Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate AO356_26645 AO356_26645 crotonase
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_26645 Length = 267 Score = 116 bits (291), Expect = 4e-31 Identities = 81/255 (31%), Positives = 127/255 (49%), Gaps = 11/255 (4%) Query: 3 ELIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAG 62 E+ VSR++ ++L NR A N ++ +L EA + V V+ F++G Sbjct: 20 EVDVSRERADIIL--NR-APLNVISMGQRDELRQVFEALDAHKGVRVIVLRSVGEHFSSG 76 Query: 63 ADLNEMAEKDLAATLNDTRPQLW--ARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAG 120 D+ E A+ W A KP+I A GY G G EL+L CD +A Sbjct: 77 GDIKGFLE----ASPEHVSKLAWNVAAPARCEKPVIVANRGYTFGVGFELSLACDFRIAS 132 Query: 121 ENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPS 180 + R+ LPE LG +PG+GG+ RL + +G + MV+ + IT QA G+ ++V P Sbjct: 133 QTTRYALPEQNLGQIPGSGGSARLQKIIGITRTKHMVMRAKRITGDQAYAWGIATEVVP- 191 Query: 181 DLTLEYALQ-LASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHE 239 D LE + L ++ R SPLA + AK+ + +++ L + E ++ L +++D E Sbjct: 192 DTELESTVDALVDELRRFSPLAQRTAKKLINDNEDAPLTVAIEMEGHCYSRLRSSKDFKE 251 Query: 240 GISAFLQKRTPDFKG 254 G+ AF KRT F G Sbjct: 252 GVEAFHSKRTAVFIG 266 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: 101 Number of extensions: 5 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: 267 Length adjustment: 25 Effective length of query: 230 Effective length of database: 242 Effective search space: 55660 Effective search space used: 55660 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 Apr 09 2024. 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