Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate SM_b20453 SM_b20453 gluconolactonase
Query= metacyc::MONOMER-13276 (356 letters) >FitnessBrowser__Smeli:SM_b20453 Length = 303 Score = 148 bits (374), Expect = 2e-40 Identities = 103/311 (33%), Positives = 156/311 (50%), Gaps = 32/311 (10%) Query: 54 RLDAILDVSTPIEVIASDIQWSEGPVWVKNGNFLLFSDPPANIMRKWTPDAGVSIFLKPS 113 R +++ S +E + +W+EGPVW + + L++SD P M +WTPD G S+F PS Sbjct: 13 RFRSLIVGSAALEELYRGCRWAEGPVWFSDLDCLIWSDIPNQRMMRWTPDGGASVFRSPS 72 Query: 114 GHAEPIPAGQFREPGSNGMKVGPDGKIWVADSGTRAIMKVDPVTRQRSVVVDNYKGKRFN 173 + NG +G++ + G R + + + R +V+ D Y+GKR N Sbjct: 73 NYV-------------NGNTRDREGRLISCEHGGRRVTRTEHDGR-ITVLADIYEGKRLN 118 Query: 174 SPNDLFFSKSGAVYFTDPPYGLTNLDESDIKEMNY--NGVFRLSP-DGRLDLIEAGLSRP 230 SPND G+++FTDP YG+ + E E V+R+ P G + + +P Sbjct: 119 SPNDAVVHSDGSIWFTDPTYGILSDYEGHKAEPEQPTRNVYRIDPLSGAIKAVVRDFIQP 178 Query: 231 NGLALSPDETKLYVSNSDRAS----PNIWVYSLDSNGLPTSRTLLRNFRKEYFDQGLAGL 286 NGLA SPDE +LY+++S A +I V+ + ++G +L N R YF G Sbjct: 179 NGLAFSPDEARLYIADSGSAKHEVPSHIRVFDVAADG------VLANDR--YFCSIDNGN 230 Query: 287 PDGMNIDKQGNLFASAPGGIYIFAPDGECLGLISGNPGQPLSNCCF-GEKGQTLFISASH 345 PDG D GNL+ SA G++ F G LG I Q +SN F G K LFI+A+ Sbjct: 231 PDGFRFDVAGNLWCSAADGVHCFDTGGTLLGKIL--VPQTVSNLTFGGPKKNRLFITATQ 288 Query: 346 NVVRVRTKTFG 356 ++ + T T G Sbjct: 289 SLYSIYTATNG 299 Lambda K H 0.317 0.135 0.409 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: 410 Number of extensions: 26 Number of successful extensions: 4 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: 356 Length of database: 303 Length adjustment: 28 Effective length of query: 328 Effective length of database: 275 Effective search space: 90200 Effective search space used: 90200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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