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Conserved domains on  [gi|987437824|ref|NP_001306920|]
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transcription elongation factor SPT5 isoform b [Homo sapiens]

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 ...
 174-261 4.32e-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: 4.32e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  174 NLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLgyWNQQMVPI 253
Cdd:cd09888     1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYL--NTIKLVPI 78


                  ....*...
gi 987437824  254 KEMTDVLK 261
Cdd:cd09888    79 KEMPDVLS 86
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 768-885 6.79e-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: 112.23  E-value: 6.79e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824    768 GSQTPMYG-SGSRTPMYGSQTP----LQDGSRTPHYGSQTPLHDG--SRTPAQSGAWdPNNPNTPSRAEEEYEYAFDDEP 840
Cdd:smart01104    1 GGRTPAWGaSGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAWGGAG-PTGSRTPAWGGASAWGNKSSEG 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 987437824    841 TPSPQA--YGGTPNPQTPGYpdpssPQVNPQYNPQTPGTPAMYNTDQ 885
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 ...
 467-517 7.64e-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: 7.64e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 987437824  467 YFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLC 517
Cdd:cd06083     1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1024-1080 2.17e-26

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: 102.59  E-value: 2.17e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 987437824 1024 EHLEPITPTKNNKVKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLRFLGKL 1080
Cdd:cd06086     1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMDSDGDIKILPMNFLAKL 57
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 416-466 1.19e-25

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: 100.27  E-value: 1.19e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 987437824  416 FQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDMLEFPAQELRK 466
Cdd:cd06082     1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 698-747 4.90e-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: 4.90e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 987437824  698 DNELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLT 747
Cdd:cd06085     2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLA 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 593-635 1.52e-19

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: 82.57  E-value: 1.52e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 987437824  593 KDIVKVIDGPHSGREGEIRHLFRSFAFLHCKKLVENGGMFVCK 635
Cdd:cd06084     1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 272-309 1.66e-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: 1.66e-17
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 987437824  272 KSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMIPRIDY 309
Cdd:cd06081     1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
PHA03269 super family cl29788
envelope glycoprotein C; Provisional
 821-966 3.36e-09

envelope glycoprotein C; Provisional


The actual alignment was detected with superfamily member PHA03269:

Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 60.90  E-value: 3.36e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  821 NPNTPSRAEEEYEYAFDDEPTPSPQayggtPNPQTPGYPDPS-SPQVNPQYNPQtpgtpamyntdqfsPYAAPSPQGSYQ 899
Cdd:PHA03269   21 NLNTNIPIPELHTSAATQKPDPAPA-----PHQAASRAPDPAvAPTSAASRKPD--------------LAQAPTPAASEK 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 987437824  900 PSPSPQSYHQV--APSPAGYQNTHSPasyhPTPSPM-----AYQASPSPSPVGYSPMTPgAPSPGGYNPHTPGS 966
Cdd:PHA03269   82 FDPAPAPHQAAsrAPDPAVAPQLAAA----PKPDAAeaftsAAQAHEAPADAGTSAASK-KPDPAAHTQHSPPP 150
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 95-168 8.49e-09

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: 53.81  E-value: 8.49e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 987437824    95 GAEDILEKA----SNIDNVVLDEDRSGARRLQNLWRDQREEELGEYYMKKYAKSSvgETVYGGSDElsDDITQQQLLP 168
Cdd:pfam11942   24 GADDFIEDDeedeDEEDGRRDDRRHRELDRRRELEEDEDAEEIAEYLKERYGRSS--SDAYRGDAE--EGVPQRLLLP 97
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 174-261 4.32e-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: 4.32e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  174 NLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLgyWNQQMVPI 253
Cdd:cd09888     1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYL--NTIKLVPI 78


                  ....*...
gi 987437824  254 KEMTDVLK 261
Cdd:cd09888    79 KEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 174-260 6.63e-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: 6.63e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   174 NLWTVKCKIGEERATAISLMRKFIAYQfTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLGywNQQMVPI 253
Cdd:pfam03439    1 KIWAVKCTPGQEREVALSLMRKILALA-KTNNLGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGL--VPGLVPI 77


                   ....*..
gi 987437824   254 KEMTDVL 260
Cdd:pfam03439   78 KEMEHLL 84
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 768-885 6.79e-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: 112.23  E-value: 6.79e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824    768 GSQTPMYG-SGSRTPMYGSQTP----LQDGSRTPHYGSQTPLHDG--SRTPAQSGAWdPNNPNTPSRAEEEYEYAFDDEP 840
Cdd:smart01104    1 GGRTPAWGaSGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAWGGAG-PTGSRTPAWGGASAWGNKSSEG 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 987437824    841 TPSPQA--YGGTPNPQTPGYpdpssPQVNPQYNPQTPGTPAMYNTDQ 885
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 ...
 467-517 7.64e-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: 7.64e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 987437824  467 YFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLC 517
Cdd:cd06083     1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1024-1080 2.17e-26

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: 102.59  E-value: 2.17e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 987437824 1024 EHLEPITPTKNNKVKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLRFLGKL 1080
Cdd:cd06086     1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMDSDGDIKILPMNFLAKL 57
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 416-466 1.19e-25

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: 100.27  E-value: 1.19e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 987437824  416 FQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDMLEFPAQELRK 466
Cdd:cd06082     1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 698-747 4.90e-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: 4.90e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 987437824  698 DNELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLT 747
Cdd:cd06085     2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLA 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 593-635 1.52e-19

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: 82.57  E-value: 1.52e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 987437824  593 KDIVKVIDGPHSGREGEIRHLFRSFAFLHCKKLVENGGMFVCK 635
Cdd:cd06084     1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 272-309 1.66e-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: 1.66e-17
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 987437824  272 KSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMIPRIDY 309
Cdd:cd06081     1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 768-826 5.27e-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: 5.27e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   768 GSQTPMYGS--GSRTPMY---GSQTPL--QDGSRTPHY--GSQTPLHD--GSRTPAQSGAWDPnnPNTPS 826
Cdd:pfam12815    1 GSRTPAYNSagGSRTPAWgadGSRTPAygGAGGRTPAYnqGGKTPAWGgaGSRTPAYYGAWGG--SRTPA 68
nusG PRK08559
transcription antitermination protein NusG; Validated
 171-312 5.63e-12

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 64.50  E-value: 5.63e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  171 KDPNLWTVKCKIGEERATAISLMRKFIAYQftdtpLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRlGYwNQQM 250
Cdd:PRK08559    4 EMSMIFAVKTTAGQERNVALMLAMRAKKEN-----LPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVR-GV-VPGE 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 987437824  251 VPIKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKM------IP---RIDYDRI 312
Cdd:PRK08559   77 ISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELleaavpIPvtvRGDQVRV 147
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 174-262 1.46e-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: 1.46e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824    174 NLWTVKCKIGEERATAISLMRKFIAYQFTDtplQIKSVVAP-EHVK----------------GYIYVEAYKQTHVKQAIE 236
Cdd:smart00738    1 NWYAVRTTSGQEKRVAENLERKAEALGLED---KIVSILVPtEEVKeirrgkkkvverklfpGYIFVEADLEDEVWTAIR 77

                            90       100       110
                    ....*....|....*....|....*....|
gi 987437824    237 GV----GNLRLGYWnQQMVPIKEMTDVLKV 262
Cdd:smart00738   78 GTpgvrGFVGGGGK-PTPVPDDEIEKILKP 106
PHA03269 PHA03269
envelope glycoprotein C; Provisional
 821-966 3.36e-09

envelope glycoprotein C; Provisional


Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 60.90  E-value: 3.36e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  821 NPNTPSRAEEEYEYAFDDEPTPSPQayggtPNPQTPGYPDPS-SPQVNPQYNPQtpgtpamyntdqfsPYAAPSPQGSYQ 899
Cdd:PHA03269   21 NLNTNIPIPELHTSAATQKPDPAPA-----PHQAASRAPDPAvAPTSAASRKPD--------------LAQAPTPAASEK 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 987437824  900 PSPSPQSYHQV--APSPAGYQNTHSPasyhPTPSPM-----AYQASPSPSPVGYSPMTPgAPSPGGYNPHTPGS 966
Cdd:PHA03269   82 FDPAPAPHQAAsrAPDPAVAPQLAAA----PKPDAAeaftsAAQAHEAPADAGTSAASK-KPDPAAHTQHSPPP 150
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 95-168 8.49e-09

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: 53.81  E-value: 8.49e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 987437824    95 GAEDILEKA----SNIDNVVLDEDRSGARRLQNLWRDQREEELGEYYMKKYAKSSvgETVYGGSDElsDDITQQQLLP 168
Cdd:pfam11942   24 GADDFIEDDeedeDEEDGRRDDRRHRELDRRRELEEDEDAEEIAEYLKERYGRSS--SDAYRGDAE--EGVPQRLLLP 97
PHA03247 PHA03247
large tegument protein UL36; Provisional
 741-958 1.42e-08

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 59.57  E-value: 1.42e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  741 VDRQRLTTVGSRRPGGMTSTYGRTPMYGSQTPMYGSGSRTPMYGSQTPlqdGSRTPHYGSQTPLHDGSRTPAQSGAWDPN 820
Cdd:PHA03247 2661 VSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTP---EPAPHALVSATPLPPGPAAARQASPALPA 2737

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  821 NPNTPsraeeeyeyafddePTPSPQAYGGTPN----PQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPqg 896
Cdd:PHA03247 2738 APAPP--------------AVPAGPATPGGPArparPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSP-- 2801

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 987437824  897 syqPSPSPQSYHQVAPSPAgYQNTHSPASYHPTPSPMAYQASPSPSPVGYSPMTP-GAPSPGG 958
Cdd:PHA03247 2802 ---WDPADPPAAVLAPAAA-LPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLgGSVAPGG 2860
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 176-304 3.68e-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: 53.36  E-value: 3.68e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   176 WTVKCKIGEERATAislmrKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRlgywnqQMVP--- 252
Cdd:TIGR00405    1 FAVKTSVGQEKNVA-----RLMARKARKSGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVR------GVVEgei 69

