Align 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial; Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain; BCKDE1A; BCKDH E1-alpha; EC 1.2.4.4 (characterized)
to candidate GFF1675 HP15_1634 branched-chain alpha-keto acid dehydrogenase complex E1 alpha subunit
Query= SwissProt::P12694 (445 letters) >FitnessBrowser__Marino:GFF1675 Length = 382 Score = 373 bits (958), Expect = e-108 Identities = 183/364 (50%), Positives = 246/364 (67%), Gaps = 1/364 (0%) Query: 76 IPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNY 135 IP ++++ + G++ ++ P L K+K L++Y++M +D + +QRQGR+SFYM Sbjct: 10 IPTFKLLKQDGKLYKSAKAPDLDKDKALRIYRAMVTTRILDERMLAAQRQGRLSFYMQCT 69 Query: 136 GEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHY 195 GEE +GSAAALD+ D++ QYRE G L YR + ++ FM Q +GN D GKGRQMPVHY Sbjct: 70 GEEAAVIGSAAALDDGDMIMAQYREQGALAYRGFTIDEFMNQLFGNEMDYGKGRQMPVHY 129 Query: 196 GCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGFNFAAT 255 G K+ +++TISSPLATQIPQA G AY K I YFGEGAASEGD HA N AA Sbjct: 130 GSKKLNYMTISSPLATQIPQAAGYAYGQKLRGEGLCTITYFGEGAASEGDFHAALNMAAV 189 Query: 256 LECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDGNDVFAVYNATKEARR 315 P+IF CRNNGYAISTP +EQ+ DG+A R GY + IRVDGND+ A+Y AT+EAR+ Sbjct: 190 HRVPVIFLCRNNGYAISTPAAEQFAADGVAPRAYGYKMDVIRVDGNDILAMYQATQEARK 249 Query: 316 RAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHPISRLRHYLLSQGWWD 375 AV N+P LIEAM+YR+ HS+SDD S YRS DE W ++D PI R+R +L S+ WW Sbjct: 250 LAVEHNRPVLIEAMSYRLAAHSSSDDPSGYRSKDEEAVWREKD-PILRMRLWLESKKWWS 308 Query: 376 EEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYG 435 E+ EK ++ RR+V+E ++A+++P P L SDVY E+P L +Q E L H+ + Sbjct: 309 EDDEKQLQENMRREVLETMKRAQKRPPPPLESLVSDVYDEVPPALAEQFEKLKAHIGRHP 368 Query: 436 EHYP 439 + YP Sbjct: 369 DEYP 372 Lambda K H 0.320 0.135 0.405 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: 500 Number of extensions: 13 Number of successful extensions: 2 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: 445 Length of database: 382 Length adjustment: 31 Effective length of query: 414 Effective length of database: 351 Effective search space: 145314 Effective search space used: 145314 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 (21.8 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