Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate PP_3180 PP_3180 Smp-30/Cgr1 family protein
Query= SwissProt::Q9I922 (299 letters) >FitnessBrowser__Putida:PP_3180 Length = 346 Score = 131 bits (330), Expect = 2e-35 Identities = 82/269 (30%), Positives = 132/269 (49%), Gaps = 7/269 (2%) Query: 16 IGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVALRKSGGYVLAMGN 75 +GES VW+E+ G L FVDI+G ++ P + A IG++AL G + Sbjct: 71 LGESLVWDERSGVLYFVDISGGRINGLTPDGEVDCLYESAARIGALALTDRGNLIFTEDA 130 Query: 76 TFSALNWEDQSVTTLARVDEDKPNNRFNDGKVDPEGRFLAGTMSQEIRPAVVERNQGSLF 135 + + + + V+ + + RFNDG DP+GRF+ G M + + N G+LF Sbjct: 131 SVAIFDVPTRKVSQHSASVHPRSTYRFNDGACDPQGRFVTGLMDEALSD-----NTGALF 185 Query: 136 TLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALDYDMKTGKSSNRRTLYK 195 S D + + GL WS D T+Y++DS + + +Y ++ G+ + Sbjct: 186 RFDWQLSDQVIHDDMGLPTGLAWSHDGHTVYFVDSAARAIYRAEYLIE-GRLGAVTLFAE 244 Query: 196 LQQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVKLPIDKTTSCCFGGPDY 255 + G PDG+ +D EG LWV Y+G ++R D G V +P+ TSCCFGGP Sbjct: 245 TPAELGRPDGLALDREGGLWVCQYHGSCLLRYDRH-GYLTDQVLMPVPCPTSCCFGGPGM 303 Query: 256 SEMYVTSACDGMDEDWKKRQPQSGGIYKI 284 + +Y+++A M + P +G +Y I Sbjct: 304 NTLYISTARYDMTPEDLHHYPDAGDLYAI 332 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: 305 Number of extensions: 20 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: 299 Length of database: 346 Length adjustment: 28 Effective length of query: 271 Effective length of database: 318 Effective search space: 86178 Effective search space used: 86178 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