GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Shewanella amazonensis SB2B

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 6937060 Sama_1231 peptide ABC transporter, ATP-binding protein (RefSeq)

Query= TCDB::Q97VF4
         (324 letters)



>FitnessBrowser__SB2B:6937060
          Length = 261

 Score =  142 bits (358), Expect = 9e-39
 Identities = 76/240 (31%), Positives = 150/240 (62%), Gaps = 10/240 (4%)

Query: 20  FKKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKN 79
           FK++   AL  +S  + +G+ L ++GE+G+GK+TL R++VG ++ +SG++ ++G ++   
Sbjct: 22  FKRQYNEALAPISFELGRGETLAIVGEAGSGKSTLARILVGAEQRSSGDIQFEGESL--- 78

Query: 80  KRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVK 139
           + +  K+  + +++I QDP ++L    ++ E+L  P+     ++  E   ++   L  V 
Sbjct: 79  ESRNLKQRCRLIRMIFQDPNTSLNPRLSIGELLEEPLRFNTGMSAHERSVQVTETLRKVG 138

Query: 140 LTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEI 199
           L P  E    YPH +S GQKQR+++AR+L ++P++I+ADE +T +D S+R  ILN L  +
Sbjct: 139 LLP--EHADFYPHMISEGQKQRVAVARALMLSPKVIIADEALTALDLSVRSQILNLLLHL 196

Query: 200 KNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLI 259
           +  + L+ +F++H++ + R   H+ DK   +V+  G+++E+  ++++ + P H YT  LI
Sbjct: 197 QKEMGLSYIFVSHNLNLVR---HVSDK--IMVLHKGQLIEKGPVQKVFESPEHEYTARLI 251


Lambda     K      H
   0.321    0.141    0.410 

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: 225
Number of extensions: 14
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: 324
Length of database: 261
Length adjustment: 26
Effective length of query: 298
Effective length of database: 235
Effective search space:    70030
Effective search space used:    70030
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 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