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 WP_012469149.1 GLOV_RS05305 2-oxoacid:acceptor oxidoreductase subunit alpha
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000020385.1:WP_012469149.1 Length = 616 Score = 114 bits (286), Expect = 5e-30 Identities = 104/358 (29%), Positives = 154/358 (43%), Gaps = 45/358 (12%) Query: 3 TQMVKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGR--------KFVQAE 54 T ++ GN+A +GA++ G YPITP++ I+ S Y + R +QAE Sbjct: 221 TFLIDGNSAAALGAIFGGVQFVAWYPITPSTSIVDHLSDYLHRLRRDPDGKATYSIIQAE 280 Query: 55 SEEAAINMVYGAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNI 114 E A I MV GA AG R MTA+SGPG+SL E + AE+PAVI DV R GP G Sbjct: 281 DELAVIGMVVGAGWAGARSMTATSGPGLSLMAEFAGYAYFAEIPAVIWDVQRMGPSTGLP 340 Query: 115 GPEQADYNQLVKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLG- 173 D GHG+ R+I L P +V E + A +LA++ + VI+L+D LG Sbjct: 341 TRTAQDDILAAYTLGHGDGRHICLIPGTVSECFEFGGMALDLAERLQTLVIVLSDLDLGL 400 Query: 174 --QMAEPLRFPERAVEH----------RPDTSW---------AVC-GSRETMKNLVTSIF 211 +P +P+R ++ R W +C + + + F Sbjct: 401 NLWPTKPFSYPDRPLDRGKVLSADELTRLQGDWKRYADLDGDGICYRTLPGTNHPAAAYF 460 Query: 212 LDFDELEEFNFYLQ--EKYAAVEENEVRYEEYM-----------VEDAEIVLVAYGISSR 258 E Y + E +AA R +Y V AE+ L++YG + Sbjct: 461 TRGTGHNEAAGYSERPEDWAANLSRLARKHDYARTIVPAPVIDPVNAAEVGLISYGSNDP 520 Query: 259 VAKSAVDTARADGIKVGLLRPITLFPFPSERIRELAEGGCTFISVEMSSGQMREDIKM 316 + A D RA G+ LR + P S ++ ++ GQMR I++ Sbjct: 521 AIREARDLLRAAGVASSYLR-LRALPLESSLTEFVSSHKRLYVVENNLDGQMRALIQL 577 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: 455 Number of extensions: 22 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: 616 Length adjustment: 33 Effective length of query: 319 Effective length of database: 583 Effective search space: 185977 Effective search space used: 185977 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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