|Viruses (default 'Bacteria')
  --gcode [N]       Genetic code / Translation table (set if --kingdom is set) (default '0')
  --gram [X]        Gram: -/neg +/pos (default '')
  --usegenus        Use genus-specific BLAST databases (needs --genus) (default OFF)
  --proteins [X]    FASTA or GBK file to use as 1st priority (default '')
  --hmms [X]        Trusted HMM to first annotate from (default '')
  --metagenome      Improve gene predictions for highly fragmented genomes (default OFF)
  --rawproduct      Do not clean up /product annotation (default OFF)
  --cdsrnaolap      Allow [tr]RNA to overlap CDS (default OFF)
Computation:
  --cpus [N]        Number of CPUs to use [0=all] (default '8')
  --fast            Fast mode - only use basic BLASTP databases (default OFF)
  --noanno          For CDS just set /product="unannotated protein" (default OFF)
  --mincontiglen [N] Minimum contig size [NCBI needs 200] (default '1')
  --evalue [n.n]    Similarity e-value cut-off (default '1e-06')
  --rfam            Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (default '0')
  --norrna          Don't run rRNA search (default OFF)
  --notrna          Don't run tRNA search (default OFF)
  --rnammer         Prefer RNAmmer over Barrnap for rRNA prediction (default OFF)
(metagenomics_practical) 

Use the options --centre X --compliant to stop prokkas complaints about ugly contig names.

[DO:] run prokka: This may take a while.

prokka data/bins/bin.1.fa --outdir data/annotation/bin1  --cpus 1 --centre X --compliant

