Alignments for a candidate for serA in Desulfobacter vibrioformis DSM 8776

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Desulfobacter vibrioformis DSM 8776

Align Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) (characterized)
to candidate WP_035238518.1 Q366_RS09695 DUF3683 domain-containing protein

Query= reanno::HerbieS:HSERO_RS19500
         (1333 letters)



>NCBI__GCF_000745975.1:WP_035238518.1
          Length = 1197

 Score =  729 bits (1883), Expect = 0.0
 Identities = 465/1306 (35%), Positives = 672/1306 (51%), Gaps = 136/1306 (10%)

Query: 24   REIPYNYTSFSDREIVIRLLGEESWSLLDELRGKRQTGRSARMLYEVLGDIWVVRRNPYL 83
            R+IP+NYTS  D +I+  L G E  S +  L   + TGRS+R+L+  +GD++++ RN +L
Sbjct: 6    RKIPFNYTSAGDDQIIAHLFGNEILSTIQILETLKGTGRSSRLLHRFMGDLFIINRNAFL 65

Query: 84   QDDLLDNPKRRAALIEALNHRLGEVDKRRLATDQAEAGDAEAQRRSASVEALLKAAKKAI 143
              +L+++P  R  L     + L  +           AG AE +     V  +L A + ++
Sbjct: 66   FQELVEHPMLRRRLFTEFENDLFNI-----------AGHAEHEE----VRIVLDACRSSL 110

Query: 144  ADFAEEFRQTYDLRKRATKVLGRFTAKDNIKFDGLSRVSHVTDATDWRVEYPFVVLTPDT 203
                ++ R     + R T+ L     K NI FD  +  SH TDATDWR   P  VL PD 
Sbjct: 111  RQLKDQIRAVAKEQTRVTRRLSPVAGKANICFDPFNITSHATDATDWRRYMPAAVLRPDR 170

Query: 204  EDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTPMSAVINTEKLEQLGAVE-MEILPG 262
            ED++  LVK    L   IIPRGGGTG TGGA PL P   +INTEKL  +  +E  +   G
Sbjct: 171  EDQIPKLVKKLKNLRFHIIPRGGGTGLTGGATPLAPDCVMINTEKLNTIFPIEHRKTKDG 230

Query: 263  LDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSAEASCIGGNVAMNAGGKKAVLWGT 322
             D  YA +   AGV+T+   DAA   G++FA DPTSA A  IGGN+A NAGGK AVL+GT
Sbjct: 231  RD--YAVMPLQAGVITQNAKDAAAAQGYIFATDPTSAWACTIGGNLAENAGGKTAVLYGT 288

Query: 323  ALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVARFKLEWSHPGEKGQKTEVFKTEIL 382
            A+DN+ ++R+  P G  L V R DH L KI   +  RF +      E GQ  +      +
Sbjct: 289  AIDNVLAFRITMPDGRLLTVARQDHPLRKIRYEDTLRFVVT----DETGQILDT-----I 339

Query: 383  EISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLITSARWILHKMPKQTRTVCLEFFGQ 442
            E++G   RK+ LGKDVT+K L G+PG+QKEGCDG+IT A +IL+       T C+EFFG 
Sbjct: 340  ELTGADIRKKHLGKDVTNKVLGGVPGLQKEGCDGIITWAEFILYPEFAHKATCCIEFFGN 399

Query: 443  -ARDAIPSIVEIKDYLDAETKKGGAILAGLEHLDERYLRAVGYATKSKRGVLPKMVLIGD 501
               +A   I ++    D         L  LEH DE Y++A+ Y TK   G   K VL+ D
Sbjct: 400  DMTEAGKVITQVCTRFD----NSDPALMALEHFDEEYIKAIKYKTKRSVGDRLKAVLLID 455

Query: 502  IVGDDENAV--AAAASEVIRMANNRVGEGFVAVSPEARKKFWLDRSRTAAIAKHTNAFKI 559
            +V +D   +       E I    ++ G        EA + +W DR R  AIA HTNAFK+
Sbjct: 456  MVSNDAVTLDQGLRGLETILEPYDKTGLSIARDRAEAAR-YWEDRKRLGAIAAHTNAFKL 514

Query: 560  NEDVVIPLNRMGEYTDGIERINIELSIKNKLQLLAELDSFFVKGNLPLGKSDDAEGDDIP 619
            NED+V+P++ + ++   +++ NIE             +  + +G + L            
Sbjct: 515  NEDIVLPIDSLADFVRFVDQTNIE-------------EKKYTQGRIIL------------ 549

Query: 620  AAEMLEDRVHQAESLLEQTHARWSYLLANLDKPLGEAKGELAALGLEKMLPVFEQRLVDQ 679
                  + +   E+ +  +  +W      L K +G  K    A  + K L +  +  ++ 
Sbjct: 550  ------NILTYLETAIPLSDPQW------LGKKVGRIKD--IAYSIRKKLDIASRDALE- 594