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 987437824   253 -IKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMI 304
Cdd:TIGR00405   70 dFEEIERFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELI 122
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 840-966 5.01e-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: 57.47  E-value: 5.01e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   840 PTPSPQAYGGTPNPQTPGYPDPSSPQVN-PQYNPQTPGTP--AMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAG 916
Cdd:pfam03154  188 PPGTTQAATAGPTPSAPSVPPQGSPATSqPPNQTQSTAAPhtLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQVSPQPLP 267

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 987437824   917 YQNTHSPASYHP---------TPSPMAYQASPSPSPVGYSPMTPG----APSPGGYNPHTPGS 966
Cdd:pfam03154  268 QPSLHGQMPPMPhslqtgpshMQHPVPPQPFPLTPQSSQSQVPPGpspaAPGQSQQRIHTPPS 330
PBP1 COG5180
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ...
 785-973 1.22e-06

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


Pssm-ID: 444064 [Multi-domain]  Cd Length: 548  Bit Score: 52.37  E-value: 1.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  785 SQTPLQ---DGSRTPHYGSQTPLHDGSRTPaQSGAWDPNNPNTPSRAEEEYEYAFDD-EPTPSPQAYGGTPNP----QTP 856
Cdd:COG5180   195 SPEKLDrpkVEVKDEAQEEPPDLTGGADHP-RPEAASSPKVDPPSTSEARSRPATVDaQPEMRPPADAKERRRaaigDTP 273

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  857 GYPDPSSPQVNPQYNPQT--PGTPAMYNTDQFSPYAAPSPQGSYQPSPS-----PQSYHQVAPSPAGYQNTHSPASYHPT 929
Cdd:COG5180   274 AAEPPGLPVLEAGSEPQSdaPEAETARPIDVKGVASAPPATRPVRPPGGardpgTPRPGQPTERPAGVPEAASDAGQPPS 353

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 987437824  930 PSPMAYQASPSpspvgySPMTPGAPSPG--GYN--PHTPGSGIEQNSS 973
Cdd:COG5180   354 AYPPAEEAVPG------KPLEQGAPRPGssGGDgaPFQPPNGAPQPGL 395
SP7_N cd22542
N-terminal domain of transcription factor Specificity Protein (SP) 7; Specificity Proteins ...
 798-966 2.24e-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: 47.59  E-value: 2.24e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  798 YGSQTPLHDgSRTPAQSGAWDPNNPNTP--------SRAEE----EYEYAFDD-----EPTPSPQA---YGGTPNPQTPG 857
Cdd:cd22542    26 FGGSSPIRD-SATPGKPGNNPGKKPYSLgsdlssakSRSSElmgdSYTATFSSgnglmSPSGSPQAsttYGNDYNPFSHS 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  858 YPDPSSPQ----VNPQYNPQTPGTPAMYNT-DQFSPY-----AAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYH 927
Cdd:cd22542   105 FPTSSGSQdpslLVSKGHPSADCLPSVYTSlDMAHPYgswykTGIHPGISSSSTNATASWWDMHSNTNWLSAQGQPDGLQ 184

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 987437824  928 PTPSPMAYQASPSPSPVGYSPMTPgaPSPGGYNPHTPGS 966
Cdd:cd22542   185 ASLQPVPAQTPLNPQLPSYTEFTT--LNPAPYPAVGISS 221
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 467-494 5.65e-05

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


Pssm-ID: 128978  Cd Length: 28  Bit Score: 40.77  E-value: 5.65e-05
                            10        20
                    ....*....|....*....|....*...
gi 987437824    467 YFKMGDHVKVIAGRFEGDTGLIVRVEEN 494
Cdd:smart00739    1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 702-733 9.57e-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: 9.57e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 987437824   702 IGQTVRISQGPYKGYIGVVKDATESTARVELH 733
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 820-956 1.99e-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: 45.53  E-value: 1.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  820 NNPNTPSRAEEEYEYAFDD-EPTPSPQAYGGTPN-PQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQG- 896
Cdd:NF033839  249 DNVNTKVEIENTVHKIFADmDAVVTKFKKGLTQDtPKEPGNKKPSAPKPGMQPSPQPEKKEVKPEPETPKPEVKPQLEKp 328

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 987437824  897 SYQPSPSPQSYH-QVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPSpvgySPMTPGAPSP 956
Cdd:NF033839  329 KPEVKPQPEKPKpEVKPQLETPKPEVKPQPEKPKPEVKPQPEKPKPE----VKPQPETPKP 385
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 471-499 2.23e-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: 2.23e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 987437824   471 GDHVKVIAGRFEGDTGLIVRVEE--NFVILF 499
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 ...
 825-964 7.73e-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: 7.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  825 PSRAEEEYEYAFDDEPTPSPQAYG----GTPNPQTPGYPDPSSPQVNPQYN-PQTPGTPAMYNTDQFSPYAAPSPQGSYQ 899
Cdd:cd21972    22 LDLEFILSNTVTSDNDNPPPPDPAypppESPESCSTVYDSDGCHPTPNAYCgPNGPGLPGHFLLAGNSPNLGPKIKTENQ 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 987437824  900 PS-------PSPQSYHQVAPS------PAGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSPmtPGAPSPGGYNPHTP 964
Cdd:cd21972   102 EQacmpvagYSGHYGPREPQRvppappPPQYAGHFQYHGHFNMFSPPLRANHPGMSTVMLTP--LSTPPLGFLSPEEA 177
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 838-964 3.44e-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: 3.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  838 DEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQynPQTPGTPAMYNTDQFSPYAAPSPQ-GSYQPSPSPQSYH-QVAPSPA 915
Cdd:NF033839  370 EKPKPEVKPQPETPKPEVKPQPEKPKPEVKPQ--PEKPKPEVKPQPEKPKPEVKPQPEkPKPEVKPQPEKPKpEVKPQPE 447

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 987437824  916 GYQNTHSPASYHPTPSPMAYQASPSPSpVGYSPMTP----GAPSPGGYNPHTP 964
Cdd:NF033839  448 KPKPEVKPQPETPKPEVKPQPEKPKPE-VKPQPEKPkpdnSKPQADDKKPSTP 499
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 592-623 7.75e-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: 35.06  E-value: 7.75e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 987437824   592 VKDIVKVIDGPHSGREGEIRHLFRSFAFLHCK 623
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 851-956 8.46e-03

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


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 38.23  E-value: 8.46e-03
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824    851 PNPQTPGYPDPSSPQVNPQYNPQTPGTPAMyntdQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTP 930
Cdd:smart00818   45 QHPPTHTLQPHHHIPVLPAQQPVVPQQPLM----PVPGQHSMTPTQHHQPNLPQPAQQPFQPQPLQPPQPQQPMQPQPPV 120

                            90       100
                    ....*....|....*....|....*.
gi 987437824    931 SPMAYQASPSPSPvgysPMTPGAPSP 956
Cdd:smart00818  121 HPIPPLPPQPPLP----PMFPMQPLP 142
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 174-261 4.32e-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: 4.32e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  174 NLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLgyWNQQMVPI 253
Cdd:cd09888     1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYL--NTIKLVPI 78


                  ....*...
gi 987437824  254 KEMTDVLK 261
Cdd:cd09888    79 KEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 174-260 6.63e-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: 6.63e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   174 NLWTVKCKIGEERATAISLMRKFIAYQfTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLGywNQQMVPI 253
Cdd:pfam03439    1 KIWAVKCTPGQEREVALSLMRKILALA-KTNNLGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGL--VPGLVPI 77


                   ....*..
gi 987437824   254 KEMTDVL 260
Cdd:pfam03439   78 KEMEHLL 84
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 768-885 6.79e-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: 112.23  E-value: 6.79e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824    768 GSQTPMYG-SGSRTPMYGSQTP----LQDGSRTPHYGSQTPLHDG--SRTPAQSGAWdPNNPNTPSRAEEEYEYAFDDEP 840
Cdd:smart01104    1 GGRTPAWGaSGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAWGGAG-PTGSRTPAWGGASAWGNKSSEG 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 987437824    841 TPSPQA--YGGTPNPQTPGYpdpssPQVNPQYNPQTPGTPAMYNTDQ 885
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 ...
 467-517 7.64e-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: 7.64e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 987437824  467 YFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLC 517
Cdd:cd06083     1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1024-1080 2.17e-26

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: 102.59  E-value: 2.17e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 987437824 1024 EHLEPITPTKNNKVKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLRFLGKL 1080
Cdd:cd06086     1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMDSDGDIKILPMNFLAKL 57
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 416-466 1.19e-25

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: 100.27  E-value: 1.19e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 987437824  416 FQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDMLEFPAQELRK 466
Cdd:cd06082     1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 698-747 4.90e-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: 4.90e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 987437824  698 DNELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLT 747
Cdd:cd06085     2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLA 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 593-635 1.52e-19

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: 82.57  E-value: 1.52e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 987437824  593 KDIVKVIDGPHSGREGEIRHLFRSFAFLHCKKLVENGGMFVCK 635
Cdd:cd06084     1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 272-309 1.66e-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: 1.66e-17
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 987437824  272 KSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMIPRIDY 309
Cdd:cd06081     1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 768-826 5.27e-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: 5.27e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   768 GSQTPMYGS--GSRTPMY---GSQTPL--QDGSRTPHY--GSQTPLHD--GSRTPAQSGAWDPnnPNTPS 826
Cdd:pfam12815    1 GSRTPAYNSagGSRTPAWgadGSRTPAygGAGGRTPAYnqGGKTPAWGgaGSRTPAYYGAWGG--SRTPA 68
nusG PRK08559
transcription antitermination protein NusG; Validated
 171-312 5.63e-12