[16:34:40] This is prokka 1.13
[16:34:40] Written by Torsten Seemann <torsten.seemann@gmail.com>
[16:34:40] Homepage is https://github.com/tseemann/prokka
[16:34:40] Local time is Tue Mar 22 16:34:40 2022
[16:34:40] You are laura
[16:34:40] Operating system is linux
[16:34:40] You have BioPerl 1.007002
[16:34:40] System has 4 cores.
[16:34:40] Will use maximum of 1 cores.
[16:34:40] Annotating as >>> Bacteria <<<
[16:34:40] Generating locus_tag from 'data/bins/bin.1.fa' contents.
[16:34:40] Setting --locustag HFHIMAGJ from MD5 1f126a0339e636dd81db632fa03976c5
[16:34:40] Enabling options to ensure Genbank/ENA/DDJB submission compliance.
[16:34:40] Creating new output folder: data/annotation/bin1
[16:34:40] Running: mkdir -p data\/annotation\/bin1
[16:34:40] Using filename prefix: PROKKA_03222022.XXX
[16:34:40] Setting HMMER_NCPU=1
[16:34:40] Writing log to: data/annotation/bin1/PROKKA_03222022.log
[16:34:40] Command: /opt/miniconda3/envs/metagenomics_practical/bin/prokka data/bins/bin.1.fa --outdir data/annotation/bin1 --cpus 1 --centre X --compliant
[16:34:40] Appending to PATH: /opt/miniconda3/envs/metagenomics_practical/bin
[16:34:40] Looking for 'aragorn' - found /opt/miniconda3/envs/metagenomics_practical/bin/aragorn
[16:34:40] Determined aragorn version is 1.2
[16:34:40] Looking for 'barrnap' - found /opt/miniconda3/envs/metagenomics_practical/bin/barrnap
[16:34:40] Determined barrnap version is 0.9
[16:34:40] Looking for 'blastp' - found /opt/miniconda3/envs/metagenomics_practical/bin/blastp
[16:34:40] Determined blastp version is 2.9
[16:34:40] Looking for 'cmpress' - found /opt/miniconda3/envs/metagenomics_practical/bin/cmpress
[16:34:40] Determined cmpress version is 1.1
[16:34:40] Looking for 'cmscan' - found /opt/miniconda3/envs/metagenomics_practical/bin/cmscan
[16:34:40] Determined cmscan version is 1.1
[16:34:40] Looking for 'egrep' - found /bin/egrep
[16:34:40] Looking for 'find' - found /usr/bin/find
[16:34:40] Looking for 'grep' - found /bin/grep
[16:34:40] Looking for 'hmmpress' - found /opt/miniconda3/envs/metagenomics_practical/bin/hmmpress
[16:34:40] Determined hmmpress version is 3.3
[16:34:40] Looking for 'hmmscan' - found /opt/miniconda3/envs/metagenomics_practical/bin/hmmscan
[16:34:40] Determined hmmscan version is 3.3
[16:34:40] Looking for 'java' - found /opt/miniconda3/envs/metagenomics_practical/bin/java
[16:34:40] Looking for 'less' - found /usr/bin/less
[16:34:40] Looking for 'makeblastdb' - found /opt/miniconda3/envs/metagenomics_practical/bin/makeblastdb
[16:34:40] Determined makeblastdb version is 2.9
[16:34:40] Looking for 'minced' - found /opt/miniconda3/envs/metagenomics_practical/bin/minced
[16:34:41] Determined minced version is 4.2
[16:34:41] Looking for 'parallel' - found /opt/miniconda3/envs/metagenomics_practical/bin/parallel
[16:34:41] Determined parallel version is 20160622
[16:34:41] Looking for 'prodigal' - found /opt/miniconda3/envs/metagenomics_practical/bin/prodigal
[16:34:41] Determined prodigal version is 2.6
[16:34:41] Looking for 'prokka-genbank_to_fasta_db' - found /opt/miniconda3/envs/metagenomics_practical/bin/prokka-genbank_to_fasta_db
[16:34:41] Looking for 'sed' - found /bin/sed
[16:34:41] Looking for 'tbl2asn' - found /opt/miniconda3/envs/metagenomics_practical/bin/tbl2asn
[16:34:41] Determined tbl2asn version is 25.8
[16:34:41] Using genetic code table 11.
[16:34:41] Loading and checking input file: data/bins/bin.1.fa
[16:34:41] Wrote 37 contigs totalling 4425020 bp.
[16:34:41] Predicting tRNAs and tmRNAs
[16:34:41] Running: aragorn -l -gc11  -w data\/annotation\/bin1\/PROKKA_03222022\.fna
[16:34:44] 1 tRNA-Ser [31831,31923] 35 (gct)
[16:34:44] 2 tRNA-Leu [59288,59374] 35 (tag)
[16:34:44] 3 tRNA-Gly [65460,65535] 34 (gcc)
[16:34:44] 4 tRNA-Cys [65630,65703] 33 (gca)
[16:34:44] 5 tRNA-Leu [65763,65854] 35 (taa)
[16:34:44] 6 tRNA-Val [281855,281929] 33 (gac)
[16:34:44] 7 tRNA-Leu c[294270,294354] 35 (cag)
[16:34:44] 8 tRNA-Trp c[379468,379558] 31 (cca)
[16:34:44] 9 tRNA-Asn c[434319,434394] 34 (gtt)
[16:34:44] 10 tRNA-Pro [523818,523894] 35 (tgg)
[16:34:44] 11 tRNA-Arg [568516,568592] 35 (tct)
[16:34:44] 12 tRNA-Lys [677102,677177] 34 (ttt)
[16:34:44] 1 tRNA-Leu c[30915,30999] 35 (gag)
[16:34:44] 2 tRNA-Phe [164483,164576] 35 (gaa)
[16:34:44] 3 tRNA-Ala [191584,191659] 34 (cgc)
[16:34:44] 4 tRNA-Lys [191686,191761] 34 (ctt)
[16:34:44] 5 tRNA-Pro [429715,429791] 35 (cgg)
[16:34:44] 1 tRNA-Phe [13659,13749] 33 (gaa)
[16:34:44] 2 tRNA-Pro [132617,132709] 33 (ggg)
[16:34:44] 3 tRNA-Pro c[138934,139010] 35 (ggg)
[16:34:44] 4 tRNA-His c[276316,276391] 34 (gtg)
[16:34:44] 5 tRNA-Val c[278421,278496] 34 (tac)
[16:34:44] tRNA [23282,23373] is a pseudo/wacky gene - skipping.
[16:34:44] 2 tRNA-Leu [88100,88184] 35 (caa)
[16:34:44] 1 tRNA-Arg c[32552,32627] 34 (cct)
[16:34:44] 2 tRNA-Met [68152,68228] 35 (cat)
[16:34:44] 1 tRNA-Thr c[173609,173684] 34 (tgt)
[16:34:44] 1 tRNA-Glu [77,152] 35 (ttc)
[16:34:44] 2 tRNA-Asp [223,299] 35 (gtc)
[16:34:44] 1 tRNA-Ser [20115,20205] 35 (cga)
[16:34:44] 2 tRNA-Thr c[108431,108506] 34 (cgt)
[16:34:44] 1 tmRNA [65777,66163] 91,123 ANDERFALAA*
[16:34:44] 1 tRNA-Ser c[6269,6359] 35 (gga)
[16:34:44] 1 tRNA-Arg [31943,32018] 34 (ccg)
[16:34:44] 2 tRNA-Met c[32532,32608] 35 (cat)
[16:34:44] 1 tRNA-Gln c[30163,30239] 35 (ttg)
[16:34:44] 2 tRNA-Met [41759,41835] 35 (cat)
[16:34:44] 3 tRNA-Arg [41895,41971] 35 (acg)
[16:34:44] 4 tRNA-Ser c[55396,55485] 35 (tga)
[16:34:44] 1 tRNA-Gly [27395,27468] 33 (ccc)
[16:34:44] 1 tRNA-Phe [7523,7598] 34 (gaa)
[16:34:44] 2 tRNA-Gly [7643,7718] 34 (gcc)
[16:34:44] 1 tRNA-Val [20761,20835] 33 (cac)
[16:34:44] 1 tRNA-Tyr [24455,24540] 35 (gta)
[16:34:44] 2 tRNA-Gly [24620,24693] 33 (tcc)
[16:34:44] 3 tRNA-Thr [24769,24843] 33 (ggt)
[16:34:44] Found 45 tRNAs
[16:34:44] Predicting Ribosomal RNAs
[16:34:44] Running Barrnap with 1 threads
[16:34:47] Found 0 rRNAs
[16:34:47] Skipping ncRNA search, enable with --rfam if desired.
[16:34:47] Total of 44 tRNA + rRNA features
[16:34:47] Searching for CRISPR repeats
[16:34:48] Found 0 CRISPRs
[16:34:48] Predicting coding sequences
[16:34:48] Contigs total 4425020 bp, so using single mode
[16:34:48] Running: prodigal -i data\/annotation\/bin1\/PROKKA_03222022\.fna -c -m -g 11 -p single -f sco -q
[16:34:53] Excluding CDS which overlaps existing RNA (tRNA) at gnl|X|HFHIMAGJ_1:377899..379779 on + strand
[16:34:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|X|HFHIMAGJ_2:164142..165458 on - strand
[16:34:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|X|HFHIMAGJ_3:13016..15067 on - strand
[16:34:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|X|HFHIMAGJ_3:131703..133025 on + strand
[16:34:57] Found 4294 CDS
[16:34:57] Connecting features back to sequences
[16:34:57] Not using genus-specific database. Try --usegenus to enable it.
[16:34:57] Annotating CDS, please be patient.
[16:34:57] Will use 1 CPUs for similarity searching.
[16:34:58] There are still 4294 unannotated CDS left (started with 4294)
[16:34:58] Will use blast to search against /opt/miniconda3/envs/metagenomics_practical/bin/../db/kingdom/Bacteria/sprot with 1 CPUs
[16:34:58] Running: cat data\/annotation\/bin1\/sprot\.faa | parallel --gnu --plain -j 1 --block 696633 --recstart '>' --pipe blastp -query - -db /opt/miniconda3/envs/metagenomics_practical/bin/../db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > data\/annotation\/bin1\/sprot\.blast 2> /dev/null
[16:39:41] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:41] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:41] Modify product: Uncharacterized protein HI_1163 => putative protein
[16:39:41] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:41] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:41] Modify product: Uncharacterized protein YisK => putative protein YisK
[16:39:41] Modify product: Putative universal stress protein SA1532 => Putative universal stress protein
[16:39:42] Modify product: UPF0394 inner membrane protein YeeE => hypothetical protein
[16:39:42] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:42] Modify product: Uncharacterized membrane protein Rv2637 => putative membrane protein
[16:39:42] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:42] Modify product: Uncharacterized protein YciH => putative protein YciH
[16:39:42] Modify product: Uncharacterized MFS-type transporter YhjX => putative MFS-type transporter YhjX
[16:39:42] Modify product: Uncharacterized NTE family protein Rv1063c => putative NTE family protein
[16:39:42] Modify product: Uncharacterized oxidoreductase SA2266 => putative oxidoreductase
[16:39:42] Modify product: RNA-binding protein HI_1333 => RNA-binding protein
[16:39:42] Modify product: Phosphate-specific transport system accessory protein PhoU homolog => Phosphate-specific transport system accessory protein PhoU 
[16:39:42] Modify product: Uncharacterized oxidoreductase YdgJ => putative oxidoreductase YdgJ
[16:39:42] Modify product: UPF0394 inner membrane protein YeeE => hypothetical protein
[16:39:42] Modify product: Uncharacterized N-acetyltransferase YsnE => putative N-acetyltransferase YsnE
[16:39:42] Modify product: Probable Fe(2+)-trafficking protein => putative Fe(2+)-trafficking protein
[16:39:42] Modify product: Uncharacterized HTH-type transcriptional regulator HI_0186 => putative HTH-type transcriptional regulator
[16:39:42] Modify product: Uncharacterized oxidoreductase SA2266 => putative oxidoreductase
[16:39:42] Modify product: Putative HTH-type transcriptional regulator Rv0890c => Putative HTH-type transcriptional regulator
[16:39:42] Modify product: Putative HTH-type transcriptional regulator Rv0890c => Putative HTH-type transcriptional regulator
[16:39:42] Modify product: Leu/Ile/Val-binding protein homolog 3 => Leu/Ile/Val-binding protein 
[16:39:42] Modify product: Uncharacterized protein PA3435 => putative protein
[16:39:42] Modify product: Probable L-asparaginase => putative L-asparaginase
[16:39:42] Modify product: UPF0434 protein NMA0874 => hypothetical protein
[16:39:42] Modify product: Probable sulfite/organosulfonate exporter TauE => putative sulfite/organosulfonate exporter TauE
[16:39:42] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:42] Modify product: Uncharacterized protein YisK => putative protein YisK
[16:39:42] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:42] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:42] Modify product: Uncharacterized oxidoreductase SA2266 => putative oxidoreductase
[16:39:42] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[16:39:42] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:42] Modify product: UPF0311 protein RPA1785 => hypothetical protein
[16:39:42] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:42] Modify product: Probable formate transporter 1 => putative formate transporter 1
[16:39:42] Modify product: Stringent starvation protein A homolog => Stringent starvation protein A 
[16:39:42] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:42] Modify product: Purine-binding protein BAB2_0673 => Purine-binding protein
[16:39:42] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS
[16:39:42] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein
[16:39:42] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein
