GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Caldicellulosiruptor hydrothermalis 108

Align ATPase (characterized, see rationale)
to candidate WP_013403450.1 CALHY_RS07950 methionine ABC transporter ATP-binding protein

Query= uniprot:Q31RN8
         (261 letters)



>NCBI__GCF_000166355.1:WP_013403450.1
          Length = 343

 Score =  167 bits (422), Expect = 4e-46
 Identities = 92/245 (37%), Positives = 150/245 (61%), Gaps = 6/245 (2%)

Query: 21  MIYAEGVEKWY---GNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRG 77
           MI  + + K Y   G   +AL  V+L +++G++  ++GPSG+GKST +R +N LE    G
Sbjct: 1   MIRIKNLTKIYHSNGIDIKALDNVNLNIEKGDIFGIIGPSGAGKSTLIRCINMLEKPTHG 60

Query: 78  EIWIEGHRLSH-DRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEA 136
            I I+G  ++     ++  +R++VG++FQ FNL    TV  N+   P+++        + 
Sbjct: 61  SIEIDGVEMTKLSPTELKEMRKKVGIIFQHFNLLSSRTVKGNVAF-PLEIAGLDKKTIDN 119

Query: 137 TARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREV 196
             ++LLE V +  + D YP QLSGGQ+QRV IARALA  P++LL DE TSALDPE    +
Sbjct: 120 RVKELLELVGLTNKTDSYPSQLSGGQKQRVGIARALANNPKVLLCDEATSALDPETTLSI 179

Query: 197 LDVMRDLASE-GMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQ 255
           L++++++  E G+T++V THE+   +++ ++V +M  GQIVE+      F  P++  A+ 
Sbjct: 180 LNLLKEINREFGITIVVVTHEMNVVKQICNKVAVMEKGQIVEQGLLTEIFANPKTKIAQN 239

Query: 256 FLAQI 260
           FL  +
Sbjct: 240 FLRSL 244


Lambda     K      H
   0.321    0.134    0.387 

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: 164
Number of extensions: 8
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: 261
Length of database: 343
Length adjustment: 27
Effective length of query: 234
Effective length of database: 316
Effective search space:    73944
Effective search space used:    73944
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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