Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011938504.1 GURA_RS08130 enoyl-CoA hydratase
Query= BRENDA::P76082 (255 letters) >NCBI__GCF_000016745.1:WP_011938504.1 Length = 261 Score = 136 bits (343), Expect = 4e-37 Identities = 83/243 (34%), Positives = 130/243 (53%), Gaps = 5/243 (2%) Query: 12 VLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGADLNEMAEK 71 + + NRP +NALN A+ LV+ L A D ++ V ++TGN F +G N++A+ Sbjct: 18 IFTICFNRPEKKNALNLAMYAALVDSLGEADRDDAVRVVLLTGNGECFTSG---NDLADF 74 Query: 72 DLAATLNDTRP--QLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFGLPE 129 A ++ P Q A + F KPL+AAV G A+G G + L CD+V AG A LP Sbjct: 75 MTAPPISAESPVMQFLAAISRFRKPLVAAVIGSAVGVGVTMLLHCDLVYAGTGAVLQLPF 134 Query: 130 ITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLTLEYALQ 189 + LG+ P AG T R +G A++++L GE +A++A G+V+ VFP L A Sbjct: 135 VNLGLCPEAGSTLLFPRLMGHQRAAELLLLGEPFSAEKACSVGIVNGVFPDVEVLAAART 194 Query: 190 LASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISAFLQKRT 249 A ++A A++ AK L++ +L+ +A E F + + E + AF+++R Sbjct: 195 KALQLAARPAAAVRLAKALLKKEYAASLEETIADEGAHFVKRLMSPEAGEALRAFMERRQ 254 Query: 250 PDF 252 PDF Sbjct: 255 PDF 257 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: 116 Number of extensions: 1 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: 261 Length adjustment: 24 Effective length of query: 231 Effective length of database: 237 Effective search space: 54747 Effective search space used: 54747 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 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