GapMind for catabolism of small carbon sources

 

Alignments for a candidate for vorB in Geotalea uraniireducens Rf4

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 WP_011939118.1 GURA_RS11370 3-methyl-2-oxobutanoate dehydrogenase subunit VorB

Query= SwissProt::P80908
         (352 letters)



>NCBI__GCF_000016745.1:WP_011939118.1
          Length = 351

 Score =  318 bits (814), Expect = 2e-91
 Identities = 166/320 (51%), Positives = 222/320 (69%), Gaps = 1/320 (0%)

Query: 6   VKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVYG 65
           VKGN AV + A+ AGC  YFGYPITP S+I    SR  P +G +F+QAESE A+INM+ G
Sbjct: 7   VKGNEAVAMAAIEAGCRYYFGYPITPQSDIPEYLSRELPKLGGEFIQAESEIASINMLLG 66

Query: 66  AAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQADYNQLV 125
           A+A G R MT+SS PG+SLKQEGIS++AG+ELP VIV++ R+GPGLG I   QADY Q V
Sbjct: 67  ASATGVRAMTSSSSPGISLKQEGISYMAGSELPGVIVNISRSGPGLGGIDASQADYFQSV 126

Query: 126 KGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRFPERA 185
           KGGGHG Y  +VLAP SVQEM DLTM AF+LAD YR P ++L D+V+GQM E L    R 
Sbjct: 127 KGGGHGGYHIVVLAPASVQEMYDLTMLAFDLADIYRMPAMVLGDSVVGQMKEALVANRRP 186

Query: 186 VEHRPDTSWAVCGSRETMKNLVTSIFLDFDELEEFNFYLQEKYAAVEENEVRYEEYMVED 245
               P   WAV G  +  + +V S+FL   ELE  N+ L  KY  ++E E R+EE+   D
Sbjct: 187 ETKLPPKDWAVRGKGDGEQRVVKSLFLGDGELEAHNWRLHAKYQELKERETRWEEFETAD 246

Query: 246 AEIVLVAYGISSRVAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAEGGCTFISVEM 305
           A++++ A+G ++R+ K+AV  AR  G+KVGLLRP+TLFPFP + + +  +     + +E+
Sbjct: 247 AQLLVTAFGSTARIVKTAVLMARDAGLKVGLLRPVTLFPFPEKALLQATQQCKKVLDIEL 306

Query: 306 SSGQMREDIKMASGCRDVEL 325
           ++GQM ED+++ S  RD E+
Sbjct: 307 NTGQMVEDVRL-SVARDAEV 325


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: 336
Number of extensions: 11
Number of successful extensions: 1
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: 351
Length adjustment: 29
Effective length of query: 323
Effective length of database: 322
Effective search space:   104006
Effective search space used:   104006
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 Apr 09 2024. 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