[16:39:42] Modify product: Probable transcriptional regulatory protein pdtaR => putative transcriptional regulatory protein pdtaR
[16:39:42] Modify product: Uncharacterized protein YbiB => putative protein YbiB
[16:39:42] Modify product: Uncharacterized protein HI_0933 => putative protein
[16:39:42] Modify product: Uncharacterized protein YqeY => putative protein YqeY
[16:39:42] Modify product: UPF0307 protein PSPTO_4464 => hypothetical protein
[16:39:42] Modify product: Acetyltransferase Atu2258 => Acetyltransferase
[16:39:42] Modify product: UPF0073 inner membrane protein YqfA => hypothetical protein
[16:39:42] Modify product: Uncharacterized ABC transporter ATP-binding protein YadG => putative ABC transporter ATP-binding protein YadG
[16:39:42] Modify product: Probable diguanylate cyclase DgcE => putative diguanylate cyclase DgcE
[16:39:42] Modify product: Uncharacterized protein Rv1364c => putative protein
[16:39:42] Modify product: Putative short-chain type dehydrogenase/reductase Rv0148 => Putative short-chain type dehydrogenase/reductase
[16:39:42] Modify product: Probable xylitol oxidase => putative xylitol oxidase
[16:39:42] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:42] Modify product: UPF0353 protein Rv1481 => hypothetical protein
[16:39:42] Modify product: Uncharacterized protein Rv2307c => putative protein
[16:39:42] Modify product: DNA-binding protein VF_0530 => DNA-binding protein
[16:39:42] Modify product: Uncharacterized protein YqjD => putative protein YqjD
[16:39:42] Modify product: Uncharacterized protein Rv1367c => putative protein
[16:39:42] Modify product: NADH dehydrogenase-like protein SA0802 => NADH dehydrogenase-like protein
[16:39:42] Modify product: Cyclic nucleotide-gated potassium channel mll3241 => Cyclic nucleotide-gated potassium channel
[16:39:42] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:42] Modify product: Probable glutamine ABC transporter permease protein GlnM => putative glutamine ABC transporter permease protein GlnM
[16:39:42] Modify product: Probable fructoselysine utilization operon transcriptional repressor => putative fructoselysine utilization operon transcriptional repressor
[16:39:43] Modify product: UPF0053 inner membrane protein YgdQ => hypothetical protein
[16:39:43] Modify product: Uncharacterized lipoprotein YfhM => putative lipoprotein YfhM
[16:39:43] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:43] Modify product: Probable D,D-dipeptide transport ATP-binding protein DdpF => putative D,D-dipeptide transport ATP-binding protein DdpF
[16:39:43] Modify product: Probable D,D-dipeptide transport system permease protein DdpC => putative D,D-dipeptide transport system permease protein DdpC
[16:39:43] Modify product: UPF0246 protein YaaA => hypothetical protein
[16:39:43] Modify product: Probable lipoprotein YiaD => putative lipoprotein YiaD
[16:39:43] Modify product: Probable D,D-dipeptide transport ATP-binding protein DdpF => putative D,D-dipeptide transport ATP-binding protein DdpF
[16:39:43] Modify product: Monocarboxylate 2-oxoacid-binding periplasmic protein all3028 => Monocarboxylate 2-oxoacid-binding periplasmic protein
[16:39:43] Modify product: Probable phosphite transport system-binding protein HtxB => putative phosphite transport system-binding protein HtxB
[16:39:43] Modify product: Probable GTPase Rv1496 => putative GTPase
[16:39:43] Modify product: RutC family protein HI_0719 => RutC family protein
[16:39:43] Modify product: Probable enoyl-CoA hydratase echA12 => putative enoyl-CoA hydratase echA12
[16:39:43] Modify product: Putative quercetin 2,3-dioxygenase Rv0181c => Putative quercetin 2,3-dioxygenase
[16:39:43] Modify product: Probable hydrolase YcaC => putative hydrolase YcaC
[16:39:43] Modify product: Putative HTH-type transcriptional regulator Rv0890c => Putative HTH-type transcriptional regulator
[16:39:43] Modify product: Putative HTH-type transcriptional regulator Rv0890c => Putative HTH-type transcriptional regulator
[16:39:43] Modify product: Putative HTH-type transcriptional regulator Rv0890c => Putative HTH-type transcriptional regulator
[16:39:43] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:43] Modify product: Probable 5-dehydro-4-deoxyglucarate dehydratase => putative 5-dehydro-4-deoxyglucarate dehydratase
[16:39:43] Modify product: Uncharacterized protein YphB => putative protein YphB
[16:39:43] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:43] Modify product: Probable D-xylose utilization operon transcriptional repressor => putative D-xylose utilization operon transcriptional repressor
[16:39:43] Modify product: Probable lipoprotein YiaD => putative lipoprotein YiaD
[16:39:43] Modify product: Solute-binding protein Dde_0634 => Solute-binding protein
[16:39:43] Modify product: Uncharacterized inner membrane transporter YedA => putative inner membrane transporter YedA
[16:39:43] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:43] Modify product: UPF0394 membrane protein XF_0765 => hypothetical protein
[16:39:43] Modify product: UPF0394 membrane protein XF_0766 => hypothetical protein
[16:39:43] Modify product: Probable glutamine ABC transporter permease protein GlnM => putative glutamine ABC transporter permease protein GlnM
[16:39:43] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase
[16:39:43] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:43] Modify product: Probable TonB-dependent receptor BfrD => putative TonB-dependent receptor BfrD
[16:39:43] Modify product: PKHD-type hydroxylase Sbal_3634 => PKHD-type hydroxylase
[16:39:43] Modify product: UPF0337 protein YjbJ => hypothetical protein
[16:39:43] Modify product: Purine-binding protein BAB2_0673 => Purine-binding protein
[16:39:43] Modify product: Uncharacterized NTE family protein Rv1063c => putative NTE family protein
[16:39:43] Modify product: Uncharacterized oxidoreductase Rv1144 => putative oxidoreductase
[16:39:43] Modify product: Probable glutamine ABC transporter permease protein GlnM => putative glutamine ABC transporter permease protein GlnM
[16:39:43] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:43] Modify product: Monocarboxylate 2-oxoacid-binding periplasmic protein all3028 => Monocarboxylate 2-oxoacid-binding periplasmic protein
[16:39:43] Modify product: Uncharacterized protein YibN => putative protein YibN
[16:39:43] Modify product: Probable CtpA-like serine protease => putative CtpA-like serine protease
[16:39:43] Modify product: Uncharacterized protein Rv2568c => putative protein
[16:39:43] Modify product: Probable sulfate transporter Rv1739c => putative sulfate transporter
[16:39:43] Modify product: UPF0235 protein YggU => hypothetical protein
[16:39:43] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[16:39:43] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase
[16:39:43] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:43] Modify product: UPF0502 protein YceH => hypothetical protein
[16:39:43] Modify product: Uncharacterized metal-dependent hydrolase YjjV => putative metal-dependent hydrolase YjjV
[16:39:43] Modify product: Uncharacterized protein Rv1480 => putative protein
[16:39:43] Modify product: UPF0353 protein Rv1481 => hypothetical protein
[16:39:43] Modify product: Purine-binding protein BAB2_0673 => Purine-binding protein
[16:39:43] Modify product: Purine-binding protein BAB2_0673 => Purine-binding protein
[16:39:43] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:43] Modify product: Uncharacterized protein HI_1028 => putative protein
[16:39:43] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:43] Modify product: Putative thiamine biosynthesis protein HI_0357 => Putative thiamine biosynthesis protein
[16:39:43] Modify product: Probable enoyl-CoA hydratase 1 => putative enoyl-CoA hydratase 1
[16:39:43] Modify product: NAD(P)H-dependent FMN reductase PA1204 => NAD(P)H-dependent FMN reductase
[16:39:43] Modify product: UPF0301 protein SO_3346 => hypothetical protein
[16:39:43] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[16:39:43] Modify product: Probable diguanylate cyclase DgcC => putative diguanylate cyclase DgcC
[16:39:43] Modify product: Uncharacterized protein YcbX => putative protein YcbX
[16:39:43] Modify product: Probable thiol:disulfide interchange protein DsbC => putative thiol:disulfide interchange protein DsbC
[16:39:43] Modify product: Probable enoyl-CoA hydratase echA8 => putative enoyl-CoA hydratase echA8
[16:39:43] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:43] Modify product: Probable FKBP-type peptidyl-prolyl cis-trans isomerase => putative FKBP-type peptidyl-prolyl cis-trans isomerase
[16:39:43] Modify product: Uncharacterized protein YisK => putative protein YisK
[16:39:43] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:43] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:44] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:44] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:44] Modify product: Probable fatty acid methyltransferase Rv3720 => putative fatty acid methyltransferase
[16:39:44] Modify product: Uncharacterized protein HI_0131 => putative protein
[16:39:44] Modify product: Probable type II secretion system protein HxcR => putative type II secretion system protein HxcR
[16:39:44] Modify product: Uncharacterized protein HI_0131 => putative protein
[16:39:44] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:44] Modify product: Uncharacterized oxidoreductase YdgJ => putative oxidoreductase YdgJ
[16:39:44] Modify product: Uncharacterized protein Rv0906 => putative protein
[16:39:44] Modify product: UPF0250 protein YbeD => hypothetical protein
[16:39:44] Modify product: Uncharacterized protein HI_0131 => putative protein
[16:39:44] Modify product: Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit => putative Ni/Fe-hydrogenase 1 B-type cytochrome subunit
[16:39:44] Modify product: Peroxiredoxin sll1621 => Peroxiredoxin
[16:39:44] Modify product: Uncharacterized GST-like protein YibF => putative GST-like protein YibF
[16:39:44] Modify product: Uncharacterized protein YaeQ => putative protein YaeQ
[16:39:44] Modify product: UPF0053 inner membrane protein YoaE => hypothetical protein
[16:39:44] Modify product: Uncharacterized glycosyltransferase Rv0539 => putative glycosyltransferase
[16:39:44] Modify product: UPF0053 inner membrane protein YoaE => hypothetical protein
[16:39:44] Modify product: Uncharacterized protein YisK => putative protein YisK
[16:39:44] Modify product: Probable enoyl-CoA hydratase echA12 => putative enoyl-CoA hydratase echA12
[16:39:44] Modify product: Uncharacterized protein Rv0628c => putative protein
[16:39:44] Modify product: Purine-binding protein BAB2_0673 => Purine-binding protein
[16:39:44] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:44] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:44] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:44] Modify product: Putative glutamine amidotransferase Rv2859c => Putative glutamine amidotransferase
[16:39:44] Modify product: Uncharacterized protein HI_0131 => putative protein
[16:39:44] Modify product: Probable D-xylose utilization operon transcriptional repressor => putative D-xylose utilization operon transcriptional repressor
[16:39:44] Modify product: Purine-binding protein BAB2_0673 => Purine-binding protein
