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 207019 DVU1569 pyruvate ferredoxin oxidoreductase, alpha subunit

Query= SwissProt::P80908
         (352 letters)



>MicrobesOnline__882:207019
          Length = 578

 Score =  111 bits (277), Expect = 5e-29
 Identities = 92/331 (27%), Positives = 143/331 (43%), Gaps = 47/331 (14%)

Query: 5   MVKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVY 64
           M++GN A+ +GA+ AG      YP+TPA+ +      +   +G    QAE E AA+NMV 
Sbjct: 190 MLQGNEAIALGALAAGVKFCAFYPMTPATSVAQNLILHAERMGVVVEQAEDEIAAMNMVL 249

Query: 65  GAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLG-NIGPEQADYNQ 123
           GA+ AG R +  +SG G +L  EG+S     E P VIV   R GP  G     EQAD + 
Sbjct: 250 GASYAGARALVPTSGGGFALMTEGVSLAGVMEQPVVIVLAQRPGPATGLPTRTEQADLD- 308

Query: 124 LVKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLG---------- 173
           L    GHG +  ++ AP + ++   LT  AF+LA++++ P  +L D  L           
Sbjct: 309 LALYAGHGEFPRVIFAPATPEDCFHLTYAAFDLAERFQIPAFVLTDQYLADSYRPVAPFD 368

Query: 174 -QMAEPLRFPERAVEHRPDTSWAVCGSRETMKNLVTS--------------IFLDFDELE 218
                PL  P+ + +  P+      G R     L  S              +  D  E  
Sbjct: 369 LDALPPLAEPDFSTDKGPE------GDRYKRYELTKSGISPRRIPGFSKSLVLADCHEHT 422

Query: 219 EFNFYLQEKYAAVEENEVRYEE-------------YMVEDAEIVLVAYGISSRVAKSAVD 265
           E  +  ++    +  ++ R  +             +  E  +++L  +G S      A  
Sbjct: 423 EQGYITEDAGLRIAMSDKRLRKGDGLRSMALPPRCFGDEAPDLLLACWGSSEGAVVEAAQ 482

Query: 266 TARADGIKVGLLRPITLFPF-PSERIRELAE 295
             RA G KVG+L    ++P  PS+ +    E
Sbjct: 483 RLRARGRKVGVLSFTQVWPLEPSQFLSRCGE 513


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: 489
Number of extensions: 33
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: 578
Length adjustment: 33
Effective length of query: 319
Effective length of database: 545
Effective search space:   173855
Effective search space used:   173855
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: 51 (24.3 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