Align 3-hydroxy-isobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate Ac3H11_2862 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= reanno::pseudo3_N2E3:AO353_25665 (368 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2862 Length = 368 Score = 271 bits (692), Expect = 3e-77 Identities = 159/354 (44%), Positives = 219/354 (61%), Gaps = 20/354 (5%) Query: 18 NDVLAEVRNHIGHLTLNRPAGLNAITLDMVRSLHRQLDAWSKDPHIHAVVLRGAGEK--- 74 +DVL+EVR +G +TLNRP LNA++L MVR L L AW D + AV +RG+ ++ Sbjct: 11 SDVLSEVRGQVGFITLNRPRALNALSLSMVRDLMAILLAWQNDARVLAVAIRGSNKEGPF 70 Query: 75 -AFCAGGDIRSLYDSFKSGGTLHEDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLV 133 AFCAGGDIR L+ + G EDFF EEYAL+ IH+Y KP +A MDG V+GGGMG+ Sbjct: 71 GAFCAGGDIRFLHQAGSQGNPQLEDFFTEEYALNHLIHNYAKPYIAFMDGIVMGGGMGIS 130 Query: 134 QGADLRVVTERSRLAMPEVAIGYFPDVGGSYFLPRIPGELGIYLGVSGVQIRAADALYCG 193 QGA LRVVTER+++AMPE AIG FPDVGG YFL R PG +G +L ++G I A DA+ Sbjct: 131 QGAALRVVTERTKMAMPETAIGLFPDVGGGYFLSRCPGRVGEWLALTGDTIGAGDAIDSQ 190 Query: 194 LADWYLESQKLAELDQHLDSLEW-HDTPLKDLQGLLAK-LALQQLPDAPLQALRPTIDHF 251 LAD L + + A + + L + + +KD + +K +A++ + L + ID + Sbjct: 191 LADGCLPADQQAAVWEALATQTFASGAAVKDY--VASKFIAIEPM----LSGAKGQIDQY 244 Query: 252 FALPDVPSIVEQLRTVTVADSHDWAMTTADLLDSRSPLAMGVTLEMLRRGRQLSLENCFA 311 FALP V IV L + ADS DWA TA L RSPL + V LE +RR R + L + Sbjct: 245 FALPTVGEIVSALES---ADS-DWARATAATLRKRSPLMLNVVLEQIRRARGMGLADDLR 300 Query: 312 LELHLDRQWF----ERGDLIEGVRALLIDKDKSPRWNPPTVQALDAKHVASFFS 361 +E + R F + + +EG+RAL +DKD +P+WNP ++ + + VA FF+ Sbjct: 301 MERDMVRHCFYLRPGQSETVEGIRALAVDKDHAPKWNPARIEDVTPEMVAPFFA 354 Lambda K H 0.321 0.138 0.418 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: 348 Number of extensions: 19 Number of successful extensions: 4 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: 368 Length of database: 368 Length adjustment: 30 Effective length of query: 338 Effective length of database: 338 Effective search space: 114244 Effective search space used: 114244 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: 49 (23.5 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