Align Xylonolactonase (EC 3.1.1.68) (characterized)
to candidate RR42_RS33665 RR42_RS33665 gluconolactonase
Query= reanno::Korea:Ga0059261_1893 (295 letters) >FitnessBrowser__Cup4G11:RR42_RS33665 Length = 300 Score = 150 bits (378), Expect = 4e-41 Identities = 96/278 (34%), Positives = 139/278 (50%), Gaps = 16/278 (5%) Query: 20 EGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCLPAANGKFVAGLQTGL 79 E P W + L++ DI + + + A+ R+W+ P G PA+ G FVAG+Q+GL Sbjct: 19 ESPFWDTQTQCLYWSDIPARTLFEWRAANAAIRTWELPEMAGCIAPASAGGFVAGMQSGL 78 Query: 80 AIFDP------ADRSFTPLTDPEPALPGNRLNDGTVDPAGRLWFGTM--DDGESEATGRI 131 P A R + P P++ R NDG D GR W GTM D +++ G + Sbjct: 79 FHLQPQPDGSMASRRLASVAHPAPSM---RFNDGRCDRQGRFWAGTMHLDMHPAQSIGSV 135 Query: 132 YRLGGDGRCVAETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIGDD---GILGDSRV 188 YR G + + + NG A SPDGRT+Y D+ V A D G+ R+ Sbjct: 136 YRFDARG-LQQQIEGLIVPNGMAWSPDGRTMYLSDSHPDVQAIWAFDYDAANGVASRRRL 194 Query: 189 FATIPNSEGFPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITKVAFGGP 248 + + G PDG AVD +GC WI + V R++P G L +A PV AFGG Sbjct: 195 WIDMRQYPGRPDGAAVDVDGCYWICGNDAGVVHRFTPEGRLDRSIALPVKKPAMCAFGGA 254 Query: 249 DLRTVYATTASKHLDADGRAEEPHAGDLFAFRVSVPGM 286 D++T++ T+ + DA +AE+P AG +FA R V G+ Sbjct: 255 DMKTLFVTSI-RPADASVQAEQPLAGGVFAVRPGVAGI 291 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: 373 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: 300 Length adjustment: 26 Effective length of query: 269 Effective length of database: 274 Effective search space: 73706 Effective search space used: 73706 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