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 64.50  E-value: 5.63e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  171 KDPNLWTVKCKIGEERATAISLMRKFIAYQftdtpLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRlGYwNQQM 250
Cdd:PRK08559    4 EMSMIFAVKTTAGQERNVALMLAMRAKKEN-----LPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVR-GV-VPGE 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 987437824  251 VPIKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKM------IP---RIDYDRI 312
Cdd:PRK08559   77 ISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELleaavpIPvtvRGDQVRV 147
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 174-260 1.11e-10

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: 59.25  E-value: 1.11e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  174 NLWTVKCKIGEERATAISLMRKFIA---------YQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLG 244
Cdd:cd08000     1 NWYVLFVKTGREEKVEKLLEKRFEAndieafvpkKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPGVIGI 80

                          90
                  ....*....|....*....
gi 987437824  245 YWN---QQMVPIKEMTDVL 260
Cdd:cd08000    81 LGNgeePSPVSDEEIEMIL 99
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 174-262 1.46e-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: 1.46e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824    174 NLWTVKCKIGEERATAISLMRKFIAYQFTDtplQIKSVVAP-EHVK----------------GYIYVEAYKQTHVKQAIE 236
Cdd:smart00738    1 NWYAVRTTSGQEKRVAENLERKAEALGLED---KIVSILVPtEEVKeirrgkkkvverklfpGYIFVEADLEDEVWTAIR 77

                            90       100       110
                    ....*....|....*....|....*....|
gi 987437824    237 GV----GNLRLGYWnQQMVPIKEMTDVLKV 262
Cdd:smart00738   78 GTpgvrGFVGGGGK-PTPVPDDEIEKILKP 106
DUF5585 pfam17823
Family of unknown function (DUF5585); This is a family of unknown function found in chordata.
 723-1042 1.10e-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: 62.28  E-value: 1.10e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   723 ATESTARVELHSTCQTISvdrqrlTTVGSRRPGGMTSTYGRT--PMYGSQTPMYGSGsrTPMYGSQTPlQDGSRTPHYGS 800
Cdd:pfam17823  170 AASPAPRTAASSTTAASS------TTAASSAPTTAASSAPATltPARGISTAATATG--HPAAGTALA-AVGNSSPAAGT 240

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   801 QTPLhDGSRTPAQSGawdpnnpnTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGypDPSSPQVNPQYNPQTPGTPAM 880
Cdd:pfam17823  241 VTAA-VGTVTPAALA--------TLAAAAGTVASAAGTINMGDPHARRLSPAKHMPS--DTMARNPAAPMGAQAQGPIIQ 309

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   881 YNTDQfsPYAAPSPqgsyQPSPSPQSYHQVAPSPAGYQNTHSPASyhPTPSPMAYQASPSPSPVGYSPMTPGA------- 953
Cdd:pfam17823  310 VSTDQ--PVHNTAG----EPTPSPSNTTLEPNTPKSVASTNLAVV--TTTKAQAKEPSASPVPVLHTSMIPEVeatsptt 381

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   954 -PSPGGYNPHTPGSGIEQNSSdwvttdiQVKVRDTyLDTQVVGQT----GVIRSVTGGMCSVYLKDSEKVVSIssehlEP 1028
Cdd:pfam17823  382 qPSPLLPTQGAAGPGILLAPE-------QVATEAT-AGTASAGPTprssGDPKTLAMASCQLSTQGQYLVVTT-----DP 448

                          330
                   ....*....|....*...
gi 987437824  1029 ITPTKNNK----VKVILG 1042
Cdd:pfam17823  449 LTPALVDKmfllVVLILG 466
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 785-966 1.46e-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: 62.48  E-value: 1.46e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   785 SQTPLQDGSRTPHYGSQTPLHDgsrtPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPtPSPQAYGGTPNPQTPGYPdPSSP 864
Cdd:pfam03154  259 SQVSPQPLPQPSLHGQMPPMPH----SLQTGPSHMQHPVPPQPFPLTPQSSQSQVP-PGPSPAAPGQSQQRIHTP-PSQS 332

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   865 QVNPQYNP-QTPGTPAMYNTdqfsPYAAPSPQGSYQPSPSPQSY----HQVAPSPagYQ-----------------NTHS 922
Cdd:pfam03154  333 QLQSQQPPrEQPLPPAPLSM----PHIKPPPTTPIPQLPNPQSHkhppHLSGPSP--FQmnsnlppppalkplsslSTHH 406

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 987437824   923 PASYHPTPSPMAYQASPSPSPVGYSPM---TPGAPSPGGYNPHTPGS 966
Cdd:pfam03154  407 PPSAHPPPLQLMPQSQQLPPPPAQPPVltqSQSLPPPAASHPPTSGL 453
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 750-815 3.03e-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: 54.37  E-value: 3.03e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 987437824   750 GSRRPGGMTSTYGRTPMY-------------GSQTPMYGSGSRTPMYGsqtplQDGSRTPHYGSQTplhDGSRTPAQSG 815
Cdd:pfam12815    1 GSRTPAYNSAGGSRTPAWgadgsrtpayggaGGRTPAYNQGGKTPAWG-----GAGSRTPAYYGAW---GGSRTPAYGG 71
PHA03269 PHA03269
envelope glycoprotein C; Provisional
 821-966 3.36e-09

envelope glycoprotein C; Provisional


Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 60.90  E-value: 3.36e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  821 NPNTPSRAEEEYEYAFDDEPTPSPQayggtPNPQTPGYPDPS-SPQVNPQYNPQtpgtpamyntdqfsPYAAPSPQGSYQ 899
Cdd:PHA03269   21 NLNTNIPIPELHTSAATQKPDPAPA-----PHQAASRAPDPAvAPTSAASRKPD--------------LAQAPTPAASEK 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 987437824  900 PSPSPQSYHQV--APSPAGYQNTHSPasyhPTPSPM-----AYQASPSPSPVGYSPMTPgAPSPGGYNPHTPGS 966
Cdd:PHA03269   82 FDPAPAPHQAAsrAPDPAVAPQLAAA----PKPDAAeaftsAAQAHEAPADAGTSAASK-KPDPAAHTQHSPPP 150
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 772-973 3.73e-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: 60.94  E-value: 3.73e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   772 PMYGSGSRTPMYGSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPsrAEEEYEYAFDDEPTPSPQayggTP 851
Cdd:pfam03154  294 PPQPFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPP--APLSMPHIKPPPTTPIPQ----LP 367

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   852 NPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQgsyqPSP---SPQSyHQVAPSPAG------YQNTHS 922
Cdd:pfam03154  368 NPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSSLSTHHPPSAH----PPPlqlMPQS-QQLPPPPAQppvltqSQSLPP 442

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 987437824   923 PASYHPTPSpmAYQASPSPSPVGYSPMTPGAP----SPGGYNPHTP--GSGIEQNSS 973
Cdd:pfam03154  443 PAASHPPTS--GLHQVPSQSPFPQHPFVPGGPppitPPSGPPTSTSsaMPGIQPPSS 497
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 95-168 8.49e-09

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: 53.81  E-value: 8.49e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 987437824    95 GAEDILEKA----SNIDNVVLDEDRSGARRLQNLWRDQREEELGEYYMKKYAKSSvgETVYGGSDElsDDITQQQLLP 168
Cdd:pfam11942   24 GADDFIEDDeedeDEEDGRRDDRRHRELDRRRELEEDEDAEEIAEYLKERYGRSS--SDAYRGDAE--EGVPQRLLLP 97
PHA03247 PHA03247
large tegument protein UL36; Provisional
 741-958 1.42e-08

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 59.57  E-value: 1.42e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  741 VDRQRLTTVGSRRPGGMTSTYGRTPMYGSQTPMYGSGSRTPMYGSQTPlqdGSRTPHYGSQTPLHDGSRTPAQSGAWDPN 820
Cdd:PHA03247 2661 VSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTP---EPAPHALVSATPLPPGPAAARQASPALPA 2737

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  821 NPNTPsraeeeyeyafddePTPSPQAYGGTPN----PQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPqg 896
Cdd:PHA03247 2738 APAPP--------------AVPAGPATPGGPArparPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSP-- 2801

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 987437824  897 syqPSPSPQSYHQVAPSPAgYQNTHSPASYHPTPSPMAYQASPSPSPVGYSPMTP-GAPSPGG 958
Cdd:PHA03247 2802 ---WDPADPPAAVLAPAAA-LPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLgGSVAPGG 2860
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 754-967 3.64e-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: 57.71  E-value: 3.64e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   754 PGGMTSTYGRTPMYGSQTPMYGSGSRTPMYGSQ-------TPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNP---- 822
Cdd:pfam09606  231 PQQMGGAPNQVAMQQQQPQQQGQQSQLGMGINQmqqmpqgVGGGAGQGGPGQPMGPPGQQPGAMPNVMSIGDQNNYqqqq 310

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   823 --NTPSRAEEEYEYAFDDEPTPS--------PQAYGGTPNPQTPGypdpssPQVNPQYNPQTPGTPAMYNTDQFSPYAAP 892
Cdd:pfam09606  311 trQQQQQQGGNHPAAHQQQMNQSvgqggqvvALGGLNHLETWNPG------NFGGLGANPMQRGQPGMMSSPSPVPGQQV 384

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 987437824   893 SPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASyHPTPSPmAYQASPSPSPVGY--SPMTPGAPSPGGyNPHTPGSG 967
Cdd:pfam09606  385 RQVTPNQFMRQSPQPSVPSPQGPGSQPPQSHPG-GMIPSP-ALIPSPSPQMSQQpaQQRTIGQDSPGG-SLNTPGQS 458
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 176-304 3.68e-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: 53.36  E-value: 3.68e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   176 WTVKCKIGEERATAislmrKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRlgywnqQMVP--- 252
Cdd:TIGR00405    1 FAVKTSVGQEKNVA-----RLMARKARKSGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVR------GVVEgei 69

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 987437824   253 -IKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMI 304
Cdd:TIGR00405   70 dFEEIERFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELI 122
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 840-966 5.01e-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: 57.47  E-value: 5.01e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   840 PTPSPQAYGGTPNPQTPGYPDPSSPQVN-PQYNPQTPGTP--AMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAG 916
Cdd:pfam03154  188 PPGTTQAATAGPTPSAPSVPPQGSPATSqPPNQTQSTAAPhtLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQVSPQPLP 267

