Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate GFF2958 PS417_15140 3-carboxymuconate cyclase
Query= uniprot:Q9HWH7 (388 letters) >FitnessBrowser__WCS417:GFF2958 Length = 391 Score = 371 bits (952), Expect = e-107 Identities = 200/382 (52%), Positives = 263/382 (68%), Gaps = 7/382 (1%) Query: 9 LLALAPLTGVAPQAQAASLYNLLVGTYTEGSSEGIQVYRFDGADGSVKG-PLRVAHTSNP 67 LL + ++ QA A Y LLVG+YT GSSEGI +F+ G G P+ A +NP Sbjct: 9 LLMAGSVGAMSVQAAPAETYELLVGSYTAGSSEGIYRLQFNSRTGQFSGKPVLAAKAANP 68 Query: 68 SYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSL 127 S+LT + DQ+ LFVVNENG G + D VGR +SY DP + +L I+QVQ+L + PT+SS+ Sbjct: 69 SWLTVSKDQKHLFVVNENGPG-QNDPVGRVSSYSIDPQNYQLTLINQVQSLGNEPTHSSV 127 Query: 128 SHDGRYLFVANYSV--QPEGSVAVLPVRADGSLAPVVQVESHQASKVHP-RQVSGHVHSV 184 + DGRY+FVANYSV P GS+A LPV A G L+ VQ+ H +S+V+P RQ S HVHSV Sbjct: 128 AADGRYVFVANYSVLEDPGGSLAALPVDATGKLSAPVQLSGHPSSRVNPERQASNHVHSV 187 Query: 185 VSSPDGQYLFAPDLGADKVFVYRYAPE-QAERPLQAADPAFVPTPPGSGPRHLIFSADGR 243 VSSPDGQY+F DLGADKVF Y Y P+ E+PL A PA V PPGSGPRHL+FSADG+ Sbjct: 188 VSSPDGQYVFVQDLGADKVFAYHYDPKANPEQPLAPASPASVQLPPGSGPRHLLFSADGK 247 Query: 244 FAYLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRG 303 A+LT E+S QV VF ++ +G+L Q Q D A ALH S+DG+FL V NRG Sbjct: 248 HAWLTTEMSAQVAVFDYK-DGQLTQTQLVDFAAGQPVSDKAGAALHASSDGKFLYVSNRG 306 Query: 304 DDNQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQ 363 NQL+ F++DPA+ L+ ++RR VEG PREF+ P GRF+L+ANQ S+++ V RDP+ Sbjct: 307 TANQLLVFSIDPATAHLKELQRRPVEGDHPREFSLDPSGRFLLIANQKSNEIVVVERDPK 366 Query: 364 SGQVGKTLQSVEVGSPSDLRFV 385 +G +GKT+Q + + +PSDL+F+ Sbjct: 367 TGLLGKTVQKMPIDAPSDLKFL 388 Lambda K H 0.318 0.135 0.395 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: 603 Number of extensions: 43 Number of successful extensions: 13 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: 388 Length of database: 391 Length adjustment: 30 Effective length of query: 358 Effective length of database: 361 Effective search space: 129238 Effective search space used: 129238 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: 50 (23.9 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