Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate YP_004140672.1 Mesci_1463 pyruvate dehydrogenase (acetyl-transferring)
Query= metacyc::MONOMER-11683 (330 letters) >NCBI__GCF_000185905.1:YP_004140672.1 Length = 342 Score = 161 bits (408), Expect = 2e-44 Identities = 106/287 (36%), Positives = 150/287 (52%), Gaps = 14/287 (4%) Query: 50 GQEAAQVGAAFALDREMDYVLPYYRDMGVVLAFGMTAKDLMMSGFAKAAD--PNSGGRQM 107 GQEA+ +G L E D + +R G +A G K + F K GG Sbjct: 62 GQEASAMGICMPL-AEDDQITSTHRGHGHCIAKGAEVKRMFAEFFGKTTGYCKGRGGSMH 120 Query: 108 PGHFGQKK---NRIVTGSSPVTTQVPHAVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHE 164 G+ N IV G P+ AVG AL+ +M K FG+G++N+G FHE Sbjct: 121 IADVGKGNLGANGIVGGGIPI------AVGAALSSKMMKTGKVVVSFFGDGANNEGAFHE 174 Query: 165 GANFAAVHKLPVIFMCENNKYAISVPYDKQVACENISDRAIGYGMPGVTVNGNDPLEVYQ 224 N AAV KLPVIF+CENN Y +S + A +NI++RA Y MPGV VNGN EV + Sbjct: 175 ALNMAAVWKLPVIFVCENNGYGMSTSTARSTAVKNIAERAAAYSMPGVIVNGNIFSEVAE 234 Query: 225 AVKEARERARRGEGPTLIETISYRLTPHSSDDDDSSYRGREEVEE-AKKSDPLLTYQAYL 283 A +A RAR GEGPTLIE+ +YR HS D + YR +EE+E+ DP+ +++ L Sbjct: 235 ASHQAVARARAGEGPTLIESKTYRHRGHSK-SDRNRYRTKEEIEDWMSNRDPITLFESEL 293 Query: 284 KETGLLSDEIEQTMLDEIMAIVNEATDEAENAPYAAPESALDYVYAK 330 +E G + D+ + + D + + E + A+ +P +YVY + Sbjct: 294 REFGFIDDKGIEAIRDAVAQEIAEGIEFAKASPSPDISETGNYVYTE 340 Lambda K H 0.316 0.132 0.377 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: 243 Number of extensions: 12 Number of successful extensions: 1 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: 330 Length of database: 342 Length adjustment: 28 Effective length of query: 302 Effective length of database: 314 Effective search space: 94828 Effective search space used: 94828 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 (21.6 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