Align BadK (characterized)
to candidate SMc01669 SMc01669 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__Smeli:SMc01669 Length = 263 Score = 156 bits (394), Expect = 5e-43 Identities = 98/265 (36%), Positives = 144/265 (54%), Gaps = 12/265 (4%) Query: 3 SNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG-NTRAF 61 S+ +L E + ++TLNRP+ LNALN L+D L L + D+ + A+++ G RAF Sbjct: 2 SDTVLIEISAGIALLTLNRPEKLNALNYELIDRLLALLDRIEIDETVQAVILTGAGDRAF 61 Query: 62 AAGADIASMAAWSYSDVYGSNFITRNW--------ETIRQIRKPVLAAVAGLAYGGGCEL 113 +AG DI +S S G N TR++ + KPV+AAV GLAYGGGCE+ Sbjct: 62 SAGGDIHE---FSGSVAKGVNAATRDFVRRGQQLTHRLEAFPKPVIAAVNGLAYGGGCEV 118 Query: 114 ALACDIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADR 173 A + IA A+FA PEIKL + P GGTQRLPR G+ +A+++ L+ + + A Sbjct: 119 TEAVHLAIASERARFAKPEIKLAMPPTFGGTQRLPRLAGRKRALELLLTGDAFSPQRALD 178 Query: 174 YGLVSRVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHA 233 GLV+ VV ++L ALA S A A+ ++ R + EG+L E + Sbjct: 179 MGLVNAVVPHEQLIASARALAGRTIRHSPLATAAIITAVTRGLNMAIGEGLLCESEQFAR 238 Query: 234 RFASADAREGIQAFLEKRAPCFSHR 258 S D +EG+ A+ E+R P ++ R Sbjct: 239 MVPSHDLKEGLAAWKERREPRYAGR 263 Lambda K H 0.321 0.135 0.389 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: 135 Number of extensions: 6 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: 258 Length of database: 263 Length adjustment: 25 Effective length of query: 233 Effective length of database: 238 Effective search space: 55454 Effective search space used: 55454 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 (21.9 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