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Conserved domains on  [gi|22094123|ref|NP_038704|]
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transcription elongation factor SPT5 isoform a [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 176-263 4.31e-44

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.


:

Pssm-ID: 193577 [Multi-domain]  Cd Length: 86  Bit Score: 154.23  E-value: 4.31e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  176 NLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLgyWNQQMVPI 255
Cdd:cd09888    1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYL--NTIKLVPI 78


                 ....*...
gi 22094123  256 KEMTDVLK 263
Cdd:cd09888   79 KEMPDVLS 86
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 766-883 4.65e-29

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.


:

Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 112.62  E-value: 4.65e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123     766 GSQTPMYG-SGSRTPMYGSQTP----LQDGSRTPHYGSQTPLHDG--SRTPAQSGAWdPNNPNTPSRAEEEYEYAFDDEP 838
Cdd:smart01104    1 GGRTPAWGaSGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAWGGAG-PTGSRTPAWGGASAWGNKSSEG 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 22094123     839 TPSPQA--YGGTPNPQTPGYpdpssPQVNPQYNPQTPGTPAMYNTDQ 883
Cdd:smart01104   80 SASSWAagPGGAYGAPTPGY-----GGTPSAYGPATPGGGAMAGSAS 121
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 469-519 7.27e-28

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.


:

Pssm-ID: 240507  Cd Length: 51  Bit Score: 106.46  E-value: 7.27e-28
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 22094123  469 YFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLC 519
Cdd:cd06083    1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 418-468 6.17e-26

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.


:

Pssm-ID: 240506  Cd Length: 51  Bit Score: 101.04  E-value: 6.17e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 22094123  418 FQPGDNVEVCEGELINLQGKVLSVDGNKITIMPKHEDLKDMLEFPAQELRK 468
Cdd:cd06082    1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 696-745 4.70e-25

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.


:

Pssm-ID: 240509  Cd Length: 52  Bit Score: 98.71  E-value: 4.70e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 22094123  696 DNELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLT 745
Cdd:cd06085    2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLA 51
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1022-1079 1.58e-24

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.


:

Pssm-ID: 240510  Cd Length: 58  Bit Score: 97.20  E-value: 1.58e-24
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 22094123 1022 EHLEPITPTKNNKVKVILGEDREATGVLLSIDGEDGIIRMDlEDQQIKILNLRFLGKL 1079
Cdd:cd06086    1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMD-SDGDIKILPMNFLAKL 57
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 595-637 6.68e-20

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.


:

Pssm-ID: 240508  Cd Length: 43  Bit Score: 83.72  E-value: 6.68e-20
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 22094123  595 KDIVKVIDGPHSGREGEIRHLYRSFAFLHCKKLVENGGMFVCK 637
Cdd:cd06084    1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 274-311 1.56e-17

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.


:

Pssm-ID: 240505  Cd Length: 38  Bit Score: 76.74  E-value: 1.56e-17
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 22094123  274 KSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMIPRIDY 311
Cdd:cd06081    1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 91-170 6.78e-12

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.


:

Pssm-ID: 463406  Cd Length: 97  Bit Score: 62.67  E-value: 6.78e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123     91 EDGAEDILEKEEIEASNIDNVVLDEDRSGARRLQNLWRDQREEELGEYYMKKYAKSSvgETVYGGSDElsDDITQQQLLP 170
Cdd:pfam11942   22 EDGADDFIEDDEEDEDEEDGRRDDRRHRELDRRRELEEDEDAEEIAEYLKERYGRSS--SDAYRGDAE--EGVPQRLLLP 97
PHA03269 super family cl29788
envelope glycoprotein C; Provisional
 819-964 3.98e-09

envelope glycoprotein C; Provisional


The actual alignment was detected with superfamily member PHA03269:

Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 60.51  E-value: 3.98e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   819 NPNTPSRAEEEYEYAFDDEPTPSPQayggtPNPQTPGYPDPS-SPQVNPQYNPQtpgtpamyntdqfsPYAAPSPQGSYQ 897
Cdd:PHA03269   21 NLNTNIPIPELHTSAATQKPDPAPA-----PHQAASRAPDPAvAPTSAASRKPD--------------LAQAPTPAASEK 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 22094123   898 PSPSPQSYHQV--APSPAGYQNTHSPasyhPTPSPM-----AYQASPSPSPVGYSPMTPgAPSPGGYNPHTPGS 964
Cdd:PHA03269   82 FDPAPAPHQAAsrAPDPAVAPQLAAA----PKPDAAeaftsAAQAHEAPADAGTSAASK-KPDPAAHTQHSPPP 150
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 176-263 4.31e-44

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.


Pssm-ID: 193577 [Multi-domain]  Cd Length: 86  Bit Score: 154.23  E-value: 4.31e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  176 NLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLgyWNQQMVPI 255
Cdd:cd09888    1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYL--NTIKLVPI 78


                 ....*...
gi 22094123  256 KEMTDVLK 263
Cdd:cd09888   79 KEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 176-262 6.62e-31

Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this 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 Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit.


Pssm-ID: 397481  Cd Length: 84  Bit Score: 116.53  E-value: 6.62e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    176 NLWTVKCKIGEERATAISLMRKFIAYQfTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLGywNQQMVPI 255
Cdd:pfam03439    1 KIWAVKCTPGQEREVALSLMRKILALA-KTNNLGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGL--VPGLVPI 77


                   ....*..
gi 22094123    256 KEMTDVL 262
Cdd:pfam03439   78 KEMEHLL 84
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 766-883 4.65e-29

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.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 112.62  E-value: 4.65e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123     766 GSQTPMYG-SGSRTPMYGSQTP----LQDGSRTPHYGSQTPLHDG--SRTPAQSGAWdPNNPNTPSRAEEEYEYAFDDEP 838
Cdd:smart01104    1 GGRTPAWGaSGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAWGGAG-PTGSRTPAWGGASAWGNKSSEG 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 22094123     839 TPSPQA--YGGTPNPQTPGYpdpssPQVNPQYNPQTPGTPAMYNTDQ 883
Cdd:smart01104   80 SASSWAagPGGAYGAPTPGY-----GGTPSAYGPATPGGGAMAGSAS 121
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 469-519 7.27e-28

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.


Pssm-ID: 240507  Cd Length: 51  Bit Score: 106.46  E-value: 7.27e-28
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 22094123  469 YFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLC 519
Cdd:cd06083    1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 418-468 6.17e-26

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.


Pssm-ID: 240506  Cd Length: 51  Bit Score: 101.04  E-value: 6.17e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 22094123  418 FQPGDNVEVCEGELINLQGKVLSVDGNKITIMPKHEDLKDMLEFPAQELRK 468
Cdd:cd06082    1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 696-745 4.70e-25

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.


Pssm-ID: 240509  Cd Length: 52  Bit Score: 98.71  E-value: 4.70e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 22094123  696 DNELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLT 745
Cdd:cd06085    2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLA 51
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1022-1079 1.58e-24

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.


Pssm-ID: 240510  Cd Length: 58  Bit Score: 97.20  E-value: 1.58e-24
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 22094123 1022 EHLEPITPTKNNKVKVILGEDREATGVLLSIDGEDGIIRMDlEDQQIKILNLRFLGKL 1079
Cdd:cd06086    1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMD-SDGDIKILPMNFLAKL 57
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 595-637 6.68e-20

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.


Pssm-ID: 240508  Cd Length: 43  Bit Score: 83.72  E-value: 6.68e-20
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 22094123  595 KDIVKVIDGPHSGREGEIRHLYRSFAFLHCKKLVENGGMFVCK 637
Cdd:cd06084    1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 274-311 1.56e-17

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.


Pssm-ID: 240505  Cd Length: 38  Bit Score: 76.74  E-value: 1.56e-17
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 22094123  274 KSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMIPRIDY 311
Cdd:cd06081    1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 766-824 5.64e-15

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.


Pssm-ID: 372327 [Multi-domain]  Cd Length: 71  Bit Score: 70.55  E-value: 5.64e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    766 GSQTPMYGS--GSRTPMY---GSQTPL--QDGSRTPHY--GSQTPLHD--GSRTPAQSGAWDPnnPNTPS 824
Cdd:pfam12815    1 GSRTPAYNSagGSRTPAWgadGSRTPAygGAGGRTPAYnqGGKTPAWGgaGSRTPAYYGAWGG--SRTPA 68
nusG PRK08559
transcription antitermination protein NusG; Validated
 173-314 4.73e-12

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 64.89  E-value: 4.73e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   173 KDPNLWTVKCKIGEERATAISLMRKFIAYQftdtpLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRlGYwNQQM 252
Cdd:PRK08559    4 EMSMIFAVKTTAGQERNVALMLAMRAKKEN-----LPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVR-GV-VPGE 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 22094123   253 VPIKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKM------IP---RIDYDRI 314
Cdd:PRK08559   77 ISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELleaavpIPvtvRGDQVRV 147
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 91-170 6.78e-12

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.


Pssm-ID: 463406  Cd Length: 97  Bit Score: 62.67  E-value: 6.78e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123     91 EDGAEDILEKEEIEASNIDNVVLDEDRSGARRLQNLWRDQREEELGEYYMKKYAKSSvgETVYGGSDElsDDITQQQLLP 170
Cdd:pfam11942   22 EDGADDFIEDDEEDEDEEDGRRDDRRHRELDRRRELEEDEDAEEIAEYLKERYGRSS--SDAYRGDAE--EGVPQRLLLP 97
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 176-264 1.27e-10

In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, this domain may confer affinity for Spt4p.Spt4p


Pssm-ID: 197850 [Multi-domain]  Cd Length: 106  Bit Score: 59.31  E-value: 1.27e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123     176 NLWTVKCKIGEERATAISLMRKFIAYQFTDtplQIKSVVAP-EHVK----------------GYIYVEAYKQTHVKQAIE 238
Cdd:smart00738    1 NWYAVRTTSGQEKRVAENLERKAEALGLED---KIVSILVPtEEVKeirrgkkkvverklfpGYIFVEADLEDEVWTAIR 77

                            90       100       110
                    ....*....|....*....|....*....|
gi 22094123     239 GV----GNLRLGYWnQQMVPIKEMTDVLKV 264
Cdd:smart00738   78 GTpgvrGFVGGGGK-PTPVPDDEIEKILKP 106
PHA03269 PHA03269
envelope glycoprotein C; Provisional
 819-964 3.98e-09

envelope glycoprotein C; Provisional


Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 60.51  E-value: 3.98e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   819 NPNTPSRAEEEYEYAFDDEPTPSPQayggtPNPQTPGYPDPS-SPQVNPQYNPQtpgtpamyntdqfsPYAAPSPQGSYQ 897
Cdd:PHA03269   21 NLNTNIPIPELHTSAATQKPDPAPA-----PHQAASRAPDPAvAPTSAASRKPD--------------LAQAPTPAASEK 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 22094123   898 PSPSPQSYHQV--APSPAGYQNTHSPasyhPTPSPM-----AYQASPSPSPVGYSPMTPgAPSPGGYNPHTPGS 964
Cdd:PHA03269   82 FDPAPAPHQAAsrAPDPAVAPQLAAA----PKPDAAeaftsAAQAHEAPADAGTSAASK-KPDPAAHTQHSPPP 150
PHA03247 PHA03247
large tegument protein UL36; Provisional
 791-956 3.25e-08

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 58.41  E-value: 3.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   791 SRTPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPsraeeeyeyafddePTPSPQAYGGTPN----PQTPGYPDPSSPQVNP 866
Cdd:PHA03247 2710 PAPHALVSATPLPPGPAAARQASPALPAAPAPP--------------AVPAGPATPGGPArparPPTTAGPPAPAPPAAP 2775

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   867 QYNPQTPGTPAMYNTDQFSPYAAPSPqgsyqPSPSPQSYHQVAPSPAgYQNTHSPASYHPTPsPMAYQASPSPSPVGYSP 946
Cdd:PHA03247 2776 AAGPPRRLTRPAVASLSESRESLPSP-----WDPADPPAAVLAPAAA-LPPAASPAGPLPPP-TSAQPTAPPPPPGPPPP 2848

                         170
                  ....*....|..
gi 22094123   947 MTP--GAPSPGG 956
Cdd:PHA03247 2849 SLPlgGSVAPGG 2860
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 178-306 3.38e-08

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.


