Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate WP_009122468.1 BUB52_RS02845 lactonase family protein
Query= uniprot:Q9HWH7 (388 letters) >NCBI__GCF_900129655.1:WP_009122468.1 Length = 372 Score = 194 bits (492), Expect = 4e-54 Identities = 128/384 (33%), Positives = 212/384 (55%), Gaps = 28/384 (7%) Query: 8 CLLALAPLTGVAPQAQAAS---LYNLLVGTYTEGSSEGIQVYRFDGADGSVKGPLRVAHT 64 C+L L+ + PQ S ++L+GTYT+G+S+GI +RF+ G+ PL Sbjct: 6 CMLGLS-MAACTPQKTVNSGEDELSMLIGTYTDGTSKGIYSFRFNQKTGTAT-PLGSVEL 63 Query: 65 SNPSYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTY 124 SNPSYLT + D + ++ V+E D+ + FD +G L+ ++ +T P Y Sbjct: 64 SNPSYLTPSEDGKFIYAVSE-----MNDSTAAVNALAFDKQTGNLRLLNSERTPGAAPCY 118 Query: 125 SSLSHDGRYLFVANYSVQPEGSVAVLPVRADGSLAPVVQVESHQASKVHP-RQVSGHVHS 183 +S +G+ + ANYS G+++V +R DG+L+P + A+ RQ+ H+H Sbjct: 119 --VSTNGKEVLTANYS---GGNMSVFRLRKDGTLSPAEALFKGTANGPDTIRQIVPHIHC 173 Query: 184 VVSSPDGQYLFAPDLGADKVFVYRYAPEQ--AERPLQAADPAFVPTPPGSGPRHLIFSAD 241 + SPDG+Y+FA D AD++ + + E + P +A D P SGPRHL FS + Sbjct: 174 ALFSPDGKYIFATDFSADRILRFTLSSEGNISRLPGEATD-----ITPDSGPRHLTFSPN 228 Query: 242 GRFAYLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLN 301 G+FAYL ELSG+V+ F + +G+L Q+Q+ +A Q + G+ +HLS DG+FL N Sbjct: 229 GKFAYLINELSGKVIAFGYT-DGKLEQIQS--IAADSLQAR-GSADIHLSPDGKFLYASN 284 Query: 302 RGDDNQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARD 361 R + + + F VD +G L + G PR F +P G+++L A ++S+ ++V+ RD Sbjct: 285 RLEGDGIAIFTVDTVNGTLTRAGYQPT-GIHPRHFNITPNGKYLLAACRDSNVIQVYERD 343 Query: 362 PQSGQVGKTLQSVEVGSPSDLRFV 385 ++G + T Q + + P ++F+ Sbjct: 344 TENGLLKDTQQDILIDKPVCVQFI 367 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: 519 Number of extensions: 52 Number of successful extensions: 14 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: 372 Length adjustment: 30 Effective length of query: 358 Effective length of database: 342 Effective search space: 122436 Effective search space used: 122436 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 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