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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

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:

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:

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:

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