Pssm-ID: 129499 [Multi-domain]  Cd Length: 145  Bit Score: 53.74  E-value: 3.38e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    178 WTVKCKIGEERATAislmrKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRlgywnqQMVP--- 254
Cdd:TIGR00405    1 FAVKTSVGQEKNVA-----RLMARKARKSGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVR------GVVEgei 69

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 22094123    255 -IKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMI 306
Cdd:TIGR00405   70 dFEEIERFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELI 122
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 838-964 6.40e-08

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.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 57.08  E-value: 6.40e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    838 PTPSPQAYGGTPNPQTPGYPDPSSPQVN-PQYNPQTPGTP--AMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAG 914
Cdd:pfam03154  188 PPGTTQAATAGPTPSAPSVPPQGSPATSqPPNQTQSTAAPhtLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQVSPQPLP 267

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 22094123    915 YQNTHSPASYHP---------TPSPMAYQASPSPSPVGYSPMTPG----APSPGGYNPHTPGS 964
Cdd:pfam03154  268 QPSLHGQMPPMPhslqtgpshMQHPVPPQPFPLTPQSSQSQVPPGpspaAPGQSQQRIHTPPS 330
PBP1 COG5180
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ...
 740-971 1.07e-06

PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification];


Pssm-ID: 444064 [Multi-domain]  Cd Length: 548  Bit Score: 52.76  E-value: 1.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  740 DRQRLTTVDSQRPGGMtSTYGRTPMYGSQTPMYgsgsrTPMYGSQTPLQDGSRTPHYGSQTPLH-------DGSRTPaQS 812
Cdd:COG5180  154 LLQRSDPILAKDPDGD-SASTLPPPAEKLDKVL-----TEPRDALKDSPEKLDRPKVEVKDEAQeeppdltGGADHP-RP 226

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  813 GAWDPNNPNTPSRAEEEYEYAFDD-EPTPSPQAYGGTPNP----QTPGYPDPSSPQVNPQYNPQT--PGTPAMYNTDQFS 885
Cdd:COG5180  227 EAASSPKVDPPSTSEARSRPATVDaQPEMRPPADAKERRRaaigDTPAAEPPGLPVLEAGSEPQSdaPEAETARPIDVKG 306

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  886 PYAAPSPQGSYQPSPS-----PQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSpspvgySPMTPGAPSPG--GYN 958
Cdd:COG5180  307 VASAPPATRPVRPPGGardpgTPRPGQPTERPAGVPEAASDAGQPPSAYPPAEEAVPG------KPLEQGAPRPGssGGD 380

                        250
                 ....*....|....*
gi 22094123  959 --PHTPGSGIEQNSS 971
Cdd:COG5180  381 gaPFQPPNGAPQPGL 395
SP7_N cd22542
N-terminal domain of transcription factor Specificity Protein (SP) 7; Specificity Proteins ...
 796-964 2.82e-05

N-terminal domain of transcription factor Specificity Protein (SP) 7; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP7, also called Osterix (Osx) in humans, is highly conserved among bone-forming vertebrates. It plays a major role, along with Runx2 and Dlx5 in driving the differentiation of mesenchymal precursor cells into osteoblasts and eventually osteocytes. SP7 also plays a regulatory role by inhibiting chondrocyte differentiation, maintaining the balance between differentiation of mesenchymal precursor cells into ossified bone or cartilage. Mutations of this gene have been associated with multiple dysfunctional bone phenotypes in vertebrates. SP7 is thought to play a role in diseases such as Osteogenesis imperfecta. SP7 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (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. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. This model represents the N-terminal domain of SP7.


Pssm-ID: 411691 [Multi-domain]  Cd Length: 297  Bit Score: 47.20  E-value: 2.82e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  796 YGSQTPLHDgSRTPAQSGAWDPNNPNTP--------SRAEE----EYEYAFDD-----EPTPSPQA---YGGTPNPQTPG 855
Cdd:cd22542   26 FGGSSPIRD-SATPGKPGNNPGKKPYSLgsdlssakSRSSElmgdSYTATFSSgnglmSPSGSPQAsttYGNDYNPFSHS 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  856 YPDPSSPQ----VNPQYNPQTPGTPAMYNT-DQFSPY-----AAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYH 925
Cdd:cd22542  105 FPTSSGSQdpslLVSKGHPSADCLPSVYTSlDMAHPYgswykTGIHPGISSSSTNATASWWDMHSNTNWLSAQGQPDGLQ 184

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 22094123  926 PTPSPMAYQASPSPSPVGYSPMTPgaPSPGGYNPHTPGS 964
Cdd:cd22542  185 ASLQPVPAQTPLNPQLPSYTEFTT--LNPAPYPAVGISS 221
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 469-496 5.43e-05

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


Pssm-ID: 128978  Cd Length: 28  Bit Score: 41.16  E-value: 5.43e-05
                            10        20
                    ....*....|....*....|....*...
gi 22094123     469 YFKMGDHVKVIAGRFEGDTGLIVRVEEN 496
Cdd:smart00739    1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 700-731 9.19e-05

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.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 40.45  E-value: 9.19e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 22094123    700 IGQTVRISQGPYKGYIGVVKDATESTARVELH 731
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 818-954 2.08e-04

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 45.14  E-value: 2.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   818 NNPNTPSRAEEEYEYAFDD-EPTPSPQAYGGTPN-PQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQG- 894
Cdd:NF033839  249 DNVNTKVEIENTVHKIFADmDAVVTKFKKGLTQDtPKEPGNKKPSAPKPGMQPSPQPEKKEVKPEPETPKPEVKPQLEKp 328

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 22094123   895 SYQPSPSPQSYH-QVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPSpvgySPMTPGAPSP 954
Cdd:NF033839  329 KPEVKPQPEKPKpEVKPQLETPKPEVKPQPEKPKPEVKPQPEKPKPE----VKPQPETPKP 385
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 473-501 2.08e-04

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.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 39.29  E-value: 2.08e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 22094123    473 GDHVKVIAGRFEGDTGLIVRVEE--NFVILF 501
Cdd:pfam00467    2 GDVVRVIAGPFKGKVGKVVEVDDkkNRVLVE 32
KLF1_2_4_N cd21972
N-terminal domain of Kruppel-like factor (KLF) 1, KLF2, KLF4, and similar proteins; Kruppel ...
 823-962 8.16e-04

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.


Pssm-ID: 409230 [Multi-domain]  Cd Length: 194  Bit Score: 41.89  E-value: 8.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  823 PSRAEEEYEYAFDDEPTPSPQAYG----GTPNPQTPGYPDPSSPQVNPQYN-PQTPGTPAMYNTDQFSPYAAPSPQGSYQ 897
Cdd:cd21972   22 LDLEFILSNTVTSDNDNPPPPDPAypppESPESCSTVYDSDGCHPTPNAYCgPNGPGLPGHFLLAGNSPNLGPKIKTENQ 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 22094123  898 PS-------PSPQSYHQVAPS------PAGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSPmtPGAPSPGGYNPHTP 962
Cdd:cd21972  102 EQacmpvagYSGHYGPREPQRvppappPPQYAGHFQYHGHFNMFSPPLRANHPGMSTVMLTP--LSTPPLGFLSPEEA 177
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 836-962 3.55e-03

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 41.29  E-value: 3.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   836 DEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQynPQTPGTPAMYNTDQFSPYAAPSPQ-GSYQPSPSPQSYH-QVAPSPA 913
Cdd:NF033839  370 EKPKPEVKPQPETPKPEVKPQPEKPKPEVKPQ--PEKPKPEVKPQPEKPKPEVKPQPEkPKPEVKPQPEKPKpEVKPQPE 447

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 22094123   914 GYQNTHSPASYHPTPSPMAYQASPSPSpVGYSPMTP----GAPSPGGYNPHTP 962
Cdd:NF033839  448 KPKPEVKPQPETPKPEVKPQPEKPKPE-VKPQPEKPkpdnSKPQADDKKPSTP 499
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 594-625 5.43e-03

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.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 35.44  E-value: 5.43e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 22094123    594 VKDIVKVIDGPHSGREGEIRHLYRSFAFLHCK 625
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 176-263 4.31e-44

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.


Pssm-ID: 193577 [Multi-domain]  Cd Length: 86  Bit Score: 154.23  E-value: 4.31e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  176 NLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLgyWNQQMVPI 255
Cdd:cd09888    1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYL--NTIKLVPI 78


                 ....*...
gi 22094123  256 KEMTDVLK 263
Cdd:cd09888   79 KEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 176-262 6.62e-31

Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this 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 Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit.


Pssm-ID: 397481  Cd Length: 84  Bit Score: 116.53  E-value: 6.62e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    176 NLWTVKCKIGEERATAISLMRKFIAYQfTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLGywNQQMVPI 255
Cdd:pfam03439    1 KIWAVKCTPGQEREVALSLMRKILALA-KTNNLGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGL--VPGLVPI 77


                   ....*..
gi 22094123    256 KEMTDVL 262
Cdd:pfam03439   78 KEMEHLL 84
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 766-883 4.65e-29

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.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 112.62  E-value: 4.65e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123     766 GSQTPMYG-SGSRTPMYGSQTP----LQDGSRTPHYGSQTPLHDG--SRTPAQSGAWdPNNPNTPSRAEEEYEYAFDDEP 838
Cdd:smart01104    1 GGRTPAWGaSGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAWGGAG-PTGSRTPAWGGASAWGNKSSEG 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 22094123     839 TPSPQA--YGGTPNPQTPGYpdpssPQVNPQYNPQTPGTPAMYNTDQ 883
Cdd:smart01104   80 SASSWAagPGGAYGAPTPGY-----GGTPSAYGPATPGGGAMAGSAS 121
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 469-519 7.27e-28

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.


Pssm-ID: 240507  Cd Length: 51  Bit Score: 106.46  E-value: 7.27e-28
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 22094123  469 YFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLC 519
Cdd:cd06083    1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 418-468 6.17e-26

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.


Pssm-ID: 240506  Cd Length: 51  Bit Score: 101.04  E-value: 6.17e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 22094123  418 FQPGDNVEVCEGELINLQGKVLSVDGNKITIMPKHEDLKDMLEFPAQELRK 468
Cdd:cd06082    1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 696-745 4.70e-25

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.


Pssm-ID: 240509  Cd Length: 52  Bit Score: 98.71  E-value: 4.70e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 22094123  696 DNELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLT 745
Cdd:cd06085    2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLA 51
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1022-1079 1.58e-24

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.


Pssm-ID: 240510  Cd Length: 58  Bit Score: 97.20  E-value: 1.58e-24
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 22094123 1022 EHLEPITPTKNNKVKVILGEDREATGVLLSIDGEDGIIRMDlEDQQIKILNLRFLGKL 1079
Cdd:cd06086    1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMD-SDGDIKILPMNFLAKL 57
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 595-637 6.68e-20

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.


Pssm-ID: 240508  Cd Length: 43  Bit Score: 83.72  E-value: 6.68e-20
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 22094123  595 KDIVKVIDGPHSGREGEIRHLYRSFAFLHCKKLVENGGMFVCK 637
Cdd:cd06084    1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 274-311 1.56e-17

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.


