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 SMc02325 SMc02325 ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Smeli:SMc02325 Length = 503 Score = 415 bits (1067), Expect = e-120 Identities = 225/499 (45%), Positives = 323/499 (64%), Gaps = 9/499 (1%) Query: 1 MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60 MKP + ++ I K FPGV AL VS+ YPG V A+VGENGAGKSTL+KI+ G+YQPD G Sbjct: 1 MKPAIALEGISKSFPGVRALSDVSLALYPGSVTALVGENGAGKSTLVKILTGIYQPDAGT 60 Query: 61 IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI-FIDYKKMYR 119 I + A AG+ + QE + D LSVAENIF+G + ID+K++ Sbjct: 61 IRLGDTETTFPTALAASRAGVTAIHQETVLFDELSVAENIFLGHAPRNRFGLIDWKQLNA 120 Query: 120 EAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEK 179 +A+ + G + DP +L IA + +V IARA+ A+V+I+DEPT++L+ KE + Sbjct: 121 DAQALLGRA-GADFDPTIRLRDLGIAKKHLVAIARALSVDARVVIMDEPTAALSHKEIHE 179 Query: 180 LFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVG 239 L+++++ LK G A++FISH+ +EIF I D+ +V RDG IG I +++++ +V MMVG Sbjct: 180 LYDLIERLKADGKAVLFISHKFDEIFRIADRYTVFRDGAMIGEGLIADVSQDDLVRMMVG 239 Query: 240 RKLEKFYIKEAHEPGEVVLEVKNLSGER----FENVSFSLRRGEILGFAGLVGAGRTELM 295 R + Y K+ G+ VL V SG R FE+++F LRRGEILGF GLVGAGR+E M Sbjct: 240 RAVGSVYPKKEVTIGQPVLTV---SGYRHPTEFEDINFELRRGEILGFYGLVGAGRSEFM 296 Query: 296 ETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPS 355 +++ G G + ++G+ + I P +AI GI VPE+R + G I+ M I NV+LPS Sbjct: 297 QSLIGITRPSAGAVKLDGEVLVIRSPAEAIRAGIVYVPEERGRQGAIIGMPIFQNVTLPS 356 Query: 356 LDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKI 415 L + F+ E LA D+R A D+ V LSGGNQQKVV+AKWLA +PK+ Sbjct: 357 LSHTSRSGFLRLAEEFALAREYTSRLDLRAAALDQDVGTLSGGNQQKVVIAKWLATRPKV 416 Query: 416 LILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGI 475 +ILDEPT+GID+G+KA ++ MS+LA +G+ VIM+SSE+PE++ MSDR+ VM G++AG Sbjct: 417 IILDEPTKGIDIGSKAAVHAFMSELAAQGLSVIMVSSEIPEIMGMSDRVIVMREGRVAGR 476 Query: 476 IDAKEASQEKVMKLAAGLE 494 + E + EK+++ AAG+E Sbjct: 477 YERSELTAEKLVRAAAGIE 495 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: 657 Number of extensions: 27 Number of successful extensions: 7 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: 494 Length of database: 503 Length adjustment: 34 Effective length of query: 460 Effective length of database: 469 Effective search space: 215740 Effective search space used: 215740 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