NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|328927069|ref|NP_001076908|]
View 

transcription elongation factor SPT5 [Bos taurus]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 174-261 4.32e-44

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


:

Pssm-ID: 193577 [Multi-domain]  Cd Length: 86  Bit Score: 154.23  E-value: 4.32e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  174 NLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLgyWNQQMVPI 253
Cdd:cd09888     1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYL--NTIKLVPI 78


                  ....*...
gi 328927069  254 KEMTDVLK 261
Cdd:cd09888    79 KEMPDVLS 86
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 768-885 1.56e-28

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: 111.07  E-value: 1.56e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069    768 GSQTPMYG-SGSRTPMYGSQTP----LQDGSRTPHYGSQTPLHDG--SRTPAQSGAWdPNNPNTPSRAEEEYEYAFDDEP 840
Cdd:smart01104    1 GGRTPAWGaSGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAWGGAG-PTGSRTPAWGGASAWGNKSSEG 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 328927069    841 TPSPQA--YGGTPNPQTPGYpdpssPQVNPQYNPQTPGTPAMYNTDQ 885
Cdd:smart01104   80 SASSWAagPGGAYGAPTPGY-----GGTPSAYGPATPGGGAMAGSAS 121
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 467-517 6.93e-28

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


:

Pssm-ID: 240507  Cd Length: 51  Bit Score: 106.46  E-value: 6.93e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 328927069  467 YFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLC 517
Cdd:cd06083     1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1024-1080 2.06e-26

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


:

Pssm-ID: 240510  Cd Length: 58  Bit Score: 102.59  E-value: 2.06e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 328927069 1024 EHLEPITPTKNNKVKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLRFLGKL 1080
Cdd:cd06086     1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMDSDGDIKILPMNFLAKL 57
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 416-466 9.38e-26

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


:

Pssm-ID: 240506  Cd Length: 51  Bit Score: 100.65  E-value: 9.38e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 328927069  416 FQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDMLEFPAQELRK 466
Cdd:cd06082     1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 698-747 4.85e-25

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


:

Pssm-ID: 240509  Cd Length: 52  Bit Score: 98.71  E-value: 4.85e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 328927069  698 DNELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLT 747
Cdd:cd06085     2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLA 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 593-635 1.53e-19

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


:

Pssm-ID: 240508  Cd Length: 43  Bit Score: 82.57  E-value: 1.53e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 328927069  593 KDIVKVIDGPHSGREGEIRHLFRSFAFLHCKKLVENGGMFVCK 635
Cdd:cd06084     1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 272-309 1.66e-17

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


:

Pssm-ID: 240505  Cd Length: 38  Bit Score: 76.74  E-value: 1.66e-17
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 328927069  272 KSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMIPRIDY 309
Cdd:cd06081     1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 95-168 3.75e-09

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


:

Pssm-ID: 463406  Cd Length: 97  Bit Score: 54.97  E-value: 3.75e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 328927069    95 GAEDILEKA----SNIDNVVLDEDRSGARRLQNLWSDQREEELGEYYMKKYAKSSvgETVYGGSDElsDDITQQQLLP 168
Cdd:pfam11942   24 GADDFIEDDeedeDEEDGRRDDRRHRELDRRRELEEDEDAEEIAEYLKERYGRSS--SDAYRGDAE--EGVPQRLLLP 97
PHA03269 super family cl29788
envelope glycoprotein C; Provisional
 821-966 5.25e-09

envelope glycoprotein C; Provisional


The actual alignment was detected with superfamily member PHA03269:

Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 60.13  E-value: 5.25e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  821 NPNTPSRAEEEYEYAFDDEPTPSPQayggtPNPQTPGYPDPS-SPQVNPQYNPQtpgtpamyntdqfsPYAAPSPQGSYQ 899
Cdd:PHA03269   21 NLNTNIPIPELHTSAATQKPDPAPA-----PHQAASRAPDPAvAPTSAASRKPD--------------LAQAPTPAASEK 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 328927069  900 PSPSPQSYHQV--APSPAGYQNTHSPasyhPTPSPM-----AYQASPSPGPVGYSPMTPgAPSPGGYNPHTPGS 966
Cdd:PHA03269   82 FDPAPAPHQAAsrAPDPAVAPQLAAA----PKPDAAeaftsAAQAHEAPADAGTSAASK-KPDPAAHTQHSPPP 150
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 174-261 4.32e-44

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


Pssm-ID: 193577 [Multi-domain]  Cd Length: 86  Bit Score: 154.23  E-value: 4.32e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  174 NLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLgyWNQQMVPI 253
Cdd:cd09888     1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYL--NTIKLVPI 78


                  ....*...
gi 328927069  254 KEMTDVLK 261
Cdd:cd09888    79 KEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 174-260 6.63e-31

Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit.


Pssm-ID: 397481  Cd Length: 84  Bit Score: 116.53  E-value: 6.63e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   174 NLWTVKCKIGEERATAISLMRKFIAYQfTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLGywNQQMVPI 253
Cdd:pfam03439    1 KIWAVKCTPGQEREVALSLMRKILALA-KTNNLGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGL--VPGLVPI 77


                   ....*..
gi 328927069   254 KEMTDVL 260
Cdd:pfam03439   78 KEMEHLL 84
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 768-885 1.56e-28

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: 111.07  E-value: 1.56e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069    768 GSQTPMYG-SGSRTPMYGSQTP----LQDGSRTPHYGSQTPLHDG--SRTPAQSGAWdPNNPNTPSRAEEEYEYAFDDEP 840
Cdd:smart01104    1 GGRTPAWGaSGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAWGGAG-PTGSRTPAWGGASAWGNKSSEG 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 328927069    841 TPSPQA--YGGTPNPQTPGYpdpssPQVNPQYNPQTPGTPAMYNTDQ 885
Cdd:smart01104   80 SASSWAagPGGAYGAPTPGY-----GGTPSAYGPATPGGGAMAGSAS 121
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 467-517 6.93e-28

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


Pssm-ID: 240507  Cd Length: 51  Bit Score: 106.46  E-value: 6.93e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 328927069  467 YFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLC 517
Cdd:cd06083     1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1024-1080 2.06e-26

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


Pssm-ID: 240510  Cd Length: 58  Bit Score: 102.59  E-value: 2.06e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 328927069 1024 EHLEPITPTKNNKVKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLRFLGKL 1080
Cdd:cd06086     1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMDSDGDIKILPMNFLAKL 57
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 416-466 9.38e-26

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


Pssm-ID: 240506  Cd Length: 51  Bit Score: 100.65  E-value: 9.38e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 328927069  416 FQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDMLEFPAQELRK 466
Cdd:cd06082     1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 698-747 4.85e-25

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


Pssm-ID: 240509  Cd Length: 52  Bit Score: 98.71  E-value: 4.85e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 328927069  698 DNELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLT 747
Cdd:cd06085     2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLA 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 593-635 1.53e-19

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


Pssm-ID: 240508  Cd Length: 43  Bit Score: 82.57  E-value: 1.53e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 328927069  593 KDIVKVIDGPHSGREGEIRHLFRSFAFLHCKKLVENGGMFVCK 635
Cdd:cd06084     1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 272-309 1.66e-17

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


Pssm-ID: 240505  Cd Length: 38  Bit Score: 76.74  E-value: 1.66e-17
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 328927069  272 KSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMIPRIDY 309
Cdd:cd06081     1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 768-826 6.47e-15

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


Pssm-ID: 372327 [Multi-domain]  Cd Length: 71  Bit Score: 70.55  E-value: 6.47e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   768 GSQTPMYGS--GSRTPMY---GSQTPL--QDGSRTPHY--GSQTPLHD--GSRTPAQSGAWDPnnPNTPS 826
Cdd:pfam12815    1 GSRTPAYNSagGSRTPAWgadGSRTPAygGAGGRTPAYnqGGKTPAWGgaGSRTPAYYGAWGG--SRTPA 68
nusG PRK08559
transcription antitermination protein NusG; Validated
 171-312 4.30e-12

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 64.89  E-value: 4.30e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  171 KDPNLWTVKCKIGEERATAISLMRKFIAYQftdtpLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRlGYwNQQM 250
Cdd:PRK08559    4 EMSMIFAVKTTAGQERNVALMLAMRAKKEN-----LPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVR-GV-VPGE 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 328927069  251 VPIKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKM------IP---RIDYDRI 312
Cdd:PRK08559   77 ISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELleaavpIPvtvRGDQVRV 147
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 174-262 1.27e-10

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


Pssm-ID: 197850 [Multi-domain]  Cd Length: 106  Bit Score: 59.31  E-value: 1.27e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069    174 NLWTVKCKIGEERATAISLMRKFIAYQFTDtplQIKSVVAP-EHVK----------------GYIYVEAYKQTHVKQAIE 236
Cdd:smart00738    1 NWYAVRTTSGQEKRVAENLERKAEALGLED---KIVSILVPtEEVKeirrgkkkvverklfpGYIFVEADLEDEVWTAIR 77

                            90       100       110
                    ....*....|....*....|....*....|
gi 328927069    237 GV----GNLRLGYWnQQMVPIKEMTDVLKV 262
Cdd:smart00738   78 GTpgvrGFVGGGGK-PTPVPDDEIEKILKP 106
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 95-168 3.75e-09

