Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_057507779.1 ABB28_RS05820 enoyl-CoA hydratase
Query= metacyc::MONOMER-15953 (257 letters) >NCBI__GCF_001431535.1:WP_057507779.1 Length = 259 Score = 180 bits (457), Expect = 2e-50 Identities = 111/247 (44%), Positives = 143/247 (57%), Gaps = 3/247 (1%) Query: 14 VRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSR-KAFAAGADIKEMAE 72 +R +T+QRPE LNALN + L LAA A QD R V+LTG+ KAF AGADI EM Sbjct: 13 IRTVTVQRPEKLNALNGETLRALAAAFEQAAQDPAVRVVILTGAGPKAFVAGADISEMNT 72 Query: 73 RDLVGILEDPRVAH--WQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARFGQP 130 V + + ++I KP+IA VNGF LGGG ELAM + IA + AR GQP Sbjct: 73 LSAVEGRDFSLLGQRLMRQIERMPKPVIARVNGFALGGGLELAMACHLRIAVDTARLGQP 132 Query: 131 EINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTIERAL 190 EI LG++PG GG+QRLLR G++ A+++ L G IDA A + GLV+EV + R Sbjct: 133 EITLGLIPGFGGSQRLLRLCGRAAALELCLLGTPIDAARALQLGLVNEVASADDLDARVA 192 Query: 191 AIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRAEGIRAFQEKR 250 +A +A APLAVR +A+ + L SGL +E F +L T D EG AF E+R Sbjct: 193 GLAERLANAAPLAVRALLDAVHVGGECSLESGLEYESAQFGLLFATHDMREGTSAFLERR 252 Query: 251 RPEFTGR 257 F R Sbjct: 253 AAMFQNR 259 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: 199 Number of extensions: 12 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 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