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 987437824   917 YQNTHSPASYHP---------TPSPMAYQASPSPSPVGYSPMTPG----APSPGGYNPHTPGS 966
Cdd:pfam03154  268 QPSLHGQMPPMPhslqtgpshMQHPVPPQPFPLTPQSSQSQVPPGpspaAPGQSQQRIHTPPS 330
NGN_Arch cd09887
Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance ...
 175-242 1.09e-07

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: 50.23  E-value: 1.09e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 987437824  175 LWTVKCKIGEERATAISLMRKFiayqfTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLR 242
Cdd:cd09887     2 IYAVKTTAGQERNVADLLAMRA-----EKENLDVYSILVPEELKGYVFVEAEDPDRVEELIRGIPHVR 64
PHA03247 PHA03247
large tegument protein UL36; Provisional
 758-978 2.03e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 55.71  E-value: 2.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  758 TSTYGRTPMYGSQTPMygsgSRTPMYGSQTPLQDGSRTPHYGSQTPLHDGSR-TPAQSGAWDPNNPNTPsRAEEEYEYAF 836
Cdd:PHA03247 2817 ALPPAASPAGPLPPPT----SAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRrPPSRSPAAKPAAPARP-PVRRLARPAV 2891

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  837 DDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQtpgtpamyntdqfsPYAAPSPQGSYQPSPSPQSYHQVAPSPAG 916
Cdd:PHA03247 2892 SRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQ--------------PQPPPPPPPRPQPPLAPTTDPAGAGEPSG 2957

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 987437824  917 YQNTHSPASYHPTPSPMAYQASPSPSPvgySPMTPGAPSPGgyNPHTPGSGIeqnsSDWVTT 978
Cdd:PHA03247 2958 AVPQPWLGALVPGRVAVPRFRVPQPAP---SREAPASSTPP--LTGHSLSRV----SSWASS 3010
PHA03378 PHA03378
EBNA-3B; Provisional
 759-958 2.05e-07

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 55.46  E-value: 2.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  759 STYGRTPMYGSQTPMYGSGSRTPMYGSQTPLQD-----------GSRTPHYGSQTPLHDGSRTPAQSGAWdPNNPNTPSR 827
Cdd:PHA03378  603 SQTPEPPTTQSHIPETSAPRQWPMPLRPIPMRPlrmqpitfnvlVFPTPHQPPQVEITPYKPTWTQIGHI-PYQPSPTGA 681

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  828 AEEEYEYAFDDEPTPSPQAYGGTPNPQTPgyPDPSS-PQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGSYQPSPSPQS 906
Cdd:PHA03378  682 NTMLPIQWAPGTMQPPPRAPTPMRPPAAP--PGRAQrPAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAA 759

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 987437824  907 YHQVAPSPAGyqnthSPASYHPTPSPMA-------YQASPSPSP---VGYSPMTPGAPSPGG 958
Cdd:PHA03378  760 APGRARPPAA-----APGAPTPQPPPQAppapqqrPRGAPTPQPppqAGPTSMQLMPRAAPG 816
PHA03377 PHA03377
EBNA-3C; Provisional
 734-964 2.44e-07

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 55.06  E-value: 2.44e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  734 STCQTISVDRQRLTTVGSRRPGGMTSTygrTPMYGSQTPMYgSGSRTPMYGSQTPLQD---GSRTPHYGSQTPLHDGSRT 810
Cdd:PHA03377  686 SVFVLPSVDAGRAQPSEESHLSSMSPT---QPISHEEQPRY-EDPDDPLDLSLHPDQApppSHQAPYSGHEEPQAQQAPY 761

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  811 PaqsGAWDPNNPNTPSRAEEEyeyafddeptpsPQAYGGTPNpQTPGY--PDPSSPQvNPQY--------------NPQT 874
Cdd:PHA03377  762 P---GYWEPRPPQAPYLGYQE------------PQAQGVQVS-SYPGYagPWGLRAQ-HPRYrhswaywsqypghgHPQG 824

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  875 PGTP-AMYNTDQFSPYAAP-----SPQGSYQPSPSP----QSYHQVAPSPAGYQNTHSPASYHPTPS----PMAYQASPS 940
Cdd:PHA03377  825 PWAPrPPHLPPQWDGSAGHgqdqvSQFPHLQSETGPprlqLSQVPQLPYSQTLVSSSAPSWSSPQPRapirPIPTRFPPP 904

                         250       260
                  ....*....|....*....|....
gi 987437824  941 PSPVGYSpMTPGAPSPGGYNPHTP 964
Cdd:PHA03377  905 PMPLQDS-MAVGCDSSGTACPSMP 927
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 419-465 2.45e-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: 48.37  E-value: 2.45e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 987437824  419 GDNVEVCEGELINLQGKILSVDG--NKITIMPKHEDLKDMLEFPAQELR 465
Cdd:cd00380     1 GDVVRVLRGPYKGREGVVVDIDPrfGIVTVKGATGSKGAELKVRFDDVD 49
PHA03247 PHA03247
large tegument protein UL36; Provisional
 785-965 6.66e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 53.79  E-value: 6.66e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  785 SQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYP----- 859
Cdd:PHA03247 2567 SVPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHppptv 2646

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  860 --------DPSSPQVNPQYNPQTPGTPAMYN--TDQFSPYAAPSPQGSYQPS---PSPQSYHQVAPSPAGYQNTHSPASY 926
Cdd:PHA03247 2647 ppperprdDPAPGRVSRPRRARRLGRAAQASspPQRPRRRAARPTVGSLTSLadpPPPPPTPEPAPHALVSATPLPPGPA 2726

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 987437824  927 HPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPG 965
Cdd:PHA03247 2727 AARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAG 2765
PHA03378 PHA03378
EBNA-3B; Provisional
 795-964 9.36e-07

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 53.15  E-value: 9.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  795 TPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEE---YEYAFDDEPTPSPQAYGGTPNPQTPGYPDPS-SPQVNPQ- 869
Cdd:PHA03378  582 TSQLASSAPSYAQTPWPVPHPSQTPEPPTTQSHIPETsapRQWPMPLRPIPMRPLRMQPITFNVLVFPTPHqPPQVEITp 661

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  870 ------------YNPQTPG---------TPAMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHP 928
Cdd:PHA03378  662 ykptwtqighipYQPSPTGantmlpiqwAPGTMQPPPRAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPAAAP 741

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 987437824  929 TPS--PMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTP 964
Cdd:PHA03378  742 GRArpPAAAPGRARPPAAAPGRARPPAAAPGAPTPQPP 779
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 839-965 1.03e-06

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 53.17  E-value: 1.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  839 EPTPSPQAYGGTPNPQtpgYPDPSSPQVNP---QYNPQTPGTPAMYNTDQFSPYAAPSP-QGSYQPSPSPQSYHQVAPSP 914
Cdd:PRK10263  370 EPVIAPAPEGYPQQSQ---YAQPAVQYNEPlqqPVQPQQPYYAPAAEQPAQQPYYAPAPeQPAQQPYYAPAPEQPVAGNA 446

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 987437824  915 AGYQNTHSPasYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPG 965
Cdd:PRK10263  447 WQAEEQQST--FAPQSTYQTEQTYQQPAAQEPLYQQPQPVEQQPVVEPEPV 495
PBP1 COG5180
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ...
 785-973 1.22e-06

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


Pssm-ID: 444064 [Multi-domain]  Cd Length: 548  Bit Score: 52.37  E-value: 1.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  785 SQTPLQ---DGSRTPHYGSQTPLHDGSRTPaQSGAWDPNNPNTPSRAEEEYEYAFDD-EPTPSPQAYGGTPNP----QTP 856
Cdd:COG5180   195 SPEKLDrpkVEVKDEAQEEPPDLTGGADHP-RPEAASSPKVDPPSTSEARSRPATVDaQPEMRPPADAKERRRaaigDTP 273

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  857 GYPDPSSPQVNPQYNPQT--PGTPAMYNTDQFSPYAAPSPQGSYQPSPS-----PQSYHQVAPSPAGYQNTHSPASYHPT 929
Cdd:COG5180   274 AAEPPGLPVLEAGSEPQSdaPEAETARPIDVKGVASAPPATRPVRPPGGardpgTPRPGQPTERPAGVPEAASDAGQPPS 353

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 987437824  930 PSPMAYQASPSpspvgySPMTPGAPSPG--GYN--PHTPGSGIEQNSS 973
Cdd:COG5180   354 AYPPAEEAVPG------KPLEQGAPRPGssGGDgaPFQPPNGAPQPGL 395
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 842-970 2.30e-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: 52.08  E-value: 2.30e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   842 PSPQAYGGTPNPQTPGYPDPSS-PQVNPqynpqTPGTPAMynTDQFSPYAAPSPQGSyQPSPSPQSYHQVAPS--PAGYQ 918
Cdd:pfam03154  172 PVLQAQSGAASPPSPPPPGTTQaATAGP-----TPSAPSV--PPQGSPATSQPPNQT-QSTAAPHTLIQQTPTlhPQRLP 243

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 987437824   919 NTHSPASYHPTPSPMAY-QASPSPSPVGYSPMTPGAPSPGGYNPHTPGSGIEQ 970
Cdd:pfam03154  244 SPHPPLQPMTQPPPPSQvSPQPLPQPSLHGQMPPMPHSLQTGPSHMQHPVPPQ 296
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 593-630 2.82e-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: 45.29  E-value: 2.82e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 987437824  593 KDIVKVIDGPHSGREGEIRHLFRSFAFLHCKKLVENGG 630
Cdd:cd00380     1 GDVVRVLRGPYKGREGVVVDIDPRFGIVTVKGATGSKG 38
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 703-746 3.53e-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: 3.53e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 987437824  703 GQTVRISQGPYKGYIGVVKDATEST--ARVELH--STCQTISVDRQRL 746
Cdd:cd00380     1 GDVVRVLRGPYKGREGVVVDIDPRFgiVTVKGAtgSKGAELKVRFDDV 48
PHA03378 PHA03378
EBNA-3B; Provisional
 744-956 3.76e-06

