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_013842280.1 DESRU_RS11505 2-oxoglutarate ferredoxin oxidoreductase subunit alpha
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000215085.1:WP_013842280.1 Length = 382 Score = 209 bits (533), Expect = 7e-59 Identities = 143/384 (37%), Positives = 203/384 (52%), Gaps = 50/384 (13%) Query: 4 QMVKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMV 63 ++++GN A GA+YAG Y GYPITP++EI +R P V KF+Q E E A++ V Sbjct: 6 RLMQGNEACAEGAIYAGMRFYAGYPITPSTEIAEILARRLPQVNGKFIQMEDEIASMAAV 65 Query: 64 YGAAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLG-NIGPEQADYN 122 GA+ G + MTA+SGPG SLKQE I + + AE+P VIV+V R GP G P Q D Sbjct: 66 VGASLTGAKSMTATSGPGFSLKQENIGYASMAEIPCVIVNVQRLGPSTGVATAPAQGDVM 125 Query: 123 QLVKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRFP 182 Q + G HG++ I L P+SV+E DLT+ AF LA+++R PVI+L D V+G M E + P Sbjct: 126 Q-ARWGTHGDHPVIALVPSSVRETFDLTVRAFNLAERFRVPVILLMDEVIGHMREKVTLP 184 Query: 183 E----------------------RAVEHRPDTSWAVCGSRETMKNLVTSIFLDFDEL--- 217 E RA H A G E + VT +F D Sbjct: 185 EPGDLPIFNRLKPDCKRDGYYPFRAEIHEA-PPMAFFG--EGYRYHVTGLFHDESGFATE 241 Query: 218 ------EEFNFYLQEKYAAVEENEVRYEEYMVEDAEIVLVAYGISSRVAKSAVDTARADG 271 + Q+ YA ++E V Y EDAE+V++AYG ++R AV AR +G Sbjct: 242 KSQIIDTQLKRLHQKIYAHLDE-IVTYHSDRTEDAELVVIAYGGTARSVARAVKLAREEG 300 Query: 272 IKVGLLRPITLFPFPSERIRELAEGGCTFISVEMSSGQMREDIK-------MASGCRDVE 324 +KVG+ RP T++PFP + + +LA G + EM+ GQ+ +++ + +GC + Sbjct: 301 LKVGVFRPQTIWPFPEKAVDQLAAAGKKLLVAEMNYGQLLLEVERISRGRCLVTGCLQAD 360 Query: 325 LVNRMGGNLIELRDILRKIREIAG 348 G L + IL KIRE+ G Sbjct: 361 ------GELTKPETILNKIREVYG 378 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: 306 Number of extensions: 17 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: 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 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