GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1692 in Flavobacterium sp. LM5

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_024982395.1 BXU11_RS05265 LPS export ABC transporter ATP-binding protein

Query= uniprot:A0A165KC78
         (242 letters)



>NCBI__GCF_002017945.1:WP_024982395.1
          Length = 250

 Score =  125 bits (313), Expect = 1e-33
 Identities = 73/237 (30%), Positives = 125/237 (52%), Gaps = 8/237 (3%)

Query: 10  LQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEYL 69
           L+ + L   Y G   VKG+  EV +GE+V L+G NGAGKTT+   I G +  N G+I   
Sbjct: 3   LRAENLIKTYKGRSVVKGISLEVNQGEIVGLLGPNGAGKTTSFYMIVGLVKPNSGHIYLD 62

Query: 70  GKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITEN----LQMGAYIRKDKAGILADIEKM 125
              I     +   ++G+  + +   VF +++I +N    LQ+  + ++++   +  +   
Sbjct: 63  DLDITQYPMYKRAQQGVGYLAQEASVFRKLSIEDNILSVLQLTNHTKEEQVAKMESLIAE 122

Query: 126 FTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVV 185
           F++   +R  +  L   +SGGE++   + R L + PK +LLDEP  G+ P+ V+ I  +V
Sbjct: 123 FSL-EHIRTNRGDL---LSGGERRRTEIARCLATDPKFILLDEPFAGVDPVAVEDIQRIV 178

Query: 186 RDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLGE 242
             +    + I++ + N    LAI D+ Y+M  G I   G  ++L+ D  VR  YLG+
Sbjct: 179 AQLKNKNIGILITDHNVQETLAITDKTYLMFEGGILKAGTPEELVEDEMVRRVYLGQ 235


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: 146
Number of extensions: 13
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: 250
Length adjustment: 24
Effective length of query: 218
Effective length of database: 226
Effective search space:    49268
Effective search space used:    49268
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 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