Align Xylonolactonase (EC 3.1.1.68) (characterized)
to candidate AZOBR_RS22710 AZOBR_RS22710 gluconolactonase
Query= reanno::Korea:Ga0059261_1893 (295 letters) >FitnessBrowser__azobra:AZOBR_RS22710 Length = 296 Score = 145 bits (365), Expect = 1e-39 Identities = 97/278 (34%), Positives = 132/278 (47%), Gaps = 12/278 (4%) Query: 20 EGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCLPAANGKFVAGLQTGL 79 E PVW + ++DI + IHR DP+SG R W P +G + +G V +TG+ Sbjct: 15 ENPVWDAERGSWTWIDIPARTIHRLDPSSGAHRRWTLPEMIGSLVLRPDGGVVCACETGV 74 Query: 80 AIFD----PADRSFTPLTDPEPALPGNRLNDGTVDPAGRLWFGTM--DDGESEATGRIYR 133 D + T L G R NDG D GR W +M D + +++G +R Sbjct: 75 FDVDLPGEGGEAVVTALATHRFPKEGMRFNDGRCDRQGRFWLSSMVMDISKGDSSGLWHR 134 Query: 134 LG-GDGRCVAETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIG---DDGILGDSRVF 189 DG T I NG A SPDGRTLY D+ V A D G + R F Sbjct: 135 FTRADGLTETGTGGYIIPNGSAFSPDGRTLYASDSHRDVRMVWAWDYDTDTGTADNRRPF 194 Query: 190 ATIPNSEGFPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITKVAFGGPD 249 + G PDG AVD +GC WI + ++R++P G+L + P+ T AFGGPD Sbjct: 195 VDMRAMVGRPDGAAVDIDGCYWICCLDEGCIKRFTPNGDLDRRIEVPMRKPTMCAFGGPD 254 Query: 250 LRTVYATTASKHLDADGRAEEPHAGDLFAFRVSVPGMP 287 LRT+ T+ S+ AD AE+PH G + F G+P Sbjct: 255 LRTMLVTSLSRG-PAD-LAEDPHGGRVLMFDPGAQGLP 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: 437 Number of extensions: 29 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