Align Enoyl-CoA-hydratase; EC 4.2.1.17 (characterized)
to candidate WP_054254926.1 BN2503_RS01750 enoyl-CoA hydratase
Query= SwissProt::G4V4T7 (265 letters) >NCBI__GCF_001298675.1:WP_054254926.1 Length = 261 Score = 133 bits (334), Expect = 4e-36 Identities = 94/249 (37%), Positives = 121/249 (48%), Gaps = 6/249 (2%) Query: 14 VAYVTMDRPAVLNAMDRRMHEELAGIWDDVEADDDVRAVVLTGAGDRAFSVGQDLKERAR 73 V +T++ PA NA+ M L D+V D+ R VVL G RAF G +LKE A+ Sbjct: 17 VVTLTLNDPARFNALGADMLAALQQALDNVARDEGARVVVLAANG-RAFCAGHNLKEMAQ 75 Query: 74 LNESGVAPTTFGSGGQAGHPRLTDRFTLSKPVVARVRGYALGGGFELVLACDIVIAAEDA 133 E F + + L PV+ARV G A G +LV CD+ +A+EDA Sbjct: 76 HPELAYYQQLFAQCSRM----MLSIHKLPVPVIARVHGMATAAGCQLVAQCDLAVASEDA 131 Query: 134 VFALPEVRLGLIAGAGGVFRLPRQLPQKVAMGYLLTGRRMDAATALRHGLVNEVVPAAEL 193 FA + GL V L R +P K AM LLTG +DA TAL GLVN VVPA L Sbjct: 132 SFATSGIHYGLFCATPSV-PLVRNVPAKRAMEMLLTGDFIDARTALEQGLVNRVVPAEAL 190 Query: 194 DQCVADWTDSLVRAAPLSVRAIKEAALRSVDLPLEEAFTTSYHWEERRRRSADAIEGVRA 253 D V S++ ++V K + +L L+ A+ + ADA EG RA Sbjct: 191 DAEVEKLVQSILGKPRVAVAMGKAVVYQHRELGLDAAYQLAGQTMAANMMDADAQEGARA 250 Query: 254 FAEKRDPIW 262 FAEKR P W Sbjct: 251 FAEKRQPAW 259 Lambda K H 0.320 0.136 0.399 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: 147 Number of extensions: 6 Number of successful extensions: 3 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: 265 Length of database: 261 Length adjustment: 25 Effective length of query: 240 Effective length of database: 236 Effective search space: 56640 Effective search space used: 56640 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 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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