Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_076479152.1 BW971_RS10155 crotonase/enoyl-CoA hydratase family protein
Query= CharProtDB::CH_091794 (261 letters) >NCBI__GCF_900156495.1:WP_076479152.1 Length = 273 Score = 117 bits (294), Expect = 2e-31 Identities = 81/253 (32%), Positives = 131/253 (51%), Gaps = 14/253 (5%) Query: 14 VAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVAGADISEMK- 72 VA VT+ P NA+ D +E+ V E++ D+EV AV+L G G K F G D+S M Sbjct: 15 VAEVTLIGPGKGNAMGPDFWRELPEVFAELDADTEVRAVVLAGRG-KHFSFGLDLSAMAG 73 Query: 73 EMNTIEGRKFGILGNKVFRRLELLEK-----------PVIAAVNGFALGGGCEIAMSCDI 121 E+ + F R+ L + PV+A + G+ +GGG ++ + DI Sbjct: 74 ELGPVLAGDALAKTRTEFHRMVLRMQGATTAVARSRTPVVAVIQGWCIGGGVDLIAAADI 133 Query: 122 RIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNK 181 R AS++A F E +G+ G QRL ++G ++L FTA++I AD ALRI LVN Sbjct: 134 RYASADATFSVREAKVGMVADMGSLQRLPAIIGDAHTRELAFTAKDIDADAALRINLVND 193 Query: 182 VVEPSE-LMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFSTE 240 V+ ++ + TA+ A +I +N P+ V+ K ++ + +D L + + ++ Sbjct: 194 VLPDADAALATARATAAQIAANPPLVVQGVKDVLDWPLTGTVDDGLRYVAAWNAAFLPSK 253 Query: 241 DQKDAMTAFIEKR 253 D +A++A EKR Sbjct: 254 DIGEAISAIFEKR 266 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: 141 Number of extensions: 7 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: 273 Length adjustment: 25 Effective length of query: 236 Effective length of database: 248 Effective search space: 58528 Effective search space used: 58528 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