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


Pssm-ID: 463406  Cd Length: 97  Bit Score: 54.97  E-value: 3.75e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 328927069    95 GAEDILEKA----SNIDNVVLDEDRSGARRLQNLWSDQREEELGEYYMKKYAKSSvgETVYGGSDElsDDITQQQLLP 168
Cdd:pfam11942   24 GADDFIEDDeedeDEEDGRRDDRRHRELDRRRELEEDEDAEEIAEYLKERYGRSS--SDAYRGDAE--EGVPQRLLLP 97
PHA03269 PHA03269
envelope glycoprotein C; Provisional
 821-966 5.25e-09

envelope glycoprotein C; Provisional


Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 60.13  E-value: 5.25e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  821 NPNTPSRAEEEYEYAFDDEPTPSPQayggtPNPQTPGYPDPS-SPQVNPQYNPQtpgtpamyntdqfsPYAAPSPQGSYQ 899
Cdd:PHA03269   21 NLNTNIPIPELHTSAATQKPDPAPA-----PHQAASRAPDPAvAPTSAASRKPD--------------LAQAPTPAASEK 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 328927069  900 PSPSPQSYHQV--APSPAGYQNTHSPasyhPTPSPM-----AYQASPSPGPVGYSPMTPgAPSPGGYNPHTPGS 966
Cdd:PHA03269   82 FDPAPAPHQAAsrAPDPAVAPQLAAA----PKPDAAeaftsAAQAHEAPADAGTSAASK-KPDPAAHTQHSPPP 150
PHA03247 PHA03247
large tegument protein UL36; Provisional
 741-958 1.04e-08

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 59.95  E-value: 1.04e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  741 VDRQRLTTVGSRRPGGMASTYGRTPMYGSQTPMYGSGSRTPMYGSQTPlqdGSRTPHYGSQTPLHDGSRTPAQSGAWDPN 820
Cdd:PHA03247 2661 VSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTP---EPAPHALVSATPLPPGPAAARQASPALPA 2737

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  821 NPNTPsraeeeyeyafddePTPSPQAYGGTPN----PQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPqg 896
Cdd:PHA03247 2738 APAPP--------------AVPAGPATPGGPArparPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSP-- 2801

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 328927069  897 syqPSPSPQSYHQVAPSPAgYQNTHSPASYHPTPsPMAYQASPSPGPVGYSPMTP--GAPSPGG 958
Cdd:PHA03247 2802 ---WDPADPPAAVLAPAAA-LPPAASPAGPLPPP-TSAQPTAPPPPPGPPPPSLPlgGSVAPGG 2860
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 176-304 3.16e-08

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


Pssm-ID: 129499 [Multi-domain]  Cd Length: 145  Bit Score: 53.74  E-value: 3.16e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   176 WTVKCKIGEERATAislmrKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRlgywnqQMVP--- 252
Cdd:TIGR00405    1 FAVKTSVGQEKNVA-----RLMARKARKSGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVR------GVVEgei 69

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 328927069   253 -IKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMI 304
Cdd:TIGR00405   70 dFEEIERFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELI 122
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 840-966 1.01e-07

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: 56.31  E-value: 1.01e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   840 PTPSPQAYGGTPNPQTPGYPDPSSPQVN-PQYNPQTPGTP--AMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAG 916
Cdd:pfam03154  188 PPGTTQAATAGPTPSAPSVPPQGSPATSqPPNQTQSTAAPhtLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQVSPQPLP 267

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 328927069   917 YQNTHSPASYHP---------TPSPMAYQASPSPGPVGYSPMTPG----APSPGGYNPHTPGS 966
Cdd:pfam03154  268 QPSLHGQMPPMPhslqtgpshMQHPVPPQPFPLTPQSSQSQVPPGpspaAPGQSQQRIHTPPS 330
PBP1 COG5180
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ...
 785-973 1.11e-06

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


Pssm-ID: 444064 [Multi-domain]  Cd Length: 548  Bit Score: 52.76  E-value: 1.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  785 SQTPL---QDGSRTPHYGSQTPLHDGSRTPaQSGAWDPNNPNTPSRAEEEYEYAFDD-EPTPSPQAYGGTPNP----QTP 856
Cdd:COG5180   195 SPEKLdrpKVEVKDEAQEEPPDLTGGADHP-RPEAASSPKVDPPSTSEARSRPATVDaQPEMRPPADAKERRRaaigDTP 273

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  857 GYPDPSSPQVNPQYNPQT--PGTPAMYNTDQFSPYAAPSPQGSYQPSPS-----PQSYHQVAPSPAGYQNTHSPASYHPT 929
Cdd:COG5180   274 AAEPPGLPVLEAGSEPQSdaPEAETARPIDVKGVASAPPATRPVRPPGGardpgTPRPGQPTERPAGVPEAASDAGQPPS 353

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 328927069  930 PSPMAYQASPSpgpvgySPMTPGAPSPG--GYN--PHTPGSGIEQNSS 973
Cdd:COG5180   354 AYPPAEEAVPG------KPLEQGAPRPGssGGDgaPFQPPNGAPQPGL 395
SP7_N cd22542
N-terminal domain of transcription factor Specificity Protein (SP) 7; Specificity Proteins ...
 798-966 5.02e-05

N-terminal domain of transcription factor Specificity Protein (SP) 7; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP7, also called Osterix (Osx) in humans, is highly conserved among bone-forming vertebrates. It plays a major role, along with Runx2 and Dlx5 in driving the differentiation of mesenchymal precursor cells into osteoblasts and eventually osteocytes. SP7 also plays a regulatory role by inhibiting chondrocyte differentiation, maintaining the balance between differentiation of mesenchymal precursor cells into ossified bone or cartilage. Mutations of this gene have been associated with multiple dysfunctional bone phenotypes in vertebrates. SP7 is thought to play a role in diseases such as Osteogenesis imperfecta. SP7 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. This model represents the N-terminal domain of SP7.


Pssm-ID: 411691 [Multi-domain]  Cd Length: 297  Bit Score: 46.43  E-value: 5.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  798 YGSQTPLHDgSRTPAQSGAWDPNNPNTP--------SRAEE----EYEYAFDD-----EPTPSPQA---YGGTPNPQTPG 857
Cdd:cd22542    26 FGGSSPIRD-SATPGKPGNNPGKKPYSLgsdlssakSRSSElmgdSYTATFSSgnglmSPSGSPQAsttYGNDYNPFSHS 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  858 YPDPSSPQ----VNPQYNPQTPGTPAMYNT-DQFSPY-----AAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYH 927
Cdd:cd22542   105 FPTSSGSQdpslLVSKGHPSADCLPSVYTSlDMAHPYgswykTGIHPGISSSSTNATASWWDMHSNTNWLSAQGQPDGLQ 184

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 328927069  928 PTPSPMAYQASPSPGPVGYSPMTPgaPSPGGYNPHTPGS 966
Cdd:cd22542   185 ASLQPVPAQTPLNPQLPSYTEFTT--LNPAPYPAVGISS 221
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 467-494 5.49e-05

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


Pssm-ID: 128978  Cd Length: 28  Bit Score: 41.16  E-value: 5.49e-05
                            10        20
                    ....*....|....*....|....*...
gi 328927069    467 YFKMGDHVKVIAGRFEGDTGLIVRVEEN 494
Cdd:smart00739    1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 702-733 9.57e-05

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


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 40.45  E-value: 9.57e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 328927069   702 IGQTVRISQGPYKGYIGVVKDATESTARVELH 733
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 820-956 1.74e-04

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


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 45.53  E-value: 1.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  820 NNPNTPSRAEEEYEYAFDD-EPTPSPQAYGGTPN-PQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPqgs 897
Cdd:NF033839  249 DNVNTKVEIENTVHKIFADmDAVVTKFKKGLTQDtPKEPGNKKPSAPKPGMQPSPQPEKKEVKPEPETPKPEVKPQL--- 325

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 328927069  898 yqPSPSPqsyhQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSP-------GPVGYSPMTPGAPSP 956
Cdd:NF033839  326 --EKPKP----EVKPQPEKPKPEVKPQLETPKPEVKPQPEKPKPevkpqpeKPKPEVKPQPETPKP 385
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 471-499 2.20e-04

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


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 39.29  E-value: 2.20e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 328927069   471 GDHVKVIAGRFEGDTGLIVRVEE--NFVILF 499
Cdd:pfam00467    2 GDVVRVIAGPFKGKVGKVVEVDDkkNRVLVE 32
KLF1_2_4_N cd21972
N-terminal domain of Kruppel-like factor (KLF) 1, KLF2, KLF4, and similar proteins; Kruppel ...
 825-964 7.18e-04

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


Pssm-ID: 409230 [Multi-domain]  Cd Length: 194  Bit Score: 41.89  E-value: 7.18e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  825 PSRAEEEYEYAFDDEPTPSPQAYG----GTPNPQTPGYPDPSSPQVNPQYN-PQTPGTPAMYNTDQFSPYAAPSPQGSYQ 899
Cdd:cd21972    22 LDLEFILSNTVTSDNDNPPPPDPAypppESPESCSTVYDSDGCHPTPNAYCgPNGPGLPGHFLLAGNSPNLGPKIKTENQ 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 328927069  900 PS-------PSPQSYHQVAPS------PAGYQNTHSPASYHPTPSPMAYQASPSPGPVGYSPmtPGAPSPGGYNPHTP 964
Cdd:cd21972   102 EQacmpvagYSGHYGPREPQRvppappPPQYAGHFQYHGHFNMFSPPLRANHPGMSTVMLTP--LSTPPLGFLSPEEA 177
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 851-956 2.34e-03

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


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 40.16  E-value: 2.34e-03
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069    851 PNPQTPGYPDPSSPQVNPQYNPQTPGTPAMyntdQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTP 930
Cdd:smart00818   45 QHPPTHTLQPHHHIPVLPAQQPVVPQQPLM----PVPGQHSMTPTQHHQPNLPQPAQQPFQPQPLQPPQPQQPMQPQPPV 120

                            90       100
                    ....*....|....*....|....*.
gi 328927069    931 SPMAYQASPSPGPvgysPMTPGAPSP 956
Cdd:smart00818  121 HPIPPLPPQPPLP----PMFPMQPLP 142
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 838-979 3.59e-03

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


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 41.29  E-value: 3.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  838 DEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQynPQTPGTPAMYNTDQFSPYAAPSPQ-GSYQPSPSPQSYH-QVAPSPA 915
Cdd:NF033839  370 EKPKPEVKPQPETPKPEVKPQPEKPKPEVKPQ--PEKPKPEVKPQPEKPKPEVKPQPEkPKPEVKPQPEKPKpEVKPQPE 447

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  916 GYQNTHSPASYHPTPSPMAYQASPSPgPVGYSPMTP----GAPSPGGYNPHTPG--SGIEQNSSDWVTTD 979
Cdd:NF033839  448 KPKPEVKPQPETPKPEVKPQPEKPKP-EVKPQPEKPkpdnSKPQADDKKPSTPNnlSKDKQPSNQASTNE 516
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 592-623 7.67e-03

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


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 35.06  E-value: 7.67e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 328927069   592 VKDIVKVIDGPHSGREGEIRHLFRSFAFLHCK 623
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 174-261 4.32e-44

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


Pssm-ID: 193577 [Multi-domain]  Cd Length: 86  Bit Score: 154.23  E-value: 4.32e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  174 NLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLgyWNQQMVPI 253
Cdd:cd09888     1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYL--NTIKLVPI 78


                  ....*...
gi 328927069  254 KEMTDVLK 261
Cdd:cd09888    79 KEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 174-260 6.63e-31

Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit.


