GapMind for catabolism of small carbon sources

 

Alignments for a candidate for vorB in Desulfovibrio vulgaris Hildenborough

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 208876 DVU3349 pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-binding domain protein

Query= SwissProt::P80908
         (352 letters)



>MicrobesOnline__882:208876
          Length = 357

 Score =  301 bits (772), Expect = 1e-86
 Identities = 165/347 (47%), Positives = 227/347 (65%), Gaps = 6/347 (1%)

Query: 6   VKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVYG 65
           +KGN A+  GA+ AGC CYFGYPITP ++I    S   P  G +FVQAESE AA NM+ G
Sbjct: 11  IKGNEAIAHGALAAGCRCYFGYPITPQNDIPEMMSSAIPAAGGEFVQAESEVAAANMLLG 70

Query: 66  AAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQADYNQLV 125
           AAA G R  T+SS PG+SL QE IS++AG+ELP VIV++ R GPGLG+IGP Q DY Q V
Sbjct: 71  AAACGVRAFTSSSSPGVSLMQEAISYMAGSELPGVIVNMNRGGPGLGDIGPSQGDYFQSV 130

Query: 126 KGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRFPERA 185
           KGGGHG+YR  VLAP + QE  D+  +AF++A ++R PV++L DA++GQM EP+  P + 
Sbjct: 131 KGGGHGDYRTYVLAPATCQECYDMMFEAFDVAYRFRTPVLVLGDAIVGQMKEPVT-PWKR 189

Query: 186 VEHRPDT---SWAVCGSRETMKNLVTSIFLDFDELEEFNFYLQEKYAAVEENEVRYEEYM 242
            +  P T    W + G++     L+ S+FL+   L   N  LQ KY A++E   R E + 
Sbjct: 190 DDLDPATEGADWRLQGAKGRPARLLKSLFLEDGALAGQNRNLQAKYEAMKE-LARAECFE 248

Query: 243 VEDAEIVLVAYGISSRVAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAEGGCTFIS 302
            EDA++V+VA+G   R+AKSA+   RA G KVGL+RP+TLFPFP + +++LA  G  F++
Sbjct: 249 TEDADLVVVAFGSIGRIAKSAIRKLRAQGHKVGLVRPVTLFPFPEKVLQDLAAKGKRFLT 308

Query: 303 VEMSSGQMREDIKMA-SGCRDVELVNRMGGNLIELRDILRKIREIAG 348
           +E + GQM +D+++A     D +    M G L    D L+ I +  G
Sbjct: 309 IEHNCGQMVDDVRLAVRAYCDSDFYGHMPGELPGSDDFLKPILDALG 355


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: 378
Number of extensions: 16
Number of successful extensions: 3
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: 357
Length adjustment: 29
Effective length of query: 323
Effective length of database: 328
Effective search space:   105944
Effective search space used:   105944
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: 49 (23.5 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