Query: 680  PEAAVFHVVQDRTVRISWKQEVRAQLRQIFSGAAFKLILEECQAIHKRVLRGRVFVALHM 739
               A  H         ++  +++  LR       +  IL   + I+   L   + +A HM
Sbjct: 595  ---AFIHTK-------NFHGQIQDHLR------GYSQILSNVEGIYNDTLSRLIVIATHM 638

Query: 740  HAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIGITKLEFLTEDE 799
            HAGDGNVH NIPV S+   ML  AH+   ++M  A +L+GV+SGEHGIG+TK ++L ED+
Sbjct: 639  HAGDGNVHVNIPVFSNDRAMLARAHMTADKVMAKAVALDGVVSGEHGIGVTKFKYLNEDQ 698

Query: 800  IGEFREYKKRVDPEGRFNKGKLLNLPGMEADLSNA-YTPSFGLMGHESLIMQQSDIGAIA 858
            + +F  Y+K+VDP G  N GKL      E D+ N  +TPSF L+  E+ I++   +  +A
Sbjct: 699  VNQFDAYRKQVDPNGLMNPGKL-----SEPDILNKMFTPSFNLLELEAQILKHGSLSDLA 753

Query: 859  SSVKDCLRCGKCKPVCSTHVPRANLLYSPRNKILATSLLVEAFLYEEQTRRGVSIKHWEE 918
            +++  C+RCGKCKP C    P  N+ + PRNK LA   L+EA LY  Q  +    K  + 
Sbjct: 754  ANISHCVRCGKCKPQCPVFYPARNMFFHPRNKNLAIGALIEALLYITQRIQSTKFKVLKN 813

Query: 919  FEDVADHCTVCHKCVTPCPVDIDFGDVSMNMRNLLRKMGKKSFNAGTNAAMFFLNATDPA 978
             E +ADHCT+CHKC+  CPV+ID G +S+  R +L+KM  K     T   + +L + +  
Sbjct: 814  LEQIADHCTICHKCLDKCPVNIDSGVISIKEREILKKMDFKHTPVSTQLTLGYLGSRNQI 873

Query: 979  TINATRKVMTQWGFKAQRLGNDLMK--KFAKKQTQKPPATVGKPPVKEQVIHFINKKMPG 1036
                 R  +   G  AQR    L K   F     +  P  +   PV +  +  +   +P 
Sbjct: 874  LNPVIRTGLLAGGSSAQRTAVKLAKPISFIPALKETRPLQMLHAPVSQPGLTTLRTHLP- 932

Query: 1037 NLPKKTARALLDIEDDKIVPIIRNPKTTTADTEAVFYFPGCGSERLFSQVGLATQAMLWN 1096
                           D+   I+ NP      T  VFYFPGCGSER+FS +  AT  +L  
Sbjct: 933  -------------HADRNQAILLNPPGRAVST--VFYFPGCGSERMFSNISKATIFLLLF 977

Query: 1097 VGVQTVLPPGYLCCGYPQRGTGDFEKGEKIITDNRVLFHRMANTLNYLDIKTVVVSCGTC 1156
             G Q VLPP YLCCGYP +      + +K+  +N ++  ++ +  N LD   V+VSCGTC
Sbjct: 978  QGHQVVLPPPYLCCGYPLKVNARTNEAQKVSLENTIIMTQIRDMFNDLDFSGVIVSCGTC 1037

Query: 1157 YDQLQGYEFEKIFPGCRIIDIHEYLLEKGVKLEGVTGTRYMYHDPCHSPMKQQDPLKTVN 1216
             + L       +F G R+ DI  YL E G+ +        +YH PCH  +K     +   
Sbjct: 1038 MESLSDLGITDLF-GARLFDISGYLFENGLTI--AQPQTCLYHTPCHDSLKGTAGAQLAK 1094

Query: 1217 SLITTIDAQKIEKNDRCCGESGTFGVSRPDVSTQVRFRKE---EEMRKGSDKVRADGFTG 1273
            +    IDA+ +     CC E+GT  +SRPD+S  +  RK+   E+ R+G DK      T 
Sbjct: 1095 A---GIDARAV---PYCCSEAGTMALSRPDISYSMFLRKQDAIEQARQGLDK------TP 1142

Query: 1274 DVKILTSCPSCFQGLSRYNEDAGTTADYIVVEMARHLLGENWMPEY 1319
              KILT+CPSC QGL R ++    TA ++ VE+AR   G  WM ++
Sbjct: 1143 KPKILTNCPSCVQGLGRQHQ---VTAVHMAVELARLTGGAGWMNQF 1185


Lambda     K      H
   0.319    0.136    0.402 

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: 3239
Number of extensions: 139
Number of successful extensions: 15
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 1333
Length of database: 1197
Length adjustment: 48
Effective length of query: 1285
Effective length of database: 1149
Effective search space:  1476465
Effective search space used:  1476465
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 (21.7 bits)
S2: 59 (27.3 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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