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Conserved domains on  [gi|11527858|gb|AAG37030|]
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transcription elongation regulator FOGGY [Danio rerio]

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 ...
 177-264 1.40e-42

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: 149.60  E-value: 1.40e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858  177 NLWTVKCKIGEERATAISLMRKFVAYQCTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKAAIEGVGNLRMgfWNQQMVPI 256
Cdd:cd09888    1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYL--NTIKLVPI 78


                 ....*...
gi 11527858  257 KEMTDVLK 264
Cdd:cd09888   79 KEMPDVLS 86
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 770-887 3.95e-29

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


:

Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 112.62  E-value: 3.95e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858     770 GSQTPIYG-TGSRTPMYGSQTP----LHDGSRTPHYGSQTPLHDG--SRTPGQSGAWdPNNPNTPSRPDDEYEFAYDDEP 842
Cdd:smart01104    1 GGRTPAWGaSGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAWGGAG-PTGSRTPAWGGASAWGNKSSEG 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 11527858     843 SPSPQ--GYGGTPNPQTPGYPEVPSPqvnpqYNPQTPGTPAMYNTDQ 887
Cdd:smart01104   80 SASSWaaGPGGAYGAPTPGYGGTPSA-----YGPATPGGGAMAGSAS 121
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 470-520 1.57e-27

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: 105.69  E-value: 1.57e-27
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 11527858  470 YFRMGDHVKVIAGRYEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLC 520
Cdd:cd06083    1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1026-1082 1.26e-25

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: 100.28  E-value: 1.26e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 11527858 1026 EHLEPVTPTKNNKVKVILGEDREATGVLLSIDGEDGIVRMELDEQLKILNLRFLGKL 1082
Cdd:cd06086    1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMDSDGDIKILPMNFLAKL 57
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 419-469 1.99e-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: 99.50  E-value: 1.99e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 11527858  419 LQAGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDPLEFPAHELRK 469
Cdd:cd06082    1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 700-749 2.54e-24

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: 96.40  E-value: 2.54e-24
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 11527858  700 DNDLIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLT 749
Cdd:cd06085    2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLA 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 596-638 9.14e-20

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


:

Pssm-ID: 240508  Cd Length: 43  Bit Score: 83.34  E-value: 9.14e-20
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 11527858  596 KDIVKVIDGPHSGREGEIRHIFRGFAFLHCKKLVENGGMFVCK 638
Cdd:cd06084    1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 275-312 1.40e-16

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: 74.04  E-value: 1.40e-16
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 11527858  275 KSWVRLKRGLYKDDIAQVDYVEPSQNTISLKMIPRIDL 312
Cdd:cd06081    1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 94-171 4.55e-14

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: 68.83  E-value: 4.55e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11527858     94 GAEDILEKEEAEVSNLDHVVLDEDHSGSRRLQNLWRDSREEALGEYYMRKYAKSSggEHFYGGSEDlsDDITQQQLLP 171
Cdd:pfam11942   24 GADDFIEDDEEDEDEEDGRRDDRRHRELDRRRELEEDEDAEEIAEYLKERYGRSS--SDAYRGDAE--EGVPQRLLLP 97
Atrophin-1 super family cl38111
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 842-968 3.45e-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.


The actual alignment was detected with superfamily member pfam03154:

Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 57.85  E-value: 3.45e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    842 PSPSPQGYG----GTPNPQTPGYPEVPSPQVN-PQYNPQTPGTP--AMYNTDQYSPYAAPSPQGSYQPSPSPQSYHQVAP 914
Cdd:pfam03154  184 PSPPPPGTTqaatAGPTPSAPSVPPQGSPATSqPPNQTQSTAAPhtLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQVSP 263

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11527858    915 SPVGYQNTHSPASYHP---------TPSPMAYQASPSPSPVGYSPMTPG----APSPGGYNPHTPGS 968
Cdd:pfam03154  264 QPLPQPSLHGQMPPMPhslqtgpshMQHPVPPQPFPLTPQSSQSQVPPGpspaAPGQSQQRIHTPPS 330
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 177-264 1.40e-42

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: 149.60  E-value: 1.40e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858  177 NLWTVKCKIGEERATAISLMRKFVAYQCTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKAAIEGVGNLRMgfWNQQMVPI 256
Cdd:cd09888    1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYL--NTIKLVPI 78


                 ....*...
gi 11527858  257 KEMTDVLK 264
Cdd:cd09888   79 KEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 177-263 1.04e-30

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: 115.76  E-value: 1.04e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    177 NLWTVKCKIGEERATAISLMRKFVAYQcTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKAAIEGVGNLRMGfwNQQMVPI 256
Cdd:pfam03439    1 KIWAVKCTPGQEREVALSLMRKILALA-KTNNLGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGL--VPGLVPI 77


                   ....*..
gi 11527858    257 KEMTDVL 263
Cdd:pfam03439   78 KEMEHLL 84
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 770-887 3.95e-29

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


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 112.62  E-value: 3.95e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858     770 GSQTPIYG-TGSRTPMYGSQTP----LHDGSRTPHYGSQTPLHDG--SRTPGQSGAWdPNNPNTPSRPDDEYEFAYDDEP 842
Cdd:smart01104    1 GGRTPAWGaSGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAWGGAG-PTGSRTPAWGGASAWGNKSSEG 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 11527858     843 SPSPQ--GYGGTPNPQTPGYPEVPSPqvnpqYNPQTPGTPAMYNTDQ 887
Cdd:smart01104   80 SASSWaaGPGGAYGAPTPGYGGTPSA-----YGPATPGGGAMAGSAS 121
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 470-520 1.57e-27

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: 105.69  E-value: 1.57e-27
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 11527858  470 YFRMGDHVKVIAGRYEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLC 520
Cdd:cd06083    1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1026-1082 1.26e-25

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: 100.28  E-value: 1.26e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 11527858 1026 EHLEPVTPTKNNKVKVILGEDREATGVLLSIDGEDGIVRMELDEQLKILNLRFLGKL 1082
Cdd:cd06086    1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMDSDGDIKILPMNFLAKL 57
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 419-469 1.99e-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: 99.50  E-value: 1.99e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 11527858  419 LQAGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDPLEFPAHELRK 469
Cdd:cd06082    1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 700-749 2.54e-24

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: 96.40  E-value: 2.54e-24
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 11527858  700 DNDLIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLT 749
Cdd:cd06085    2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLA 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 596-638 9.14e-20

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


Pssm-ID: 240508  Cd Length: 43  Bit Score: 83.34  E-value: 9.14e-20
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 11527858  596 KDIVKVIDGPHSGREGEIRHIFRGFAFLHCKKLVENGGMFVCK 638
Cdd:cd06084    1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 275-312 1.40e-16

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: 74.04  E-value: 1.40e-16
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 11527858  275 KSWVRLKRGLYKDDIAQVDYVEPSQNTISLKMIPRIDL 312
Cdd:cd06081    1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 770-828 2.15e-14

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: 69.01  E-value: 2.15e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    770 GSQTPIYGT--GSRTPMY---GSQTPLHD--GSRTPHY--GSQTPLHD--GSRTPGQSGAWDPnnPNTPS 828
Cdd:pfam12815    1 GSRTPAYNSagGSRTPAWgadGSRTPAYGgaGGRTPAYnqGGKTPAWGgaGSRTPAYYGAWGG--SRTPA 68
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 94-171 4.55e-14

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: 68.83  E-value: 4.55e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11527858     94 GAEDILEKEEAEVSNLDHVVLDEDHSGSRRLQNLWRDSREEALGEYYMRKYAKSSggEHFYGGSEDlsDDITQQQLLP 171
Cdd:pfam11942   24 GADDFIEDDEEDEDEEDGRRDDRRHRELDRRRELEEDEDAEEIAEYLKERYGRSS--SDAYRGDAE--EGVPQRLLLP 97
nusG PRK08559
transcription antitermination protein NusG; Validated
 174-307 9.04e-12

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 64.12  E-value: 9.04e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   174 KDPNLWTVKCKIGEERATAISLMRKFVAYQctdtpLQIKSVVAPEHVKGYIYVEAYKQTHVKAAIEGVGNLRMGFwnQQM 253
Cdd:PRK08559    4 EMSMIFAVKTTAGQERNVALMLAMRAKKEN-----LPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVRGVV--PGE 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 11527858   254 VPIKEMTDVLKVVKEVTNLKPKSWVRLKRGLYKDDIAQVDYVEPSQNTISLKMI 307
Cdd:PRK08559   77 ISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELL 130
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 177-265 2.33e-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: 58.54  E-value: 2.33e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858     177 NLWTVKCKIGEERATAISLMRKFVAYQCTDtplQIKSVVAP-EHVK----------------GYIYVEAYKQTHVKAAIE 239
Cdd:smart00738    1 NWYAVRTTSGQEKRVAENLERKAEALGLED---KIVSILVPtEEVKeirrgkkkvverklfpGYIFVEADLEDEVWTAIR 77

                            90       100       110
                    ....*....|....*....|....*....|
gi 11527858     240 GVGNLRmGF----WNQQMVPIKEMTDVLKV 265
Cdd:smart00738   78 GTPGVR-GFvgggGKPTPVPDDEIEKILKP 106
PHA03247 PHA03247
large tegument protein UL36; Provisional
 744-960 1.13e-09

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 63.03  E-value: 1.13e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   744 DRQRLTTVGGKERQGRSSTHLRTPMYGSQTPiygTGSRT----PMYGSQTPLHD--------GSRTPHYGSQTPLHDGSR 811
Cdd:PHA03247 2650 ERPRDDPAPGRVSRPRRARRLGRAAQASSPP---QRPRRraarPTVGSLTSLADpppppptpEPAPHALVSATPLPPGPA 2726

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   812 TPGQSGAWDPNNPNTPSRPddeyefayddEPSPSPQGYGGTPNPQTPGYPEVPSPQVNPQYNPQTPGTPAMYNTDQYSPY 891
Cdd:PHA03247 2727 AARQASPALPAAPAPPAVP----------AGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRE 2796

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 11527858   892 AAPSPqgsyqPSPSPQSYHQVAPSPvGYQNTHSPASYHPTPsPMAYQASPSPSPVGYSPMTP--GAPSPGG 960
Cdd:PHA03247 2797 SLPSP-----WDPADPPAAVLAPAA-ALPPAASPAGPLPPP-TSAQPTAPPPPPGPPPPSLPlgGSVAPGG 2860
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 842-968 3.45e-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: 57.85  E-value: 3.45e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    842 PSPSPQGYG----GTPNPQTPGYPEVPSPQVN-PQYNPQTPGTP--AMYNTDQYSPYAAPSPQGSYQPSPSPQSYHQVAP 914
Cdd:pfam03154  184 PSPPPPGTTqaatAGPTPSAPSVPPQGSPATSqPPNQTQSTAAPhtLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQVSP 263

