Align xylono-1,5-lactonase (EC 3.1.1.110) (characterized)
to candidate WP_086510992.1 BZY95_RS16570 SMP-30/gluconolactonase/LRE family protein
Query= metacyc::MONOMER-20628 (289 letters) >NCBI__GCF_002151265.1:WP_086510992.1 Length = 304 Score = 181 bits (460), Expect = 1e-50 Identities = 108/290 (37%), Positives = 149/290 (51%), Gaps = 18/290 (6%) Query: 3 AQVTCVWDLKATLGEGPIW-----HGDTLWFVDIKQRKIHNYHPATGERFSFDAPDQVTF 57 A + +W +A LG GP+W L FVDI +R ++ + A+G + + + Sbjct: 13 AMIQRIWRGRAQLGGGPLWCPGQGEAGRLLFVDILRRALYVHDFASGTTRGWPLEEACCW 72 Query: 58 LAPIVGATGFVVGLKTGIHRFHPATGFSLLLE---VEDAALNNRPNDATVDAQGRLWFGT 114 L P GF+ GL + + +++ + NR N+A VD GRLWFG+ Sbjct: 73 LVPRADGDGFIAGLASRLVHLRLEEHGPRIVDDWVTPEEPAGNRFNNAAVDTLGRLWFGS 132 Query: 115 MHDGEENNS----GSLYRMDLTGVARMDRDICITNGPCVSPDGKTFYHTDTLEKTIYAFD 170 M + E+ + G+LYR+D G+ R+D + NGP VSPDG+T YH+DT +YA++ Sbjct: 133 MSENEQESGEPGQGALYRLDGAGLRRVDHGYGVANGPAVSPDGRTLYHSDTAAGIVYAYE 192 Query: 171 LAEDGLLSNKRVFVQFALGDDVYPDGSVVDSEGYLWTALWGGFGAVRFSPQGDAVTRIEL 230 LA DG L+ +R ++F G YPDG D EG LW A WGG RF P G + L Sbjct: 193 LAADGELTGRREHLRFH-GAQGYPDGMTCDVEGGLWVAHWGGGRVSRFLPDGTLDETLLL 251 Query: 231 PAPNVTKPCFGGPDLKTLYFTTARKGLSDETLAQYPLAGGVFAVPVDVAG 280 PA VT FGGP+L LY TTA G E LAG +F V V G Sbjct: 252 PASRVTSCAFGGPELDQLYITTAADGRDQEA-----LAGSLFRVAPGVRG 296 Lambda K H 0.321 0.139 0.442 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: 363 Number of extensions: 22 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: 289 Length of database: 304 Length adjustment: 26 Effective length of query: 263 Effective length of database: 278 Effective search space: 73114 Effective search space used: 73114 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 (21.8 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