Align BadK (characterized)
to candidate HSERO_RS12745 HSERO_RS12745 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__HerbieS:HSERO_RS12745 Length = 260 Score = 133 bits (334), Expect = 4e-36 Identities = 96/252 (38%), Positives = 128/252 (50%), Gaps = 13/252 (5%) Query: 9 ETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGN-TRAFAAGADI 67 E G ++TL+ P AL D L + +AD I +V+ G + F+AGAD+ Sbjct: 10 EKTGHTAVLTLSNPPANTWTRAALAD-LTRLVKELNADRDIYTLVVTGEGEKFFSAGADL 68 Query: 68 ASMA------AWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVI 121 A A + +G F ET+ R +AA+ G A GGG E ALACDI I Sbjct: 69 KLFADGDKAMAREMARRFGEAF-----ETLSAFRGVSIAAINGYAMGGGLECALACDIRI 123 Query: 122 AGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVV 181 A A+ ALPE +GLLP AGGTQ LP +G+ A M L +NAE A R GLV VV Sbjct: 124 AEEQAQMALPEAAVGLLPCAGGTQNLPWLVGEGWAKRMILCGERVNAETALRIGLVEEVV 183 Query: 182 DDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAR 241 + R+ +ALA S ++ A K+ + A + L + ER F + D R Sbjct: 184 PRGQARERALALAQQAEKQSPSSVAASKQLIQGARHNPLGTILQTERELFVDLFDTQDQR 243 Query: 242 EGIQAFLEKRAP 253 EG+QAFLEKR+P Sbjct: 244 EGVQAFLEKRSP 255 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: 137 Number of extensions: 8 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: 258 Length of database: 260 Length adjustment: 24 Effective length of query: 234 Effective length of database: 236 Effective search space: 55224 Effective search space used: 55224 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