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 51.22  E-value: 3.76e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  744 QRLTTVGSRRPGGMTSTYGRTP---MYGSQTPmygsgsRTPMYGSQTP-LQDGSRTPHYGSQTPLHDGSRTPAQSGAWDP 819
Cdd:PHA03378  575 QPLTSPTTSQLASSAPSYAQTPwpvPHPSQTP------EPPTTQSHIPeTSAPRQWPMPLRPIPMRPLRMQPITFNVLVF 648

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  820 NNPNTPSRAEeeyeyafddeptPSPQAYGGTPNPQTPGYPDPSSPQVN--PQYNPQTPGTPAMYNTDQFSPYAAPS---- 893
Cdd:PHA03378  649 PTPHQPPQVE------------ITPYKPTWTQIGHIPYQPSPTGANTMlpIQWAPGTMQPPPRAPTPMRPPAAPPGraqr 716

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 987437824  894 PQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPS-PMAYQASPSPSPVGyspmTPGAPSP 956
Cdd:PHA03378  717 PAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRArPPAAAPGRARPPAA----APGAPTP 776
PHA03247 PHA03247
large tegument protein UL36; Provisional
 807-962 4.25e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 51.09  E-value: 4.25e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  807 GSRTPAQSGAWDPNNPNTPSRAEEEYeyaFDDEPTPSP-----------------QAYGGTPNPQTPGYPDPSSPQV--N 867
Cdd:PHA03247 2494 AAPDPGGGGPPDPDAPPAPSRLAPAI---LPDEPVGEPvhprmltwirgleelasDDAGDPPPPLPPAAPPAAPDRSvpP 2570

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  868 PQYNPQTPGtPAMyNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQA-SPSPSPVGY 946
Cdd:PHA03247 2571 PRPAPRPSE-PAV-TSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPdPHPPPTVPP 2648

                         170
                  ....*....|....*.
gi 987437824  947 SPMTPGAPSPGGYNPH 962
Cdd:PHA03247 2649 PERPRDDPAPGRVSRP 2664
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 471-515 4.51e-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: 4.51e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 987437824  471 GDHVKVIAGRFEGDTGLIVRVEENFVIL----FSDLTMHELKVLPRDLQ 515
Cdd:cd00380     1 GDVVRVLRGPYKGREGVVVDIDPRFGIVtvkgATGSKGAELKVRFDDVD 49
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 734-957 7.32e-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: 50.30  E-value: 7.32e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   734 STCQTISVdrqrlTTVGSRRPGGMTStyGRTPMYGSQTPM-YGSGSRTPMYGSQTPLQDgSRTPHYGSQTPlhdGSRTPA 812
Cdd:pfam05109  463 STGPTVST-----ADVTSPTPAGTTS--GASPVTPSPSPRdNGTESKAPDMTSPTSAVT-TPTPNATSPTP---AVTTPT 531

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   813 QSGAWDPNNPNTPSRAeeeYEYAFDDEPTPSPQAYGGTPNPQTPGY-------------PDPSSPQV---NPQYNPQ--- 873
Cdd:pfam05109  532 PNATSPTLGKTSPTSA---VTTPTPNATSPTPAVTTPTPNATIPTLgktsptsavttptPNATSPTVgetSPQANTTnht 608

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   874 ---TPGTPAMYNTDQFSPYAAPSPQGSYQPSPS------PQSYHQ-VAPSPAGYQNTHSP--ASYHPTPSPMAYQASPSP 941
Cdd:pfam05109  609 lggTSSTPVVTSPPKNATSAVTTGQHNITSSSTssmslrPSSISEtLSPSTSDNSTSHMPllTSAHPTGGENITQVTPAS 688

                          250
                   ....*....|....*.
gi 987437824   942 SPVGYSPMTPGAPSPG 957
Cdd:pfam05109  689 TSTHHVSTSSPAPRPG 704
Pro-rich pfam15240
Proline-rich protein; This family includes several eukaryotic proline-rich proteins.
 812-964 1.16e-05

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


Pssm-ID: 464580 [Multi-domain]  Cd Length: 167  Bit Score: 46.95  E-value: 1.16e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   812 AQSGAWDPNNPNTPSR-AEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQfsPYA 890
Cdd:pfam15240   16 AQSSSEDVSQEDSPSLiSEEEGQSQQGGQGPQGPPPGGFPPQPPASDDPPGPPPPGGPQQPPPQGGKQKPQGPPP--QGG 93

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 987437824   891 APSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPSPvGYSPMTPGAPSPGGyNPHTP 964
Cdd:pfam15240   94 PRPPPGKPQGPPPQGGNQQQGPPPPGKPQGPPPQGGGPPPQGGNQQGPPPPPP-GNPQGPPQRPPQPG-NPQGP 165
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 861-972 1.40e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 49.31  E-value: 1.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  861 PSSPQVNPQYNPQTpgtpamynTDQFSPYAAPSPQGSYQPSPSPQSYHQ-VAPSPAGYQNTHSPASYHPTPSPMAYQASP 939
Cdd:PRK10263  740 PHEPLFTPIVEPVQ--------QPQQPVAPQQQYQQPQQPVAPQPQYQQpQQPVAPQPQYQQPQQPVAPQPQYQQPQQPV 811

                          90       100       110
                  ....*....|....*....|....*....|...
gi 987437824  940 SPSPVGYSPMTPGAPSPGGYNPHTPGSGIEQNS 972
Cdd:PRK10263  812 APQPQYQQPQQPVAPQPQYQQPQQPVAPQPQDT 844
PHA03291 PHA03291
envelope glycoprotein I; Provisional
 835-982 1.43e-05

envelope glycoprotein I; Provisional


Pssm-ID: 223033 [Multi-domain]  Cd Length: 401  Bit Score: 48.80  E-value: 1.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  835 AFDDEPTPSPQAYGGTPnpqTPGYPDPSSPQVNPQYNPqtpgtpamynTDQFSPyAAPSPQGSYQPSPspqsyhQVAPSP 914
Cdd:PHA03291  165 AFPAEGTLAAPPLGEGS---ADGSCDPALPLSAPRLGP----------ADVFVP-ATPRPTPRTTASP------ETTPTP 224

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 987437824  915 AgyqNTHSPASyHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPGSGIEQNSSDWVTTDIQV 982
Cdd:PHA03291  225 S---TTTSPPS-TTIPAPSTTIAAPQAGTTPEAEGTPAPPTPGGGEAPPANATPAPEASRYELTVTQI 288
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 787-974 1.60e-05

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 49.40  E-value: 1.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  787 TPLQDGSRTPHYGSQ-----------TPLHDGSRTPAqSGAWDPNNPNTPSRAEE-EYEYAFDDEPTPSPQAYGGTPNPQ 854
Cdd:PHA03307   26 ATPGDAADDLLSGSQgqlvsdsaelaAVTVVAGAAAC-DRFEPPTGPPPGPGTEApANESRSTPTWSLSTLAPASPAREG 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  855 TPGYPDPSSPqvnpqynpqtPGTPAMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNThSPASYHPTP---- 930
Cdd:PHA03307  105 SPTPPGPSSP----------DPPPPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPA-AVASDAASSrqaa 173

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 987437824  931 --SPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPGSGIEQNSSD 974
Cdd:PHA03307  174 lpLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASS 219
SP7_N cd22542
N-terminal domain of transcription factor Specificity Protein (SP) 7; Specificity Proteins ...
 798-966 2.24e-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: 47.59  E-value: 2.24e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  798 YGSQTPLHDgSRTPAQSGAWDPNNPNTP--------SRAEE----EYEYAFDD-----EPTPSPQA---YGGTPNPQTPG 857
Cdd:cd22542    26 FGGSSPIRD-SATPGKPGNNPGKKPYSLgsdlssakSRSSElmgdSYTATFSSgnglmSPSGSPQAsttYGNDYNPFSHS 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  858 YPDPSSPQ----VNPQYNPQTPGTPAMYNT-DQFSPY-----AAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYH 927
Cdd:cd22542   105 FPTSSGSQdpslLVSKGHPSADCLPSVYTSlDMAHPYgswykTGIHPGISSSSTNATASWWDMHSNTNWLSAQGQPDGLQ 184

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 987437824  928 PTPSPMAYQASPSPSPVGYSPMTPgaPSPGGYNPHTPGS 966
Cdd:cd22542   185 ASLQPVPAQTPLNPQLPSYTEFTT--LNPAPYPAVGISS 221
PHA03247 PHA03247
large tegument protein UL36; Provisional
 743-1001 2.56e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 48.78  E-value: 2.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  743 RQRLTTVGSRRPGGMTSTYGRTPMYGSQ--TPMYGSGSRTPmyGSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPN 820
Cdd:PHA03247 2711 APHALVSATPLPPGPAAARQASPALPAApaPPAVPAGPATP--GGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAV 2788

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  821 NPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFS-----PYAAPSPQ 895
Cdd:PHA03247 2789 ASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSvapggDVRRRPPS 2868

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  896 GSYQPSPSPQSYHQVA--PSPAGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPGSGIEQNSS 973
Cdd:PHA03247 2869 RSPAAKPAAPARPPVRrlARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTD 2948

                         250       260
                  ....*....|....*....|....*...
gi 987437824  974 DWVTTDIQVKVRDTYLDTQVVGQTGVIR 1001
Cdd:PHA03247 2949 PAGAGEPSGAVPQPWLGALVPGRVAVPR 2976
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 839-962 3.52e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 48.06  E-value: 3.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  839 EPTPSPQAYGGTPNPQTPGyPDPSSPQVNPQYNPQTPGTPAmyntdqfsPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQ 918
Cdd:PRK07764  391 AGAPAAAAPSAAAAAPAAA-PAPAAAAPAAAAAPAPAAAPQ--------PAPAPAPAPAPPSPAGNAPAGGAPSPPPAAA 461

