Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate SMc01669 SMc01669 enoyl-CoA hydratase
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__Smeli:SMc01669 Length = 263 Score = 162 bits (409), Expect = 8e-45 Identities = 99/251 (39%), Positives = 146/251 (58%), Gaps = 7/251 (2%) Query: 12 VLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNA-RFFAAGADLNE--- 67 + LLTLNRP NALN L+ +L+ L+ D ++ ++TG R F+AG D++E Sbjct: 13 IALLTLNRPEKLNALNYELIDRLLALLDRIEIDETVQAVILTGAGDRAFSAGGDIHEFSG 72 Query: 68 -MAEKDLAATLNDTR--PQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENAR 124 +A+ AAT + R QL RL+AF KP+IAAVNG A G GCE+ + +A E AR Sbjct: 73 SVAKGVNAATRDFVRRGQQLTHRLEAFPKPVIAAVNGLAYGGGCEVTEAVHLAIASERAR 132 Query: 125 FGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTL 184 F PEI L + P GGTQRL R G+ A +++L+G++ + Q+A GLV+ V P + + Sbjct: 133 FAKPEIKLAMPPTFGGTQRLPRLAGRKRALELLLTGDAFSPQRALDMGLVNAVVPHEQLI 192 Query: 185 EYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAF 244 A LA + RHSPLA A A+ + +A+ GL E + F + + D EG++A+ Sbjct: 193 ASARALAGRTIRHSPLATAAIITAVTRGLNMAIGEGLLCESEQFARMVPSHDLKEGLAAW 252 Query: 245 LQKRTPDFKGR 255 ++R P + GR Sbjct: 253 KERREPRYAGR 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: 120 Number of extensions: 4 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