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11527858    915 SPVGYQNTHSPASYHP---------TPSPMAYQASPSPSPVGYSPMTPG----APSPGGYNPHTPGS 968
Cdd:pfam03154  264 QPLPQPSLHGQMPPMPhslqtgpshMQHPVPPQPFPLTPQSSQSQVPPGpspaAPGQSQQRIHTPPS 330
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 179-307 4.78e-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: 4.78e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    179 WTVKCKIGEERATAislmrKFVAYQCTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKAAIEGVGNLRmGFWNQQmVPIKE 258
Cdd:TIGR00405    1 FAVKTSVGQEKNVA-----RLMARKARKSGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVR-GVVEGE-IDFEE 73

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 11527858    259 MTDVLKVVKEVTNLKPKSWVRLKRGLYKDDIAQVDYVEPSQNTISLKMI 307
Cdd:TIGR00405   74 IERFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELI 122
PHA03247 PHA03247
large tegument protein UL36; Provisional
 821-966 4.88e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 54.56  E-value: 4.88e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   821 PNNPNTPSRPDDEYEFAYDDEPSPspqGYGGTPNPQTPGYPEVPSPQVNPQYNPQTPGTPAMY----NTDQYSPYAAPSP 896
Cdd:PHA03247 2475 PGAPVYRRPAEARFPFAAGAAPDP---GGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLtwirGLEELASDDAGDP 2551

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 11527858   897 QGSYQPSPSPQSYHQVAPSPvgyqnthSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAP--SPGGYNPHTP 966
Cdd:PHA03247 2552 PPPLPPAAPPAAPDRSVPPP-------RPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDrgDPRGPAPPSP 2616
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 788-963 9.62e-06

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: 49.77  E-value: 9.62e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   788 QTPLHDGSRTPHyGSQTPLHDGSRTPGQSGAWDPNNPNTPSRPDDEYEfayDDEPSPSPQGYG-------GTPNPQTPGY 860
Cdd:NF033839  282 DTPKEPGNKKPS-APKPGMQPSPQPEKKEVKPEPETPKPEVKPQLEKP---KPEVKPQPEKPKpevkpqlETPKPEVKPQ 357

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   861 PEVPSPQVNPQYNPQTPGTPAMYNTDQYSPYAAPS-PQGSYQPSPSpQSYHQVAPSPVGYQNTHSPASYHPTPS--PMAY 937
Cdd:NF033839  358 PEKPKPEVKPQPEKPKPEVKPQPETPKPEVKPQPEkPKPEVKPQPE-KPKPEVKPQPEKPKPEVKPQPEKPKPEvkPQPE 436

                         170       180
                  ....*....|....*....|....*.
gi 11527858   938 QASPSPSPVGYSPMTPGAPSPGGYNP 963
Cdd:NF033839  437 KPKPEVKPQPEKPKPEVKPQPETPKP 462
KLF1_2_4_N cd21972
N-terminal domain of Kruppel-like factor (KLF) 1, KLF2, KLF4, and similar proteins; Kruppel ...
 835-966 1.05e-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: 44.59  E-value: 1.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858  835 EFAYDDEPSPSPQGYG--GTPNPQTPGYPEVPSPQVNPQYN-PQTPGTPAMYNTDQYSPYAAPSPQgsyqPSPSPQSYHQ 911
Cdd:cd21972   32 VTSDNDNPPPPDPAYPppESPESCSTVYDSDGCHPTPNAYCgPNGPGLPGHFLLAGNSPNLGPKIK----TENQEQACMP 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 11527858  912 VAPSPVGY---QNTHSPASYHPTP--------------SPMAYQASPSPSPVGYSPmtPGAPSPGGYNPHTP 966
Cdd:cd21972  108 VAGYSGHYgprEPQRVPPAPPPPQyaghfqyhghfnmfSPPLRANHPGMSTVMLTP--LSTPPLGFLSPEEA 177
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 824-963 1.13e-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: 46.30  E-value: 1.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   824 PNTPSRPDDEYEFAYDDEPSPSPQGYGGTPNPQT-PGYPEV------PSPQVNPQYNPQTPGTPAMYNTdqyspyaaPSP 896
Cdd:NF033839  281 QDTPKEPGNKKPSAPKPGMQPSPQPEKKEVKPEPeTPKPEVkpqlekPKPEVKPQPEKPKPEVKPQLET--------PKP 352

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   897 QGSYQPS-PSPqsyhQVAPSPVGYQNTHSPASYHPTPSPMAYQASPSP--SPVGYSPMTPGAPSPGGYNP 963
Cdd:NF033839  353 EVKPQPEkPKP----EVKPQPEKPKPEVKPQPETPKPEVKPQPEKPKPevKPQPEKPKPEVKPQPEKPKP 418
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 704-735 1.19e-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: 40.06  E-value: 1.19e-04
                           10        20        30
                   ....*....|....*....|....*....|..
gi 11527858    704 IGQTVRISQGPYKGYIGVVKDATESTARVELH 735
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
SP7_N cd22542
N-terminal domain of transcription factor Specificity Protein (SP) 7; Specificity Proteins ...
 800-968 1.28e-04

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: 45.27  E-value: 1.28e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858  800 YGSQTPLHDgSRTPGQSGAWDPNNPNTPS---------RPD---DEYEFAYDD-----EPSPSPQ---GYGGTPNPQTPG 859
Cdd:cd22542   26 FGGSSPIRD-SATPGKPGNNPGKKPYSLGsdlssaksrSSElmgDSYTATFSSgnglmSPSGSPQastTYGNDYNPFSHS 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858  860 YPEVPSPQ----VNPQYNPQTPGTPAMYNT-DQYSPY-----AAPSPQGSYQPSPSPQSYHQVAPSPVGYQNTHSPASYH 929
Cdd:cd22542  105 FPTSSGSQdpslLVSKGHPSADCLPSVYTSlDMAHPYgswykTGIHPGISSSSTNATASWWDMHSNTNWLSAQGQPDGLQ 184

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 11527858  930 PTPSPMAYQASPSPSPVGYSPMTPgaPSPGGYNPHTPGS 968
Cdd:cd22542  185 ASLQPVPAQTPLNPQLPSYTEFTT--LNPAPYPAVGISS 221
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 470-497 1.32e-04

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


Pssm-ID: 128978  Cd Length: 28  Bit Score: 40.00  E-value: 1.32e-04
                            10        20
                    ....*....|....*....|....*...
gi 11527858     470 YFRMGDHVKVIAGRYEGDTGLIVRVEEN 497
Cdd:smart00739    1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 474-502 3.68e-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: 38.91  E-value: 3.68e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 11527858    474 GDHVKVIAGRYEGDTGLIVRVEE--NFVILF 502
Cdd:pfam00467    2 GDVVRVIAGPFKGKVGKVVEVDDkkNRVLVE 32
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 595-626 1.79e-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: 36.98  E-value: 1.79e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 11527858    595 VKDIVKVIDGPHSGREGEIRHIFRGFAFLHCK 626
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 592-618 7.52e-03

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


Pssm-ID: 128978  Cd Length: 28  Bit Score: 35.00  E-value: 7.52e-03
                            10        20
                    ....*....|....*....|....*..
gi 11527858     592 NIHVKDIVKVIDGPHSGREGEIRHIFR 618
Cdd:smart00739    1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 177-264 1.40e-42

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: 149.60  E-value: 1.40e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858  177 NLWTVKCKIGEERATAISLMRKFVAYQCTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKAAIEGVGNLRMgfWNQQMVPI 256
Cdd:cd09888    1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYL--NTIKLVPI 78


                 ....*...
gi 11527858  257 KEMTDVLK 264
Cdd:cd09888   79 KEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 177-263 1.04e-30

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: 115.76  E-value: 1.04e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    177 NLWTVKCKIGEERATAISLMRKFVAYQcTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKAAIEGVGNLRMGfwNQQMVPI 256
Cdd:pfam03439    1 KIWAVKCTPGQEREVALSLMRKILALA-KTNNLGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGL--VPGLVPI 77


                   ....*..
gi 11527858    257 KEMTDVL 263
Cdd:pfam03439   78 KEMEHLL 84
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 770-887 3.95e-29

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


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 112.62  E-value: 3.95e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858     770 GSQTPIYG-TGSRTPMYGSQTP----LHDGSRTPHYGSQTPLHDG--SRTPGQSGAWdPNNPNTPSRPDDEYEFAYDDEP 842
Cdd:smart01104    1 GGRTPAWGaSGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAWGGAG-PTGSRTPAWGGASAWGNKSSEG 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 11527858     843 SPSPQ--GYGGTPNPQTPGYPEVPSPqvnpqYNPQTPGTPAMYNTDQ 887
Cdd:smart01104   80 SASSWaaGPGGAYGAPTPGYGGTPSA-----YGPATPGGGAMAGSAS 121
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 470-520 1.57e-27

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: 105.69  E-value: 1.57e-27
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 11527858  470 YFRMGDHVKVIAGRYEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLC 520
Cdd:cd06083    1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1026-1082 1.26e-25

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: 100.28  E-value: 1.26e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 11527858 1026 EHLEPVTPTKNNKVKVILGEDREATGVLLSIDGEDGIVRMELDEQLKILNLRFLGKL 1082
Cdd:cd06086    1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMDSDGDIKILPMNFLAKL 57
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 419-469 1.99e-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: 99.50  E-value: 1.99e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 11527858  419 LQAGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDPLEFPAHELRK 469
Cdd:cd06082    1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 700-749 2.54e-24

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: 96.40  E-value: 2.54e-24
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 11527858  700 DNDLIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLT 749
Cdd:cd06085    2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLA 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 596-638 9.14e-20

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


Pssm-ID: 240508  Cd Length: 43  Bit Score: 83.34  E-value: 9.14e-20
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 11527858  596 KDIVKVIDGPHSGREGEIRHIFRGFAFLHCKKLVENGGMFVCK 638
Cdd:cd06084    1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 275-312 1.40e-16

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: 74.04  E-value: 1.40e-16
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 11527858  275 KSWVRLKRGLYKDDIAQVDYVEPSQNTISLKMIPRIDL 312
Cdd:cd06081    1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 770-828 2.15e-14

