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_012469685.1 GLOV_RS08075 2-oxoglutarate ferredoxin oxidoreductase subunit alpha
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000020385.1:WP_012469685.1 Length = 377 Score = 211 bits (538), Expect = 2e-59 Identities = 138/370 (37%), Positives = 200/370 (54%), Gaps = 30/370 (8%) Query: 6 VKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVYG 65 ++GN A GA+YAGC + GYPITP++E+ S P VG KF+Q E E A+ + G Sbjct: 8 LQGNEAAAHGALYAGCKFFAGYPITPSTEVSEVLSIELPKVGGKFIQMEDEIGAMAALLG 67 Query: 66 AAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLG-NIGPEQADYNQL 124 A AG + +T++SGPG+SLKQE I + AE+P V+ +VMR GP G GP Q+D Sbjct: 68 GALAGQKALTSTSGPGLSLKQELIGYGCIAEIPCVVYNVMRGGPSTGMPTGPSQSDV-MC 126 Query: 125 VKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRFPER 184 + G HG++ I L P SVQE D+ + AF LA+KYR PV +L D ++ M E + F E Sbjct: 127 ARWGTHGDHATIALMPASVQETYDMIVRAFNLAEKYRMPVHVLPDEIVAHMRERIEFREP 186 Query: 185 A--------------VEHRP-DTSWAVCGSRETMKNLVTSIFLDFDELEE-FNFYLQEKY 228 E++P DT + + ++L + F E Sbjct: 187 GELEVIDRTAPSVPPSEYKPYDTKFGDVPPLAAFGSGYKFHVTGLNKLPDGFPTTKAEYV 246 Query: 229 AAVEENEVR-----------YEEYMVEDAEIVLVAYGISSRVAKSAVDTARADGIKVGLL 277 A EE ++R +EE+M++DAEI +VAYG +SR A+ AV+ AR GIK G+ Sbjct: 247 QAEEERQIRKVTANIDEIVEFEEFMLDDAEICVVAYGSTSRSARYAVNEAREKGIKAGMF 306 Query: 278 RPITLFPFPSERIRELAEGGCTFISVEMSSGQMREDI-KMASGCRDVELVNRMGGNLIEL 336 R T +PFP ++I+ LA+ FI EM+ G +I + A G + +NR+ G I Sbjct: 307 RIKTFWPFPDKQIKALADKVKGFIVPEMNLGMCSLEIERCAQGKAQILGINRVDGEPINP 366 Query: 337 RDILRKIREI 346 IL K++E+ Sbjct: 367 EQILEKMKEV 376 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: 311 Number of extensions: 13 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: 352 Length of database: 377 Length adjustment: 29 Effective length of query: 323 Effective length of database: 348 Effective search space: 112404 Effective search space used: 112404 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 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