GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Flavobacterium sp. LM5

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_024982395.1 BXU11_RS05265 LPS export ABC transporter ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_002017945.1:WP_024982395.1
          Length = 250

 Score =  138 bits (348), Expect = 1e-37
 Identities = 87/249 (34%), Positives = 132/249 (53%), Gaps = 16/249 (6%)

Query: 12  LAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFD 71
           L A  L K++ G   V+   +EV QG I GL+GPNGAGKTT F ++   ++P+ G +  D
Sbjct: 3   LRAENLIKTYKGRSVVKGISLEVNQGEIVGLLGPNGAGKTTSFYMIVGLVKPNSGHIYLD 62

Query: 72  GEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVK 131
              I Q   ++ AQQG+    Q A    +LS+ +N+L   Q            + + V K
Sbjct: 63  DLDITQYPMYKRAQQGVGYLAQEASVFRKLSIEDNILSVLQLTN-------HTKEEQVAK 115

Query: 132 EEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVN 191
            E  + E   F LE +   +        LSGG+R+  E+ R L T+PK ILLDEP AGV+
Sbjct: 116 MESLIAE---FSLEHIRTNR-----GDLLSGGERRRTEIARCLATDPKFILLDEPFAGVD 167

Query: 192 PRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTNS 251
           P  ++DI  RI+   +   +  LI +HN+   +++ D+ +++ EG  L  GTP E+  + 
Sbjct: 168 PVAVEDI-QRIVAQLKNKNIGILITDHNVQETLAITDKTYLMFEGGILKAGTPEELVEDE 226

Query: 252 QVLEAYLGK 260
            V   YLG+
Sbjct: 227 MVRRVYLGQ 235


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: 134
Number of extensions: 7
Number of successful extensions: 4
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: 250
Length adjustment: 24
Effective length of query: 236
Effective length of database: 226
Effective search space:    53336
Effective search space used:    53336
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