GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Lysobacter daejeonensis GH1-9

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_084087424.1 N800_RS09205 ABC transporter ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_000768355.1:WP_084087424.1
          Length = 560

 Score = 75.5 bits (184), Expect = 2e-18
 Identities = 70/230 (30%), Positives = 105/230 (45%), Gaps = 30/230 (13%)

Query: 16  GLCKSFGGIKAVQEA-RIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGEP 74
           G+  ++ G  A+ E+  + +  G    + GPNGAGK+TL +LL  F+ PD+GRV+ DG  
Sbjct: 339 GVGFAYPGRPALYESLNLSIRVGETVAITGPNGAGKSTLAHLLLRFVAPDQGRVLLDGVD 398

Query: 75  IQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVKEEK 134
           I +L+   +     + + QV   L   +VL+N+                  P     E +
Sbjct: 399 ISELRLSNLRSHVGLVSQQV--LLFHGTVLDNIAYG--------------HPTAGQAEVE 442

Query: 135 QLQEQAMFLLESVGLAKKAYEYAGG----LSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190
                AM     VGL        G     LSGGQR+ + + R L+ NP +I+LDE  A  
Sbjct: 443 AAANAAMAHDFIVGLPDGYRTVVGDQGVRLSGGQRQRIALARVLLRNPAVIVLDEATAMF 502

Query: 191 NP---RLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQ 237
           +P   R     C  +L     +G T L+I H     ++L DRV  L  G+
Sbjct: 503 DPEAERAFIARCHAVL-----EGRTVLLITHR-PASLALADRVLRLDGGR 546


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: 267
Number of extensions: 15
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 260
Length of database: 560
Length adjustment: 30
Effective length of query: 230
Effective length of database: 530
Effective search space:   121900
Effective search space used:   121900
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: 50 (23.9 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