GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Lacinutrix algicola AKS293

Align NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_055435882.1 ASC41_RS06790 ATP-binding cassette domain-containing protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_001418085.1:WP_055435882.1
          Length = 308

 Score =  111 bits (278), Expect = 2e-29
 Identities = 74/237 (31%), Positives = 121/237 (51%), Gaps = 31/237 (13%)

Query: 11  LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70
           LL A  + K+FG   A+    I V +GSI GL+GPNGAGKTTL  +++    PDKG+V+ 
Sbjct: 4   LLEAQSVSKNFGDFTALNNVSISVEKGSIFGLLGPNGAGKTTLIRIINQITMPDKGQVLL 63

Query: 71  DGEPIQQLQPHQIA----QQGMVRTFQVARTLSRLSVLENMLLA-AQKQTGENFWQVQLQ 125
           DGEP+Q+     I     ++G+ +T +V      L+ L+ +  A A+K+  E F ++++ 
Sbjct: 64  DGEPLQRHHIQNIGYLPEERGLYKTMKVGEQALYLAQLKGLDKAEAKKRLHEWFERLEIG 123

Query: 126 PQVVVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDE 185
                   K++QE                     LS G  + ++    ++  PKL++ DE
Sbjct: 124 DW----WNKKIQE---------------------LSKGMAQKIQFVVTVLHQPKLLIFDE 158

Query: 186 PAAGVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADG 242
           P +G +P   D I + IL   R+DG T +   H M+ +  LCD + ++ +   + DG
Sbjct: 159 PFSGFDPINADIIKNEILRL-REDGATVIFSTHRMESVEELCDHIALIHKSNKILDG 214


Lambda     K      H
   0.319    0.136    0.391 

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: 145
Number of extensions: 6
Number of successful extensions: 3
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: 260
Length of database: 308
Length adjustment: 26
Effective length of query: 234
Effective length of database: 282
Effective search space:    65988
Effective search space used:    65988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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