Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate BPHYT_RS28015 BPHYT_RS28015 enoyl-CoA hydratase
Query= reanno::Cup4G11:RR42_RS28545 (384 letters) >FitnessBrowser__BFirm:BPHYT_RS28015 Length = 382 Score = 327 bits (839), Expect = 3e-94 Identities = 179/365 (49%), Positives = 222/365 (60%), Gaps = 5/365 (1%) Query: 19 ADDEVRFDEINGIGLITLNRPRQLNALSYPMIGLLDAQLAAWAARDDIAAVVLRGAGPKA 78 A+ E+ F +N + +ITLNRP LNALS+ M+ L + D I A+VL+GAG K Sbjct: 15 AEREILFRVVNRVAIITLNRPAALNALSHAMVRELAVLVEHCRTDDGIVALVLKGAGAKG 74 Query: 79 FCAGGDIRALYDSFHAGTALHRQFFVDEYQLDYRLHCYPKPVVALMDGIVMGGGMGLAQA 138 FCAGGD+R + + FFVDEY+LDY LH +PKPVVAL+DGI MGGGMGL Q Sbjct: 75 FCAGGDVREVQRLAKNNDSRWLAFFVDEYRLDYALHTFPKPVVALLDGIAMGGGMGLGQG 134 Query: 139 AHLRVLTERSRVAMPETGIGLVPDVGASHFLSKLPLALALYVGLTGVTLGAADTLLCKLA 198 A LR++TERS++AMPET IG +PDVGA+ FLS +P L LYVGLTG TL AD L +LA Sbjct: 135 ARLRIVTERSKIAMPETRIGFLPDVGATRFLSVMPAELELYVGLTGATLSGADALRLQLA 194 Query: 199 DIAVPAASLEHFEQTLAAINRTGDVLADLRAALQATPDAGEQAAPLQSVLPAVLRHF--- 255 D+ VPA L FE+ L + GD++A LR + P APL + +LRHF Sbjct: 195 DLCVPAEWLASFEERLQRMPLEGDLMAALRGVFE-PPCNIIPHAPLAAFTQLILRHFDRR 253 Query: 256 -RADASVAGLLDSLAAESDPAYADWAARTLDILRGRSPLMMAVTRELLLRGRDLDLADCF 314 D VA + L E W T D L G SP M+ VTRE LLRGR + LA+CF Sbjct: 254 SSIDRMVATVRHDLLREPPREVKQWLQSTYDALTGHSPTMLYVTREALLRGRQMTLAECF 313 Query: 315 RMELGVVSHAFSQGDFIEGVRALIVDKDNAPRWRVKDASEVSEAVVQSFFDSPWPREPHP 374 RMELG+V +GDF EGVRA ++DKD RW +EV V+ F SPW + HP Sbjct: 314 RMELGIVKRVIEEGDFCEGVRAQLIDKDRKARWAPATLAEVRPERVRHFLASPWKSDAHP 373 Query: 375 LAMLG 379 LA LG Sbjct: 374 LAALG 378 Lambda K H 0.322 0.137 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: 383 Number of extensions: 15 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: 384 Length of database: 382 Length adjustment: 30 Effective length of query: 354 Effective length of database: 352 Effective search space: 124608 Effective search space used: 124608 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: 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