[16:39:44] Modify product: Putative quercetin 2,3-dioxygenase Rv0181c => Putative quercetin 2,3-dioxygenase
[16:39:44] Modify product: UPF0702 transmembrane protein YetF => hypothetical protein
[16:39:44] Modify product: Uncharacterized oxidoreductase Rv0945 => putative oxidoreductase
[16:39:44] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[16:39:44] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:44] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:44] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:44] Modify product: Leu/Ile/Val-binding protein homolog 3 => Leu/Ile/Val-binding protein 
[16:39:44] Modify product: Leu/Ile/Val-binding protein homolog 3 => Leu/Ile/Val-binding protein 
[16:39:44] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv2564 => putative ABC transporter ATP-binding protein
[16:39:44] Modify product: Uncharacterized protein YpbG => putative protein YpbG
[16:39:44] Modify product: UPF0225 protein YchJ => hypothetical protein
[16:39:44] Modify product: Uncharacterized GTP-binding protein YjiA => putative GTP-binding protein YjiA
[16:39:44] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein
[16:39:44] Modify product: Probable amino-acid permease protein YxeN => putative amino-acid permease protein YxeN
[16:39:44] Modify product: Probable xanthine dehydrogenase subunit C => putative xanthine dehydrogenase subunit C
[16:39:44] Modify product: Probable xanthine dehydrogenase subunit D => putative xanthine dehydrogenase subunit D
[16:39:44] Modify product: Probable xanthine dehydrogenase subunit E => putative xanthine dehydrogenase subunit E
[16:39:44] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:44] Modify product: Uncharacterized acyl-CoA thioester hydrolase HI_0827 => putative acyl-CoA thioester hydrolase
[16:39:44] Modify product: UPF0213 protein BH0048 => hypothetical protein
[16:39:44] Modify product: Uncharacterized HTH-type transcriptional regulator YybR => putative HTH-type transcriptional regulator YybR
[16:39:44] Modify product: UPF0176 protein lpg2838 => hypothetical protein
[16:39:44] Modify product: Probable phosphite transport system-binding protein PtxB => putative phosphite transport system-binding protein PtxB
[16:39:44] Modify product: Probable 2,4-dienoyl-CoA reductase => putative 2,4-dienoyl-CoA reductase
[16:39:44] Modify product: Probable ECF RNA polymerase sigma factor SigI => putative ECF RNA polymerase sigma factor SigI
[16:39:44] Modify product: UPF0126 inner membrane protein YicG => hypothetical protein
[16:39:44] Modify product: Uncharacterized NAD-dependent oxidoreductase MAP_4146 => putative NAD-dependent oxidoreductase
[16:39:44] Modify product: Probable 3-hydroxyacyl-CoA dehydrogenase => putative 3-hydroxyacyl-CoA dehydrogenase
[16:39:44] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase
[16:39:44] Modify product: Probable S-adenosylmethionine-dependent methyltransferase MSMEG_2350/MSMEI_2290 => putative S-adenosylmethionine-dependent methyltransferase/MSMEI_2290
[16:39:44] Modify product: Uncharacterized protein RP789 => putative protein RP789
[16:39:44] Modify product: Probable diacyglycerol O-acyltransferase tgs1 => putative diacyglycerol O-acyltransferase tgs1
[16:39:44] Modify product: Stringent starvation protein B homolog => Stringent starvation protein B 
[16:39:44] Modify product: Leu/Ile/Val-binding protein homolog 3 => Leu/Ile/Val-binding protein 
[16:39:44] Modify product: Probable enoyl-CoA hydratase echA8 => putative enoyl-CoA hydratase echA8
[16:39:44] Modify product: Probable bifunctional transcriptional activator/DNA repair enzyme AlkA => putative bifunctional transcriptional activator/DNA repair enzyme AlkA
[16:39:44] Modify product: Sulfurtransferase Alvin_2599 => Sulfurtransferase
[16:39:44] Modify product: Probable TonB-dependent receptor NMB0964 => putative TonB-dependent receptor
[16:39:44] Modify product: Uncharacterized protein YyaP => putative protein YyaP
[16:39:44] Modify product: Probable hydrolase YcaC => putative hydrolase YcaC
[16:39:44] Modify product: Probable copper-importing P-type ATPase A => putative copper-importing P-type ATPase A
[16:39:44] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:45] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase
[16:39:45] Modify product: Uncharacterized MFS-type transporter YhjX => putative MFS-type transporter YhjX
[16:39:45] Modify product: Probable 2-dehydro-3-deoxygalactonokinase DgoK1 => putative 2-dehydro-3-deoxygalactonokinase DgoK1
[16:39:45] Modify product: Probable D,D-dipeptide transport system permease protein DdpC => putative D,D-dipeptide transport system permease protein DdpC
[16:39:45] Modify product: Solute-binding protein Veis_3954 => Solute-binding protein
[16:39:45] Modify product: Uncharacterized aminopeptidase Rv1333 => putative aminopeptidase
[16:39:45] Modify product: Probable copper-importing P-type ATPase A => putative copper-importing P-type ATPase A
[16:39:45] Modify product: Uncharacterized protein Rv0906 => putative protein
[16:39:45] Modify product: Protease HtpX homolog => Protease HtpX 
[16:39:45] Modify product: Probable DNA endonuclease SmrA => putative DNA endonuclease SmrA
[16:39:45] Modify product: UPF0758 protein YsxA => hypothetical protein
[16:39:45] Modify product: Uncharacterized protein YciO => putative protein YciO
[16:39:45] Modify product: Uncharacterized protein Rv2575 => putative protein
[16:39:45] Modify product: Chemotaxis protein CheY homolog => Chemotaxis protein CheY 
[16:39:45] Modify product: UPF0053 inner membrane protein YtfL => hypothetical protein
[16:39:45] Modify product: Uncharacterized protein Rv2715 => putative protein
[16:39:45] Modify product: Probable glycerol-3-phosphate acyltransferase => putative glycerol-3-phosphate acyltransferase
[16:39:45] Modify product: UPF0234 protein HI_1034 => hypothetical protein
[16:39:45] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[16:39:45] Modify product: Uncharacterized MFS-type transporter YfcJ => putative MFS-type transporter YfcJ
[16:39:45] Modify product: Uncharacterized protein Rv2569c => putative protein
[16:39:45] Modify product: UPF0153 protein YeiW => hypothetical protein
[16:39:45] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
[16:39:45] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase
[16:39:45] Modify product: Putative esterase HI_1161 => Putative esterase
[16:39:45] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:45] Modify product: Outer membrane porin protein BP0840 => Outer membrane porin protein
[16:39:45] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:45] Modify product: UPF0173 metal-dependent hydrolase SA1529 => hypothetical protein
[16:39:45] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:45] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:45] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:45] Modify product: Probable tartrate dehydrogenase/decarboxylase TtuC' => putative tartrate dehydrogenase/decarboxylase TtuC'
[16:39:45] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:45] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:45] Modify product: Uncharacterized HTH-type transcriptional regulator Rv1985c => putative HTH-type transcriptional regulator
[16:39:45] Modify product: Putative phosphoribosyl transferase MT0597 => Putative phosphoribosyl transferase
[16:39:45] Modify product: Uncharacterized protein MT2089 => putative protein
[16:39:45] Modify product: Cyclic di-GMP phosphodiesterase PA4781 => Cyclic di-GMP phosphodiesterase
[16:39:45] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:45] Modify product: Uncharacterized NTE family protein Rv1063c => putative NTE family protein
[16:39:45] Modify product: Uncharacterized NTE family protein Rv2565 => putative NTE family protein
[16:39:45] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:45] Modify product: Uncharacterized protein YbaA => putative protein YbaA
[16:39:45] Modify product: Putative acyltransferase Rv0859 => Putative acyltransferase
[16:39:45] Modify product: UPF0070 protein HI_0370 => hypothetical protein
[16:39:45] Modify product: Segregation and condensation protein B homolog => Segregation and condensation protein B 
[16:39:45] Modify product: Probable ATP-dependent helicase DinG => putative ATP-dependent helicase DinG
[16:39:45] Modify product: Uncharacterized protein Rv2569c => putative protein
[16:39:45] Modify product: Uncharacterized protein Rv2567 => putative protein
[16:39:45] Modify product: Uncharacterized protein Rv2569c => putative protein
[16:39:45] Modify product: Uncharacterized oxidoreductase SA2266 => putative oxidoreductase
[16:39:45] Modify product: Uncharacterized protein NMB0928 => putative protein
[16:39:45] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:45] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:45] Modify product: Uncharacterized protein HI_1048 => putative protein
[16:39:45] Modify product: Uncharacterized protein Rv2307c => putative protein
[16:39:46] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein
[16:39:46] Modify product: Probable type II secretion system protein HxcR => putative type II secretion system protein HxcR
[16:39:46] Modify product: Putative transport protein Rv0205 => Putative transport protein
[16:39:46] Modify product: Probable phosphatase Rv3661 => putative phosphatase
[16:39:46] Modify product: Probable multidrug-efflux transporter Rv1258c => putative multidrug-efflux transporter
[16:39:46] Modify product: Probable xanthine dehydrogenase subunit A => putative xanthine dehydrogenase subunit A
[16:39:46] Modify product: UPF0337 protein PA4738 => hypothetical protein
[16:39:46] Modify product: Solute-binding protein Bamb_6123 => Solute-binding protein
[16:39:46] Modify product: Solute-binding protein Rfer_1840 => Solute-binding protein
[16:39:46] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase
[16:39:46] Modify product: UPF0761 membrane protein YihY => hypothetical protein
[16:39:46] Modify product: Probable 3-phenylpropionic acid transporter => putative 3-phenylpropionic acid transporter
[16:39:46] Modify product: Solute-binding protein Veis_3954 => Solute-binding protein
[16:39:46] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:46] Modify product: Probable D-xylose utilization operon transcriptional repressor => putative D-xylose utilization operon transcriptional repressor
[16:39:46] Modify product: Stringent starvation protein A homolog => Stringent starvation protein A 
[16:39:46] Modify product: Stress response UPF0229 protein YhbH => hypothetical protein
[16:39:46] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:46] Modify product: Probable 5-dehydro-4-deoxyglucarate dehydratase => putative 5-dehydro-4-deoxyglucarate dehydratase
[16:39:46] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:46] Modify product: Solute-binding protein Bpro_3107 => Solute-binding protein
[16:39:46] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:46] Modify product: Uncharacterized protein HI_0131 => putative protein
[16:39:46] Modify product: Uncharacterized protein HI_0131 => putative protein
[16:39:46] Modify product: Uncharacterized oxidoreductase Rv1144 => putative oxidoreductase
[16:39:46] Modify product: Leu/Ile/Val-binding protein homolog 3 => Leu/Ile/Val-binding protein 
