Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate BWI76_RS20065 BWI76_RS20065 1,4-dihydroxy-2-naphthoyl-CoA synthase
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__Koxy:BWI76_RS20065 Length = 285 Score = 110 bits (276), Expect = 2e-29 Identities = 82/245 (33%), Positives = 126/245 (51%), Gaps = 10/245 (4%) Query: 15 LTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNA-RFFAAGADLNEMAE--- 70 +T+NRP RNA + +++ L A D +I V V+TG + F AG D + Sbjct: 37 ITINRPQVRNAFRPLTVKEMIQALADARYDDNIGVIVLTGEGDKAFCAGGDQKVRGDYGG 96 Query: 71 -KDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFGLPE 129 +D + + +++ KP++A V GY++G G L ++CD+ +A ENA FG Sbjct: 97 YQDDSGVHHLNVLDFQRQIRTCPKPVLAMVAGYSIGGGHVLHMMCDLTIAAENAIFGQTG 156 Query: 130 ITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFP-SDLTLEYAL 188 +G G G + R VG+ A ++ AQQA GLV+ V P +DL E + Sbjct: 157 PKVGSFDGGWGASYMARIVGQKKAREIWFLCRQYDAQQALDMGLVNTVVPLADLEKE-TV 215 Query: 189 QLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLL-AATEDRHEGISAFLQK 247 + +M ++SP+AL+ K AL + + QAGL + T+L TE+ EG +AF QK Sbjct: 216 RWCREMLQNSPMALRCLKAAL--NADCDGQAGLQELAGNATMLFYMTEEGQEGRNAFNQK 273 Query: 248 RTPDF 252 R PDF Sbjct: 274 RQPDF 278 Lambda K H 0.318 0.130 0.356 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: 109 Number of extensions: 6 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: 255 Length of database: 285 Length adjustment: 25 Effective length of query: 230 Effective length of database: 260 Effective search space: 59800 Effective search space used: 59800 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: 41 (21.8 bits) S2: 47 (22.7 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