Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate WP_035239607.1 Q366_RS13010 1,4-dihydroxy-2-naphthoyl-CoA synthase
Query= BRENDA::Q5SLK3 (254 letters) >NCBI__GCF_000745975.1:WP_035239607.1 Length = 274 Score = 97.1 bits (240), Expect = 3e-25 Identities = 80/258 (31%), Positives = 127/258 (49%), Gaps = 20/258 (7%) Query: 5 ERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAG-RAFSAGQDL 63 E +G+ +T+NR NA + + +L+ ED+ + ++LTGAG AF AG D Sbjct: 19 EYYEGIGKITINRERYRNAFRPTTVHEISESLRLCREDKRINVIVLTGAGDTAFCAGGDQ 78 Query: 64 TEFGDRKPDYEAHLRRYN--RVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVG 121 T G + R N V + + + KP++ VNG A G G L + D+ +A+ Sbjct: 79 TVKGAGGYIDKDGTPRLNILEVQKQIRSMPKPVIAMVNGFAIGGGHVLHVVCDITIASEN 138 Query: 122 ASFTTAFVRIGLVPDSGL-SFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAE 180 A F ++G D+GL S L +G KA+E+ + + +A +AL +GLV++VVP + Sbjct: 139 AIFGQTGPKVGSF-DAGLGSSYLASTIGQKKAREIWFMCRQYTAAQALEMGLVNKVVPLD 197 Query: 181 KLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQ-------T 233 +L +E ++ A ++ + L L +L L L + LQ AG T Sbjct: 198 QLEDETVAWAMKMQE--------HSPLALRMIKLGLNAELDGQVGLQEFAGNATLLYYLT 249 Query: 234 QDHEEGVRAFREKRPPRF 251 Q+ +EG AF EKR P F Sbjct: 250 QEAQEGKNAFLEKRKPDF 267 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: 144 Number of extensions: 6 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 24 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