Align Xylonolactonase (EC 3.1.1.68) (characterized)
to candidate RR42_RS30140 RR42_RS30140 gluconolaconase
Query= reanno::Korea:Ga0059261_1893 (295 letters) >FitnessBrowser__Cup4G11:RR42_RS30140 Length = 292 Score = 295 bits (756), Expect = 6e-85 Identities = 148/280 (52%), Positives = 188/280 (67%), Gaps = 1/280 (0%) Query: 8 PEPVWALGAPLLEGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCLPAA 67 P VW LGA L EGPVW Q +A++FVDIK RIHRF A+G RSW +Q GF +P Sbjct: 6 PLCVWQLGAELGEGPVWHQGSSAVYFVDIKGRRIHRFAIATGAMRSWPVDSQPGFIVPLD 65 Query: 68 NGKFVAGLQTGLAIFDPADRSFTPLTDPEPALPGNRLNDGTVDPAGRLWFGTMDDGESEA 127 +G F+ G+Q GL FDPAD + L + EP LPGNR+NDG VDPAGRLWFGTMDDGE+ Sbjct: 66 DGGFLCGMQDGLYRFDPADGACRRLKEVEPDLPGNRINDGFVDPAGRLWFGTMDDGEAAP 125 Query: 128 TGRIYRLGGDGRCVAETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIGDDGILGDSR 187 +G +Y++G DGR + I+NGPA+SPD RTLYH DT+ ++++ +G DG L R Sbjct: 126 SGSLYQVGDDGRTWRRDSGYVITNGPAMSPDARTLYHADTVKRLVYAFDVGQDGALSRRR 185 Query: 188 VFATIPNSEGFPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITKVAFGG 247 FA + + G+PDG AVDA+G +WI ++ GA + R+SP G L VV FP +TK+AFGG Sbjct: 186 EFARLCGT-GYPDGMAVDADGHLWIAVFGGARIERWSPDGRLAGVVRFPCDNVTKLAFGG 244 Query: 248 PDLRTVYATTASKHLDADGRAEEPHAGDLFAFRVSVPGMP 287 DLRTVY TTA K L A +P AG LF+FR G+P Sbjct: 245 DDLRTVYVTTARKGLSPAALALQPLAGGLFSFRAPTRGLP 284 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: 473 Number of extensions: 35 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: 292 Length adjustment: 26 Effective length of query: 269 Effective length of database: 266 Effective search space: 71554 Effective search space used: 71554 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