Pssm-ID: 240505  Cd Length: 38  Bit Score: 76.74  E-value: 1.56e-17
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 22094123  274 KSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMIPRIDY 311
Cdd:cd06081    1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 766-824 5.64e-15

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.


Pssm-ID: 372327 [Multi-domain]  Cd Length: 71  Bit Score: 70.55  E-value: 5.64e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    766 GSQTPMYGS--GSRTPMY---GSQTPL--QDGSRTPHY--GSQTPLHD--GSRTPAQSGAWDPnnPNTPS 824
Cdd:pfam12815    1 GSRTPAYNSagGSRTPAWgadGSRTPAygGAGGRTPAYnqGGKTPAWGgaGSRTPAYYGAWGG--SRTPA 68
nusG PRK08559
transcription antitermination protein NusG; Validated
 173-314 4.73e-12

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 64.89  E-value: 4.73e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   173 KDPNLWTVKCKIGEERATAISLMRKFIAYQftdtpLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRlGYwNQQM 252
Cdd:PRK08559    4 EMSMIFAVKTTAGQERNVALMLAMRAKKEN-----LPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVR-GV-VPGE 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 22094123   253 VPIKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKM------IP---RIDYDRI 314
Cdd:PRK08559   77 ISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELleaavpIPvtvRGDQVRV 147
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 91-170 6.78e-12

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.


Pssm-ID: 463406  Cd Length: 97  Bit Score: 62.67  E-value: 6.78e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123     91 EDGAEDILEKEEIEASNIDNVVLDEDRSGARRLQNLWRDQREEELGEYYMKKYAKSSvgETVYGGSDElsDDITQQQLLP 170
Cdd:pfam11942   22 EDGADDFIEDDEEDEDEEDGRRDDRRHRELDRRRELEEDEDAEEIAEYLKERYGRSS--SDAYRGDAE--EGVPQRLLLP 97
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 176-262 9.12e-11

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.


Pssm-ID: 193574 [Multi-domain]  Cd Length: 99  Bit Score: 59.64  E-value: 9.12e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  176 NLWTVKCKIGEERATAISLMRKFIA---------YQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLG 246
Cdd:cd08000    1 NWYVLFVKTGREEKVEKLLEKRFEAndieafvpkKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPGVIGI 80

                         90
                 ....*....|....*....
gi 22094123  247 YWN---QQMVPIKEMTDVL 262
Cdd:cd08000   81 LGNgeePSPVSDEEIEMIL 99
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 176-264 1.27e-10

In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, this domain may confer affinity for Spt4p.Spt4p


Pssm-ID: 197850 [Multi-domain]  Cd Length: 106  Bit Score: 59.31  E-value: 1.27e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123     176 NLWTVKCKIGEERATAISLMRKFIAYQFTDtplQIKSVVAP-EHVK----------------GYIYVEAYKQTHVKQAIE 238
Cdd:smart00738    1 NWYAVRTTSGQEKRVAENLERKAEALGLED---KIVSILVPtEEVKeirrgkkkvverklfpGYIFVEADLEDEVWTAIR 77

                            90       100       110
                    ....*....|....*....|....*....|
gi 22094123     239 GV----GNLRLGYWnQQMVPIKEMTDVLKV 264
Cdd:smart00738   78 GTpgvrGFVGGGGK-PTPVPDDEIEKILKP 106
DUF5585 pfam17823
Family of unknown function (DUF5585); This is a family of unknown function found in chordata.
 721-1040 1.55e-09

Family of unknown function (DUF5585); This is a family of unknown function found in chordata.


Pssm-ID: 465521 [Multi-domain]  Cd Length: 506  Bit Score: 61.90  E-value: 1.55e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    721 ATESTARVELHSTCQTISvdrqrlTTVDSQRPGGMTSTYGRT--PMYGSQTPMYGSGsrTPMYGSQTPlQDGSRTPHYGS 798
Cdd:pfam17823  170 AASPAPRTAASSTTAASS------TTAASSAPTTAASSAPATltPARGISTAATATG--HPAAGTALA-AVGNSSPAAGT 240

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    799 QTPLhDGSRTPAQSGawdpnnpnTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGypDPSSPQVNPQYNPQTPGTPAM 878
Cdd:pfam17823  241 VTAA-VGTVTPAALA--------TLAAAAGTVASAAGTINMGDPHARRLSPAKHMPS--DTMARNPAAPMGAQAQGPIIQ 309

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    879 YNTDQfsPYAAPSPqgsyQPSPSPQSYHQVAPSPAGYQNTHSPASyhPTPSPMAYQASPSPSPVGYSPMTPGA------- 951
Cdd:pfam17823  310 VSTDQ--PVHNTAG----EPTPSPSNTTLEPNTPKSVASTNLAVV--TTTKAQAKEPSASPVPVLHTSMIPEVeatsptt 381

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    952 -PSPGGYNPHTPGSGIEQNSSdwvttdiQVKVRDTyLDTQIVGQT----GVIRSVTGGMCSVYLKDSEKVVSIssehlEP 1026
Cdd:pfam17823  382 qPSPLLPTQGAAGPGILLAPE-------QVATEAT-AGTASAGPTprssGDPKTLAMASCQLSTQGQYLVVTT-----DP 448

                          330
                   ....*....|....*...
gi 22094123   1027 ITPTKNNK----VKVILG 1040
Cdd:pfam17823  449 LTPALVDKmfllVVLILG 466
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 783-964 2.14e-09

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.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 61.71  E-value: 2.14e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    783 SQTPLQDGSRTPHYGSQTPLHDgsrtPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPtPSPQAYGGTPNPQTPGYPdPSSP 862
Cdd:pfam03154  259 SQVSPQPLPQPSLHGQMPPMPH----SLQTGPSHMQHPVPPQPFPLTPQSSQSQVP-PGPSPAAPGQSQQRIHTP-PSQS 332

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    863 QVNPQYNP-QTPGTPAMYNTdqfsPYAAPSPQGSYQPSPSPQSY----HQVAPSPagYQ-----------------NTHS 920
Cdd:pfam03154  333 QLQSQQPPrEQPLPPAPLSM----PHIKPPPTTPIPQLPNPQSHkhppHLSGPSP--FQmnsnlppppalkplsslSTHH 406

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 22094123    921 PASYHPTPSPMAYQASPSPSPVGYSPM---TPGAPSPGGYNPHTPGS 964
Cdd:pfam03154  407 PPSAHPPPLQLMPQSQQLPPPPAQPPVltqSQSLPPPAASHPPTSGL 453
PHA03269 PHA03269
envelope glycoprotein C; Provisional
 819-964 3.98e-09

envelope glycoprotein C; Provisional


Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 60.51  E-value: 3.98e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   819 NPNTPSRAEEEYEYAFDDEPTPSPQayggtPNPQTPGYPDPS-SPQVNPQYNPQtpgtpamyntdqfsPYAAPSPQGSYQ 897
Cdd:PHA03269   21 NLNTNIPIPELHTSAATQKPDPAPA-----PHQAASRAPDPAvAPTSAASRKPD--------------LAQAPTPAASEK 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 22094123   898 PSPSPQSYHQV--APSPAGYQNTHSPasyhPTPSPM-----AYQASPSPSPVGYSPMTPgAPSPGGYNPHTPGS 964
Cdd:PHA03269   82 FDPAPAPHQAAsrAPDPAVAPQLAAA----PKPDAAeaftsAAQAHEAPADAGTSAASK-KPDPAAHTQHSPPP 150
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 770-971 5.46e-09

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.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 60.55  E-value: 5.46e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    770 PMYGSGSRTPMYGSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPsrAEEEYEYAFDDEPTPSPQayggTP 849
Cdd:pfam03154  294 PPQPFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPP--APLSMPHIKPPPTTPIPQ----LP 367

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    850 NPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQgsyqPSP---SPQSyHQVAPSPAG------YQNTHS 920
Cdd:pfam03154  368 NPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSSLSTHHPPSAH----PPPlqlMPQS-QQLPPPPAQppvltqSQSLPP 442

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 22094123    921 PASYHPTPSpmAYQASPSPSPVGYSPMTPGAP----SPGGYNPHTP--GSGIEQNSS 971
Cdd:pfam03154  443 PAASHPPTS--GLHQVPSQSPFPQHPFVPGGPppitPPSGPPTSTSsaMPGIQPPSS 497
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 753-813 9.98e-09

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.


Pssm-ID: 372327 [Multi-domain]  Cd Length: 71  Bit Score: 52.83  E-value: 9.98e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 22094123    753 GGMTSTYG----RTPMYG---SQTPMYGSGSRTPMYGsqtplQDGSRTPHYGSQTplhDGSRTPAQSG 813
Cdd:pfam12815   12 GSRTPAWGadgsRTPAYGgagGRTPAYNQGGKTPAWG-----GAGSRTPAYYGAW---GGSRTPAYGG 71
PHA03247 PHA03247
large tegument protein UL36; Provisional
 791-956 3.25e-08

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 58.41  E-value: 3.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   791 SRTPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPsraeeeyeyafddePTPSPQAYGGTPN----PQTPGYPDPSSPQVNP 866
Cdd:PHA03247 2710 PAPHALVSATPLPPGPAAARQASPALPAAPAPP--------------AVPAGPATPGGPArparPPTTAGPPAPAPPAAP 2775

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   867 QYNPQTPGTPAMYNTDQFSPYAAPSPqgsyqPSPSPQSYHQVAPSPAgYQNTHSPASYHPTPsPMAYQASPSPSPVGYSP 946
Cdd:PHA03247 2776 AAGPPRRLTRPAVASLSESRESLPSP-----WDPADPPAAVLAPAAA-LPPAASPAGPLPPP-TSAQPTAPPPPPGPPPP 2848

                         170
                  ....*....|..
gi 22094123   947 MTP--GAPSPGG 956
Cdd:PHA03247 2849 SLPlgGSVAPGG 2860
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 178-306 3.38e-08

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.


Pssm-ID: 129499 [Multi-domain]  Cd Length: 145  Bit Score: 53.74  E-value: 3.38e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    178 WTVKCKIGEERATAislmrKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRlgywnqQMVP--- 254
Cdd:TIGR00405    1 FAVKTSVGQEKNVA-----RLMARKARKSGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVR------GVVEgei 69

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 22094123    255 -IKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMI 306
Cdd:TIGR00405   70 dFEEIERFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELI 122
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 752-965 5.81e-08

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 56.94  E-value: 5.81e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    752 PGGMTSTYGRTPMYGSQTPMYGSGSRTPMYGSQ-------TPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNP---- 820
Cdd:pfam09606  231 PQQMGGAPNQVAMQQQQPQQQGQQSQLGMGINQmqqmpqgVGGGAGQGGPGQPMGPPGQQPGAMPNVMSIGDQNNYqqqq 310

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    821 --NTPSRAEEEYEYAFDDEPTPS--------PQAYGGTPNPQTPGypdpssPQVNPQYNPQTPGTPAMYNTDQFSPYAAP 890
Cdd:pfam09606  311 trQQQQQQGGNHPAAHQQQMNQSvgqggqvvALGGLNHLETWNPG------NFGGLGANPMQRGQPGMMSSPSPVPGQQV 384

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 22094123    891 SPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASyHPTPSPmAYQASPSPSPVGY--SPMTPGAPSPGGyNPHTPGSG 965
Cdd:pfam09606  385 RQVTPNQFMRQSPQPSVPSPQGPGSQPPQSHPG-GMIPSP-ALIPSPSPQMSQQpaQQRTIGQDSPGG-SLNTPGQS 458
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 838-964 6.40e-08

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.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 57.08  E-value: 6.40e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    838 PTPSPQAYGGTPNPQTPGYPDPSSPQVN-PQYNPQTPGTP--AMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAG 914
Cdd:pfam03154  188 PPGTTQAATAGPTPSAPSVPPQGSPATSqPPNQTQSTAAPhtLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQVSPQPLP 267

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 22094123    915 YQNTHSPASYHP---------TPSPMAYQASPSPSPVGYSPMTPG----APSPGGYNPHTPGS 964
Cdd:pfam03154  268 QPSLHGQMPPMPhslqtgpshMQHPVPPQPFPLTPQSSQSQVPPGpspaAPGQSQQRIHTPPS 330
NGN_Arch cd09887
Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance ...
 177-244 9.33e-08

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.


