Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate N515DRAFT_1164 N515DRAFT_1164 enoyl-CoA hydratase
Query= uniprot:A0A2Z5MCI7 (262 letters) >FitnessBrowser__Dyella79:N515DRAFT_1164 Length = 260 Score = 119 bits (299), Expect = 5e-32 Identities = 82/247 (33%), Positives = 122/247 (49%), Gaps = 6/247 (2%) Query: 18 VLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGA-DNFFCAGGNLNRLLENR 76 ++T++ P NAL+ D A +D ++R VV+ GA D F AG ++ E Sbjct: 16 IITVNRPDKLNALNRDTLNELTLAFAQAAQDDAVRTVVLAGAGDKAFVAGADI---AEMN 72 Query: 77 AKDPSVQAQSIDLLAEWI-SALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKFV 135 P VQAQ + + S++ KPV+A + G A G G LA+AC L VA++ A+F Sbjct: 73 GYTP-VQAQGFSRAGQRLMSSIERLGKPVVARIQGFALGGGMELAMACHLRVASEKARFG 131 Query: 136 MSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARDA 195 +GL P GG+ L + R A E+ + G +GA R +ELGVVN++ P + Sbjct: 132 QPEINLGLIPGFGGTQRLLRLAGRGAALELCLTGAMVGAQRAYELGVVNRVVAPEALDET 191 Query: 196 AVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFLE 255 A AD+L +P + A I + G L + L E F + + EG +AFLE Sbjct: 192 VDALADQLAASAPLAAAGILDAILQGGEMALDQGLEFETQAFALAFSTEDMREGTTAFLE 251 Query: 256 KRAPVYK 262 KR +K Sbjct: 252 KRKAEFK 258 Lambda K H 0.317 0.132 0.377 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: 130 Number of extensions: 5 Number of successful extensions: 1 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: 262 Length of database: 260 Length adjustment: 25 Effective length of query: 237 Effective length of database: 235 Effective search space: 55695 Effective search space used: 55695 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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