Align Xylonolactonase (EC 3.1.1.68) (characterized)
to candidate PP_1170 PP_1170 Gluconolactonase
Query= reanno::Korea:Ga0059261_1893 (295 letters) >FitnessBrowser__Putida:PP_1170 Length = 293 Score = 132 bits (331), Expect = 1e-35 Identities = 90/279 (32%), Positives = 135/279 (48%), Gaps = 14/279 (5%) Query: 20 EGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCLPAANGKFVAGLQTGL 79 E PVW + AL++VDI + ++HR+ A G+ + W + C+ + +VAG+++G+ Sbjct: 15 ESPVWHPGEQALYWVDIPARQLHRWQAADGKHQCWQGDEMLA-CIARSGQGWVAGMESGI 73 Query: 80 -AIFDPADRSFTP--LTDPEPALPGNRLNDGTVDPAGRLWFGTM--DDGESEATGRIYRL 134 + AD S L++ + A G R NDG D GR W GTM D + G +YR Sbjct: 74 FQLQAKADGSLDSRLLSNVQHAQAGMRFNDGRCDRQGRFWAGTMLLDMQQGAHVGALYRH 133 Query: 135 GGDGRCVAETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIG---DDGILGDSRVFAT 191 G+G + + + NG A SPDG+ +Y D+ V A D G +F Sbjct: 134 DGEGHLHLQQDGMIVPNGLAFSPDGKRMYLSDSHPNVQKVWAFDYDTDSGTPHGKHLFVD 193 Query: 192 IPNSEGFPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITKVAFGGPDLR 251 + N G PDG A+D +GC WI + + R++P G L ++ PV AFGG L Sbjct: 194 MRNYPGRPDGAAIDQDGCYWICGNDAGQIHRFTPEGRLDRSLSVPVKKPAMCAFGGASLD 253 Query: 252 TVYATTASKHLDADGRAEEPHAGDLFAFRVSVPGMPGTE 290 +Y T S +++P AG +FA PG G E Sbjct: 254 ILYVT--SIRPTGIDLSDQPLAGGVFALD---PGTKGLE 287 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: 420 Number of extensions: 28 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: 293 Length adjustment: 26 Effective length of query: 269 Effective length of database: 267 Effective search space: 71823 Effective search space used: 71823 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