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 987437824  919 NTHSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPH 962
Cdd:PRK07764  462 PSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAG 505
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 467-494 5.65e-05

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


Pssm-ID: 128978  Cd Length: 28  Bit Score: 40.77  E-value: 5.65e-05
                            10        20
                    ....*....|....*....|....*...
gi 987437824    467 YFKMGDHVKVIAGRFEGDTGLIVRVEEN 494
Cdd:smart00739    1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 840-954 8.82e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 46.60  E-value: 8.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  840 PTPSPQAYGGTPNPQTPGyPDPSSPQVNPQYNPQTPGTPAmyntdqfsPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQN 919
Cdd:PRK14959  387 EGPASGGAATIPTPGTQG-PQGTAPAAGMTPSSAAPATPA--------PSAAPSPRVPWDDAPPAPPRSGIPPRPAPRMP 457

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 987437824  920 THSPASYHPTPSPMAYQASPSPS-PVGYSPMTPGAP 954
Cdd:PRK14959  458 EASPVPGAPDSVASASDAPPTLGdPSDTAEHTPSGP 493
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 737-956 8.83e-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: 46.68  E-value: 8.83e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   737 QTISVDRQRLTTVGSRRPGGMTS-TYGRTPMYGSQTPMYGSGSRTPMYGSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSG 815
Cdd:pfam03154   24 QTASPDGRASPTNEDLRSSGRNSpSAASTSSNDSKAESMKKSSKKIKEEAPSPLKSAKRQREKGASDTEEPERATAKKSK 103

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   816 AWDPNNPNTPSRAEEEYE--YAFDDEPTPSPQAYGGTPNPQTPGYPDP--------SS----------PQVNPQYNPQTP 875
Cdd:pfam03154  104 TQEISRPNSPSEGEGESSdgRSVNDEGSSDPKDIDQDNRSTSPSIPSPqdnesdsdSSaqqqilqtqpPVLQAQSGAASP 183

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   876 GTPAMYNTDQfSPYAAPSPQGsyqPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPSPvGYSPMTPGAPS 955
Cdd:pfam03154  184 PSPPPPGTTQ-AATAGPTPSA---PSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSPHP-PLQPMTQPPPP 258


                   .
gi 987437824   956 P 956
Cdd:pfam03154  259 S 259
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 702-733 9.57e-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: 9.57e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 987437824   702 IGQTVRISQGPYKGYIGVVKDATESTARVELH 733
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 841-956 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 987437824   841 TPSPQAYGGTPNPQTPGY--PD-----PSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPS 913
Cdd:pfam05109  422 SKAPESTTTSPTLNTTGFaaPNtttglPSSTHVPTNLTAPASTGPTVSTADVTSPTPAGTTSGASPVTPSPSPRDNGTES 501

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 987437824   914 PAgyQNTHSPASYHPTPSPMAyqasPSPSPVGYSPmTPGAPSP 956
Cdd:pfam05109  502 KA--PDMTSPTSAVTTPTPNA----TSPTPAVTTP-TPNATSP 537
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 791-979 1.60e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 45.75  E-value: 1.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  791 DGSRTPHYGSQTPLHDGSR--TPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNP 868
Cdd:PRK07764  596 GGEGPPAPASSGPPEEAARpaAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGG 675

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  869 QYNPQTPGTPAMyntdqfSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSP 948
Cdd:PRK07764  676 AAPAAPPPAPAP------AAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPP 749

                         170       180       190
                  ....*....|....*....|....*....|.
gi 987437824  949 MTPGAPSPGGYNPHTPGSGIEQNSSDWVTTD 979
Cdd:PRK07764  750 DPAGAPAQPPPPPAPAPAAAPAAAPPPSPPS 780
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 820-956 1.99e-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: 45.53  E-value: 1.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  820 NNPNTPSRAEEEYEYAFDD-EPTPSPQAYGGTPN-PQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQG- 896
Cdd:NF033839  249 DNVNTKVEIENTVHKIFADmDAVVTKFKKGLTQDtPKEPGNKKPSAPKPGMQPSPQPEKKEVKPEPETPKPEVKPQLEKp 328

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 987437824  897 SYQPSPSPQSYH-QVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPSpvgySPMTPGAPSP 956
Cdd:NF033839  329 KPEVKPQPEKPKpEVKPQLETPKPEVKPQPEKPKPEVKPQPEKPKPE----VKPQPETPKP 385
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 806-966 2.12e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 45.55  E-value: 2.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  806 DGSRTPAQSGAWDPNNPNTPSRAeeeyeyAFDDEPTPSPQAYGGTPNPQTPGYPDPSSP--QVNPQYNPQTPGTPAMYNT 883
Cdd:PHA03307  238 DSSSSESSGCGWGPENECPLPRP------APITLPTRIWEASGWNGPSSRPGPASSSSSprERSPSPSPSSPGSGPAPSS 311

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  884 DQFSPYAAPSPQGSyQPSPSPQSyhqVAPSPAGyqnTHSPASYHPTPSPmayqASPSPSPVGYSPMTPGAPSPGGYNPHT 963
Cdd:PHA03307  312 PRASSSSSSSRESS-SSSTSSSS---ESSRGAA---VSPGPSPSRSPSP----SRPPPPADPSSPRKRPRPSRAPSSPAA 380


                  ...
gi 987437824  964 PGS 966
Cdd:PHA03307  381 SAG 383
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 812-956 2.13e-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: 45.53  E-value: 2.13e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   812 AQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQayGGTPNPQTPGYPDPSSP-----QVNPQYNPQTpgTPAMYNTDQF 886
Cdd:pfam03154  176 AQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQ--GSPATSQPPNQTQSTAAphtliQQTPTLHPQR--LPSPHPPLQP 251

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   887 SPYAAPSPQGSYQPSPSPQSY------------------HQVAPSPAGYQNTHSPASYHPTPSPMAyqASPSPSPVGYSP 948
Cdd:pfam03154  252 MTQPPPPSQVSPQPLPQPSLHgqmppmphslqtgpshmqHPVPPQPFPLTPQSSQSQVPPGPSPAA--PGQSQQRIHTPP 329


                   ....*...
gi 987437824   949 MTPGAPSP 956
Cdd:pfam03154  330 SQSQLQSQ 337
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 471-499 2.23e-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: 2.23e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 987437824   471 GDHVKVIAGRFEGDTGLIVRVEE--NFVILF 499
Cdd:pfam00467    2 GDVVRVIAGPFKGKVGKVVEVDDkkNRVLVE 32
dnaA PRK14086
chromosomal replication initiator protein DnaA;
781-945 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 987437824  781 PMY-GSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNnPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYP 859
Cdd:PRK14086  103 RRTsEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLPTAR-PAYPAYQQRPEPGAWPRAADDYGWQQQRLGFPPRAPYA 181

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  860 DPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGSY-------QPSPSPQSYHQV--APSPAGYQNTHSPASYHPTP 930
Cdd:PRK14086  182 SPASYAPEQERDREPYDAGRPEYDQRRRDYDHPRPDWDRprrdrtdRPEPPPGAGHVHrgGPGPPERDDAPVVPIRPSAP 261

                         170
                  ....*....|....*
gi 987437824  931 SPMAYQASPSPSPVG 945
Cdd:PRK14086  262 GPLAAQPAPAPGPGE 276
PHA03247 PHA03247
large tegument protein UL36; Provisional
 822-964 2.39e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 45.70  E-value: 2.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  822 PNTPS-RAEEEYEYAFDDEPTPSPQAyGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMY----NTDQFSPYAAPSPQG 896
Cdd:PHA03247 2475 PGAPVyRRPAEARFPFAAGAAPDPGG-GGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLtwirGLEELASDDAGDPPP 2553

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  897 SYQPSPSPQSYHQVAPSPagyqnthSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAP--SPGGYNPHTP 964
Cdd:PHA03247 2554 PLPPAAPPAAPDRSVPPP-------RPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDrgDPRGPAPPSP 2616
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 811-966 2.53e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 45.36  E-value: 2.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  811 PAQSGAWDPNNPNTPSRAEEEYEYAfdDEPTPS---PQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFS 887
Cdd:PRK07764  592 PGAAGGEGPPAPASSGPPEEAARPA--APAAPAapaAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGW 669

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  888 PYAAPSPQGSyQPSPSPQSYHQVAPS--PAGYQNTHSPASYHP---------TPSPMAYQASPSPSPVGYSPMTPGAPSP 956
Cdd:PRK07764  670 PAKAGGAAPA-APPPAPAPAAPAAPAgaAPAQPAPAPAATPPAgqaddpaaqPPQAAQGASAPSPAADDPVPLPPEPDDP 748

                         170
                  ....*....|
gi 987437824  957 GGYNPHTPGS 966
Cdd:PRK07764  749 PDPAGAPAQP 758
Pneumo_att_G pfam05539
Pneumovirinae attachment membrane glycoprotein G;
769-930 3.07e-04

Pneumovirinae attachment membrane glycoprotein G;


Pssm-ID: 114270 [Multi-domain]  Cd Length: 408  Bit Score: 44.65  E-value: 3.07e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   769 SQTPMYGSGSRTPMYGSQT----PLQDG-SRTPHYGSQTPLHDgSRTPAQSGAWDP--NNPNTPSRAEEEYEYAFDDEPT 841
Cdd:pfam05539  215 STEPVGTQGTTTSSNPEPQteppPSQRGpSGSPQHPPSTTSQD-QSTTGDGQEHTQrrKTPPATSNRRSPHSTATPPPTT 293

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   842 PSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPyaaPSPQ------GSYQPSpSPQSYHQVAPSPA 915
Cdd:pfam05539  294 KRQETGRPTPRPTATTQSGSSPPHSSPPGVQANPTTQNLVDCKELDP---PKPNsicygvGIYNEA-LPRGCDIVVPLCS 369

