Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1); The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli, and has a variety of functions such as its involvement in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. Spt5-like is homologous to the Spt5 proteins present in all eukaryotes, which is unique as it encodes a protein with an additional long carboxy-terminal extension that contains WG/GW motifs. Spt5-like, or KTF1 (KOW domain-containing Transcription Factor 1), is a RNA-directed DNA methylation (RdDM) pathway effector in plants.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653  194 NLWMVKCKMGEEKATAVTLMRKFIAYQVQDEPLQIKSVIAVEGLKGYIYVESYKQTHVKHAIEGIGNLRlgLWTQQMVPI 273
Cdd:cd09888     1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVY--LNTIKLVPI 78

                  ....*...
gi 291241653  274 KEMPDVLK 281
Cdd:cd09888    79 KEMPDVLS 86

KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 291241653 1033 DHLEPVMPSKQDKVKVILGEDRESTGTLINIDGQDGIVKMDqavgSDVQLKILHLGHLGKFV 1094
Cdd:cd06086     1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMD----SDGDIKILPMNFLAKLV 58

KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 291241653  438 LAPGDSVEVIEGELVHLQGKIIGVDGDKITIMPKHEDLKEPLDFPARELRK 488
Cdd:cd06082     1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653    784 PGQTPMY---GSRTPMYGSQTP----LHDGSRTPHYGSQTPLHDG--SRTPGQtGAWDPTNRNTPARtdefdyrfdeptp 854
Cdd:smart01104    1 GGRTPAWgasGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAW-GGAGPTGSRTPAW------------- 66

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 291241653    855 SPAYGGTPNPATPGYSADTPPSNGPYTPATPGSSTMYSSsdhtYSPyqhsstPSPGGYQGTPSPA 919
Cdd:smart01104   67 GGASAWGNKSSEGSASSWAAGPGGAYGAPTPGYGGTPSA----YGP------ATPGGGAMAGSAS 121

Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653    95 FILDEADVDDDYDDAVEEEEVEEGFQDLIDRNATTGDVEGDSHGAR------RLHQMWREQKEDEIEEYYKRKYADTTSg 168
Cdd:pfam11942    1 FIDDEAEVDDDEEEEEDEDEDEDGADDFIEDDEEDEDEEDGRRDDRrhreldRRRELEEDEDAEEIAEYLKERYGRSSS- 79

                           90       100
                   ....*....|....*....|
gi 291241653   169 GRYDSnyEMSDDITQQGLLP 188
Cdd:pfam11942   80 DAYRG--DAEEGVPQRLLLP 97

Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1); The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli, and has a variety of functions such as its involvement in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. Spt5-like is homologous to the Spt5 proteins present in all eukaryotes, which is unique as it encodes a protein with an additional long carboxy-terminal extension that contains WG/GW motifs. Spt5-like, or KTF1 (KOW domain-containing Transcription Factor 1), is a RNA-directed DNA methylation (RdDM) pathway effector in plants.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653  194 NLWMVKCKMGEEKATAVTLMRKFIAYQVQDEPLQIKSVIAVEGLKGYIYVESYKQTHVKHAIEGIGNLRlgLWTQQMVPI 273
Cdd:cd09888     1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVY--LNTIKLVPI 78

                  ....*...
gi 291241653  274 KEMPDVLK 281
Cdd:cd09888    79 KEMPDVLS 86

KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 291241653  489 HFRMGDHVKVIGGRYEGDTGLIVRVEDNMVILFSDLTMHELKVLPRDLQLC 539
Cdd:cd06083     1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51

KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 291241653  714 DMELIGQTVRIREGPFKGYIGIVKDATESTARVELHTNCKTISVDKNRLNP 764
Cdd:cd06085     2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLAV 52

KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 291241653  615 KDIVKVIDGPHSGRQGEVKHIYRSFAFLHSRLMTENGGIFVCR 657
Cdd:cd06084     1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43

KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 291241653  292 KSWVRLKRGVFKDDLAQVDYVEPAQNQVTLKLVPRVDY 329
Cdd:cd06081     1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteriztic TPA motif.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291241653   785 GQTPMY----GSRTPMY---GSQTPLHD--GSRTPHY--GSQTPLHD--GSRTPGQTGAWDPTnrNTPA 840
Cdd:pfam12815    2 SRTPAYnsagGSRTPAWgadGSRTPAYGgaGGRTPAYnqGGKTPAWGgaGSRTPAYYGAWGGS--RTPA 68

transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial NusG and the uL24 (previously L24p/L26e) family of ribosomal proteins. The most recent papers and crystal structures make this a transcription elongation factor rather than a ribosomal protein.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653   198 VKCKMGEEKATAVTLMRKfiayqVQDEPLQIKSVIAVEGLKGYIYVESYKQTHVKHAIEGIGNLRlGLwTQQMVPIKEMP 277
Cdd:TIGR00405    3 VKTSVGQEKNVARLMARK-----ARKSGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVR-GV-VEGEIDFEEIE 75

