Align Putative enoyl-CoA hydratase protein; EC 4.2.1.17 (characterized, see rationale)
to candidate WP_090447225.1 BLS63_RS18325 enoyl-CoA hydratase
Query= uniprot:Q92VJ6 (261 letters) >NCBI__GCF_900100495.1:WP_090447225.1 Length = 265 Score = 126 bits (317), Expect = 4e-34 Identities = 81/251 (32%), Positives = 119/251 (47%), Gaps = 1/251 (0%) Query: 12 QRGVARVTLARSEKHNALSATMIGELTAVVGRLATDASIRAVILDAEGKSFCAGGDLDWM 71 + GV +TL R + NA+S M+ EL AV+ + + +RA++L G FCAGGD+ M Sbjct: 15 EAGVLHITLNRPDSRNAMSLAMVEELRAVLAAVNDELDVRAIVLRGTGGHFCAGGDIKDM 74 Query: 72 RQQFSADRPTRIAEATRLAMMLKALNDLPKPLIARVHGNAFGGGVGLISVCDTVIAASGA 131 + +L+ P+ L+A + G GGG GL V D IA A Sbjct: 75 ATARAQGEQAYRELNRAFGSLLEEAQRAPQVLVAVLEGAVLGGGFGLACVSDIAIARQEA 134 Query: 132 QFGLTETRLGLIPATISPYVIARTGEARARPLFMSARVF-GAEEAKVAGFVTTVVDGTML 190 QFGL ET LG++PA I+P+V+ R G +AR L ++A F GAE A++ L Sbjct: 135 QFGLPETSLGILPAQIAPFVVGRIGLTQARRLALTAARFNGAEAARLGLVHFCEASSEAL 194 Query: 191 DGAVEAAVTAYLVAAPGAAGRAKRLARSLGLPITDAVIAATIEQLADTWETDEAREGVSA 250 + +E + AP A K L + +++ Q A+ E EG A Sbjct: 195 ERRLEETLAQIRQCAPQANAATKALLLATETENLGSLLDHAAGQFAEAVLGAEGSEGTLA 254 Query: 251 FFERRNPSWRQ 261 F ++R P W Q Sbjct: 255 FVQKRAPKWAQ 265 Lambda K H 0.321 0.133 0.383 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: 166 Number of extensions: 11 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: 265 Length adjustment: 25 Effective length of query: 236 Effective length of database: 240 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 (21.9 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