GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CBS in Echinicola vietnamensis KMM 6221, DSM 17526

Align Putative cystathionine beta-synthase MT1108; EC 4.2.1.22; Beta-thionase; Serine sulfhydrase (uncharacterized)
to candidate Echvi_0220 Echvi_0220 cysteine synthase B

Query= curated2:P9WP50
         (464 letters)



>FitnessBrowser__Cola:Echvi_0220
          Length = 292

 Score =  195 bits (495), Expect = 2e-54
 Identities = 118/299 (39%), Positives = 166/299 (55%), Gaps = 13/299 (4%)

Query: 9   ELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLKPGGTIV 68
           ELIG TPLV L  +  +    +  K+E  NPGGS KDR A  MI+ A   G LK G  +V
Sbjct: 5   ELIGNTPLVELEHIPTNPNVKIYCKLEGQNPGGSVKDRAAYSMIKRAMDRGDLKQGDRVV 64

Query: 69  EPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPPHDPASY 128
           E TSGNTG+ LA++A+  G +   + PD  + ++   + AYGA+V++ P A        Y
Sbjct: 65  EATSGNTGIALAMIAKVLGVEMTLIMPDNSTRERVVSMEAYGAKVILTPAA----KTIEY 120

Query: 129 YSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGTGGTITG 188
                  +   +G +  +Q+ANP+   +HY  TGPEI  DT G++THFV+ +GT GTI G
Sbjct: 121 SRTLAEEMAKNEGYYILNQFANPDNYQAHYEGTGPEIMRDTNGEITHFVSAMGTTGTIMG 180

Query: 189 AGRYLKEVSGGRVRIVGADP-EGSVYSGGAGRPYLVEGVGEDFWPAAYDPSVPDEIIAVS 247
             RYLKE     V+IVG  P +GS   G       +     +F P  YD S  D+II VS
Sbjct: 181 VSRYLKEQKPA-VQIVGTQPTDGSSIPG-------IRRWSPEFLPKIYDASRVDQIIDVS 232

Query: 248 DSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRGYMSKIF 306
             ++ +MTRR+A+EE +L G S G A+ AA+K+AE      ++ +    G R   S +F
Sbjct: 233 QEEATEMTRRMAKEEGILAGMSSGGALHAAVKLAESLDSGVIVCITCDRGDRYLSSDLF 291


Lambda     K      H
   0.316    0.135    0.398 

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: 356
Number of extensions: 12
Number of successful extensions: 3
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: 464
Length of database: 292
Length adjustment: 30
Effective length of query: 434
Effective length of database: 262
Effective search space:   113708
Effective search space used:   113708
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: 41 (21.6 bits)
S2: 49 (23.5 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