Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate CCNA_01891 CCNA_01891 enoyl-CoA hydratase/carnithine racemase
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__Caulo:CCNA_01891 Length = 275 Score = 142 bits (358), Expect = 7e-39 Identities = 87/260 (33%), Positives = 142/260 (54%), Gaps = 10/260 (3%) Query: 1 MSELIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFA 60 MS L + + V +TL P N+ + ++++L +A + ++T + F Sbjct: 21 MSCLKIEVEDFVATVTLANPPV-NSASVDMMLELTAAFDAFNESPDVRAVLLTAEGKTFC 79 Query: 61 AGADLNEMAEKDLAATLNDTRPQL-----WARLQAFNKPLIAAVNGYALGAGCELALLCD 115 AGADL D A R ++ W+ ++ +KP++ AVNG ALGAG + CD Sbjct: 80 AGADLKNRPGPDAPAGTAFARQRMAREMSWSMVEC-SKPVVVAVNGAALGAGLGIVASCD 138 Query: 116 VVVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVS 175 ++VA E A FGLPEI +G+ AGG + +R + SLA +MVL+G + A++ + GL+ Sbjct: 139 IIVASERAVFGLPEIDVGL---AGGAKHAVRFIPHSLARRMVLTGWRVPAEELYRRGLIE 195 Query: 176 DVFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATE 235 P + L+YA +A ++A SP+A+ AAK +L ++L+ G E+ L+ +E Sbjct: 196 AALPHEEFLDYARGIAKEIASKSPVAVAAAKDSLNVIDNLSLRDGYRYEQGNTYKLSKSE 255 Query: 236 DRHEGISAFLQKRTPDFKGR 255 D E + AF++KR P F+GR Sbjct: 256 DAKEAVRAFIEKRPPVFQGR 275 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: 128 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: 275 Length adjustment: 25 Effective length of query: 230 Effective length of database: 250 Effective search space: 57500 Effective search space used: 57500 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