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 AO356_00965 AO356_00965 sugar ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_00965 Length = 517 Score = 343 bits (879), Expect = 1e-98 Identities = 190/474 (40%), Positives = 288/474 (60%), Gaps = 3/474 (0%) Query: 20 LKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINA 79 L +++ GEV A+ GENGAGKSTL KII G+ P G++ ++G+ R ++A Sbjct: 24 LTDINLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGQDYRPGSRTQAEEL 83 Query: 80 GIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFMKEEFGIEIDPEEKL 139 G+ V QEL+++ LSVAEN+F+ + G +I K++ + A + M + IDP+ + Sbjct: 84 GVRMVMQELNLLPTLSVAENLFLDNLPSHGGWISRKQLRKAAIEAMAQVGLDAIDPDTLV 143 Query: 140 GKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAIIFISH 199 G+ I QQMVEIAR + VLILDEPT+ LT +E E LFE + L+ +GVAII+ISH Sbjct: 144 GELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVAIIYISH 203 Query: 200 RLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEKFYIKEAHEPGEVVLE 259 RLEE+ + +++VLRDG + + + N E++V +MVGR+L + + G L Sbjct: 204 RLEELARVAQRIAVLRDGNLVCVEPMANYDSEQLVTLMVGRELGEHIDLGPRQIGAPALT 263 Query: 260 VKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYI--EGKRV 316 VK L+ ++ +VSF +R GEI G +GL+GAGRTEL+ IFG P G + + + V Sbjct: 264 VKGLTRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGADPADSGTVALGSPARVV 323 Query: 317 EINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADW 376 I P DA+ GI L+ EDRK GL+L SI N++L ++ I ++ E LA Sbjct: 324 SIRSPSDAVAHGIALITEDRKGEGLLLTQSIAANIALGNMPEISSAGLVNGSAELALAQR 383 Query: 377 AIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRI 436 + IR + P + V LSGGNQQKVV+ +WL +++ DEPTRGIDVGAK +IY + Sbjct: 384 QVDAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCAVMLFDEPTRGIDVGAKFDIYAL 443 Query: 437 MSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLA 490 + +L ++G ++++SS+L E++ + DRI V+S G+L + +Q+ ++ A Sbjct: 444 LGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDLLAAA 497 Score = 86.7 bits (213), Expect = 2e-21 Identities = 65/225 (28%), Positives = 112/225 (49%), Gaps = 5/225 (2%) Query: 270 NVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGI 329 +++ +L RGE+L G GAG++ L + I G G++ +G+ A E G+ Sbjct: 26 DINLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGQDYRPGSRTQAEELGV 85 Query: 330 GLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPD 389 +V ++ L L+ +S+ N+ L +L G +IS K+ ++ A A+ + PD Sbjct: 86 RMVMQE---LNLLPTLSVAENLFLDNLP--SHGGWISRKQLRKAAIEAMAQVGLDAIDPD 140 Query: 390 RKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIM 449 V L G+QQ V +A+ L +LILDEPT + ++ +++L GV +I Sbjct: 141 TLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVAIIY 200 Query: 450 ISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494 IS L E+ +++ RIAV+ G L + E+++ L G E Sbjct: 201 ISHRLEELARVAQRIAVLRDGNLVCVEPMANYDSEQLVTLMVGRE 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: 584 Number of extensions: 29 Number of successful extensions: 7 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: 517 Length adjustment: 34 Effective length of query: 460 Effective length of database: 483 Effective search space: 222180 Effective search space used: 222180 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