GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Crocosphaera subtropica ATCC 51142

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_009545830.1 CCE_RS09615 LPS export ABC transporter ATP-binding protein

Query= TCDB::Q55164
         (267 letters)



>NCBI__GCF_000017845.1:WP_009545830.1
          Length = 238

 Score =  120 bits (300), Expect = 3e-32
 Identities = 77/251 (30%), Positives = 129/251 (51%), Gaps = 18/251 (7%)

Query: 19  LLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLFN 78
           L+ + + K++G    V+  ++ V  G I GL+GPNGAGKTT F + +  I+P++G V  N
Sbjct: 3   LILENIHKTYGKRDIVNRVNLKVAPGEIVGLLGPNGAGKTTTFYIATGLIKPNKGRVWLN 62

Query: 79  GDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQK 138
              + +L  ++ A  G     Q   +   L+V EN+ +A   QT   F  R      + K
Sbjct: 63  QQEVTRLPLNKRARLGIGYMTQQPSIFRHLSVAENIQVA-LEQTNVPFRQRPQRLHTLLK 121

Query: 139 EERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARAL---MSNPKLILLDEPAA 195
           E R         LE +     A      +SGG+R+  E+AR+L      P  +LLDEP A
Sbjct: 122 EFR---------LEKI-----AHTKGSQVSGGERRRTELARSLAVGQQGPDFLLLDEPFA 167

Query: 196 GVNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQS 255
           GV+P  + +I   I     + +  L+ +HN+   + + +  +++ +G+ LA G+ E+I +
Sbjct: 168 GVDPIAVSEIQTMIAQLCDRQMGILITDHNVQATLAITNRAYIMRDGQILAAGSAEEIYN 227

Query: 256 DPRVLEAYLGD 266
           +P V + YLG+
Sbjct: 228 NPLVRQYYLGN 238


Lambda     K      H
   0.319    0.136    0.389 

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: 130
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: 267
Length of database: 238
Length adjustment: 24
Effective length of query: 243
Effective length of database: 214
Effective search space:    52002
Effective search space used:    52002
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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