Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate 207416 DVU1946 pyruvate ferredoxin oxidoreductase, beta subunit, putative
Query= SwissProt::P80907 (478 letters) >MicrobesOnline__882:207416 Length = 276 Score = 102 bits (253), Expect = 2e-26 Identities = 78/267 (29%), Positives = 118/267 (44%), Gaps = 41/267 (15%) Query: 29 YCAGCGHGILHKLIGEAIDELGI-QERSVMISPVGCAVFAYYYFDCGNVQVAHGRAPAVG 87 +CAGCGHGI+ + ++ LG+ ++ V+++ +GC+ Y D V HGRA Sbjct: 22 FCAGCGHGIVLGSLIRSVHALGLPKDDVVVVAGIGCSGRLAVYVDFNTVHTTHGRALTFA 81 Query: 88 TGISRAEDTPVVLLYQGDGDLASIGLNETIQAANRGEKMAVFFVNNTVYGMTGGQMAPTT 147 TGI A V+ GDGD SIG N I AA R + +NN +YGMTGGQ + T Sbjct: 82 TGIKMANPRLKVICVMGDGDAMSIGGNHLIHAARRNIGVTALVLNNHIYGMTGGQCSSAT 141 Query: 148 LIGEVTVTCPGGRDPRYAGYPLHMCELLDNLQAPVFIERVSLADPKSIRKAKR----AVK 203 G++++T P G L D+ F+E A + + + Sbjct: 142 PQGDISMTTPYG-------------ALEDSFD---FVEMAKAAGANYVARGTSFHALMLD 185 Query: 204 RALEIQRDGKGYAFVEVLSPCPT-----NLRQDAEGAERFLKEEM-------------ER 245 + + G++ VEV SPCPT N + A ++LK+ + Sbjct: 186 KLITSAIMHPGFSMVEVFSPCPTQYGRKNKFRSAVDMYKWLKKNTVKIETLKEGEKPEDG 245 Query: 246 EFPVKNFRDRSSETEPLIRSESDFSRE 272 P+ FRDR +T L +D R+ Sbjct: 246 RIPIGVFRDR--QTPGLEERYADMQRK 270 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: 333 Number of extensions: 14 Number of successful extensions: 3 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: 478 Length of database: 276 Length adjustment: 29 Effective length of query: 449 Effective length of database: 247 Effective search space: 110903 Effective search space used: 110903 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)
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