Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate AO353_23650 AO353_23650 3-carboxymuconate cyclase
Query= uniprot:Q9HWH7 (388 letters) >FitnessBrowser__pseudo3_N2E3:AO353_23650 Length = 391 Score = 395 bits (1015), Expect = e-114 Identities = 214/389 (55%), Positives = 277/389 (71%), Gaps = 9/389 (2%) Query: 1 MRRLPTLCLLALAPLTGVAPQAQAASLYNLLVGTYTEGSSEGIQVYRFDGADGSVKG-PL 59 MR+L L + G++ + +A + LLVGTYT+G S+GI +FD G + PL Sbjct: 3 MRKLWPLLMAGSVGAMGLS--SASAESFQLLVGTYTQGQSQGIYRLKFDSQSGQLDATPL 60 Query: 60 RVAHTSNPSYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLA 119 +V ++NPS+LT + DQR LFVVNENG G + D VGR +S+ +P + L I+QVQ+L Sbjct: 61 QVVKSANPSWLTLSSDQRRLFVVNENGPG-QADPVGRVSSFAVEPNTHALSLINQVQSLG 119 Query: 120 DHPTYSSLSHDGRYLFVANYSV--QPEGSVAVLPVRADGSLAPVVQVESHQASKVHP-RQ 176 + PT+SSLS DG+YLFV+NYSV P G++A LPV DG LAP VQ+ SHQ S+V+P RQ Sbjct: 120 NEPTHSSLSADGKYLFVSNYSVAEDPGGNLAALPVSTDGKLAPPVQLSSHQPSRVNPERQ 179 Query: 177 VSGHVHSVVSSPDGQYLFAPDLGADKVFVYRYAPE-QAERPLQAADPAFVPTPPGSGPRH 235 +S HVHS VSSPDGQY+FA DLGADKVFVYRY P+ ERPL AA PA V PPGSGPRH Sbjct: 180 MSAHVHSTVSSPDGQYVFANDLGADKVFVYRYDPKANPERPLTAATPASVQLPPGSGPRH 239 Query: 236 LIFSADGRFAYLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGR 295 L+FSADG+ AYLTLE+S QV VF ++ G+L Q Q DLA + A ALH S+DG+ Sbjct: 240 LLFSADGKHAYLTLEMSAQVAVFDYQA-GKLTQRQMVDLAAGKPAAQKAAAALHASSDGK 298 Query: 296 FLGVLNRGDDNQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQL 355 FL V NRG N+L+ FA+DPASG+L+ ++RR VEG PREF+ P G+FVLVANQ S+Q+ Sbjct: 299 FLYVSNRGTTNELLVFAIDPASGELKELQRRPVEGDHPREFSLDPSGKFVLVANQKSNQI 358 Query: 356 RVFARDPQSGQVGKTLQSVEVGSPSDLRF 384 + ARD ++G +GKT+Q + SPSD++F Sbjct: 359 VIIARDVKTGLLGKTVQKLPFDSPSDIKF 387 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: 569 Number of extensions: 38 Number of successful extensions: 15 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