Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_012760683.1 RLEG_RS34755 carnitinyl-CoA dehydratase
Query= metacyc::MONOMER-15953 (257 letters) >NCBI__GCF_000023185.1:WP_012760683.1 Length = 260 Score = 117 bits (292), Expect = 3e-31 Identities = 84/251 (33%), Positives = 127/251 (50%), Gaps = 8/251 (3%) Query: 13 GVRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGS-RKAFAAGADIKEMA 71 GV + + RP+A NA++ L D R +++G+ K F AG D+K A Sbjct: 12 GVLEVVIDRPKA-NAIDLATSRALGLIFRNFRDDPALRVAIVSGAGEKFFCAGWDLKAAA 70 Query: 72 ERDLV-GILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARFGQP 130 D V G Q + +KP+I AVNG C GGG E+A+ AD+++A E A F P Sbjct: 71 SGDAVDGDYGVGGFGGLQELRDLNKPVICAVNGICCGGGLEIALSADLILAAEHATFALP 130 Query: 131 EINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTIERAL 190 EI G + A +L + + +AM M+L+G+ +D A R G ++EV E +ERA Sbjct: 131 EIRSGTVADAASI-KLPKRIPYHIAMDMLLTGRWLDVHEAHRWGFINEVLPAERLMERAW 189 Query: 191 AIARVIAQKAPLAVRLAKEALLKAEDTDLASGLR--FERHAFTV--LAGTADRAEGIRAF 246 +AR++ L KE + +AE + + + +R TV L + D+ EG RAF Sbjct: 190 ELARLLESGPSLVHAAIKEIVREAEGSTFQTAMNKITKRQFATVDRLYSSEDQLEGARAF 249 Query: 247 QEKRRPEFTGR 257 EKR P + G+ Sbjct: 250 AEKRSPIWKGK 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: 159 Number of extensions: 9 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: 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