Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_029133990.1 A3GO_RS0114405 enoyl-CoA hydratase
Query= metacyc::MONOMER-15953 (257 letters) >NCBI__GCF_000428045.1:WP_029133990.1 Length = 261 Score = 191 bits (484), Expect = 2e-53 Identities = 103/250 (41%), Positives = 154/250 (61%), Gaps = 3/250 (1%) Query: 11 EQGVRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSR-KAFAAGADIKE 69 E G+ +T+ RP + NALN+ LDE+ A + R +++TG+ KAF AGADI E Sbjct: 12 ETGIYKLTVNRPRSFNALNSATLDEIYAAGEQLANTPDARVLLVTGAGDKAFVAGADIAE 71 Query: 70 MAERDLVG--ILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARF 127 M ++ + + + ++R+ P+IA VNG+CLGGG ELAM D +IA E A+F Sbjct: 72 MRDKSAIEGQVFSQKGMRAFRRLETLDIPVIAVVNGYCLGGGNELAMSCDWIIASEKAQF 131 Query: 128 GQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTIE 187 GQPE+NLG+ PG GG+QRL R +G++ AM+++++G+ I A A GL + V + +E Sbjct: 132 GQPEVNLGVSPGFGGSQRLTRLIGRAKAMELLVTGRQIKADEALAWGLANHVYAADELME 191 Query: 188 RALAIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRAEGIRAFQ 247 +AL AR+I QK P++VRL K+A+ + +D DL + E F + T D+ EG+ AF Sbjct: 192 KALETARLINQKGPVSVRLTKQAVQRGQDLDLDNACLLESQVFGLCFSTEDQKEGMGAFL 251 Query: 248 EKRRPEFTGR 257 EKR +F R Sbjct: 252 EKRAAQFKAR 261 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: 152 Number of extensions: 7 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: 261 Length adjustment: 24 Effective length of query: 233 Effective length of database: 237 Effective search space: 55221 Effective search space used: 55221 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