Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate BWI76_RS23720 BWI76_RS23720 calcium-binding protein
Query= SwissProt::Q9I922 (299 letters) >FitnessBrowser__Koxy:BWI76_RS23720 Length = 292 Score = 157 bits (396), Expect = 4e-43 Identities = 99/298 (33%), Positives = 157/298 (52%), Gaps = 8/298 (2%) Query: 4 IKIECVVSETYKIGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVAL 63 ++IE ++ ++GESPVW+ ++ L +VD ++ + ++S V IGS AL Sbjct: 1 MRIEVLLDLKTRLGESPVWDIEQQRLWWVDSLDGRLFACNAQGGAIKSWDVRQKIGSFAL 60 Query: 64 RKSG-GYVLAMGNTFSALNWEDQSVTTLARVDEDKPNNRFNDGKVDPEGRFLAGTMSQEI 122 R++G G V+A+ N L++ +T L + D+P NR NDGKVD +GRFL G+M Sbjct: 61 RQNGEGAVVALQNGVHLLDFASGGLTLLHHPEADRPFNRLNDGKVDRQGRFLFGSMDMR- 119 Query: 123 RPAVVERNQGSLFTLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALDYDM 182 E G+L+ L D S+ + +SN WS +T Y+ D+ + ++ A DY+ Sbjct: 120 ----EEEPSGALYRLDADLSLHVLKKNIIVSNAPCWSPSGETFYFADTWTGEICAWDYNT 175 Query: 183 KTGKSSNRRTLYKLQQDE-GIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVKLP 241 TG S R + + E G DG +D+EG LW A G+++R PE G+ + +++P Sbjct: 176 ATGDLSGERVFCHVDRSEGGAADGATVDSEGYLWNALVYAGKLVRYTPE-GEVDRIIEMP 234 Query: 242 IDKTTSCCFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPTAFAG 299 + K TS FGG + +YVTS + + G ++ I LGV G+A FAG Sbjct: 235 VKKVTSVMFGGENLDVLYVTSMAQPPLPRFPEDNQLRGSLFAIYDLGVTGVAERRFAG 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: 296 Number of extensions: 24 Number of successful extensions: 8 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 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