Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate WP_057509054.1 ABB28_RS13170 SMP-30/gluconolactonase/LRE family protein
Query= SwissProt::Q9I922 (299 letters) >NCBI__GCF_001431535.1:WP_057509054.1 Length = 308 Score = 124 bits (310), Expect = 4e-33 Identities = 89/293 (30%), Positives = 146/293 (49%), Gaps = 21/293 (7%) Query: 16 IGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVALRKSGGYVLAMGN 75 +GES W +E L + DI G+++ R +P T Q S +GS+AL +SG +L M Sbjct: 23 LGESITWCARERVLWWTDINGRRIWRGNPDTGNAQWWSTPGRVGSLALCESGRLLLGMEK 82 Query: 76 TFSALNWEDQS---------VTTLARVDEDKPNNRFNDGKVDPEGRFLAGTMSQEIRPAV 126 AL + D S + V D R NDG++D G F+ G ++++ PA Sbjct: 83 ---ALYFADPSREEPGAGLNCEQVCEVPMDGAALRINDGRLDRAGNFVFGCINED--PA- 136 Query: 127 VERNQGSLFTLYPDHSVVKHFDM--VDISNGLDWSLDHKTLYYIDSLSFKVDALDYDMKT 184 R + + F Y ++ + V I+NG+ + D + +YY DSL ++ YD T Sbjct: 137 --RARAARFHQYSIAQGLRALALEPVAIANGICFDPDGQGMYYCDSLQGRIMHAGYDAAT 194 Query: 185 GKSSNRRTLYKLQQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVKLPIDK 244 S+ R ++ + PDG +DA+G++W A + GRV+R G+ + + +P + Sbjct: 195 ATVSDPR-VFAVIDGGAEPDGAVVDADGRVWGAQWGAGRVVRYSA-AGEVDRILPVPALQ 252 Query: 245 TTSCCFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPTAF 297 T F G +YVTSA DG+D + QP SGG+++++ G +G+ F Sbjct: 253 PTCVAFAGDGLGTLYVTSARDGLDVAMLQDQPTSGGVFRVSLEGARGLPDLRF 305 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: 292 Number of extensions: 14 Number of successful extensions: 6 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: 308 Length adjustment: 27 Effective length of query: 272 Effective length of database: 281 Effective search space: 76432 Effective search space used: 76432 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