Align BadK (characterized)
to candidate Ga0059261_2668 Ga0059261_2668 Enoyl-CoA hydratase/carnithine racemase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__Korea:Ga0059261_2668 Length = 256 Score = 144 bits (364), Expect = 1e-39 Identities = 100/261 (38%), Positives = 141/261 (54%), Gaps = 11/261 (4%) Query: 3 SNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG-NTRAF 61 ++ +L V ITLNRP LNAL + AL ++ A ++ D + +VI G +AF Sbjct: 2 TDDLLFTVADHVATITLNRPAKLNALTPEMAAALIASVSACNSSDAVRCVVITGAGEKAF 61 Query: 62 AAGADIASMAAWSYSDVYGSNFITRN----WETIRQIRKPVLAAVAGLAYGGGCELALAC 117 +AG+DI ++ D Y + + RN + +R RKPV+AA+ G A GGG E A+A Sbjct: 62 SAGSDITTL------DGYATPWDFRNRDDYCDALRACRKPVVAAINGYALGGGLETAMAA 115 Query: 118 DIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLV 177 DI IA +A+FA PEIKLG + G G L ++G + A M + ++AE+A +GLV Sbjct: 116 DIRIASTNARFAAPEIKLGWIGGGGMAAGLTYSMGASNAALMLFTGDMIDAEKALAWGLV 175 Query: 178 SRVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFAS 237 S VV D L +A TIA+ + A K +L A + I +ER FA+ Sbjct: 176 SEVVAPDALLARAQEIARTIASRAPIAAETAKLNLRAAHTMPWDKAIEYERDLQAICFAT 235 Query: 238 ADAREGIQAFLEKRAPCFSHR 258 DA+EG AF EKRAP F R Sbjct: 236 DDAKEGRAAFAEKRAPVFRRR 256 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: 134 Number of extensions: 6 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: 258 Length of database: 256 Length adjustment: 24 Effective length of query: 234 Effective length of database: 232 Effective search space: 54288 Effective search space used: 54288 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