Align xylono-1,5-lactonase (EC 3.1.1.110) (characterized)
to candidate SMa0060 SMa0060 gluconolactonase
Query= metacyc::MONOMER-20628 (289 letters) >FitnessBrowser__Smeli:SMa0060 Length = 311 Score = 130 bits (326), Expect = 5e-35 Identities = 99/290 (34%), Positives = 141/290 (48%), Gaps = 21/290 (7%) Query: 1 MTAQVTCVWDLKATLGEGPIWHGD--TLWFVDIKQRKIHNYHPATGERFSFDAPDQVTFL 58 M+A V+ + D K +GE +W GD L++VDI ++IH P G ++ PD VT + Sbjct: 1 MSATVSLLLDAKDIVGESILWCGDEKALYWVDIVGKRIHRLEPENGRHDTWPTPDFVTSI 60 Query: 59 APIVGATGFVVGLKTGIHRFHPATGFSLLLEVEDAALNNRPNDATVDAQGRLWFGTMHDG 118 GF+VGL + + P F E NR N+ V G W TM Sbjct: 61 GMRKDG-GFIVGLSRNVCLWTPDGPFEEFAMPEPDLPENRLNEGRVAPDGSFWVATMQSN 119 Query: 119 ---------EENNSGSLYRMDLTG-VARMD-RDICITNGPCVSPDGKTFYHTDTLEKTIY 167 + SG++YR+D TG V+++ + ITN + D + F+ DTL IY Sbjct: 120 LDAGGSPKDMDRQSGAVYRIDPTGHVSQLTPNEYGITNTMGWTRDNR-FFFADTLANEIY 178 Query: 168 AFD--LAEDGLLSNKRVFVQFALGDDVYPDGSVVDSEGYLWTA-LWGGFGAVRFSPQGDA 224 FD LA + + + + FA G PDGS +D++ LW + GG F G Sbjct: 179 MFDCDLAARRIDNRRTIVAGFARG---LPDGSCLDADDRLWNCRVAGGAAVAGFDGAGRL 235 Query: 225 VTRIELPAPNVTKPCFGGPDLKTLYFTTARKGLSDETLAQYPLAGGVFAV 274 + IELPA T FGGP L TLY T+AR ++ + L +PL GG+FAV Sbjct: 236 MHLIELPASWPTSCTFGGPVLSTLYVTSARFTMTGDHLDMHPLEGGLFAV 285 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: 352 Number of extensions: 32 Number of successful extensions: 7 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: 311 Length adjustment: 27 Effective length of query: 262 Effective length of database: 284 Effective search space: 74408 Effective search space used: 74408 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 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