[16:39:46] Modify product: Putative monooxygenase Rv1533 => Putative monooxygenase
[16:39:46] Modify product: Uncharacterized protein Rv2411c => putative protein
[16:39:46] Modify product: Uncharacterized protein PA3922 => putative protein
[16:39:46] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:46] Modify product: UPF0324 inner membrane protein YeiH => hypothetical protein
[16:39:46] Modify product: Probable L-galactonate transporter => putative L-galactonate transporter
[16:39:46] Modify product: Uncharacterized ABC transporter ATP-binding protein YejF => putative ABC transporter ATP-binding protein YejF
[16:39:46] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[16:39:46] Modify product: Acetyltransferase SACOL1063 => Acetyltransferase
[16:39:46] Modify product: Probable intracellular septation protein A => putative intracellular septation protein A
[16:39:46] Modify product: Probable parvulin-type peptidyl-prolyl cis-trans isomerase => putative parvulin-type peptidyl-prolyl cis-trans isomerase
[16:39:46] Modify product: Uncharacterized oxidoreductase YgfF => putative oxidoreductase YgfF
[16:39:46] Modify product: UPF0056 inner membrane protein MarC => hypothetical protein
[16:39:46] Modify product: Probable phospholipid import ATP-binding protein MlaF => putative phospholipid import ATP-binding protein MlaF
[16:39:46] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[16:39:46] Modify product: Probable membrane transporter protein YfcA => putative membrane transporter protein YfcA
[16:39:46] Modify product: Probable deferrochelatase/peroxidase YfeX => putative deferrochelatase/peroxidase YfeX
[16:39:46] Modify product: Probable multidrug resistance protein EmrY => putative multidrug resistance protein EmrY
[16:39:46] Modify product: Leu/Ile/Val-binding protein homolog 3 => Leu/Ile/Val-binding protein 
[16:39:46] Modify product: Probable D,D-dipeptide transport ATP-binding protein DdpF => putative D,D-dipeptide transport ATP-binding protein DdpF
[16:39:46] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:46] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:46] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:46] Modify product: Probable cystine transporter YijE => putative cystine transporter YijE
[16:39:46] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:46] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase
[16:39:46] Modify product: Uncharacterized protein YphB => putative protein YphB
[16:39:46] Modify product: SCO1 protein homolog => SCO1 protein 
[16:39:46] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:46] Modify product: Probable diguanylate cyclase DgcC => putative diguanylate cyclase DgcC
[16:39:46] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[16:39:46] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[16:39:46] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1281c => putative ABC transporter ATP-binding protein
[16:39:46] Modify product: UPF0701 protein HI_0467 => hypothetical protein
[16:39:46] Modify product: Cyclic di-GMP phosphodiesterase PA4781 => Cyclic di-GMP phosphodiesterase
[16:39:46] Modify product: UPF0176 protein lpg2838 => hypothetical protein
[16:39:46] Modify product: Putative quercetin 2,3-dioxygenase Rv0181c => Putative quercetin 2,3-dioxygenase
[16:39:46] Modify product: UPF0098 protein CT_736 => hypothetical protein
[16:39:46] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein
[16:39:46] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit B => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit B
[16:39:46] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit A => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit A
[16:39:47] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:47] Modify product: Uncharacterized protein Rv2913c => putative protein
[16:39:47] Modify product: Uncharacterized GMC-type oxidoreductase Rv0492c => putative GMC-type oxidoreductase
[16:39:47] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN
[16:39:47] Modify product: Co-chaperone protein HscB homolog => Co-chaperone protein HscB 
[16:39:47] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:47] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[16:39:47] Modify product: Uncharacterized protein MT3212 => putative protein
[16:39:47] Modify product: Probable hydrolase YcaC => putative hydrolase YcaC
[16:39:47] Modify product: Uncharacterized protein Rv2568c => putative protein
[16:39:47] Modify product: UPF0065 protein in clcB-clcD intergenic region => hypothetical protein
[16:39:47] Modify product: Uncharacterized ABC transporter ATP-binding protein YadG => putative ABC transporter ATP-binding protein YadG
[16:39:47] Modify product: Probable phospholipid-binding protein MlaC => putative phospholipid-binding protein MlaC
[16:39:47] Modify product: Probable phospholipid-binding lipoprotein MlaA => putative phospholipid-binding lipoprotein MlaA
[16:39:47] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[16:39:47] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[16:39:47] Modify product: Probable phospholipid import ATP-binding protein MlaF => putative phospholipid import ATP-binding protein MlaF
[16:39:47] Modify product: Probable peptidoglycan D,D-transpeptidase PenA => putative peptidoglycan D,D-transpeptidase PenA
[16:39:47] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW
[16:39:47] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase
[16:39:47] Modify product: GTP cyclohydrolase 1 type 2 homolog => GTP cyclohydrolase 1 type 2 
[16:39:47] Cleaned 358 /product names
[16:39:47] Deleting unwanted file: data/annotation/bin1/sprot.faa
[16:39:47] Deleting unwanted file: data/annotation/bin1/sprot.blast
[16:39:47] There are still 1430 unannotated CDS left (started with 4294)
[16:39:47] Will use hmmer3 to search against /opt/miniconda3/envs/metagenomics_practical/bin/../db/hmm/HAMAP.hmm with 1 CPUs
[16:39:47] Running: cat data\/annotation\/bin1\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 173344 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /opt/miniconda3/envs/metagenomics_practical/bin/../db/hmm/HAMAP.hmm /dev/stdin > data\/annotation\/bin1\/HAMAP\.hmm\.hmmer3 2> /dev/null
[16:40:27] Modify product: Uncharacterized Nudix hydrolase NudL => putative Nudix hydrolase NudL
[16:40:27] Cleaned 1 /product names
[16:40:27] Deleting unwanted file: data/annotation/bin1/HAMAP.hmm.faa
[16:40:27] Deleting unwanted file: data/annotation/bin1/HAMAP.hmm.hmmer3
[16:40:27] Labelling remaining 1338 proteins as 'hypothetical protein'
[16:40:27] Possible /pseudo '2-isopropylmalate synthase' at gnl|X|HFHIMAGJ_1 position 429143
[16:40:27] Possible /pseudo 'Putative aliphatic sulfonates-binding protein' at gnl|X|HFHIMAGJ_1 position 450886
[16:40:27] Possible /pseudo 'Putative aliphatic sulfonates-binding protein' at gnl|X|HFHIMAGJ_1 position 457008
[16:40:27] Possible /pseudo 'Putative aliphatic sulfonates-binding protein' at gnl|X|HFHIMAGJ_1 position 457987
[16:40:27] Possible /pseudo 'Putative HTH-type transcriptional regulator' at gnl|X|HFHIMAGJ_1 position 490964
[16:40:27] Possible /pseudo 'Riboflavin transport system permease protein RibX' at gnl|X|HFHIMAGJ_1 position 497782
[16:40:27] Possible /pseudo 'Isocitrate dehydrogenase [NADP]' at gnl|X|HFHIMAGJ_1 position 594202
[16:40:27] Possible /pseudo 'Alpha-keto acid-binding periplasmic protein TakP' at gnl|X|HFHIMAGJ_2 position 153845
[16:40:27] Possible /pseudo 'Alpha-keto acid-binding periplasmic protein TakP' at gnl|X|HFHIMAGJ_2 position 155058
[16:40:27] Possible /pseudo 'Putative HTH-type transcriptional regulator' at gnl|X|HFHIMAGJ_3 position 48146
[16:40:27] Possible /pseudo 'Short-chain-enoyl-CoA hydratase' at gnl|X|HFHIMAGJ_5 position 197926
[16:40:27] Possible /pseudo 'Heme/hemopexin-binding protein' at gnl|X|HFHIMAGJ_6 position 52625
[16:40:27] Possible /pseudo 'Lipid A biosynthesis lauroyltransferase' at gnl|X|HFHIMAGJ_7 position 30350
[16:40:27] Possible /pseudo 'L-cystine-binding protein FliY' at gnl|X|HFHIMAGJ_7 position 165912
[16:40:27] Possible /pseudo 'D-methionine-binding lipoprotein MetQ' at gnl|X|HFHIMAGJ_7 position 176506
[16:40:27] Possible /pseudo 'Dibenzothiophene desulfurization enzyme C' at gnl|X|HFHIMAGJ_7 position 180000
[16:40:27] Possible /pseudo 'Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein' at gnl|X|HFHIMAGJ_8 position 54470
[16:40:27] Possible /pseudo 'Type I secretion system ATP-binding protein PrsD' at gnl|X|HFHIMAGJ_8 position 133595
[16:40:27] Possible /pseudo 'Methylxanthine N1-demethylase NdmA' at gnl|X|HFHIMAGJ_9 position 79193
[16:40:27] Possible /pseudo 'A-type flagellin' at gnl|X|HFHIMAGJ_10 position 71977
[16:40:27] Possible /pseudo 'Cyanophycin synthetase' at gnl|X|HFHIMAGJ_11 position 25117
[16:40:27] Possible /pseudo 'Signal transduction histidine-protein kinase BarA' at gnl|X|HFHIMAGJ_12 position 68081
[16:40:27] Possible /pseudo 'Chromate transport protein' at gnl|X|HFHIMAGJ_12 position 100187
[16:40:27] Possible /pseudo 'putative protein' at gnl|X|HFHIMAGJ_13 position 10031
[16:40:27] Possible /pseudo 'Autoinducer 2 sensor kinase/phosphatase LuxQ' at gnl|X|HFHIMAGJ_16 position 4119
[16:40:27] Possible /pseudo 'CAI-1 autoinducer sensor kinase/phosphatase CqsS' at gnl|X|HFHIMAGJ_16 position 96763
[16:40:27] Possible /pseudo 'Biopolymer transport protein ExbD' at gnl|X|HFHIMAGJ_18 position 8843
[16:40:27] Possible /pseudo 'Homoprotocatechuate catabolism bifunctional isomerase/decarboxylase' at gnl|X|HFHIMAGJ_18 position 45718
[16:40:27] Possible /pseudo 'putative zinc protease' at gnl|X|HFHIMAGJ_19 position 14616
[16:40:27] Possible /pseudo 'Cytochrome c oxidase subunit 2' at gnl|X|HFHIMAGJ_20 position 28494
[16:40:27] Possible /pseudo 'Cytochrome c oxidase subunit 2' at gnl|X|HFHIMAGJ_20 position 28879
[16:40:27] Possible /pseudo 'Methyl-accepting chemotaxis protein I' at gnl|X|HFHIMAGJ_20 position 49736
[16:40:27] Found 1914 unique /gene codes.
[16:40:27] Fixed 6 duplicate /gene - cph1_1 cph1_2 cph1_3 cph1_4 cph1_5 cph1_6
[16:40:27] Fixed 5 duplicate /gene - gsiD_1 gsiD_2 gsiD_3 gsiD_4 gsiD_5
[16:40:27] Fixed 3 duplicate /gene - cpdA_1 cpdA_2 cpdA_3
[16:40:27] Fixed 3 duplicate /gene - paaG_1 paaG_2 paaG_3
[16:40:27] Fixed 3 duplicate /gene - trxA_1 trxA_2 trxA_3
[16:40:27] Fixed 2 duplicate /gene - yadH_1 yadH_2
[16:40:27] Fixed 5 duplicate /gene - ssuC_1 ssuC_2 ssuC_3 ssuC_4 ssuC_5
[16:40:27] Fixed 3 duplicate /gene - arcB_1 arcB_2 arcB_3
[16:40:27] Fixed 2 duplicate /gene - fmt_1 fmt_2
[16:40:27] Fixed 2 duplicate /gene - thiE_1 thiE_2
[16:40:27] Fixed 4 duplicate /gene - soxC_1 soxC_2 soxC_3 soxC_4
[16:40:27] Fixed 4 duplicate /gene - rhlE_1 rhlE_2 rhlE_3 rhlE_4
[16:40:27] Fixed 2 duplicate /gene - hpcE_1 hpcE_2
[16:40:27] Fixed 2 duplicate /gene - rnr_1 rnr_2
[16:40:27] Fixed 2 duplicate /gene - hemN_1 hemN_2
[16:40:27] Fixed 2 duplicate /gene - greA_1 greA_2
[16:40:27] Fixed 5 duplicate /gene - bepA_1 bepA_2 bepA_3 bepA_4 bepA_5
[16:40:27] Fixed 2 duplicate /gene - hexR_1 hexR_2
[16:40:27] Fixed 4 duplicate /gene - hyuA_1 hyuA_2 hyuA_3 hyuA_4
[16:40:27] Fixed 3 duplicate /gene - rutB_1 rutB_2 rutB_3
[16:40:27] Fixed 3 duplicate /gene - prkC_1 prkC_2 prkC_3
[16:40:27] Fixed 2 duplicate /gene - fosB_1 fosB_2
[16:40:27] Fixed 2 duplicate /gene - otnK_1 otnK_2
