Alignments for a candidate for serA in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Burkholderia phytofirmans PsJN

Align Phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate BPHYT_RS03150 BPHYT_RS03150 FAD-linked oxidase

Query= reanno::BFirm:BPHYT_RS03150
         (1364 letters)



>FitnessBrowser__BFirm:BPHYT_RS03150
          Length = 1364

 Score = 2742 bits (7107), Expect = 0.0
 Identities = 1364/1364 (100%), Positives = 1364/1364 (100%)

Query: 1    MNAPQVFDPHGAAATVAADPEARLREIPYNYTSFSDREIVIRLLGDEAWAVLAELRAERR 60
            MNAPQVFDPHGAAATVAADPEARLREIPYNYTSFSDREIVIRLLGDEAWAVLAELRAERR
Sbjct: 1    MNAPQVFDPHGAAATVAADPEARLREIPYNYTSFSDREIVIRLLGDEAWAVLAELRAERR 60

Query: 61   TGRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRAMLIEALHHRLSEIEKRRRADLTEH 120
            TGRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRAMLIEALHHRLSEIEKRRRADLTEH
Sbjct: 61   TGRSARMLYEVLGDIWVVRRNPYLQDDLLDNPKRRAMLIEALHHRLSEIEKRRRADLTEH 120

Query: 121  GDEAGVDRAARVETLVQAARRAVDEFASEFQKTYDLRKRATKVLGKVTEKDNIKFDGLSR 180
            GDEAGVDRAARVETLVQAARRAVDEFASEFQKTYDLRKRATKVLGKVTEKDNIKFDGLSR
Sbjct: 121  GDEAGVDRAARVETLVQAARRAVDEFASEFQKTYDLRKRATKVLGKVTEKDNIKFDGLSR 180

Query: 181  VSHVTDATDWRVEYPFVVLTPDTEAEIAGMIKACFELGLTVIPRGGGTGYTGGAVPLTPF 240
            VSHVTDATDWRVEYPFVVLTPDTEAEIAGMIKACFELGLTVIPRGGGTGYTGGAVPLTPF
Sbjct: 181  VSHVTDATDWRVEYPFVVLTPDTEAEIAGMIKACFELGLTVIPRGGGTGYTGGAVPLTPF 240

Query: 241  SAVINTEKLEQLGAVEMTELPGVDRKVATIFSGAGVVTRRVTEAAEQAGFVFAVDPTSLD 300
            SAVINTEKLEQLGAVEMTELPGVDRKVATIFSGAGVVTRRVTEAAEQAGFVFAVDPTSLD
Sbjct: 241  SAVINTEKLEQLGAVEMTELPGVDRKVATIFSGAGVVTRRVTEAAEQAGFVFAVDPTSLD 300

Query: 301  ASCVGGNVAMNAGGKKAVLWGTALDNLAWWRMVDPEGNWLEVTRLDHNMGKIHDIEVARF 360
            ASCVGGNVAMNAGGKKAVLWGTALDNLAWWRMVDPEGNWLEVTRLDHNMGKIHDIEVARF
Sbjct: 301  ASCVGGNVAMNAGGKKAVLWGTALDNLAWWRMVDPEGNWLEVTRLDHNMGKIHDIEVARF 360

Query: 361  RLDWFDGNYAPGEKLMRTEALDIKGRVFRKEGLGKDVTDKFLAGLPGVQKEGCDGLITSA 420
            RLDWFDGNYAPGEKLMRTEALDIKGRVFRKEGLGKDVTDKFLAGLPGVQKEGCDGLITSA
Sbjct: 361  RLDWFDGNYAPGEKLMRTEALDIKGRVFRKEGLGKDVTDKFLAGLPGVQKEGCDGLITSA 420

Query: 421  RWVLHKMPAHTRTVCLEFFGQARDAIPSIVEIKDYLFETSKQGGAILAGLEHLDERYLRA 480
            RWVLHKMPAHTRTVCLEFFGQARDAIPSIVEIKDYLFETSKQGGAILAGLEHLDERYLRA
Sbjct: 421  RWVLHKMPAHTRTVCLEFFGQARDAIPSIVEIKDYLFETSKQGGAILAGLEHLDERYLRA 480

Query: 481  VGYATKSKRNAFPKMVLIGDIVGDDADAVAQATSEVVRMANGKSGEGFVAVNAEARKRFW 540
            VGYATKSKRNAFPKMVLIGDIVGDDADAVAQATSEVVRMANGKSGEGFVAVNAEARKRFW
Sbjct: 481  VGYATKSKRNAFPKMVLIGDIVGDDADAVAQATSEVVRMANGKSGEGFVAVNAEARKRFW 540

Query: 541  LDRSRTAAIAKHTNAFKINEDVVIPLDRMGEYTDGIERINIELSIKNKLQLVDALEAFFK 600
            LDRSRTAAIAKHTNAFKINEDVVIPLDRMGEYTDGIERINIELSIKNKLQLVDALEAFFK
Sbjct: 541  LDRSRTAAIAKHTNAFKINEDVVIPLDRMGEYTDGIERINIELSIKNKLQLVDALEAFFK 600

Query: 601  GGKLPLGKSDDANEIPSAELLEDRVQQALDLLKRVRTRWEFLRDKLDLSLREAQHYLVGL 660
            GGKLPLGKSDDANEIPSAELLEDRVQQALDLLKRVRTRWEFLRDKLDLSLREAQHYLVGL
Sbjct: 601  GGKLPLGKSDDANEIPSAELLEDRVQQALDLLKRVRTRWEFLRDKLDLSLREAQHYLVGL 660

