Align Regucalcin; RC; Gluconolactonase; GNL; Senescence marker protein 30; SMP-30; xSMP-30; EC 3.1.1.17 (characterized)
to candidate SMa0717 SMa0717 hypothetical protein
Query= SwissProt::Q9I922 (299 letters) >FitnessBrowser__Smeli:SMa0717 Length = 569 Score = 170 bits (431), Expect = 6e-47 Identities = 98/294 (33%), Positives = 158/294 (53%), Gaps = 8/294 (2%) Query: 6 IECVVSETYKIGESPVWEEKEGTLLFVDITGQKVCRWDPSTKKVQSVSVEAPIGSVALRK 65 ++CV+ ++GE+PVW E+E L +VDI V R+DP T K +S +V + +V + Sbjct: 283 VQCVLPWGAQLGEAPVWVEREKRLYWVDILHPAVHRFDPVTGKNESCNVAKLVSAVLPTR 342 Query: 66 SGGYVLAMGNTFSALNWEDQSVTTLARVDEDKPNNRFNDGKVDPEGRFLAGTMSQEIRPA 125 + G ++A + +++ A + P NR ND KVDP GR G+M + Sbjct: 343 NEGLIVASQDGVEHFDFDRGDFNPFAEPEPGLPENRLNDAKVDPSGRLWVGSMRLD---- 398 Query: 126 VVERNQGSLFTLYPDHSVVKHFDMVDISNGLDWSLDHKTLYYIDSLSFKVDALDYDMKTG 185 V R GSL+ L V + ++NGL WS D T Y++D++ + A D+D + G Sbjct: 399 -VSRPTGSLYRLTSAGEVTRAGSGFTVANGLAWSPDSSTFYFVDTVPGIIYAYDFDAREG 457 Query: 186 KSSNRRTLYKLQQDEGIPDGMCIDAEGKLWVACYNGGRVIRIDPETGKQIQTVKLPIDKT 245 +NRR + + EG PDG+ +DA+G +W A ++G RV R P+ G+ + V+LP+ + Sbjct: 458 SIANRRVFVTVPEAEGRPDGLAVDADGGVWCAIWDGWRVNRYRPD-GRLDRAVELPVPRP 516 Query: 246 TSCCFGGPDYSEMYVTSACDGMDEDWKKRQPQSGGIYKITGLGVKGIAPTAFAG 299 TS FGG + + +++TSA + P SGGI+ G +G+ PT+ G Sbjct: 517 TSVAFGGDELATLFITSARTRLPASTLTEAPLSGGIFACNP-GARGL-PTSLFG 568 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: 484 Number of extensions: 30 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: 569 Length adjustment: 31 Effective length of query: 268 Effective length of database: 538 Effective search space: 144184 Effective search space used: 144184 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: 50 (23.9 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