Align Xylonolactonase (EC 3.1.1.68) (characterized)
to candidate PP_3180 PP_3180 Smp-30/Cgr1 family protein
Query= reanno::Korea:Ga0059261_1893 (295 letters) >FitnessBrowser__Putida:PP_3180 Length = 346 Score = 141 bits (355), Expect = 2e-38 Identities = 90/271 (33%), Positives = 126/271 (46%) Query: 16 APLLEGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCLPAANGKFVAGL 75 A L E VW +R L+FVDI RI+ P +++ A++G G + Sbjct: 69 ADLGESLVWDERSGVLYFVDISGGRINGLTPDGEVDCLYESAARIGALALTDRGNLIFTE 128 Query: 76 QTGLAIFDPADRSFTPLTDPEPALPGNRLNDGTVDPAGRLWFGTMDDGESEATGRIYRLG 135 +AIFD R + + R NDG DP GR G MD+ S+ TG ++R Sbjct: 129 DASVAIFDVPTRKVSQHSASVHPRSTYRFNDGACDPQGRFVTGLMDEALSDNTGALFRFD 188 Query: 136 GDGRCVAETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIGDDGILGDSRVFATIPNS 195 + + G A S DG T+Y VD+ I+ A +G LG +FA P Sbjct: 189 WQLSDQVIHDDMGLPTGLAWSHDGHTVYFVDSAARAIYRAEYLIEGRLGAVTLFAETPAE 248 Query: 196 EGFPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITKVAFGGPDLRTVYA 255 G PDG A+D EG +W+ Y+G+ + RY G L D V PV T FGGP + T+Y Sbjct: 249 LGRPDGLALDREGGLWVCQYHGSCLLRYDRHGYLTDQVLMPVPCPTSCCFGGPGMNTLYI 308 Query: 256 TTASKHLDADGRAEEPHAGDLFAFRVSVPGM 286 +TA + + P AGDL+A R G+ Sbjct: 309 STARYDMTPEDLHHYPDAGDLYAIRPETGGV 339 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: 321 Number of extensions: 23 Number of successful extensions: 3 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: 346 Length adjustment: 28 Effective length of query: 267 Effective length of database: 318 Effective search space: 84906 Effective search space used: 84906 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