Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate 18115 b4087 fused D-allose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Keio:18115 Length = 510 Score = 375 bits (962), Expect = e-108 Identities = 209/504 (41%), Positives = 325/504 (64%), Gaps = 17/504 (3%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 P + + I K F VHALK V++ YPGE+HA++GENGAGKSTLMK+++G+++P +G I Sbjct: 4 PYISMAGIGKSFGPVHALKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPTKGTIT 63 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI----FIDYKKMY 118 A GI ++QELSV+D L+V EN+++G + I ID+++M Sbjct: 64 INNISYNKLDHKLAAQLGIGIIYQELSVIDELTVLENLYIGRHLTKKICGVNIIDWREM- 122 Query: 119 REAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETE 178 R M G+++D +EK+ SI+ +QM+EIA+ + AKV+I+DEPTSSLT KE + Sbjct: 123 RVRAAMMLLRVGLKVDLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTNKEVD 182 Query: 179 KLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238 LF ++ L+++G AI++ISH+L EI ICD+ +V++DG + + + +++ + IV +MV Sbjct: 183 YLFLIMNQLRKEGTAIVYISHKLAEIRRICDRYTVMKDGSSVCSGIVSDVSNDDIVRLMV 242 Query: 239 GRKLEKFY--IKE--AHEPGEVVLEVKNLSG---ERFENVSFSLRRGEILGFAGLVGAGR 291 GR+L+ + +KE ++ E V EV+N++ ++ ++SFS+ RGEILGFAGLVG+GR Sbjct: 243 GRELQNRFNAMKENVSNLAHETVFEVRNVTSRDRKKVRDISFSVCRGEILGFAGLVGSGR 302 Query: 292 TELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNV 351 TELM +FG + GGEI + GK + PLDA+++G+ + E R+ G SI N+ Sbjct: 303 TELMNCLFGVDKRAGGEIRLNGKDISPRSPLDAVKKGMAYITESRRDNGFFPNFSIAQNM 362 Query: 352 SLPSL--DRIKKGPFISFKR--EKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAK 407 ++ D KG F E+ A+ + ++ ++ + LSGGNQQKV+++K Sbjct: 363 AISRSLKDGGYKGAMGLFHEVDEQRTAENQRELLALKCHSVNQNITELSGGNQQKVLISK 422 Query: 408 WLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVM 467 WL P+++I DEPTRGIDVGAKAEIY++M QLA +G ++M+SSELPE++ + DRIAV Sbjct: 423 WLCCCPEVIIFDEPTRGIDVGAKAEIYKVMRQLADDGKVILMVSSELPEIITVCDRIAVF 482 Query: 468 SFGKLAGII-DAKEASQEKVMKLA 490 G+L I+ + + S+E++M A Sbjct: 483 CEGRLTQILTNRDDMSEEEIMAWA 506 Score = 78.2 bits (191), Expect = 6e-19 Identities = 64/231 (27%), Positives = 119/231 (51%), Gaps = 12/231 (5%) Query: 269 ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRV-EINHPLDAIEQ 327 ++V+ ++ GEI G GAG++ LM+ + G G I I +++H L A + Sbjct: 22 KSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPTKGTITINNISYNKLDHKL-AAQL 80 Query: 328 GIGLVPEDRKKLGLILIMSIMHNVSLPS--LDRIKKGPFISFKREKELADWAIKTFDIRP 385 GIG++ ++ L +I ++++ N+ + +I I ++ + A + ++ Sbjct: 81 GIGIIYQE---LSVIDELTVLENLYIGRHLTKKICGVNIIDWREMRVRAAMMLLRVGLKV 137 Query: 386 AYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGV 445 D KV LS ++Q + +AK L L K++I+DEPT + ++ IM+QL KEG Sbjct: 138 DL-DEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTNKEVDYLFLIMNQLRKEGT 196 Query: 446 GVIMISSELPEVLQMSDRIAVMSFGK--LAGIIDAKEASQEKVMKLAAGLE 494 ++ IS +L E+ ++ DR VM G +GI+ + S + +++L G E Sbjct: 197 AIVYISHKLAEIRRICDRYTVMKDGSSVCSGIV--SDVSNDDIVRLMVGRE 245 Lambda K H 0.318 0.138 0.385 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: 722 Number of extensions: 28 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 494 Length of database: 510 Length adjustment: 34 Effective length of query: 460 Effective length of database: 476 Effective search space: 218960 Effective search space used: 218960 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 (21.7 bits) S2: 52 (24.6 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