Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate PfGW456L13_3427 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= BRENDA::O87873 (258 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3427 Length = 272 Score = 94.0 bits (232), Expect = 3e-24 Identities = 82/252 (32%), Positives = 122/252 (48%), Gaps = 13/252 (5%) Query: 10 VWLERDGSLLRLRLARPKA-NIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPH-FSFG 67 V LERD + + L RP+ N ++ + + QAL Q P +R +++ EG F G Sbjct: 17 VRLERDAMVGWVVLTRPRQINAINDEIRQGVPQALALLQQDPDIRVIVIRGEGDRGFCAG 76 Query: 68 ASVDEHMPDQCAQMLKSLHGLVR--EMLDSPV-PILVALRGQCLGGGLEVAAAGNLLFAA 124 A + E + + ++ VR E LD P++ A+ G C+GGGLE+ A ++ FAA Sbjct: 77 ADIKERRGPESSLQVRQRMENVRWIETLDGITKPVIAAIHGYCMGGGLELVLACDIRFAA 136 Query: 125 PDAKFGQPEIRLGVFAPAASCLLPPRV---GQACAEDLLWSGRSIDGAEGHRIGLIDVLA 181 PDA F PE LG+ RV GQA D+L +G + + RIGL+ LA Sbjct: 137 PDAVFALPETGLGLIPGGGGTQRLSRVVAPGQAL--DMLLTGDRVGAEQAQRIGLVSRLA 194 Query: 182 EDPE--AAALRWFDEHIARLSASSLRFAVRAARCDSVPRIKQKLDTVEALYLEELMASHD 239 D +R F + IA ++ F +AAR +K+ LD +E L + D Sbjct: 195 SDSANLVQEVRAFAQRIASKPPTASAFVKQAARAALEMDLKRGLD-LELDLFALLAPTKD 253 Query: 240 AVEGLKAFLEKR 251 A E +AF E+R Sbjct: 254 AREAAQAFSERR 265 Lambda K H 0.321 0.135 0.402 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: 172 Number of extensions: 9 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: 258 Length of database: 272 Length adjustment: 25 Effective length of query: 233 Effective length of database: 247 Effective search space: 57551 Effective search space used: 57551 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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