Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate H281DRAFT_05949 H281DRAFT_05949 gluconolactonase
Query= metacyc::MONOMER-13276 (356 letters) >FitnessBrowser__Burk376:H281DRAFT_05949 Length = 302 Score = 160 bits (405), Expect = 4e-44 Identities = 102/304 (33%), Positives = 165/304 (54%), Gaps = 33/304 (10%) Query: 53 PRLDAILDVSTPIEVIASDIQWSEGPVWVKNGNFLLFSDPPANIMRKWTPDAGVSIFLKP 112 PR +L + ++ + + W+EGPV+ + L++SD P N M +W P GV ++ P Sbjct: 11 PRFRLLLQPNASMDKLTGECLWAEGPVYFPATDLLIWSDIPNNRMLRWAPGMGVGVYRGP 70 Query: 113 SGHAEPIPAGQFREPGSNGMKVGPDGKIWVADSGTRAIMKVDPVTRQRSVVVDNYKGKRF 172 S + SNG +G++ + G R + + + +V+ +++GKR Sbjct: 71 SNY-------------SNGNTRDREGRLVSCEHGERRVTRTEH-DGSITVIASHFEGKRL 116 Query: 173 NSPNDLFFSKSGAVYFTDPPYGLTNLDES--DIKEMNYNGVFRLSP-DGRLDLIEAGLSR 229 NSPND+ GA++FTDP YG+ + E E+ V+R+SP D ++ L+ + Sbjct: 117 NSPNDVIVDSEGAIWFTDPDYGIISDYEGYRSDSEIGRCNVYRVSPGDTQVRLVSDDFVK 176 Query: 230 PNGLALSPDETKLYVSNS-----DRASPNIWVYSLDSNGLPTSRTLLRNFRKEYFDQGLA 284 PNGLA SPDE+KLY+++S D A +I V+ + SNG LRN R F + + Sbjct: 177 PNGLAFSPDESKLYIADSAASHDDNAPRHIRVFDVASNG------ALRNGR--VFVEMQS 228 Query: 285 GLPDGMNIDKQGNLFASAPGGIYIFAPDGECLGLISGNPGQPLSNCCF-GEKGQTLFISA 343 G+PDGM +D+ GN++ SA G++ +APDG LG I + ++N F G + LFI+A Sbjct: 229 GVPDGMRVDEHGNVWTSAEDGVHCYAPDGTLLGKIL--IPEVVANLTFGGPRRNRLFITA 286 Query: 344 SHNV 347 + +V Sbjct: 287 TSSV 290 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: 406 Number of extensions: 35 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: 356 Length of database: 302 Length adjustment: 28 Effective length of query: 328 Effective length of database: 274 Effective search space: 89872 Effective search space used: 89872 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