GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metC in Shewanella sp. ANA-3

Align Cystathionine beta-lyase; CBL; EC 4.4.1.13; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase (uncharacterized)
to candidate 7026472 Shewana3_3614 cystathionine gamma-synthase (RefSeq)

Query= curated2:P0C2T9
         (380 letters)



>lcl|FitnessBrowser__ANA3:7026472 Shewana3_3614 cystathionine
           gamma-synthase (RefSeq)
          Length = 393

 Score =  322 bits (826), Expect = 9e-93
 Identities = 172/375 (45%), Positives = 237/375 (63%), Gaps = 1/375 (0%)

Query: 4   LKTKVIHGGISTDRTTGAVSVPIYQTSTYKQNGLGQPKEYEYSRSGNPTRHALEELIADL 63
           L T  +  GI +D   GAV  PIY ++ Y  +G   P+E++YSRSGNPTR  L + +A L
Sbjct: 12  LATLAVRQGIESDTQYGAVVPPIYLSTNYAFDGHKNPREFDYSRSGNPTRSILGDALAKL 71

Query: 64  EGGVQGFAFSSGLAGIHAVLSLFSAGDHIILADDVYGGTFRLVDKVLTKTGIIYDLVDLS 123
           E G  G    +G+A I  V +L    D +++  D YGG++RL   +  K      +VD +
Sbjct: 72  EKGATGVVTCTGMAAITLVTTLLGPDDLLVVPHDCYGGSYRLFTNLAKKGQFKLLVVDQT 131

Query: 124 NLEDLKAAFKAETKAVYFETPSNPLLKVLDIKEISSIAKAHNALTLVDNTFATPYLQQPI 183
           + + L+ A   + K V+ ETPSNPLL+V+DI+ I+  + A  AL +VDNTF +P LQQP+
Sbjct: 132 DAQALEQAIAQQPKMVWIETPSNPLLRVVDIEAIAKASHAVGALVVVDNTFLSPILQQPL 191

Query: 184 ALGADIVLHSATKYLGGHSDVVAGLVTTNSNELAIEIGFLQNSIGAVLGPQDSWLVQRGI 243
            LGADIV+HS TKY+ GHSDVV G V     +L   + +  N++G      DS+   RG+
Sbjct: 192 LLGADIVIHSTTKYINGHSDVVGGAVIAKDPQLGETLHWWSNTLGLTGSAFDSYQTLRGL 251

Query: 244 KTLAPRMEAHSANAQKIAEFLEASQAVSKVYYPGLVNHEGHEIAKKQMTAFGGMISFELT 303
           +TLA R+  H +NAQ+I + L +S  VSKVYYPGL +H GH IA KQ   FG M+SFEL 
Sbjct: 252 RTLAVRIREHQSNAQRIVDVLTSSPVVSKVYYPGLADHPGHAIAAKQQKGFGAMLSFELK 311

Query: 304 -DENAVKNFVENLRYFTLAESLGGVESLIEVPAVMTHASIPKELREEIGIKDGLIRLSVG 362
             E  V  F++ L  F++AESLGGVESL+ VPA MTH ++  + R E GIKD L+RLSVG
Sbjct: 312 GGEAEVVAFLDALSLFSVAESLGGVESLVAVPATMTHRAMEPQARFEAGIKDTLLRLSVG 371

Query: 363 VEALEDLLTDLKEAL 377
           +E  +DL+ D++  L
Sbjct: 372 IEDADDLVADIQAGL 386


Lambda     K      H
   0.315    0.133    0.367 

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: 403
Number of extensions: 13
Number of successful extensions: 2
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: 380
Length of database: 393
Length adjustment: 30
Effective length of query: 350
Effective length of database: 363
Effective search space:   127050
Effective search space used:   127050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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