Pssm-ID: 397481  Cd Length: 84  Bit Score: 116.53  E-value: 6.63e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   174 NLWTVKCKIGEERATAISLMRKFIAYQfTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLGywNQQMVPI 253
Cdd:pfam03439    1 KIWAVKCTPGQEREVALSLMRKILALA-KTNNLGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGL--VPGLVPI 77


                   ....*..
gi 328927069   254 KEMTDVL 260
Cdd:pfam03439   78 KEMEHLL 84
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 768-885 1.56e-28

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: 111.07  E-value: 1.56e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069    768 GSQTPMYG-SGSRTPMYGSQTP----LQDGSRTPHYGSQTPLHDG--SRTPAQSGAWdPNNPNTPSRAEEEYEYAFDDEP 840
Cdd:smart01104    1 GGRTPAWGaSGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAWGGAG-PTGSRTPAWGGASAWGNKSSEG 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 328927069    841 TPSPQA--YGGTPNPQTPGYpdpssPQVNPQYNPQTPGTPAMYNTDQ 885
Cdd:smart01104   80 SASSWAagPGGAYGAPTPGY-----GGTPSAYGPATPGGGAMAGSAS 121
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 467-517 6.93e-28

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


Pssm-ID: 240507  Cd Length: 51  Bit Score: 106.46  E-value: 6.93e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 328927069  467 YFKMGDHVKVIAGRFEGDTGLIVRVEENFVILFSDLTMHELKVLPRDLQLC 517
Cdd:cd06083     1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1024-1080 2.06e-26

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


Pssm-ID: 240510  Cd Length: 58  Bit Score: 102.59  E-value: 2.06e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 328927069 1024 EHLEPITPTKNNKVKVILGEDREATGVLLSIDGEDGIVRMDLDEQLKILNLRFLGKL 1080
Cdd:cd06086     1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMDSDGDIKILPMNFLAKL 57
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 416-466 9.38e-26

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


Pssm-ID: 240506  Cd Length: 51  Bit Score: 100.65  E-value: 9.38e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 328927069  416 FQPGDNVEVCEGELINLQGKILSVDGNKITIMPKHEDLKDMLEFPAQELRK 466
Cdd:cd06082     1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 698-747 4.85e-25

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


Pssm-ID: 240509  Cd Length: 52  Bit Score: 98.71  E-value: 4.85e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 328927069  698 DNELIGQTVRISQGPYKGYIGVVKDATESTARVELHSTCQTISVDRQRLT 747
Cdd:cd06085     2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLA 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 593-635 1.53e-19

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


Pssm-ID: 240508  Cd Length: 43  Bit Score: 82.57  E-value: 1.53e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 328927069  593 KDIVKVIDGPHSGREGEIRHLFRSFAFLHCKKLVENGGMFVCK 635
Cdd:cd06084     1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 272-309 1.66e-17

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


Pssm-ID: 240505  Cd Length: 38  Bit Score: 76.74  E-value: 1.66e-17
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 328927069  272 KSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMIPRIDY 309
Cdd:cd06081     1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 768-826 6.47e-15

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


Pssm-ID: 372327 [Multi-domain]  Cd Length: 71  Bit Score: 70.55  E-value: 6.47e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   768 GSQTPMYGS--GSRTPMY---GSQTPL--QDGSRTPHY--GSQTPLHD--GSRTPAQSGAWDPnnPNTPS 826
Cdd:pfam12815    1 GSRTPAYNSagGSRTPAWgadGSRTPAygGAGGRTPAYnqGGKTPAWGgaGSRTPAYYGAWGG--SRTPA 68
nusG PRK08559
transcription antitermination protein NusG; Validated
 171-312 4.30e-12

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 64.89  E-value: 4.30e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  171 KDPNLWTVKCKIGEERATAISLMRKFIAYQftdtpLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRlGYwNQQM 250
Cdd:PRK08559    4 EMSMIFAVKTTAGQERNVALMLAMRAKKEN-----LPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVR-GV-VPGE 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 328927069  251 VPIKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKM------IP---RIDYDRI 312
Cdd:PRK08559   77 ISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELleaavpIPvtvRGDQVRV 147
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 174-260 9.97e-11

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


Pssm-ID: 193574 [Multi-domain]  Cd Length: 99  Bit Score: 59.64  E-value: 9.97e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  174 NLWTVKCKIGEERATAISLMRKFIA---------YQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLG 244
Cdd:cd08000     1 NWYVLFVKTGREEKVEKLLEKRFEAndieafvpkKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPGVIGI 80

                          90
                  ....*....|....*....
gi 328927069  245 YWN---QQMVPIKEMTDVL 260
Cdd:cd08000    81 LGNgeePSPVSDEEIEMIL 99
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 174-262 1.27e-10

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


Pssm-ID: 197850 [Multi-domain]  Cd Length: 106  Bit Score: 59.31  E-value: 1.27e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069    174 NLWTVKCKIGEERATAISLMRKFIAYQFTDtplQIKSVVAP-EHVK----------------GYIYVEAYKQTHVKQAIE 236
Cdd:smart00738    1 NWYAVRTTSGQEKRVAENLERKAEALGLED---KIVSILVPtEEVKeirrgkkkvverklfpGYIFVEADLEDEVWTAIR 77

                            90       100       110
                    ....*....|....*....|....*....|
gi 328927069    237 GV----GNLRLGYWnQQMVPIKEMTDVLKV 262
Cdd:smart00738   78 GTpgvrGFVGGGGK-PTPVPDDEIEKILKP 106
DUF5585 pfam17823
Family of unknown function (DUF5585); This is a family of unknown function found in chordata.
 720-1042 1.35e-09

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


Pssm-ID: 465521 [Multi-domain]  Cd Length: 506  Bit Score: 61.90  E-value: 1.35e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   720 VKDATESTARVELHSTCQTISVDRQRLTTVGSRRPGGMASTYGRTPMYGSQTPMygSGSRTPMYGSQTPlQDGSRTPHYG 799
Cdd:pfam17823  156 AAPRAAIAAASAPHAASPAPRTAASSTTAASSTTAASSAPTTAASSAPATLTPA--RGISTAATATGHP-AAGTALAAVG 232

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   800 SQTPLhdgSRT-PAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGypDPSSPQVNPQYNPQTPGTP 878
Cdd:pfam17823  233 NSSPA---AGTvTAAVGTVTPAALATLAAAAGTVASAAGTINMGDPHARRLSPAKHMPS--DTMARNPAAPMGAQAQGPI 307

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   879 AMYNTDQfsPYAAPSPqgsyQPSPSPQSYHQVAPSPAGYQNTHSPASyhPTPSPMAYQASPSPGPVGYSPMTPGA----- 953
Cdd:pfam17823  308 IQVSTDQ--PVHNTAG----EPTPSPSNTTLEPNTPKSVASTNLAVV--TTTKAQAKEPSASPVPVLHTSMIPEVeatsp 379

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   954 ---PSPGGYNPHTPGSGIEQNSSdwvttdiQVKVRDTyLDTQVVGQT----GVIRSVTGGMCSVYLKDSEKVVSIssehl 1026
Cdd:pfam17823  380 ttqPSPLLPTQGAAGPGILLAPE-------QVATEAT-AGTASAGPTprssGDPKTLAMASCQLSTQGQYLVVTT----- 446

                          330       340
                   ....*....|....*....|
gi 328927069  1027 EPITPTKNNK----VKVILG 1042
Cdd:pfam17823  447 DPLTPALVDKmfllVVLILG 466
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 750-815 3.21e-09

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


Pssm-ID: 372327 [Multi-domain]  Cd Length: 71  Bit Score: 54.37  E-value: 3.21e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 328927069   750 GSRRPGGMASTYGRTPMY-------------GSQTPMYGSGSRTPMYGsqtplQDGSRTPHYGSQTplhDGSRTPAQSG 815
Cdd:pfam12815    1 GSRTPAYNSAGGSRTPAWgadgsrtpayggaGGRTPAYNQGGKTPAWG-----GAGSRTPAYYGAW---GGSRTPAYGG 71
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 785-966 3.54e-09

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


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 60.94  E-value: 3.54e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   785 SQTPLQDGSRTPHYGSQTPLHDgsrtPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPtPSPQAYGGTPNPQTPGYPdPSSP 864
Cdd:pfam03154  259 SQVSPQPLPQPSLHGQMPPMPH----SLQTGPSHMQHPVPPQPFPLTPQSSQSQVP-PGPSPAAPGQSQQRIHTP-PSQS 332

