Align BadK (characterized)
to candidate 3610342 Dshi_3723 Enoyl-CoA hydratase/isomerase (RefSeq)
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__Dino:3610342 Length = 267 Score = 133 bits (334), Expect = 4e-36 Identities = 87/253 (34%), Positives = 130/253 (51%), Gaps = 4/253 (1%) Query: 6 ILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGA 65 I + + G I L R +N ++ D L A A DADD + IV+ F++G Sbjct: 19 IEVDAEAERGDIVLERAP-MNVISMDQRDQLRAAFEALDADDAVRVIVLRAEGEHFSSGG 77 Query: 66 DIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRS 125 I S V + + N + KPV+AA G +G G E++LACD IA +S Sbjct: 78 YIHGFLDASPEHV---SHLADNVAAPWRCAKPVIAANKGYTFGVGFEISLACDFRIAAKS 134 Query: 126 AKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDR 185 +ALPE KLG +PG+GG+ RL IG A+ D+ + +R ++ ++A +G+ +V+DD+ Sbjct: 135 TFYALPEQKLGQIPGSGGSARLQALIGLARTKDVVMRSRRISGQQAFDWGIAVELVEDDK 194 Query: 186 LRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQ 245 L + T L + +FS A K+ LN + +T+A GI E S D EG++ Sbjct: 195 LEEATAKLVNELRSFSPMAQRTAKKLLNDSENATVATGIELEGHCYSRLRQSEDFAEGVK 254 Query: 246 AFLEKRAPCFSHR 258 AF EKR P F R Sbjct: 255 AFHEKRKPTFVGR 267 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: 92 Number of extensions: 2 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: 267 Length adjustment: 25 Effective length of query: 233 Effective length of database: 242 Effective search space: 56386 Effective search space used: 56386 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