                          170
                   ....*....|....*
gi 987437824   916 GYqNTHSPASYHPTP 930
Cdd:pfam05539  370 TY-TIMCMDTYYSKP 383
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 792-964 3.97e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 44.78  E-value: 3.97e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  792 GSRTPHYGSQTPLHDGSRTPAQSGAWDPnnPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQvnPQYN 871
Cdd:PHA03307  773 ALLEPAEPQRGAGSSPPVRAEAAFRRPG--RLRRSGPAADAASRTASKRKSRSHTPDGGSESSGPARPPGAAAR--PPPA 848

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  872 PQTPGTPAMyntDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASyHPTPSPMAyqaspsPSPVGYSPMTP 951
Cdd:PHA03307  849 RSSESSKSK---PAAAGGRARGKNGRRRPRPPEPRARPGAAAPPKAAAAAPPAG-APAPRPRP------APRVKLGPMPP 918

                         170       180
                  ....*....|....*....|
gi 987437824  952 GAPSP-GGY------NPHTP 964
Cdd:PHA03307  919 GGPDPrGGFrrvppgDLHTP 938
PTZ00395 PTZ00395
Sec24-related protein; Provisional
 784-962 4.27e-04

Sec24-related protein; Provisional


Pssm-ID: 185594 [Multi-domain]  Cd Length: 1560  Bit Score: 44.68  E-value: 4.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  784 GSQTPLQDGSRTPHYGSQTPL-HDGSRTPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTP--NP--QTPGY 858
Cdd:PTZ00395  345 GSPNAASAGAPFNGLGNQADGgHINQVHPDARGAWAGGPHSNASYNCAAYSNAAQSNAAQSNAGFSNAGysNPgnSNPGY 424

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  859 PDP---SSPQVNPQY------NPQTPGTPamYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPT 929
Cdd:PTZ00395  425 NNApnsNTPYNNPPNsntpysNPPNSNPP--YSNLPYSNTPYSNAPLSNAPPSSAKDHHSAYHAAYQHRAANQPAANLPT 502

                         170       180       190
                  ....*....|....*....|....*....|...
gi 987437824  930 PSPMAyqASPSPSPVGYSPMTPGAPSPGGYNPH 962
Cdd:PTZ00395  503 ANQPA--ANNFHGAAGNSVGNPFASRPFGSAPY 533
DUF1373 pfam07117
Protein of unknown function (DUF1373); This family consists of several hypothetical proteins ...
 822-936 4.34e-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: 4.34e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   822 PNTPSRAEEEYEY----AFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGS 897
Cdd:pfam07117   42 PPRPEEEEGQGGGggtfPFPGSPEPEPGGGGSGPMPMSASAPEPEPAKAKPQRPAPAQGHGHGGGGDSDSSGSGSGHQGS 121

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 987437824   898 YQP---SPSPQSYHQVAPSPAGYQNTHSPasyHPTPSPMAYQ 936
Cdd:pfam07117  122 GGAgagAGAPGHQHEQEQESSSSDDDDED---EFEFTPEEDE 160
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
842-973 4.47e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 44.48  E-value: 4.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  842 PSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTH 921
Cdd:PRK12323  392 PAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRP 471

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 987437824  922 SPASYHPTPSPMAYQASPSPSPVGYSP---MTPGAPSPGGYNPHTPGSGIEQNSS 973
Cdd:PRK12323  472 VAAAAAAAPARAAPAAAPAPADDDPPPweeLPPEFASPAPAQPDAAPAGWVAESI 526
dnaA PRK14086
chromosomal replication initiator protein DnaA;
839-965 5.44e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 44.05  E-value: 5.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  839 EPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGSYQPSPSPQsyhqvAPSPAGYQ 918
Cdd:PRK14086   94 EPAPPPPHARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLPTARPAYPAYQQRPEPGAWPR-----AADDYGWQ 168

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 987437824  919 NT-HSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGyNPHTPG 965
Cdd:PRK14086  169 QQrLGFPPRAPYASPASYAPEQERDREPYDAGRPEYDQRRR-DYDHPR 215
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 788-957 5.71e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 44.01  E-value: 5.71e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  788 PLQDGSRTPHYGSQT--PLHDGSRTPAQSGAWDPNNP-------NTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGY 858
Cdd:PHA03307  195 PSTPPAAASPRPPRRssPISASASSPAPAPGRSAADDagasssdSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASG 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  859 PDPSSPQVNPQYNPQTPGtpamyntdqfSPYAAPSP---QGSYQPSPSPQSYHQVAPSPAGyqnTHSPASYHPTPSPMAY 935
Cdd:PHA03307  275 WNGPSSRPGPASSSSSPR----------ERSPSPSPsspGSGPAPSSPRASSSSSSSRESS---SSSTSSSSESSRGAAV 341

                         170       180
                  ....*....|....*....|..
gi 987437824  936 QASPSPSPVGYSPMTPGAPSPG 957
Cdd:PHA03307  342 SPGPSPSRSPSPSRPPPPADPS 363
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 851-1037 5.86e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 44.03  E-value: 5.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  851 PNPQTPGYPDPSSPQVNPQYNPQTPGTPAMyntdqfspyAAPSPQGSYQPSPSPQSyhQVAPSPAGYQNTHSPASYHPTP 930
Cdd:PRK14950  364 PAPQPAKPTAAAPSPVRPTPAPSTRPKAAA---------AANIPPKEPVRETATPP--PVPPRPVAPPVPHTPESAPKLT 432

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  931 spmayqasPSPSPVGYSPMTPGAPSPGGYNP--HTPGSGIEQNSSDWVTTDIQVKVRDTYLdtQVVGQTGViRSVTggmc 1008
Cdd:PRK14950  433 --------RAAIPVDEKPKYTPPAPPKEEEKalIADGDVLEQLEAIWKQILRDVPPRSPAV--QALLSSGV-RPVS---- 497

                         170       180       190
                  ....*....|....*....|....*....|
gi 987437824 1009 svyLKDSEKVVSISSE-HLEPITPTKNNKV 1037
Cdd:PRK14950  498 ---VEKNTLTLSFKSKfHKDKIEEPENRKI 524
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 781-946 6.30e-04

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 43.92  E-value: 6.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  781 PMYGSQTPLQDGSR--TPHYGSQTPlhDGSRTPAQSGaWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGY 858
Cdd:PRK10263  345 PVASVDVPPAQPTVawQPVPGPQTG--EPVIAPAPEG-YPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAEQPAQQPYY 421

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  859 -PDPSSPQVNPQYNPQtPGTPAMYNtdqfsPYAAPSPQGSYQPSPSPQSYHQ-VAPSPAGYQNTHSPASYHPT---PSPM 933
Cdd:PRK10263  422 aPAPEQPAQQPYYAPA-PEQPVAGN-----AWQAEEQQSTFAPQSTYQTEQTyQQPAAQEPLYQQPQPVEQQPvvePEPV 495

                         170
                  ....*....|...
gi 987437824  934 AYQASPSPSPVGY 946
Cdd:PRK10263  496 VEETKPARPPLYY 508
Med26_M pfam15694
Mediator complex subunit 26 middle domain; Med26_M is the middle domain of subunit 26 of ...
 854-970 7.22e-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: 42.55  E-value: 7.22e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824   854 QTPGYPDPSSPQvNPQYNPQTpgTPAMYNTDQFSPYAapsPQGSY-QPSPSPQSYHQVAPSPAGYQNTHSP--------A 924
Cdd:pfam15694   81 ETGGPPQPKSPR-CSSFSPRN--SRHETFARRSSTYA---PKGSVpSPSPRSQVLDAQVPSPLPLSQPSTPpvqakrleK 154

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 987437824   925 SYHPTP-SPMAYQASPS-----PSPVGYSPMTPGAPSPGGYNPHTPGSGIEQ 970
Cdd:pfam15694  155 PPQSSPeSSQHWLEQSDseshqRHQDGSATLLSQSVSPGCKTPLHPGENSLP 206
KLF1_2_4_N cd21972
N-terminal domain of Kruppel-like factor (KLF) 1, KLF2, KLF4, and similar proteins; Kruppel ...
 825-964 7.73e-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: 7.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  825 PSRAEEEYEYAFDDEPTPSPQAYG----GTPNPQTPGYPDPSSPQVNPQYN-PQTPGTPAMYNTDQFSPYAAPSPQGSYQ 899
Cdd:cd21972    22 LDLEFILSNTVTSDNDNPPPPDPAypppESPESCSTVYDSDGCHPTPNAYCgPNGPGLPGHFLLAGNSPNLGPKIKTENQ 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 987437824  900 PS-------PSPQSYHQVAPS------PAGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSPmtPGAPSPGGYNPHTP 964
Cdd:cd21972   102 EQacmpvagYSGHYGPREPQRvppappPPQYAGHFQYHGHFNMFSPPLRANHPGMSTVMLTP--LSTPPLGFLSPEEA 177
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 763-956 9.82e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 43.24  E-value: 9.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  763 RTPMYGSQTPMYGSGSRTPMYGSQTPLQDGSRTPhygsQTPLHDGSRTPAQSGAwDPNNPNTPSRAEeeyeyafdDEPTP 842
Cdd:PHA03307   64 RFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAP----ASPAREGSPTPPGPSS-PDPPPPTPPPAS--------PPPSP 130

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  843 SPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTdqfSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGyqnths 922
Cdd:PHA03307  131 APDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQ---AALPLSSPEETARAPSSPPAEPPPSTPPAA------ 201

                         170       180       190
                  ....*....|....*....|....*....|....
gi 987437824  923 PASYHPTPSPMAyqASPSPSPVGYSPMTPGAPSP 956
Cdd:PHA03307  202 ASPRPPRRSSPI--SASASSPAPAPGRSAADDAG 233
KLF3_N cd21577
N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called ...
 887-962 1.12e-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: 41.56  E-value: 1.12e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 987437824  887 SPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHsPASYHP--TPSPMAYQASPSPSPVGYSPMTpgAPSPGGYNPH 962
Cdd:cd21577    41 SSSSSSSSPSSRASPPSPYSKSSPPSPPQQRPLSP-PLSLPPpvAPPPLSPGSVPGGLPVISPVMV--QPVPVLYPPH 115
PHA03369 PHA03369
capsid maturational protease; Provisional
 810-907 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 987437824  810 TPAQSGAWDPNnPNTPSRAEEE-YEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVnpqynPQTPGTPAMYNTDQFSP 888
Cdd:PHA03369  353 LTAPSRVLAAA-AKVAVIAAPQtHTGPADRQRPQRPDGIPYSVPARSPMTAYPPVPQF-----CGDPGLVSPYNPQSPGT 426