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   865 QVNPQYNP-QTPGTPAMYNTdqfsPYAAPSPQGSYQPSPSPQSY----HQVAPSPagYQ-----------------NTHS 922
Cdd:pfam03154  333 QLQSQQPPrEQPLPPAPLSM----PHIKPPPTTPIPQLPNPQSHkhppHLSGPSP--FQmnsnlppppalkplsslSTHH 406

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 328927069   923 PASYHPTPSPMAYQASPSPGPVGYSPM---TPGAPSPGGYNPHTPGS 966
Cdd:pfam03154  407 PPSAHPPPLQLMPQSQQLPPPPAQPPVltqSQSLPPPAASHPPTSGL 453
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 95-168 3.75e-09

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


Pssm-ID: 463406  Cd Length: 97  Bit Score: 54.97  E-value: 3.75e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 328927069    95 GAEDILEKA----SNIDNVVLDEDRSGARRLQNLWSDQREEELGEYYMKKYAKSSvgETVYGGSDElsDDITQQQLLP 168
Cdd:pfam11942   24 GADDFIEDDeedeDEEDGRRDDRRHRELDRRRELEEDEDAEEIAEYLKERYGRSS--SDAYRGDAE--EGVPQRLLLP 97
PHA03269 PHA03269
envelope glycoprotein C; Provisional
 821-966 5.25e-09

envelope glycoprotein C; Provisional


Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 60.13  E-value: 5.25e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  821 NPNTPSRAEEEYEYAFDDEPTPSPQayggtPNPQTPGYPDPS-SPQVNPQYNPQtpgtpamyntdqfsPYAAPSPQGSYQ 899
Cdd:PHA03269   21 NLNTNIPIPELHTSAATQKPDPAPA-----PHQAASRAPDPAvAPTSAASRKPD--------------LAQAPTPAASEK 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 328927069  900 PSPSPQSYHQV--APSPAGYQNTHSPasyhPTPSPM-----AYQASPSPGPVGYSPMTPgAPSPGGYNPHTPGS 966
Cdd:PHA03269   82 FDPAPAPHQAAsrAPDPAVAPQLAAA----PKPDAAeaftsAAQAHEAPADAGTSAASK-KPDPAAHTQHSPPP 150
PHA03247 PHA03247
large tegument protein UL36; Provisional
 741-958 1.04e-08

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 59.95  E-value: 1.04e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  741 VDRQRLTTVGSRRPGGMASTYGRTPMYGSQTPMYGSGSRTPMYGSQTPlqdGSRTPHYGSQTPLHDGSRTPAQSGAWDPN 820
Cdd:PHA03247 2661 VSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTP---EPAPHALVSATPLPPGPAAARQASPALPA 2737

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  821 NPNTPsraeeeyeyafddePTPSPQAYGGTPN----PQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPqg 896
Cdd:PHA03247 2738 APAPP--------------AVPAGPATPGGPArparPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSP-- 2801

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 328927069  897 syqPSPSPQSYHQVAPSPAgYQNTHSPASYHPTPsPMAYQASPSPGPVGYSPMTP--GAPSPGG 958
Cdd:PHA03247 2802 ---WDPADPPAAVLAPAAA-LPPAASPAGPLPPP-TSAQPTAPPPPPGPPPPSLPlgGSVAPGG 2860
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 754-967 2.89e-08

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


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 58.10  E-value: 2.89e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   754 PGGMASTYGRTPMYGSQTPMYGSGSRTPMYGSQ-------TPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNP---- 822
Cdd:pfam09606  231 PQQMGGAPNQVAMQQQQPQQQGQQSQLGMGINQmqqmpqgVGGGAGQGGPGQPMGPPGQQPGAMPNVMSIGDQNNYqqqq 310

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   823 --NTPSRAEEEYEYAFDDEPTPS--------PQAYGGTPNPQTPGypdpssPQVNPQYNPQTPGTPAMYNTDQFSPYAAP 892
Cdd:pfam09606  311 trQQQQQQGGNHPAAHQQQMNQSvgqggqvvALGGLNHLETWNPG------NFGGLGANPMQRGQPGMMSSPSPVPGQQV 384

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 328927069   893 SPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASyHPTPSPmAYQASPSPGPVGY--SPMTPGAPSPGGyNPHTPGSG 967
Cdd:pfam09606  385 RQVTPNQFMRQSPQPSVPSPQGPGSQPPQSHPG-GMIPSP-ALIPSPSPQMSQQpaQQRTIGQDSPGG-SLNTPGQS 458
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 176-304 3.16e-08

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


Pssm-ID: 129499 [Multi-domain]  Cd Length: 145  Bit Score: 53.74  E-value: 3.16e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   176 WTVKCKIGEERATAislmrKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRlgywnqQMVP--- 252
Cdd:TIGR00405    1 FAVKTSVGQEKNVA-----RLMARKARKSGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVR------GVVEgei 69

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 328927069   253 -IKEMTDVLKVVKEVANLKPKSWVRLKRGIYKDDIAQVDYVEPSQNTISLKMI 304
Cdd:TIGR00405   70 dFEEIERFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELI 122
NGN_Arch cd09887
Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance ...
 175-242 9.24e-08

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


Pssm-ID: 193576  Cd Length: 82  Bit Score: 50.62  E-value: 9.24e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 328927069  175 LWTVKCKIGEERATAISLMRKFiayqfTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLR 242
Cdd:cd09887     2 IYAVKTTAGQERNVADLLAMRA-----EKENLDVYSILVPEELKGYVFVEAEDPDRVEELIRGIPHVR 64
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 840-966 1.01e-07

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: 56.31  E-value: 1.01e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   840 PTPSPQAYGGTPNPQTPGYPDPSSPQVN-PQYNPQTPGTP--AMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAG 916
Cdd:pfam03154  188 PPGTTQAATAGPTPSAPSVPPQGSPATSqPPNQTQSTAAPhtLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQVSPQPLP 267

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 328927069   917 YQNTHSPASYHP---------TPSPMAYQASPSPGPVGYSPMTPG----APSPGGYNPHTPGS 966
Cdd:pfam03154  268 QPSLHGQMPPMPhslqtgpshMQHPVPPQPFPLTPQSSQSQVPPGpspaAPGQSQQRIHTPPS 330
PHA03247 PHA03247
large tegument protein UL36; Provisional
 758-978 1.73e-07

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 55.71  E-value: 1.73e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  758 ASTYGRTPMYGSQTPMygsgSRTPMYGSQTPLQDGSRTPHYGSQTPLHDGSR-TPAQSGAWDPNNPNTPsRAEEEYEYAF 836
Cdd:PHA03247 2817 ALPPAASPAGPLPPPT----SAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRrPPSRSPAAKPAAPARP-PVRRLARPAV 2891

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  837 DDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQtpgtpamyntdqfsPYAAPSPQGSYQPSPSPQSYHQVAPSPAG 916
Cdd:PHA03247 2892 SRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQ--------------PQPPPPPPPRPQPPLAPTTDPAGAGEPSG 2957

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 328927069  917 YQNTHSPASYHPTPSPMAYQASPSPGPvgySPMTPGAPSPGgyNPHTPGSGIeqnsSDWVTT 978
Cdd:PHA03247 2958 AVPQPWLGALVPGRVAVPRFRVPQPAP---SREAPASSTPP--LTGHSLSRV----SSWASS 3010
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 419-465 2.43e-07

KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues.


Pssm-ID: 240504  Cd Length: 49  Bit Score: 48.37  E-value: 2.43e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 328927069  419 GDNVEVCEGELINLQGKILSVDG--NKITIMPKHEDLKDMLEFPAQELR 465
Cdd:cd00380     1 GDVVRVLRGPYKGREGVVVDIDPrfGIVTVKGATGSKGAELKVRFDDVD 49
PHA03378 PHA03378
EBNA-3B; Provisional
 759-958 3.87e-07

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 54.30  E-value: 3.87e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  759 STYGRTPMYGSQTPMYGSGSRTPMYGSQTPLQD-----------GSRTPHYGSQTPLHDGSRTPAQSGAWdPNNPNTPSR 827
Cdd:PHA03378  603 SQTPEPPTTQSHIPETSAPRQWPMPLRPIPMRPlrmqpitfnvlVFPTPHQPPQVEITPYKPTWTQIGHI-PYQPSPTGA 681

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  828 AEEEYEYAFDDEPTPSPQAYGGTPNPQTPgyPDPSS-PQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGSYQPSPSPQS 906
Cdd:PHA03378  682 NTMLPIQWAPGTMQPPPRAPTPMRPPAAP--PGRAQrPAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAA 759

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 328927069  907 YHQVAPSPAGyqnthSPASYHPTPSPMA-------YQASPSPGP---VGYSPMTPGAPSPGG 958
Cdd:PHA03378  760 APGRARPPAA-----APGAPTPQPPPQAppapqqrPRGAPTPQPppqAGPTSMQLMPRAAPG 816
PHA03378 PHA03378
EBNA-3B; Provisional
 744-956 9.05e-07

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 53.15  E-value: 9.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  744 QRLTTVGSRRPGGMASTYGRTP---MYGSQTPmygsgsRTPMYGSQTP-LQDGSRTPHYGSQTPLHDGSRTPAQSGAWDP 819
Cdd:PHA03378  575 QPLTSPTTSQLASSAPSYAQTPwpvPHPSQTP------EPPTTQSHIPeTSAPRQWPMPLRPIPMRPLRMQPITFNVLVF 648

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  820 NNPNTPSRAEeeyeyafddeptPSPQAYGGTPNPQTPGYPDPSSPQVN--PQYNPQTPGTPAMYNTDQFSPYAAPS---- 893
Cdd:PHA03378  649 PTPHQPPQVE------------ITPYKPTWTQIGHIPYQPSPTGANTMlpIQWAPGTMQPPPRAPTPMRPPAAPPGraqr 716