Pssm-ID: 193576  Cd Length: 82  Bit Score: 50.62  E-value: 9.33e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 22094123  177 LWTVKCKIGEERATAISLMRKFiayqfTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLR 244
Cdd:cd09887    2 IYAVKTTAGQERNVADLLAMRA-----EKENLDVYSILVPEELKGYVFVEAEDPDRVEELIRGIPHVR 64
PHA03377 PHA03377
EBNA-3C; Provisional
 732-962 9.99e-08

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 56.21  E-value: 9.99e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   732 STCQTISVDRQRLTTVDSQRPGGMTSTygrTPMYGSQTPMYgSGSRTPMYGSQTPLQD---GSRTPHYGSQTPLHDGSRT 808
Cdd:PHA03377  686 SVFVLPSVDAGRAQPSEESHLSSMSPT---QPISHEEQPRY-EDPDDPLDLSLHPDQApppSHQAPYSGHEEPQAQQAPY 761

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   809 PaqsGAWDPNNPNTPSRAEEEyeyafddeptpsPQAYGGTPNpQTPGY--PDPSSPQvNPQY--------------NPQT 872
Cdd:PHA03377  762 P---GYWEPRPPQAPYLGYQE------------PQAQGVQVS-SYPGYagPWGLRAQ-HPRYrhswaywsqypghgHPQG 824

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   873 PGTP-AMYNTDQFSPYAAP-----SPQGSYQPSPSP----QSYHQVAPSPAGYQNTHSPASYHPTPS----PMAYQASPS 938
Cdd:PHA03377  825 PWAPrPPHLPPQWDGSAGHgqdqvSQFPHLQSETGPprlqLSQVPQLPYSQTLVSSSAPSWSSPQPRapirPIPTRFPPP 904

                         250       260
                  ....*....|....*....|....
gi 22094123   939 PSPVGYSpMTPGAPSPGGYNPHTP 962
Cdd:PHA03377  905 PMPLQDS-MAVGCDSSGTACPSMP 927
PHA03247 PHA03247
large tegument protein UL36; Provisional
 756-976 1.91e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 55.71  E-value: 1.91e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   756 TSTYGRTPMYGSQTPMygsgSRTPMYGSQTPLQDGSRTPHYGSQTPLHDGSR-TPAQSGAWDPNNPNTPsRAEEEYEYAF 834
Cdd:PHA03247 2817 ALPPAASPAGPLPPPT----SAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRrPPSRSPAAKPAAPARP-PVRRLARPAV 2891

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   835 DDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQtpgtpamyntdqfsPYAAPSPQGSYQPSPSPQSYHQVAPSPAG 914
Cdd:PHA03247 2892 SRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQ--------------PQPPPPPPPRPQPPLAPTTDPAGAGEPSG 2957

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 22094123   915 YQNTHSPASYHPTPSPMAYQASPSPSPvgySPMTPGAPSPGgyNPHTPGSGIeqnsSDWVTT 976
Cdd:PHA03247 2958 AVPQPWLGALVPGRVAVPRFRVPQPAP---SREAPASSTPP--LTGHSLSRV----SSWASS 3010
PHA03378 PHA03378
EBNA-3B; Provisional
 749-956 1.93e-07

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 55.46  E-value: 1.93e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   749 SQRPGGMT--STYGRTPMYGSQTPMYGSGSRTPMYGSQTPLQD-----------GSRTPHYGSQTPLHDGSRTPAQSGAW 815
Cdd:PHA03378  593 AQTPWPVPhpSQTPEPPTTQSHIPETSAPRQWPMPLRPIPMRPlrmqpitfnvlVFPTPHQPPQVEITPYKPTWTQIGHI 672

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   816 dPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPgyPDPSS-PQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQG 894
Cdd:PHA03378  673 -PYQPSPTGANTMLPIQWAPGTMQPPPRAPTPMRPPAAP--PGRAQrPAAATGRARPPAAAPGRARPPAAAPGRARPPAA 749

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 22094123   895 SYQPSPSPQSYHQVAPSPAGyqnthSPASYHPTPSPMA-------YQASPSPSP---VGYSPMTPGAPSPGG 956
Cdd:PHA03378  750 APGRARPPAAAPGRARPPAA-----APGAPTPQPPPQAppapqqrPRGAPTPQPppqAGPTSMQLMPRAAPG 816
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 421-467 2.81e-07

KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); 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. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues.


Pssm-ID: 240504  Cd Length: 49  Bit Score: 47.98  E-value: 2.81e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 22094123  421 GDNVEVCEGELINLQGKVLSVDG--NKITIMPKHEDLKDMLEFPAQELR 467
Cdd:cd00380    1 GDVVRVLRGPYKGREGVVVDIDPrfGIVTVKGATGSKGAELKVRFDDVD 49
PHA03247 PHA03247
large tegument protein UL36; Provisional
 783-965 9.01e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 53.40  E-value: 9.01e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   783 SQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYP----- 857
Cdd:PHA03247 2567 SVPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHppptv 2646

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   858 --------DPSSPQVNPQYNPQTPGTPAMYN--TDQFSPYAAPSPQGSY-----------QPSPSPQSYHQVAPSPAGYQ 916
Cdd:PHA03247 2647 ppperprdDPAPGRVSRPRRARRLGRAAQASspPQRPRRRAARPTVGSLtsladppppppTPEPAPHALVSATPLPPGPA 2726

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 22094123   917 NTHS-----PASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGynPHTPGSG 965
Cdd:PHA03247 2727 AARQaspalPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAP--PAAPAAG 2778
PHA03378 PHA03378
EBNA-3B; Provisional
 793-962 1.04e-06

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 53.15  E-value: 1.04e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   793 TPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEE---YEYAFDDEPTPSPQAYGGTPNPQTPGYPDPS-SPQVNPQ- 867
Cdd:PHA03378  582 TSQLASSAPSYAQTPWPVPHPSQTPEPPTTQSHIPETsapRQWPMPLRPIPMRPLRMQPITFNVLVFPTPHqPPQVEITp 661

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   868 ------------YNPQTPG---------TPAMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHP 926
Cdd:PHA03378  662 ykptwtqighipYQPSPTGantmlpiqwAPGTMQPPPRAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPAAAP 741

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 22094123   927 TPS--PMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTP 962
Cdd:PHA03378  742 GRArpPAAAPGRARPPAAAPGRARPPAAAPGAPTPQPP 779
PBP1 COG5180
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ...
 740-971 1.07e-06

PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification];


Pssm-ID: 444064 [Multi-domain]  Cd Length: 548  Bit Score: 52.76  E-value: 1.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  740 DRQRLTTVDSQRPGGMtSTYGRTPMYGSQTPMYgsgsrTPMYGSQTPLQDGSRTPHYGSQTPLH-------DGSRTPaQS 812
Cdd:COG5180  154 LLQRSDPILAKDPDGD-SASTLPPPAEKLDKVL-----TEPRDALKDSPEKLDRPKVEVKDEAQeeppdltGGADHP-RP 226

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  813 GAWDPNNPNTPSRAEEEYEYAFDD-EPTPSPQAYGGTPNP----QTPGYPDPSSPQVNPQYNPQT--PGTPAMYNTDQFS 885
Cdd:COG5180  227 EAASSPKVDPPSTSEARSRPATVDaQPEMRPPADAKERRRaaigDTPAAEPPGLPVLEAGSEPQSdaPEAETARPIDVKG 306

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  886 PYAAPSPQGSYQPSPS-----PQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSpspvgySPMTPGAPSPG--GYN 958
Cdd:COG5180  307 VASAPPATRPVRPPGGardpgTPRPGQPTERPAGVPEAASDAGQPPSAYPPAEEAVPG------KPLEQGAPRPGssGGD 380

                        250
                 ....*....|....*
gi 22094123  959 --PHTPGSGIEQNSS 971
Cdd:COG5180  381 gaPFQPPNGAPQPGL 395
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 837-963 1.10e-06

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 53.17  E-value: 1.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   837 EPTPSPQAYGGTPNPQtpgYPDPSSPQVNP---QYNPQTPGTPAMYNTDQFSPYAAPSP-QGSYQPSPSPQSYHQVAPSP 912
Cdd:PRK10263  370 EPVIAPAPEGYPQQSQ---YAQPAVQYNEPlqqPVQPQQPYYAPAAEQPAQQPYYAPAPeQPAQQPYYAPAPEQPVAGNA 446

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 22094123   913 AGYQNTHSPasYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPG 963
Cdd:PRK10263  447 WQAEEQQST--FAPQSTYQTEQTYQQPAAQEPLYQQPQPVEQQPVVEPEPV 495
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 840-968 2.97e-06

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.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 51.69  E-value: 2.97e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    840 PSPQAYGGTPNPQTPGYPDPSS-PQVNPqynpqTPGTPAMynTDQFSPYAAPSPQGSyQPSPSPQSYHQVAPS--PAGYQ 916
Cdd:pfam03154  172 PVLQAQSGAASPPSPPPPGTTQaATAGP-----TPSAPSV--PPQGSPATSQPPNQT-QSTAAPHTLIQQTPTlhPQRLP 243

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 22094123    917 NTHSPASYHPTPSPMAY-QASPSPSPVGYSPMTPGAPSPGGYNPHTPGSGIEQ 968
Cdd:pfam03154  244 SPHPPLQPMTQPPPPSQvSPQPLPQPSLHGQMPPMPHSLQTGPSHMQHPVPPQ 296
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 701-744 3.20e-06

KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); 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. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues.


