Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_108402835.1 B9Z44_RS06720 enoyl-CoA hydratase
Query= metacyc::MONOMER-15953 (257 letters) >NCBI__GCF_003063475.1:WP_108402835.1 Length = 268 Score = 164 bits (415), Expect = 2e-45 Identities = 105/259 (40%), Positives = 141/259 (54%), Gaps = 6/259 (2%) Query: 4 TLSVDAPEQGVRLITLQRPEALNALNTQL-LDELAAELALAEQDAETRAVVLTGS-RKAF 61 TL V + L RPE NALNTQ+ +D L + L + + R VVLTG+ K F Sbjct: 11 TLECTQVSDHVLQVCLNRPEVGNALNTQMGVDLLDLWVRLTDVPGDLRCVVLTGAGAKIF 70 Query: 62 AAGADIKE---MAERDLVGILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADI 118 G D+KE M + E +W I P+I A+NG GGG E+A+ D Sbjct: 71 CGGGDLKERNGMTPQAWQYQHEIFERLYWALID-LPLPVIGAINGHAYGGGLEMALCCDF 129 Query: 119 LIAGEDARFGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSE 178 L A +DARF PE+ LGIMPG GGTQ L RA+G+ A ++ L+G+ A A GLV++ Sbjct: 130 LYASQDARFALPEVTLGIMPGMGGTQNLPRALGERRAKELALTGRPFSAEQALAWGLVNQ 189 Query: 179 VTLPELTIERALAIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTAD 238 V P+ + AL A+ IA APL+VR K+++ +L + RFE A+ L T D Sbjct: 190 VAAPDAVLALALETAQRIAANAPLSVRQIKKSIRYGGQMELRTAYRFEVEAYNRLVDTDD 249 Query: 239 RAEGIRAFQEKRRPEFTGR 257 R EG+ AF +KR P F GR Sbjct: 250 RREGVAAFNDKRPPVFKGR 268 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: 180 Number of extensions: 11 Number of successful extensions: 2 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: 268 Length adjustment: 25 Effective length of query: 232 Effective length of database: 243 Effective search space: 56376 Effective search space used: 56376 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 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