GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Btheta:349858 BT0330 ketoisovalerate
           oxidoreductase subunit vorA (NCBI ptt file)
          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)



>lcl|FitnessBrowser__Btheta:349857 BT0329 ketoisovalerate
           oxidoreductase subunit vorA (NCBI ptt file)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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