GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1692 in Dethiosulfovibrio salsuginis USBA 82

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_085545426.1 B9Y55_RS11110 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC78
         (242 letters)



>NCBI__GCF_900177735.1:WP_085545426.1
          Length = 321

 Score =  112 bits (281), Expect = 7e-30
 Identities = 84/241 (34%), Positives = 121/241 (50%), Gaps = 36/241 (14%)

Query: 10  LQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEYL 69
           L+++GL  ++ G +AVK +   V +GE++SL+G +G GKTTT+K I G    + GNI   
Sbjct: 3   LELRGLNKSFQGSRAVKDLSLTVEQGEMISLLGPSGCGKTTTLKMIGGFCLPDSGNIVLE 62

Query: 70  GKSIKGKGAWDLVKEGLVMVPEGR---------GVFARMTITENLQMGAYIRKDKAGILA 120
           G+ I              M PEGR          +F  M++  N+  G   +    GI  
Sbjct: 63  GEDITS------------MAPEGRPTATVFQSYALFPHMSVMGNVTYGLKFK----GIHK 106

Query: 121 DIEKMFTIFPRLRERKDQLAGT-------MSGGEQQMLAMGRALMSQPKVLLLDEPSMGL 173
           D     T   R    K  L G+       +SGGEQQ +A+ R+LM QPKVLLLDEP   L
Sbjct: 107 DRR---TSMGREMLEKVGLPGSGNKGIHQLSGGEQQRVALARSLMIQPKVLLLDEPLSNL 163

Query: 174 -SPIMVDKIFEVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLND 232
            + + V    E+ R    LG+T V V  +   A+A++DR  VME G I   G  +++  +
Sbjct: 164 DAKLRVKMRAEIRRIQRELGITAVYVTHDQEEAMALSDRIAVMEKGSIVQIGTPREVYGE 223

Query: 233 P 233
           P
Sbjct: 224 P 224


Lambda     K      H
   0.317    0.136    0.373 

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: 190
Number of extensions: 10
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: 242
Length of database: 321
Length adjustment: 25
Effective length of query: 217
Effective length of database: 296
Effective search space:    64232
Effective search space used:    64232
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 (21.7 bits)
S2: 47 (22.7 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