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_084511225.1 G491_RS0101620 2-oxoglutarate synthase subunit alpha
Query= SwissProt::P80908 (352 letters) >NCBI__GCF_000429905.1:WP_084511225.1 Length = 372 Score = 219 bits (558), Expect = 9e-62 Identities = 135/373 (36%), Positives = 208/373 (55%), Gaps = 36/373 (9%) Query: 8 GNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVYGAA 67 G+ A GA+ AGC + GYPITPA+E+ S P +G ++Q E E AA+ + GA+ Sbjct: 3 GDVACAEGALAAGCLFFGGYPITPATEVAERMSHRLPEIGGTYIQMEDEIAAMASIVGAS 62 Query: 68 AAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLGNIGPEQADYNQLVKG 127 AG + MT++SGPG SL E + E P V+V+V RAGP G P Q +++ Sbjct: 63 CAGAKSMTSTSGPGFSLMMENLGLAVITETPCVVVNVQRAGPSTGL--PTQGAQGDMMQA 120 Query: 128 --GGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRFPE-- 183 G HG+Y I +AP S QE+ T+DAF LA+KYR PV+I+ D V+G M+E + P+ Sbjct: 121 RWGSHGDYEIIAMAPASAQEIFYQTIDAFNLAEKYRTPVLIMTDEVIGHMSERVVIPDAR 180 Query: 184 ------------RAVEHRPDTSW-----AVCGSRETMKNLVTSIFLDFDELEEFNFYLQE 226 R +RP + + + + K VT L DE+ ++ Sbjct: 181 EIKTIERVKAKGRKDRYRPYAAGDLGVPPMANAGDGYKVHVTG--LTHDEMGYPAMTVEA 238 Query: 227 KYAAVE----------ENEVRYEEYMVEDAEIVLVAYGISSRVAKSAVDTARADGIKVGL 276 + A +E ++ +RYEE+M+EDA+ ++V YG+S+R ++AV+ ARA GIKVG+ Sbjct: 239 QAAMMERLMGKIQNNRDDIIRYEEFMIEDADYIIVTYGVSARTGRAAVEEARAQGIKVGM 298 Query: 277 LRPITLFPFPSERIRELAEGGCTFISVEMSSGQMREDI-KMASGCRDVELVNRMGGNLIE 335 LR IT++PF E+IR+LA ++VE++ GQ+ ++ + +G V+LV GG LI Sbjct: 299 LRLITVWPFAEEKIRDLASKAKGMVTVEINLGQVHLEVERCVAGRVPVKLVGHPGGTLIS 358 Query: 336 LRDILRKIREIAG 348 ++ I++ G Sbjct: 359 PDTVIHTIKQEFG 371 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: 308 Number of extensions: 9 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: 1 Length of query: 352 Length of database: 372 Length adjustment: 29 Effective length of query: 323 Effective length of database: 343 Effective search space: 110789 Effective search space used: 110789 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