Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_042119745.1 RHE_RS23495 carnitinyl-CoA dehydratase
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_000092045.1:WP_042119745.1 Length = 260 Score = 125 bits (313), Expect = 1e-33 Identities = 83/259 (32%), Positives = 132/259 (50%), Gaps = 8/259 (3%) Query: 6 IETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAG 64 + T+++G + + ++RP K NA++ + DPE+RV II+G G K FCAG Sbjct: 5 VRTRRDGAVLEVVIDRP-KANAIDLATSRAMGLIFRDFRDDPELRVAIISGAGEKFFCAG 63 Query: 65 ADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAA 124 D+ + + G + ++ L+KP I +NG GGGLE+AL+ D+ IAA Sbjct: 64 WDLKAAASGDAVDG-DYGVGGFGGLQELRDLNKPVICAVNGLCCGGGLEIALSTDLIIAA 122 Query: 125 EEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPL 184 E A LPEI G + +L + I A++M++TG + +A ++G VN VVP Sbjct: 123 EHATFALPEIRSGTVAD-AASIKLPKRIPYHIAMDMLLTGRWLDVHEAHRWGFVNEVVPA 181 Query: 185 ANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGL----ALESVGWGVVFSTED 240 L + +LA + P+ A IKE+V S + + + ++S+ED Sbjct: 182 ERLMERAWELARLLESGPPLVYAAIKEIVREAEGSTFQTAMNKITKRQFATVDRLYSSED 241 Query: 241 KKEGVSAFLEKREPTFKGK 259 + EG AF EKR P +KG+ Sbjct: 242 QLEGARAFAEKRSPIWKGR 260 Lambda K H 0.315 0.135 0.382 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: 130 Number of extensions: 7 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: 259 Length of database: 260 Length adjustment: 24 Effective length of query: 235 Effective length of database: 236 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: 42 (22.0 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