[16:40:27] Fixed 2 duplicate /gene - hosA_1 hosA_2
[16:40:27] Fixed 2 duplicate /gene - mepM_1 mepM_2
[16:40:27] Fixed 2 duplicate /gene - uvrA_1 uvrA_2
[16:40:27] Fixed 2 duplicate /gene - cheA_1 cheA_2
[16:40:27] Fixed 2 duplicate /gene - loiP_1 loiP_2
[16:40:27] Fixed 4 duplicate /gene - ctaC_1 ctaC_2 ctaC_3 ctaC_4
[16:40:27] Fixed 2 duplicate /gene - rpoE_1 rpoE_2
[16:40:27] Fixed 2 duplicate /gene - tam_1 tam_2
[16:40:27] Fixed 2 duplicate /gene - dhaT_1 dhaT_2
[16:40:27] Fixed 2 duplicate /gene - ltnD_1 ltnD_2
[16:40:27] Fixed 2 duplicate /gene - mrcA_1 mrcA_2
[16:40:27] Fixed 2 duplicate /gene - dnaJ_1 dnaJ_2
[16:40:27] Fixed 3 duplicate /gene - oatA_1 oatA_2 oatA_3
[16:40:27] Fixed 2 duplicate /gene - srkA_1 srkA_2
[16:40:27] Fixed 6 duplicate /gene - cysA_1 cysA_2 cysA_3 cysA_4 cysA_5 cysA_6
[16:40:27] Fixed 2 duplicate /gene - flhA_1 flhA_2
[16:40:27] Fixed 2 duplicate /gene - mobA_1 mobA_2
[16:40:27] Fixed 6 duplicate /gene - exbD_1 exbD_2 exbD_3 exbD_4 exbD_5 exbD_6
[16:40:27] Fixed 4 duplicate /gene - pilT_1 pilT_2 pilT_3 pilT_4
[16:40:27] Fixed 2 duplicate /gene - fliC_1 fliC_2
[16:40:27] Fixed 2 duplicate /gene - dapA_1 dapA_2
[16:40:27] Fixed 2 duplicate /gene - nuoB_1 nuoB_2
[16:40:27] Fixed 2 duplicate /gene - todS_1 todS_2
[16:40:27] Fixed 2 duplicate /gene - slcC_1 slcC_2
[16:40:27] Fixed 2 duplicate /gene - mscM_1 mscM_2
[16:40:27] Fixed 2 duplicate /gene - dcmA_1 dcmA_2
[16:40:27] Fixed 2 duplicate /gene - hpd_1 hpd_2
[16:40:27] Fixed 3 duplicate /gene - nlhH_1 nlhH_2 nlhH_3
[16:40:27] Fixed 2 duplicate /gene - tas_1 tas_2
[16:40:27] Fixed 3 duplicate /gene - iolS_1 iolS_2 iolS_3
[16:40:27] Fixed 2 duplicate /gene - prmA_1 prmA_2
[16:40:27] Fixed 2 duplicate /gene - cckA_1 cckA_2
[16:40:27] Fixed 2 duplicate /gene - bcr_1 bcr_2
[16:40:27] Fixed 2 duplicate /gene - ompR_1 ompR_2
[16:40:27] Fixed 6 duplicate /gene - dctM_1 dctM_2 dctM_3 dctM_4 dctM_5 dctM_6
[16:40:27] Fixed 8 duplicate /gene - crp_1 crp_2 crp_3 crp_4 crp_5 crp_6 crp_7 crp_8
[16:40:27] Fixed 2 duplicate /gene - liaR_1 liaR_2
[16:40:27] Fixed 5 duplicate /gene - cmpD_1 cmpD_2 cmpD_3 cmpD_4 cmpD_5
[16:40:27] Fixed 2 duplicate /gene - grxC_1 grxC_2
[16:40:27] Fixed 2 duplicate /gene - kefC_1 kefC_2
[16:40:27] Fixed 2 duplicate /gene - rsmI_1 rsmI_2
[16:40:27] Fixed 3 duplicate /gene - trxB_1 trxB_2 trxB_3
[16:40:27] Fixed 2 duplicate /gene - stkP_1 stkP_2
[16:40:27] Fixed 2 duplicate /gene - cmpR_1 cmpR_2
[16:40:27] Fixed 10 duplicate /gene - rspR_1 rspR_2 rspR_3 rspR_4 rspR_5 rspR_6 rspR_7 rspR_8 rspR_9 rspR_10
[16:40:27] Fixed 2 duplicate /gene - kup_1 kup_2
[16:40:27] Fixed 2 duplicate /gene - metXA_1 metXA_2
[16:40:27] Fixed 2 duplicate /gene - araQ_1 araQ_2
[16:40:27] Fixed 2 duplicate /gene - egtB_1 egtB_2
[16:40:27] Fixed 2 duplicate /gene - apc3_1 apc3_2
[16:40:27] Fixed 5 duplicate /gene - lrp_1 lrp_2 lrp_3 lrp_4 lrp_5
[16:40:27] Fixed 8 duplicate /gene - uctC_1 uctC_2 uctC_3 uctC_4 uctC_5 uctC_6 uctC_7 uctC_8
[16:40:27] Fixed 2 duplicate /gene - chrR_1 chrR_2
[16:40:27] Fixed 2 duplicate /gene - vraR_1 vraR_2
[16:40:27] Fixed 4 duplicate /gene - oprM_1 oprM_2 oprM_3 oprM_4
[16:40:27] Fixed 2 duplicate /gene - garA_1 garA_2
[16:40:27] Fixed 5 duplicate /gene - crt_1 crt_2 crt_3 crt_4 crt_5
[16:40:27] Fixed 2 duplicate /gene - phoB_1 phoB_2
[16:40:27] Fixed 2 duplicate /gene - lpxH_1 lpxH_2
[16:40:27] Fixed 2 duplicate /gene - icd_1 icd_2
[16:40:27] Fixed 4 duplicate /gene - acsA_1 acsA_2 acsA_3 acsA_4
[16:40:27] Fixed 2 duplicate /gene - aspC_1 aspC_2
[16:40:27] Fixed 2 duplicate /gene - mshD_1 mshD_2
[16:40:27] Fixed 2 duplicate /gene - livJ_1 livJ_2
[16:40:27] Fixed 2 duplicate /gene - hmrR_1 hmrR_2
[16:40:27] Fixed 2 duplicate /gene - dnaK_1 dnaK_2
[16:40:27] Fixed 2 duplicate /gene - btsR_1 btsR_2
[16:40:27] Fixed 2 duplicate /gene - rlmN_1 rlmN_2
[16:40:27] Fixed 3 duplicate /gene - lpxL_1 lpxL_2 lpxL_3
[16:40:27] Fixed 2 duplicate /gene - chrA1_1 chrA1_2
[16:40:27] Fixed 2 duplicate /gene - nrtA_1 nrtA_2
[16:40:27] Fixed 2 duplicate /gene - hmuU_1 hmuU_2
[16:40:27] Fixed 2 duplicate /gene - sttH_1 sttH_2
[16:40:27] Fixed 4 duplicate /gene - ugpC_1 ugpC_2 ugpC_3 ugpC_4
[16:40:27] Fixed 2 duplicate /gene - rsxB_1 rsxB_2
[16:40:27] Fixed 2 duplicate /gene - livK_1 livK_2
[16:40:27] Fixed 2 duplicate /gene - corA_1 corA_2
[16:40:27] Fixed 2 duplicate /gene - hisF_1 hisF_2
[16:40:27] Fixed 3 duplicate /gene - dppC_1 dppC_2 dppC_3
[16:40:27] Fixed 3 duplicate /gene - tolC_1 tolC_2 tolC_3
[16:40:27] Fixed 2 duplicate /gene - pcpR_1 pcpR_2
[16:40:27] Fixed 2 duplicate /gene - ligA_1 ligA_2
[16:40:27] Fixed 2 duplicate /gene - prpC_1 prpC_2
[16:40:27] Fixed 2 duplicate /gene - fbp_1 fbp_2
[16:40:27] Fixed 2 duplicate /gene - metI_1 metI_2
[16:40:27] Fixed 4 duplicate /gene - barA_1 barA_2 barA_3 barA_4
[16:40:27] Fixed 2 duplicate /gene - gpx1_1 gpx1_2
[16:40:27] Fixed 3 duplicate /gene - uvrY_1 uvrY_2 uvrY_3
[16:40:27] Fixed 7 duplicate /gene - ribX_1 ribX_2 ribX_3 ribX_4 ribX_5 ribX_6 ribX_7
[16:40:27] Fixed 4 duplicate /gene - potA_1 potA_2 potA_3 potA_4
[16:40:27] Fixed 5 duplicate /gene - aam_1 aam_2 aam_3 aam_4 aam_5
[16:40:27] Fixed 2 duplicate /gene - fcuA_1 fcuA_2
[16:40:27] Fixed 2 duplicate /gene - thiD_1 thiD_2
[16:40:27] Fixed 3 duplicate /gene - clcD_1 clcD_2 clcD_3
[16:40:27] Fixed 2 duplicate /gene - entS_1 entS_2
[16:40:27] Fixed 3 duplicate /gene - dauA_1 dauA_2 dauA_3
[16:40:27] Fixed 3 duplicate /gene - pspB_1 pspB_2 pspB_3
[16:40:27] Fixed 2 duplicate /gene - fdx_1 fdx_2
[16:40:27] Fixed 2 duplicate /gene - echA8_1 echA8_2
[16:40:27] Fixed 2 duplicate /gene - sugB_1 sugB_2
[16:40:27] Fixed 2 duplicate /gene - mcbR_1 mcbR_2
[16:40:27] Fixed 2 duplicate /gene - glpE_1 glpE_2
[16:40:27] Fixed 2 duplicate /gene - argE_1 argE_2
[16:40:27] Fixed 2 duplicate /gene - yjiE_1 yjiE_2
[16:40:27] Fixed 2 duplicate /gene - efe_1 efe_2
[16:40:27] Fixed 4 duplicate /gene - yisK_1 yisK_2 yisK_3 yisK_4
[16:40:27] Fixed 2 duplicate /gene - fabI_1 fabI_2
[16:40:27] Fixed 3 duplicate /gene - trg_1 trg_2 trg_3
[16:40:27] Fixed 2 duplicate /gene - rimI_1 rimI_2
[16:40:27] Fixed 3 duplicate /gene - dpgD_1 dpgD_2 dpgD_3
[16:40:27] Fixed 2 duplicate /gene - degU_1 degU_2
[16:40:27] Fixed 3 duplicate /gene - takP_1 takP_2 takP_3
[16:40:27] Fixed 3 duplicate /gene - catD_1 catD_2 catD_3
[16:40:27] Fixed 4 duplicate /gene - lutR_1 lutR_2 lutR_3 lutR_4
[16:40:27] Fixed 5 duplicate /gene - qseC_1 qseC_2 qseC_3 qseC_4 qseC_5
[16:40:27] Fixed 2 duplicate /gene - katE_1 katE_2
[16:40:27] Fixed 2 duplicate /gene - scpA_1 scpA_2
[16:40:27] Fixed 2 duplicate /gene - bvgS_1 bvgS_2
[16:40:27] Fixed 4 duplicate /gene - tsr_1 tsr_2 tsr_3 tsr_4
[16:40:27] Fixed 3 duplicate /gene - metQ_1 metQ_2 metQ_3
[16:40:27] Fixed 2 duplicate /gene - leuC_1 leuC_2
[16:40:27] Fixed 2 duplicate /gene - hbpA_1 hbpA_2
[16:40:27] Fixed 2 duplicate /gene - modA_1 modA_2
[16:40:27] Fixed 2 duplicate /gene - cphA_1 cphA_2
[16:40:27] Fixed 2 duplicate /gene - btuB_1 btuB_2
[16:40:27] Fixed 3 duplicate /gene - gltI_1 gltI_2 gltI_3
[16:40:27] Fixed 2 duplicate /gene - occR_1 occR_2
[16:40:27] Fixed 4 duplicate /gene - rhtB_1 rhtB_2 rhtB_3 rhtB_4
[16:40:27] Fixed 2 duplicate /gene - yeaW_1 yeaW_2
[16:40:27] Fixed 3 duplicate /gene - tctD_1 tctD_2 tctD_3
[16:40:27] Fixed 2 duplicate /gene - ftsH_1 ftsH_2
[16:40:27] Fixed 2 duplicate /gene - dmoA_1 dmoA_2
[16:40:27] Fixed 3 duplicate /gene - yiaM_1 yiaM_2 yiaM_3
[16:40:27] Fixed 2 duplicate /gene - tdiR_1 tdiR_2
[16:40:27] Fixed 3 duplicate /gene - cqsS_1 cqsS_2 cqsS_3
[16:40:27] Fixed 3 duplicate /gene - iorB_1 iorB_2 iorB_3
[16:40:27] Fixed 2 duplicate /gene - ydbM_1 ydbM_2
[16:40:27] Fixed 2 duplicate /gene - accA1_1 accA1_2
[16:40:27] Fixed 2 duplicate /gene - hisH_1 hisH_2
[16:40:27] Fixed 6 duplicate /gene - cynR_1 cynR_2 cynR_3 cynR_4 cynR_5 cynR_6
[16:40:27] Fixed 4 duplicate /gene - menH_1 menH_2 menH_3 menH_4
[16:40:27] Fixed 3 duplicate /gene - mshA_1 mshA_2 mshA_3
[16:40:27] Fixed 2 duplicate /gene - ligC_1 ligC_2
[16:40:27] Fixed 3 duplicate /gene - epsE_1 epsE_2 epsE_3
[16:40:27] Fixed 2 duplicate /gene - moeA_1 moeA_2
[16:40:27] Fixed 2 duplicate /gene - nicS_1 nicS_2
[16:40:27] Fixed 4 duplicate /gene - resA_1 resA_2 resA_3 resA_4
[16:40:27] Fixed 2 duplicate /gene - nfdA_1 nfdA_2
[16:40:27] Fixed 9 duplicate /gene - fabG_1 fabG_2 fabG_3 fabG_4 fabG_5 fabG_6 fabG_7 fabG_8 fabG_9
[16:40:27] Fixed 2 duplicate /gene - cysW_1 cysW_2
[16:40:27] Fixed 2 duplicate /gene - kstR2_1 kstR2_2
[16:40:27] Fixed 3 duplicate /gene - ydcV_1 ydcV_2 ydcV_3
[16:40:27] Fixed 2 duplicate /gene - nagK_1 nagK_2
[16:40:27] Fixed 4 duplicate /gene - ribN_1 ribN_2 ribN_3 ribN_4
[16:40:27] Fixed 2 duplicate /gene - cpg2_1 cpg2_2
[16:40:27] Fixed 2 duplicate /gene - der_1 der_2
[16:40:27] Fixed 2 duplicate /gene - qorA_1 qorA_2
[16:40:27] Fixed 5 duplicate /gene - tolQ_1 tolQ_2 tolQ_3 tolQ_4 tolQ_5
[16:40:27] Fixed 2 duplicate /gene - pitA_1 pitA_2
[16:40:27] Fixed 2 duplicate /gene - nnr_1 nnr_2
[16:40:27] Fixed 3 duplicate /gene - plsC_1 plsC_2 plsC_3
[16:40:27] Fixed 2 duplicate /gene - ctaD_1 ctaD_2
[16:40:27] Fixed 2 duplicate /gene - pimB_1 pimB_2
[16:40:27] Fixed 3 duplicate /gene - ycaC_1 ycaC_2 ycaC_3
[16:40:27] Fixed 2 duplicate /gene - desR_1 desR_2
[16:40:27] Fixed 2 duplicate /gene - soj_1 soj_2
[16:40:27] Fixed 3 duplicate /gene - rpfC_1 rpfC_2 rpfC_3
[16:40:27] Fixed 3 duplicate /gene - fadA_1 fadA_2 fadA_3
[16:40:27] Fixed 17 duplicate /gene - livF_1 livF_2 livF_3 livF_4 livF_5 livF_6 livF_7 livF_8 livF_9 livF_10 livF_11 livF_12 livF_13 livF_14 livF_15 livF_16 livF_17
[16:40:27] Fixed 2 duplicate /gene - leuA_1 leuA_2
[16:40:27] Fixed 2 duplicate /gene - yiaO_1 yiaO_2
[16:40:27] Fixed 2 duplicate /gene - rluB_1 rluB_2
[16:40:27] Fixed 2 duplicate /gene - alkA_1 alkA_2
[16:40:27] Fixed 2 duplicate /gene - tauD_1 tauD_2
[16:40:27] Fixed 2 duplicate /gene - cheR_1 cheR_2
[16:40:27] Fixed 2 duplicate /gene - aqpZ_1 aqpZ_2
[16:40:27] Fixed 2 duplicate /gene - ugpB_1 ugpB_2
[16:40:27] Fixed 3 duplicate /gene - luxQ_1 luxQ_2 luxQ_3
[16:40:27] Fixed 2 duplicate /gene - hxcR_1 hxcR_2
[16:40:27] Fixed 3 duplicate /gene - pytH_1 pytH_2 pytH_3
[16:40:27] Fixed 2 duplicate /gene - fdhF_1 fdhF_2
[16:40:27] Fixed 5 duplicate /gene - ssuB_1 ssuB_2 ssuB_3 ssuB_4 ssuB_5
[16:40:27] Fixed 2 duplicate /gene - rutR_1 rutR_2
[16:40:27] Fixed 3 duplicate /gene - slt_1 slt_2 slt_3
[16:40:27] Fixed 3 duplicate /gene - glxR_1 glxR_2 glxR_3
[16:40:27] Fixed 2 duplicate /gene - stp_1 stp_2
[16:40:27] Fixed 2 duplicate /gene - garD_1 garD_2
[16:40:27] Fixed 5 duplicate /gene - hipO_1 hipO_2 hipO_3 hipO_4 hipO_5
[16:40:27] Fixed 3 duplicate /gene - slyA_1 slyA_2 slyA_3
[16:40:27] Fixed 2 duplicate /gene - mtnN_1 mtnN_2
[16:40:27] Fixed 2 duplicate /gene - cysE_1 cysE_2
[16:40:27] Fixed 2 duplicate /gene - nuoF_1 nuoF_2
[16:40:27] Fixed 2 duplicate /gene - ispD_1 ispD_2
[16:40:27] Fixed 3 duplicate /gene - potB_1 potB_2 potB_3
[16:40:27] Fixed 2 duplicate /gene - prmC_1 prmC_2
[16:40:27] Fixed 2 duplicate /gene - guaD_1 guaD_2
[16:40:27] Fixed 2 duplicate /gene - apc4_1 apc4_2
[16:40:27] Fixed 2 duplicate /gene - clsB_1 clsB_2
[16:40:27] Fixed 2 duplicate /gene - yngG_1 yngG_2
[16:40:27] Fixed 2 duplicate /gene - ifcA_1 ifcA_2
[16:40:27] Fixed 5 duplicate /gene - ribY_1 ribY_2 ribY_3 ribY_4 ribY_5
