GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Burkholderia phytofirmans PsJN

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate BPHYT_RS15595 BPHYT_RS15595 ABC transporter

Query= TCDB::Q55164
         (267 letters)



>FitnessBrowser__BFirm:BPHYT_RS15595
          Length = 257

 Score =  190 bits (483), Expect = 2e-53
 Identities = 99/247 (40%), Positives = 154/247 (62%)

Query: 19  LLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLFN 78
           L  +G++K FGGL+A+    + +K G I GLIGPNGAGKTT FN+++    PD GE   +
Sbjct: 7   LSVKGVNKRFGGLQALSEVGLEIKSGQIYGLIGPNGAGKTTFFNVITGLYTPDSGEFKLD 66

Query: 79  GDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQK 138
           G++    A +Q+A  G  RTFQ  ++   +T LEN+++    +T    +  +      +K
Sbjct: 67  GENYTPTAVYQVAKAGIARTFQNIRLFGGMTALENVMVGRHVRTKHGLIGAVFQTPAERK 126

Query: 139 EERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGVN 198
           EER  +E+A+ +LE VG+   A   +  LS G ++ LE+ARAL ++PKL+ LDEPAAG+N
Sbjct: 127 EEREIKERAIELLEYVGIAQYADYTSRNLSYGHQRRLEIARALATDPKLLALDEPAAGMN 186

Query: 199 PTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSDPR 258
            T   ++ + +      G T L+IEH++ ++M LC+ + VL  G+ +A G P+ +Q DP+
Sbjct: 187 ATEKVELTKLLDKIRADGKTILLIEHDVKLVMGLCNQMTVLDYGKVIAQGLPQDVQKDPK 246

Query: 259 VLEAYLG 265
           V+EAYLG
Sbjct: 247 VIEAYLG 253


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: 206
Number of extensions: 8
Number of successful extensions: 1
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: 257
Length adjustment: 25
Effective length of query: 242
Effective length of database: 232
Effective search space:    56144
Effective search space used:    56144
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 17 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