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: 69.01  E-value: 2.15e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    770 GSQTPIYGT--GSRTPMY---GSQTPLHD--GSRTPHY--GSQTPLHD--GSRTPGQSGAWDPnnPNTPS 828
Cdd:pfam12815    1 GSRTPAYNSagGSRTPAWgadGSRTPAYGgaGGRTPAYnqGGKTPAWGgaGSRTPAYYGAWGG--SRTPA 68
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 94-171 4.55e-14

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: 68.83  E-value: 4.55e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11527858     94 GAEDILEKEEAEVSNLDHVVLDEDHSGSRRLQNLWRDSREEALGEYYMRKYAKSSggEHFYGGSEDlsDDITQQQLLP 171
Cdd:pfam11942   24 GADDFIEDDEEDEDEEDGRRDDRRHRELDRRRELEEDEDAEEIAEYLKERYGRSS--SDAYRGDAE--EGVPQRLLLP 97
nusG PRK08559
transcription antitermination protein NusG; Validated
 174-307 9.04e-12

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 64.12  E-value: 9.04e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   174 KDPNLWTVKCKIGEERATAISLMRKFVAYQctdtpLQIKSVVAPEHVKGYIYVEAYKQTHVKAAIEGVGNLRMGFwnQQM 253
Cdd:PRK08559    4 EMSMIFAVKTTAGQERNVALMLAMRAKKEN-----LPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVRGVV--PGE 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 11527858   254 VPIKEMTDVLKVVKEVTNLKPKSWVRLKRGLYKDDIAQVDYVEPSQNTISLKMI 307
Cdd:PRK08559   77 ISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELL 130
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 765-817 2.70e-11

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: 60.15  E-value: 2.70e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 11527858    765 RTPMY---GSQTPIYGT-GSRTPMY--GSQTPLHD--GSRTPHYGSQTplhDGSRTPGQSG 817
Cdd:pfam12815   14 RTPAWgadGSRTPAYGGaGGRTPAYnqGGKTPAWGgaGSRTPAYYGAW---GGSRTPAYGG 71
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 177-265 2.33e-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: 58.54  E-value: 2.33e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858     177 NLWTVKCKIGEERATAISLMRKFVAYQCTDtplQIKSVVAP-EHVK----------------GYIYVEAYKQTHVKAAIE 239
Cdd:smart00738    1 NWYAVRTTSGQEKRVAENLERKAEALGLED---KIVSILVPtEEVKeirrgkkkvverklfpGYIFVEADLEDEVWTAIR 77

                            90       100       110
                    ....*....|....*....|....*....|
gi 11527858     240 GVGNLRmGF----WNQQMVPIKEMTDVLKV 265
Cdd:smart00738   78 GTPGVR-GFvgggGKPTPVPDDEIEKILKP 106
PHA03247 PHA03247
large tegument protein UL36; Provisional
 744-960 1.13e-09

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 63.03  E-value: 1.13e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   744 DRQRLTTVGGKERQGRSSTHLRTPMYGSQTPiygTGSRT----PMYGSQTPLHD--------GSRTPHYGSQTPLHDGSR 811
Cdd:PHA03247 2650 ERPRDDPAPGRVSRPRRARRLGRAAQASSPP---QRPRRraarPTVGSLTSLADpppppptpEPAPHALVSATPLPPGPA 2726

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   812 TPGQSGAWDPNNPNTPSRPddeyefayddEPSPSPQGYGGTPNPQTPGYPEVPSPQVNPQYNPQTPGTPAMYNTDQYSPY 891
Cdd:PHA03247 2727 AARQASPALPAAPAPPAVP----------AGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRE 2796

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 11527858   892 AAPSPqgsyqPSPSPQSYHQVAPSPvGYQNTHSPASYHPTPsPMAYQASPSPSPVGYSPMTP--GAPSPGG 960
Cdd:PHA03247 2797 SLPSP-----WDPADPPAAVLAPAA-ALPPAASPAGPLPPP-TSAQPTAPPPPPGPPPPSLPlgGSVAPGG 2860
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 795-969 5.56e-09

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


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 60.55  E-value: 5.56e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    795 SRTPHYGSQTPLHDGSRTPG----QSGAWDPNNPnTPSRPDDEYEFAYDDEPSPSPQGYGGTPNPQTPGYP---EVPSPQ 867
Cdd:pfam03154  259 SQVSPQPLPQPSLHGQMPPMphslQTGPSHMQHP-VPPQPFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPpsqSQLQSQ 337

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    868 VNPQYNPQTPGTPAMyntdqysPYAAPSPQGSYQPSPSPQSY----HQVAPSP---------------VGYQNTHSPASY 928
Cdd:pfam03154  338 QPPREQPLPPAPLSM-------PHIKPPPTTPIPQLPNPQSHkhppHLSGPSPfqmnsnlppppalkpLSSLSTHHPPSA 410

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 11527858    929 HPTPSPMAYQASPSPSPVGYSPM---TPGAPSPGGYNPHTPGSN 969
Cdd:pfam03154  411 HPPPLQLMPQSQQLPPPPAQPPVltqSQSLPPPAASHPPTSGLH 454
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 177-263 7.69e-09

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: 54.25  E-value: 7.69e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858  177 NLWTVKCKIGEERATAISLMRKFVA---------YQCTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKAAIEGVGNLRMG 247
Cdd:cd08000    1 NWYVLFVKTGREEKVEKLLEKRFEAndieafvpkKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPGVIGI 80

                         90
                 ....*....|....*....
gi 11527858  248 FWN---QQMVPIKEMTDVL 263
Cdd:cd08000   81 LGNgeePSPVSDEEIEMIL 99
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 762-968 2.54e-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: 58.24  E-value: 2.54e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    762 THLRTPMygsqtPIYGTGSRTPMYGSQTPLHDGSRTPHYGSQTPlhdgSRTPGQSGAWDPNNPNTPSRPDDEYEFAYDDE 841
Cdd:pfam03154  287 SHMQHPV-----PPQPFPLTPQSSQSQVPPGPSPAAPGQSQQRI----HTPPSQSQLQSQQPPREQPLPPAPLSMPHIKP 357

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    842 P--SPSPQgyggTPNPQT---PGYPEVPSPQvnpQYNPQTPGTPAMYNTDQYSPYAAPS---------PQGSYQPSPSPQ 907
Cdd:pfam03154  358 PptTPIPQ----LPNPQShkhPPHLSGPSPF---QMNSNLPPPPALKPLSSLSTHHPPSahppplqlmPQSQQLPPPPAQ 430

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 11527858    908 SyhqvaPSPVGYQNTHSPASYHPTPSpmAYQASPSPSPVGYSPMTPGAP----SPGGYNPHTPGS 968
Cdd:pfam03154  431 P-----PVLTQSQSLPPPAASHPPTS--GLHQVPSQSPFPQHPFVPGGPppitPPSGPPTSTSSA 488
PHA03247 PHA03247
large tegument protein UL36; Provisional
 773-980 2.92e-08

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 58.41  E-value: 2.92e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   773 TPIYGTGSRTPMYGSQTPLHDGSRTPHYGSQTPLHDGSRTPGQSGAwdPNNPNTPSRPDDEYEFAydDEPSPSPQGYGGT 852
Cdd:PHA03247 2826 GPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSP--AAKPAAPARPPVRRLAR--PAVSRSTESFALP 2901

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   853 PNPQTPgyPEVPSPQVNPQYNPQTPGTPamyntdqySPYAAPSPQGSYQPSPSPQSYHQVAPSPVGYQNTHSPASYHPTP 932
Cdd:PHA03247 2902 PDQPER--PPQPQAPPPPQPQPQPPPPP--------QPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGR 2971

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 11527858   933 SPMAYQASPSPSPvgySPMTPgAPSpggynPHTPGSNIDQASNDWVTT 980
Cdd:PHA03247 2972 VAVPRFRVPQPAP---SREAP-ASS-----TPPLTGHSLSRVSSWASS 3010
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 842-968 3.45e-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: 57.85  E-value: 3.45e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    842 PSPSPQGYG----GTPNPQTPGYPEVPSPQVN-PQYNPQTPGTP--AMYNTDQYSPYAAPSPQGSYQPSPSPQSYHQVAP 914
Cdd:pfam03154  184 PSPPPPGTTqaatAGPTPSAPSVPPQGSPATSqPPNQTQSTAAPhtLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQVSP 263

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11527858    915 SPVGYQNTHSPASYHP---------TPSPMAYQASPSPSPVGYSPMTPG----APSPGGYNPHTPGS 968
Cdd:pfam03154  264 QPLPQPSLHGQMPPMPhslqtgpshMQHPVPPQPFPLTPQSSQSQVPPGpspaAPGQSQQRIHTPPS 330
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 179-307 4.78e-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: 4.78e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    179 WTVKCKIGEERATAislmrKFVAYQCTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKAAIEGVGNLRmGFWNQQmVPIKE 258
Cdd:TIGR00405    1 FAVKTSVGQEKNVA-----RLMARKARKSGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVR-GVVEGE-IDFEE 73

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 11527858    259 MTDVLKVVKEVTNLKPKSWVRLKRGLYKDDIAQVDYVEPSQNTISLKMI 307
Cdd:TIGR00405   74 IERFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELI 122
PHA03378 PHA03378
EBNA-3B; Provisional
 761-960 1.33e-07

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 55.84  E-value: 1.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   761 STHLRTPMYGSQTPIYGTGSRTPMYGSQTPLHD-----------GSRTPHYGSQTPLHDGSRTPGQSGAWD----PNNPN 825
Cdd:PHA03378  603 SQTPEPPTTQSHIPETSAPRQWPMPLRPIPMRPlrmqpitfnvlVFPTPHQPPQVEITPYKPTWTQIGHIPyqpsPTGAN 682

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   826 TPSRPDdeyefAYDDEPSPSPQGYGGTPNPQTPGYPEVPsPQVNPQYNPQTPGTPAMYNTDQYSPYAAPSPQGSYQPSPS 905
Cdd:PHA03378  683 TMLPIQ-----WAPGTMQPPPRAPTPMRPPAAPPGRAQR-PAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARP 756