Pssm-ID: 240504  Cd Length: 49  Bit Score: 44.90  E-value: 3.20e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 22094123  701 GQTVRISQGPYKGYIGVVKDATEST--ARVELH--STCQTISVDRQRL 744
Cdd:cd00380    1 GDVVRVLRGPYKGREGVVVDIDPRFgiVTVKGAtgSKGAELKVRFDDV 48
PHA03378 PHA03378
EBNA-3B; Provisional
 742-954 3.60e-06

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 51.22  E-value: 3.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   742 QRLTTVDSQRPGGMTSTYGRTP---MYGSQTPmygsgsRTPMYGSQTP-LQDGSRTPHYGSQTPLHDGSRTPAQSGAWDP 817
Cdd:PHA03378  575 QPLTSPTTSQLASSAPSYAQTPwpvPHPSQTP------EPPTTQSHIPeTSAPRQWPMPLRPIPMRPLRMQPITFNVLVF 648

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   818 NNPNTPSRAEeeyeyafddeptPSPQAYGGTPNPQTPGYPDPSSPQVN--PQYNPQTPGTPAMYNTDQFSPYAAPS---- 891
Cdd:PHA03378  649 PTPHQPPQVE------------ITPYKPTWTQIGHIPYQPSPTGANTMlpIQWAPGTMQPPPRAPTPMRPPAAPPGraqr 716

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 22094123   892 PQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPS-PMAYQASPSPSPVGyspmTPGAPSP 954
Cdd:PHA03378  717 PAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRArPPAAAPGRARPPAA----APGAPTP 776
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 744-955 3.80e-06

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 51.07  E-value: 3.80e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    744 LTTVDSQRPGGMTSTYGRTPMYGSQTPM-YGSGSRTPMYGSQTPLQDgSRTPHYGSQTPlhdGSRTPAQSGAWDPNNPNT 822
Cdd:pfam05109  468 VSTADVTSPTPAGTTSGASPVTPSPSPRdNGTESKAPDMTSPTSAVT-TPTPNATSPTP---AVTTPTPNATSPTLGKTS 543

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    823 PSRAeeeYEYAFDDEPTPSPQAYGGTPNPQTPGY-------------PDPSSPQV---NPQYNPQ------TPGTPAMYN 880
Cdd:pfam05109  544 PTSA---VTTPTPNATSPTPAVTTPTPNATIPTLgktsptsavttptPNATSPTVgetSPQANTTnhtlggTSSTPVVTS 620

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    881 TDQFSPYAAPSPQGSYQPSPS------PQSYHQ-VAPSPAGYQNTHSP--ASYHPTPSPMAYQASPSPSPVGYSPMTPGA 951
Cdd:pfam05109  621 PPKNATSAVTTGQHNITSSSTssmslrPSSISEtLSPSTSDNSTSHMPllTSAHPTGGENITQVTPASTSTHHVSTSSPA 700


                   ....
gi 22094123    952 PSPG 955
Cdd:pfam05109  701 PRPG 704
PHA03247 PHA03247
large tegument protein UL36; Provisional
 805-960 3.81e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 51.48  E-value: 3.81e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   805 GSRTPAQSGAWDPNNPNTPSRAEEEYeyaFDDEPTPSP-----------------QAYGGTPNPQTPGYPDPSSPQV--N 865
Cdd:PHA03247 2494 AAPDPGGGGPPDPDAPPAPSRLAPAI---LPDEPVGEPvhprmltwirgleelasDDAGDPPPPLPPAAPPAAPDRSvpP 2570

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   866 PQYNPQTPGtPAMyNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQA-SPSPSPVGY 944
Cdd:PHA03247 2571 PRPAPRPSE-PAV-TSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPdPHPPPTVPP 2648

                         170
                  ....*....|....*.
gi 22094123   945 SPMTPGAPSPGGYNPH 960
Cdd:PHA03247 2649 PERPRDDPAPGRVSRP 2664
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 473-517 4.34e-06

KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); 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. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues.


Pssm-ID: 240504  Cd Length: 49  Bit Score: 44.52  E-value: 4.34e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 22094123  473 GDHVKVIAGRFEGDTGLIVRVEENFVIL----FSDLTMHELKVLPRDLQ 517
Cdd:cd00380    1 GDVVRVLRGPYKGREGVVVDIDPRFGIVtvkgATGSKGAELKVRFDDVD 49
PHA03291 PHA03291
envelope glycoprotein I; Provisional
 833-1010 4.81e-06

envelope glycoprotein I; Provisional


Pssm-ID: 223033 [Multi-domain]  Cd Length: 401  Bit Score: 50.34  E-value: 4.81e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   833 AFDDEPTPSPQAYGGTPnpqTPGYPDPSSPQVNPQYNPqtpgtpamynTDQFSPyAAPSPQGSYQPSPspqsyhQVAPSP 912
Cdd:PHA03291  165 AFPAEGTLAAPPLGEGS---ADGSCDPALPLSAPRLGP----------ADVFVP-ATPRPTPRTTASP------ETTPTP 224

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   913 AgyqNTHSPASyHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPGSGIEQNSSDWVTTDIQVkvrdtyldTQIV 992
Cdd:PHA03291  225 S---TTTSPPS-TTIPAPSTTIAAPQAGTTPEAEGTPAPPTPGGGEAPPANATPAPEASRYELTVTQI--------IQIA 292

                         170
                  ....*....|....*...
gi 22094123   993 GQTGVIRSVTGGMCSVYL 1010
Cdd:PHA03291  293 IPASIIACVFLGSCACCL 310
PHA03247 PHA03247
large tegument protein UL36; Provisional
 809-966 1.07e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 49.94  E-value: 1.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   809 PAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQV-----NPQYNPQTPGTPAMyNTDQ 883
Cdd:PHA03247 2694 SLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPAtpggpARPARPPTTAGPPA-PAPP 2772

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   884 FSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPAS-YHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTP 962
Cdd:PHA03247 2773 AAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLaPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPL 2852


                  ....
gi 22094123   963 GSGI 966
Cdd:PHA03247 2853 GGSV 2856
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 785-972 1.38e-05

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 49.40  E-value: 1.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   785 TPLQDGSRTPHYGSQ-----------TPLHDGSRTPAqSGAWDPNNPNTPSRAEE-EYEYAFDDEPTPSPQAYGGTPNPQ 852
Cdd:PHA03307   26 ATPGDAADDLLSGSQgqlvsdsaelaAVTVVAGAAAC-DRFEPPTGPPPGPGTEApANESRSTPTWSLSTLAPASPAREG 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   853 TPGYPDPSSPqvnpqynpqtPGTPAMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNThSPASYHPTP---- 928
Cdd:PHA03307  105 SPTPPGPSSP----------DPPPPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPA-AVASDAASSrqaa 173

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 22094123   929 --SPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPGSGIEQNSSD 972
Cdd:PHA03307  174 lpLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASS 219
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 595-632 1.39e-05

KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); 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. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues.


Pssm-ID: 240504  Cd Length: 49  Bit Score: 43.36  E-value: 1.39e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 22094123  595 KDIVKVIDGPHSGREGEIRHLYRSFAFLHCKKLVENGG 632
Cdd:cd00380    1 GDVVRVLRGPYKGREGVVVDIDPRFGIVTVKGATGSKG 38
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 859-970 1.41e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 49.31  E-value: 1.41e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   859 PSSPQVNPQYNPQTpgtpamynTDQFSPYAAPSPQGSYQPSPSPQSYHQ-VAPSPAGYQNTHSPASYHPTPSPMAYQASP 937
Cdd:PRK10263  740 PHEPLFTPIVEPVQ--------QPQQPVAPQQQYQQPQQPVAPQPQYQQpQQPVAPQPQYQQPQQPVAPQPQYQQPQQPV 811

                          90       100       110
                  ....*....|....*....|....*....|...
gi 22094123   938 SPSPVGYSPMTPGAPSPGGYNPHTPGSGIEQNS 970
Cdd:PRK10263  812 APQPQYQQPQQPVAPQPQYQQPQQPVAPQPQDT 844
Pro-rich pfam15240
Proline-rich protein; This family includes several eukaryotic proline-rich proteins.
 810-962 2.07e-05

Proline-rich protein; This family includes several eukaryotic proline-rich proteins.


Pssm-ID: 464580 [Multi-domain]  Cd Length: 167  Bit Score: 46.18  E-value: 2.07e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    810 AQSGAWDPNNPNTPSR-AEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQfsPYA 888
Cdd:pfam15240   16 AQSSSEDVSQEDSPSLiSEEEGQSQQGGQGPQGPPPGGFPPQPPASDDPPGPPPPGGPQQPPPQGGKQKPQGPPP--QGG 93

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 22094123    889 APSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPSPvGYSPMTPGAPSPGGyNPHTP 962
Cdd:pfam15240   94 PRPPPGKPQGPPPQGGNQQQGPPPPGKPQGPPPQGGGPPPQGGNQQGPPPPPP-GNPQGPPQRPPQPG-NPQGP 165
SP7_N cd22542
N-terminal domain of transcription factor Specificity Protein (SP) 7; Specificity Proteins ...
 796-964 2.82e-05

N-terminal domain of transcription factor Specificity Protein (SP) 7; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP7, also called Osterix (Osx) in humans, is highly conserved among bone-forming vertebrates. It plays a major role, along with Runx2 and Dlx5 in driving the differentiation of mesenchymal precursor cells into osteoblasts and eventually osteocytes. SP7 also plays a regulatory role by inhibiting chondrocyte differentiation, maintaining the balance between differentiation of mesenchymal precursor cells into ossified bone or cartilage. Mutations of this gene have been associated with multiple dysfunctional bone phenotypes in vertebrates. SP7 is thought to play a role in diseases such as Osteogenesis imperfecta. SP7 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (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. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. This model represents the N-terminal domain of SP7.


Pssm-ID: 411691 [Multi-domain]  Cd Length: 297  Bit Score: 47.20  E-value: 2.82e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  796 YGSQTPLHDgSRTPAQSGAWDPNNPNTP--------SRAEE----EYEYAFDD-----EPTPSPQA---YGGTPNPQTPG 855
Cdd:cd22542   26 FGGSSPIRD-SATPGKPGNNPGKKPYSLgsdlssakSRSSElmgdSYTATFSSgnglmSPSGSPQAsttYGNDYNPFSHS 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  856 YPDPSSPQ----VNPQYNPQTPGTPAMYNT-DQFSPY-----AAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYH 925
Cdd:cd22542  105 FPTSSGSQdpslLVSKGHPSADCLPSVYTSlDMAHPYgswykTGIHPGISSSSTNATASWWDMHSNTNWLSAQGQPDGLQ 184

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 22094123  926 PTPSPMAYQASPSPSPVGYSPMTPgaPSPGGYNPHTPGS 964
Cdd:cd22542  185 ASLQPVPAQTPLNPQLPSYTEFTT--LNPAPYPAVGISS 221
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 837-960 3.25e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 48.06  E-value: 3.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   837 EPTPSPQAYGGTPNPQTPGyPDPSSPQVNPQYNPQTPGTPAmyntdqfsPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQ 916
Cdd:PRK07764  391 AGAPAAAAPSAAAAAPAAA-PAPAAAAPAAAAAPAPAAAPQ--------PAPAPAPAPAPPSPAGNAPAGGAPSPPPAAA 461

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 22094123   917 NTHSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPH 960
Cdd:PRK07764  462 PSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAG 505
PHA03247 PHA03247
large tegument protein UL36; Provisional
 769-962 3.74e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 48.01  E-value: 3.74e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   769 TPMYGSGSRTPmyGSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGT 848
Cdd:PHA03247 2741 PPAVPAGPATP--GGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAAL 2818

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   849 PNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFS-----PYAAPSPQGSYQPSPSPQSYHQVA--PSPAGYQNTHS- 920
Cdd:PHA03247 2819 PPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSvapggDVRRRPPSRSPAAKPAAPARPPVRrlARPAVSRSTESf 2898

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 22094123   921 ---PASYHPTPSPMAyQASPSPSPVGYSPMTPGAPSPGGYNPHTP 962
Cdd:PHA03247 2899 alpPDQPERPPQPQA-PPPPQPQPQPPPPPQPQPPPPPPPRPQPP 2942
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 735-954 4.08e-05

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.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 47.84  E-value: 4.08e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    735 QTISVDRQRLTTVDSQRPGGMTS-TYGRTPMYGSQTPMYGSGSRTPMYGSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSG 813
Cdd:pfam03154   24 QTASPDGRASPTNEDLRSSGRNSpSAASTSSNDSKAESMKKSSKKIKEEAPSPLKSAKRQREKGASDTEEPERATAKKSK 103

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    814 AWDPNNPNTPSRAEEEYE--YAFDDEPTPSPQAYGGTPNPQTPGYPDP--------SS----------PQVNPQYNPQTP 873
Cdd:pfam03154  104 TQEISRPNSPSEGEGESSdgRSVNDEGSSDPKDIDQDNRSTSPSIPSPqdnesdsdSSaqqqilqtqpPVLQAQSGAASP 183

