GapMind for catabolism of small carbon sources

 

Aligments for a candidate for vorB in Desulfovibrio vulgaris Miyazaki F

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 8501322 DvMF_2055 2-ketoisovalerate ferredoxin reductase (RefSeq)

Query= SwissProt::P80908
         (352 letters)



>lcl|FitnessBrowser__Miya:8501322 DvMF_2055 2-ketoisovalerate
           ferredoxin reductase (RefSeq)
          Length = 361

 Score =  313 bits (802), Expect = 4e-90
 Identities = 169/345 (48%), Positives = 228/345 (66%), Gaps = 3/345 (0%)

Query: 6   VKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVYG 65
           +KGN A+  GA+ AGC CYFGYPITP ++I    S   P  G +FVQAESE A+ NM+ G
Sbjct: 16  IKGNEAIAHGALAAGCRCYFGYPITPQNDIPEMMSYALPDAGGEFVQAESEVASANMLLG 75

Query: 66  AAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQADYNQLV 125
           AAAAG R +T+SS PG+SL QE IS++AG+ELP VIV++ R GPGLG+IGP Q DY Q V
Sbjct: 76  AAAAGIRALTSSSSPGISLMQEAISYMAGSELPGVIVNMNRGGPGLGDIGPSQGDYFQSV 135

Query: 126 KGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLR-FPER 184
           KGGGHG+Y+  VLAP + QE  D+ + AF+LA KYRNPV++L DA++GQM EP+  +   
Sbjct: 136 KGGGHGDYKLFVLAPATCQECYDMMVQAFDLAFKYRNPVMVLGDAIVGQMKEPVTPWKPA 195

Query: 185 AVEHRPDTSWAVCGSRETMKNLVTSIFLDFDELEEFNFYLQEKYAAVEENEVRYEEYMVE 244
           AV       W + G++     L+ S+FL+   L   N +LQ KYAA++  E + E ++ +
Sbjct: 196 AVPATEAADWRLEGAKGRKPRLLKSLFLEDGALAGQNRHLQAKYAAMQA-EAKAESFLTD 254

Query: 245 DAEIVLVAYGISSRVAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAEGGCTFISVE 304
           DAE+++VAYG   R+AKSA+   RA G KVGL+RP TLFPFP   +R LAE G  F+++E
Sbjct: 255 DAELIVVAYGSIGRIAKSAIRKLRAQGHKVGLVRPQTLFPFPGPLLRGLAEQGKRFLTIE 314

Query: 305 MSSGQMREDIKMA-SGCRDVELVNRMGGNLIELRDILRKIREIAG 348
            + GQM ED++++  G  D      M G +    D L  I +  G
Sbjct: 315 HNCGQMVEDVRLSIRGIVDSAFYGHMPGEMPGSDDFLAPILDAMG 359


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: 375
Number of extensions: 15
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: 361
Length adjustment: 29
Effective length of query: 323
Effective length of database: 332
Effective search space:   107236
Effective search space used:   107236
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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