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 11527858   906 PQSYHQVAPSPVGyqnthSPASYHPTPSPMA-------YQASPSPSP---VGYSPMTPGAPSPGG 960
Cdd:PHA03378  757 PAAAPGRARPPAA-----APGAPTPQPPPQAppapqqrPRGAPTPQPppqAGPTSMQLMPRAAPG 816
PHA03247 PHA03247
large tegument protein UL36; Provisional
 809-964 3.09e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 54.94  E-value: 3.09e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   809 GSRTPGQSGAWDPNNPNTPSRP-----DDE-----------------YEFAYDDEPSPSPQGYGGTPNPQTPgyPEVPSP 866
Cdd:PHA03247 2494 AAPDPGGGGPPDPDAPPAPSRLapailPDEpvgepvhprmltwirglEELASDDAGDPPPPLPPAAPPAAPD--RSVPPP 2571

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   867 QVNP-------QYNPQTPGTPAMYNTDQySPYAAP-SPQGSYQPSPSPQSYHQVAPSPvgyqnthspasyhPTPSPMAYQ 938
Cdd:PHA03247 2572 RPAPrpsepavTSRARRPDAPPQSARPR-APVDDRgDPRGPAPPSPLPPDTHAPDPPP-------------PSPSPAANE 2637

                         170       180
                  ....*....|....*....|....*..
gi 11527858   939 A-SPSPSPVGYSPMTPGAPSPGGYNPH 964
Cdd:PHA03247 2638 PdPHPPPTVPPPERPRDDPAPGRVSRP 2664
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 846-967 3.58e-07

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: 54.24  E-value: 3.58e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    846 PQGYGGTPNPQTPGypevpsPQVNPQYNPQTPGTPAMYNTDQYSPYAAPSPQGSYQPSPSPQSYHQVAPSPVGYQNTHSP 925
Cdd:pfam09606  342 ALGGLNHLETWNPG------NFGGLGANPMQRGQPGMMSSPSPVPGQQVRQVTPNQFMRQSPQPSVPSPQGPGSQPPQSH 415

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 11527858    926 ASyHPTPSPmAYQASPSPSPVGY--SPMTPGAPSPGGyNPHTPG 967
Cdd:pfam09606  416 PG-GMIPSP-ALIPSPSPQMSQQpaQQRTIGQDSPGG-SLNTPG 456
NGN_Arch cd09887
Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance ...
 178-245 4.05e-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: 48.69  E-value: 4.05e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11527858  178 LWTVKCKIGEERATAISLMRKfvayqCTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKAAIEGVGNLR 245
Cdd:cd09887    2 IYAVKTTAGQERNVADLLAMR-----AEKENLDVYSILVPEELKGYVFVEAEDPDRVEELIRGIPHVR 64
PHA03247 PHA03247
large tegument protein UL36; Provisional
 821-966 4.88e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 54.56  E-value: 4.88e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   821 PNNPNTPSRPDDEYEFAYDDEPSPspqGYGGTPNPQTPGYPEVPSPQVNPQYNPQTPGTPAMY----NTDQYSPYAAPSP 896
Cdd:PHA03247 2475 PGAPVYRRPAEARFPFAAGAAPDP---GGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLtwirGLEELASDDAGDP 2551

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 11527858   897 QGSYQPSPSPQSYHQVAPSPvgyqnthSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAP--SPGGYNPHTP 966
Cdd:PHA03247 2552 PPPLPPAAPPAAPDRSVPPP-------RPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDrgDPRGPAPPSP 2616
PHA03247 PHA03247
large tegument protein UL36; Provisional
 811-967 6.34e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 54.17  E-value: 6.34e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   811 RTPGQ-SGAWDPNNPNTPSRPDDeyefAYDDEPSPSPQ-------GYGGTPNPQTPGYPEVPSP-QVNPQYNPQTPGTPA 881
Cdd:PHA03247 2599 RAPVDdRGDPRGPAPPSPLPPDT----HAPDPPPPSPSpaanepdPHPPPTVPPPERPRDDPAPgRVSRPRRARRLGRAA 2674

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   882 MYN--TDQYSPYAAPSPQGSYQPS---PSPQSYHQVAPSPVGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAP 956
Cdd:PHA03247 2675 QASspPQRPRRRAARPTVGSLTSLadpPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGP 2754

                         170
                  ....*....|.
gi 11527858   957 SPGGYNPHTPG 967
Cdd:PHA03247 2755 ARPARPPTTAG 2765
PHA03377 PHA03377
EBNA-3C; Provisional
 755-974 7.61e-07

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 53.52  E-value: 7.61e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   755 ERQGRSSTHLRTPMYGSQTPIYgTGSRTPMYGSQTPLHD---GSRTPHYGSQTPLHDGSRTPGQsgaWDPNNPNTPSRPD 831
Cdd:PHA03377  702 EESHLSSMSPTQPISHEEQPRY-EDPDDPLDLSLHPDQApppSHQAPYSGHEEPQAQQAPYPGY---WEPRPPQAPYLGY 777

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   832 DEYEfAYDDEPSPSPqGYGG--TPNPQTPGY--PEVPSPQvNPQY-NPQTPGTP-AMYNTDQYSPYAAP-----SPQGSY 900
Cdd:PHA03377  778 QEPQ-AQGVQVSSYP-GYAGpwGLRAQHPRYrhSWAYWSQ-YPGHgHPQGPWAPrPPHLPPQWDGSAGHgqdqvSQFPHL 854

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   901 QPSPSP----QSYHQVAPSPVGYQNTHSPASYHPTPS----PMAYQASPSPSPVGYSpMTPGAPSPGGYNPHTP-GSNID 971
Cdd:PHA03377  855 QSETGPprlqLSQVPQLPYSQTLVSSSAPSWSSPQPRapirPIPTRFPPPPMPLQDS-MAVGCDSSGTACPSMPfASDYS 933


                  ...
gi 11527858   972 QAS 974
Cdd:PHA03377  934 QGA 936
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 791-967 1.99e-06

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 52.39  E-value: 1.99e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   791 LHDGSRT--PHYGSQTPLHDG------------SRTPGQSGAwDPNNPNTPSRPDDEYEFA-----YDDEPSPSPQGYGG 851
Cdd:PRK10263  293 LFSGNRAtqPEYDEYDPLLNGapitepvavaaaATTATQSWA-APVEPVTQTPPVASVDVPpaqptVAWQPVPGPQTGEP 371

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   852 TPNPQTPGYPEVP---SPQVNPQ------YNPQTPGTPAMYNTDQYSPYAAPSP-QGSYQPSPSPQSYHQVAPSPVGYQN 921
Cdd:PRK10263  372 VIAPAPEGYPQQSqyaQPAVQYNeplqqpVQPQQPYYAPAAEQPAQQPYYAPAPeQPAQQPYYAPAPEQPVAGNAWQAEE 451

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 11527858   922 THSPasYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPG 967
Cdd:PRK10263  452 QQST--FAPQSTYQTEQTYQQPAAQEPLYQQPQPVEQQPVVEPEPV 495
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 474-518 2.39e-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: 2.39e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 11527858  474 GDHVKVIAGRYEGDTGLIVRVEENFVIL----FSDLTMHELKVLPRDLQ 518
Cdd:cd00380    1 GDVVRVLRGPYKGREGVVVDIDPRFGIVtvkgATGSKGAELKVRFDDVD 49
PHA02682 PHA02682
ORF080 virion core protein; Provisional
 811-946 3.08e-06

ORF080 virion core protein; Provisional


Pssm-ID: 177464 [Multi-domain]  Cd Length: 280  Bit Score: 50.24  E-value: 3.08e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   811 RTPGQSgawdPNNPnTPSRPDDEYEFAYDDEPSPSPQGYGGTPNPQTP--GYPEVPSPQVNPQYNPQTPGTPAmyNTDQY 888
Cdd:PHA02682   75 RPSGQS----PLAP-SPACAAPAPACPACAPAAPAPAVTCPAPAPACPpaTAPTCPPPAVCPAPARPAPACPP--STRQC 147

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 11527858   889 SPyAAPSPQgsyqPSPSPqsyhqvAPSPVGYQNTHSPASYhPTPSPMAYQASPSPSPV 946
Cdd:PHA02682  148 PP-APPLPT----PKPAP------AAKPIFLHNQLPPPDY-PAASCPTIETAPAASPV 193
PHA03247 PHA03247
large tegument protein UL36; Provisional
 821-974 3.12e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 51.86  E-value: 3.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   821 PNNPNTPSRP-DDEYEFAYDDEPSPSPQGyggTPNPQTPgyPEVPSPQVNPQYNPQTPGTPAMYNTDQYS-------PYA 892
Cdd:PHA03247 2592 PPQSARPRAPvDDRGDPRGPAPPSPLPPD---THAPDPP--PPSPSPAANEPDPHPPPTVPPPERPRDDPapgrvsrPRR 2666

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   893 APSPQGSYQPSPSPQSYHQ-VAPSPVGyqnthSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPGSNID 971
Cdd:PHA03247 2667 ARRLGRAAQASSPPQRPRRrAARPTVG-----SLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAP 2741


                  ...
gi 11527858   972 QAS 974
Cdd:PHA03247 2742 PAV 2744
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 422-468 5.44e-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: 5.44e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 11527858  422 GDNVEVCEGELINLQGKILSVDG--NKITIMPKHEDLKDPLEFPAHELR 468
Cdd:cd00380    1 GDVVRVLRGPYKGREGVVVDIDPrfGIVTVKGATGSKGAELKVRFDDVD 49
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 705-748 5.50e-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: 5.50e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 11527858  705 GQTVRISQGPYKGYIGVVKDATEST--ARVELH--STCQTISVDRQRL 748
Cdd:cd00380    1 GDVVRVLRGPYKGREGVVVDIDPRFgiVTVKGAtgSKGAELKVRFDDV 48
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 596-633 6.31e-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: 44.13  E-value: 6.31e-06
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 11527858  596 KDIVKVIDGPHSGREGEIRHIFRGFAFLHCKKLVENGG 633
Cdd:cd00380    1 GDVVRVLRGPYKGREGVVVDIDPRFGIVTVKGATGSKG 38
PHA03247 PHA03247
large tegument protein UL36; Provisional
 812-986 6.66e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 50.71  E-value: 6.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   812 TPGQSGAWDPNNPNTPSRPDDEYEFAYDDEPSPSPqgyggTPNPQTPGYPEVPSPQVNPQYNP----------------- 874
Cdd:PHA03247 2795 RESLPSPWDPADPPAAVLAPAAALPPAASPAGPLP-----PPTSAQPTAPPPPPGPPPPSLPLggsvapggdvrrrppsr 2869

