Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate BWI76_RS21470 BWI76_RS21470 gluconolaconase
Query= SwissProt::Q9I922 (299 letters) >FitnessBrowser__Koxy:BWI76_RS21470 Length = 290 Score = 130 bits (326), Expect = 5e-35 Identities = 89/276 (32%), Positives = 133/276 (48%), Gaps = 15/276 (5%) Query: 13 TYKIGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVALRKSGGYVLA 72 T + E P W E E L + DI ++ R+D T + Q + G ALR GG+++A Sbjct: 11 TGHLPECPTWSEAEQALYWADIMECEIHRYDVRTGEHQVLQFPEEPGCFALRAKGGFIVA 70 Query: 73 MGNTFSALNWEDQSVTTLARVDEDKPNN----RFNDGKVDPEGRFLAGTMSQEIRPAVVE 128 + + W + L R D P+N RFNDG D +GRF AGT + Sbjct: 71 LRSGI----WLTDAHGLLQRKVCDNPSNPQLARFNDGGTDRDGRFYAGTFW-----GPGD 121 Query: 129 RNQGSLFTLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALDYDMKTGKSS 188 N L + D S + +NGL +S D + +Y D+ + + D K G++ Sbjct: 122 FNGALLMRIDSDLSPQVIQCDIHGANGLAFSEDKRWMYTSDTPNAVIYRTPLD-KRGEAG 180 Query: 189 NRRTLYKLQQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVKLPIDKTTSC 248 R + EGIPDG IDAEG W A ++G R+ R P TG+Q++ +LP+ T Sbjct: 181 KREVFRRFHPGEGIPDGAAIDAEGCYWSAMFDGWRIARFSP-TGEQLEEHRLPVRCPTMV 239 Query: 249 CFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKI 284 CFGG D +Y+T+ + MD + + P SG I+ + Sbjct: 240 CFGGTDMKTLYITTTRENMDAEEVAKYPLSGAIFTL 275 Lambda K H 0.316 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: 279 Number of extensions: 20 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: 299 Length of database: 290 Length adjustment: 26 Effective length of query: 273 Effective length of database: 264 Effective search space: 72072 Effective search space used: 72072 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: 48 (23.1 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