GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CBS in Paraburkholderia bryophila 376MFSha3.1

Align Putative cystathionine beta-synthase MT1108; EC 4.2.1.22; Beta-thionase; Serine sulfhydrase (uncharacterized)
to candidate H281DRAFT_03911 H281DRAFT_03911 cysteine synthase

Query= curated2:P9WP50
         (464 letters)



>FitnessBrowser__Burk376:H281DRAFT_03911
          Length = 300

 Score =  200 bits (509), Expect = 5e-56
 Identities = 126/302 (41%), Positives = 174/302 (57%), Gaps = 18/302 (5%)

Query: 7   ISELIGGTPLVRLNSVVPDGA----GTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLK 62
           I + IG TPLV+L  +  D        V AK+E  NP GS KDR A+ MI+ AEA G++K
Sbjct: 6   IEDTIGNTPLVQLVRLPDDEIRSRNNVVLAKLEGNNPAGSVKDRPALSMIKKAEARGRIK 65

Query: 63  PGGTIVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPP 122
           PG T++E TSGNTG+ LA+ A  RGYK V + P+ +S ++R  + AYGA++++ P     
Sbjct: 66  PGDTLIESTSGNTGIALAMAAAIRGYKMVLIMPEDLSVERRQSMAAYGAQIILTPVT--- 122

Query: 123 HDPASYYSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGT 182
                   +++++ RD  G    DQ+ANP+ PA+H   TGPEIW DTEG++THFV+ +GT
Sbjct: 123 GGMEYARDLAEQMQRDGKGIIL-DQFANPDNPAAHVEGTGPEIWRDTEGRITHFVSSMGT 181

Query: 183 GGTITGAGRYLKEVSGGRVRIVGADP-EGSVYSGGAGRPYLVEGVGEDFWPAAYDPSVPD 241
            GTI G   YLK+     + IVGA P EGS   G    P       E + P  +D S  D
Sbjct: 182 TGTIMGVSSYLKQ-QNQAIEIVGAQPEEGSRIPGIRKWP-------EAYMPKIFDRSRVD 233

Query: 242 EIIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRGY 301
            +  VS + +  M RRLA  E +  G S G A   AL+VA +   +A IV ++ D G  Y
Sbjct: 234 RVENVSQAAAEAMARRLASVEGIFAGISSGGACEVALRVARQV-ENATIVFIVCDRGDRY 292

Query: 302 MS 303
           +S
Sbjct: 293 LS 294


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: 387
Number of extensions: 24
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: 464
Length of database: 300
Length adjustment: 30
Effective length of query: 434
Effective length of database: 270
Effective search space:   117180
Effective search space used:   117180
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