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 WP_092484692.1 BM299_RS12340 ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >NCBI__GCF_900115975.1:WP_092484692.1 Length = 509 Score = 339 bits (869), Expect = 2e-97 Identities = 177/497 (35%), Positives = 306/497 (61%), Gaps = 10/497 (2%) Query: 4 ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63 ++E+K+I KRFPGV A V+ GE+H ++GENG+GKSTLM ++AG+Y+PDEGEII Sbjct: 6 LIELKNITKRFPGVIANDKVNFNVKQGEIHVLLGENGSGKSTLMSVLAGLYRPDEGEIIV 65 Query: 64 EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEK 123 G + + P +AI+AG+ V Q ++D+ SVAEN+ +GD + ++ K + + Sbjct: 66 RGTQMVFRSPGDAISAGVGMVHQHFKLIDSFSVAENVILGDHNVAPV-LNMKDIENNLAQ 124 Query: 124 FMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEV 183 + + +G+ IDP ++ + S+ +Q VEI + +Y+ ++VLILDEPT+ LT +ET +LF+ Sbjct: 125 -LSQRYGLHIDPSARVWQLSVGEKQRVEIVKMLYRGSRVLILDEPTAVLTPQETAELFKN 183 Query: 184 VKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLE 243 ++ + G ++ I+H+++E+ EI D+V+VLR G+ + T + + + + +MVG+ + Sbjct: 184 LREMARSGRGVVVITHKMQEVMEIADRVTVLRKGKAVATLEKKQINRRDLAWLMVGQDVV 243 Query: 244 KFYIKEAHEPGEVVLEVK------NLSGERFENVSFSLRRGEILGFAGLVGAGRTELMET 297 + Y K++ VLE++ +L +NV+F++ GEI G AG+ G G+ EL E Sbjct: 244 RQYKKKSPPGEHKVLELQGVHCMNDLGRPCLQNVTFTVHSGEIFGIAGVAGNGQRELAEV 303 Query: 298 IFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPS-- 355 + G RP GG IYI+G + P I+ G+ LVPEDR GL+ + + N+ L Sbjct: 304 VSGLRPVTGGSIYIKGNEITGGSPRRIIDHGVALVPEDRLGTGLVPNLGAVDNLILKDYR 363 Query: 356 LDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKI 415 ++++GPF++ ++ +E + F+I+ + D V LSGGN Q+++LA+ + +P + Sbjct: 364 TGKLQRGPFLNLRQARENTKNLVNRFEIKLSSLDAPVKLLSGGNLQRLLLAREITAEPHL 423 Query: 416 LILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGI 475 L+ P RG+D+ A I+ ++ Q ++G+ +++IS +L E+ ++SDRI V+ G++ GI Sbjct: 424 LVAVYPVRGLDIKATEAIHNLLLQQREKGMAILLISEDLDEIFKLSDRIGVLCNGQITGI 483 Query: 476 IDAKEASQEKVMKLAAG 492 I A+ E+V L G Sbjct: 484 IPAEMTDIEEVGLLMMG 500 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: 669 Number of extensions: 37 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: 509 Length adjustment: 34 Effective length of query: 460 Effective length of database: 475 Effective search space: 218500 Effective search space used: 218500 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 Apr 09 2024. 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