Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate RR42_RS12795 RR42_RS12795 3-hydroxyisobutyryl-CoA hydrolase
Query= reanno::Cup4G11:RR42_RS28545 (384 letters) >FitnessBrowser__Cup4G11:RR42_RS12795 Length = 362 Score = 298 bits (762), Expect = 2e-85 Identities = 176/355 (49%), Positives = 225/355 (63%), Gaps = 14/355 (3%) Query: 30 GIGLITLNRPRQLNALSYPMIGLLDAQLAAWAARDDIAAVVLRGAGPKAFCAGGDIRALY 89 GIG +TLNRP+ LNALS MI + L AWA ++AAVV+ GAG KAFCAGGDIR + Sbjct: 16 GIGYLTLNRPQALNALSLEMIRAITQALNAWAVAPEVAAVVIAGAGGKAFCAGGDIRFFH 75 Query: 90 DSFHAGTALHRQFFVDEYQLDYRLHCYPKPVVALMDGIVMGGGMGLAQAAHLRVLTERSR 149 + AG QFFV+EY L++ +H Y KP +ALMDG+VMGGGMG++Q A R++TER++ Sbjct: 76 KAALAGDPALDQFFVEEYALNHLIHTYAKPYIALMDGVVMGGGMGISQGARRRLVTERTK 135 Query: 150 VAMPETGIGLVPDVGASHFLSKLPLALALYVGLTGVTLGAADTLLCKLADIAVPAASLEH 209 +AMPET IGL PDVG FLS+ P L Y+GLTG + AAD L LAD +P ++ Sbjct: 136 MAMPETNIGLFPDVGGGWFLSRTPGRLGEYLGLTGAMIHAADALYAGLADAYLPGNAMAE 195 Query: 210 FEQTLAAIN-RTGD-VLA---DLRAALQATPDAGE-QAAPLQSVLPAVLRHFRADASVAG 263 + L A GD VLA + AA +A GE Q A LQ + + A ASV G Sbjct: 196 LVEVLRARQFADGDAVLACVDEATAAHRAACPPGESQLAKLQEEIDGLF----AGASVTG 251 Query: 264 LLDSLAAESDPAYADWAARTLDILRGRSPLMMAVTRELLLRGRDLDLADCFRMELGVVSH 323 + +AA SD A +DWAA+T +LR RSPLM+ VT E + R R + L D RMEL ++ H Sbjct: 252 I---VAAVSD-AGSDWAAQTAAMLRTRSPLMLNVTLEQIRRARTMALNDELRMELDMMYH 307 Query: 324 AFSQGDFIEGVRALIVDKDNAPRWRVKDASEVSEAVVQSFFDSPWPREPHPLAML 378 F GD +EG+RAL VDKD+AP+W+ EV+ V +FFDSPW HPLA L Sbjct: 308 VFRHGDGVEGIRALAVDKDHAPKWQPARLDEVTRERVHAFFDSPWAHGEHPLAAL 362 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: 349 Number of extensions: 17 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: 384 Length of database: 362 Length adjustment: 30 Effective length of query: 354 Effective length of database: 332 Effective search space: 117528 Effective search space used: 117528 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