[16:40:27] Fixed 4 duplicate /gene - dadA1_1 dadA1_2 dadA1_3 dadA1_4
[16:40:27] Fixed 2 duplicate /gene - cnbA_1 cnbA_2
[16:40:27] Fixed 2 duplicate /gene - araD_1 araD_2
[16:40:27] Fixed 2 duplicate /gene - dkgB_1 dkgB_2
[16:40:27] Fixed 2 duplicate /gene - todT_1 todT_2
[16:40:27] Fixed 2 duplicate /gene - pbpG_1 pbpG_2
[16:40:27] Fixed 4 duplicate /gene - cloR_1 cloR_2 cloR_3 cloR_4
[16:40:27] Fixed 6 duplicate /gene - braC_1 braC_2 braC_3 braC_4 braC_5 braC_6
[16:40:27] Fixed 2 duplicate /gene - ogt_1 ogt_2
[16:40:27] Fixed 2 duplicate /gene - yadG_1 yadG_2
[16:40:27] Fixed 3 duplicate /gene - btsS_1 btsS_2 btsS_3
[16:40:27] Fixed 3 duplicate /gene - cobD_1 cobD_2 cobD_3
[16:40:27] Fixed 8 duplicate /gene - ssuA_1 ssuA_2 ssuA_3 ssuA_4 ssuA_5 ssuA_6 ssuA_7 ssuA_8
[16:40:27] Fixed 3 duplicate /gene - htpX_1 htpX_2 htpX_3
[16:40:27] Fixed 3 duplicate /gene - siaP_1 siaP_2 siaP_3
[16:40:27] Fixed 3 duplicate /gene - lldR_1 lldR_2 lldR_3
[16:40:27] Fixed 2 duplicate /gene - czcA_1 czcA_2
[16:40:27] Fixed 5 duplicate /gene - yfcG_1 yfcG_2 yfcG_3 yfcG_4 yfcG_5
[16:40:27] Fixed 3 duplicate /gene - phoR_1 phoR_2 phoR_3
[16:40:27] Fixed 2 duplicate /gene - mlaF_1 mlaF_2
[16:40:27] Fixed 2 duplicate /gene - yiaD_1 yiaD_2
[16:40:27] Fixed 3 duplicate /gene - glnM_1 glnM_2 glnM_3
[16:40:27] Fixed 2 duplicate /gene - eno_1 eno_2
[16:40:27] Fixed 2 duplicate /gene - cheW_1 cheW_2
[16:40:27] Fixed 2 duplicate /gene - bepE_1 bepE_2
[16:40:27] Fixed 2 duplicate /gene - osmY_1 osmY_2
[16:40:27] Fixed 2 duplicate /gene - rimO_1 rimO_2
[16:40:27] Fixed 2 duplicate /gene - alaS_1 alaS_2
[16:40:27] Fixed 2 duplicate /gene - phaC_1 phaC_2
[16:40:27] Fixed 3 duplicate /gene - copA_1 copA_2 copA_3
[16:40:27] Fixed 2 duplicate /gene - lemA_1 lemA_2
[16:40:27] Fixed 2 duplicate /gene - pcm_1 pcm_2
[16:40:27] Fixed 2 duplicate /gene - fixJ_1 fixJ_2
[16:40:27] Fixed 6 duplicate /gene - oppD_1 oppD_2 oppD_3 oppD_4 oppD_5 oppD_6
[16:40:27] Fixed 2 duplicate /gene - ydgJ_1 ydgJ_2
[16:40:27] Fixed 2 duplicate /gene - sbp_1 sbp_2
[16:40:27] Fixed 2 duplicate /gene - nreB_1 nreB_2
[16:40:27] Fixed 2 duplicate /gene - tmoT_1 tmoT_2
[16:40:27] Fixed 2 duplicate /gene - curA_1 curA_2
[16:40:27] Fixed 2 duplicate /gene - ribBA_1 ribBA_2
[16:40:27] Fixed 2 duplicate /gene - hyuC_1 hyuC_2
[16:40:27] Fixed 3 duplicate /gene - pilE_1 pilE_2 pilE_3
[16:40:27] Fixed 2 duplicate /gene - yajR_1 yajR_2
[16:40:27] Fixed 17 duplicate /gene - livH_1 livH_2 livH_3 livH_4 livH_5 livH_6 livH_7 livH_8 livH_9 livH_10 livH_11 livH_12 livH_13 livH_14 livH_15 livH_16 livH_17
[16:40:27] Fixed 2 duplicate /gene - dgoD_1 dgoD_2
[16:40:27] Fixed 6 duplicate /gene - mmgC_1 mmgC_2 mmgC_3 mmgC_4 mmgC_5 mmgC_6
[16:40:27] Fixed 2 duplicate /gene - xthA_1 xthA_2
[16:40:27] Fixed 2 duplicate /gene - pgdA_1 pgdA_2
[16:40:27] Fixed 3 duplicate /gene - tauB_1 tauB_2 tauB_3
[16:40:27] Fixed 4 duplicate /gene - fadD_1 fadD_2 fadD_3 fadD_4
[16:40:27] Fixed 2 duplicate /gene - yhaJ_1 yhaJ_2
[16:40:27] Fixed 2 duplicate /gene - mdtC_1 mdtC_2
[16:40:27] Fixed 3 duplicate /gene - ydiK_1 ydiK_2 ydiK_3
[16:40:27] Fixed 2 duplicate /gene - sugA_1 sugA_2
[16:40:27] Fixed 9 duplicate /gene - gsiC_1 gsiC_2 gsiC_3 gsiC_4 gsiC_5 gsiC_6 gsiC_7 gsiC_8 gsiC_9
[16:40:27] Fixed 2 duplicate /gene - frc_1 frc_2
[16:40:27] Fixed 2 duplicate /gene - yhjX_1 yhjX_2
[16:40:27] Fixed 3 duplicate /gene - fabH_1 fabH_2 fabH_3
[16:40:27] Fixed 2 duplicate /gene - mdtA_1 mdtA_2
[16:40:27] Fixed 2 duplicate /gene - dmdB_1 dmdB_2
[16:40:27] Fixed 2 duplicate /gene - mepA_1 mepA_2
[16:40:27] Fixed 2 duplicate /gene - limB_1 limB_2
[16:40:27] Fixed 2 duplicate /gene - metN_1 metN_2
[16:40:27] Fixed 2 duplicate /gene - cyaA_1 cyaA_2
[16:40:27] Fixed 2 duplicate /gene - atpH_1 atpH_2
[16:40:27] Fixed 3 duplicate /gene - dppA_1 dppA_2 dppA_3
[16:40:27] Fixed 3 duplicate /gene - rbsA_1 rbsA_2 rbsA_3
[16:40:27] Fixed 13 duplicate /gene - lptB_1 lptB_2 lptB_3 lptB_4 lptB_5 lptB_6 lptB_7 lptB_8 lptB_9 lptB_10 lptB_11 lptB_12 lptB_13
[16:40:27] Fixed 4 duplicate /gene - yabJ_1 yabJ_2 yabJ_3 yabJ_4
[16:40:27] Fixed 2 duplicate /gene - amiC_1 amiC_2
[16:40:27] Fixed 2 duplicate /gene - ybaK_1 ybaK_2
[16:40:27] Fixed 2 duplicate /gene - guaB_1 guaB_2
[16:40:27] Fixed 2 duplicate /gene - nagC_1 nagC_2
[16:40:27] Fixed 2 duplicate /gene - gstA_1 gstA_2
[16:40:27] Fixed 2 duplicate /gene - ohrR_1 ohrR_2
[16:40:27] Fixed 5 duplicate /gene - gsiB_1 gsiB_2 gsiB_3 gsiB_4 gsiB_5
[16:40:27] Fixed 3 duplicate /gene - lysN_1 lysN_2 lysN_3
[16:40:27] Fixed 3 duplicate /gene - proA_1 proA_2 proA_3
[16:40:27] Fixed 2 duplicate /gene - ycf3_1 ycf3_2
[16:40:27] Fixed 7 duplicate /gene - glnQ_1 glnQ_2 glnQ_3 glnQ_4 glnQ_5 glnQ_6 glnQ_7
[16:40:27] Fixed 2 duplicate /gene - kdgR_1 kdgR_2
[16:40:27] Fixed 2 duplicate /gene - ppsC_1 ppsC_2
[16:40:27] Fixed 2 duplicate /gene - thadh_1 thadh_2
[16:40:27] Fixed 3 duplicate /gene - pgrR_1 pgrR_2 pgrR_3
[16:40:27] Fixed 2 duplicate /gene - arsC_1 arsC_2
[16:40:27] Fixed 3 duplicate /gene - fliY_1 fliY_2 fliY_3
[16:40:27] Fixed 2 duplicate /gene - rluA_1 rluA_2
[16:40:27] Fixed 2 duplicate /gene - tsaC1_1 tsaC1_2
[16:40:27] Fixed 2 duplicate /gene - dgcC_1 dgcC_2
[16:40:27] Fixed 2 duplicate /gene - comM_1 comM_2
[16:40:27] Fixed 3 duplicate /gene - gno_1 gno_2 gno_3
[16:40:27] Fixed 3 duplicate /gene - dppD_1 dppD_2 dppD_3
[16:40:27] Fixed 2 duplicate /gene - zntR_1 zntR_2
[16:40:27] Fixed 3 duplicate /gene - lcfB_1 lcfB_2 lcfB_3
[16:40:27] Fixed 2 duplicate /gene - ddpC_1 ddpC_2
[16:40:27] Fixed 3 duplicate /gene - cmpB_1 cmpB_2 cmpB_3
[16:40:27] Fixed 2 duplicate /gene - mlaE_1 mlaE_2
[16:40:27] Fixed 4 duplicate /gene - dapE_1 dapE_2 dapE_3 dapE_4
[16:40:27] Fixed 2 duplicate /gene - estA_1 estA_2
[16:40:27] Fixed 2 duplicate /gene - prsD_1 prsD_2
[16:40:27] Fixed 6 duplicate /gene - fixL_1 fixL_2 fixL_3 fixL_4 fixL_5 fixL_6
[16:40:27] Fixed 3 duplicate /gene - cpo_1 cpo_2 cpo_3
[16:40:27] Fixed 2 duplicate /gene - bclA_1 bclA_2
[16:40:27] Fixed 3 duplicate /gene - dan_1 dan_2 dan_3
[16:40:27] Fixed 2 duplicate /gene - nasD_1 nasD_2
[16:40:27] Fixed 4 duplicate /gene - gntR_1 gntR_2 gntR_3 gntR_4
[16:40:27] Fixed 2 duplicate /gene - gltA_1 gltA_2
[16:40:27] Fixed 3 duplicate /gene - cadA_1 cadA_2 cadA_3
[16:40:27] Fixed 2 duplicate /gene - xerC_1 xerC_2
[16:40:27] Fixed 4 duplicate /gene - gcvA_1 gcvA_2 gcvA_3 gcvA_4
[16:40:27] Fixed 3 duplicate /gene - dmdC_1 dmdC_2 dmdC_3
[16:40:27] Fixed 2 duplicate /gene - ftsA_1 ftsA_2
[16:40:27] Fixed 3 duplicate /gene - cheB_1 cheB_2 cheB_3
[16:40:27] Fixed 2 duplicate /gene - amtB_1 amtB_2
[16:40:27] Fixed 2 duplicate /gene - msrAB_1 msrAB_2
[16:40:27] Fixed 3 duplicate /gene - sspA_1 sspA_2 sspA_3
[16:40:27] Fixed 5 duplicate /gene - oppF_1 oppF_2 oppF_3 oppF_4 oppF_5
[16:40:27] Fixed 3 duplicate /gene - cc4_1 cc4_2 cc4_3
[16:40:27] Fixed 12 duplicate /gene - dmlR_1 dmlR_2 dmlR_3 dmlR_4 dmlR_5 dmlR_6 dmlR_7 dmlR_8 dmlR_9 dmlR_10 dmlR_11 dmlR_12
[16:40:27] Fixed 2 duplicate /gene - speE_1 speE_2
[16:40:27] Fixed 2 duplicate /gene - glrR_1 glrR_2
[16:40:27] Fixed 2 duplicate /gene - lolA_1 lolA_2
[16:40:27] Fixed 2 duplicate /gene - algE5_1 algE5_2
[16:40:27] Fixed 2 duplicate /gene - infA_1 infA_2
[16:40:27] Fixed 3 duplicate /gene - soxA_1 soxA_2 soxA_3
[16:40:27] Fixed 3 duplicate /gene - crnA_1 crnA_2 crnA_3
[16:40:27] Fixed 4 duplicate /gene - cya_1 cya_2 cya_3 cya_4
[16:40:27] Fixed 4 duplicate /gene - siaM_1 siaM_2 siaM_3 siaM_4
[16:40:27] Fixed 2 duplicate /gene - gloB_1 gloB_2
[16:40:27] Fixed 2 duplicate /gene - acdA_1 acdA_2
[16:40:27] Fixed 2 duplicate /gene - qseB_1 qseB_2
[16:40:27] Fixed 3 duplicate /gene - ddpF_1 ddpF_2 ddpF_3
[16:40:27] Fixed 2 duplicate /gene - yphB_1 yphB_2
[16:40:27] Fixed 2 duplicate /gene - siaQ_1 siaQ_2
[16:40:27] Fixed 5 duplicate /gene - tar_1 tar_2 tar_3 tar_4 tar_5
[16:40:27] Fixed 2 duplicate /gene - metH_1 metH_2
[16:40:27] Fixed 4 duplicate /gene - clsC_1 clsC_2 clsC_3 clsC_4
[16:40:27] Fixed 3 duplicate /gene - iorA_1 iorA_2 iorA_3
[16:40:27] Fixed 2 duplicate /gene - glpQ_1 glpQ_2
[16:40:27] Fixed 2 duplicate /gene - mexR_1 mexR_2
[16:40:27] Fixed 3 duplicate /gene - xerD_1 xerD_2 xerD_3
[16:40:27] Fixed 2 duplicate /gene - btuF_1 btuF_2
[16:40:27] Fixed 4 duplicate /gene - cheY_1 cheY_2 cheY_3 cheY_4
[16:40:28] Fixed 2 duplicate /gene - gstB_1 gstB_2
[16:40:28] Fixed 2 duplicate /gene - pyrE_1 pyrE_2
[16:40:28] Fixed 2 duplicate /gene - ndmA_1 ndmA_2
[16:40:28] Fixed 2 duplicate /gene - sdpR_1 sdpR_2
[16:40:28] Fixed 2 duplicate /gene - slyD_1 slyD_2
[16:40:28] Fixed 5 duplicate /gene - cyaB_1 cyaB_2 cyaB_3 cyaB_4 cyaB_5
[16:40:28] Fixed 2 duplicate /gene - aroK_1 aroK_2
[16:40:28] Fixed 2 duplicate /gene - ypdB_1 ypdB_2
[16:40:28] Fixed 3 duplicate /gene - hxuA_1 hxuA_2 hxuA_3
[16:40:28] Fixed 2 duplicate /gene - evgS_1 evgS_2
[16:40:28] Fixed 2 duplicate /gene - ccpA_1 ccpA_2
[16:40:28] Fixed 3 duplicate /gene - rclR_1 rclR_2 rclR_3
[16:40:28] Fixed 2 duplicate /gene - iclR_1 iclR_2
[16:40:28] Fixed 3 duplicate /gene - ais_1 ais_2 ais_3
[16:40:28] Fixed 2 duplicate /gene - czcB_1 czcB_2
[16:40:28] Fixed 2 duplicate /gene - zraR_1 zraR_2
[16:40:28] Fixed 2 duplicate /gene - mdtB_1 mdtB_2
[16:40:28] Fixed 384 colliding /gene names.
[16:40:28] Adding /locus_tag identifiers
[16:40:28] Assigned 4339 locus_tags to CDS and RNA features.
[16:40:28] Writing outputs to data/annotation/bin1/
[16:40:31] Generating annotation statistics file
[16:40:31] Generating Genbank and Sequin files
[16:40:31] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.13 from https://github.com/tseemann/prokka' -Z data\/annotation\/bin1\/PROKKA_03222022\.err -i data\/annotation\/bin1\/PROKKA_03222022\.fsa 2> /dev/null
[16:40:40] Deleting unwanted file: data/annotation/bin1/errorsummary.val
[16:40:40] Deleting unwanted file: data/annotation/bin1/PROKKA_03222022.dr
[16:40:40] Deleting unwanted file: data/annotation/bin1/PROKKA_03222022.fixedproducts
[16:40:40] Deleting unwanted file: data/annotation/bin1/PROKKA_03222022.ecn
[16:40:40] Deleting unwanted file: data/annotation/bin1/PROKKA_03222022.val
[16:40:40] Repairing broken .GBK output that tbl2asn produces...
[16:40:40] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < data\/annotation\/bin1\/PROKKA_03222022\.gbf > data\/annotation\/bin1\/PROKKA_03222022\.gbk
[16:40:40] Deleting unwanted file: data/annotation/bin1/PROKKA_03222022.gbf
[16:40:40] Output files:
[16:40:40] data/annotation/bin1/PROKKA_03222022.log
[16:40:40] data/annotation/bin1/PROKKA_03222022.fna
[16:40:40] data/annotation/bin1/PROKKA_03222022.gff
[16:40:40] data/annotation/bin1/PROKKA_03222022.faa
[16:40:40] data/annotation/bin1/PROKKA_03222022.ffn
[16:40:40] data/annotation/bin1/PROKKA_03222022.tbl
[16:40:40] data/annotation/bin1/PROKKA_03222022.fsa
[16:40:40] data/annotation/bin1/PROKKA_03222022.tsv
[16:40:40] data/annotation/bin1/PROKKA_03222022.txt
[16:40:40] data/annotation/bin1/PROKKA_03222022.sqn
[16:40:40] data/annotation/bin1/PROKKA_03222022.err
[16:40:40] data/annotation/bin1/PROKKA_03222022.gbk
[16:40:40] Annotation finished successfully.
[16:40:40] Walltime used: 6.00 minutes
[16:40:40] If you use this result please cite the Prokka paper:
[16:40:40] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[16:40:40] Type 'prokka --citation' for more details.
[16:40:40] Thank you, come again.
(metagenomics_practical) 

