Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate WP_032984929.1 BN137_RS00940 SMP-30/gluconolactonase/LRE family protein
Query= SwissProt::Q9I922 (299 letters) >NCBI__GCF_000319285.1:WP_032984929.1 Length = 292 Score = 134 bits (336), Expect = 3e-36 Identities = 90/290 (31%), Positives = 140/290 (48%), Gaps = 24/290 (8%) Query: 18 ESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVALRKSGGYVLAMGNTF 77 E P W+ +E L + DI Q++ R+DP + + + +G ALR+ GG+++A+ + Sbjct: 19 ECPTWDAQEQALYWADILEQEIHRYDPQSAEHRVWQFPEEVGCFALREKGGFIVALRSAI 78 Query: 78 SALNWEDQSVTTLARVDEDKPNN----RFNDGKVDPEGRFLAGTM--SQEIRPAVVERNQ 131 W L + D PNN RFNDG D +GRF AGT + + A++ R Sbjct: 79 ----WLADERGLLVQKICDNPNNPALARFNDGGTDHDGRFYAGTFWAPGDYKGALLVR-- 132 Query: 132 GSLFTLYPDHSVVKHFDMVDI--SNGLDWSLDHKTLYYIDSLSFKVDALDYDMKTGKSSN 189 D + H DI +NGL +S D + +Y D+ + D + G+ Sbjct: 133 -------VDSDLSAHVIQSDIHGANGLAFSPDKRWMYTSDTPKGVIYRTPLD-ELGEPGK 184 Query: 190 RRTLYKLQQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVKLPIDKTTSCC 249 R + EGIPDG +D EG W A Y+G R+ R P+ G+Q++ +LP+ T C Sbjct: 185 REIFKIFGEGEGIPDGAALDVEGCYWTAMYDGHRIARFSPQ-GEQLEEYRLPVRCPTMVC 243 Query: 250 FGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPTAFAG 299 FGG D +Y+TS + MD + + P SG ++ + V G+ F G Sbjct: 244 FGGADMKTLYITSTRENMDLEELAKFPLSGALFTLE-TSVAGLPKPKFKG 292 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: 273 Number of extensions: 14 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: 292 Length adjustment: 26 Effective length of query: 273 Effective length of database: 266 Effective search space: 72618 Effective search space used: 72618 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 24 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