GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metC in Echinicola vietnamensis KMM 6221, DSM 17526

Align Cystathionine beta-lyase; CBL; EC 4.4.1.13; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase (uncharacterized)
to candidate Echvi_2283 Echvi_2283 Cystathionine beta-lyases/cystathionine gamma-synthases

Query= curated2:P0C2T9
         (380 letters)



>lcl|FitnessBrowser__Cola:Echvi_2283 Echvi_2283 Cystathionine
           beta-lyases/cystathionine gamma-synthases
          Length = 391

 Score =  258 bits (660), Expect = 2e-73
 Identities = 142/367 (38%), Positives = 216/367 (58%), Gaps = 11/367 (2%)

Query: 23  SVPIYQTSTYKQNGLGQPKEYE--------YSRSGNPTRHALEELIADLEGGVQGFAFSS 74
           S PIY TS++  +   + ++          YSR  NP    L E +  +EG   G A +S
Sbjct: 24  SAPIYMTSSFTFDSAEEARQMFAEEIPGNIYSRYANPNSSDLIEKVCAVEGTEDGIATAS 83

Query: 75  GLAGIH-AVLSLFSAGDHIILADDVYGGTFRLVDKVLTKTGIIYDLVDLSNLEDLKAAFK 133
           G+A +  ++ SL   GDHI+ +  ++G T +L+ +V  K GI     D+S++E+     K
Sbjct: 84  GMAAMFGSMASLLEQGDHILASRSLFGSTHQLLTRVFPKWGITSTYGDISDIENWDKLVK 143

Query: 134 AETKAVYFETPSNPLLKVLDIKEISSIAKAHNALTLVDNTFATPYLQQPIALGADIVLHS 193
             TK ++ ETPSNP L+V+D++ I   AKAHN + +VDN FATPYLQQP   GADIV HS
Sbjct: 144 PNTKMLFIETPSNPGLEVIDLEWIGKFAKAHNLILVVDNCFATPYLQQPAKWGADIVAHS 203

Query: 194 ATKYLGGHSDVVAGLVTTNSNELAIEIGFLQNSIGAVLGPQDSWLVQRGIKTLAPRMEAH 253
           ATKY+ G   V+ GL+     EL  E+ F     G  + P ++W++ R ++TLA RME H
Sbjct: 204 ATKYIDGQGRVLGGLI-LGKQELIKEVQFFTRHTGPSISPFNAWILSRSMETLAIRMERH 262

Query: 254 SANAQKIAEFLEASQAVSKVYYPGLVNHEGHEIAKKQMTAFGGMISFELTDE-NAVKNFV 312
            ANA  +A + + ++ +  V YP L +H  H++AKKQM   GG+++  L       + F+
Sbjct: 263 CANALAVASYFQDNKELEFVKYPFLKSHPQHDLAKKQMKHGGGIVTLTLKGGIERAQRFI 322

Query: 313 ENLRYFTLAESLGGVESLIEVPAVMTHASIPKELREEIGIKDGLIRLSVGVEALEDLLTD 372
           + L+  T+  +LG   S+I  PA  TH+ + +E R+ +GI  GLIRLS G+E  +D++ D
Sbjct: 323 DELQMITVTANLGDTRSIITHPASTTHSKLTEEERQRVGILPGLIRLSAGLEHHDDIIAD 382

Query: 373 LKEALEK 379
           ++ ALE+
Sbjct: 383 IERALER 389


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: 363
Number of extensions: 11
Number of successful extensions: 4
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: 391
Length adjustment: 30
Effective length of query: 350
Effective length of database: 361
Effective search space:   126350
Effective search space used:   126350
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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