                          90
                  ....*....|....*....
gi 987437824  889 YAAPSPQGSYQPSPSPQSY 907
Cdd:PHA03369  427 SYGPEPVGPVPPQPTNPYV 445
PHA03269 PHA03269
envelope glycoprotein C; Provisional
 871-978 1.57e-03

envelope glycoprotein C; Provisional


Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 42.41  E-value: 1.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  871 NPQTP-GTPAMYN---TDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPSPVGY 946
Cdd:PHA03269   21 NLNTNiPIPELHTsaaTQKPDPAPAPHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQAASRAPDPAV 100

                          90       100       110
                  ....*....|....*....|....*....|..
gi 987437824  947 SPMTPGAPSPggyNPHTPGSGIEQNSSDWVTT 978
Cdd:PHA03269  101 APQLAAAPKP---DAAEAFTSAAQAHEAPADA 129
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 848-967 1.60e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 42.67  E-value: 1.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  848 GGTPNPQTPGYPDPSSPQVnPQYNPQTPGTPAMyntdqfspyAAPSPQGSYQPSPSPQSYHQVAPSPAgyqnthSPASYH 927
Cdd:PRK07764  389 GGAGAPAAAAPSAAAAAPA-AAPAPAAAAPAAA---------AAPAPAAAPQPAPAPAPAPAPPSPAG------NAPAGG 452

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 987437824  928 PTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPGSG 967
Cdd:PRK07764  453 APSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAA 492
PHA03369 PHA03369
capsid maturational protease; Provisional
 850-987 1.75e-03

capsid maturational protease; Provisional


Pssm-ID: 223061 [Multi-domain]  Cd Length: 663  Bit Score: 42.29  E-value: 1.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  850 TPNPQTPGYPDPSSPQVNPqynPQTPGTPAM---YNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSpAGYQNTHSPASY 926
Cdd:PHA03369  353 LTAPSRVLAAAAKVAVIAA---PQTHTGPADrqrPQRPDGIPYSVPARSPMTAYPPVPQFCGDPGLV-SPYNPQSPGTSY 428

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 987437824  927 HPTPSPMAYQASPSPS--PVGYSPMT-PGAPSPGGYnpHTPGS-GIEQNSSDWVTTDIQVKVRDT 987
Cdd:PHA03369  429 GPEPVGPVPPQPTNPYvmPISMANMVyPGHPQEHGH--ERKRKrGGELKEELIETLKLVKKLKEE 491
PHA03325 PHA03325
nuclear-egress-membrane-like protein; Provisional
 800-961 1.98e-03

nuclear-egress-membrane-like protein; Provisional


Pssm-ID: 223044  Cd Length: 418  Bit Score: 41.79  E-value: 1.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  800 SQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAyggtpnpqtpgYPDPSSPQVNPQYNPQTPGTPA 879
Cdd:PHA03325  266 SSLPTSAPKRRSRRAGAMRAAAGETADLADDDGSEHSDPEPLPASLP-----------PPPVRRPRVKHPEAGKEEPDGA 334

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  880 MYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGyqnthSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGY 959
Cdd:PHA03325  335 RNAEAKEPAQPATSTSSKGSSSAQNKDSGSTGPGSSL-----AAASSFLEDDDFGSPPLDLTTSLRHMPSPSVTSAPEPP 409


                  ..
gi 987437824  960 NP 961
Cdd:PHA03325  410 SI 411
dnaA PRK14086
chromosomal replication initiator protein DnaA;
819-967 2.02e-03

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 42.12  E-value: 2.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  819 PNNPNTPSRAEEeyeyafddeptPSPQAYGGTPNPQTPGYPDPSSPQVNPQYnPQTPGTPAMY--NTDQFSPYAAPSPQG 896
Cdd:PRK14086   96 APPPPHARRTSE-----------PELPRPGRRPYEGYGGPRADDRPPGLPRQ-DQLPTARPAYpaYQQRPEPGAWPRAAD 163

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  897 SYQPSPSPQSYhqvaPSPAGYQnthSPASYHPTPSPMAY----------QASPSPSPVGYSPMTPGA-------PSPGGY 959
Cdd:PRK14086  164 DYGWQQQRLGF----PPRAPYA---SPASYAPEQERDREpydagrpeydQRRRDYDHPRPDWDRPRRdrtdrpePPPGAG 236


                  ....*...
gi 987437824  960 NPHTPGSG 967
Cdd:PRK14086  237 HVHRGGPG 244
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 840-957 2.94e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.90  E-value: 2.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  840 PTPSPQAYGGTPNPQTPgypDPSSPQVNPQYNPQTPGTPAmyntdqfSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQN 919
Cdd:PRK07764  404 AAPAAAPAPAAAAPAAA---AAPAPAAAPQPAPAPAPAPA-------PPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAA 473

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 987437824  920 THSPASyhPTPSPMAYQASPSPSPVgysPMTPGAPSPG 957
Cdd:PRK07764  474 PEPTAA--PAPAPPAAPAPAAAPAA---PAAPAAPAGA 506
KREPA2 cd23959
Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of ...
 765-956 3.39e-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: 3.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  765 PMYGSQTPMYGSGSRTPMYGSQTPLQDGSRTPHYGSQTPLhDGSRTPAQSGAWDPNNP----NTPSRAEEEYEYAFDDEP 840
Cdd:cd23959    56 PLYGAVSPEGENPFDGPGLVTASTVSDCYVGNANFYEVDM-SDAFAMAPDESLGPFRAarvpNPFSASSSTQRETHKTAQ 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  841 TPSPQAYGGTPnPQTPGYPDPSSPQVNPqynPQTPGTPAMYNTDQ-FSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQN 919
Cdd:cd23959   135 VAPPKAEPQTA-PVTPFGQLPMFGQHPP---PAKPLPAAAAAQQSsASPGEVASPFASGTVSASPFATATDTAPSSGAPD 210

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 987437824  920 THSPASyhPTPSPMAyqASPSPSPVGYSPMTPGAPSP 956
Cdd:cd23959   211 GFPAEA--SAPSPFA--APASAASFPAAPVANGEAAT 243
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 838-964 3.44e-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: 3.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  838 DEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQynPQTPGTPAMYNTDQFSPYAAPSPQ-GSYQPSPSPQSYH-QVAPSPA 915
Cdd:NF033839  370 EKPKPEVKPQPETPKPEVKPQPEKPKPEVKPQ--PEKPKPEVKPQPEKPKPEVKPQPEkPKPEVKPQPEKPKpEVKPQPE 447

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 987437824  916 GYQNTHSPASYHPTPSPMAYQASPSPSpVGYSPMTP----GAPSPGGYNPHTP 964
Cdd:NF033839  448 KPKPEVKPQPETPKPEVKPQPEKPKPE-VKPQPEKPkpdnSKPQADDKKPSTP 499
KLF1_N cd21581
N-terminal domain of Kruppel-like Factor 1; Kruppel-like Factor 1 (KLF1, also known as ...
 768-962 5.36e-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: 40.03  E-value: 5.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  768 GSQTPMYGSGSRTPMYGSQTPLQdgsrtPHYGSQTPLHDGSRTpaqsgAWDPnnpntpsraeeeyEYAFDDEPTPSPQAy 847
Cdd:cd21581    26 EGQLPLDGPPDKLSPSGSEQLQV-----SQPMTEELLDDDSQA-----SWDI-------------EFLLSNWSSPSLNP- 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  848 GGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYN----------TDQFSPYAAPSPQ-GSYQPSPSPQSYHQVAP---- 912
Cdd:cd21581    82 SLDNNTQALPQEEQPGAYYEPPKKDQPGTEGLQVGgpglmaellsPEESTGWAPPEPHhGYPDAFVGPALFPAPANvdqf 161

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 987437824  913 --SPAGYQNTH---------SPASYHPT--PSPMAYQASPSPSPVGYSPMTPgAPSPGGYNPH 962
Cdd:cd21581   162 gfPQGGSVDRRgnlsksgswDFGSYYPQqhPSVVAFPDSRFGPLSGPQALTP-DPQHYGYFQL 223
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 777-915 5.66e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 40.74  E-value: 5.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824  777 GSRTPMYGSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEEYEyafddeptPSPQAYGGTPNPQTP 856
Cdd:PRK07764  674 GGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASA--------PSPAADDPVPLPPEP 745

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 987437824  857 GYPDPSSPQVNPQYNPQTPGTPAmyntdqfspyAAPSPQGSYQPSPSPQSYHQVAPSPA 915
Cdd:PRK07764  746 DDPPDPAGAPAQPPPPPAPAPAA----------APAAAPPPSPPSEEEEMAEDDAPSMD 794
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 592-623 7.75e-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: 35.06  E-value: 7.75e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 987437824   592 VKDIVKVIDGPHSGREGEIRHLFRSFAFLHCK 623
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 851-956 8.46e-03

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


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 38.23  E-value: 8.46e-03
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 987437824    851 PNPQTPGYPDPSSPQVNPQYNPQTPGTPAMyntdQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTP 930
Cdd:smart00818   45 QHPPTHTLQPHHHIPVLPAQQPVVPQQPLM----PVPGQHSMTPTQHHQPNLPQPAQQPFQPQPLQPPQPQQPMQPQPPV 120

                            90       100
                    ....*....|....*....|....*.
gi 987437824    931 SPMAYQASPSPSPvgysPMTPGAPSP 956
Cdd:smart00818  121 HPIPPLPPQPPLP----PMFPMQPLP 142
 
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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