Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate H281DRAFT_00300 H281DRAFT_00300 6-phosphogluconolactonase
Query= uniprot:Q9HWH7 (388 letters) >FitnessBrowser__Burk376:H281DRAFT_00300 Length = 434 Score = 327 bits (837), Expect = 5e-94 Identities = 178/372 (47%), Positives = 235/372 (63%), Gaps = 6/372 (1%) Query: 19 APQAQAASLYNLLVGTYTEGSSEGIQVYRFDGADGSVKGPLRVAHTSNPSYLTFAPDQRT 78 A A A +Y++LVGTYT G SEG+ VYRFD G + VA T NPSYL + D+R Sbjct: 63 AGPAPADGVYDMLVGTYTGGKSEGLYVYRFDTKTGDATR-VSVAQTVNPSYLVVSRDRRF 121 Query: 79 LFVVNE-NGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSLSHDGRYLFVA 137 ++ VNE G G G +++RFD SG+L +++V + P Y SLS DG+YL A Sbjct: 122 VYAVNELPGDNGPASQRGGISAFRFDAASGQLSFLNKVSADGNDPCYLSLSPDGKYLLTA 181 Query: 138 NYSV--QPEGSVAVLPVRADGSL-APVVQVESHQASKVHPRQVSGHVHSVVSSPDGQYLF 194 NYSV P GS AV PV+ADG L A V+ V V RQ + HVHS V SPDG+YLF Sbjct: 182 NYSVAADPGGSFAVFPVQADGQLGASVLTVHHEGGGPVKGRQDNSHVHSTVFSPDGRYLF 241 Query: 195 APDLGADKVFVYRYAPEQAERPLQAADPAFVPTPPGSGPRHLIFSADGRFAYLTLELSGQ 254 A DLGADK++ YRY P+ + D + PG+GPRHL+F DG+ AYLT EL+ Sbjct: 242 AQDLGADKLYSYRYTPDGSRGLFGPTDWRYTQEKPGTGPRHLVFGVDGKHAYLTSELAAT 301 Query: 255 VMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRGDDNQLVTFAVD 314 V +F ++ +G+L Q+QT L GF+G VGA A+HLS DGRFL NRGD N++V F+VD Sbjct: 302 VSIFNYD-DGKLTQVQTVSLTEPGFKGAVGAAAIHLSPDGRFLYATNRGDANEIVIFSVD 360 Query: 315 PASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSGQVGKTLQSV 374 P +G L+ + +S G PREFA P G++++V NQNSD + VF RDPQSG + + + Sbjct: 361 PTNGHLKKIGHQSSLGKSPREFAIDPTGKWLIVGNQNSDTVYVFRRDPQSGLLEANPKRI 420 Query: 375 EVGSPSDLRFVA 386 E+GSP D + V+ Sbjct: 421 EIGSPVDFKLVS 432 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: 691 Number of extensions: 47 Number of successful extensions: 12 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: 434 Length adjustment: 31 Effective length of query: 357 Effective length of database: 403 Effective search space: 143871 Effective search space used: 143871 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