GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Mesorhizobium ciceri biovar biserrulae WSM1271

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_013529094.1 MESCI_RS06155 ATP-binding cassette domain-containing protein

Query= TCDB::Q55164
         (267 letters)



>NCBI__GCF_000185905.1:WP_013529094.1
          Length = 518

 Score =  176 bits (446), Expect = 9e-49
 Identities = 104/260 (40%), Positives = 154/260 (59%), Gaps = 12/260 (4%)

Query: 17  SLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVL 76
           ++L    LS  FGGL A+       K G IT LIGPNGAGKTT+FN ++ F +P +G + 
Sbjct: 16  AILQVDHLSMKFGGLVAIGDLSFAAKRGEITALIGPNGAGKTTVFNCITGFYKPSEGMIT 75

Query: 77  FNGDS-----IGQLAPHQIALRGSV-RTFQVAKVLSRLTVLENMLLADQHQ----TGEKF 126
            N +      + +L  H+I  R  V RTFQ  ++ S +T+LEN+L+A  ++    +G   
Sbjct: 76  LNRNDGSTFLLERLPNHEIPARAKVARTFQNIRLFSGMTLLENLLVAQHNKLMKASGYTV 135

Query: 127 LPRLINFRRVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPK 186
           L  L  F   +K    + E A   LE   L  +A D AG L  G ++ LE+ARA+ + P+
Sbjct: 136 L-GLFGFSGYRKASAESVELAKHWLEKADLVDRADDPAGDLPYGAQRRLEIARAMCTGPE 194

Query: 187 LILLDEPAAGVNPTLIGQICEHIVN-WNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNL 245
           L+ LDEPAAG+NP     + E +++  N  G + L+IEH+M V+M +  HV VL  GR +
Sbjct: 195 LLCLDEPAAGLNPKESAALNELLIDIKNTSGASILLIEHDMSVVMQISDHVVVLEYGRKI 254

Query: 246 ADGTPEQIQSDPRVLEAYLG 265
           +DG+P+ +++DPRV+ AYLG
Sbjct: 255 SDGSPQSVRTDPRVIAAYLG 274


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: 306
Number of extensions: 11
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: 267
Length of database: 518
Length adjustment: 30
Effective length of query: 237
Effective length of database: 488
Effective search space:   115656
Effective search space used:   115656
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: 49 (23.5 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