Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate HSERO_RS20090 HSERO_RS20090 gluconolactonase
Query= metacyc::MONOMER-13276 (356 letters) >FitnessBrowser__HerbieS:HSERO_RS20090 Length = 305 Score = 135 bits (340), Expect = 1e-36 Identities = 95/310 (30%), Positives = 159/310 (51%), Gaps = 35/310 (11%) Query: 51 FSPRLDAILDVSTPIEVIASDIQWSEGPVWVKNGNFLLFSDPPANIMRKWTPDAGVSIFL 110 F R ++ + ++ + + +W+EGPVW+ L++SD P N + +W+ AG +F Sbjct: 11 FDARFRRMVIDTAQVDCLYTGCRWAEGPVWLPATQELIWSDIPNNRLMRWSEGAGAGVFR 70 Query: 111 KPSGHAEPIPAGQFREPGSNGMKVGPDGKIWVADSGTRAIMKVDPVTRQRSVVVDNYKGK 170 +PS +NG + +G+I G RA+++ + + + +++GK Sbjct: 71 QPSNF-------------NNGNTLDREGRIVGCLHGGRAVVRTEH-DGSITTLASHWQGK 116 Query: 171 RFNSPNDLFFSKSGAVYFTDPPYGLTNLDE--SDIKEMNYNGVFRLSPD-GRLDLIEAGL 227 R NSPND+ G+++FTDP YG+ + E E+ V+R+ D G + ++ + L Sbjct: 117 RLNSPNDVVVKSDGSIWFTDPDYGINSDYEGYQAQSEIGACNVYRIDGDSGEISIVASDL 176 Query: 228 SRPNGLALSPDETKLYVSN---SDRAS--PNIWVYS-LDSNGLPTSRTLLRNFRKEYFDQ 281 RPNGLA S DE +LY+++ + RA +I V+ +D L E F Sbjct: 177 ERPNGLAFSTDERRLYIADTGLTHRAGGPHHIRVFDVVDGISLKVG---------EVFAT 227 Query: 282 GLAGLPDGMNIDKQGNLFASAPGGIYIFAPDGECLGLISGNPGQPLSNCCF-GEKGQTLF 340 GL DG +D QGN++ SA G++ +APDG LG I + +SN F G +G LF Sbjct: 228 IDPGLADGFRLDAQGNVWTSAGDGVHCYAPDGTLLGKIL--IPEVVSNVVFGGPRGNRLF 285 Query: 341 ISASHNVVRV 350 I+A+ ++ V Sbjct: 286 ITATTSLYAV 295 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: 378 Number of extensions: 32 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: 305 Length adjustment: 28 Effective length of query: 328 Effective length of database: 277 Effective search space: 90856 Effective search space used: 90856 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