Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217368995  898 MRRTPIGTDRNHNRYWLFSDEVPGLFIEKGWvhdsidyrfnhhckdhtvsgdedycprskkanlgknasmntqhgtatev 977
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFDPGTGRLFVESPS------------------------------------------------- 31

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 2217368995  978 avetttpkqgQNLWFLCDSQKELDELLNCLHPQGIRESQLKERLEKRF 1025
Cdd:pfam15613   32 ----------DGEWGVYSSKEQLDALIASLNPRGVRESALKEALEKIK 69

WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2217368995  727 EFLEKLETSEFFELTSEEKLQILTALCHRILMTYSVQDHME 767
Cdd:pfam15612    6 GLLETLKKGGYYELSPEEKLKILKALCDLLLSSSAIRDEIE 46

Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217368995  898 MRRTPIGTDRNHNRYWLFSDEVPGLFIEKGWvhdsidyrfnhhckdhtvsgdedycprskkanlgknasmntqhgtatev 977
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFDPGTGRLFVESPS------------------------------------------------- 31

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 2217368995  978 avetttpkqgQNLWFLCDSQKELDELLNCLHPQGIRESQLKERLEKRF 1025
Cdd:pfam15613   32 ----------DGEWGVYSSKEQLDALIASLNPRGVRESALKEALEKIK 69

WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2217368995  727 EFLEKLETSEFFELTSEEKLQILTALCHRILMTYSVQDHME 767
Cdd:pfam15612    6 GLLETLKKGGYYELSPEEKLKILKALCDLLLSSSAIRDEIE 46

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217368995  785 KEENDKKRAEKQKRKEMEAKNKEngkvENGLGKTDRKKEIVKFEPQVDTEAEDMISAVK-----SRRLLAIQAKKEREIQ 859
Cdd:TIGR02794   65 KEQERQKKLEQQAEEAEKQRAAE----QARQKELEQRAAAEKAAKQAEQAAKQAEEKQKqaeeaKAKQAAEAKAKAEAEA 140

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 2217368995  860 EREMKVKLERQAEEERIRKHKAAAEKAFQEGIAKAK 895
Cdd:TIGR02794  141 ERKAKEEAAKQAEEEAKAKAAAEAKKKAEEAKKKAE 176

Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217368995  898 MRRTPIGTDRNHNRYWLFSDEVPGLFIEKGWvhdsidyrfnhhckdhtvsgdedycprskkanlgknasmntqhgtatev 977
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFDPGTGRLFVESPS------------------------------------------------- 31

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 2217368995  978 avetttpkqgQNLWFLCDSQKELDELLNCLHPQGIRESQLKERLEKRF 1025
Cdd:pfam15613   32 ----------DGEWGVYSSKEQLDALIASLNPRGVRESALKEALEKIK 69

WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2217368995  727 EFLEKLETSEFFELTSEEKLQILTALCHRILMTYSVQDHME 767
Cdd:pfam15612    6 GLLETLKKGGYYELSPEEKLKILKALCDLLLSSSAIRDEIE 46

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217368995  785 KEENDKKRAEKQKRKEMEAKNKEngkvENGLGKTDRKKEIVKFEPQVDTEAEDMISAVK-----SRRLLAIQAKKEREIQ 859
Cdd:TIGR02794   65 KEQERQKKLEQQAEEAEKQRAAE----QARQKELEQRAAAEKAAKQAEQAAKQAEEKQKqaeeaKAKQAAEAKAKAEAEA 140

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 2217368995  860 EREMKVKLERQAEEERIRKHKAAAEKAFQEGIAKAK 895
Cdd:TIGR02794  141 ERKAKEEAAKQAEEEAKAKAAAEAKKKAEEAKKKAE 176

MAEBL; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217368995  785 KEENDKKRAEKQKRKEMEAKNKEngkvENGLGKTDRKK---EIVKFEPQVDTEAEDMISAVKSRRLLAIQAKKEREIQER 861
Cdd:PTZ00121  1669 KAEEDKKKAEEAKKAEEDEKKAA----EALKKEAEEAKkaeELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKK 1744

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 2217368995  862 EMKVKLERQAEEERIRKHKAAAEKAFQEGIAKAKLVMR 899
Cdd:PTZ00121  1745 KAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIE 1782