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 291241653   278 DVLKVVKEVVTLKPKSWVRLKRGVFKDDLAQVDYVEPAQNQVTLKLV 324
Cdd:TIGR00405   76 RFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELI 122

Transcription elongation factor SPT5 [Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653  768 PTSRGSTTSYRHT----PlhPGQTpmyGSRTPM--YGSQTPLHDGSRTPHYGSQT----PLHDGSRTPGQTGAWDPTNRN 837
Cdd:COG5164    21 AGSQGSTKPAQNQgstrP--AGNT---GGTRPAqnQGSTTPAGNTGGTRPAGNQGatgpAQNQGGTTPAQNQGGTRPAGN 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653  838 TPARTDEFDYRFDEPtpsPAYGGTPNPATPGYSAdTPPSNGPYTPATPGSSTmysssdhtysPYQHSSTpSPGGYQGTPS 917
Cdd:COG5164    96 TGGTTPAGDGGATGP---PDDGGATGPPDDGGST-TPPSGGSTTPPGDGGST----------PPGPGST-GPGGSTTPPG 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 291241653  918 PANYQPAPSPGGYQPTPSPAYQQSPSPGGYQLTPSPGGypmtpGAPSPGGFNPLTPGASLDSG 980
Cdd:COG5164   161 DGGSTTPPGPGGSTTPPDDGGSTTPPNKGETGTDIPTG-----GTPRQGPDGPVKKDDKNGKG 218

N-terminal domain of Kruppel-like factor (KLF) 1, KLF2, KLF4, and similar proteins; Kruppel/Krueppel-like transcription factors (KLFs) belong to a family of proteins called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specifity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the related N-terminal domains of KLF1, KLF2, KLF4, and similar proteins.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653  852 PTPSPAYG--GTPNPATPGYSADTPPSNGPYTPATPGSSTM------YSSSDHTYSPYQ-------HSSTPSPGGYqGTP 916
Cdd:cd21972    40 PPPDPAYPppESPESCSTVYDSDGCHPTPNAYCGPNGPGLPghfllaGNSPNLGPKIKTenqeqacMPVAGYSGHY-GPR 118

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 291241653  917 SPANYQPAPSPGGYQPTPSP-AYQQSPSPGGYQLTPSPGGYPMTP-GAPSPGGFNPLTP 973
Cdd:cd21972   119 EPQRVPPAPPPPQYAGHFQYhGHFNMFSPPLRANHPGMSTVMLTPlSTPPLGFLSPEEA 177

KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG.

                           10        20        30
                   ....*....|....*....|....*....|..
gi 291241653   718 IGQTVRIREGPFKGYIGIVKDATESTARVELH 749
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32

Domain of unknown function (DUF4813); This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 345 and 672 amino acids in length.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653   919 ANYQPAPS---PGGYQPTPSPAYQQSPSPGGYQLTPS---PGG---YPMTPGAPSPGGFNPLTPGASLDSGSSEWQtihi 989
Cdd:pfam16072    2 ATYHPAGAtyhPGGYAPAGATYHPAGQVPAGATYYPSggvPHGatyYPQAPVAAVPAGATYLPAGAAIPAGATYYP---- 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 291241653   990 evkvKATHEDSALIYKIGVIRGISGG--MCSVFIPDEGRVV 1028
Cdd:pfam16072   78 ----QAPKSSSGLGLGTGLIAGALGGaiLGHALTPTQTRVV 114

KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.

                            10        20
                    ....*....|....*....|....*..
gi 291241653    611 NIQVKDIVKVIDGPHSGRQGEVKHIYR 637
Cdd:smart00739    1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653    854 PSPAYGGTP------NPATPgYSADTPPSNG----PYTPATPGSSTMYSSSDHTYSPYQHSSTPSPGGYQGTPSPANYQP 923
Cdd:smart00818   22 PYPSYGYEPmggwlhHQIIP-VSQQHPPTHTlqphHHIPVLPAQQPVVPQQPLMPVPGQHSMTPTQHHQPNLPQPAQQPF 100

