Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate 203808 SO4739 naphthoate synthase (NCBI ptt file)
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__MR1:203808 Length = 300 Score = 80.9 bits (198), Expect = 3e-20 Identities = 79/271 (29%), Positives = 123/271 (45%), Gaps = 29/271 (10%) Query: 4 KERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRA------F 57 + + G + + +NRP+ LNA + +D LY AL + +V LLTG G + F Sbjct: 29 RAKAHGTVRIAINRPDCLNAFRPKTVDELYIALDHARQWSDVGCALLTGNGPSAKGQYSF 88 Query: 58 SAGQDLTEFGDRKPDYE------AHLRRYNR-----VVEALSGLEKPLVVAVNGVAAGAG 106 S+G D G YE A L R R V + + K ++ V G A G G Sbjct: 89 SSGGDQRIRGKDGYKYEGAEEGKADLARMGRLHILEVQRLIRFMPKVVIAVVPGWAVGGG 148 Query: 107 MSLALWGDLRLAAVG-ASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAE 165 SL + DL LA+ A F + S L +++G +A+E+ SA+ Sbjct: 149 HSLHVVCDLTLASKEHAIFKQTDPDVASFDSGYGSAYLAKMIGQKRAREIFFCGFNYSAD 208 Query: 166 EALALGLVHRVVPAEKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLT-EALALEA 224 EA A+G+V++ VP +L EAL AKE+ A + K Y ++T + + + Sbjct: 209 EAFAMGMVNKSVPHAELEVEALRWAKEINSKSPTAMRMLK------YGFNMTDDGMVGQQ 262 Query: 225 VLQGQAGQ----TQDHEEGVRAFREKRPPRF 251 + G+A + + + +EG AF EKR F Sbjct: 263 LFAGEATRLAYASAEAQEGRDAFLEKRDQDF 293 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: 151 Number of extensions: 10 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: 254 Length of database: 300 Length adjustment: 25 Effective length of query: 229 Effective length of database: 275 Effective search space: 62975 Effective search space used: 62975 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