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 328927069  894 PQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPspmAYQASPSPGPVGYSPMTPGAPSP 956
Cdd:PHA03378  717 PAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGR---ARPPAAAPGRARPPAAAPGAPTP 776
PHA03247 PHA03247
large tegument protein UL36; Provisional
 785-965 1.01e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 53.40  E-value: 1.01e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  785 SQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYP----- 859
Cdd:PHA03247 2567 SVPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHppptv 2646

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  860 --------DPSSPQVNPQYNPQTPGTPAMYN--TDQFSPYAAPSPQGSYQPS---PSPQSYHQVAPSPAGYQNTHSPASY 926
Cdd:PHA03247 2647 ppperprdDPAPGRVSRPRRARRLGRAAQASspPQRPRRRAARPTVGSLTSLadpPPPPPTPEPAPHALVSATPLPPGPA 2726

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 328927069  927 HPTPSPMAYQASPSPGPVGYSPMTPGAPSPGGYNPHTPG 965
Cdd:PHA03247 2727 AARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAG 2765
PBP1 COG5180
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ...
 785-973 1.11e-06

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


Pssm-ID: 444064 [Multi-domain]  Cd Length: 548  Bit Score: 52.76  E-value: 1.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  785 SQTPL---QDGSRTPHYGSQTPLHDGSRTPaQSGAWDPNNPNTPSRAEEEYEYAFDD-EPTPSPQAYGGTPNP----QTP 856
Cdd:COG5180   195 SPEKLdrpKVEVKDEAQEEPPDLTGGADHP-RPEAASSPKVDPPSTSEARSRPATVDaQPEMRPPADAKERRRaaigDTP 273

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  857 GYPDPSSPQVNPQYNPQT--PGTPAMYNTDQFSPYAAPSPQGSYQPSPS-----PQSYHQVAPSPAGYQNTHSPASYHPT 929
Cdd:COG5180   274 AAEPPGLPVLEAGSEPQSdaPEAETARPIDVKGVASAPPATRPVRPPGGardpgTPRPGQPTERPAGVPEAASDAGQPPS 353

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 328927069  930 PSPMAYQASPSpgpvgySPMTPGAPSPG--GYN--PHTPGSGIEQNSS 973
Cdd:COG5180   354 AYPPAEEAVPG------KPLEQGAPRPGssGGDgaPFQPPNGAPQPGL 395
PHA03378 PHA03378
EBNA-3B; Provisional
 795-964 1.18e-06

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 52.76  E-value: 1.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  795 TPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEE---YEYAFDDEPTPSPQAYGGTPNPQTPGYPDPS-SPQVNPQ- 869
Cdd:PHA03378  582 TSQLASSAPSYAQTPWPVPHPSQTPEPPTTQSHIPETsapRQWPMPLRPIPMRPLRMQPITFNVLVFPTPHqPPQVEITp 661

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  870 ------------YNPQTPG---------TPAMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHP 928
Cdd:PHA03378  662 ykptwtqighipYQPSPTGantmlpiqwAPGTMQPPPRAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPAAAP 741

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 328927069  929 TPS--PMAYQASPSPGPVGYSPMTPGAPSPGGYNPHTP 964
Cdd:PHA03378  742 GRArpPAAAPGRARPPAAAPGRARPPAAAPGAPTPQPP 779
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 839-965 1.39e-06

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 52.78  E-value: 1.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  839 EPTPSPQAYGGTPNPQtpgYPDPSSPQVNP---QYNPQTPGTPAMYNTDQFSPYAAPSP-QGSYQPSPSPQSYHQVAPSP 914
Cdd:PRK10263  370 EPVIAPAPEGYPQQSQ---YAQPAVQYNEPlqqPVQPQQPYYAPAAEQPAQQPYYAPAPeQPAQQPYYAPAPEQPVAGNA 446

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 328927069  915 AGYQNTHSPasYHPTPSPMAYQASPSPGPVGYSPMTPGAPSPGGYNPHTPG 965
Cdd:PRK10263  447 WQAEEQQST--FAPQSTYQTEQTYQQPAAQEPLYQQPQPVEQQPVVEPEPV 495
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 593-630 2.82e-06

KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues.


Pssm-ID: 240504  Cd Length: 49  Bit Score: 45.29  E-value: 2.82e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 328927069  593 KDIVKVIDGPHSGREGEIRHLFRSFAFLHCKKLVENGG 630
Cdd:cd00380     1 GDVVRVLRGPYKGREGVVVDIDPRFGIVTVKGATGSKG 38
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 703-746 3.50e-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: 44.90  E-value: 3.50e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 328927069  703 GQTVRISQGPYKGYIGVVKDATEST--ARVELH--STCQTISVDRQRL 746
Cdd:cd00380     1 GDVVRVLRGPYKGREGVVVDIDPRFgiVTVKGAtgSKGAELKVRFDDV 48
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 471-515 4.47e-06

KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues.


Pssm-ID: 240504  Cd Length: 49  Bit Score: 44.52  E-value: 4.47e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 328927069  471 GDHVKVIAGRFEGDTGLIVRVEENFVIL----FSDLTMHELKVLPRDLQ 515
Cdd:cd00380     1 GDVVRVLRGPYKGREGVVVDIDPRFGIVtvkgATGSKGAELKVRFDDVD 49
PHA03247 PHA03247
large tegument protein UL36; Provisional
 807-962 5.08e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 51.09  E-value: 5.08e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  807 GSRTPAQSGAWDPNNPNTPSRAEEEYeyaFDDEPTPSP-----------------QAYGGTPNPQTPGYPDPSSPQV--N 867
Cdd:PHA03247 2494 AAPDPGGGGPPDPDAPPAPSRLAPAI---LPDEPVGEPvhprmltwirgleelasDDAGDPPPPLPPAAPPAAPDRSvpP 2570

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  868 PQYNPQTPGtPAMyNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQA-SPSPGPVGY 946
Cdd:PHA03247 2571 PRPAPRPSE-PAV-TSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPdPHPPPTVPP 2648

                         170
                  ....*....|....*.
gi 328927069  947 SPMTPGAPSPGGYNPH 962
Cdd:PHA03247 2649 PERPRDDPAPGRVSRP 2664
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 842-970 6.26e-06

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


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 50.54  E-value: 6.26e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   842 PSPQAYGGTPNPQTPGYPDPSS-PQVNPqynpqTPGTPAMynTDQFSPYAAPSPQGSyQPSPSPQSYHQVAPS--PAGYQ 918
Cdd:pfam03154  172 PVLQAQSGAASPPSPPPPGTTQaATAGP-----TPSAPSV--PPQGSPATSQPPNQT-QSTAAPHTLIQQTPTlhPQRLP 243

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 328927069   919 NTHSPASYHPTPSPMAY-QASPSPGPVGYSPMTPGAPSPGGYNPHTPGSGIEQ 970
Cdd:pfam03154  244 SPHPPLQPMTQPPPPSQvSPQPLPQPSLHGQMPPMPHSLQTGPSHMQHPVPPQ 296
PHA03291 PHA03291
envelope glycoprotein I; Provisional
 835-982 8.92e-06

envelope glycoprotein I; Provisional


Pssm-ID: 223033 [Multi-domain]  Cd Length: 401  Bit Score: 49.57  E-value: 8.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  835 AFDDEPTPSPQAYGGTPnpqTPGYPDPSSPQVNPQYNPqtpgtpamynTDQFSPyAAPSPQGSYQPSPspqsyhQVAPSP 914
Cdd:PHA03291  165 AFPAEGTLAAPPLGEGS---ADGSCDPALPLSAPRLGP----------ADVFVP-ATPRPTPRTTASP------ETTPTP 224

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 328927069  915 AgyqNTHSPASyHPTPSPMAYQASPSPGPVGYSPMTPGAPSPGGYNPHTPGSGIEQNSSDWVTTDIQV 982
Cdd:PHA03291  225 S---TTTSPPS-TTIPAPSTTIAAPQAGTTPEAEGTPAPPTPGGGEAPPANATPAPEASRYELTVTQI 288
PHA03247 PHA03247
large tegument protein UL36; Provisional
 743-1001 1.43e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 49.55  E-value: 1.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  743 RQRLTTVGSRRPGGMASTYGRTPMYGSQ--TPMYGSGSRTPmyGSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPN 820
Cdd:PHA03247 2711 APHALVSATPLPPGPAAARQASPALPAApaPPAVPAGPATP--GGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAV 2788

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  821 NPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFS-----PYAAPSPQ 895
Cdd:PHA03247 2789 ASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSvapggDVRRRPPS 2868

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  896 GSYQPSPSPQSYHQVA--PSPAGYQNTHSPASYHPTPSPMAYQASPSPGPVGYSPMTPGAPSPGGYNPHTPGSGIEQNSS 973
Cdd:PHA03247 2869 RSPAAKPAAPARPPVRrlARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTD 2948

                         250       260
                  ....*....|....*....|....*...
gi 328927069  974 DWVTTDIQVKVRDTYLDTQVVGQTGVIR 1001
Cdd:PHA03247 2949 PAGAGEPSGAVPQPWLGALVPGRVAVPR 2976
Pro-rich pfam15240
Proline-rich protein; This family includes several eukaryotic proline-rich proteins.
 812-964 1.80e-05

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


Pssm-ID: 464580 [Multi-domain]  Cd Length: 167  Bit Score: 46.18  E-value: 1.80e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   812 AQSGAWDPNNPNTPSR-AEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQfsPYA 890
Cdd:pfam15240   16 AQSSSEDVSQEDSPSLiSEEEGQSQQGGQGPQGPPPGGFPPQPPASDDPPGPPPPGGPQQPPPQGGKQKPQGPPP--QGG 93

