Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate GFF1676 PGA1_c16990 putative enoyl-CoA hydratase FadB
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__Phaeo:GFF1676 Length = 258 Score = 125 bits (315), Expect = 7e-34 Identities = 85/256 (33%), Positives = 130/256 (50%), Gaps = 5/256 (1%) Query: 3 ELIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAG 62 E++ S + + ++TLNRPA NAL ++ + ++ A + V+TG+ F +G Sbjct: 5 EILFSLEDGLAVVTLNRPAKMNALTGLTRAEITHAMQRAGKEAR--AVVLTGSGVSFCSG 62 Query: 63 ADLNEMAEK---DLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVA 119 DL++ A + DL TL D + + P IAAVNG A GAG LAL DVV+A Sbjct: 63 QDLSDAASQGKLDLERTLRDEYTPMLEAIYNCPVPTIAAVNGPAAGAGANLALAADVVIA 122 Query: 120 GENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFP 179 E+A F +G+MP AGGT + R +G + A L + I+A+QA G++ + P Sbjct: 123 TESAYFMQAFARIGLMPDAGGTWFMPRQMGMAKAMGAALFADKISAKQASDWGMIWEAIP 182 Query: 180 SDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHE 239 + A+ +A A A K A+R +L L++E L T D E Sbjct: 183 DAEFDAHWRARAAYLASGPTRAFGAIKTAIRDGYGNSLPEQLSEEAHLQGQCGKTRDFME 242 Query: 240 GISAFLQKRTPDFKGR 255 G++AF++KR F+GR Sbjct: 243 GVTAFMEKRPAKFEGR 258 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: 122 Number of extensions: 9 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: 255 Length of database: 258 Length adjustment: 24 Effective length of query: 231 Effective length of database: 234 Effective search space: 54054 Effective search space used: 54054 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