Align Xylonolactonase (EC 3.1.1.68) (characterized)
to candidate WP_047094223.1 AAV99_RS11825 SMP-30/gluconolactonase/LRE family protein
Query= reanno::Korea:Ga0059261_1893 (295 letters) >NCBI__GCF_001013305.1:WP_047094223.1 Length = 294 Score = 225 bits (573), Expect = 1e-63 Identities = 122/277 (44%), Positives = 156/277 (56%), Gaps = 3/277 (1%) Query: 20 EGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCLPAANGKFVAGLQTGL 79 EG +W +WFVDIK HR+ +DP +G +AP Q+G+ LPA NG + GLQ GL Sbjct: 19 EGVLWDAARGVVWFVDIKQHRLWHYDPDTGSNSFTEAPGQIGWALPADNGMLLCGLQDGL 78 Query: 80 AIFDPADRSFTPLTDPEPALPGNRLNDGTVDPAGRLWFGTMDDGESEATGRIYRLGGDGR 139 +F P +F L NRLND DP GR+WFG+MDD ES A+GR Y Sbjct: 79 YVFHPELSTFEKLAAVPGEPAANRLNDACTDPWGRVWFGSMDDTESAASGRFYCFDRGEI 138 Query: 140 CVAETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIGDDGILGDSRVFATIPN--SEG 197 A + ++I+NGPAV+ G +Y DT I A + DG+ G++R FA + Sbjct: 139 TPAGPSGITITNGPAVNAQGDRIYFTDTTAQKIMVANLTPDGV-GEARPFADTGALFPDA 197 Query: 198 FPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITKVAFGGPDLRTVYATT 257 +PDGP VDAE VW GLY G V R+SP GEL + P ITK+AFGG D RT Y T+ Sbjct: 198 YPDGPVVDAEDHVWTGLYLGGRVARFSPDGELTATIDMPARDITKLAFGGADFRTGYVTS 257 Query: 258 ASKHLDADGRAEEPHAGDLFAFRVSVPGMPGTEVSVG 294 A+K++ D A P AG LFAF V G T V +G Sbjct: 258 ATKNMTEDDMALYPQAGSLFAFDAPVAGFAQTRVRIG 294 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: 414 Number of extensions: 35 Number of successful extensions: 2 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: 294 Length adjustment: 26 Effective length of query: 269 Effective length of database: 268 Effective search space: 72092 Effective search space used: 72092 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 24 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