Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate WP_034279790.1 BA81_RS01220 lactonase family protein
Query= uniprot:Q9HWH7 (388 letters) >NCBI__GCF_000691165.1:WP_034279790.1 Length = 347 Score = 161 bits (407), Expect = 3e-44 Identities = 106/356 (29%), Positives = 178/356 (50%), Gaps = 19/356 (5%) Query: 32 VGTYTEGSSEGIQVYRFDGADGSVKGPLRVAHTSNPSYLTFAPDQRTLFVVNENGRGGKG 91 +GTYT+G S+G+ + + ++ A NP+YLT + DQ+ ++ V + G Sbjct: 8 IGTYTKGDSKGVYTFTLNTDKQQIEQVEVAAELENPTYLTVSEDQKFVYAVVKKG----- 62 Query: 92 DTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSLSHDGRYLFVANYSVQPEGSVAVLP 151 + G +Y+ D +GRL I+Q P + S+ + + ANY +G+ + Sbjct: 63 -SQGGLAAYQIDSTTGRLHFINQELADGASPCHVSVDSQTKTAYTANYH---KGTAEMYE 118 Query: 152 VRAD-GSLAPVVQVESHQASKVHP-RQVSGHVHSVVSSPDGQYLFAPDLGADKVFVYRYA 209 + A+ GS+ + H+ + + RQ H H + +PD Q+ A DLG D ++ Y+ Sbjct: 119 IDAENGSVIRTLSQAQHEGTGPNEDRQEKPHTHFMGLTPDEQFAVAVDLGTDGIYTYK-- 176 Query: 210 PEQAERPLQAADPAFVPTPPGSGPRHLIFSADGRFAYLTLELSGQVMVFAHEGNGRLRQL 269 + + L+ A T PGSGPRH+ F AY+ ELS +V+V + +G ++ Sbjct: 177 --KEDGKLELAHT--FETKPGSGPRHITFHPTKPVAYVMTELSSEVIVLRYFEDGHFEEI 232 Query: 270 QTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRGDDNQLVTFAVDPASGQLRFVERRSVE 329 QT P+ F A+H+S+DG+F+ NRG D+ + A D GQL VE S E Sbjct: 233 QTIATIPSDFTENNQGSAIHVSSDGQFVYAGNRGHDSIAIFKADD--DGQLSLVEIASSE 290 Query: 330 GTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSGQVGKTLQSVEVGSPSDLRFV 385 G PR+F P F++ +NQ S L ++ RD ++G++ + V P ++F+ Sbjct: 291 GNWPRDFVLDPTEEFLVGSNQESSNLVLYKRDKETGRLTVLQSDITVPHPVCVKFL 346 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: 431 Number of extensions: 34 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 388 Length of database: 347 Length adjustment: 30 Effective length of query: 358 Effective length of database: 317 Effective search space: 113486 Effective search space used: 113486 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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