Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate GFF1302 PGA1_c13180 ABC transporter, ATP binding protein
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__Phaeo:GFF1302 Length = 334 Score = 201 bits (510), Expect = 3e-56 Identities = 128/354 (36%), Positives = 181/354 (51%), Gaps = 27/354 (7%) Query: 2 LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61 ++L + K G I P DL +E G V +GP+ GK++L+RL+AGL+ T G+I D Sbjct: 4 IKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTIRID 63 Query: 62 GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121 G D T +P KR +AMV+Q + YP ++V NIA PM+++G A R + AA L L Sbjct: 64 GEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAALNL 123 Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181 T YLDR P LSGGQ+QR A+ RA+V+ + L DEPL+NLD LR +R E+ ++ + Sbjct: 124 TDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELHKRL 183 Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241 +Y T + EA+ + L G + Q G +E+YR P N+ AG P +N L Sbjct: 184 ATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKMNLL- 242 Query: 242 VTKSGNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQARTL-VSE 300 T P H A TI P HL ++ G + A T+ VSE Sbjct: 243 --------TGPQAA-----QHNA------ATIGIRPEHLSISETEG----MWAGTIGVSE 279 Query: 301 ITGSESFVHLEYDGVRWVMLAHGIHDIDPDMEVEAFL--DTRHLMAFGSDGRAI 352 GS++F H++ D + ++D FL D HL FGSDG I Sbjct: 280 HLGSDTFFHVQCDAFDDPLTVRASGELDLGYGERVFLTPDMTHLHRFGSDGLRI 333 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: 325 Number of extensions: 14 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: 358 Length of database: 334 Length adjustment: 29 Effective length of query: 329 Effective length of database: 305 Effective search space: 100345 Effective search space used: 100345 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