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    874 GTPAMYNTDQfSPYAAPSPQGsyqPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPSPvGYSPMTPGAPS 953
Cdd:pfam03154  184 PSPPPPGTTQ-AATAGPTPSA---PSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSPHP-PLQPMTQPPPP 258


                   .
gi 22094123    954 P 954
Cdd:pfam03154  259 S 259
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 469-496 5.43e-05

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


Pssm-ID: 128978  Cd Length: 28  Bit Score: 41.16  E-value: 5.43e-05
                            10        20
                    ....*....|....*....|....*...
gi 22094123     469 YFKMGDHVKVIAGRFEGDTGLIVRVEEN 496
Cdd:smart00739    1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 838-952 7.49e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 46.60  E-value: 7.49e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   838 PTPSPQAYGGTPNPQTPGyPDPSSPQVNPQYNPQTPGTPAmyntdqfsPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQN 917
Cdd:PRK14959  387 EGPASGGAATIPTPGTQG-PQGTAPAAGMTPSSAAPATPA--------PSAAPSPRVPWDDAPPAPPRSGIPPRPAPRMP 457

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 22094123   918 THSPASYHPTPSPMAYQASPSPS-PVGYSPMTPGAP 952
Cdd:PRK14959  458 EASPVPGAPDSVASASDAPPTLGdPSDTAEHTPSGP 493
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 700-731 9.19e-05

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.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 40.45  E-value: 9.19e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 22094123    700 IGQTVRISQGPYKGYIGVVKDATESTARVELH 731
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
PHA03247 PHA03247
large tegument protein UL36; Provisional
 777-956 1.06e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.86  E-value: 1.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   777 RTPMYGSQTPLQDGSRTPHYGSQTPLhdgsRTPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPS--------------P 842
Cdd:PHA03247 2599 RAPVDDRGDPRGPAPPSPLPPDTHAP----DPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGrvsrprrarrlgraA 2674

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   843 QAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAP-SPQGSYQPSPSPQSYHQVAPSPAGyqnTHSP 921
Cdd:PHA03247 2675 QASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPpGPAAARQASPALPAAPAPPAVPAG---PATP 2751

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 22094123   922 ASYHPTPSPMAYQASPSPSPVGYSPMTP--GAPSPGG 956
Cdd:PHA03247 2752 GGPARPARPPTTAGPPAPAPPAAPAAGPprRLTRPAV 2788
Pneumo_att_G pfam05539
Pneumovirinae attachment membrane glycoprotein G;
746-928 1.20e-04

Pneumovirinae attachment membrane glycoprotein G;


Pssm-ID: 114270 [Multi-domain]  Cd Length: 408  Bit Score: 45.81  E-value: 1.20e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    746 TVDSQRPGGMTSTYGRTPMYGSQTPMYGSGSRTPMYGSQT----PLQDG-SRTPHYGSQTPLHDgSRTPAQSGAWDP--N 818
Cdd:pfam05539  194 TPQSQPATQGHQTATANQRLSSTEPVGTQGTTTSSNPEPQteppPSQRGpSGSPQHPPSTTSQD-QSTTGDGQEHTQrrK 272

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    819 NPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPyaaPSPQ----- 893
Cdd:pfam05539  273 TPPATSNRRSPHSTATPPPTTKRQETGRPTPRPTATTQSGSSPPHSSPPGVQANPTTQNLVDCKELDP---PKPNsicyg 349

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 22094123    894 -GSYQPSpSPQSYHQVAPSPAGYqNTHSPASYHPTP 928
Cdd:pfam05539  350 vGIYNEA-LPRGCDIVVPLCSTY-TIMCMDTYYSKP 383
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 839-954 1.29e-04

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 46.06  E-value: 1.29e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    839 TPSPQAYGGTPNPQTPGY--PD-----PSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPS 911
Cdd:pfam05109  422 SKAPESTTTSPTLNTTGFaaPNtttglPSSTHVPTNLTAPASTGPTVSTADVTSPTPAGTTSGASPVTPSPSPRDNGTES 501

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 22094123    912 PAgyQNTHSPASYHPTPSPMAyqasPSPSPVGYSPmTPGAPSP 954
Cdd:pfam05109  502 KA--PDMTSPTSAVTTPTPNA----TSPTPAVTTP-TPNATSP 537
PHA03247 PHA03247
large tegument protein UL36; Provisional
 776-954 1.38e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.47  E-value: 1.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   776 SRTPMYGSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEEyeyAFDDEPTPsPQAYGGTPNPQTPG 855
Cdd:PHA03247 2710 PAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTT---AGPPAPAP-PAAPAAGPPRRLTR 2785

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   856 YP----DPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPqgsyqPSPSPQSYHQVAPSPA-----------GYQNTHS 920
Cdd:PHA03247 2786 PAvaslSESRESLPSPWDPADPPAAVLAPAAALPPAASPAG-----PLPPPTSAQPTAPPPPpgppppslplgGSVAPGG 2860

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 22094123   921 PASYHPTP-SPMAYQASPSPSPVGYSPMTPGAPSP 954
Cdd:PHA03247 2861 DVRRRPPSrSPAAKPAAPARPPVRRLARPAVSRST 2895
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 789-977 1.48e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 46.13  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   789 DGSRTPHYGSQTPLHDGSR--TPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNP 866
Cdd:PRK07764  596 GGEGPPAPASSGPPEEAARpaAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGG 675

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   867 QYNPQTPGTPAMyntdqfSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSP 946
Cdd:PRK07764  676 AAPAAPPPAPAP------AAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPP 749

                         170       180       190
                  ....*....|....*....|....*....|.
gi 22094123   947 MTPGAPSPGGYNPHTPGSGIEQNSSDWVTTD 977
Cdd:PRK07764  750 DPAGAPAQPPPPPAPAPAAAPAAAPPPSPPS 780
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 804-964 1.98e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 45.55  E-value: 1.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   804 DGSRTPAQSGAWDPNNPNTPSRAeeeyeyAFDDEPTPSPQAYGGTPNPQTPGYPDPSSP--QVNPQYNPQTPGTPAMYNT 881
Cdd:PHA03307  238 DSSSSESSGCGWGPENECPLPRP------APITLPTRIWEASGWNGPSSRPGPASSSSSprERSPSPSPSSPGSGPAPSS 311

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   882 DQFSPYAAPSPQGSyQPSPSPQSyhqVAPSPAGyqnTHSPASYHPTPSPmayqASPSPSPVGYSPMTPGAPSPGGYNPHT 961
Cdd:PHA03307  312 PRASSSSSSSRESS-SSSTSSSS---ESSRGAA---VSPGPSPSRSPSP----SRPPPPADPSSPRKRPRPSRAPSSPAA 380


                  ...
gi 22094123   962 PGS 964
Cdd:PHA03307  381 SAG 383
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 849-1035 2.03e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 45.19  E-value: 2.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   849 PNPQTPGYPDPSSPQVNPQYNPQTPGTPAMyntdqfspyAAPSPQGSYQPSPSPQSyhQVAPSPAGYQNTHSPASYHPTP 928
Cdd:PRK14950  364 PAPQPAKPTAAAPSPVRPTPAPSTRPKAAA---------AANIPPKEPVRETATPP--PVPPRPVAPPVPHTPESAPKLT 432

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   929 spmayqasPSPSPVGYSPMTPGAPSPGGYNP--HTPGSGIEQNSSDWVTTDIQVKVRDTYLdtQIVGQTGViRSVTggmc 1006
Cdd:PRK14950  433 --------RAAIPVDEKPKYTPPAPPKEEEKalIADGDVLEQLEAIWKQILRDVPPRSPAV--QALLSSGV-RPVS---- 497

                         170       180       190
                  ....*....|....*....|....*....|
gi 22094123  1007 svyLKDSEKVVSISSE-HLEPITPTKNNKV 1035
Cdd:PRK14950  498 ---VEKNTLTLSFKSKfHKDKIEEPENRKI 524
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 818-954 2.08e-04

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 45.14  E-value: 2.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   818 NNPNTPSRAEEEYEYAFDD-EPTPSPQAYGGTPN-PQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQG- 894
Cdd:NF033839  249 DNVNTKVEIENTVHKIFADmDAVVTKFKKGLTQDtPKEPGNKKPSAPKPGMQPSPQPEKKEVKPEPETPKPEVKPQLEKp 328

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 22094123   895 SYQPSPSPQSYH-QVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPSpvgySPMTPGAPSP 954
Cdd:NF033839  329 KPEVKPQPEKPKpEVKPQLETPKPEVKPQPEKPKPEVKPQPEKPKPE----VKPQPETPKP 385
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 473-501 2.08e-04

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.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 39.29  E-value: 2.08e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 22094123    473 GDHVKVIAGRFEGDTGLIVRVEE--NFVILF 501
Cdd:pfam00467    2 GDVVRVIAGPFKGKVGKVVEVDDkkNRVLVE 32
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 809-964 2.22e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 45.36  E-value: 2.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   809 PAQSGAWDPNNPNTPSRAEEEYEYAfdDEPTPS---PQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFS 885
Cdd:PRK07764  592 PGAAGGEGPPAPASSGPPEEAARPA--APAAPAapaAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGW 669

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   886 PYAAPSPQGSyQPSPSPQSYHQVAPS--PAGYQNTHSPASYHP---------TPSPMAYQASPSPSPVGYSPMTPGAPSP 954
Cdd:PRK07764  670 PAKAGGAAPA-APPPAPAPAAPAAPAgaAPAQPAPAPAATPPAgqaddpaaqPPQAAQGASAPSPAADDPVPLPPEPDDP 748

                         170
                  ....*....|
gi 22094123   955 GGYNPHTPGS 964
Cdd:PRK07764  749 PDPAGAPAQP 758
PHA03247 PHA03247
large tegument protein UL36; Provisional
 820-962 2.31e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 45.70  E-value: 2.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   820 PNTPS-RAEEEYEYAFDDEPTPSPQAyGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMY----NTDQFSPYAAPSPQG 894
Cdd:PHA03247 2475 PGAPVyRRPAEARFPFAAGAAPDPGG-GGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLtwirGLEELASDDAGDPPP 2553

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   895 SYQPSPSPQSYHQVAPSPagyqnthSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAP--SPGGYNPHTP 962
Cdd:PHA03247 2554 PLPPAAPPAAPDRSVPPP-------RPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDrgDPRGPAPPSP 2616
dnaA PRK14086
chromosomal replication initiator protein DnaA;
779-943 2.33e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 45.20  E-value: 2.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   779 PMY-GSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNnPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYP 857
Cdd:PRK14086  103 RRTsEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLPTAR-PAYPAYQQRPEPGAWPRAADDYGWQQQRLGFPPRAPYA 181

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   858 DPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGSY-------QPSPSPQSYHQV--APSPAGYQNTHSPASYHPTP 928
Cdd:PRK14086  182 SPASYAPEQERDREPYDAGRPEYDQRRRDYDHPRPDWDRprrdrtdRPEPPPGAGHVHrgGPGPPERDDAPVVPIRPSAP 261

                         170
                  ....*....|....*
gi 22094123   929 SPMAYQASPSPSPVG 943
Cdd:PRK14086  262 GPLAAQPAPAPGPGE 276
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 810-954 2.84e-04

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.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 45.14  E-value: 2.84e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    810 AQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQayGGTPNPQTPGYPDPSSP-----QVNPQYNPQTpgTPAMYNTDQF 884
Cdd:pfam03154  176 AQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQ--GSPATSQPPNQTQSTAAphtliQQTPTLHPQR--LPSPHPPLQP 251

