GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Bacteroides thetaiotaomicron VPI-5482

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 349829 BT0301 ATP-binding transport protein natA (Na+ ABC transporter) (NCBI ptt file)

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__Btheta:349829
          Length = 503

 Score = 72.0 bits (175), Expect = 2e-17
 Identities = 49/158 (31%), Positives = 82/158 (51%), Gaps = 12/158 (7%)

Query: 23  QAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEYLGKSIKGKGAWDLV 82
           +A++GV FE++ G +  L+G NGAGK+T M+ I G    + G+I   G   +      + 
Sbjct: 230 KALRGVSFEIQTG-MFGLLGPNGAGKSTLMRVICGIFEQSYGSIWINGLDTR------IY 282

Query: 83  KEGLV----MVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFTIFP-RLRERKD 137
           +E L      +P+  G +  MT  E L   A ++    G L      + +    + ERKD
Sbjct: 283 REELQSLIGFLPQEFGTYENMTSWEFLDYQAILKGIVDGDLRRERLDYVLKAVHMYERKD 342

Query: 138 QLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSP 175
           +  G+ SGG +Q + +   L+  P++L++DEP+ GL P
Sbjct: 343 EKIGSFSGGMKQRIGIALILLHLPRILVVDEPTAGLDP 380


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: 231
Number of extensions: 16
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: 503
Length adjustment: 29
Effective length of query: 213
Effective length of database: 474
Effective search space:   100962
Effective search space used:   100962
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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