Align xylono-1,5-lactonase (EC 3.1.1.110) (characterized)
to candidate AZOBR_RS31230 AZOBR_RS31230 gluconolactonase
Query= metacyc::MONOMER-20628 (289 letters) >FitnessBrowser__azobra:AZOBR_RS31230 Length = 299 Score = 202 bits (513), Expect = 1e-56 Identities = 118/291 (40%), Positives = 155/291 (53%), Gaps = 10/291 (3%) Query: 1 MTAQVTCVWDLKATLGEGPIWHGD--TLWFVDIKQRKIHNYHPATGERFSFDAPDQVTFL 58 M +V CVW +A LGEGP+W + ++FVDI +I + G + + D +L Sbjct: 1 MPQEVRCVWPARALLGEGPLWSPEQGAVFFVDIHGSRILRHGLDDGSQADWALEDAACWL 60 Query: 59 APIVGATGFVVGLKTG-IHRFHPATGFSL----LLEVEDAALNNRPNDATVDAQGRLWFG 113 GF+ GL++ + R G ++ L ++ NR NDA DAQGRLW G Sbjct: 61 VECADGDGFIAGLRSRRVVRLRLEPGRAVIAGELARIDPDRPGNRLNDAKADAQGRLWIG 120 Query: 114 TMHDGEENNSGSLYRMDLTG-VARMDRDICITNGPCVSPDGKTFYHTDTLEKTIYAFDLA 172 +M DGEE SG+ +R+D G + RMD + NGP +SPDG+T YHTD+ +TI+AFDL Sbjct: 121 SMDDGEETPSGAFHRLDPDGSITRMDEGYTVANGPALSPDGRTLYHTDSAARTIHAFDLD 180 Query: 173 EDGLLSNKRVFVQFALGDDVYPDGSVVDSEGYLWTALWGGFGAVRFSPQGDAVTRIELPA 232 G LS KR ++FA D YPDG D+EG LW A W G RF P G I LP Sbjct: 181 GAGRLSGKRAHIRFAEADG-YPDGMTCDAEGGLWVAHWDGGRVSRFRPDGTLDRAIALPV 239 Query: 233 PNVTKPCFGGPDLKTLYFTTARKGLSDETLAQYPLAGGVFAV-PVDVAGQP 282 VT F GP L L+ TTA G+ + PLAG +F P V G P Sbjct: 240 SRVTSCVFAGPALDRLFVTTAAHGIGRDGRPDEPLAGALFECDPGGVRGLP 290 Lambda K H 0.321 0.139 0.442 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: 403 Number of extensions: 34 Number of successful extensions: 6 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: 289 Length of database: 299 Length adjustment: 26 Effective length of query: 263 Effective length of database: 273 Effective search space: 71799 Effective search space used: 71799 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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