GapMind for catabolism of small carbon sources

 

Alignments for a candidate for vorB in Bacteroides thetaiotaomicron VPI-5482

Align Ketoisovalerate oxidoreductase subunit VorB; VOR; 2-oxoisovalerate ferredoxin reductase subunit beta; 2-oxoisovalerate oxidoreductase beta chain; EC 1.2.7.7 (characterized)
to candidate 349859 BT0331 ketoisovalerate oxidoreductase subunit vorB (NCBI ptt file)

Query= SwissProt::P80908
         (352 letters)



>FitnessBrowser__Btheta:349859
          Length = 295

 Score =  266 bits (680), Expect = 5e-76
 Identities = 149/291 (51%), Positives = 194/291 (66%), Gaps = 7/291 (2%)

Query: 62  MVYGAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQADY 121
           MVYG A +G  V+T+SS PG+SLKQEGIS++AGAELP +IV+VMR GPGLG I P QADY
Sbjct: 1   MVYGGAGSGKMVLTSSSSPGVSLKQEGISYIAGAELPCLIVNVMRGGPGLGTIQPSQADY 60

Query: 122 NQLVKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAE---- 177
            Q VKGGGHG+YR I LAP SVQEM D     FELA KYRNP IILAD V+GQM E    
Sbjct: 61  FQTVKGGGHGDYRLIALAPASVQEMADFVALGFELAFKYRNPAIILADGVIGQMMEKVVL 120

Query: 178 PLRFPERA-VEHRPDTSWAVCGSRETMK-NLVTSIFLDFDELEEFNFYLQEKYAAVEENE 235
           P + P R   E      WA  G  +  K N++TS+ L  + +E  N   Q KY  +EENE
Sbjct: 121 PAQKPRRTDAEVIEQCPWAATGKAKGRKPNIITSLELKPEAMEINNIRFQAKYKQIEENE 180

Query: 236 VRYEEYMVEDAEIVLVAYGISSRVAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAE 295
           VR+EE   EDAE ++VA+G  +R+ + A++ AR  GIKVG+LRPITL+PFPS+ I   A+
Sbjct: 181 VRFEEINCEDAEYLIVAFGSMARIGQKAMELAREKGIKVGILRPITLWPFPSKAIAAYAD 240

Query: 296 GGCTFISVEMSSGQMREDIKMA-SGCRDVELVNRMGGNLIELRDILRKIRE 345
                +  E+++GQM ED+++A +G   VE   R+GG + +  +I+  + E
Sbjct: 241 KVKGMLVTELNAGQMIEDVRLAVNGKVKVEHFGRLGGIVPDPDEIVTALEE 291


Lambda     K      H
   0.319    0.136    0.390 

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: 290
Number of extensions: 4
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: 352
Length of database: 295
Length adjustment: 28
Effective length of query: 324
Effective length of database: 267
Effective search space:    86508
Effective search space used:    86508
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 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