Query: 661  GYEAMAEKFADRVDAQPDVNVFHVTQDRTIRVSWKQEIRAELRQIFNGGEFKPILDEAQA 720
            GYEAMAEKFADRVDAQPDVNVFHVTQDRTIRVSWKQEIRAELRQIFNGGEFKPILDEAQA
Sbjct: 661  GYEAMAEKFADRVDAQPDVNVFHVTQDRTIRVSWKQEIRAELRQIFNGGEFKPILDEAQA 720

Query: 721  IHKQVLRGRVFVALHMHAGDGNVHTNLPVNSDNYEMLQDAHTAVARIMKLARSLDGVISG 780
            IHKQVLRGRVFVALHMHAGDGNVHTNLPVNSDNYEMLQDAHTAVARIMKLARSLDGVISG
Sbjct: 721  IHKQVLRGRVFVALHMHAGDGNVHTNLPVNSDNYEMLQDAHTAVARIMKLARSLDGVISG 780

Query: 781  EHGIGITKLEFLTEDEISEFRQYKQRVDPHGRFNAGKLLEGADLRNAYTPSFGLMGYESL 840
            EHGIGITKLEFLTEDEISEFRQYKQRVDPHGRFNAGKLLEGADLRNAYTPSFGLMGYESL
Sbjct: 781  EHGIGITKLEFLTEDEISEFRQYKQRVDPHGRFNAGKLLEGADLRNAYTPSFGLMGYESL 840

Query: 841  IMQQSDIGAISESIKDCLRCGKCKPVCATHVPRANLLYSPRNKILATSLLVEAFLYEEQT 900
            IMQQSDIGAISESIKDCLRCGKCKPVCATHVPRANLLYSPRNKILATSLLVEAFLYEEQT
Sbjct: 841  IMQQSDIGAISESIKDCLRCGKCKPVCATHVPRANLLYSPRNKILATSLLVEAFLYEEQT 900

Query: 901  RRGVSIKHWDEFNDVADHCTVCHKCVTPCPVKIDFGDVTMNMRNLLRKMGKKKFNPGNAA 960
            RRGVSIKHWDEFNDVADHCTVCHKCVTPCPVKIDFGDVTMNMRNLLRKMGKKKFNPGNAA
Sbjct: 901  RRGVSIKHWDEFNDVADHCTVCHKCVTPCPVKIDFGDVTMNMRNLLRKMGKKKFNPGNAA 960

Query: 961  GMFFLNATNPQTINLARTAMMGVGYKAQRLGNEVLKKFTKKQTAHPPATVGKPPVTQQVI 1020
            GMFFLNATNPQTINLARTAMMGVGYKAQRLGNEVLKKFTKKQTAHPPATVGKPPVTQQVI
Sbjct: 961  GMFFLNATNPQTINLARTAMMGVGYKAQRLGNEVLKKFTKKQTAHPPATVGKPPVTQQVI 1020

Query: 1021 HFMNKKMPGNLPKKTARALLDIEDNKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVG 1080
            HFMNKKMPGNLPKKTARALLDIEDNKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVG
Sbjct: 1021 HFMNKKMPGNLPKKTARALLDIEDNKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVG 1080

Query: 1081 LATQAMLWEAGVQTVLPPGYLCCGYPQRGSGQFDKAEQIVTDNRVLFHRVANTLNYLDIK 1140
            LATQAMLWEAGVQTVLPPGYLCCGYPQRGSGQFDKAEQIVTDNRVLFHRVANTLNYLDIK
Sbjct: 1081 LATQAMLWEAGVQTVLPPGYLCCGYPQRGSGQFDKAEQIVTDNRVLFHRVANTLNYLDIK 1140

Query: 1141 TVVVSCGTCYDQLAGYEFEKIFPGCRIIDIHEFLLEKGMKLDGVNGVRYMYHDPCHTPIK 1200
            TVVVSCGTCYDQLAGYEFEKIFPGCRIIDIHEFLLEKGMKLDGVNGVRYMYHDPCHTPIK
Sbjct: 1141 TVVVSCGTCYDQLAGYEFEKIFPGCRIIDIHEFLLEKGMKLDGVNGVRYMYHDPCHTPIK 1200

Query: 1201 TMDPIKLVNQLMGSEKDGYKIEKNDRCCGESGTLAVTRPDISTQVRFRKEEEIRKGAAKL 1260
            TMDPIKLVNQLMGSEKDGYKIEKNDRCCGESGTLAVTRPDISTQVRFRKEEEIRKGAAKL
Sbjct: 1201 TMDPIKLVNQLMGSEKDGYKIEKNDRCCGESGTLAVTRPDISTQVRFRKEEEIRKGAAKL 1260

Query: 1261 RGIPLVAEAGANGINPANASAGSAGAPEGSVLKAGDGPQPKGATDVKILTSCPSCLQGLS 1320
            RGIPLVAEAGANGINPANASAGSAGAPEGSVLKAGDGPQPKGATDVKILTSCPSCLQGLS
Sbjct: 1261 RGIPLVAEAGANGINPANASAGSAGAPEGSVLKAGDGPQPKGATDVKILTSCPSCLQGLS 1320

Query: 1321 RYNEDAGIEADYIVVEMARHVLGEDWMVDYVQRANNGGIERVLV 1364
            RYNEDAGIEADYIVVEMARHVLGEDWMVDYVQRANNGGIERVLV
Sbjct: 1321 RYNEDAGIEADYIVVEMARHVLGEDWMVDYVQRANNGGIERVLV 1364


Lambda     K      H
   0.320    0.136    0.406 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 5002
Number of extensions: 180
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1364
Length of database: 1364
Length adjustment: 49
Effective length of query: 1315
Effective length of database: 1315
Effective search space:  1729225
Effective search space used:  1729225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (27.7 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis