Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_094507764.1 CEV31_RS14480 enoyl-CoA hydratase/isomerase family protein
Query= CharProtDB::CH_091794 (261 letters) >NCBI__GCF_002252445.1:WP_094507764.1 Length = 257 Score = 147 bits (372), Expect = 2e-40 Identities = 82/249 (32%), Positives = 134/249 (53%), Gaps = 1/249 (0%) Query: 6 VILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVAG 65 ++ + V +T+NRP+ +NA N+ ++ E + V AVILTGAGE++F AG Sbjct: 5 ILTSLKNSVLTITLNRPEVMNAWNTAMRDQLIEAFQAAEENVAVKAVILTGAGERAFGAG 64 Query: 66 ADISEMKEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDIRIAS 125 D++E K N + K++ R+ L KP+IAA+NG A G ++A+ CDIRIA Sbjct: 65 QDLNETKTFNADRAEIWIGEWEKLYTRIRTLSKPIIAALNGVAAGSAFQVALLCDIRIAH 124 Query: 126 SNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNKVVEP 185 S R GQPE+ GI P G+ + ++G L+ T + + +DEA RIGL+N +V Sbjct: 125 SGVRIGQPEINSGI-PTTTGSWIMREMIGFARTVDLVLTGRLLDSDEAHRIGLINTIVAQ 183 Query: 186 SELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFSTEDQKDA 245 ++ A+ + ++ S PVA++L++Q + + AL+ E ++T + Sbjct: 184 DQVQAAAQALGEELASKPPVAMRLNRQRFYEMTETGLQDALSAGVRIQREAYATGEPARM 243 Query: 246 MTAFIEKRK 254 M AF R+ Sbjct: 244 MEAFFAARQ 252 Lambda K H 0.317 0.134 0.365 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: 160 Number of extensions: 8 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: 261 Length of database: 257 Length adjustment: 24 Effective length of query: 237 Effective length of database: 233 Effective search space: 55221 Effective search space used: 55221 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 (21.6 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