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 328927069   891 APSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPgPVGYSPMTPGAPSPGGyNPHTP 964
Cdd:pfam15240   94 PRPPPGKPQGPPPQGGNQQQGPPPPGKPQGPPPQGGGPPPQGGNQQGPPPP-PPGNPQGPPQRPPQPG-NPQGP 165
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 861-972 1.90e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 48.93  E-value: 1.90e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  861 PSSPQVNPQYNPQTpgtpamynTDQFSPYAAPSPQGSYQPSPSPQSYHQ-VAPSPAGYQNTHSPASYHPTPSPMAYQASP 939
Cdd:PRK10263  740 PHEPLFTPIVEPVQ--------QPQQPVAPQQQYQQPQQPVAPQPQYQQpQQPVAPQPQYQQPQQPVAPQPQYQQPQQPV 811

                          90       100       110
                  ....*....|....*....|....*....|...
gi 328927069  940 SPGPVGYSPMTPGAPSPGGYNPHTPGSGIEQNS 972
Cdd:PRK10263  812 APQPQYQQPQQPVAPQPQYQQPQQPVAPQPQDT 844
SP7_N cd22542
N-terminal domain of transcription factor Specificity Protein (SP) 7; Specificity Proteins ...
 798-966 5.02e-05

N-terminal domain of transcription factor Specificity Protein (SP) 7; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP7, also called Osterix (Osx) in humans, is highly conserved among bone-forming vertebrates. It plays a major role, along with Runx2 and Dlx5 in driving the differentiation of mesenchymal precursor cells into osteoblasts and eventually osteocytes. SP7 also plays a regulatory role by inhibiting chondrocyte differentiation, maintaining the balance between differentiation of mesenchymal precursor cells into ossified bone or cartilage. Mutations of this gene have been associated with multiple dysfunctional bone phenotypes in vertebrates. SP7 is thought to play a role in diseases such as Osteogenesis imperfecta. SP7 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. This model represents the N-terminal domain of SP7.


Pssm-ID: 411691 [Multi-domain]  Cd Length: 297  Bit Score: 46.43  E-value: 5.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  798 YGSQTPLHDgSRTPAQSGAWDPNNPNTP--------SRAEE----EYEYAFDD-----EPTPSPQA---YGGTPNPQTPG 857
Cdd:cd22542    26 FGGSSPIRD-SATPGKPGNNPGKKPYSLgsdlssakSRSSElmgdSYTATFSSgnglmSPSGSPQAsttYGNDYNPFSHS 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  858 YPDPSSPQ----VNPQYNPQTPGTPAMYNT-DQFSPY-----AAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYH 927
Cdd:cd22542   105 FPTSSGSQdpslLVSKGHPSADCLPSVYTSlDMAHPYgswykTGIHPGISSSSTNATASWWDMHSNTNWLSAQGQPDGLQ 184

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 328927069  928 PTPSPMAYQASPSPGPVGYSPMTPgaPSPGGYNPHTPGS 966
Cdd:cd22542   185 ASLQPVPAQTPLNPQLPSYTEFTT--LNPAPYPAVGISS 221
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 467-494 5.49e-05

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


Pssm-ID: 128978  Cd Length: 28  Bit Score: 41.16  E-value: 5.49e-05
                            10        20
                    ....*....|....*....|....*...
gi 328927069    467 YFKMGDHVKVIAGRFEGDTGLIVRVEEN 494
Cdd:smart00739    1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28
dnaA PRK14086
chromosomal replication initiator protein DnaA;
781-945 6.00e-05

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 47.13  E-value: 6.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  781 PMY-GSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNnPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYP 859
Cdd:PRK14086  103 RRTsEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLPTAR-PAYPAYQQRPEPGAWPRAADDYGWQQQRLGFPPRAPYA 181

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  860 DPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGSY-------QPSPSPQSYHQV--APSPAGYQNTHSPASYHPTP 930
Cdd:PRK14086  182 SPASYAPEQERDREPYDAGRPEYDQRRRDYDHPRPDWDRprrdrtdRPEPPPGAGHVHrgGPGPPERDDAPVVPIRPSAP 261

                         170
                  ....*....|....*
gi 328927069  931 SPMAYQASPSPGPVG 945
Cdd:PRK14086  262 GPLAAQPAPAPGPGE 276
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 840-954 6.11e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 46.98  E-value: 6.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  840 PTPSPQAYGGTPNPQTPGyPDPSSPQVNPQYNPQTPGTPAmyntdqfsPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQN 919
Cdd:PRK14959  387 EGPASGGAATIPTPGTQG-PQGTAPAAGMTPSSAAPATPA--------PSAAPSPRVPWDDAPPAPPRSGIPPRPAPRMP 457

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 328927069  920 THSPASYHPTPSPMAYQASPSPG-PVGYSPMTPGAP 954
Cdd:PRK14959  458 EASPVPGAPDSVASASDAPPTLGdPSDTAEHTPSGP 493
PTZ00395 PTZ00395
Sec24-related protein; Provisional
 784-962 6.76e-05

Sec24-related protein; Provisional


Pssm-ID: 185594 [Multi-domain]  Cd Length: 1560  Bit Score: 47.38  E-value: 6.76e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  784 GSQTPLQDGSRTPHYGSQTPL-HDGSRTPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTP--NP--QTPGY 858
Cdd:PTZ00395  345 GSPNAASAGAPFNGLGNQADGgHINQVHPDARGAWAGGPHSNASYNCAAYSNAAQSNAAQSNAGFSNAGysNPgnSNPGY 424

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  859 PDP---SSPQVNPQY------NPQTPGTPamYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPT 929
Cdd:PTZ00395  425 NNApnsNTPYNNPPNsntpysNPPNSNPP--YSNLPYSNTPYSNAPLSNAPPSSAKDHHSAYHAAYQHRAANQPAANLPT 502

                         170       180       190
                  ....*....|....*....|....*....|...
gi 328927069  930 PSPMAyqASPSPGPVGYSPMTPGAPSPGGYNPH 962
Cdd:PTZ00395  503 ANQPA--ANNFHGAAGNSVGNPFASRPFGSAPY 533
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 839-962 7.62e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 46.90  E-value: 7.62e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  839 EPTPSPQAYGGTPNPQTPGyPDPSSPQVNPQYNPQTPGTPAmyntdqfsPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQ 918
Cdd:PRK07764  391 AGAPAAAAPSAAAAAPAAA-PAPAAAAPAAAAAPAPAAAPQ--------PAPAPAPAPAPPSPAGNAPAGGAPSPPPAAA 461

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 328927069  919 NTHSPASYHPTPSPMAYQASPSPGPVGYSPMTPGAPSPGGYNPH 962
Cdd:PRK07764  462 PSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAG 505
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 702-733 9.57e-05

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


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 40.45  E-value: 9.57e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 328927069   702 IGQTVRISQGPYKGYIGVVKDATESTARVELH 733
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 812-964 1.23e-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: 1.23e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   812 AQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQayGGTPNPQTPGYPDPSSP-----QVNPQYNPQTpgTPAMYNTDQF 886
Cdd:pfam03154  176 AQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQ--GSPATSQPPNQTQSTAAphtliQQTPTLHPQR--LPSPHPPLQP 251

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   887 SPYAAPSPQGSYQPSPSPQSY------------------HQVAPSPAGYQNTHSPASYHPTPSPMAyqaspsPGPVGYSP 948
Cdd:pfam03154  252 MTQPPPPSQVSPQPLPQPSLHgqmppmphslqtgpshmqHPVPPQPFPLTPQSSQSQVPPGPSPAA------PGQSQQRI 325

                          170
                   ....*....|....*.
gi 328927069   949 MTPgAPSPGGYNPHTP 964
Cdd:pfam03154  326 HTP-PSQSQLQSQQPP 340
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 787-956 1.32e-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: 1.32e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   787 TPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEEYE--YAFDDEPTPSPQAYGGTPNPQTPGYPDP--- 861
Cdd:pfam03154   75 SPLKSAKRQREKGASDTEEPERATAKKSKTQEISRPNSPSEGEGESSdgRSVNDEGSSDPKDIDQDNRSTSPSIPSPqdn 154

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   862 -----SS----------PQVNPQYNPQTPGTPAMYNTDQfSPYAAPSPQGsyqPSPSPQSYHQVAPSPAGYQNTHSPASY 926
Cdd:pfam03154  155 esdsdSSaqqqilqtqpPVLQAQSGAASPPSPPPPGTTQ-AATAGPTPSA---PSVPPQGSPATSQPPNQTQSTAAPHTL 230

                          170       180       190
                   ....*....|....*....|....*....|
gi 328927069   927 HPTPSPMAYQASPSPGPvGYSPMTPGAPSP 956
Cdd:pfam03154  231 IQQTPTLHPQRLPSPHP-PLQPMTQPPPPS 259
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 791-979 1.54e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 45.75  E-value: 1.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  791 DGSRTPHYGSQTPLHDGSR--TPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNP 868
Cdd:PRK07764  596 GGEGPPAPASSGPPEEAARpaAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGG 675

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  869 QYNPQTPGTPAMyntdqfSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSPGPVGYSP 948
Cdd:PRK07764  676 AAPAAPPPAPAP------AAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPP 749

                         170       180       190
                  ....*....|....*....|....*....|.
gi 328927069  949 MTPGAPSPGGYNPHTPGSGIEQNSSDWVTTD 979
Cdd:PRK07764  750 DPAGAPAQPPPPPAPAPAAAPAAAPPPSPPS 780
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 820-956 1.74e-04

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


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 45.53  E-value: 1.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  820 NNPNTPSRAEEEYEYAFDD-EPTPSPQAYGGTPN-PQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPqgs 897
Cdd:NF033839  249 DNVNTKVEIENTVHKIFADmDAVVTKFKKGLTQDtPKEPGNKKPSAPKPGMQPSPQPEKKEVKPEPETPKPEVKPQL--- 325

