GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Desulfovibrio vulgaris Miyazaki F

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 8501378 DvMF_2110 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q97VF4
         (324 letters)



>FitnessBrowser__Miya:8501378
          Length = 316

 Score =  158 bits (399), Expect = 2e-43
 Identities = 98/305 (32%), Positives = 165/305 (54%), Gaps = 44/305 (14%)

Query: 27  ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86
           A+  VSL++++G  L ++GESG GK+TL R++VGL  P++G+V+ DG        ++F  
Sbjct: 11  AVDGVSLTLDRGRTLGLVGESGCGKSTLARMVVGLLPPSAGQVLLDG--------RLFAG 62

Query: 87  YRKD-----------------------VQLIPQDPYSTLPFNKTVEEILVAPILRWEKIN 123
              D                       VQ++ QDP+S+L   +TV    +   L    + 
Sbjct: 63  TDGDAANGGASGHSADLAISRAEAAQLVQMVFQDPFSSLNPRRTVGAS-IGEALAVAGVP 121

Query: 124 KDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTM 183
             E R ++ ++L+LV L    E   +YPH+ SGGQ+QR+++AR+L  +P ++V DEPV+ 
Sbjct: 122 GPERRAKVADMLQLVGLRA--EHADRYPHEFSGGQRQRVAVARALITHPALVVCDEPVSS 179

Query: 184 VDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADL 243
           +DAS++  +LN L E++  + L  +FI+HD+ +     H+ D  +  VM+ G++VE A  
Sbjct: 180 LDASVQAQVLNLLRELQEHMGLAYLFISHDLGVVG---HMSD--HVAVMYLGKVVEEAPR 234

Query: 244 EEILKDPLHPYTNDLIKLTPSIDNLYKEINVKINYE-----RVEKGCPYRLRCPFAMDIC 298
           + +   P HPYT  L+   P  D   +  +  ++ +         GCP+  RCP  MD+C
Sbjct: 235 DVLFAAPAHPYTRALLASVPVRDPSRRAEHPALSGDLPSPIAPPPGCPFHPRCPQVMDVC 294

Query: 299 KNEEP 303
           + + P
Sbjct: 295 RRQVP 299


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: 264
Number of extensions: 11
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: 324
Length of database: 316
Length adjustment: 28
Effective length of query: 296
Effective length of database: 288
Effective search space:    85248
Effective search space used:    85248
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