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   875 QTPGTPAMYNTDQYSPYAAPSPQGSYQPSPSPQSYHQVAPSPvgyqnthsPASYHPTPSPMAyQASPSPSPVGYSPMTPG 954
Cdd:PHA03247 2870 SPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQP--------QAPPPPQPQPQP-PPPPQPQPPPPPPPRPQ 2940

                         170       180       190
                  ....*....|....*....|....*....|..
gi 11527858   955 APSPGGYNPHTPGSNIDQASNDWVTTDIMVRV 986
Cdd:PHA03247 2941 PPLAPTTDPAGAGEPSGAVPQPWLGALVPGRV 2972
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 757-969 7.95e-06

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 50.08  E-value: 7.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   757 QGRSSTHLRTPmYGSQTPIYGTGSRTPMYGSQTPLHdGSRTPHYGSQTPlhdGSRTPGQSGAWDPNNPNTPSRPDDEYEF 836
Cdd:PRK10263  390 AVQYNEPLQQP-VQPQQPYYAPAAEQPAQQPYYAPA-PEQPAQQPYYAP---APEQPVAGNAWQAEEQQSTFAPQSTYQT 464

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   837 aYDDEPSPSPQGYggtPNPQTPGYPEVPSPQVNPQYNPQTPGTPAMY-----------NTDQYSPYAAPSPQGSYQP--- 902
Cdd:PRK10263  465 -EQTYQQPAAQEP---LYQQPQPVEQQPVVEPEPVVEETKPARPPLYyfeeveekrarEREQLAAWYQPIPEPVKEPepi 540

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   903 SPSPQSYHQVAPSPVGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPG---GYNPHTPGSN 969
Cdd:PRK10263  541 KSSLKAPSVAAVPPVEAAAAVSPLASGVKKATLATGAAATVAAPVFSLANSGGPRPQvkeGIGPQLPRPK 610
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 809-968 8.02e-06

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 49.98  E-value: 8.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   809 GSRTPGQSGAWDPNNPNTPSRPDdeyefAYDDEPSPSPQGYGGTPNPQTPGYPEVPSPQVNPQYNPQTPGTPAMYNTDQY 888
Cdd:PRK07764  594 AAGGEGPPAPASSGPPEEAARPA-----APAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDG 668

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   889 SPYAAPSPQGSyQPSPSPQSYHQVAPSPV--GYQNTHSPASYHP---------TPSPMAYQASPSPSPVGYSPMTPGAPS 957
Cdd:PRK07764  669 WPAKAGGAAPA-APPPAPAPAAPAAPAGAapAQPAPAPAATPPAgqaddpaaqPPQAAQGASAPSPAADDPVPLPPEPDD 747

                         170
                  ....*....|.
gi 11527858   958 PGGYNPHTPGS 968
Cdd:PRK07764  748 PPDPAGAPAQP 758
PHA03378 PHA03378
EBNA-3B; Provisional
 797-966 8.22e-06

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 50.07  E-value: 8.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   797 TPHYGSQTPLHDGSRTPGQSGAWDPNNPNTPSRP---DDEYEFAYDDEP--------SPSPQGYGGTPNPQTPGYPEVPS 865
Cdd:PHA03378  582 TSQLASSAPSYAQTPWPVPHPSQTPEPPTTQSHIpetSAPRQWPMPLRPipmrplrmQPITFNVLVFPTPHQPPQVEITP 661

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   866 PQVN------PQYNPQTPG---------TPAMYNTDQYSPYAAPSPQGSYQPSPSPQSYHQVAPSPVGYQNTHSPASYHP 930
Cdd:PHA03378  662 YKPTwtqighIPYQPSPTGantmlpiqwAPGTMQPPPRAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPAAAP 741

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 11527858   931 TPS--PMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTP 966
Cdd:PHA03378  742 GRArpPAAAPGRARPPAAAPGRARPPAAAPGAPTPQPP 779
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 788-963 9.62e-06

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: 49.77  E-value: 9.62e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   788 QTPLHDGSRTPHyGSQTPLHDGSRTPGQSGAWDPNNPNTPSRPDDEYEfayDDEPSPSPQGYG-------GTPNPQTPGY 860
Cdd:NF033839  282 DTPKEPGNKKPS-APKPGMQPSPQPEKKEVKPEPETPKPEVKPQLEKP---KPEVKPQPEKPKpevkpqlETPKPEVKPQ 357

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   861 PEVPSPQVNPQYNPQTPGTPAMYNTDQYSPYAAPS-PQGSYQPSPSpQSYHQVAPSPVGYQNTHSPASYHPTPS--PMAY 937
Cdd:NF033839  358 PEKPKPEVKPQPEKPKPEVKPQPETPKPEVKPQPEkPKPEVKPQPE-KPKPEVKPQPEKPKPEVKPQPEKPKPEvkPQPE 436

                         170       180
                  ....*....|....*....|....*.
gi 11527858   938 QASPSPSPVGYSPMTPGAPSPGGYNP 963
Cdd:NF033839  437 KPKPEVKPQPEKPKPEVKPQPETPKP 462
Pro-rich pfam15240
Proline-rich protein; This family includes several eukaryotic proline-rich proteins.
 831-966 1.13e-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: 1.13e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    831 DDEYEFAYDDEPSPSPQGYGGTPNPQTPGYPEVPSPQVNPQYNPQTPGTPAMYNTDQysPYAAPSPQGSYQPSPSPQSYH 910
Cdd:pfam15240   34 EEEGQSQQGGQGPQGPPPGGFPPQPPASDDPPGPPPPGGPQQPPPQGGKQKPQGPPP--QGGPRPPPGKPQGPPPQGGNQ 111

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 11527858    911 QVAPSPVGYQNTHSPASYHPTPSPMAYQASPSPSPvGYSPMTPGAPSPGGyNPHTP 966
Cdd:pfam15240  112 QQGPPPPGKPQGPPPQGGGPPPQGGNQQGPPPPPP-GNPQGPPQRPPQPG-NPQGP 165
PTZ00395 PTZ00395
Sec24-related protein; Provisional
 786-1027 1.72e-05

Sec24-related protein; Provisional


Pssm-ID: 185594 [Multi-domain]  Cd Length: 1560  Bit Score: 49.30  E-value: 1.72e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   786 GSQTPLHDGSRTPHYGSQTPL-HDGSRTPGQSGAWDPNNPNTPSRPDDEYEFAYDDEPSPSPQGYGGTP--NP--QTPGY 860
Cdd:PTZ00395  345 GSPNAASAGAPFNGLGNQADGgHINQVHPDARGAWAGGPHSNASYNCAAYSNAAQSNAAQSNAGFSNAGysNPgnSNPGY 424

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   861 PEVP---SPQVNPQY------NPQTPGTPamYNTDQYSPYAAPSPQGSYQPSPSPQSYHQVAPSPVGYQNTHSPASYHPT 931
Cdd:PTZ00395  425 NNAPnsnTPYNNPPNsntpysNPPNSNPP--YSNLPYSNTPYSNAPLSNAPPSSAKDHHSAYHAAYQHRAANQPAANLPT 502

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   932 PSPMAyqASPSPSPVGYSPMTPGAPSPGGYNPHtpgsnidqASNDWVTTDIMVRVKDTFLDGGVINQTGIIRSvtggmcs 1011
Cdd:PTZ00395  503 ANQPA--ANNFHGAAGNSVGNPFASRPFGSAPY--------GGNAATTADPNGIAKREDHPEGGTNRQKYEQS------- 565

                         250
                  ....*....|....*.
gi 11527858  1012 vflqDTEKVVSISSEH 1027
Cdd:PTZ00395  566 ----DEESVESSSSEN 577
dnaA PRK14086
chromosomal replication initiator protein DnaA;
820-969 1.76e-05

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 48.67  E-value: 1.76e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   820 DPNNPNTPSRPDDEYEFAYDDEPSPSPQGYGGTPNPQ-------TPGYPEVPSPQ-VNPQYNPQT-----PGTPAMYNTD 886
Cdd:PRK14086   89 DPSAGEPAPPPPHARRTSEPELPRPGRRPYEGYGGPRaddrppgLPRQDQLPTARpAYPAYQQRPepgawPRAADDYGWQ 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   887 Q----YSPYAAPSPQGSYQPSPSP--QSYHQVAPS-PVGYQNTHSPASYH----------PTPSPMA---YQASPSPSPV 946
Cdd:PRK14086  169 QqrlgFPPRAPYASPASYAPEQERdrEPYDAGRPEyDQRRRDYDHPRPDWdrprrdrtdrPEPPPGAghvHRGGPGPPER 248

                         170       180
                  ....*....|....*....|...
gi 11527858   947 GYSPMTPGAPSPGGYNPHTPGSN 969
Cdd:PRK14086  249 DDAPVVPIRPSAPGPLAAQPAPA 271
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 794-966 1.77e-05

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 49.01  E-value: 1.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   794 GSRTPHYGSQTPLHDGSRTPGQSGAWDPnnPNTPSRPDDEYEFAYDDEPSPSPQGYGGTPNPQTPGYPevPSPQVNPQYN 873
Cdd:PHA03307  773 ALLEPAEPQRGAGSSPPVRAEAAFRRPG--RLRRSGPAADAASRTASKRKSRSHTPDGGSESSGPARP--PGAAARPPPA 848

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   874 PQTPGTPAMyntDQYSPYAAPSPQGSYQPSPSPQSYHQVAPSPVGYQNTHSPASyHPTPSPMAyqaspsPSPVGYSPMTP 953
Cdd:PHA03307  849 RSSESSKSK---PAAAGGRARGKNGRRRPRPPEPRARPGAAAPPKAAAAAPPAG-APAPRPRP------APRVKLGPMPP 918

                         170       180
                  ....*....|....*....|
gi 11527858   954 GAPSP-GGY------NPHTP 966
Cdd:PHA03307  919 GGPDPrGGFrrvppgDLHTP 938
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 861-974 2.69e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 48.54  E-value: 2.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   861 PEVP--SPQVNPQYNPQTPgtpamyntdqysPYAAPSPQGSYQPSPSPQSYHQ-VAPSPVGYQNTHSPASYHPTPSPMAY 937
Cdd:PRK10263  740 PHEPlfTPIVEPVQQPQQP------------VAPQQQYQQPQQPVAPQPQYQQpQQPVAPQPQYQQPQQPVAPQPQYQQP 807

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 11527858   938 QASPSPSPVGYSPMTPGAPSPGGYNPHTPGSNIDQAS 974
Cdd:PRK10263  808 QQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQDT 844
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 845-956 4.10e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 47.75  E-value: 4.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   845 SPQGYGGTPNPQTPGYPEVPSP-QVNPQ-------YNPQT--PGTPAmyntdqysPYAAPSPQGSYQPSPSPQSYHQVAP 914
Cdd:PRK14959  379 SAPSGSAAEGPASGGAATIPTPgTQGPQgtapaagMTPSSaaPATPA--------PSAAPSPRVPWDDAPPAPPRSGIPP 450

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 11527858   915 SPVGYQNTHSPASYHPTPSPMAYQASPSPS-PVGYSPMTPGAP 956
Cdd:PRK14959  451 RPAPRMPEASPVPGAPDSVASASDAPPTLGdPSDTAEHTPSGP 493
DUF3824 pfam12868
Domain of unknwon function (DUF3824); This is a repeating domain found in fungal proteins. It ...
 828-916 5.23e-05

Domain of unknwon function (DUF3824); This is a repeating domain found in fungal proteins. It is proline-rich, and the function is not known.


