Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate AZOBR_RS26485 AZOBR_RS26485 enoyl-CoA hydratase
Query= CharProtDB::CH_091794 (261 letters) >FitnessBrowser__azobra:AZOBR_RS26485 Length = 262 Score = 209 bits (532), Expect = 5e-59 Identities = 105/250 (42%), Positives = 161/250 (64%), Gaps = 1/250 (0%) Query: 6 VILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVAG 65 ++ ++G V ++TINRP LNAL+ TL E++ +GE+E+D V +++TGAGE++FVAG Sbjct: 7 ILTSRDGAVGLITINRPTTLNALDVPTLLELERALGELESDDGVHVIVVTGAGERAFVAG 66 Query: 66 ADISEMKEMNTIEGR-KFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDIRIA 124 DI+++ + F + ++VFRR E +KP IAAVNG+ALGGG E+ +S DIRIA Sbjct: 67 GDIADLDSRQGLAHYLDFAEVVHRVFRRFETCDKPTIAAVNGWALGGGTELVLSLDIRIA 126 Query: 125 SSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNKVVE 184 + A+FG PE+ LG+ PG GGTQR+ R + A++L+FT A EA+ GLVN+ V Sbjct: 127 ADTAKFGLPEINLGLFPGAGGTQRILRQIPPCRARELVFTGDQFTAAEAVAWGLVNRAVP 186 Query: 185 PSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFSTEDQKD 244 ++LM A A KI + +P+ +KL+K+ + G + + +LA+E G ++D + Sbjct: 187 KADLMAEAMATAQKIAAKSPLILKLTKRTLRHGAEMPLGASLAYEQAMIGLVLDSQDAHE 246 Query: 245 AMTAFIEKRK 254 AF+EKRK Sbjct: 247 GCRAFLEKRK 256 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: 177 Number of extensions: 5 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: 262 Length adjustment: 25 Effective length of query: 236 Effective length of database: 237 Effective search space: 55932 Effective search space used: 55932 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