Align 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial; Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain; EC 1.2.4.4 (characterized)
to candidate 201483 SO2339 alpha keto acid dehydrogenase complex, E1 component, alpha subunit (NCBI ptt file)
Query= SwissProt::O45924 (431 letters) >FitnessBrowser__MR1:201483 Length = 392 Score = 372 bits (955), Expect = e-107 Identities = 188/365 (51%), Positives = 242/365 (66%), Gaps = 3/365 (0%) Query: 59 LPIYRVTNAVGDVIDKSQDPNFDEQTSLKMYKTMTQLNIMDRILYDSQRQGRISFYMTSF 118 +PI R+ A G + + P DE ++K+Y T ++D + +QRQGRISFYMT Sbjct: 24 IPILRILQADGTTYETAVLPVIDEALAIKIYDTCVFTRVLDERMLGAQRQGRISFYMTCT 83 Query: 119 GEEGNHVGSAAALEPQDLIYGQYREAGVLLWRGYTMENFMNQCYGNADDLGKGRQMPMHF 178 GEE VGS AAL+P+D+I QYRE L +RG+T E FMNQ + N DLGKGRQMP+H+ Sbjct: 84 GEEAAIVGSVAALDPEDVILAQYREHAALRYRGFTTEQFMNQMFSNEKDLGKGRQMPIHY 143 Query: 179 GTKERNFVTISSPLTTQLPQAVGSAYAFKQQKDNNRIAVVYFGDGAASEGDAHAAFNFAA 238 G N+ TISSPL TQ+PQA G Y+ K Q N +AV YFG+GAASEGD HA N AA Sbjct: 144 GCAALNYQTISSPLATQIPQATGVGYSLKMQGKRN-VAVCYFGEGAASEGDFHAGLNMAA 202 Query: 239 TLKCPIIFFCRNNGYAISTPTSEQYGGDGIAGKGPAYGLHTIRVDGNDLLAVYNATKEAR 298 LKCP+IFFCRNNGYAISTPT EQ+ G+GIA +G YG+HTIRVDGND+LAV AT++AR Sbjct: 203 VLKCPVIFFCRNNGYAISTPTEEQFAGNGIASRGVGYGMHTIRVDGNDMLAVLAATQQAR 262 Query: 299 RVALT-NRPVLIEAMTYRLGHHSTSDDSTAYRSSDEVQTWGDKDHPITRFKKYITERGWW 357 A+ N PVLIEAMTYRLG HS+SDD + YRS +E W D P+ RFK ++ +GW Sbjct: 263 AYAIEHNAPVLIEAMTYRLGAHSSSDDPSGYRSKEEEAKWQQHD-PVKRFKLWLINKGWL 321 Query: 358 NEEKEMEWQKEVKKRVLTEFAAAEKRKKAHYHDLFEDVYDELPLRLRRQRDELDAHVAEY 417 E + + ++ ++ VL AEK ++ EDVYD+ L++Q EL H+ +Y Sbjct: 322 AEADDAQRYEKYREEVLAAVKVAEKLPIPMLDEIIEDVYDKPTPALKKQLSELKEHIKKY 381 Query: 418 KEHYP 422 + YP Sbjct: 382 PQSYP 386 Lambda K H 0.317 0.132 0.391 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: 480 Number of extensions: 20 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 431 Length of database: 392 Length adjustment: 31 Effective length of query: 400 Effective length of database: 361 Effective search space: 144400 Effective search space used: 144400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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