Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate 354228 BT4702 dihydroxynapthoic acid synthetase (NCBI ptt file)
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__Btheta:354228 Length = 274 Score = 102 bits (254), Expect = 8e-27 Identities = 81/261 (31%), Positives = 130/261 (49%), Gaps = 18/261 (6%) Query: 2 VLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAG-RAFSAG 60 +L + +G+ +T+NR NA T + AL+ E+ ++ +++TGAG +AF +G Sbjct: 16 ILFDYYNGIARITINRERYRNAFTPTTTAEMSDALRICREEADIDVIVITGAGDKAFCSG 75 Query: 61 QDLTEFGDRKPDYEAHLRRYN--RVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLA 118 D G + + R + V + + + KP++ AVNG A G G L + DL +A Sbjct: 76 GDQNVKGRGGYIGKDGVPRLSVLDVQKQIRSIPKPVIAAVNGFAIGGGHVLHVVCDLSIA 135 Query: 119 AVGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVP 178 + A F R+G + L R+VG KA+E+ L + +A+EAL +GLV++VVP Sbjct: 136 SENAIFGQTGPRVGSFDAGFGASYLARVVGQKKAREIWFLCRKYNAQEALDMGLVNKVVP 195 Query: 179 AEKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQ------ 232 E+L +E + A+E+ L L L + L L +A +Q AG Sbjct: 196 LEQLEDEYVQWAEEM--------MLLSPLALRMIKAGLNAELDGQAGIQELAGDATLLYY 247 Query: 233 -TQDHEEGVRAFREKRPPRFQ 252 T + +EG AF EKR P F+ Sbjct: 248 LTDEAQEGKNAFLEKRKPNFK 268 Lambda K H 0.318 0.135 0.371 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: 156 Number of extensions: 8 Number of successful extensions: 3 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: 254 Length of database: 274 Length adjustment: 25 Effective length of query: 229 Effective length of database: 249 Effective search space: 57021 Effective search space used: 57021 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