Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_042119745.1 RHE_RS23495 carnitinyl-CoA dehydratase
Query= metacyc::MONOMER-15953 (257 letters) >NCBI__GCF_000092045.1:WP_042119745.1 Length = 260 Score = 121 bits (304), Expect = 1e-32 Identities = 85/247 (34%), Positives = 126/247 (51%), Gaps = 8/247 (3%) Query: 17 ITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGS-RKAFAAGADIKEMAERDL 75 + + RP+A NA++ + D E R +++G+ K F AG D+K A D Sbjct: 16 VVIDRPKA-NAIDLATSRAMGLIFRDFRDDPELRVAIISGAGEKFFCAGWDLKAAASGDA 74 Query: 76 V-GILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARFGQPEINL 134 V G Q + +KP+I AVNG C GGG E+A+ D++IA E A F PEI Sbjct: 75 VDGDYGVGGFGGLQELRDLNKPVICAVNGLCCGGGLEIALSTDLIIAAEHATFALPEIRS 134 Query: 135 GIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTIERALAIAR 194 G + A +L + + +AM M+L+G+ +D A R G V+EV E +ERA +AR Sbjct: 135 GTVADAASI-KLPKRIPYHIAMDMLLTGRWLDVHEAHRWGFVNEVVPAERLMERAWELAR 193 Query: 195 VIAQKAPLAVRLAKEALLKAEDTDLASGLR--FERHAFTV--LAGTADRAEGIRAFQEKR 250 ++ PL KE + +AE + + + +R TV L + D+ EG RAF EKR Sbjct: 194 LLESGPPLVYAAIKEIVREAEGSTFQTAMNKITKRQFATVDRLYSSEDQLEGARAFAEKR 253 Query: 251 RPEFTGR 257 P + GR Sbjct: 254 SPIWKGR 260 Lambda K H 0.320 0.134 0.374 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: 160 Number of extensions: 9 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: 257 Length of database: 260 Length adjustment: 24 Effective length of query: 233 Effective length of database: 236 Effective search space: 54988 Effective search space used: 54988 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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