Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_012757048.1 RLEG_RS07315 enoyl-CoA hydratase/isomerase family protein
Query= metacyc::MONOMER-15953 (257 letters) >NCBI__GCF_000023185.1:WP_012757048.1 Length = 259 Score = 141 bits (356), Expect = 1e-38 Identities = 93/248 (37%), Positives = 125/248 (50%), Gaps = 9/248 (3%) Query: 14 VRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKEMA-- 71 V +T+ RPE LNAL+ +L LA E +A RA +LTG K F+AG DIK Sbjct: 14 VATLTISRPEKLNALDLDMLKALADAADEVEANANVRAAILTGEGKGFSAGGDIKAWGGM 73 Query: 72 ---ERDLVGILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARFG 128 E + + R+ ++R+A PLIAA+NG LGGG ELA ADI +A E + G Sbjct: 74 LPQEFGHLWVRHGHRI--FERLATLRVPLIAALNGHALGGGLELAGVADIRLAEEQIKIG 131 Query: 129 QPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTIER 188 PE LG++PG GTQRL+R +M L G+ A A+ G+V V + Sbjct: 132 LPETGLGMVPGWSGTQRLVRRFSAQAVRRMALGGEIFTAEEARLLGIVDAVVPTGNALAA 191 Query: 189 ALAIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRAEGIRAFQE 248 A A+ IA + P A +AK + A D +G E + A T D EG+ +F E Sbjct: 192 AREYAQRIAARGPAATEIAKLMIASANGED--NGTAVEALGSILAAKTGDLKEGVASFSE 249 Query: 249 KRRPEFTG 256 KR F G Sbjct: 250 KRPATFKG 257 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: 208 Number of extensions: 14 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: 259 Length adjustment: 24 Effective length of query: 233 Effective length of database: 235 Effective search space: 54755 Effective search space used: 54755 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