Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate 354228 BT4702 dihydroxynapthoic acid synthetase (NCBI ptt file)
Query= BRENDA::Q1D5Y4 (258 letters) >FitnessBrowser__Btheta:354228 Length = 274 Score = 118 bits (295), Expect = 1e-31 Identities = 83/248 (33%), Positives = 126/248 (50%), Gaps = 14/248 (5%) Query: 16 TIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADLKERAT---M 72 TI+ E RNA + E+ + + D+ +VITGAGDKAFC+G D + + Sbjct: 28 TINRERYRNAFTPTTTAEMSDALRICREEADIDVIVITGAGDKAFCSGGDQNVKGRGGYI 87 Query: 73 AEDEV-RAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPAAELGLT 131 +D V R + +++ R+I K IAA+NG A+GGG L + CDL +A+ A G T Sbjct: 88 GKDGVPRLSVLDVQKQIRSIPKP---VIAAVNGFAIGGGHVLHVVCDLSIASENAIFGQT 144 Query: 132 EVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGHLLAVAY 191 ++G G G LAR+VG +A+++ R+ NA EA +GL N++ P L Sbjct: 145 GPRVGSFDAGFGASYLARVVGQKKAREIWFLCRKYNAQEALDMGLVNKVVPLEQLEDEYV 204 Query: 192 GLAESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEIL---KTEDRLEGLRAFA 248 AE ++ +P+A+ I G ELD ++ + L T++ EG AF Sbjct: 205 QWAEEMMLLSPLAL----RMIKAGLNAELDGQAGIQELAGDATLLYYLTDEAQEGKNAFL 260 Query: 249 EKRAPVYK 256 EKR P +K Sbjct: 261 EKRKPNFK 268 Lambda K H 0.319 0.136 0.380 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: 117 Number of extensions: 6 Number of successful extensions: 2 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: 274 Length adjustment: 25 Effective length of query: 233 Effective length of database: 249 Effective search space: 58017 Effective search space used: 58017 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 (21.7 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