Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate CCNA_01282 CCNA_01282 gluconolactonase
Query= metacyc::MONOMER-13276 (356 letters) >FitnessBrowser__Caulo:CCNA_01282 Length = 347 Score = 293 bits (751), Expect = 4e-84 Identities = 157/354 (44%), Positives = 213/354 (60%), Gaps = 16/354 (4%) Query: 7 SRRECLSAAVMVPIAAMTATATITGSAQAAKNNMNGSTIGKITKFSPRLDAILDVSTPIE 66 +RR L A V + A A G+ IG+I + SP LDA++D + PIE Sbjct: 3 TRRAMLGAGVALIAGAQGFAAQARGAGSPK--------IGRIRRLSPELDAVVDANAPIE 54 Query: 67 VIASDIQWSEGPVWVKNGNFLLFSDPPANIMRKWTPDAGVSIFLKPSGHAEPIPAGQFRE 126 + I W+EGP WV NG++LLFSD P N+M +W G + FL+PSG+ P P FRE Sbjct: 55 QLTDGITWAEGPAWVANGSYLLFSDVPGNVMHRWDAKGGKTDFLRPSGYDGP-PTKIFRE 113 Query: 127 PGSNGMKVGPDGKIWVADSGTRAIMKVDPVTRQRSVVVDNYKGKRFNSPNDLFFSK---- 182 G+NG + G++ V D G RA+ ++D TR+++++ + GK+FNSPNDL + Sbjct: 114 AGTNGAIISTAGELLVCDCGNRAVARIDLSTRKKTLLATTFNGKKFNSPNDLVEVRHGPL 173 Query: 183 SGAVYFTDPPYGLTNLDESDIKEMNYNGVFRLSPDGRLDLIEAGLSRPNGLALSPDETKL 242 G++YFTDPPYGL D S KE +NGV+ L P+G + L++ LS PNG+ LSPD +L Sbjct: 174 KGSLYFTDPPYGLEGGDASPAKEQAFNGVYLLRPNGEVALVDGSLSFPNGVGLSPDGRRL 233 Query: 243 YVSNSDRASPNIWVYSLDSNGLPTSRTLLRNFRKEYFDQGLAGLPDGMNIDKQGNLFASA 302 YV+ SD P I Y L ++GLPT+ + + + G GLPDGM +D QG LFAS Sbjct: 234 YVAISDPKRPVIMAYDLGADGLPTASRVFFD-ASDLLKAGGPGLPDGMKVDAQGRLFASG 292 Query: 303 PGGIYIFAPDGECLGLISGNPGQPLSNCCFGEKGQTLFISASHNVVRVRTKTFG 356 PG I I PD + LG+I G P +NC FGE G TLFI+++H V RVRTKT G Sbjct: 293 PGCIMILTPDAKLLGVI--ETGFPAANCVFGEDGGTLFITSNHLVARVRTKTKG 344 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: 493 Number of extensions: 43 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: 347 Length adjustment: 29 Effective length of query: 327 Effective length of database: 318 Effective search space: 103986 Effective search space used: 103986 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