Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate GFF929 HP15_908 enoyl-CoA hydratase/isomerase
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__Marino:GFF929 Length = 259 Score = 162 bits (411), Expect = 5e-45 Identities = 100/260 (38%), Positives = 151/260 (58%), Gaps = 6/260 (2%) Query: 1 MSELI-VSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNA-RF 58 MS+LI + ++ + +LT+N P A N L+ L N ++ D I V+TG +F Sbjct: 1 MSDLIQLEKRGHIAVLTINNPPA-NTWTKDSLIALTNIVKELNEDRDIFALVMTGQGEKF 59 Query: 59 FAAGADLNEMAEKDLAAT--LNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDV 116 ++AGADL A+ D A + + ++ LQ F IAAVNGYA+G G E A+ CD+ Sbjct: 60 YSAGADLKTFADGDKARANEMGQLFGEAFSTLQRFRGVSIAAVNGYAMGGGLECAMACDI 119 Query: 117 VVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSD 176 +A E+A+ LPE +G++P AGGTQ L VG+ A +M+L GE + A A + GLV + Sbjct: 120 RIAEEHAQMALPEAGVGLLPCAGGTQNLPWLVGEGWAKRMILCGERVKADTALRIGLVEE 179 Query: 177 VFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQE-VALQAGLAQERQLFTLLAATE 235 V PS L+ AL+LA + SP + K + +++ + G ER+LF L +TE Sbjct: 180 VVPSGQGLDKALELAEMACQQSPSSTARCKTLVMSARDGRSHDDGWRMERELFVELFSTE 239 Query: 236 DRHEGISAFLQKRTPDFKGR 255 D+ EG++AFL+KR P++K R Sbjct: 240 DQKEGVNAFLEKRKPEWKNR 259 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: 125 Number of extensions: 10 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: 259 Length adjustment: 24 Effective length of query: 231 Effective length of database: 235 Effective search space: 54285 Effective search space used: 54285 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