Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate H281DRAFT_03749 H281DRAFT_03749 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__Burk376:H281DRAFT_03749 Length = 360 Score = 192 bits (487), Expect = 2e-53 Identities = 115/356 (32%), Positives = 182/356 (51%), Gaps = 14/356 (3%) Query: 2 LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61 ++L K G ++ DL ++ G VL+GP+ GK++LMR++AGL+ +GG + Sbjct: 4 VQLSGIFKRYGDTQVVHGIDLHIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDLMIG 63 Query: 62 GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121 GT + Q+RN++MV+Q + YP L+VY NIA RI + A + AA++L L Sbjct: 64 GTRANNLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESPANFKPRIEAAAKMLNL 123 Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181 YLDR P LSGGQ+QR A+ RA+V+ SL L DEPL+NLD KLR ++R E+ + + Sbjct: 124 GGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKALHQRL 183 Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241 +Y T + EA+ + +N GR+ Q G +E+Y P NL A P +N + Sbjct: 184 KNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSMNFAE 243 Query: 242 VTKSGNVFTRPSGVTIPVPSHLAVVPDG---------PVTIAFHPHHLGLAPQTGDAARL 292 T+ SG+ + + +V +G VT+ P H+ QT D + Sbjct: 244 GVLVNR--TQGSGLALKLADGGEIVLEGAPASATVGAKVTLGVRPEHIETITQTPD---V 298 Query: 293 QARTLVSEITGSESFVHLEYDGVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSD 348 + V E TG+E+ ++ + G W + ++P V L H+ F ++ Sbjct: 299 TMQVEVVEPTGAETHLYGKIGGDTWCVTTRQRSKVEPGERVTLRLPAAHIHLFDTE 354 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: 344 Number of extensions: 21 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: 360 Length adjustment: 29 Effective length of query: 329 Effective length of database: 331 Effective search space: 108899 Effective search space used: 108899 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