Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate AO356_23060 AO356_23060 gluconolactonase
Query= SwissProt::Q9I922 (299 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23060 Length = 301 Score = 147 bits (371), Expect = 3e-40 Identities = 95/301 (31%), Positives = 151/301 (50%), Gaps = 11/301 (3%) Query: 4 IKIECVVSETYKIGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVAL 63 ++ E +V +GESPVW +E L +V+I + RW+ S+ K+Q + +A Sbjct: 1 MQAELIVDARNAVGESPVWVPEENALYWVNIPSGGLQRWNASSGKIQGWEAPEMLACIAR 60 Query: 64 RKSGGYVLAMGNTFSALNWEDQ---SVTTLARVDEDKPNNRFNDGKVDPEGRFLAGTMSQ 120 + GG+V M + F L+ D V+ + + R NDG+ D +GRF AG+M Sbjct: 61 HQDGGWVAGMESGFFRLHPHDDGSLDSELCGSVEHSRVDMRLNDGRCDRQGRFWAGSMVL 120 Query: 121 EIRPAVVERNQGSLFTLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDS--LSFKVDAL 178 + A V+ + + V + NGL +S D +T+Y DS LS ++ A Sbjct: 121 NM-AANVDEGRMYRYEAGQRSPVEAQLSGFIVPNGLGFSPDGRTMYLSDSHPLSQQIWAF 179 Query: 179 DYDMKTGKSSNRRTLYKLQQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTV 238 DYD+ +G SNRR + G PDG +DA+G W+ + G + R P+ G+ +++ Sbjct: 180 DYDIDSGTPSNRRLFVDMLPLAGRPDGAAVDADGCYWICANDAGLIHRFTPD-GRLDRSL 238 Query: 239 KLPIDKTTSCCFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPTAFA 298 ++P+ K T C FGG ++VTS G D D Q +GG++ + GVKG+A F Sbjct: 239 EVPVKKPTMCAFGGSRLDTLFVTSIRPGDDND---PQSLAGGVFALKP-GVKGLAEPVFG 294 Query: 299 G 299 G Sbjct: 295 G 295 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: 343 Number of extensions: 26 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: 301 Length adjustment: 27 Effective length of query: 272 Effective length of database: 274 Effective search space: 74528 Effective search space used: 74528 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