GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Rhodobacter viridis JA737

Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate WP_110806514.1 C8J30_RS14100 ABC transporter permease

Query= uniprot:A0A0C4Y7K0
         (337 letters)



>NCBI__GCF_003217355.1:WP_110806514.1
          Length = 339

 Score =  192 bits (488), Expect = 1e-53
 Identities = 121/318 (38%), Positives = 178/318 (55%), Gaps = 24/318 (7%)

Query: 33  LGMLPVLVLLCIGFSVLTENFAGWQ------NLSIIAQQASINMVLAAGMTFVILTGGID 86
           + +L VLV + + F +L   F G         L I+  Q S+  +++ G+T VI+ GGID
Sbjct: 22  VNILFVLVGIALVFEILGWIFQGQSFLMSIDRLKIMILQVSVIGIISVGVTQVIIAGGID 81

Query: 87  LSVGSILSISAVVAMLVS--------LMPQL----GMLSVPAALLCGLLFGIVNGALVAF 134
           LS GS++   A+ AM  +        + P L     ++ +   L+ G L G++NGAL+A+
Sbjct: 82  LSSGSVVGAVAMFAMSFAQVSTYARAVYPDLTDLPAIVPIALGLMAGALVGLINGALIAY 141

Query: 135 MKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAVVAV 194
            K+PPFI TLGT+   RG A+       I  P   FAFIG G +      V I  AV A+
Sbjct: 142 AKIPPFIATLGTMVTARGFAKWYTKGQPISFPTDDFAFIGKGMMP-----VAIFLAVAAI 196

Query: 195 SWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAA 254
               ++ T  G   YA+G N +AAR+SGI V   L+ VY V+  LA L G++ +AR   A
Sbjct: 197 FHVAMKYTRYGKFTYAIGANQQAARVSGINVEHHLIKVYVVAATLAALAGMVVAARGQTA 256

Query: 255 NGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYI 314
               +G +YELDAIA  ++GG S  GG GSI+GT++G +I  V+ +G   L +   +Q +
Sbjct: 257 QA-GMGLAYELDAIAMAVIGGVSLTGGRGSILGTMIGMVIFGVIISGFTFLRLDAYYQEM 315

Query: 315 IKGLVIIGAVALDSYRRK 332
           IKG++I+ AV  D YR+K
Sbjct: 316 IKGVIIVAAVVADVYRQK 333


Lambda     K      H
   0.325    0.141    0.409 

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: 343
Number of extensions: 21
Number of successful extensions: 5
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: 337
Length of database: 339
Length adjustment: 28
Effective length of query: 309
Effective length of database: 311
Effective search space:    96099
Effective search space used:    96099
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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