Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 170 bits (431), Expect = 5e-47 Identities = 106/314 (33%), Positives = 160/314 (50%), Gaps = 35/314 (11%) Query: 21 DLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMPVQKRNVAMVYQ 80 +L + G V++GP+ GK++L+RL+AGL+ P+ G I V +P + R++AMV+Q Sbjct: 54 NLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDRLPAKARDIAMVFQ 113 Query: 81 QFINYPALTVYNNIASPMRISG------------------------KDAATIDREVRKAA 116 + YP L+VY+N+A +R G + A I R VR+ A Sbjct: 114 SYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPEQEARIKRRVREVA 173 Query: 117 ELLKLTPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPK 176 +L+L LDR P LSGGQ+QR AL RA+ +N + LMDEPL+NLD KLR E R ++ Sbjct: 174 TMLQLDTLLDRQPKQLSGGQKQRVALGRAIARNPQVFLMDEPLSNLDAKLRAETRAQIVS 233 Query: 177 IFAQSGAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPP 236 + Q G +Y T + +EA+ +G A LN+G + Q +E+Y RP N A PP Sbjct: 234 LQRQLGVTTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDRPANRFVAQFIGSPP 293 Query: 237 LNTLDVTKSGNVFTRPSGVTIPVPSH----LAVVPDGPVTIAFHPHHLGLAPQTGDAARL 292 +N + VT + +P L + V + P HL + G AA Sbjct: 294 MNLIPVTVRAPLQLTTENFRCTLPEAWEPVLRLYDGQTVELGIRPEHL----EVGAAA-- 347 Query: 293 QARTLVSEITGSES 306 ++ L+ +TG E+ Sbjct: 348 -SKNLLITVTGVEA 360 Lambda K H 0.319 0.136 0.392 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: 356 Number of extensions: 14 Number of successful extensions: 2 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: 358 Length of database: 417 Length adjustment: 30 Effective length of query: 328 Effective length of database: 387 Effective search space: 126936 Effective search space used: 126936 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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