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 291241653    924 APSPGGYQPTPSPAYQQSPSPGGYQLTPSPGGYPMTPGAPSPggfnPLTPGASLDSgsseWQ 985
Cdd:smart00818  101 QPQPLQPPQPQQPMQPQPPVHPIPPLPPQPPLPPMFPMQPLP----PLLPDLPLEA----WP 154

Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1); The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli, and has a variety of functions such as its involvement in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. Spt5-like is homologous to the Spt5 proteins present in all eukaryotes, which is unique as it encodes a protein with an additional long carboxy-terminal extension that contains WG/GW motifs. Spt5-like, or KTF1 (KOW domain-containing Transcription Factor 1), is a RNA-directed DNA methylation (RdDM) pathway effector in plants.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653  194 NLWMVKCKMGEEKATAVTLMRKFIAYQVQDEPLQIKSVIAVEGLKGYIYVESYKQTHVKHAIEGIGNLRlgLWTQQMVPI 273
Cdd:cd09888     1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVY--LNTIKLVPI 78

                  ....*...
gi 291241653  274 KEMPDVLK 281
Cdd:cd09888    79 KEMPDVLS 86

KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 291241653  489 HFRMGDHVKVIGGRYEGDTGLIVRVEDNMVILFSDLTMHELKVLPRDLQLC 539
Cdd:cd06083     1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51

KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 291241653  714 DMELIGQTVRIREGPFKGYIGIVKDATESTARVELHTNCKTISVDKNRLNP 764
Cdd:cd06085     2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLAV 52

KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 291241653  615 KDIVKVIDGPHSGRQGEVKHIYRSFAFLHSRLMTENGGIFVCR 657
Cdd:cd06084     1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43

KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 291241653  292 KSWVRLKRGVFKDDLAQVDYVEPAQNQVTLKLVPRVDY 329
Cdd:cd06081     1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteriztic TPA motif.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 291241653   785 GQTPMY----GSRTPMY---GSQTPLHD--GSRTPHY--GSQTPLHD--GSRTPGQTGAWDPTnrNTPA 840
Cdd:pfam12815    2 SRTPAYnsagGSRTPAWgadGSRTPAYGgaGGRTPAYnqGGKTPAWGgaGSRTPAYYGAWGGS--RTPA 68

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653    791 GSRTPMYGSqtplhDGSRTPHYGSQTPlhdgsrtpgqtgawdptnrntpartdefdyrfdeptpspAYGGTPNPATPGYS 870
Cdd:smart01104    1 GGRTPAWGA-----SGSKTPAWGSRTP---------------------------------------GTAAGGAPTARGGS 36

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653    871 ADTPPSNGPYTPATPGSSTMYSSSDHTySPYQHSSTPSPGGYQGTPSPANYQPAPSPGGyqptPSPAYQQSPSPGGYqlt 950
Cdd:smart01104   37 GSRTPAWGGAGSRTPAWGGAGPTGSRT-PAWGGASAWGNKSSEGSASSWAAGPGGAYGA----PTPGYGGTPSAYGP--- 108

                           170
                    ....*....|...
gi 291241653    951 PSPGGYPMTPGAP 963
Cdd:smart01104  109 ATPGGGAMAGSAS 121

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteriztic TPA motif.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653   791 GSRTPMYGSqtplHDGSRTPHY---GSQTPLHD--GSRTP-----GQTGAWDPTNRNTPARTDEFDyrfDEPTpsPAYGG 860
Cdd:pfam12815    1 GSRTPAYNS----AGGSRTPAWgadGSRTPAYGgaGGRTPaynqgGKTPAWGGAGSRTPAYYGAWG---GSRT--PAYGG 71

EBNA-3B; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653  725 REGP--FKGYIGIVKDATESTARVeLHTNCKTISVDKNRLNPVNQPTS---RGSTTSYRHTP---LHPGQTPmygsRTPM 796
Cdd:PHA03378  536 RRAPcvYTEDLDIESDEPASTEPV-HDQLLPAPGLGPLQIQPLTSPTTsqlASSAPSYAQTPwpvPHPSQTP----EPPT 610

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653  797 YGSQTP-LHDGSRTPHYGSQTPLHDGSRTPGqtgAWDPTNRNTPARTDEFDYRFDEPTPSPAYGGTPNPATPGYSADTPP 875
Cdd:PHA03378  611 TQSHIPeTSAPRQWPMPLRPIPMRPLRMQPI---TFNVLVFPTPHQPPQVEITPYKPTWTQIGHIPYQPSPTGANTMLPI 687

