Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate SMc04142 SMc04142 hypothetical protein
Query= SwissProt::Q9I922 (299 letters) >FitnessBrowser__Smeli:SMc04142 Length = 294 Score = 139 bits (351), Expect = 6e-38 Identities = 98/295 (33%), Positives = 142/295 (48%), Gaps = 11/295 (3%) Query: 4 IKIECVVSETYKIGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVAL 63 + EC++ + ESPV++E+ L FVDI + R D S ++E S L Sbjct: 5 LTFECLLDSRCDVAESPVFDERRNCLFFVDIGRSALHRVDLSGAGHVEWTIEGGACSTGL 64 Query: 64 RKSGGYVLAMGNTFSALNWEDQSVTT-LARVDEDKPNNRFNDGKVDPEGRFLAGTMSQEI 122 +SG VLA + + + +VT +A ++ D + R NDGKV P+G F GTM Sbjct: 65 ARSGRLVLAQRDRVVLFDPDAGAVTREIAAIEPDIADTRLNDGKVGPDGAFWVGTMHD-- 122 Query: 123 RPAVVERNQGSLFTLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALDYDM 182 R SL+ + P+ +V + + V SNGL WS D L++ DS +D +D Sbjct: 123 --VPDRRPVASLYRVSPEGAVERKVEGVVCSNGLAWSGDGSLLFHSDSRGAWIDRWQFDP 180 Query: 183 KTGKSSNRRTLYKLQQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVKLPI 242 TG S RR L L + G PDG DAE W A + G V R PE G+ + T + P+ Sbjct: 181 ATGALSGRRRLASLDEASGRPDGAATDAEAHYWSAGVSAGIVNRFSPE-GRLVGTHRFPV 239 Query: 243 DKTTSCCFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPTAF 297 T CF GPD + VTS + ++ +SGGI+ + V G+A F Sbjct: 240 PAPTMPCFAGPDLKTLLVTS----LRPAGIGKENRSGGIF-VARSPVAGVAVHRF 289 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: 17 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: 294 Length adjustment: 26 Effective length of query: 273 Effective length of database: 268 Effective search space: 73164 Effective search space used: 73164 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