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.
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:
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