Pssm-ID: 372351 [Multi-domain]  Cd Length: 145  Bit Score: 44.35  E-value: 5.23e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    828 SRPDDEYEFAYDDEPSPSPQGY-----------------------GGTPNPQTPGYPEVPSPQVNPQYNPQTPGTpamyn 884
Cdd:pfam12868   42 RRYEDDYRDYYEDPYSPSPYPPspagpyasqgqyypetnyfppppGSTPQPPVDPQPNAPPPPYNPADYPPPPGA----- 116

                           90       100       110
                   ....*....|....*....|....*....|..
gi 11527858    885 tdqyspyAAPSPQGSYQPSPSPQSYhqvAPSP 916
Cdd:pfam12868  117 -------APPPQPYQYPPPPGPDPY---APRP 138
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 810-958 5.58e-05

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: 47.22  E-value: 5.58e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    810 SRTP-GQSGAWDPNNPnTPSRPDDEYEFAYDDEPSPSPQGYGGTPNPQTPGyPEVPSPQVNPQynpqtpgTPAMYNTDQY 888
Cdd:pfam05109  475 SPTPaGTTSGASPVTP-SPSPRDNGTESKAPDMTSPTSAVTTPTPNATSPT-PAVTTPTPNAT-------SPTLGKTSPT 545

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 11527858    889 SPYAAPSPQGS------YQPSPSPQSYHQVAPSPVGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSP 958
Cdd:pfam05109  546 SAVTTPTPNATsptpavTTPTPNATIPTLGKTSPTSAVTTPTPNATSPTVGETSPQANTTNHTLGGTSSTPVVTSP 621
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 797-946 6.16e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 47.39  E-value: 6.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   797 TPHYGSQTPLHDGSRTPGQSGAWDPN--NPNTPSRPDDEYEfaYDDEPSPSPQGYggtpnpQTPGYPEVPSPQVNpqyNP 874
Cdd:PRK10263  739 GPHEPLFTPIVEPVQQPQQPVAPQQQyqQPQQPVAPQPQYQ--QPQQPVAPQPQY------QQPQQPVAPQPQYQ---QP 807

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11527858   875 QTPGTPAMYNTDQYSPYAAPSPQGSYQPSPSPQSYHQVApSPVGYQNTHSPASYHP-TPSPMAYQASPSPSPV 946
Cdd:PRK10263  808 QQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQDTLL-HPLLMRNGDSRPLHKPtTPLPSLDLLTPPPSEV 879
dnaA PRK14086
chromosomal replication initiator protein DnaA;
841-976 7.77e-05

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 46.74  E-value: 7.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   841 EPSPSPQGYGGTPNPQTPGYPEVPSPQVNPQYNPQTPGTPAMYNTDQYSPYAAPSPQGSYQPSPSPQsyhqvAPSPVGYQ 920
Cdd:PRK14086   94 EPAPPPPHARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLPTARPAYPAYQQRPEPGAWPR-----AADDYGWQ 168

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 11527858   921 NT-HSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGyNPHTPGSNIDQASND 976
Cdd:PRK14086  169 QQrLGFPPRAPYASPASYAPEQERDREPYDAGRPEYDQRRR-DYDHPRPDWDRPRRD 224
PHA03291 PHA03291
envelope glycoprotein I; Provisional
 819-976 8.16e-05

envelope glycoprotein I; Provisional


Pssm-ID: 223033 [Multi-domain]  Cd Length: 401  Bit Score: 46.49  E-value: 8.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   819 WDPNNPNTPSRPDDEYEFAYDDEPSPSPQGYGGTPNPQTPGYPeVPSPQVNPQ--YNPQTPGTPAMYNTdqySPYAAPSP 896
Cdd:PHA03291  149 WVEGATNASLFPLGLAAFPAEGTLAAPPLGEGSADGSCDPALP-LSAPRLGPAdvFVPATPRPTPRTTA---SPETTPTP 224

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   897 QGSYQPSPSPqsyhqvapspvgyqnthspasyhpTPSPMAYQASPSPSPVGYSPMTPGAPSPGGynPHTPGSNIDQASND 976
Cdd:PHA03291  225 STTTSPPSTT------------------------IPAPSTTIAAPQAGTTPEAEGTPAPPTPGG--GEAPPANATPAPEA 278
KLF1_2_4_N cd21972
N-terminal domain of Kruppel-like factor (KLF) 1, KLF2, KLF4, and similar proteins; Kruppel ...
 835-966 1.05e-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: 44.59  E-value: 1.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858  835 EFAYDDEPSPSPQGYG--GTPNPQTPGYPEVPSPQVNPQYN-PQTPGTPAMYNTDQYSPYAAPSPQgsyqPSPSPQSYHQ 911
Cdd:cd21972   32 VTSDNDNPPPPDPAYPppESPESCSTVYDSDGCHPTPNAYCgPNGPGLPGHFLLAGNSPNLGPKIK----TENQEQACMP 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 11527858  912 VAPSPVGY---QNTHSPASYHPTP--------------SPMAYQASPSPSPVGYSPmtPGAPSPGGYNPHTP 966
Cdd:cd21972  108 VAGYSGHYgprEPQRVPPAPPPPQyaghfqyhghfnmfSPPLRANHPGMSTVMLTP--LSTPPLGFLSPEEA 177
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 824-963 1.13e-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: 46.30  E-value: 1.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   824 PNTPSRPDDEYEFAYDDEPSPSPQGYGGTPNPQT-PGYPEV------PSPQVNPQYNPQTPGTPAMYNTdqyspyaaPSP 896
Cdd:NF033839  281 QDTPKEPGNKKPSAPKPGMQPSPQPEKKEVKPEPeTPKPEVkpqlekPKPEVKPQPEKPKPEVKPQLET--------PKP 352

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   897 QGSYQPS-PSPqsyhQVAPSPVGYQNTHSPASYHPTPSPMAYQASPSP--SPVGYSPMTPGAPSPGGYNP 963
Cdd:NF033839  353 EVKPQPEkPKP----EVKPQPEKPKPEVKPQPETPKPEVKPQPEKPKPevKPQPEKPKPEVKPQPEKPKP 418
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 704-735 1.19e-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: 40.06  E-value: 1.19e-04
                           10        20        30
                   ....*....|....*....|....*....|..
gi 11527858    704 IGQTVRISQGPYKGYIGVVKDATESTARVELH 735
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
PHA03247 PHA03247
large tegument protein UL36; Provisional
 821-970 1.23e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.47  E-value: 1.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   821 PNNPNTPSRPDDEYEFAYDDEPSPSPQGYGGTPNPQTPGYPEVPSPQV-----NPQYNPQTPGTPAMyNTDQYSPYAAPs 895
Cdd:PHA03247 2702 PPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPAtpggpARPARPPTTAGPPA-PAPPAAPAAGP- 2779

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11527858   896 PQGSYQPSPSPQSYH-QVAPSPVGYQNTHSPAS-YHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPGSNI 970
Cdd:PHA03247 2780 PRRLTRPAVASLSESrESLPSPWDPADPPAAVLaPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSV 2856
SP7_N cd22542
N-terminal domain of transcription factor Specificity Protein (SP) 7; Specificity Proteins ...
 800-968 1.28e-04

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: 45.27  E-value: 1.28e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858  800 YGSQTPLHDgSRTPGQSGAWDPNNPNTPS---------RPD---DEYEFAYDD-----EPSPSPQ---GYGGTPNPQTPG 859
Cdd:cd22542   26 FGGSSPIRD-SATPGKPGNNPGKKPYSLGsdlssaksrSSElmgDSYTATFSSgnglmSPSGSPQastTYGNDYNPFSHS 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858  860 YPEVPSPQ----VNPQYNPQTPGTPAMYNT-DQYSPY-----AAPSPQGSYQPSPSPQSYHQVAPSPVGYQNTHSPASYH 929
Cdd:cd22542  105 FPTSSGSQdpslLVSKGHPSADCLPSVYTSlDMAHPYgswykTGIHPGISSSSTNATASWWDMHSNTNWLSAQGQPDGLQ 184

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 11527858  930 PTPSPMAYQASPSPSPVGYSPMTPgaPSPGGYNPHTPGS 968
Cdd:cd22542  185 ASLQPVPAQTPLNPQLPSYTEFTT--LNPAPYPAVGISS 221
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 470-497 1.32e-04

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


Pssm-ID: 128978  Cd Length: 28  Bit Score: 40.00  E-value: 1.32e-04
                            10        20
                    ....*....|....*....|....*...
gi 11527858     470 YFRMGDHVKVIAGRYEGDTGLIVRVEEN 497
Cdd:smart00739    1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 824-975 1.34e-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: 46.30  E-value: 1.34e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    824 PNTPSRPDDEYEFAYDDEPSPSPQGYGGTPNPQTPGYPEVPSPQVNP----QYNPQ--TPGTPAMYNTDQYSPYAAPSPQ 897
Cdd:pfam03154  181 ASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPhtliQQTPTlhPQRLPSPHPPLQPMTQPPPPSQ 260

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    898 GSYQPSPSPQSY------------------HQVAPSPVGYQNTHSPASYHPTPSPMA-------------YQASPSPSPV 946
Cdd:pfam03154  261 VSPQPLPQPSLHgqmppmphslqtgpshmqHPVPPQPFPLTPQSSQSQVPPGPSPAApgqsqqrihtppsQSQLQSQQPP 340

