Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 5209192 Shew_1670 enoyl-CoA hydratase (RefSeq)
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__PV4:5209192 Length = 257 Score = 162 bits (410), Expect = 6e-45 Identities = 100/247 (40%), Positives = 142/247 (57%), Gaps = 8/247 (3%) Query: 14 LLTLNRPAARN--ALNNALLMQLVNELEAAATDTSISVCVITGNA-RFFAAGADLNEMAE 70 +LT+N P A A + ALL Q V EL A + I V+TG +FF+AGADL A+ Sbjct: 14 VLTMNNPPANTWTADSLALLKQKVTELNA---NKEIYALVLTGEGEKFFSAGADLKLFAD 70 Query: 71 KDL--AATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFGLP 128 D AAT+ + + L F IAA+NGYA+G G E+AL CD+ +A A LP Sbjct: 71 GDKGNAATMAKHFGEAFEALSGFRGVSIAAINGYAMGGGLEVALACDIRIAEAQAVMALP 130 Query: 129 EITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTLEYAL 188 E T+G++P AGGTQ L VG+ A +M+L GE + A +A GL+ +V L+ A+ Sbjct: 131 EATVGLLPCAGGTQNLTAMVGEGWAKRMILCGERVGADKALSIGLIEEVVDKGAALDTAM 190 Query: 189 QLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAFLQKR 248 LA K+A SP ++ KQ ++ + + L ER+LF L TED+ EG++AFL+KR Sbjct: 191 ALAEKVANQSPSSVTVCKQLIQSGRAMPRTQALPLERELFVGLFDTEDQAEGVNAFLEKR 250 Query: 249 TPDFKGR 255 ++K R Sbjct: 251 KANWKNR 257 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: 116 Number of extensions: 4 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: 257 Length adjustment: 24 Effective length of query: 231 Effective length of database: 233 Effective search space: 53823 Effective search space used: 53823 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