Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate BPHYT_RS06110 BPHYT_RS06110 3-carboxymuconate cyclase
Query= uniprot:Q9HWH7 (388 letters) >FitnessBrowser__BFirm:BPHYT_RS06110 Length = 385 Score = 307 bits (787), Expect = 3e-88 Identities = 176/380 (46%), Positives = 231/380 (60%), Gaps = 9/380 (2%) Query: 11 ALAPLTGVAPQAQAASLYNLLVGTYTEGSSEGIQVYRFDGADGSVKGPLRVAHTSNPSYL 70 A A +G AP A +Y++LVGTYT SEG+ VYRFD G + A T NPSYL Sbjct: 9 AFAQDSGPAP---ADGVYDMLVGTYTGPKSEGLYVYRFDTKTGEATR-VSAAQTVNPSYL 64 Query: 71 TFAPDQRTLFVVNEN-GRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSLSH 129 + D+R ++ VNE G G G +++RFD SG+L +++V + + P Y SLS Sbjct: 65 VVSRDRRFVYAVNEMPGDNGPATQRGGISAFRFDAASGQLTFLNKVSSDGNDPCYLSLSP 124 Query: 130 DGRYLFVANYSV--QPEGSVAVLPVRADGSL-APVVQVESHQASKVHPRQVSGHVHSVVS 186 DG+YL ANYSV P GS AV P++ADG + A V+ V V RQ + HVHS V Sbjct: 125 DGKYLLTANYSVAADPGGSFAVFPLQADGQVGASVLTVHHEGGGPVKGRQDNSHVHSTVF 184 Query: 187 SPDGQYLFAPDLGADKVFVYRYAPEQAERPLQAADPAFVPTPPGSGPRHLIFSADGRFAY 246 SPDG YLFA DLGADK++ YRY P+ + D + GSGPRHL+F ADG+ AY Sbjct: 185 SPDGHYLFAQDLGADKLYSYRYTPDGSRGLFGPTDWRYNQEKAGSGPRHLVFGADGKHAY 244 Query: 247 LTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRGDDN 306 LT E++ V F + +G+L Q+QT L GF+G VGA A+HLS DGRFL NRGD N Sbjct: 245 LTSEMAATVSTFDYN-DGKLTQVQTLPLTEPGFKGAVGAAAIHLSPDGRFLYATNRGDAN 303 Query: 307 QLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSGQ 366 +V F+VDP +G L+ V +S G PREFA P G +++V NQNSD + VF RD QSG Sbjct: 304 DIVIFSVDPTNGHLKKVGHQSSMGKSPREFAIDPTGNWLIVGNQNSDTVYVFKRDQQSGL 363 Query: 367 VGKTLQSVEVGSPSDLRFVA 386 + + E+G+P D + V+ Sbjct: 364 LEANPKHFELGAPVDFKLVS 383 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: 627 Number of extensions: 40 Number of successful extensions: 10 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: 385 Length adjustment: 30 Effective length of query: 358 Effective length of database: 355 Effective search space: 127090 Effective search space used: 127090 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