Align Xylonolactonase (EC 3.1.1.68) (characterized)
to candidate Pf6N2E2_488 Gluconolactonase (EC 3.1.1.17)
Query= reanno::Korea:Ga0059261_1893 (295 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_488 Length = 301 Score = 130 bits (326), Expect = 5e-35 Identities = 91/277 (32%), Positives = 133/277 (48%), Gaps = 13/277 (4%) Query: 20 EGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCLPAANGKFVAGLQTGL 79 E PVWV + AL++V+I S + ++ +SG+ + W+AP + +G +VAG+++G Sbjct: 15 ESPVWVPEENALYWVNIPSGGLQCWNASSGKLQGWEAPEMLACIARHQDGGWVAGMESGF 74 Query: 80 AIFDPADRSFTP---LTDPEPALPGNRLNDGTVDPAGRLWFGTM--DDGESEATGRIYRL 134 P D + E + RLNDG D GR W G+M + G + GR+YR Sbjct: 75 FRLHPNDDGSLDSELCANVEHSRTDMRLNDGRCDRQGRFWAGSMVLNMGANADEGRMYRY 134 Query: 135 GGDGRCVAET--AAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIG---DDGILGDSRVF 189 R E + + NG SPDGRT+Y D+ V A D G + R+F Sbjct: 135 EAGQRSPVEAQLSGFIVPNGLGFSPDGRTMYLSDSHPLVQQIWAFDYDIDSGTPSNRRLF 194 Query: 190 ATIPNSEGFPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITKVAFGGPD 249 + G PDG AVDA+GC WI + + R++P G L + PV T AFGG Sbjct: 195 VDMMPLAGRPDGAAVDADGCYWICANDAGLIHRFTPDGRLDRSLQVPVKKPTMCAFGGSR 254 Query: 250 LRTVYATTASKHLDADGRAEEPHAGDLFAFRVSVPGM 286 L T++ T+ D D + AG +FA V G+ Sbjct: 255 LDTLFVTSIRPGDDND---PQSLAGGVFALNPGVKGL 288 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: 397 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: 301 Length adjustment: 26 Effective length of query: 269 Effective length of database: 275 Effective search space: 73975 Effective search space used: 73975 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