Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_012755571.1 RLEG_RS26045 crotonase/enoyl-CoA hydratase family protein
Query= CharProtDB::CH_091794 (261 letters) >NCBI__GCF_000023185.1:WP_012755571.1 Length = 267 Score = 183 bits (465), Expect = 3e-51 Identities = 101/255 (39%), Positives = 144/255 (56%), Gaps = 4/255 (1%) Query: 4 NNVILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFV 63 + V+++ +A +T+NRP+ LNALN + + ++ IE D + VILTG+GE++F Sbjct: 3 DTVLIDSRDGIATLTLNRPEKLNALNYALIDRLLAILDAIETDRSIRVVILTGSGERAFS 62 Query: 64 AGADISEMKEMNT----IEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSC 119 AG DI E E + R F G ++ RLE KPVIAAVNG A GGGCEI + Sbjct: 63 AGGDIYEFSESVAQGADVAMRDFVARGQRLTARLEAYHKPVIAAVNGLAFGGGCEITEAV 122 Query: 120 DIRIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLV 179 + IAS A F +PE+ L + P FGGTQRL RL G A +L+ T AL +GLV Sbjct: 123 PLAIASERALFAKPEINLAMPPTFGGTQRLPRLAGRKRALELLLTGDAFSPQRALELGLV 182 Query: 180 NKVVEPSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFST 239 N++V LM A ++A +I+ ++P+A A+ RG+ I L E E F T Sbjct: 183 NQLVPHDALMPAAHDLARRILRHSPLAAASILTAVTRGINQSIAEGLLIEGEQFARMAPT 242 Query: 240 EDQKDAMTAFIEKRK 254 D ++ + A+IE+RK Sbjct: 243 ADLREGLDAWIERRK 257 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: 165 Number of extensions: 4 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: 261 Length of database: 267 Length adjustment: 25 Effective length of query: 236 Effective length of database: 242 Effective search space: 57112 Effective search space used: 57112 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 Apr 09 2024. 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