Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate AO356_30355 AO356_30355 enoyl-CoA hydratase
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30355 Length = 264 Score = 164 bits (415), Expect = 2e-45 Identities = 95/261 (36%), Positives = 145/261 (55%), Gaps = 7/261 (2%) Query: 6 IETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGA 65 +E G + LNRP+K NAL+ +L+ L A+ A+ + +I +ITG G AFC+G Sbjct: 4 LEVSTVGRVMVAKLNRPEKKNALSESMLDSLRTALLAADENDDIGCFVITGAGDAFCSGG 63 Query: 66 DI------TQFNQLTPAEAW-KFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALAC 118 D+ + TP E + K ++ IE KP IA +NG A+G G++L+L C Sbjct: 64 DLGRRAAESAEGDPTPLERKIRLQKVTHQVALAIENFEKPLIAAVNGAAVGAGMDLSLQC 123 Query: 119 DIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLV 178 D+R A+E A+ I +G+ PG GG L R++G +ALE++ TGD + ++A G+V Sbjct: 124 DMRFASESARFAEAYIRVGLIPGNGGCYLLPRIVGTAKALELLWTGDFVSAEEALALGIV 183 Query: 179 NRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFST 238 NRV L Q+T A ++A PI IK+++ + L + L + L + VV ST Sbjct: 184 NRVFSDDELMQQTLDFATRLADGPPIQQRSIKKLLYQSLRTDLRTSLESVAAQMAVVQST 243 Query: 239 EDKKEGVSAFLEKREPTFKGK 259 +D KE + A+ EKR+P F GK Sbjct: 244 DDYKEAIKAYKEKRKPRFIGK 264 Lambda K H 0.315 0.135 0.382 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: 139 Number of extensions: 7 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: 259 Length of database: 264 Length adjustment: 25 Effective length of query: 234 Effective length of database: 239 Effective search space: 55926 Effective search space used: 55926 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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