Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate AZOBR_RS09775 AZOBR_RS09775 enoyl-CoA hydratase
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__azobra:AZOBR_RS09775 Length = 263 Score = 156 bits (394), Expect = 5e-43 Identities = 92/242 (38%), Positives = 135/242 (55%), Gaps = 6/242 (2%) Query: 12 VLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITG-NARFFAAGADLNEMA- 69 + LTLNRPA NA++ AL +++ L+A D ++ ++TG R F+AGAD+ E Sbjct: 22 IATLTLNRPAKLNAISTALAAAMLDTLDALEVDAAVRAIIVTGAGERAFSAGADIAEFTP 81 Query: 70 --EKDLAATLNDTRP--QLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARF 125 + A + RP L AR+++F KP+IAAVNG G GCE+ + VA E A F Sbjct: 82 AVRRGPEAAVRAFRPGQTLCARIESFPKPIIAAVNGICYGGGCEILEASHLAVASERASF 141 Query: 126 GLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTLE 185 EI LG+MP GGTQRL R+ G+ A + +L+G++ A GLV+ V P D L Sbjct: 142 SKAEIRLGMMPTFGGTQRLPRNAGRKRALEWLLTGDTFPPAMALAVGLVNQVVPHDALLP 201 Query: 186 YALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAFL 245 A +LA ++ RHSP A+ A+ + + + GLA E + F LA D +G+ A+L Sbjct: 202 AAFELAGRIVRHSPAAVSGILGAVTRGLNMTIGEGLAVETERFARLAPGADLRDGLEAWL 261 Query: 246 QK 247 + Sbjct: 262 AR 263 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: 6 Number of successful extensions: 1 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: 263 Length adjustment: 24 Effective length of query: 231 Effective length of database: 239 Effective search space: 55209 Effective search space used: 55209 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