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 WP_086509735.1 BZY95_RS09715 thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha
Query= SwissProt::P12694 (445 letters) >NCBI__GCF_002151265.1:WP_086509735.1 Length = 407 Score = 382 bits (982), Expect = e-111 Identities = 184/364 (50%), Positives = 251/364 (68%), Gaps = 1/364 (0%) Query: 76 IPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMDRILYESQRQGRISFYMTNY 135 IP +R++ + G + +E P L ++K L++Y++M + +D + +QRQGR+SFYM Sbjct: 20 IPTFRLLQQDGSLCEGAEAPELDRDKALRIYRAMLVTRVLDERMMAAQRQGRLSFYMQCT 79 Query: 136 GEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMAQCYGNISDLGKGRQMPVHY 195 GEE +G+ AALD+ D++ QYRE G L+YR + + FM Q +GN D GKGRQMP+HY Sbjct: 80 GEEAAVIGATAALDDADMIMAQYREQGALVYRGFSYDEFMNQLFGNELDYGKGRQMPIHY 139 Query: 196 GCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYFGEGAASEGDAHAGFNFAAT 255 G ++ H++TISSPLATQIPQA G AY K A I +FGEGAASEGD HA N A+ Sbjct: 140 GSRKLHYMTISSPLATQIPQATGYAYGQKLAGEGHCTITFFGEGAASEGDFHAALNMASV 199 Query: 256 LECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSIRVDGNDVFAVYNATKEARR 315 + P+IFFCRNNGYAISTP SEQ+ DGIA R GY + IRVDGNDV AVY AT+EAR+ Sbjct: 200 HKVPVIFFCRNNGYAISTPASEQFAADGIAPRAFGYRMHVIRVDGNDVLAVYRATQEARK 259 Query: 316 RAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDKQDHPISRLRHYLLSQGWWD 375 AV +NQP LIEAMTYR+ HS+SDD S YRS E W ++D PI R++ +L+ GWW Sbjct: 260 IAVEQNQPVLIEAMTYRLAAHSSSDDPSGYRSRKEEEAWREKD-PILRMQRWLIDGGWWS 318 Query: 376 EEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEMPAQLRKQQESLARHLQTYG 435 EE+EK ++ RR+V+E ++AE++P P L +DVY ++ L++Q ++L H++ Y Sbjct: 319 EEEEKELQESLRREVLETMKRAEKRPPPPLESLVTDVYADVTPALQRQLDALKTHIRKYP 378 Query: 436 EHYP 439 + YP Sbjct: 379 DAYP 382 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: 539 Number of extensions: 15 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: 407 Length adjustment: 32 Effective length of query: 413 Effective length of database: 375 Effective search space: 154875 Effective search space used: 154875 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: 51 (24.3 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