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 328927069  898 yqPSPSPqsyhQVAPSPAGYQNTHSPASYHPTPSPMAYQASPSP-------GPVGYSPMTPGAPSP 956
Cdd:NF033839  326 --EKPKP----EVKPQPEKPKPEVKPQLETPKPEVKPQPEKPKPevkpqpeKPKPEVKPQPETPKP 385
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 471-499 2.20e-04

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


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 39.29  E-value: 2.20e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 328927069   471 GDHVKVIAGRFEGDTGLIVRVEE--NFVILF 499
Cdd:pfam00467    2 GDVVRVIAGPFKGKVGKVVEVDDkkNRVLVE 32
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 792-964 2.43e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 45.55  E-value: 2.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  792 GSRTPHYGSQTPLHDGSRTPAQSGAWDPnnPNTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQvnPQYN 871
Cdd:PHA03307  773 ALLEPAEPQRGAGSSPPVRAEAAFRRPG--RLRRSGPAADAASRTASKRKSRSHTPDGGSESSGPARPPGAAAR--PPPA 848

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  872 PQTPGTPAMyntDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASyHPTPSPMAyqaspsPGPVGYSPMTP 951
Cdd:PHA03307  849 RSSESSKSK---PAAAGGRARGKNGRRRPRPPEPRARPGAAAPPKAAAAAPPAG-APAPRPRP------APRVKLGPMPP 918

                         170       180
                  ....*....|....*....|
gi 328927069  952 GAPSP-GGY------NPHTP 964
Cdd:PHA03307  919 GGPDPrGGFrrvppgDLHTP 938
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 811-966 3.07e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 44.98  E-value: 3.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  811 PAQSGAWDPNNPNTPSRAEEEYEYAfdDEPTPS---PQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFS 887
Cdd:PRK07764  592 PGAAGGEGPPAPASSGPPEEAARPA--APAAPAapaAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGW 669

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  888 PYAAPSPQGSyQPSPSPQSYHQVAPS--PAGYQNTHSPASYHP---------TPSPMAYQASPSPGPVGYSPMTPGAPSP 956
Cdd:PRK07764  670 PAKAGGAAPA-APPPAPAPAAPAAPAgaAPAQPAPAPAATPPAgqaddpaaqPPQAAQGASAPSPAADDPVPLPPEPDDP 748

                         170
                  ....*....|
gi 328927069  957 GGYNPHTPGS 966
Cdd:PRK07764  749 PDPAGAPAQP 758
Pneumo_att_G pfam05539
Pneumovirinae attachment membrane glycoprotein G;
769-930 3.20e-04

Pneumovirinae attachment membrane glycoprotein G;


Pssm-ID: 114270 [Multi-domain]  Cd Length: 408  Bit Score: 44.27  E-value: 3.20e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   769 SQTPMYGSGSRTPMYGSQT----PLQDG-SRTPHYGSQTPLHDgSRTPAQSGAWDP--NNPNTPSRAEEEYEYAFDDEPT 841
Cdd:pfam05539  215 STEPVGTQGTTTSSNPEPQteppPSQRGpSGSPQHPPSTTSQD-QSTTGDGQEHTQrrKTPPATSNRRSPHSTATPPPTT 293

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   842 PSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPyaaPSPQ------GSYQPSpSPQSYHQVAPSPA 915
Cdd:pfam05539  294 KRQETGRPTPRPTATTQSGSSPPHSSPPGVQANPTTQNLVDCKELDP---PKPNsicygvGIYNEA-LPRGCDIVVPLCS 369

                          170
                   ....*....|....*
gi 328927069   916 GYqNTHSPASYHPTP 930
Cdd:pfam05539  370 TY-TIMCMDTYYSKP 383
PHA03247 PHA03247
large tegument protein UL36; Provisional
 822-964 3.53e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 44.93  E-value: 3.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  822 PNTPS-RAEEEYEYAFDDEPTPSPQAyGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMY----NTDQFSPYAAPSPQG 896
Cdd:PHA03247 2475 PGAPVyRRPAEARFPFAAGAAPDPGG-GGPPDPDAPPAPSRLAPAILPDEPVGEPVHPRMLtwirGLEELASDDAGDPPP 2553

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  897 SYQPSPSPQSYHQVAPSPagyqnthSPASYHPTPSPMAYQASPSPGPVGYSPMTPGAP--SPGGYNPHTP 964
Cdd:PHA03247 2554 PLPPAAPPAAPDRSVPPP-------RPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDrgDPRGPAPPSP 2616
DUF1373 pfam07117
Protein of unknown function (DUF1373); This family consists of several hypothetical proteins ...
 822-936 4.75e-04

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


Pssm-ID: 462093 [Multi-domain]  Cd Length: 212  Bit Score: 42.86  E-value: 4.75e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   822 PNTPSRAEEEYEY----AFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGS 897
Cdd:pfam07117   42 PPRPEEEEGQGGGggtfPFPGSPEPEPGGGGSGPMPMSASAPEPEPAKAKPQRPAPAQGHGHGGGGDSDSSGSGSGHQGS 121

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 328927069   898 YQP---SPSPQSYHQVAPSPAGYQNTHSPasyHPTPSPMAYQ 936
Cdd:pfam07117  122 GGAgagAGAPGHQHEQEQESSSSDDDDED---EFEFTPEEDE 160
PLN02983 PLN02983
biotin carboxyl carrier protein of acetyl-CoA carboxylase
 859-942 5.01e-04

biotin carboxyl carrier protein of acetyl-CoA carboxylase


Pssm-ID: 215533 [Multi-domain]  Cd Length: 274  Bit Score: 43.29  E-value: 5.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  859 PDPSSPQVNPQYNPQTPGTPAMyntdqfSPYAAPSPQGsyqPSPSPqsyhqvAPSPAGYQNTHSPASYHPT-PSPMA--- 934
Cdd:PLN02983  144 PPPPAPVVMMQPPPPHAMPPAS------PPAAQPAPSA---PASSP------PPTPASPPPAKAPKSSHPPlKSPMAgtf 208


                  ....*...
gi 328927069  935 YQaSPSPG 942
Cdd:PLN02983  209 YR-SPAPG 215
DUF1373 pfam07117
Protein of unknown function (DUF1373); This family consists of several hypothetical proteins ...
 840-979 5.12e-04

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


Pssm-ID: 462093 [Multi-domain]  Cd Length: 212  Bit Score: 42.86  E-value: 5.12e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   840 PTPSPQAYGGTPNPQTPGYPDPSSpqvnpQYNPQTPGTpamyntdqFSPyaAPSPQGSYQPSPsPQSYHQVAPSPAgyqn 919
Cdd:pfam07117   29 PMSLPLPPGQEPEPPRPEEEEGQG-----GGGGTFPFP--------GSP--EPEPGGGGSGPM-PMSASAPEPEPA---- 88

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 328927069   920 thsPASYHpTPSPMAYQASPSPGPVGYSPMTPGAPSPGGYNPHTPGSG--IEQNSSDWVTTD 979
Cdd:pfam07117   89 ---KAKPQ-RPAPAQGHGHGGGGDSDSSGSGSGHQGSGGAGAGAGAPGhqHEQEQESSSSDD 146
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 788-956 5.48e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 44.39  E-value: 5.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  788 PLQDGSRTPHYGSQT--PLHDGSRTPAQSGAWDPNNP-------NTPSRAEEEYEYAFDDEPTPSPQAYGGTPNPQTPGY 858
Cdd:PHA03307  195 PSTPPAAASPRPPRRssPISASASSPAPAPGRSAADDagasssdSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASG 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  859 PDPSSPQVNPQYNPQTPGTPamyntdqfSPYAAPS-PQGSYQPSPSPQSYHQVAPSPAGyqnTHSPASYHPTPSPMA--Y 935
Cdd:PHA03307  275 WNGPSSRPGPASSSSSPRER--------SPSPSPSsPGSGPAPSSPRASSSSSSSRESS---SSSTSSSSESSRGAAvsP 343

                         170       180
                  ....*....|....*....|.
gi 328927069  936 QASPSPGPVGYSPMTPGAPSP 956
Cdd:PHA03307  344 GPSPSRSPSPSRPPPPADPSS 364
dnaA PRK14086
chromosomal replication initiator protein DnaA;
839-965 5.92e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 44.05  E-value: 5.92e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  839 EPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGSYQPSPSPQsyhqvAPSPAGYQ 918
Cdd:PRK14086   94 EPAPPPPHARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLPTARPAYPAYQQRPEPGAWPR-----AADDYGWQ 168

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 328927069  919 NT-HSPASYHPTPSPMAYQASPSPGPVGYSPMTPGAPSPGGyNPHTPG 965
Cdd:PRK14086  169 QQrLGFPPRAPYASPASYAPEQERDREPYDAGRPEYDQRRR-DYDHPR 215
KLF1_2_4_N cd21972
N-terminal domain of Kruppel-like factor (KLF) 1, KLF2, KLF4, and similar proteins; Kruppel ...
 825-964 7.18e-04

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


Pssm-ID: 409230 [Multi-domain]  Cd Length: 194  Bit Score: 41.89  E-value: 7.18e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  825 PSRAEEEYEYAFDDEPTPSPQAYG----GTPNPQTPGYPDPSSPQVNPQYN-PQTPGTPAMYNTDQFSPYAAPSPQGSYQ 899
Cdd:cd21972    22 LDLEFILSNTVTSDNDNPPPPDPAypppESPESCSTVYDSDGCHPTPNAYCgPNGPGLPGHFLLAGNSPNLGPKIKTENQ 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 328927069  900 PS-------PSPQSYHQVAPS------PAGYQNTHSPASYHPTPSPMAYQASPSPGPVGYSPmtPGAPSPGGYNPHTP 964
Cdd:cd21972   102 EQacmpvagYSGHYGPREPQRvppappPPQYAGHFQYHGHFNMFSPPLRANHPGMSTVMLTP--LSTPPLGFLSPEEA 177
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
842-973 7.57e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 43.71  E-value: 7.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  842 PSPQAYGGTPNPQTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTH 921
Cdd:PRK12323  392 PAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRP 471

