GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Bacteroides clarus YIT 12056

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_087412571.1 BUB52_RS05180 phosphate ABC transporter ATP-binding protein

Query= uniprot:D8IUY7
         (241 letters)



>NCBI__GCF_900129655.1:WP_087412571.1
          Length = 250

 Score = 93.2 bits (230), Expect = 4e-24
 Identities = 72/238 (30%), Positives = 122/238 (51%), Gaps = 13/238 (5%)

Query: 4   NILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAIT---GTLPASRV 60
           N ++ + ++  YG   A+KGI +++ E  +V  IG +G GK+T L+ +      +P +R+
Sbjct: 2   NKIETRDVNFWYGDFHALKGISMDIAEKSVVAFIGPSGCGKSTFLRLLNRMNDLIPDTRL 61

Query: 61  EGHIEYLGQPL--KGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSD--DKGQI 116
            G I   GQ +  KG +  EL K+ + MV +    F + SI EN+  G   +   D   I
Sbjct: 62  TGEILIDGQDIYKKGVQVDELRKN-VGMVFQRPNPFPK-SIFENVAYGLRVNGVTDNAFI 119

Query: 117 AADID---KWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSP 173
              ++   K  A++  +K++    A  LSGG+QQ L +ARA+   P +LL+DEP+  L P
Sbjct: 120 RRRVEETLKGAALWDEVKDKLKVSAYALSGGQQQRLCIARAMAVSPSVLLMDEPASALDP 179

Query: 174 IMVEKIFEVIRNVSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDP 231
           I   K+ E+I  +  Q  TI++V  N + A   +        G +   G  +++  +P
Sbjct: 180 ISTAKVEELIHELKKQ-YTIVIVTHNMQQAARVSDSTAFFYMGEMVEFGDTKKIFTNP 236


Lambda     K      H
   0.317    0.134    0.365 

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: 112
Number of extensions: 6
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: 241
Length of database: 250
Length adjustment: 24
Effective length of query: 217
Effective length of database: 226
Effective search space:    49042
Effective search space used:    49042
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: 46 (22.3 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