GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1692 in Pseudarthrobacter sulfonivorans Ar51

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_058929181.1 AU252_RS01290 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC78
         (242 letters)



>NCBI__GCF_001484605.1:WP_058929181.1
          Length = 239

 Score =  180 bits (457), Expect = 2e-50
 Identities = 97/226 (42%), Positives = 145/226 (64%), Gaps = 1/226 (0%)

Query: 4   KSNKVLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMND 63
           + ++ LL V+ L V YG I+AV GV   V  GE V L G+NGAGK+TT+KAI G++  + 
Sbjct: 5   RRDEELLAVRDLVVNYGPIRAVSGVSIGVHRGETVVLCGANGAGKSTTIKAIMGSVPASS 64

Query: 64  GNIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIE 123
           G++   G+ I    A    + G+ + PEGR VFA MT+ EN+++GA+  K        +E
Sbjct: 65  GSVHLDGQPITTVSAALRARRGIRLSPEGRQVFATMTVEENIRIGAHQLK-ATDRNTRVE 123

Query: 124 KMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFE 183
           ++F  FP L ER+   AG +SGG+QQ++AMGRA+ S+P++LLLDEP +GL+PI +  + +
Sbjct: 124 ELFDTFPLLAERRRSRAGDLSGGQQQIVAMGRAMASRPRLLLLDEPFLGLAPIWIASVSD 183

Query: 184 VVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQL 229
            +R V A G  +++ EQ A  AL +ADRGYV++ G I   G   ++
Sbjct: 184 AIRTVQAAGTALLISEQMARPALELADRGYVLKHGSIARRGTADEV 229


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: 140
Number of extensions: 4
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: 242
Length of database: 239
Length adjustment: 23
Effective length of query: 219
Effective length of database: 216
Effective search space:    47304
Effective search space used:    47304
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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