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    885 SPYAAPSPQGSYQPSPSPQSY------------------HQVAPSPAGYQNTHSPASYHPTPSPMAyqASPSPSPVGYSP 946
Cdd:pfam03154  252 MTQPPPPSQVSPQPLPQPSLHgqmppmphslqtgpshmqHPVPPQPFPLTPQSSQSQVPPGPSPAA--PGQSQQRIHTPP 329


                   ....*...
gi 22094123    947 MTPGAPSP 954
Cdd:pfam03154  330 SQSQLQSQ 337
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 790-962 3.44e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 44.78  E-value: 3.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   790 GSRTPHYGSQTPLHDGSRTPAQSGAWDPnnPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQvnPQYN 869
Cdd:PHA03307  773 ALLEPAEPQRGAGSSPPVRAEAAFRRPG--RLRRSGPAADAASRTASKRKSRSHTPDGGSESSGPARPPGAAAR--PPPA 848

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   870 PQTPGTPAMyntDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASyHPTPSPMAyqaspsPSPVGYSPMTP 949
Cdd:PHA03307  849 RSSESSKSK---PAAAGGRARGKNGRRRPRPPEPRARPGAAAPPKAAAAAPPAG-APAPRPRP------APRVKLGPMPP 918

                         170       180
                  ....*....|....*....|
gi 22094123   950 GAPSP-GGY------NPHTP 962
Cdd:PHA03307  919 GGPDPrGGFrrvppgDLHTP 938
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
840-971 4.24e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 44.48  E-value: 4.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   840 PSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTH 919
Cdd:PRK12323  392 PAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRP 471

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 22094123   920 SPASYHPTPSPMAYQASPSPSPVGYSP---MTPGAPSPGGYNPHTPGSGIEQNSS 971
Cdd:PRK12323  472 VAAAAAAAPARAAPAAAPAPADDDPPPweeLPPEFASPAPAQPDAAPAGWVAESI 526
PTZ00395 PTZ00395
Sec24-related protein; Provisional
 782-960 4.68e-04

Sec24-related protein; Provisional


Pssm-ID: 185594 [Multi-domain]  Cd Length: 1560  Bit Score: 44.30  E-value: 4.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   782 GSQTPLQDGSRTPHYGSQTPL-HDGSRTPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTP--NP--QTPGY 856
Cdd:PTZ00395  345 GSPNAASAGAPFNGLGNQADGgHINQVHPDARGAWAGGPHSNASYNCAAYSNAAQSNAAQSNAGFSNAGysNPgnSNPGY 424

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   857 PDP---SSPQVNPQY------NPQTPGTPamYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPT 927
Cdd:PTZ00395  425 NNApnsNTPYNNPPNsntpysNPPNSNPP--YSNLPYSNTPYSNAPLSNAPPSSAKDHHSAYHAAYQHRAANQPAANLPT 502

                         170       180       190
                  ....*....|....*....|....*....|...
gi 22094123   928 PSPMAyqASPSPSPVGYSPMTPGAPSPGGYNPH 960
Cdd:PTZ00395  503 ANQPA--ANNFHGAAGNSVGNPFASRPFGSAPY 533
DUF1373 pfam07117
Protein of unknown function (DUF1373); This family consists of several hypothetical proteins ...
 820-934 5.06e-04

Protein of unknown function (DUF1373); This family consists of several hypothetical proteins which seem to be specific to Oryzias latipes (Japanese ricefish). Members of this family are typically around 200 residues in length. The function of this family is unknown.


Pssm-ID: 462093 [Multi-domain]  Cd Length: 212  Bit Score: 42.86  E-value: 5.06e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    820 PNTPSRAEEEYEY----AFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGS 895
Cdd:pfam07117   42 PPRPEEEEGQGGGggtfPFPGSPEPEPGGGGSGPMPMSASAPEPEPAKAKPQRPAPAQGHGHGGGGDSDSSGSGSGHQGS 121

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 22094123    896 YQP---SPSPQSYHQVAPSPAGYQNTHSPasyHPTPSPMAYQ 934
Cdd:pfam07117  122 GGAgagAGAPGHQHEQEQESSSSDDDDED---EFEFTPEEDE 160
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 786-955 5.07e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 44.39  E-value: 5.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   786 PLQDGSRTPHYGSQT--PLHDGSRTPAQSGAWDPNNP-------NTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGY 856
Cdd:PHA03307  195 PSTPPAAASPRPPRRssPISASASSPAPAPGRSAADDagasssdSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASG 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   857 PDPSSPQVNPQYNPQTPGtpamyntdqfSPYAAPSPQ---GSYQPSPSPQSYHQVAPSPAGyqnTHSPASYHPTPSPMAY 933
Cdd:PHA03307  275 WNGPSSRPGPASSSSSPR----------ERSPSPSPSspgSGPAPSSPRASSSSSSSRESS---SSSTSSSSESSRGAAV 341

                         170       180
                  ....*....|....*....|..
gi 22094123   934 QASPSPSPVGYSPMTPGAPSPG 955
Cdd:PHA03307  342 SPGPSPSRSPSPSRPPPPADPS 363
dnaA PRK14086
chromosomal replication initiator protein DnaA;
837-963 5.34e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 44.05  E-value: 5.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   837 EPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGSYQPSPSPQsyhqvAPSPAGYQ 916
Cdd:PRK14086   94 EPAPPPPHARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLPTARPAYPAYQQRPEPGAWPR-----AADDYGWQ 168

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 22094123   917 NT-HSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGyNPHTPG 963
Cdd:PRK14086  169 QQrLGFPPRAPYASPASYAPEQERDREPYDAGRPEYDQRRR-DYDHPR 215
Pneumo_att_G pfam05539
Pneumovirinae attachment membrane glycoprotein G;
806-1009 6.45e-04

Pneumovirinae attachment membrane glycoprotein G;


Pssm-ID: 114270 [Multi-domain]  Cd Length: 408  Bit Score: 43.50  E-value: 6.45e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    806 SRTPAQSGAWDPN--NPNTPS-RAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQvnPQYNPqtpgtPAMYNTD 882
Cdd:pfam05539  171 AVTTSKTTSWPTEvsHPTYPSqVTPQSQPATQGHQTATANQRLSSTEPVGTQGTTTSSNPE--PQTEP-----PPSQRGP 243

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    883 QFSPYAAPS-PQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASyHPTPSPM-----AYQASPSPSPVGYSPMTPGAPSPGG 956
Cdd:pfam05539  244 SGSPQHPPStTSQDQSTTGDGQEHTQRRKTPPATSNRRSPHS-TATPPPTtkrqeTGRPTPRPTATTQSGSSPPHSSPPG 322

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 22094123    957 --YNPHTpgsgieQNSSDWVTTDIQVKVRDTY-LDTQIVGQTGVIRSVTgGMCSVY 1009
Cdd:pfam05539  323 vqANPTT------QNLVDCKELDPPKPNSICYgVGIYNEALPRGCDIVV-PLCSTY 371
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 779-944 6.56e-04

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 43.92  E-value: 6.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   779 PMYGSQTPLQDGSR--TPHYGSQTPlhDGSRTPAQSGaWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGY 856
Cdd:PRK10263  345 PVASVDVPPAQPTVawQPVPGPQTG--EPVIAPAPEG-YPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAEQPAQQPYY 421

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   857 -PDPSSPQVNPQYNPQtPGTPAMYNtdqfsPYAAPSPQGSYQPSPSPQSYHQ-VAPSPAGYQNTHSPASYHPT---PSPM 931
Cdd:PRK10263  422 aPAPEQPAQQPYYAPA-PEQPVAGN-----AWQAEEQQSTFAPQSTYQTEQTyQQPAAQEPLYQQPQPVEQQPvvePEPV 495

                         170
                  ....*....|...
gi 22094123   932 AYQASPSPSPVGY 944
Cdd:PRK10263  496 VEETKPARPPLYY 508
KLF1_2_4_N cd21972
N-terminal domain of Kruppel-like factor (KLF) 1, KLF2, KLF4, and similar proteins; Kruppel ...
 823-962 8.16e-04

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.


Pssm-ID: 409230 [Multi-domain]  Cd Length: 194  Bit Score: 41.89  E-value: 8.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  823 PSRAEEEYEYAFDDEPTPSPQAYG----GTPNPQTPGYPDPSSPQVNPQYN-PQTPGTPAMYNTDQFSPYAAPSPQGSYQ 897
Cdd:cd21972   22 LDLEFILSNTVTSDNDNPPPPDPAypppESPESCSTVYDSDGCHPTPNAYCgPNGPGLPGHFLLAGNSPNLGPKIKTENQ 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 22094123  898 PS-------PSPQSYHQVAPS------PAGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSPmtPGAPSPGGYNPHTP 962
Cdd:cd21972  102 EQacmpvagYSGHYGPREPQRvppappPPQYAGHFQYHGHFNMFSPPLRANHPGMSTVMLTP--LSTPPLGFLSPEEA 177
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 761-954 8.28e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 43.62  E-value: 8.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   761 RTPMYGSQTPMYGSGSRTPMYGSQTPLQDGSRTPhygsQTPLHDGSRTPAQSGAWDPNnPNTPSRAEeeyeyafdDEPTP 840
Cdd:PHA03307   64 RFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAP----ASPAREGSPTPPGPSSPDPP-PPTPPPAS--------PPPSP 130

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   841 SPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTdqfSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGyqnths 920
Cdd:PHA03307  131 APDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQ---AALPLSSPEETARAPSSPPAEPPPSTPPAA------ 201

                         170       180       190
                  ....*....|....*....|....*....|....
gi 22094123   921 PASYHPTPSPMAyqASPSPSPVGYSPMTPGAPSP 954
Cdd:PHA03307  202 ASPRPPRRSSPI--SASASSPAPAPGRSAADDAG 233
Med26_M pfam15694
Mediator complex subunit 26 middle domain; Med26_M is the middle domain of subunit 26 of ...
 852-968 9.52e-04

Mediator complex subunit 26 middle domain; Med26_M is the middle domain of subunit 26 of Mediator. Med19 and Med26 act synergistically to mediate the interaction between REST (a Kruppel-type zinc finger transcription factor that binds to a 21-bp RE1 silencing element present in over 900 human genes) and Mediator.


Pssm-ID: 464807 [Multi-domain]  Cd Length: 255  Bit Score: 42.17  E-value: 9.52e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123    852 QTPGYPDPSSPQvNPQYNPQTpgTPAMYNTDQFSPYAapsPQGSY-QPSPSPQSYHQVAPSPAGYQNTHSP--------A 922
Cdd:pfam15694   81 ETGGPPQPKSPR-CSSFSPRN--SRHETFARRSSTYA---PKGSVpSPSPRSQVLDAQVPSPLPLSQPSTPpvqakrleK 154

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 22094123    923 SYHPTP-SPMAYQASPS-----PSPVGYSPMTPGAPSPGGYNPHTPGSGIEQ 968
Cdd:pfam15694  155 PPQSSPeSSQHWLEQSDseshqRHQDGSATLLSQSVSPGCKTPLHPGENSLP 206
PHA03369 PHA03369
capsid maturational protease; Provisional
 808-905 1.17e-03

capsid maturational protease; Provisional


Pssm-ID: 223061 [Multi-domain]  Cd Length: 663  Bit Score: 43.06  E-value: 1.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   808 TPAQSGAWDPNnPNTPSRAEEE-YEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVnpqynPQTPGTPAMYNTDQFSP 886
Cdd:PHA03369  353 LTAPSRVLAAA-AKVAVIAAPQtHTGPADRQRPQRPDGIPYSVPARSPMTAYPPVPQF-----CGDPGLVSPYNPQSPGT 426

                          90
                  ....*....|....*....
gi 22094123   887 YAAPSPQGSYQPSPSPQSY 905
Cdd:PHA03369  427 SYGPEPVGPVPPQPTNPYV 445
KLF3_N cd21577
N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called ...
 885-960 1.46e-03

N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called Krueppel-like factor 3 and originally called Basic Kruppel-like Factor/BKLF), was the third member of the KLF family of zinc finger transcription factors to be discovered. KLF3 possesses a wide range of biological impacts on regulating apoptosis, differentiation, and proliferation in various tissues during the entire progression process. It has been proposed as a tumor suppressor in colorectal cancer. It appears to function predominantly as a repressor of transcription, turning genes off by recruiting the C-terminal Binding Protein co-repressors CtBP1 and CtBP2. CtBP docks onto a short motif (residues 61-65) in the N-terminus of KLF3, through the Proline-X-Aspartate-Leucine-Serine (PXDLS) motif. CtBP in turn recruits histone modifying enzymes to alter chromatin and repress gene expression. KLF3 belongs 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 specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF3.


