Align SMP-30/Gluconolaconase/LRE domain protein (characterized, see rationale)
to candidate WP_053938787.1 WG78_RS15705 SMP-30/gluconolactonase/LRE family protein
Query= uniprot:B2UIY8 (300 letters) >NCBI__GCF_001294205.1:WP_053938787.1 Length = 301 Score = 79.0 bits (193), Expect = 1e-19 Identities = 57/174 (32%), Positives = 83/174 (47%), Gaps = 35/174 (20%) Query: 134 PLGKLYRLDAAAARTGRVDAVIDDLIVPNGLAFSPEGKTMYLSDSHASRQTVWAFDYDID 193 P ++R+D GRV A+I D++ PNGLAFSP+ + +Y++DS S ++ Sbjct: 151 PQCHVFRIDPL----GRVQAMISDMVKPNGLAFSPDERLLYVADSGGSH---------VE 197 Query: 194 TGTPHNRRVFIDMNAY-----------PGRPDGAAVDADGCYWICGNDAGFVHRFTPDGR 242 G H RR +D + PG PDG VD G W D VH ++P G+ Sbjct: 198 NGPHHIRRFALDEHGVLSNQGVLAEISPGMPDGIKVDELGHIWSSAADG--VHCYSPAGQ 255 Query: 243 LDRSIAIPTSKPAMCAFGGPGLDTLFVTSIRIGDDPLSGATFAVRPGVTGLPEP 296 L I +P + +C FGGP + LF+T+ S + +AV V G P Sbjct: 256 LLGKIRLPETVSNLC-FGGPKRNRLFITA--------SSSVYAVYVAVRGARLP 300 Lambda K H 0.322 0.140 0.466 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: 333 Number of extensions: 20 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 300 Length of database: 301 Length adjustment: 27 Effective length of query: 273 Effective length of database: 274 Effective search space: 74802 Effective search space used: 74802 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 (21.9 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