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653  876 SNGPYT----PATPGSSTMYSSSDHTYSPYQHSSTPSPGGyQGTPSPANyQPAPSPGGYQPTPSPAYQQSPSPGGYQLTP 951
Cdd:PHA03378  688 QWAPGTmqppPRAPTPMRPPAAPPGRAQRPAAATGRARPP-AAAPGRAR-PPAAAPGRARPPAAAPGRARPPAAAPGRAR 765

                         250
                  ....*....|....
gi 291241653  952 SPGGypmTPGAPSP 965
Cdd:PHA03378  766 PPAA---APGAPTP 776

N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization Substance G (NusG) and its eukaryotic homolog Spt5 are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus in bacteria and archaea. The eukaryotic ortholog, Spt5, is a large protein composed of an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. Spt5 forms a Spt4-Spt5 complex that is an essential RNA Polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli and has a variety of functions, such as being involved in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but its functions and requirements are different. The diverse activities suggest that, after diverging from a common ancestor, NusG proteins became specialized in different bacteria.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653  194 NLWMVKCKMGEEKATAVTLMRKFIA---------YQVQDEPLQIKSVIAVEGLKGYIYVESYKQTHVKHAIEGIGNLRLG 264
Cdd:cd08000     1 NWYVLFVKTGREEKVEKLLEKRFEAndieafvpkKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPGVIGI 80

                          90
                  ....*....|....*....
gi 291241653  265 LW---TQQMVPIKEMPDVL 280
Cdd:cd08000    81 LGngeEPSPVSDEEIEMIL 99

Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. Transcription in archaea has a eukaryotic-type transcription apparatus, but contains bacterial-type transcription factors. NusG is one of the few archaeal transcription factors that has orthologs in both bacteria and eukaryotes. Archaeal NusG is similar to bacterial NusG, composed of an NGN domain and a Kyrpides Ouzounis and Woese (KOW) repeat. The eukaryotic ortholog, Spt5, is a large protein composed of an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. NusG was originally discovered as a N-dependent antitermination enhancing activity in Escherichia coli and has a variety of functions, such as being involved in RNA polymerase elongation and Rho-termination in bacteria. Archaeal NusG forms a complex with DNA-directed RNA polymerase subunit E (rpoE) that is similar to the Spt5-Spt4 complex in eukaryotes.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 291241653  195 LWMVKCKMGEEKATAVTLMRKfiayqVQDEPLQIKSVIAVEGLKGYIYVESYKQTHVKHAIEGIGNLR 262
Cdd:cd09887     2 IYAVKTTAGQERNVADLLAMR-----AEKENLDVYSILVPEELKGYVFVEAEDPDRVEELIRGIPHVR 64

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653   779 HTPlHPGQTPMYGSRTPMYGSQTPLHDGSRTPHYGSQTPLHDGSRTPGQTGawDPTnRNTPARTDEFDYRFDEPTPSPAY 858
Cdd:pfam03154  288 HMQ-HPVPPQPFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPSQSQLQSQ--QPP-REQPLPPAPLSMPHIKPPPTTPI 363

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653   859 GGTPNPAT----PGYSADTP---PSNGPYTPATPGSSTMysSSDHTYSPYQHSSTPSPGGYQGTPSPAnyQPapsPGGYQ 931
Cdd:pfam03154  364 PQLPNPQShkhpPHLSGPSPfqmNSNLPPPPALKPLSSL--STHHPPSAHPPPLQLMPQSQQLPPPPA--QP---PVLTQ 436

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 291241653   932 -PTPSPAYQQSPSPGGYQLTPSPGGYPMTPGAP--SPGGFNPLTPGASLDSGSSEWQ 985
Cdd:pfam03154  437 sQSLPPPAASHPPTSGLHQVPSQSPFPQHPFVPggPPPITPPSGPPTSTSSAMPGIQ 493

Chitinase [Carbohydrate transport and metabolism];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653  809 TPHYGSQTPLHDGSRTPGQTGAWDPTNRNTPARTDEFDYRfdePTPSPAYGGTPNPATPGYSADTPPSNGPYTPATPGSS 888
Cdd:COG3469    57 AGSGTGTTAASSTAATSSTTSTTATATAAAAAATSTSATL---VATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGST 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 291241653  889 TMYSSSDHTYSPYqHSSTPSPGGYQGTPSPANYQPAPSPGGYQPTPSPAYQQSPSPGGYQLTPSPggyPMTPGAPSPGGF 968
Cdd:COG3469   134 TTSGASATSSAGS-TTTTTTVSGTETATGGTTTTSTTTTTTSASTTPSATTTATATTASGATTPS---ATTTATTTGPPT 209

                  ....
gi 291241653  969 NPLT 972
Cdd:COG3469   210 PGLP 213