Investigating prokka output

The prokka output is very elaborate and can be used to many ends. We will quickly visualise the output for the purpose of this practical. To investigate the prokka output, you can use two webservers that both can place the annotations from prokka in metabolic KEGG pathways. First, we'll inspect the contents of a GFF file.

[DO:] View prokka output: (look for the .gff file)

ls data/annotation/bin1

PROKKA_03222022.err  PROKKA_03222022.fsa  PROKKA_03222022.sqn
PROKKA_03222022.faa  PROKKA_03222022.gbk  PROKKA_03222022.tbl
PROKKA_03222022.ffn  PROKKA_03222022.gff  PROKKA_03222022.tsv
PROKKA_03222022.fna  PROKKA_03222022.log  PROKKA_03222022.txt
(metagenomics_practical) 

head data/annotation/bin1/PROKKA_03222022.txt

organism: Genus species strain 
contigs: 37
bases: 4425020
gene: 4339
tRNA: 44
CDS: 4294
tmRNA: 1
(metagenomics_practical) 

grep -v '#' data/annotation/bin1/PROKKA_03222022.gff | head

gnl|X|HFHIMAGJ_1	Prodigal:2.6	CDS	394	1284	.	-	0	ID=HFHIMAGJ_00001;Parent=HFHIMAGJ_00001_gene;inference=ab initio prediction:Prodigal:2.6;locus_tag=HFHIMAGJ_00001;product=hypothetical protein;protein_id=gnl|X|HFHIMAGJ_00001
gnl|X|HFHIMAGJ_1	prokka	gene	394	1284	.	-	.	ID=HFHIMAGJ_00001_gene;locus_tag=HFHIMAGJ_00001
gnl|X|HFHIMAGJ_1	Prodigal:2.6	CDS	1291	1719	.	-	0	ID=HFHIMAGJ_00002;Parent=HFHIMAGJ_00002_gene;Name=exbD_1;dbxref=COG:COG0848;gene=exbD_1;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P0ABV2;locus_tag=HFHIMAGJ_00002;product=Biopolymer transport protein ExbD;protein_id=gnl|X|HFHIMAGJ_00002
gnl|X|HFHIMAGJ_1	prokka	gene	1291	1719	.	-	.	ID=HFHIMAGJ_00002_gene;Name=exbD_1;gene=exbD_1;locus_tag=HFHIMAGJ_00002
gnl|X|HFHIMAGJ_1	Prodigal:2.6	CDS	1721	2413	.	-	0	ID=HFHIMAGJ_00003;Parent=HFHIMAGJ_00003_gene;Name=tolQ_1;dbxref=COG:COG0811;gene=tolQ_1;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P0ABU9;locus_tag=HFHIMAGJ_00003;product=Protein TolQ;protein_id=gnl|X|HFHIMAGJ_00003
gnl|X|HFHIMAGJ_1	prokka	gene	1721	2413	.	-	.	ID=HFHIMAGJ_00003_gene;Name=tolQ_1;gene=tolQ_1;locus_tag=HFHIMAGJ_00003
gnl|X|HFHIMAGJ_1	Prodigal:2.6	CDS	2410	2811	.	-	0	ID=HFHIMAGJ_00004;Parent=HFHIMAGJ_00004_gene;eC_number=3.1.2.-;Name=ybgC;dbxref=COG:COG0824;gene=ybgC;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P44679;locus_tag=HFHIMAGJ_00004;product=Acyl-CoA thioesterase YbgC;protein_id=gnl|X|HFHIMAGJ_00004
gnl|X|HFHIMAGJ_1	prokka	gene	2410	2811	.	-	.	ID=HFHIMAGJ_00004_gene;Name=ybgC;gene=ybgC;locus_tag=HFHIMAGJ_00004
gnl|X|HFHIMAGJ_1	Prodigal:2.6	CDS	2808	4001	.	-	0	ID=HFHIMAGJ_00005;Parent=HFHIMAGJ_00005_gene;eC_number=2.6.1.-;Name=patA;dbxref=COG:COG0436;gene=patA;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P16524;locus_tag=HFHIMAGJ_00005;product=Putative N-acetyl-LL-diaminopimelate aminotransferase;protein_id=gnl|X|HFHIMAGJ_00005
gnl|X|HFHIMAGJ_1	prokka	gene	2808	4001	.	-	.	ID=HFHIMAGJ_00005_gene;Name=patA;gene=patA;locus_tag=HFHIMAGJ_00005
grep: write error: Broken pipe

Visualisation in IPath3 onpathways.embl.de

For visualisation in pathways.embl.de we need to add the word 'UNIRPOT:' to the list of IDs like so:

Prokka gives UniProt IDs in the gff files first we will collect these IDs and discard all other information. However, we need to make sure that IPath3 understands these are UniprotIDs. The code below helps you to do so.

[DO:] take the uniprot IDs out of the gff file:

grep -o 'UniProt.*' data/annotation/bin1/PROKKA_03222022.gff| cut -d';' -f1 | cut -d':' -f2 | sed 's/^/UNIPROT:/g'

UNIPROT:P0ABV2
UNIPROT:P0ABU9
UNIPROT:P44679
UNIPROT:P16524
UNIPROT:P0A780
UNIPROT:P11998
UNIPROT:A5U2B7
UNIPROT:P51961
UNIPROT:P25539
UNIPROT:P02974
UNIPROT:S0HPF7
UNIPROT:P0A8D0
UNIPROT:P0A2E2
UNIPROT:P0AGC3
UNIPROT:P76346
UNIPROT:Q9I2V0
UNIPROT:P83221
UNIPROT:P23869
UNIPROT:P21888
UNIPROT:P37878
UNIPROT:Q9HXZ2
UNIPROT:P52097
UNIPROT:C3JXY0
UNIPROT:Q9KR66
UNIPROT:P0ACG8
UNIPROT:P45336
UNIPROT:P0CL17
UNIPROT:B3EWP1
UNIPROT:P14375
UNIPROT:P21175
UNIPROT:P45073
UNIPROT:P22731
UNIPROT:P0AEX7
UNIPROT:P25026
UNIPROT:P23871
UNIPROT:P0ADP0
UNIPROT:P37269
UNIPROT:Q6N3F2
UNIPROT:P76397
UNIPROT:P13511
UNIPROT:Q9JZ37
UNIPROT:Q9JZ38
UNIPROT:P0A6H1
UNIPROT:P0A9M0
UNIPROT:O05412
UNIPROT:P14407
UNIPROT:P33950
UNIPROT:P75798
UNIPROT:P75799
UNIPROT:P24137
UNIPROT:P24136
UNIPROT:Q6DTN4
UNIPROT:P05042
UNIPROT:P13738
UNIPROT:P27550
UNIPROT:P15452
UNIPROT:P9WKJ5
UNIPROT:Q47141
UNIPROT:P60955
UNIPROT:P0ACM2
UNIPROT:B3EWP1
UNIPROT:O07610
UNIPROT:Q9R381
UNIPROT:Q57252
UNIPROT:P0ACM2
UNIPROT:P55819
UNIPROT:B3EWP1
UNIPROT:P76518
UNIPROT:P52046
UNIPROT:Q9ZHQ1
UNIPROT:P75797
UNIPROT:P75798
UNIPROT:P26904
UNIPROT:P24136
UNIPROT:P24137
UNIPROT:P45493
UNIPROT:P07658
UNIPROT:A8GQT6
UNIPROT:P69902
UNIPROT:P23222
UNIPROT:P69902
UNIPROT:P40149
UNIPROT:B3EWP1
UNIPROT:O06724
UNIPROT:Q55459
UNIPROT:P23882
UNIPROT:P23878
UNIPROT:Q56992
UNIPROT:O32102
UNIPROT:P40883
UNIPROT:P17315
UNIPROT:Q9HTW3
UNIPROT:P06129
UNIPROT:P29931
UNIPROT:P37028
UNIPROT:Q56992
UNIPROT:P15031
UNIPROT:P31570
UNIPROT:P9WP93
UNIPROT:P97084
UNIPROT:P9WP95
UNIPROT:Q7SIC7
UNIPROT:Q7A551
UNIPROT:Q9KJX5
UNIPROT:P76397
UNIPROT:B7M458
UNIPROT:A7ZNP9
UNIPROT:Q51487
UNIPROT:A9BJC1
UNIPROT:Q08IS0
UNIPROT:P15452
UNIPROT:O08498
UNIPROT:O53838
UNIPROT:P33015
UNIPROT:P0AB83
UNIPROT:Q9F1R2
UNIPROT:B3EWP1
UNIPROT:O05218
UNIPROT:Q9F466
UNIPROT:P76114
UNIPROT:P0AFR9
UNIPROT:P0AFK4
UNIPROT:P0AFK9
UNIPROT:P69874
UNIPROT:P9WP07
UNIPROT:A0A0K8P8E7
UNIPROT:P42419
UNIPROT:P80064
UNIPROT:P0A6D5
UNIPROT:P37676
UNIPROT:Q9KR66
UNIPROT:P37674
UNIPROT:Q88FX7
UNIPROT:Q72LL6
UNIPROT:P23836
UNIPROT:D0ZV89
UNIPROT:P77526
UNIPROT:O32242
UNIPROT:P21161
UNIPROT:P52003
UNIPROT:Q46871
UNIPROT:O34360
UNIPROT:P16575
UNIPROT:P71040
UNIPROT:P9WNH5
UNIPROT:B3EWP1
UNIPROT:P0A0H9
UNIPROT:A0A0A1H8I4
UNIPROT:Q07806
UNIPROT:O34816
UNIPROT:O32130
UNIPROT:P25888
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[DO:] Go to the the website linked above, and past in your IDs in the search field. You can now browse through the pathways encoded by those genes.

Visualising in KEGG

Visualising in KEGG ( the Kyoto Encyclopedia of Genes and Genomes) allows us to zoom in further into the metabolism. The best way to approach this, is to take all protein sequences produced by prokka (the .faa file) and do a protein blast to the KEGG database with blastKOala. This takes quite some time and requires an account, so I did this for you already. The files are available in the data/blastKOala directory. Note that the bin numbers may not match up between my example and your own run, this is just for illustration of what's possible with the method.

[DO:] Upload and visualise these simple tables on KEGG reconstruct pathway

You may feel overwhelmed by the number of pathways, modules and genes available to you. For this specific case, we are interested in Nitrogen metabolism. You may have a look at the Dijkhuizen et al. 2018 paper on Azolla endophytes. Figure 4 of that paper shows the nitrogen metabolism of multiple microbes is plotted. Next, some hypotheses are derived and tested in the wet lab. Does your plot of the nitrogen metabolism overlap with the one published? Or did you maybe discover a new endophyte!

http://www.genome.jp/kegg/tool/map_module.html

ls data/blastKOala -1

bin_1_KO.txt
bin_2_KO.txt
bin_3_KO.txt
bin_4_KO.txt
bin_5_KO.txt
bin_6_KO.txt
KO_combined.txt

A snapshot of the KEGG nitrogen metabolism pathway looks like this (with the KO_combined.txt file as input).

You may feel overwhelmed by the number of pathways, modules and genes available to you. For this specific case, we are interested in Nitrogen metabolism. You may have a look at the Dijkhuizen et al. 2018 paper on Azolla endophytes. Find of that paper, this shows the nitrogen metabolism of multiple microbes. Next, some hypotheses are derived and tested in the wet lab. Does your plot of the nitrogen metabolism overlap with the one published? Or did you maybe discover a new endophyte!