Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate GFF4068 Psest_4141 3-carboxymuconate cyclase
Query= uniprot:Q9HWH7 (388 letters) >FitnessBrowser__psRCH2:GFF4068 Length = 397 Score = 338 bits (866), Expect = 2e-97 Identities = 194/391 (49%), Positives = 254/391 (64%), Gaps = 14/391 (3%) Query: 5 PTLCLLALAPLTGV----APQAQAASLYNLLVGTYTEGS-SEGIQVYRFDGADGSVKG-P 58 PTL L A L G +A+ ++ +L+G+YT S S GI RFD A G + P Sbjct: 10 PTLLRLVFALLVGALLAGGARAETDDMH-ILIGSYTHDSDSPGILRLRFDPATGQIDPKP 68 Query: 59 LRVAHTSNPSYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTL 118 ++ + NPS+L + L+ NENG D VGR ++++ D S Q I Q +L Sbjct: 69 VQTLTSDNPSWLVLDDKRGRLYATNENGPA-HADPVGRVSAWQLDS-SSEHQLIGQNISL 126 Query: 119 ADHPTYSSLSHDGRYLFVANYSVQPE--GSVAVLPVRADGSLAPVVQVESHQASKVHP-R 175 D PT++SLSHDGRYLF++NY +P GS+AV+P+ DG PV Q+ +HQ+S VHP R Sbjct: 127 GDEPTHASLSHDGRYLFISNYGSRPNPGGSLAVMPLAEDGHPLPVTQILAHQSSGVHPER 186 Query: 176 QVSGHVHSVVSSPDGQYLFAPDLGADKVFVYRYAPEQAERPLQAADPAFVPTPPGSGPRH 235 Q S HVHS V SPDG+ L DLGAD+VFVYRY P+ AERPLQA +PA + PPGSGPRH Sbjct: 187 QRSAHVHSAVPSPDGKRLLVSDLGADRVFVYRYDPQNAERPLQADEPASIELPPGSGPRH 246 Query: 236 LIFSADGRFAYLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGR 295 L+F +G+ AYL LELS QV F + NG L + Q DL AG + GA+H SADGR Sbjct: 247 LVFHPNGKHAYLALELSAQVASFDYT-NGTLTRRQLLDLKDAGNDVRHSPGAIHSSADGR 305 Query: 296 FLGVLNRGDDNQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQL 355 FL V +RGD N ++ FA++ A G LR ++RRS EG EPREFA + GRF+L+ANQ SD+L Sbjct: 306 FLYVSDRGDYNHIIVFAIE-ADGTLREIQRRSSEGREPREFAITADGRFMLIANQLSDEL 364 Query: 356 RVFARDPQSGQVGKTLQSVEVGSPSDLRFVA 386 V RDP SGQ+G+ LQ++ VG PSD++ +A Sbjct: 365 VVIRRDPDSGQLGEKLQTLTVGRPSDIKLLA 395 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: 590 Number of extensions: 47 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: 397 Length adjustment: 31 Effective length of query: 357 Effective length of database: 366 Effective search space: 130662 Effective search space used: 130662 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