Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate H281DRAFT_05978 H281DRAFT_05978 Sugar lactone lactonase YvrE
Query= SwissProt::Q9I922 (299 letters) >FitnessBrowser__Burk376:H281DRAFT_05978 Length = 303 Score = 178 bits (452), Expect = 1e-49 Identities = 106/294 (36%), Positives = 156/294 (53%), Gaps = 7/294 (2%) Query: 6 IECVVSETYKIGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVALRK 65 I+ V S +GES +W+EK L +VD GQ + R D S+ +S ++ IGS+ LR Sbjct: 17 IDVVDSTPDVLGESIIWDEKTQLLWWVDGIGQSIHRLDISSGAKKSWPMQEEIGSIGLRA 76 Query: 66 SGGYVLAMGNTFSALNWEDQSVTTLARVDEDKPNNRFNDGKVDPEGRFLAGTMSQEIRPA 125 GG ++ M + F + E +T +AR D ++P NRFNDGK D GR+ +GT+ A Sbjct: 77 KGGLIVGMRSGFYFFSPETGELTEVARPDAERPKNRFNDGKCDRHGRYWSGTVE-----A 131 Query: 126 VVERNQGSLFTLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALDYDMKTG 185 +G LF L PD + + NGL +S D++ +Y DS S ++D DYD G Sbjct: 132 AAYTPRGRLFRLDPDLKPKLIMEGITCINGLSFSPDNRLMYMTDSFSCQIDVFDYDSVDG 191 Query: 186 KSSNRRTLYKLQQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVKLPIDKT 245 NRR ++ GI DG +DA+G W A +G V R DP G+ + LP+ + Sbjct: 192 AIYNRRKFAEVPLGRGICDGSTVDADGCFWSANMDGWCVTRYDPR-GRIDMVINLPVRRV 250 Query: 246 TSCCFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPTAFAG 299 +S CFGGPD +++T+A M E +QP +G + + GVKG+ F G Sbjct: 251 SSLCFGGPDLDTLFITTARRRMSEKELAQQPLAGNVLAVRP-GVKGLPEPEFLG 303 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: 316 Number of extensions: 28 Number of successful extensions: 3 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: 303 Length adjustment: 27 Effective length of query: 272 Effective length of database: 276 Effective search space: 75072 Effective search space used: 75072 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