GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Bacillus altitudinis 41KF2b

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_017358586.1 BA79_RS12600 glycine betaine/L-proline ABC transporter ATP-binding protein

Query= TCDB::P73650
         (240 letters)



>NCBI__GCF_000691145.1:WP_017358586.1
          Length = 421

 Score =  101 bits (252), Expect = 2e-26
 Identities = 63/209 (30%), Positives = 111/209 (53%), Gaps = 6/209 (2%)

Query: 25  NFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQ---IVRRG 81
           NF +  GE+  ++G +G+GKSTL + +  L+ P+ GEI   G+ IT +  DQ   + R+ 
Sbjct: 53  NFDVYDGEIFVIMGLSGSGKSTLVRLLNRLIEPTSGEIYIDGDMITNMSKDQLREVRRKK 112

Query: 82  MCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFPKLAQR--RNQRAGTLSG 139
           +  V Q   +F   T+ EN + G  L     +  + +       +       Q    LSG
Sbjct: 113 ISMVFQNFALFPHRTILENTEYGLELQGVEKEQRRSKALESLKLVGLEGFEEQYPNQLSG 172

Query: 140 GERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAIN-ATGKAIILVEQNAKQ 198
           G +Q + + RAL  DPD+LL+DE  +AL P++ KD+  ++  ++ + GK II +  +  +
Sbjct: 173 GMQQRVGLARALANDPDILLMDEAFSALDPLIRKDMQDELLELHTSVGKTIIFITHDLDE 232

Query: 199 ALMMADRGYVLENGRDKLEGSGQSLLNDP 227
           AL + DR  ++++G     G+ + +L +P
Sbjct: 233 ALRIGDRIVLMKDGNIVQIGTPEEILMNP 261


Lambda     K      H
   0.320    0.139    0.393 

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: 164
Number of extensions: 8
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: 240
Length of database: 421
Length adjustment: 27
Effective length of query: 213
Effective length of database: 394
Effective search space:    83922
Effective search space used:    83922
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 (21.8 bits)
S2: 48 (23.1 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