Align 3-methyl-2-oxobutanoate dehydrogenase subunit beta; Branched-chain alpha-ketoacid dehydrogenase E1 component subunit beta; BCKADH E1-beta; EC 1.2.4.4 (characterized)
to candidate N515DRAFT_0481 N515DRAFT_0481 2-oxoisovalerate dehydrogenase E1 component
Query= SwissProt::P9WIS1 (348 letters) >FitnessBrowser__Dyella79:N515DRAFT_0481 Length = 755 Score = 156 bits (394), Expect = 2e-42 Identities = 114/333 (34%), Positives = 166/333 (49%), Gaps = 22/333 (6%) Query: 32 INRALYDAMAADERVLVFGEDVAVEGGVFRVTEGLADTFGADRCFDTPLAESAIIGIAVG 91 I +AL++ MA L+FGEDVA++GGV+ VT+GL TF +R F+T L E+ I+G+A G Sbjct: 426 IGQALHEVMAKYPESLLFGEDVALKGGVYTVTKGLFKTFKGNRVFNTLLDETVILGLAQG 485 Query: 92 LALRGFVPVPEIQFDGFSYPAFDQVVSHLAKYRTRTRGEVDMPVTVRIPSFG---GIGAA 148 A G +P+PEIQ+ + + A DQ+ + + + P+ +R+ + G G G Sbjct: 486 YANMGMLPMPEIQYLAYFHNACDQIRGEACSLQFFSNDQYRNPLVMRVAALGYQKGFG-G 544 Query: 149 EHHSDSTESYWVHTAGLKVVVPSTPGDAYWLLRHAIACP----------DPVMYLEPKRR 198 H+D++ + GL V PS DA +LR +A +P+ K Sbjct: 545 HFHNDNSIAALRDIPGLVVGCPSRGDDAAAMLRTLMALAKVDGRVCAFLEPIALYMTKDL 604 Query: 199 YH-GRGMVDTSRPEP----PIGHAMV-RRSGTDVTVVTYGNLVSTALSSADTAEQQHDWS 252 Y G G + P P P+G V + D+ V T+GN V AL +A E++H W Sbjct: 605 YEAGDGQWQFAYPAPGEALPLGEGRVYEQDADDLVVFTFGNGVPMALRAAREIEKKHGWR 664 Query: 253 LEVIDLRSLAPLDFDTIAASIQRTGRCVVMHEGPRSLGYGAGLAARIQEEMFYQLEAPVL 312 V+DLR LAPL+ IA + R +V+ EG RS G G G+ I E P+ Sbjct: 665 TRVVDLRWLAPLNDKFIAGQARNARRILVLDEGRRSAGVGEGIITAIVEGGCG--ATPLQ 722 Query: 313 RACGFDTPYPPARLEKLWLPGPDRLLDCVERVL 345 R G DT P A L LPG ++ ER+L Sbjct: 723 RVVGADTYTPLAGAALLVLPGEAEIVAAAERML 755 Lambda K H 0.321 0.137 0.417 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: 630 Number of extensions: 26 Number of successful extensions: 3 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: 348 Length of database: 755 Length adjustment: 34 Effective length of query: 314 Effective length of database: 721 Effective search space: 226394 Effective search space used: 226394 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 (21.9 bits) S2: 52 (24.6 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