Align Methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate Echvi_0069 Echvi_0069 Enoyl-CoA hydratase/carnithine racemase
Query= reanno::Pedo557:CA265_RS09125 (258 letters) >FitnessBrowser__Cola:Echvi_0069 Length = 260 Score = 112 bits (279), Expect = 1e-29 Identities = 75/242 (30%), Positives = 128/242 (52%), Gaps = 5/242 (2%) Query: 16 ITINRPEKKNALNPQLIAELTAAFIKASEDDLVKVVILNANGDAFSAGADL-AYLQQLQY 74 I I+RP NALN +++ EL AAF +A++ + V+ V+L G AF +G DL A L Sbjct: 17 IAIDRPAVFNALNFEVLEELKAAFDQAAQAETVRCVVLTGGGGAFCSGQDLKAVGTDLDG 76 Query: 75 NTFEENVADSNHLKKLFTTIYYLPKVVIAQVEGHAIAGGCGLATICDIVFATPESNFGYT 134 F+E + + L + L K +I ++ G A+ GC LA D++ A+ E+ Sbjct: 77 IPFKEII--RKYYNPLIIQMRNLSKPIICKLNGAAVGAGCSLALATDVIIASKEAYLAEM 134 Query: 135 EVKIGFV-PAIVSCFLKEKVSESIAKEILLTGKIFSAEEALKYNLINFVTNSSDIHQIVR 193 IG V A + FL ++V +A E+ TG+ AEEA + L+N S + + V Sbjct: 135 FAHIGLVMDAGSNYFLPKRVGYPLAFELATTGRKVYAEEAERLGLVNKAIEHSALDETVA 194 Query: 194 EFALSLCSGSSGNSLMITKQLITQTTNPLLEKCLETAVQINARVRESEDFKKGISSFLNK 253 ++ + + +SG+++ + K+++ ++ LE+ LE + +DFK+G++SFL K Sbjct: 195 QY-VEVYVNASGSAIGMIKEMLRKSNGMSLEEVLEMEAVYQEKAGSHQDFKEGVTSFLEK 253 Query: 254 EK 255 K Sbjct: 254 RK 255 Lambda K H 0.318 0.133 0.367 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: 131 Number of extensions: 8 Number of successful extensions: 4 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 ( 7.3 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