GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Pseudarthrobacter sulfonivorans Ar51

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_058929663.1 AU252_RS04335 ABC transporter ATP-binding protein

Query= TCDB::Q55164
         (267 letters)



>NCBI__GCF_001484605.1:WP_058929663.1
          Length = 345

 Score =  224 bits (572), Expect = 1e-63
 Identities = 114/248 (45%), Positives = 166/248 (66%), Gaps = 1/248 (0%)

Query: 18  LLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLF 77
           +++A+ +++SFGG+ AVD   + +    IT LIGPNGAGKTTLFNLL+ F  P+ G+  F
Sbjct: 38  IVVAENVTRSFGGINAVDVEYLEIPRHKITALIGPNGAGKTTLFNLLTGFDMPNSGKWQF 97

Query: 78  NGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQ 137
            G+S+  ++P+++A  G VRTFQ+ KV+ +LTV+ENM L    Q GE+    L       
Sbjct: 98  EGNSLAGISPYKVARMGMVRTFQLTKVMGKLTVMENMRLGGSEQPGERLSKALFKGLWGG 157

Query: 138 KEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGV 197
           +E+    + A  +LE   L AK  DYA +LSGGQRKLLEMAR+LM  PKL++LDEP AGV
Sbjct: 158 REKEITAQ-ANVLLEKFKLDAKKDDYAASLSGGQRKLLEMARSLMVRPKLVMLDEPMAGV 216

Query: 198 NPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSDP 257
           NP L   + +HI N   +G+T L +EH+M+++  +   V V+AEG+ +A+G P ++  +P
Sbjct: 217 NPALTQSLLDHIKNLKAEGMTVLFVEHDMNMVRHIADWVVVMAEGKIVAEGPPGEVMKNP 276

Query: 258 RVLEAYLG 265
            V++AYLG
Sbjct: 277 AVIDAYLG 284


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: 248
Number of extensions: 12
Number of successful extensions: 2
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: 345
Length adjustment: 27
Effective length of query: 240
Effective length of database: 318
Effective search space:    76320
Effective search space used:    76320
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: 48 (23.1 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