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 8499838 DvMF_0603 2-oxoglutarate ferredoxin oxidoreductase subunit alpha (RefSeq)
Query= SwissProt::P80908 (352 letters) >FitnessBrowser__Miya:8499838 Length = 382 Score = 202 bits (515), Expect = 9e-57 Identities = 134/366 (36%), Positives = 191/366 (52%), Gaps = 31/366 (8%) Query: 8 GNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLV-GRKFVQAESEEAAINMVYGA 66 GN AV GA+ AGC Y GYPITP++EI+ + PL+ F+Q E E A++ GA Sbjct: 17 GNEAVAEGALLAGCSFYAGYPITPSTEIMEVMANRLPLIEDGVFIQMEDEIASMGATIGA 76 Query: 67 AAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLG-NIGPEQADYNQLV 125 + AG + MTA+SGPG +L QE I + E P V+V+VMR GP G P QAD Q+ Sbjct: 77 SLAGRKAMTATSGPGFALMQEHIGYACMVEAPLVVVNVMRGGPSTGLPTSPAQADV-QMA 135 Query: 126 KGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRFPE-- 183 + G HG++ IVL+ ++VQE ++T+ AF A+KYR PVI+L D V E + P+ Sbjct: 136 RWGTHGDHPIIVLSASNVQECLEMTVTAFNFAEKYRTPVILLLDEVTAHTREKITVPDPD 195 Query: 184 -----RAVEHRPDTSW------------AVCGSRETMKNLVTSIFLDF--------DELE 218 VE W A+ + VT + D DE++ Sbjct: 196 EVEILSRVEPTVPPEWFKPYADTARGVPAMAPIGSGYRTHVTGLTHDVMGYPTQRPDEVK 255 Query: 219 EFNFYLQEKYAAVEENEVRYEEYMVEDAEIVLVAYGISSRVAKSAVDTARADGIKVGLLR 278 + L K + +EYM++DAE+ +VAYG +R A AV+ AR G K GLL Sbjct: 256 DAMLRLFRKIDQYYGDIQMSDEYMLDDAEVAVVAYGSVARSAHLAVEQARERGAKAGLLT 315 Query: 279 PITLFPFPSERIRELAEGGCTFISVEMSSGQMREDIK-MASGCRDVELVNRMGGNLIELR 337 TLFPFP + +L T + EM+ GQM ++K + +G V +NR+ G +I Sbjct: 316 LKTLFPFPRPAVEKLTHRCHTVVVPEMNMGQMSREVKRVNNGRTKVRTINRVDGQIITPS 375 Query: 338 DILRKI 343 +IL+ I Sbjct: 376 EILKAI 381 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: 307 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 352 Length of database: 382 Length adjustment: 30 Effective length of query: 322 Effective length of database: 352 Effective search space: 113344 Effective search space used: 113344 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 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