Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate Ga0059261_2840 Ga0059261_2840 Enoyl-CoA hydratase/carnithine racemase
Query= BRENDA::Q13825 (339 letters) >FitnessBrowser__Korea:Ga0059261_2840 Length = 263 Score = 122 bits (305), Expect = 1e-32 Identities = 83/259 (32%), Positives = 127/259 (49%), Gaps = 9/259 (3%) Query: 82 LEEENRGIVVLGINRAYGKNSLSKNLIKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAGA 141 ++ + GIV+ INR N++ +NLI D L +D++ R +I+ FCAGA Sbjct: 6 IDRHDGGIVIATINRPARMNAIDRNLIASFEALFDRLDADREARVLILTG-AGRAFCAGA 64 Query: 142 DLKERAKMSSSEVGPFVSKIRA--VINDIANLPVPTIAAIDGLALGGGLELALACDIRVA 199 DLK S+ S++R ++ IANL P IAA++G A GGG LA DIR+A Sbjct: 65 DLKSDFVESAGPEESLASQLRLARLMERIANLRQPVIAAVNGAAAGGGFAFTLAADIRIA 124 Query: 200 ASSAKMGLVETKLAIIPGGGG-TQRLPRAIGMSLAKELIFSARVLDGKEAKAVGLISHVL 258 SA + +L + G G + LPR IG+S A EL+ + R D +EA+ +G + + Sbjct: 125 GRSAHFSIANARLGLSAGECGISWLLPRLIGLSRAFELMLTGRKFDAEEAERIGYVVRTV 184 Query: 259 EQNQEGDAAYRKALDLAREFLPQGPVAMRVAKLAINQGME-VDLVTGLAIEEACYAQTIP 317 D AL+ AR P + + K + + +E + +A+E Sbjct: 185 AD----DVLLDTALETARLIAANAPFGVAMTKDVVRRNLETASMQAAIALEARTQLLCGG 240 Query: 318 TKDRLEGLLAFKEKRPPRY 336 + D E + AF EKRPP + Sbjct: 241 SGDFREAVSAFLEKRPPDF 259 Lambda K H 0.318 0.135 0.386 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: 177 Number of extensions: 12 Number of successful extensions: 5 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: 339 Length of database: 263 Length adjustment: 27 Effective length of query: 312 Effective length of database: 236 Effective search space: 73632 Effective search space used: 73632 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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