GapMind for catabolism of small carbon sources

 

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

Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate 349858 BT0330 ketoisovalerate oxidoreductase subunit vorA (NCBI ptt file)

Query= SwissProt::P80907
         (478 letters)



>FitnessBrowser__Btheta:349858
          Length = 235

 Score =  236 bits (603), Expect = 5e-67
 Identities = 110/230 (47%), Positives = 154/230 (66%)

Query: 26  ATHYCAGCGHGILHKLIGEAIDELGIQERSVMISPVGCAVFAYYYFDCGNVQVAHGRAPA 85
           A HYC GC HG++HKL+ E I+E+G++E++V +SPVGCAVFAY Y D    + AHGRAPA
Sbjct: 5   AMHYCPGCSHGVVHKLVAEVIEEMGMEEKTVGVSPVGCAVFAYNYLDIDWQEAAHGRAPA 64

Query: 86  VGTGISRAEDTPVVLLYQGDGDLASIGLNETIQAANRGEKMAVFFVNNTVYGMTGGQMAP 145
           V T I R     +V  YQGDGDLA IG  ETI A NRGE + + F+NN +YGMTGGQMAP
Sbjct: 65  VATAIKRLWPDRLVFTYQGDGDLACIGTAETIHALNRGENITIIFINNAIYGMTGGQMAP 124

Query: 146 TTLIGEVTVTCPGGRDPRYAGYPLHMCELLDNLQAPVFIERVSLADPKSIRKAKRAVKRA 205
           TTL+G  + TCP GRD    GYPL + E+   L+   ++ R S+    +IRKAK+A+++A
Sbjct: 125 TTLVGMKSSTCPYGRDVELHGYPLKITEIAAQLEGTAYVTRQSVQSVPAIRKAKKAIRKA 184

Query: 206 LEIQRDGKGYAFVEVLSPCPTNLRQDAEGAERFLKEEMEREFPVKNFRDR 255
            E   +GKG   VE++S C +  +   E + ++++E M   +P+ + +D+
Sbjct: 185 FENSMNGKGSNLVEIVSTCSSGWKMTPEKSNKWMEEHMFPFYPLGDLKDK 234


Lambda     K      H
   0.318    0.137    0.402 

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: 300
Number of extensions: 9
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: 478
Length of database: 235
Length adjustment: 28
Effective length of query: 450
Effective length of database: 207
Effective search space:    93150
Effective search space used:    93150
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate 349857 BT0329 ketoisovalerate oxidoreductase subunit vorA (NCBI ptt file)

Query= SwissProt::P80907
         (478 letters)



>FitnessBrowser__Btheta:349857
          Length = 180

 Score =  114 bits (284), Expect = 3e-30
 Identities = 55/132 (41%), Positives = 84/132 (63%), Gaps = 1/132 (0%)

Query: 301 IAGFGGQGVLSMGLTLAQAACSEGRHTSWYPAYGPEQRGGTSSCGVVISGERVGSPAVDT 360
           IAGFGGQGVLSMG  LA +   EG+  SW PAYGPEQRGGT++  V++S +++ SP +  
Sbjct: 7   IAGFGGQGVLSMGKILAYSGLMEGKEVSWMPAYGPEQRGGTANVTVIVSDDKISSPILSK 66

Query: 361 PDVLVAFNQPSLDEFAGDVREGGIVLYD-TATADFSKKENLRAIGVPALEIAKEHGTGRA 419
            D  +  NQPSL++F   V+ GGI++YD     +   +++++   + A++ A E    +A
Sbjct: 67  YDTAIILNQPSLEKFESRVKPGGILIYDGYGIINPPTRKDIKVYRIDAMDAANEMNNAKA 126

Query: 420 ANTAMLGVMMAL 431
            N  +LG ++ L
Sbjct: 127 FNMIVLGGLLQL 138


Lambda     K      H
   0.318    0.137    0.402 

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: 187
Number of extensions: 9
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: 478
Length of database: 180
Length adjustment: 26
Effective length of query: 452
Effective length of database: 154
Effective search space:    69608
Effective search space used:    69608
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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