Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_042119745.1 RHE_RS23495 carnitinyl-CoA dehydratase
Query= CharProtDB::CH_091794 (261 letters) >NCBI__GCF_000092045.1:WP_042119745.1 Length = 260 Score = 126 bits (316), Expect = 5e-34 Identities = 83/248 (33%), Positives = 127/248 (51%), Gaps = 7/248 (2%) Query: 10 KEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVAGADIS 69 ++G V V I+RPKA NA++ T + M + + +D E+ I++GAGEK F AG D+ Sbjct: 9 RDGAVLEVVIDRPKA-NAIDLATSRAMGLIFRDFRDDPELRVAIISGAGEKFFCAGWDLK 67 Query: 70 EMKEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDIRIASSNAR 129 + ++G +G+ G + L L KPVI AVNG GGG EIA+S D+ IA+ +A Sbjct: 68 AAASGDAVDG-DYGVGGFGGLQELRDLNKPVICAVNGLCCGGGLEIALSTDLIIAAEHAT 126 Query: 130 FGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNKVVEPSELM 189 F PE+ G T + +L + + +A ++ T + + EA R G VN+VV LM Sbjct: 127 FALPEIRSG-TVADAASIKLPKRIPYHIAMDMLLTGRWLDVHEAHRWGFVNEVVPAERLM 185 Query: 190 NTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTAL----AFESEAFGECFSTEDQKDA 245 A E+A + S P+ K+ + TA+ + +S+EDQ + Sbjct: 186 ERAWELARLLESGPPLVYAAIKEIVREAEGSTFQTAMNKITKRQFATVDRLYSSEDQLEG 245 Query: 246 MTAFIEKR 253 AF EKR Sbjct: 246 ARAFAEKR 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: 144 Number of extensions: 11 Number of successful extensions: 4 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 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