Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate RR42_RS28550 RR42_RS28550 enoyl-CoA hydratase
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__Cup4G11:RR42_RS28550 Length = 256 Score = 153 bits (386), Expect = 4e-42 Identities = 107/245 (43%), Positives = 142/245 (57%), Gaps = 9/245 (3%) Query: 15 LTLNRPAAR--NALNNALLMQLVNELEAAATDTSISVCVITGN-ARFFAAGADLNEMAEK 71 LTL RP A NA A L QLV L A DT + VITG+ +RFF+AGADLN A+ Sbjct: 13 LTLKRPPANAFNAEGLAQLQQLVATLNA---DTRVRAIVITGDGSRFFSAGADLNGFADG 69 Query: 72 DLA-ATLNDTR-PQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFGLPE 129 D A A L R + LQ +IAA+NGYA+G G E AL CDV +A E A+ LPE Sbjct: 70 DRAHARLMAQRFGAAFEALQNARPLVIAAINGYAMGGGLECALACDVRIAEEQAQMALPE 129 Query: 130 ITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTLEYALQ 189 +G++P GTQ L VG+ A +M+L+ E I A A + GLV ++ P+ L+ AL+ Sbjct: 130 AGVGLLPCGCGTQTLPWLVGEGWAKRMILANERIDAATALRIGLVEEMVPTGQALDAALR 189 Query: 190 LASKMARHSPLALQAAKQALRQS-QEVALQAGLAQERQLFTLLAATEDRHEGISAFLQKR 248 LA + + SP A +KQ + + Q V LA ER+ F L ED+ EG++AFLQKR Sbjct: 190 LAERASNVSPRAAAYSKQLVHLARQGVPRGPALALERERFVDLFDGEDQREGVNAFLQKR 249 Query: 249 TPDFK 253 P ++ Sbjct: 250 APQWR 254 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: 127 Number of extensions: 8 Number of successful extensions: 4 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: 256 Length adjustment: 24 Effective length of query: 231 Effective length of database: 232 Effective search space: 53592 Effective search space used: 53592 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