Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate PfGW456L13_3314 3-carboxymuconate cyclase
Query= uniprot:Q9HWH7 (388 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3314 Length = 389 Score = 378 bits (970), Expect = e-109 Identities = 206/382 (53%), Positives = 265/382 (69%), Gaps = 7/382 (1%) Query: 9 LLALAPLTGVAPQAQAASLYNLLVGTYTEGSSEGIQVYRFDGADGSVKG-PLRVAHTSNP 67 LL + + Q +A Y LLVG+YT G S+GI FD G + PL+V ++NP Sbjct: 7 LLMAGSIGAMGVQVASAEDYQLLVGSYTAGQSQGIYRLAFDSRTGQIDASPLQVIKSANP 66 Query: 68 SYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSL 127 S+LT + DQR LFVVNENG G + D VGR +S+ DP + L ISQVQ+L + PT+SSL Sbjct: 67 SWLTLSKDQRHLFVVNENGPG-QTDPVGRVSSFAIDPKTHALSLISQVQSLGNEPTHSSL 125 Query: 128 SHDGRYLFVANYSV--QPEGSVAVLPVRADGSLAPVVQVESHQASKVHP-RQVSGHVHSV 184 S DG +LFV+NYSV P G++AVLPV ADG L VVQ+ SH AS+V+P RQ S HVHS Sbjct: 126 SIDGSHLFVSNYSVAEDPGGTLAVLPVAADGKLKAVVQMSSHPASRVNPERQASAHVHST 185 Query: 185 VSSPDGQYLFAPDLGADKVFVYRYAPE-QAERPLQAADPAFVPTPPGSGPRHLIFSADGR 243 + SPDG+Y+FA DLGADKVF YR+ P+ E PL A PAFV PPGSGPRHL+FSADG+ Sbjct: 186 IPSPDGRYVFANDLGADKVFAYRFDPKANPELPLTPATPAFVQLPPGSGPRHLLFSADGK 245 Query: 244 FAYLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRG 303 A+LT+E+S QV VF + +G+L Q Q DLA A ALH SADG+FL V NRG Sbjct: 246 HAWLTMEMSAQVAVFDYH-DGQLEQTQMVDLAAGQPVSDKAAAALHASADGKFLYVSNRG 304 Query: 304 DDNQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQ 363 NQL+ FA+DPA+G L ++RR+VEG PREF+ P G+F+L+ANQ S+Q+ V RD + Sbjct: 305 TANQLLVFAIDPATGHLSELQRRAVEGDHPREFSLDPSGKFLLIANQKSNQIVVVERDAR 364 Query: 364 SGQVGKTLQSVEVGSPSDLRFV 385 +G +GKT+Q + + +PSDLRF+ Sbjct: 365 TGLLGKTVQKLPMDAPSDLRFL 386 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: 589 Number of extensions: 37 Number of successful extensions: 14 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: 389 Length adjustment: 30 Effective length of query: 358 Effective length of database: 359 Effective search space: 128522 Effective search space used: 128522 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