Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate 15516 b1394 enoyl-CoA hydratase (NCBI)
Query= BRENDA::Q13825 (339 letters) >FitnessBrowser__Keio:15516 Length = 262 Score = 112 bits (280), Expect = 1e-29 Identities = 81/262 (30%), Positives = 126/262 (48%), Gaps = 9/262 (3%) Query: 82 LEEENRGIVVLGINRAYGKNSLSKNLIKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAGA 141 L +G++ L +NR NS + + L++ + ++ D +R +++ G FCAG Sbjct: 6 LSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRG-FCAGQ 64 Query: 142 DLKER---AKMSSSEVGPFVSKI-RAVINDIANLPVPTIAAIDGLALGGGLELALACDIR 197 DL +R + ++G V + ++ +A LP P I A++G+A G G LAL DI Sbjct: 65 DLNDRNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIV 124 Query: 198 VAASSAKMGLVETKLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGKEAKAVGLISHV 257 +AA SAK + +KL +IP GGT LPR G + A L L ++A G+I V Sbjct: 125 IAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQV 184 Query: 258 LEQNQEGDAAYRKALDLAREFLPQGPVAMRVAKLAINQGMEVDLVTGLAIEEACYAQTIP 317 ++ D A + LAR Q + + K AIN L T L +E Sbjct: 185 VDDETLADTAQQ----LARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGR 240 Query: 318 TKDRLEGLLAFKEKRPPRYKGE 339 + D EG+ AF KR P++ G+ Sbjct: 241 SADYREGVSAFLAKRSPQFTGK 262 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: 174 Number of extensions: 9 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: 339 Length of database: 262 Length adjustment: 26 Effective length of query: 313 Effective length of database: 236 Effective search space: 73868 Effective search space used: 73868 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 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