Align Xylonolactonase (EC 3.1.1.68) (characterized)
to candidate GFF363 Psest_0364 Gluconolactonase
Query= reanno::Korea:Ga0059261_1893 (295 letters) >FitnessBrowser__psRCH2:GFF363 Length = 296 Score = 131 bits (330), Expect = 2e-35 Identities = 94/284 (33%), Positives = 135/284 (47%), Gaps = 15/284 (5%) Query: 14 LGAPLLEGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCLPAANGKFVA 73 LG E PVWV + AL++VDI + + R++ A G+ W + C+ +VA Sbjct: 11 LGCATGESPVWVAAEQALYWVDIPNRELLRWNAADGQISRWQGDEMLA-CIARHGDGWVA 69 Query: 74 GLQTGLAIFD--PADRSFTPLTDP-EPALPGNRLNDGTVDPAGRLWFGTM--DDGESEAT 128 G+++G P R + L + LP R+NDG D GR W G+M D Sbjct: 70 GMESGFFSLQTRPDGRLDSHLLATIDHQLPAMRMNDGRCDREGRFWAGSMALDMAAGHPV 129 Query: 129 GRIYRLGG---DGRCVAETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIG---DDGI 182 G +YRL D V + + NG A SPDGRT+Y D+ V A D G Sbjct: 130 GALYRLDSKSIDAPLVPQLDGFIVPNGLAFSPDGRTMYLSDSHPSVQKIWAFDYDIDSGT 189 Query: 183 LGDSRVFATIPNSEGFPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITK 242 R+F + + G PDG AVDA+GC WI + + R++P G L +A PV + Sbjct: 190 PSRRRLFVDMLDHPGRPDGAAVDADGCYWICGNDAGFIHRFTPDGRLDRSLAVPVKKPSM 249 Query: 243 VAFGGPDLRTVYATTASKHLDADGRAEEPHAGDLFAFRVSVPGM 286 AFGG L T++ T+ D +++P AG +FA V G+ Sbjct: 250 CAFGGARLDTLFVTSIRPGGDL---SDQPLAGGVFALNPGVTGL 290 Lambda K H 0.319 0.139 0.439 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: 411 Number of extensions: 34 Number of successful extensions: 5 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: 295 Length of database: 296 Length adjustment: 26 Effective length of query: 269 Effective length of database: 270 Effective search space: 72630 Effective search space used: 72630 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 (21.7 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