Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate 350650 BT1122 conserved hypothetical protein (NCBI ptt file)
Query= uniprot:Q9HWH7 (388 letters) >FitnessBrowser__Btheta:350650 Length = 384 Score = 163 bits (413), Expect = 7e-45 Identities = 110/363 (30%), Positives = 188/363 (51%), Gaps = 22/363 (6%) Query: 30 LLVGTYTEGSSEGIQVYRFDGADGSVKGPLRVAHTSNPSYLTFAPDQRTLFVVNENGRGG 89 LLVG Y + EG+++YRFDG V P + SNP++LT ++ + ++ G Sbjct: 37 LLVGCYMKPDEEGVRMYRFDGQTADVDYPCGLRGISNPAFLTSDSTGNRIYAIGDDE--G 94 Query: 90 KGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSLSHDGRYLFVANYSVQPEGSVAV 149 K T A + FD SG L ++ T + P Y +LS ++ ANY GS+ V Sbjct: 95 KSST---ANALLFDKESGLLSLLNSQSTDGELPIYITLSPKEYFVLTANYK---GGSITV 148 Query: 150 LPVRADGSL---APVVQVESHQASKVHPRQVSGHVHSVVSSPDGQYLFAPDLGADKVFVY 206 G L +++ + +K RQ H+H V +PDG++L A DLG D ++++ Sbjct: 149 FSQDKKGKLQRDTKIIRFAGNGPNK--KRQEQSHLHCVTFTPDGKFLLATDLGTDCIYLF 206 Query: 207 RYA--PE--QAERPLQAADPAFVPTPPGSGPRHLIFSADGRFAYLTLELSGQVMVFAHEG 262 PE +A L + + GSGPRH+ F +GRFAYL ELSG++ VF++ Sbjct: 207 PIGKRPEAGKAHSLLDESRVVRIQMDSGSGPRHICFHPNGRFAYLISELSGKITVFSY-N 265 Query: 263 NGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRGDDNQLVTFAVDPASGQLRF 322 G+L +LQT P +G +H+S+DG+FL ++ ++ +++D G L Sbjct: 266 EGKLERLQTIVCDPFVAEGNAD---IHVSSDGKFLYASKHLKEDGIIVYSIDSQKGTLVQ 322 Query: 323 VERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSGQVGKTLQSVEVGSPSDL 382 + + G PR FA SP G ++ V ++++ +++F R+ +G + T +++ + P+ + Sbjct: 323 IGFQPT-GLYPRSFAISPDGCYLAVVCRDANCIQIFERNRNTGLLKNTGKNIRLERPAFV 381 Query: 383 RFV 385 +F+ Sbjct: 382 KFL 384 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: 488 Number of extensions: 36 Number of successful extensions: 9 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: 384 Length adjustment: 30 Effective length of query: 358 Effective length of database: 354 Effective search space: 126732 Effective search space used: 126732 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