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 5209454 Shew_1925 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (RefSeq)
Query= SwissProt::P12694 (445 letters) >FitnessBrowser__PV4:5209454 Length = 392 Score = 368 bits (945), Expect = e-106 Identities = 183/383 (47%), Positives = 250/383 (65%), Gaps = 2/383 (0%) Query: 57 ASAEFIDKLEFIQPNVISGIPIYRVMDRQGQIINPSEDPHLPKEKVLKLYKSMTLLNTMD 116 ++ E + ++ F+ + +S IPI +++ G + P + ++ K+Y + +D Sbjct: 6 SNTETVHRVSFLDKDSLS-IPILKILQADGTTFENAVLPVIDQDLAAKIYDTCVFTRVLD 64 Query: 117 RILYESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFMA 176 + +QRQGRISFYMT GEE VGS AALD D++ QYRE + YR + E FM Sbjct: 65 ERMLAAQRQGRISFYMTCTGEEAAVVGSVAALDQDDVILAQYREHAAIRYRGFTTEQFMN 124 Query: 177 QCYGNISDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVICYF 236 Q + N DLGKGRQMP+HYGC+ ++ TISSPLATQIPQA G Y+ K V ICYF Sbjct: 125 QMFSNEKDLGKGRQMPIHYGCEALNYQTISSPLATQIPQATGVGYSLKMQGKRNVAICYF 184 Query: 237 GEGAASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGIMSI 296 GEGAASEGD HAG N AA L P+IFFCRNNGYAISTPT+EQ+ G+GIA+RG GYG+ +I Sbjct: 185 GEGAASEGDFHAGLNMAAVLNSPVIFFCRNNGYAISTPTNEQFAGNGIASRGVGYGMHTI 244 Query: 297 RVDGNDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVNYWDK 356 RVDGND+ AV AT++AR A+ N+P LIEAMTYR+G HS+SDD S YRS DE W + Sbjct: 245 RVDGNDMLAVMAATQQARAYALEHNKPVLIEAMTYRLGAHSSSDDPSGYRSKDEEAKWQQ 304 Query: 357 QDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDVYQEM 416 D P+ R + +L+++GW E + A ++ R +V+ A + AE+ P P + + DV E Sbjct: 305 HD-PVKRFKLWLINKGWLAESDDAALYEKYREEVLAAVKVAEKLPAPKIDEIIEDVLDEP 363 Query: 417 PAQLRKQQESLARHLQTYGEHYP 439 +L++Q L +H++ Y + YP Sbjct: 364 TPRLKQQLTELKQHIKKYPDSYP 386 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: 453 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: 392 Length adjustment: 32 Effective length of query: 413 Effective length of database: 360 Effective search space: 148680 Effective search space used: 148680 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