Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate 8501323 DvMF_2056 thiamine pyrophosphate protein domain protein TPP-binding (RefSeq)
Query= SwissProt::P80907 (478 letters) >FitnessBrowser__Miya:8501323 Length = 263 Score = 253 bits (645), Expect = 7e-72 Identities = 118/229 (51%), Positives = 158/229 (68%) Query: 26 ATHYCAGCGHGILHKLIGEAIDELGIQERSVMISPVGCAVFAYYYFDCGNVQVAHGRAPA 85 ATHYC GC HGI H+L+ E ++E+G+ + ++ ++ +GC+VF Y Y +V+ HGRAPA Sbjct: 27 ATHYCPGCHHGIAHRLVAEVLEEMGVVDDTICVASIGCSVFIYNYLAVDSVEAPHGRAPA 86 Query: 86 VGTGISRAEDTPVVLLYQGDGDLASIGLNETIQAANRGEKMAVFFVNNTVYGMTGGQMAP 145 V TG+ R +V YQGDGDLASIGL E + AANRGE++ + FVNNTVYGMTGGQMAP Sbjct: 87 VATGVKRGRTDKIVFTYQGDGDLASIGLAEVMHAANRGERITIVFVNNTVYGMTGGQMAP 146 Query: 146 TTLIGEVTVTCPGGRDPRYAGYPLHMCELLDNLQAPVFIERVSLADPKSIRKAKRAVKRA 205 TTLIG+ T TCPGGR G P+ M E++ L + R SL K+IR AK+AV++A Sbjct: 147 TTLIGQKTTTCPGGRCRDREGMPIRMAEIIAGLGGVAYSARASLDSVKNIRAAKKAVRKA 206 Query: 206 LEIQRDGKGYAFVEVLSPCPTNLRQDAEGAERFLKEEMEREFPVKNFRD 254 ++Q+ G G+ FVE+LS CPTN R DA A ++EEM FP+ ++D Sbjct: 207 FDVQQQGLGFGFVELLSGCPTNWRMDAVKANTRIREEMIPYFPLGVYKD 255 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: 367 Number of extensions: 20 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: 263 Length adjustment: 29 Effective length of query: 449 Effective length of database: 234 Effective search space: 105066 Effective search space used: 105066 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 8501324 DvMF_2057 pyruvate ferredoxin/flavodoxin oxidoreductase (RefSeq)
Query= SwissProt::P80907 (478 letters) >FitnessBrowser__Miya:8501324 Length = 180 Score = 120 bits (301), Expect = 4e-32 Identities = 71/176 (40%), Positives = 104/176 (59%), Gaps = 7/176 (3%) Query: 299 VKIAGFGGQGVLSMGLTLAQAACSEGRHTSWYPAYGPEQRGGTSSCGVVISGERVGSPAV 358 V +AGFGGQGV+ +G LA A + G + ++ P YGPE RGGT++C VV+S E +GSP + Sbjct: 7 VIMAGFGGQGVMLIGNLLAYAGMNAGLNVTYIPVYGPEMRGGTANCTVVVSDEDIGSPII 66 Query: 359 DTPDVLVAFNQPSLDEFAGDVREGGIVLYDTATADFSKKE-NLRAIGVPALEIAKEHGTG 417 P L+ NQPSLD+F + +GG+ + +T+ D S+ E +R + VPA +IA + G Sbjct: 67 QRPKSLIVMNQPSLDKFQPRLEDGGVQVLNTSLVDASQAEARVRTVCVPANDIADKLGNT 126 Query: 418 RAANTAMLGV-MMALGITGLD--EESFRDAIRFTFSGKDKIIDINLKILEAGADWA 470 + AN LG + A G+ LD ++S I +S +I N L+AG D A Sbjct: 127 KMANMVALGAYVRATGVVDLDVVKKSLSSVISAHYS---HLIPKNADALQAGFDHA 179 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: 172 Number of extensions: 7 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