Pssm-ID: 410554 [Multi-domain]  Cd Length: 214  Bit Score: 41.18  E-value: 1.46e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 22094123  885 SPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHsPASYHP--TPSPMAYQASPSPSPVGYSPMTpgAPSPGGYNPH 960
Cdd:cd21577   41 SSSSSSSSPSSRASPPSPYSKSSPPSPPQQRPLSP-PLSLPPpvAPPPLSPGSVPGGLPVISPVMV--QPVPVLYPPH 115
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 846-965 1.52e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 42.67  E-value: 1.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   846 GGTPNPQTPGYPDPSSPQVnPQYNPQTPGTPAMyntdqfspyAAPSPQGSYQPSPSPQSYHQVAPSPAgyqnthSPASYH 925
Cdd:PRK07764  389 GGAGAPAAAAPSAAAAAPA-AAPAPAAAAPAAA---------AAPAPAAAPQPAPAPAPAPAPPSPAG------NAPAGG 452

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 22094123   926 PTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPGSG 965
Cdd:PRK07764  453 APSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAA 492
PHA03269 PHA03269
envelope glycoprotein C; Provisional
 869-976 1.72e-03

envelope glycoprotein C; Provisional


Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 42.41  E-value: 1.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   869 NPQTP-GTPAMYN---TDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPSPVGY 944
Cdd:PHA03269   21 NLNTNiPIPELHTsaaTQKPDPAPAPHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQAASRAPDPAV 100

                          90       100       110
                  ....*....|....*....|....*....|..
gi 22094123   945 SPMTPGAPSPggyNPHTPGSGIEQNSSDWVTT 976
Cdd:PHA03269  101 APQLAAAPKP---DAAEAFTSAAQAHEAPADA 129
PHA03369 PHA03369
capsid maturational protease; Provisional
 848-985 1.73e-03

capsid maturational protease; Provisional


Pssm-ID: 223061 [Multi-domain]  Cd Length: 663  Bit Score: 42.29  E-value: 1.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   848 TPNPQTPGYPDPSSPQVNPqynPQTPGTPAM---YNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSpAGYQNTHSPASY 924
Cdd:PHA03369  353 LTAPSRVLAAAAKVAVIAA---PQTHTGPADrqrPQRPDGIPYSVPARSPMTAYPPVPQFCGDPGLV-SPYNPQSPGTSY 428

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 22094123   925 HPTPSPMAYQASPSPS--PVGYSPMT-PGAPSPGGYnpHTPGS-GIEQNSSDWVTTDIQVKVRDT 985
Cdd:PHA03369  429 GPEPVGPVPPQPTNPYvmPISMANMVyPGHPQEHGH--ERKRKrGGELKEELIETLKLVKKLKEE 491
dnaA PRK14086
chromosomal replication initiator protein DnaA;
817-965 1.99e-03

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 42.12  E-value: 1.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   817 PNNPNTPSRAEEeyeyafddeptPSPQAYGGTPNPQTPGYPDPSSPQVNPQYnPQTPGTPAMY--NTDQFSPYAAPSPQG 894
Cdd:PRK14086   96 APPPPHARRTSE-----------PELPRPGRRPYEGYGGPRADDRPPGLPRQ-DQLPTARPAYpaYQQRPEPGAWPRAAD 163

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   895 SYQPSPSPQSYhqvaPSPAGYQnthSPASYHPTPSPMAY----------QASPSPSPVGYSPMTPGA-------PSPGGY 957
Cdd:PRK14086  164 DYGWQQQRLGF----PPRAPYA---SPASYAPEQERDREpydagrpeydQRRRDYDHPRPDWDRPRRdrtdrpePPPGAG 236


                  ....*...
gi 22094123   958 NPHTPGSG 965
Cdd:PRK14086  237 HVHRGGPG 244
PHA03325 PHA03325
nuclear-egress-membrane-like protein; Provisional
 798-959 2.10e-03

nuclear-egress-membrane-like protein; Provisional


Pssm-ID: 223044  Cd Length: 418  Bit Score: 41.79  E-value: 2.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   798 SQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAyggtpnpqtpgYPDPSSPQVNPQYNPQTPGTPA 877
Cdd:PHA03325  266 SSLPTSAPKRRSRRAGAMRAAAGETADLADDDGSEHSDPEPLPASLP-----------PPPVRRPRVKHPEAGKEEPDGA 334

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   878 MYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGyqnthSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGY 957
Cdd:PHA03325  335 RNAEAKEPAQPATSTSSKGSSSAQNKDSGSTGPGSSL-----AAASSFLEDDDFGSPPLDLTTSLRHMPSPSVTSAPEPP 409


                  ..
gi 22094123   958 NP 959
Cdd:PHA03325  410 SI 411
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 838-955 2.91e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.90  E-value: 2.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   838 PTPSPQAYGGTPNPQTPgypDPSSPQVNPQYNPQTPGTPAmyntdqfSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQN 917
Cdd:PRK07764  404 AAPAAAPAPAAAAPAAA---AAPAPAAAPQPAPAPAPAPA-------PPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAA 473

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 22094123   918 THSPASyhPTPSPMAYQASPSPSPVgysPMTPGAPSPG 955
Cdd:PRK07764  474 PEPTAA--PAPAPPAAPAPAAAPAA---PAAPAAPAGA 506
KREPA2 cd23959
Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of ...
 763-954 3.33e-03

Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of the parasitic protozoan's KREPA RNA editing catalytic complex (RECC). Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPAs are responsible for the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. Apart from the conserved C-terminal OB-fold domain, KREPA1, KREPA2, and KREPA3 contain two conserved C2H2 zinc-finger domains. KREPA2 and kinetoplastid RNA editing ligase 1 (KREL1) are specific for ligation post-U-deletion and are paralogous to KREL2 and KREPA1 that are specific for ligation post-U-insertion. KREPA2, is critical for RECC stability and KREL1 integration into the complex.


Pssm-ID: 467780 [Multi-domain]  Cd Length: 424  Bit Score: 41.01  E-value: 3.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  763 PMYGSQTPMYGSGSRTPMYGSQTPLQDGSRTPHYGSQTPLhDGSRTPAQSGAWDPNNP----NTPSRAEEEYEYAFDDEP 838
Cdd:cd23959   56 PLYGAVSPEGENPFDGPGLVTASTVSDCYVGNANFYEVDM-SDAFAMAPDESLGPFRAarvpNPFSASSSTQRETHKTAQ 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  839 TPSPQAYGGTPnPQTPGYPDPSSPQVNPqynPQTPGTPAMYNTDQ-FSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQN 917
Cdd:cd23959  135 VAPPKAEPQTA-PVTPFGQLPMFGQHPP---PAKPLPAAAAAQQSsASPGEVASPFASGTVSASPFATATDTAPSSGAPD 210

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 22094123  918 THSPASyhPTPSPMAyqASPSPSPVGYSPMTPGAPSP 954
Cdd:cd23959  211 GFPAEA--SAPSPFA--APASAASFPAAPVANGEAAT 243
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 836-962 3.55e-03

pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A.


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 41.29  E-value: 3.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   836 DEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQynPQTPGTPAMYNTDQFSPYAAPSPQ-GSYQPSPSPQSYH-QVAPSPA 913
Cdd:NF033839  370 EKPKPEVKPQPETPKPEVKPQPEKPKPEVKPQ--PEKPKPEVKPQPEKPKPEVKPQPEkPKPEVKPQPEKPKpEVKPQPE 447

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 22094123   914 GYQNTHSPASYHPTPSPMAYQASPSPSpVGYSPMTP----GAPSPGGYNPHTP 962
Cdd:NF033839  448 KPKPEVKPQPETPKPEVKPQPEKPKPE-VKPQPEKPkpdnSKPQADDKKPSTP 499
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 775-913 5.06e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.12  E-value: 5.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123   775 GSRTPMYGSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEEYEyafddeptPSPQAYGGTPNPQTP 854
Cdd:PRK07764  674 GGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASA--------PSPAADDPVPLPPEP 745

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 22094123   855 GYPDPSSPQVNPQYNPQTPGTPAmyntdqfspyAAPSPQGSYQPSPSPQSYHQVAPSPA 913
Cdd:PRK07764  746 DDPPDPAGAPAQPPPPPAPAPAA----------APAAAPPPSPPSEEEEMAEDDAPSMD 794
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 594-625 5.43e-03

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.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 35.44  E-value: 5.43e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 22094123    594 VKDIVKVIDGPHSGREGEIRHLYRSFAFLHCK 625
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
KLF1_N cd21581
N-terminal domain of Kruppel-like Factor 1; Kruppel-like Factor 1 (KLF1, also known as ...
 766-960 7.36e-03

N-terminal domain of Kruppel-like Factor 1; Kruppel-like Factor 1 (KLF1, also known as Krueppel-like factor 1 or Erythroid Kruppel-like Factor/EKLF) was the first Kruppel-like factor discovered. It was found to be vitally important for embryonic erythropoiesis in promoting the switch from fetal hemoglobin (Hemoglobin F) to adult hemoglobin (Hemoglobin A) gene expression by binding to highly conserved CACCC domains. EKLF ablation in mouse embryos produces a lethal anemic phenotype, causing death by embryonic day 14, and natural mutations lead to beta+ thalassemia in humans. However, expression of embryonic hemoglobin and fetal hemoglobin genes is normal in EKLF-deficient mice, suggesting other factors may be involved. KLF1 functions as a transcriptional activator. It belongs 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 N-terminal domain of KLF1, which is related to the N-terminal domains of KLF2 and KLF4.


Pssm-ID: 409227 [Multi-domain]  Cd Length: 278  Bit Score: 39.64  E-value: 7.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  766 GSQTPMYGSGSRTPMYGSQTPLQdgsrtPHYGSQTPLHDGSRTpaqsgAWDPnnpntpsraeeeyEYAFDDEPTPSPQAy 845
Cdd:cd21581   26 EGQLPLDGPPDKLSPSGSEQLQV-----SQPMTEELLDDDSQA-----SWDI-------------EFLLSNWSSPSLNP- 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22094123  846 GGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYN----------TDQFSPYAAPSPQ-GSYQPSPSPQSYHQVAP---- 910
Cdd:cd21581   82 SLDNNTQALPQEEQPGAYYEPPKKDQPGTEGLQVGgpglmaellsPEESTGWAPPEPHhGYPDAFVGPALFPAPANvdqf 161

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 22094123  911 --SPAGYQNTH---------SPASYHPT--PSPMAYQASPSPSPVGYSPMTPgAPSPGGYNPH 960
Cdd:cd21581  162 gfPQGGSVDRRgnlsksgswDFGSYYPQqhPSVVAFPDSRFGPLSGPQALTP-DPQHYGYFQL 223
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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