GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__ANA3:7026472
          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:

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