Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate WP_066330220.1 BLR17_RS12195 lactonase family protein
Query= uniprot:Q9HWH7 (388 letters) >NCBI__GCF_900100165.1:WP_066330220.1 Length = 369 Score = 187 bits (476), Expect = 3e-52 Identities = 124/378 (32%), Positives = 203/378 (53%), Gaps = 19/378 (5%) Query: 9 LLALAPLTGVAPQAQAASLYNLLVGTYTEG-SSEGIQVYRFDGADGSVKGPLRVAHTSNP 67 L+ L L+ + QAQ +NL++GTYT+ S+GI VY F+ G + + NP Sbjct: 6 LITLLLLSCICIQAQEKK-FNLIIGTYTKSCESKGIYVYDFNAETGDFQFKSSTENVINP 64 Query: 68 SYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSL 127 S+++ + + ++ VNE+G +++++D + +++ +++ + P Y + Sbjct: 65 SFVSVSKNNDFIYSVNEDG------PKSTVSAFKYDTSNAKIEFVNKQEIHNPGPCY--I 116 Query: 128 SHDGRYLFVANYSVQPEGSVAVLPVRADGSLAPVVQVESHQASKVHP-RQVSGHVHSVVS 186 +D + + ANY+ GSVAV +GSL + Q+ H ++P RQ HVHSV Sbjct: 117 INDDKNVITANYT---GGSVAVFGKNKNGSLTELKQLIKHSGKGINPARQEKSHVHSVQF 173 Query: 187 SPDGQYLFAPDLGADKVFVYRYAPEQAERPLQAADPAFVPTPPGSGPRHLIFSADGRFAY 246 SPD Q++ A DLG DK+++Y+Y P+ A +PL+ D + GSGPRH FS +G+ Y Sbjct: 174 SPDHQFVLATDLGTDKMYLYQYNPKVA-KPLELKDS--IKVKAGSGPRHFAFSKNGQQLY 230 Query: 247 LTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRGDDN 306 L EL G + VF + G+L +Q + F+G A +H+S D RFL NR + N Sbjct: 231 LLQELDGTLSVFNY-NKGKLVLVQETTVLAPDFKGTSTAADIHISPDQRFLYATNRKEAN 289 Query: 307 QLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSGQ 366 + F + G+L R S G PR FA P G F+LV +Q ++ + VF R+ ++G Sbjct: 290 TISCFKI-LKDGKLALASRTSSLGDGPRNFAIDPTGNFLLVGHQYTNNVVVFKRNKETGA 348 Query: 367 VGKTLQSVEVGSPSDLRF 384 + T + +E+ +P L F Sbjct: 349 LTDTGKRIELCAPVCLVF 366 Score = 25.0 bits (53), Expect = 0.004 Identities = 13/49 (26%), Positives = 27/49 (55%) Query: 338 FSPGGRFVLVANQNSDQLRVFARDPQSGQVGKTLQSVEVGSPSDLRFVA 386 FSP +FVL + +D++ ++ +P+ + + S++V + S R A Sbjct: 173 FSPDHQFVLATDLGTDKMYLYQYNPKVAKPLELKDSIKVKAGSGPRHFA 221 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: 397 Number of extensions: 29 Number of successful extensions: 11 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 388 Length of database: 369 Length adjustment: 30 Effective length of query: 358 Effective length of database: 339 Effective search space: 121362 Effective search space used: 121362 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