GapMind for catabolism of small carbon sources

 

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

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 353166 BT3640 lipoprotein releasing system ATP-binding protein (NCBI ptt file)

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__Btheta:353166
          Length = 218

 Score = 91.3 bits (225), Expect = 1e-23
 Identities = 66/217 (30%), Positives = 111/217 (51%), Gaps = 7/217 (3%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMND-GNIE 67
           +++++G+  ++G +Q +KG+D E+ +GE+VS++G +GAGKTT ++ I GTL   D G + 
Sbjct: 1   MIKLEGITKSFGSLQVLKGIDLEINKGEIVSIVGPSGAGKTTLLQ-IMGTLDEPDAGTVA 59

Query: 68  YLG---KSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEK 124
             G     +K K       + +  V +   +    T  EN+ + A+I    +    +   
Sbjct: 60  IDGTVVSRMKEKELSAFRNKNIGFVFQFHQLLPEFTALENVMIPAFIAGVSSKEANERAM 119

Query: 125 MFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEV 184
               F  L +R       +SGGE+Q +A+ RAL++ P V+L DEPS  L     + + ++
Sbjct: 120 EILAFMGLTDRASHKPNELSGGEKQRVAVARALINHPAVILADEPSGSLDTHNKEDLHQL 179

Query: 185 VRDVY-ALGVTIVLVEQNASRALAIADRGYVMESGLI 220
             D+   LG T V+V  +   A  I DR   M  G I
Sbjct: 180 FFDLRDRLGQTFVIVTHDEGLA-KITDRTVHMVDGTI 215


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: 120
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: 242
Length of database: 218
Length adjustment: 23
Effective length of query: 219
Effective length of database: 195
Effective search space:    42705
Effective search space used:    42705
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 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