Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate HSERO_RS12745 HSERO_RS12745 enoyl-CoA hydratase
Query= CharProtDB::CH_091794 (261 letters) >FitnessBrowser__HerbieS:HSERO_RS12745 Length = 260 Score = 167 bits (424), Expect = 2e-46 Identities = 93/249 (37%), Positives = 138/249 (55%), Gaps = 1/249 (0%) Query: 5 NVILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVA 64 N+ LEK G AV+T++ P A N L ++ ++ E+ D ++ +++TG GEK F A Sbjct: 6 NLKLEKTGHTAVLTLSNPPA-NTWTRAALADLTRLVKELNADRDIYTLVVTGEGEKFFSA 64 Query: 65 GADISEMKEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDIRIA 124 GAD+ + + R+ + F L IAA+NG+A+GGG E A++CDIRIA Sbjct: 65 GADLKLFADGDKAMAREMARRFGEAFETLSAFRGVSIAAINGYAMGGGLECALACDIRIA 124 Query: 125 SSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNKVVE 184 A+ PE +G+ P GGTQ L LVG G AK++I + + A+ ALRIGLV +VV Sbjct: 125 EEQAQMALPEAAVGLLPCAGGTQNLPWLVGEGWAKRMILCGERVNAETALRIGLVEEVVP 184 Query: 185 PSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFSTEDQKD 244 + A +A + +P +V SKQ I + T L E E F + F T+DQ++ Sbjct: 185 RGQARERALALAQQAEKQSPSSVAASKQLIQGARHNPLGTILQTERELFVDLFDTQDQRE 244 Query: 245 AMTAFIEKR 253 + AF+EKR Sbjct: 245 GVQAFLEKR 253 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: 178 Number of extensions: 10 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: 261 Length of database: 260 Length adjustment: 25 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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 17 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