Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate 349840 BT0312 2-oxoisovalerate dehydrogenase beta subunit (NCBI ptt file)
Query= metacyc::MONOMER-11684 (327 letters) >FitnessBrowser__Btheta:349840 Length = 678 Score = 215 bits (547), Expect = 3e-60 Identities = 124/328 (37%), Positives = 185/328 (56%), Gaps = 9/328 (2%) Query: 7 IDAINLAMKEEMERDSRVFVLGEDVGR--KGGVFKATAGLYEQFGEERVMDTPLAESAIA 64 ++AIN +K E + F+ G+DV KGGVF T G+ ++FGE RV P+AE I Sbjct: 353 VNAINETLKAEFRHNPDTFIWGQDVANREKGGVFNVTKGMQQEFGEARVFSAPIAEDYIV 412 Query: 65 GVGIGAAMYGMR---PIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGG 121 G G + + + I +FAD+ PAV Q + E +RSN ++ I +R GG Sbjct: 413 GTANGMSRFDPKIHVVIEGAEFADYFWPAVEQYV-ECTHEYWRSNGKFAPNITLRLASGG 471 Query: 122 GVHGALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLIK 181 + G LYHSQ++E PG +IV PS DA GLL+ ++R + LF E K Y ++ Sbjct: 472 YIGGGLYHSQNIEGALTTLPGARIVCPSFADDAAGLLRTSMRSKGFTLFLEPKALYNSVE 531 Query: 182 -GEVPADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKD-GISAHVVDLRTV 239 V +D+ +P GKA ++REG D+++ITYG HF L AE+LEK+ G V+D+R++ Sbjct: 532 AAAVVPEDFEVPFGKARIRREGTDLSIITYGNTTHFCLHVAEQLEKESGWKVEVIDIRSL 591 Query: 240 YPLDKEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPA 299 PLDKEAI E+ KT K L+V ED +E+AA+I LD P++R+ G Sbjct: 592 IPLDKEAIFESVKKTSKALVVHEDKVFSGFGAELAAMIGTDMFRYLDGPVQRV-GSTFTP 650 Query: 300 MPYAPTMEKYFMVNPDKVEAAMRELAEF 327 + + P +EK + + K+ A ++L E+ Sbjct: 651 VGFNPILEKEILPDEAKIYEAAKKLLEY 678 Lambda K H 0.319 0.136 0.392 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: 497 Number of extensions: 28 Number of successful extensions: 6 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: 327 Length of database: 678 Length adjustment: 33 Effective length of query: 294 Effective length of database: 645 Effective search space: 189630 Effective search space used: 189630 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 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