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_011939077.1 GURA_RS11115 2-oxoacid:acceptor oxidoreductase subunit alpha
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000016745.1:WP_011939077.1 Length = 377 Score = 221 bits (562), Expect = 3e-62 Identities = 145/372 (38%), Positives = 205/372 (55%), Gaps = 34/372 (9%) Query: 6 VKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVYG 65 ++GN A GA+YAGC + GYPITP++E+ S P +G KF+Q E E A+ V G Sbjct: 8 MQGNEAATHGALYAGCKFFAGYPITPSTEVAEVMSAELPKIGGKFIQMEDEIGAMAAVIG 67 Query: 66 AAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLG-NIGPEQADYNQL 124 A+ AG +V+T++SGPG+SLKQE I + AE P VI++VMR GP G GP Q+D Sbjct: 68 ASLAGSKVLTSTSGPGLSLKQELIGYACIAETPCVIINVMRGGPSTGMPTGPSQSDV-MS 126 Query: 125 VKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRFPER 184 K G HG++ I L P SVQE+ + T+ AF LA+KYR PV+++ D ++ M E + FPE+ Sbjct: 127 AKWGTHGDHPAICLVPASVQELFEETVRAFNLAEKYRTPVMVMPDEIVAHMRERIVFPEK 186 Query: 185 AVEHRPDTSWAVCGSRETMKNLVTSIFLDFDELEEF----NFYL--------------QE 226 D + A S E K T F D L F F++ Sbjct: 187 GELEVIDRT-APSVSPEQYKPYDTK-FGDVPPLAAFGSGYRFHVTGLNKAEDGFPTTKAS 244 Query: 227 KYAAVEENEVR-----------YEEYMVEDAEIVLVAYGISSRVAKSAVDTARADGIKVG 275 A EE +VR +EEYM++DAE+ +VA+G +SR A+ AV+ AR GIK G Sbjct: 245 LVQAEEERQVRKVDANVDDIVKFEEYMLDDAEVAIVAFGSTSRSARFAVNEARKQGIKAG 304 Query: 276 LLRPITLFPFPSERIRELAEGGCTFISVEMSSGQMREDI-KMASGCRDVELVNRMGGNLI 334 L R T +PFP ++++ LA FI+ EM+ G ++ + A G V + R+ G I Sbjct: 305 LFRIKTFWPFPDKQLKALASRVKAFITPEMNLGMCTVEVQRCAEGKAPVHGIFRVDGEPI 364 Query: 335 ELRDILRKIREI 346 IL KI+E+ Sbjct: 365 NPGQILDKIKEV 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: 302 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 Apr 09 2024. 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