Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate WP_038017558.1 HA49_RS11685 lactonase family protein
Query= uniprot:Q9HWH7 (388 letters) >NCBI__GCF_000757425.2:WP_038017558.1 Length = 364 Score = 217 bits (552), Expect = 5e-61 Identities = 145/355 (40%), Positives = 202/355 (56%), Gaps = 19/355 (5%) Query: 36 TEGSSEGIQVYRFDG-ADGSVKGPLRVAHTSNPSYLTFAPDQRTLFVVNENGRGGKGDTV 94 T SEGI YR ADGS++ R+ T NPS++ + DQR L+ NE+ Sbjct: 23 TAHPSEGI--YRLQLLADGSLQVVDRLK-TDNPSWIVLSQDQRFLYTTNES-------ET 72 Query: 95 GRATSYRFDPISGRLQQISQVQTLADHPTYSSLSHDGRYLFVANYSV-QPEGSVAVLPVR 153 GR ++ P G L+ ++ QT HPT++ L+ DGRYL ANYS V P+ Sbjct: 73 GRVSAIEITP-QGPLRLLNSQQTRGAHPTHACLTPDGRYLLAANYSDGMNNAGFIVFPLV 131 Query: 154 ADGSLAPVVQVE--SHQASKVHPRQVSGHVHSVVSSPDGQYLFAPDLGADKVFVYRYAPE 211 G + VQ + ++ V RQ SGH HSV SPDG+ L+ DLGAD V +Y Y P Sbjct: 132 DSGEIGEAVQHVRFAEGSAVVAERQQSGHAHSVNISPDGKILYVADLGADIVRIYHYQP- 190 Query: 212 QAERPLQAADPAFVPTPPGSGPRHLIFSADGRFAYLTLELSGQVMVFAHEGNGRLRQLQT 271 Q + P + P G+GPRH+ FS DGRF + E+S QV +F G+L +QT Sbjct: 191 QNDTPFLHQPQDDIRLPGGAGPRHIAFSDDGRFVCVVSEMSAQVHLF-QMNEGQLNAIQT 249 Query: 272 HDLAPA-GFQGKVGAGALHLSADGRFLGVLNRGDDNQLVTFAVDPASGQLRFVERRSVEG 330 +LA + + K GAG L+ S DGRFL V NR N++V F+VDP SG+L ++ S G Sbjct: 250 LELADSDSAEDKAGAGVLY-SPDGRFLYVGNRQQRNEIVVFSVDPHSGRLSDRQQFSSGG 308 Query: 331 TEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSGQVGKTLQSVEVGSPSDLRFV 385 EPR FAF G F+LVAN S+++ V ARDP +G + T S+++G+P+D++F+ Sbjct: 309 IEPRAFAFDNTGHFLLVANVWSNRVTVLARDPHNGGLRPTGNSLDIGTPTDIKFL 363 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: 529 Number of extensions: 38 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: 364 Length adjustment: 30 Effective length of query: 358 Effective length of database: 334 Effective search space: 119572 Effective search space used: 119572 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