                          170       180
                   ....*....|....*....|....*....
gi 11527858    947 GYSPMTPgAPSPGGYNPHTPGSNIDQASN 975
Cdd:pfam03154  341 REQPLPP-APLSMPHIKPPPTTPIPQLPN 368
PHA03269 PHA03269
envelope glycoprotein C; Provisional
 852-980 1.36e-04

envelope glycoprotein C; Provisional


Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 45.87  E-value: 1.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   852 TPNPQTPgypeVPSPQVNPQYNPQTPgtpamyntdqySPYAAPSPQGSYQPSPSPQSYHQVAPSPVGYQNTHSPASYHPT 931
Cdd:PHA03269   19 IANLNTN----IPIPELHTSAATQKP-----------DPAPAPHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFD 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 11527858   932 PSPMAYQASPSPSPVGYSPMTPGAPSPggyNPHTPGSNIDQASNDWVTT 980
Cdd:PHA03269   84 PAPAPHQAASRAPDPAVAPQLAAAPKP---DAAEAFTSAAQAHEAPADA 129
dnaA PRK14086
chromosomal replication initiator protein DnaA;
790-947 1.44e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 45.97  E-value: 1.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   790 PLHDGSRTPHYGSQT-PLHDGSRTPGQSGAWDPNNPNTPSRPddeyefAY-DDEPSPSPQGYGGTPNPQTPGYPEVPSPQ 867
Cdd:PRK14086  103 RRTSEPELPRPGRRPyEGYGGPRADDRPPGLPRQDQLPTARP------AYpAYQQRPEPGAWPRAADDYGWQQQRLGFPP 176

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   868 VNPQYNPQTPGTPAMYNTDQY----SPYAAPSPQGSY--------------QPSPSPQSYHQV--APSPVGYQNTHSPAS 927
Cdd:PRK14086  177 RAPYASPASYAPEQERDREPYdagrPEYDQRRRDYDHprpdwdrprrdrtdRPEPPPGAGHVHrgGPGPPERDDAPVVPI 256

                         170       180
                  ....*....|....*....|
gi 11527858   928 YHPTPSPMAYQASPSPSPVG 947
Cdd:PRK14086  257 RPSAPGPLAAQPAPAPGPGE 276
KLF9_13_N-like cd21975
Kruppel-like factor (KLF) 9, KLF13, KLF14, KLF16, and similar proteins; Kruppel/Krueppel-like ...
 842-963 1.44e-04

Kruppel-like factor (KLF) 9, KLF13, KLF14, KLF16, 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. KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved alpha-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. 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 related N-terminal domains of KLF9, KLF13, KLF14, KLF16, and similar proteins.


Pssm-ID: 409240 [Multi-domain]  Cd Length: 163  Bit Score: 43.53  E-value: 1.44e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858  842 PSPSPQGYGGT---------PNPQTPGYPEVPSPQVNPqyNPQTPGT--PAMYNTDQYSPYAAPSPQGSYQPSP--SPQS 908
Cdd:cd21975   21 VRPDPEGAGLAagldvratrEVAKGPGPPGPAWKPDGA--DSPGLVTaaPHLLAANVLAPLRGPSVEGSSLESGdaDMGS 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 11527858  909 YHQVAPSPvGYQNTHSPASYHPTPSPmayqasPSPSPVGYspmtPGAPSPGGYNP 963
Cdd:cd21975   99 DSDVAPAS-GAAASTSPESSSDAASS------PSPLSLLH----PGEAGLEPERP 142
KLF1_N cd21581
N-terminal domain of Kruppel-like Factor 1; Kruppel-like Factor 1 (KLF1, also known as ...
 787-964 1.55e-04

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: 45.04  E-value: 1.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858  787 SQTPLHDGSRTPHYGSQTPLHDGSRTpgqsgAWDPnnpntpsrpddeyEFAYDDEPSPSPQGyGGTPNPQTPGYPEVPSP 866
Cdd:cd21581   38 LSPSGSEQLQVSQPMTEELLDDDSQA-----SWDI-------------EFLLSNWSSPSLNP-SLDNNTQALPQEEQPGA 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858  867 QVNPQYNPQTPGTPAMYN----------TDQYSPYAAPSPQ-GSYQPSPSPQSYHQVAP------SPVGYQNTH------ 923
Cdd:cd21581   99 YYEPPKKDQPGTEGLQVGgpglmaellsPEESTGWAPPEPHhGYPDAFVGPALFPAPANvdqfgfPQGGSVDRRgnlsks 178

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 11527858  924 ---SPASYHPT--PSPMAYQASPSPSPVGYSPMTPgAPSPGGYNPH 964
Cdd:cd21581  179 gswDFGSYYPQqhPSVVAFPDSRFGPLSGPQALTP-DPQHYGYFQL 223
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 789-968 1.68e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 45.93  E-value: 1.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   789 TPLHDGSRTPHygsqtPLHDGSRTPGQSGAwdpnnPNTPSRPDDEYEFAYDDEPSPSPQGYGGTPNPQTPGYPEVPSPQV 868
Cdd:PHA03307  197 TPPAAASPRPP-----RRSSPISASASSPA-----PAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLP 266

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   869 NPQYNPQTPGTPAMYNTDQYSPYAAPSPQGSYQPSPSPQSYHQVAPSPVGYQ------NTHSPASYHPTPSPMAYQ---- 938
Cdd:PHA03307  267 TRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSsssresSSSSTSSSSESSRGAAVSpgps 346

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 11527858   939 -------ASPSPSPVGYSPMTPGAPSPGGYNPHTPGS 968
Cdd:PHA03307  347 psrspspSRPPPPADPSSPRKRPRPSRAPSSPAASAG 383
DUF1373 pfam07117
Protein of unknown function (DUF1373); This family consists of several hypothetical proteins ...
 824-938 1.83e-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: 44.01  E-value: 1.83e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    824 PNTPSRPDDEYE----FAYDDEPSPSPQGYGGTPNPQTPGYPEVPSPQVNPQYNPQTPGTPAMYNTDQYSPYAAPSPQGS 899
Cdd:pfam07117   42 PPRPEEEEGQGGgggtFPFPGSPEPEPGGGGSGPMPMSASAPEPEPAKAKPQRPAPAQGHGHGGGGDSDSSGSGSGHQGS 121

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 11527858    900 YQP---SPSPQSYHQVAPSPVGYQNTHSPasyHPTPSPMAYQ 938
Cdd:pfam07117  122 GGAgagAGAPGHQHEQEQESSSSDDDDED---EFEFTPEEDE 160
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 827-964 2.03e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 45.36  E-value: 2.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   827 PSRPDDEYEFAYDDEPSPSPQGYGGTPNP----QTPGYPEVPSPQVNPQ-YNPQTPGTPAMYNTDQysPYAAPSPQGSYQ 901
Cdd:PRK07764  365 PSASDDERGLLARLERLERRLGVAGGAGApaaaAPSAAAAAPAAAPAPAaAAPAAAAAPAPAAAPQ--PAPAPAPAPAPP 442

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11527858   902 PSPSPQSYHQVAPSPVGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPH 964
Cdd:PRK07764  443 SPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAG 505
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 841-974 2.06e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 45.36  E-value: 2.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   841 EPSPSPQGYGGTPNPQTPGYPEVPSPQVNPQYnPQTPGTPAMYNTDQYSPYAAPSPQGSYQPSPSPQSYHQVAPSPVGYQ 920
Cdd:PRK07764  598 EGPPAPASSGPPEEAARPAAPAAPAAPAAPAP-AGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGA 676

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 11527858   921 nthSPASYHPTPSPMAYQA-SPSPSPVGYSPMTPGAPSPGGYNPHTPGSNIDQAS 974
Cdd:PRK07764  677 ---APAAPPPAPAPAAPAApAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGA 728
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 828-960 2.17e-04

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 45.30  E-value: 2.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   828 SRPDDEYEfAYDD-----EPSPSPQGYGGTPNPQTPGYPEVP-SPQVNPQYNPQTPGTPAMYNTDQYSPYAAPSPQGSYQ 901
Cdd:PLN03209  435 TRPLSPYA-RYEDlkpptSPSPTAPTGVSPSVSSTSSVPAVPdTAPATAATDAAAPPPANMRPLSPYAVYDDLKPPTSPS 513

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11527858   902 P-SPSPQSYHQVAPSPVGYQNTHSPASyhptPSPMAYQASPSPSPVgySPMT-------PGAPSPGG 960
Cdd:PLN03209  514 PaAPVGKVAPSSTNEVVKVGNSAPPTA----LADEQHHAQPKPRPL--SPYTmyedlkpPTSPTPSP 574
DUF1373 pfam07117
Protein of unknown function (DUF1373); This family consists of several hypothetical proteins ...
 827-934 3.30e-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: 43.24  E-value: 3.30e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    827 PSRPDDEYefayddePSPSPQGYGgtpnpqTPGYPEVPSPQvnpqynPQTPGTPAMYNTDQYsPYAAPSPQGSYQPSPSP 906
Cdd:pfam07117   40 PEPPRPEE-------EEGQGGGGG------TFPFPGSPEPE------PGGGGSGPMPMSASA-PEPEPAKAKPQRPAPAQ 99

                           90       100       110
                   ....*....|....*....|....*....|..
gi 11527858    907 QSYH----QVAPSPVGYQNTHSPASYHPTPSP 934
Cdd:pfam07117  100 GHGHggggDSDSSGSGSGHQGSGGAGAGAGAP 131
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 474-502 3.68e-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: 38.91  E-value: 3.68e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 11527858    474 GDHVKVIAGRYEGDTGLIVRVEE--NFVILF 502
Cdd:pfam00467    2 GDVVRVIAGPFKGKVGKVVEVDDkkNRVLVE 32
PHA03264 PHA03264
envelope glycoprotein D; Provisional
 834-947 4.30e-04

envelope glycoprotein D; Provisional


Pssm-ID: 223029 [Multi-domain]  Cd Length: 416  Bit Score: 44.23  E-value: 4.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   834 YEFAYDDEPSPSPQGygGTPNPqtpgyPEVPSPQVNPQYNPQTPGTPAMYNTDQYSPYAAPSPQGSY--QPSPSPQSYHQ 911
Cdd:PHA03264  258 FEESKGYEPPPAPSG--GSPAP-----PGDDRPEAKPEPGPVEDGAPGRETGGEGEGPEPAGRDGAAggEPKPGPPRPAP 330

