Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate SMc01499 SMc01499 ATP-binding transport ABC transporter protein
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__Smeli:SMc01499 Length = 333 Score = 204 bits (519), Expect = 3e-57 Identities = 115/314 (36%), Positives = 176/314 (56%), Gaps = 23/314 (7%) Query: 2 LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61 + L+N +K+ GA I DL + G V +GP+ GK++L+RL+AGL+ + G I D Sbjct: 4 ITLKNVSKVFGAHAVIPSIDLDITDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGEIVID 63 Query: 62 GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121 G + T +P +R ++MV+Q + YP ++V +NIA P++++G+D A+ID++V AA +L L Sbjct: 64 GRNATELPPARRGLSMVFQSYALYPHMSVRSNIAFPLKMAGEDKASIDKKVEDAARVLNL 123 Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181 T YLDR P LSGGQ+QR A+ RA+V+ L DEPL+NLD LR +R E+ ++ Q Sbjct: 124 TDYLDRKPRQLSGGQRQRVAIGRAIVRQPEAFLFDEPLSNLDAALRVNMRLEISQLHQQL 183 Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241 VY T + EA+ + LN+GR+ Q G +++YRRP NL AG P +N + Sbjct: 184 KTTMVYVTHDQVEAMTMADKIVVLNRGRIEQVGSPLDLYRRPDNLFVAGFIGSPKMNFV- 242 Query: 242 VTKSGNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQARTLVSEI 301 P +H A TI P H+ L+ D + V+E Sbjct: 243 -------------TGAPAAAHQA------HTIGIRPEHIALSK---DQGTWRGTVGVAEH 280 Query: 302 TGSESFVHLEYDGV 315 GS++F+H+ DG+ Sbjct: 281 LGSDTFLHVNADGI 294 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: 288 Number of extensions: 11 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: 333 Length adjustment: 29 Effective length of query: 329 Effective length of database: 304 Effective search space: 100016 Effective search space used: 100016 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: 49 (23.5 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