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 11527858   912 VAPSPVGYQNThsPASYHPTPSPmAYQASPSPSPVG 947
Cdd:PHA03264  331 DADRPEGWPSL--EAITFPPPTP-ATPAVPRARPVI 363
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
811-983 6.13e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 43.71  E-value: 6.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   811 RTPGQSGAWDPNNPNTPSRPDDEYEFAYDDEPSPSPqgyggTPNPQTPGYPEVPSPQVNPQYNPQTPGTPAMYNTDQYSP 890
Cdd:PRK12323  364 RPGQSGGGAGPATAAAAPVAQPAPAAAAPAAAAPAP-----AAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQ 438

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   891 YAAPSPQGSYQPSPSPQSYHQVAPSPVGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSP---MTPGAPSPGGYnphtpg 967
Cdd:PRK12323  439 ASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPPPweeLPPEFASPAPA------ 512

                         170
                  ....*....|....*.
gi 11527858   968 sNIDQASNDWVTTDIM 983
Cdd:PRK12323  513 -QPDAAPAGWVAESIP 527
PHA03132 PHA03132
thymidine kinase; Provisional
 823-958 8.44e-04

thymidine kinase; Provisional


Pssm-ID: 222997 [Multi-domain]  Cd Length: 580  Bit Score: 43.21  E-value: 8.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   823 NPNTPSRPDDEYEFAYDDEP---SPSPQGYGGTPNPQTPGYPEVPSPQV----NPQYNPQTPGTPAMYNTDQYSPYAAPS 895
Cdd:PHA03132   34 DDFLTPLGSTSEATSEDDDDlypPRETGSGGGVATSTIYTVPRPPRGPEqtldKPDSLPASRELPPGPTPVPPGGFRGAS 113

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11527858   896 PQGSYQPSPSPQSYHQVAPSPVGYQNTHSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSP 958
Cdd:PHA03132  114 SPRLGADSTSPRFLYQVNFPVILAPIGESNSSSEELSEEEEHSRPPPSESLKVKNGGKVYPKG 176
Med26_M pfam15694
Mediator complex subunit 26 middle domain; Med26_M is the middle domain of subunit 26 of ...
 842-972 1.40e-03

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: 41.78  E-value: 1.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    842 PSPSPQGYGGTPNP----------------QTPGYPEVPSPQvNPQYNPQTpgTPAMYNTDQYSPYAapsPQGSY-QPSP 904
Cdd:pfam15694   51 PHTSSPGLGKPPSTssllkaavlqqqarldETGGPPQPKSPR-CSSFSPRN--SRHETFARRSSTYA---PKGSVpSPSP 124

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    905 SPQSYHQVAPSPVGYQNTHSP--------ASYHPTP-SPMAYQASPS-----PSPVGYSPMTPGAPSPGGYNPHTPGSNI 970
Cdd:pfam15694  125 RSQVLDAQVPSPLPLSQPSTPpvqakrleKPPQSSPeSSQHWLEQSDseshqRHQDGSATLLSQSVSPGCKTPLHPGENS 204


                   ..
gi 11527858    971 DQ 972
Cdd:pfam15694  205 LP 206
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 846-967 1.40e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 42.78  E-value: 1.40e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   846 PQGYGGTPNP---QTPGYPEVPSPQVNPQYNPQTPGTPAMYNTDQYSPYAAPSPQGSYQPSPSPQSYHQVAPSPVG---- 918
Cdd:PRK14951  366 PAAAAEAAAPaekKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAApaav 445

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 11527858   919 YQNTHSPASYHPTPSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPG 967
Cdd:PRK14951  446 ALAPAPPAQAAPETVAIPVRVAPEPAVASAAPAPAAAPAAARLTPTEEG 494
KREPA2 cd23959
Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of ...
 855-958 1.46e-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: 42.16  E-value: 1.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858  855 PQTPgYPEVPSPQVNPQynPQTPGTPAMYNTDQ-YSPYAAPSPQGSYQPSPSPQSYHQVAPSPVGYQNTHSPASyhPTPS 933
Cdd:cd23959  146 PVTP-FGQLPMFGQHPP--PAKPLPAAAAAQQSsASPGEVASPFASGTVSASPFATATDTAPSSGAPDGFPAEA--SAPS 220

                         90       100
                 ....*....|....*....|....*
gi 11527858  934 PMAyqASPSPSPVGYSPMTPGAPSP 958
Cdd:cd23959  221 PFA--APASAASFPAAPVANGEAAT 243
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 789-976 1.56e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 42.85  E-value: 1.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   789 TPLHDGSRTPHYGSQ----TPLHDGSRTPGQSGAW------DPNNPNT---------PSRPDDEYEFAYDDEPSPSPQGY 849
Cdd:PHA03307   26 ATPGDAADDLLSGSQgqlvSDSAELAAVTVVAGAAacdrfePPTGPPPgpgteapanESRSTPTWSLSTLAPASPAREGS 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   850 GGTPNPQTPGYPEVPSPQVNPqynPQTPGtpamyntdqysPYAAPSPQGSYQPSPSPQSYHQVAPSPVGYQNTHSPASYH 929
Cdd:PHA03307  106 PTPPGPSSPDPPPPTPPPASP---PPSPA-----------PDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRQ 171

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 11527858   930 PT-PSPMAYQASPSPSPVGYSPMTPGAPSPGGYNPHTPGSNIDQASND 976
Cdd:PHA03307  172 AAlPLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASS 219
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 765-958 1.73e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 42.47  E-value: 1.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   765 RTPMYGSQTPIYGTGSRTPMYGSQTPLHDGSRTPhygsQTPLHDGSRTPGQSGAWDPnnPNTPSRPDDEYEFAYDDEPSP 844
Cdd:PHA03307   64 RFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAP----ASPAREGSPTPPGPSSPDP--PPPTPPPASPPPSPAPDLSEM 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   845 SPQGYGGTPNPQTPGyPEVPSPQVNPQYNPQTPGTPAmyntdqyspYAAPSPQGSYQPSPSPQsyhqvAPSPVGYQNTHS 924
Cdd:PHA03307  138 LRPVGSPGPPPAASP-PAAGASPAAVASDAASSRQAA---------LPLSSPEETARAPSSPP-----AEPPPSTPPAAA 202

                         170       180       190
                  ....*....|....*....|....*....|....
gi 11527858   925 PASYHPTPSPMAyqaSPSPSPVGYSPMTPGAPSP 958
Cdd:PHA03307  203 SPRPPRRSSPIS---ASASSPAPAPGRSAADDAG 233
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 595-626 1.79e-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: 36.98  E-value: 1.79e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 11527858    595 VKDIVKVIDGPHSGREGEIRHIFRGFAFLHCK 626
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 777-916 2.13e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 42.28  E-value: 2.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   777 GTGSRTPMYGSQTPLHDGSRTPHYGSQTPLHDGSRTPGQSGAWDPNNPNTPSRPDDEyefayddePSPSPQGYGGTPNPQ 856
Cdd:PRK07764  672 KAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGA--------SAPSPAADDPVPLPP 743

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   857 TPGYPEVPSPQVNPQYNPQTPGTPAmyntdqyspyAAPSPQGSYQPSPSPQSYHQVAPSP 916
Cdd:PRK07764  744 EPDDPPDPAGAPAQPPPPPAPAPAA----------APAAAPPPSPPSEEEEMAEDDAPSM 793
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 793-935 2.35e-03

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: 41.92  E-value: 2.35e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858    793 DGSRTPHYGSQTPLHDGSRTPGQSGAWDPNNPNTPSRPDDEyefayddePS-PSPQGYGGTPNPQTPGYPeVPSPQVNPQ 871
Cdd:pfam09606  358 GGLGANPMQRGQPGMMSSPSPVPGQQVRQVTPNQFMRQSPQ--------PSvPSPQGPGSQPPQSHPGGM-IPSPALIPS 428

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 11527858    872 YNPQTPGTPamyntdqyspyAAPSPQGSYQPSPSPQSYHQVA-PSPVGYQNTH----SPASYHPTPSPM 935
Cdd:pfam09606  429 PSPQMSQQP-----------AQQRTIGQDSPGGSLNTPGQSAvNSPLNPQEEQlyreKYRQLTKYIEPL 486
KLF3_N cd21577
N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called ...
 889-964 3.15e-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: 40.41  E-value: 3.15e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11527858  889 SPYAAPSPQGSYQPSPSPQSYHQVAPSPVGYQNTHsPASYHP--TPSPMAYQASPSPSPVGYSPMTpgAPSPGGYNPH 964
Cdd:cd21577   41 SSSSSSSSPSSRASPPSPYSKSSPPSPPQQRPLSP-PLSLPPpvAPPPLSPGSVPGGLPVISPVMV--QPVPVLYPPH 115
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 770-945 3.93e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.12  E-value: 3.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   770 GSQTPIYGTGSRTPMYGSQTPLHDGSRTPHYGSQTPLHDGSRTPGQSGAWDPNNPNTPSRPddeyefAYDDEPSPSPQGY 849
Cdd:PRK07764  623 APAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPP------APAPAAPAAPAGA 696

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   850 GGTPNPQTPGYPEVPSPQVNPQYNPQTPGTPAmyntdqyspyAAPSPQGSYQPSPSPQSYHQVAPSPVGYQNTHSPASYH 929
Cdd:PRK07764  697 APAQPAPAPAATPPAGQADDPAAQPPQAAQGA----------SAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAP 766

                         170
                  ....*....|....*.
gi 11527858   930 PTPSPMAYQASPSPSP 945
Cdd:PRK07764  767 AAAPAAAPPPSPPSEE 782
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 837-947 5.91e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 40.74  E-value: 5.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11527858   837 AYDDEPSP-SPQGYGGTPNPQTPGYPEVPSPQVNPQYNPQTPGTPAMYNTDQySPYAAPSPQGSYQPSPSPQSYHQVAPS 915
Cdd:PRK07764  401 AAAAAPAAaPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGG-APSPPPAAAPSAQPAPAPAAAPEPTAA 479

                          90       100       110
                  ....*....|....*....|....*....|..
gi 11527858   916 PVGYQNTHSPASYHPTPSPmayQASPSPSPVG 947
Cdd:PRK07764  480 PAPAPPAAPAPAAAPAAPA---APAAPAGADD 508
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 592-618 7.52e-03

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


Pssm-ID: 128978  Cd Length: 28  Bit Score: 35.00  E-value: 7.52e-03
                            10        20
                    ....*....|....*....|....*..
gi 11527858     592 NIHVKDIVKVIDGPHSGREGEIRHIFR 618
Cdd:smart00739    1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27
 
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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