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 328927069  922 SPASYHPTPSPMAYQASPSPGPVGYSP---MTPGAPSPGGYNPHTPGSGIEQNSS 973
Cdd:PRK12323  472 VAAAAAAAPARAAPAAAPAPADDDPPPweeLPPEFASPAPAQPDAAPAGWVAESI 526
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 750-957 8.58e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 43.62  E-value: 8.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  750 GSRRPGGMASTYGRTPMYGSQTPMYGSG----SRTPMYGSQTPLQDGSR----TPHYGSQTPLHDGSRTPAQ--SGAWDP 819
Cdd:PHA03307  221 APAPGRSAADDAGASSSDSSSSESSGCGwgpeNECPLPRPAPITLPTRIweasGWNGPSSRPGPASSSSSPRerSPSPSP 300

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  820 NNP-----NTPSRAEEEYEyAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPqvnpqynPQTPGTPAmyntdqfSPYAAPSP 894
Cdd:PHA03307  301 SSPgsgpaPSSPRASSSSS-SSRESSSSSTSSSSESSRGAAVSPGPSPSR-------SPSPSRPP-------PPADPSSP 365

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 328927069  895 QGSYQPSPSPQSYHQVAPSP----AGYQNTHSPASYH---------PTPSPMAYQASPSPGPVGYSPMTP-GAPSPG 957
Cdd:PHA03307  366 RKRPRPSRAPSSPAASAGRPtrrrARAAVAGRARRRDatgrfpagrPRPSPLDAGAASGAFYARYPLLTPsGEPWPG 442
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 848-967 9.35e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 43.44  E-value: 9.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  848 GGTPNPQTPGYPDPSSPQVnPQYNPQTPGTPAMyntdqfspyAAPSPQGSYQPSPSPQSYHQVAPSPAgyqnthSPASYH 927
Cdd:PRK07764  389 GGAGAPAAAAPSAAAAAPA-AAPAPAAAAPAAA---------AAPAPAAAPQPAPAPAPAPAPPSPAG------NAPAGG 452

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 328927069  928 PTPSPMAYQASPSPGPVGYSPMTPGAPSPGGYNPHTPGSG 967
Cdd:PRK07764  453 APSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAA 492
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 806-966 9.99e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 43.24  E-value: 9.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  806 DGSRTPAQSGAWDPNNPNTPSRAeeeyeyAFDDEPTPSPQAYGGTPNPQTPGYPDPSSP--QVNPQYNPQTPGTPAMYNT 883
Cdd:PHA03307  238 DSSSSESSGCGWGPENECPLPRP------APITLPTRIWEASGWNGPSSRPGPASSSSSprERSPSPSPSSPGSGPAPSS 311

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  884 DQFSPYAAPSPQGSyQPSPSPQSyhqVAPSPAGyqnTHSPASYHPTPSPmayqASPSPGPVGYSPMTPGAPSPGGYNPHT 963
Cdd:PHA03307  312 PRASSSSSSSRESS-SSSTSSSS---ESSRGAA---VSPGPSPSRSPSP----SRPPPPADPSSPRKRPRPSRAPSSPAA 380


                  ...
gi 328927069  964 PGS 966
Cdd:PHA03307  381 SAG 383
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 851-1037 1.07e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 42.87  E-value: 1.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  851 PNPQTPGYPDPSSPQVNPQYNPQTPGTPAMyntdqfspyAAPSPQGSYQPSPSPQSyhQVAPSPAGYQNTHSPASYHPTP 930
Cdd:PRK14950  364 PAPQPAKPTAAAPSPVRPTPAPSTRPKAAA---------AANIPPKEPVRETATPP--PVPPRPVAPPVPHTPESAPKLT 432

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  931 spmayqasPSPGPVGYSPMTPGAPSPGGYNP--HTPGSGIEQNSSDWVTTDIQVKVRDTYLdtQVVGQTGViRSVTggmc 1008
Cdd:PRK14950  433 --------RAAIPVDEKPKYTPPAPPKEEEKalIADGDVLEQLEAIWKQILRDVPPRSPAV--QALLSSGV-RPVS---- 497

                         170       180       190
                  ....*....|....*....|....*....|
gi 328927069 1009 svyLKDSEKVVSISSE-HLEPITPTKNNKV 1037
Cdd:PRK14950  498 ---VEKNTLTLSFKSKfHKDKIEEPENRKI 524
PHA03369 PHA03369
capsid maturational protease; Provisional
 810-907 1.16e-03

capsid maturational protease; Provisional


Pssm-ID: 223061 [Multi-domain]  Cd Length: 663  Bit Score: 43.06  E-value: 1.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  810 TPAQSGAWDPNnPNTPSRAEEE-YEYAFDDEPTPSPQAYGGTPNPQTPGYPDPSSPQVnpqynPQTPGTPAMYNTDQFSP 888
Cdd:PHA03369  353 LTAPSRVLAAA-AKVAVIAAPQtHTGPADRQRPQRPDGIPYSVPARSPMTAYPPVPQF-----CGDPGLVSPYNPQSPGT 426

                          90
                  ....*....|....*....
gi 328927069  889 YAAPSPQGSYQPSPSPQSY 907
Cdd:PHA03369  427 SYGPEPVGPVPPQPTNPYV 445
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 793-974 1.85e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 42.47  E-value: 1.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  793 SRTPHYGSQTPLHDGSRTPAQSGAwdPNNPNTPSRAEeeyeyafDDEPTPSPQayggtpnpqtPGYPDPSSPQVNPQYNP 872
Cdd:PHA03307   79 APANESRSTPTWSLSTLAPASPAR--EGSPTPPGPSS-------PDPPPPTPP----------PASPPPSPAPDLSEMLR 139

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  873 QTPGTPAMYNTDQFSPYAAPSPQGSYQPSPSPQSYhqvaPSPAGYQNTHSPASYHPTPSPMAYQASPSPGP-VGYSPMTP 951
Cdd:PHA03307  140 PVGSPGPPPAASPPAAGASPAAVASDAASSRQAAL----PLSSPEETARAPSSPPAEPPPSTPPAAASPRPpRRSSPISA 215

                         170       180
                  ....*....|....*....|...
gi 328927069  952 GAPSPGGYNPHTPGSGIEQNSSD 974
Cdd:PHA03307  216 SASSPAPAPGRSAADDAGASSSD 238
Med26_M pfam15694
Mediator complex subunit 26 middle domain; Med26_M is the middle domain of subunit 26 of ...
 854-970 1.86e-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: 41.40  E-value: 1.86e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069   854 QTPGYPDPSSPQvNPQYNPQTpgTPAMYNTDQFSPYAapsPQGSY-QPSPSPQSYHQVAPSPAGYQNTHSP--------A 924
Cdd:pfam15694   81 ETGGPPQPKSPR-CSSFSPRN--SRHETFARRSSTYA---PKGSVpSPSPRSQVLDAQVPSPLPLSQPSTPpvqakrleK 154

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 328927069   925 SYHPTP-SPMAYQASPS-----PGPVGYSPMTPGAPSPGGYNPHTPGSGIEQ 970
Cdd:pfam15694  155 PPQSSPeSSQHWLEQSDseshqRHQDGSATLLSQSVSPGCKTPLHPGENSLP 206
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 851-956 2.34e-03

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


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 40.16  E-value: 2.34e-03
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069    851 PNPQTPGYPDPSSPQVNPQYNPQTPGTPAMyntdQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQNTHSPASYHPTP 930
Cdd:smart00818   45 QHPPTHTLQPHHHIPVLPAQQPVVPQQPLM----PVPGQHSMTPTQHHQPNLPQPAQQPFQPQPLQPPQPQQPMQPQPPV 120

                            90       100
                    ....*....|....*....|....*.
gi 328927069    931 SPMAYQASPSPGPvgysPMTPGAPSP 956
Cdd:smart00818  121 HPIPPLPPQPPLP----PMFPMQPLP 142
PHA03325 PHA03325
nuclear-egress-membrane-like protein; Provisional
 800-961 2.66e-03

nuclear-egress-membrane-like protein; Provisional


Pssm-ID: 223044  Cd Length: 418  Bit Score: 41.41  E-value: 2.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  800 SQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEEYEYAFDDEPTPSPQAyggtpnpqtpgYPDPSSPQVNPQYNPQTPGTPA 879
Cdd:PHA03325  266 SSLPTSAPKRRSRRAGAMRAAAGETADLADDDGSEHSDPEPLPASLP-----------PPPVRRPRVKHPEAGKEEPDGA 334

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  880 MYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGyqnthSPASYHPTPSPMAYQASPSPGPVGYSPMTPGAPSPGGY 959
Cdd:PHA03325  335 RNAEAKEPAQPATSTSSKGSSSAQNKDSGSTGPGSSL-----AAASSFLEDDDFGSPPLDLTTSLRHMPSPSVTSAPEPP 409


                  ..
gi 328927069  960 NP 961
Cdd:PHA03325  410 SI 411
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 844-965 3.05e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 41.62  E-value: 3.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  844 PQAYGGTPNP---QTPGYPDPSSPQVNPQYNPQTPGTPAMYNTDQFSPYAAPSPQGSYQPSPSPQSYHQVAPSPAG---- 916
Cdd:PRK14951  366 PAAAAEAAAPaekKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAApaav 445

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 328927069  917 YQNTHSPASYHPTPSPMAYQASPSPGPVGYSPMTPGAPSPGGYNPHTPG 965
Cdd:PRK14951  446 ALAPAPPAQAAPETVAIPVRVAPEPAVASAAPAPAAAPAAARLTPTEEG 494
PspC_subgroup_2 NF033839
pneumococcal surface protein PspC, LPXTG-anchored form; The pneumococcal surface protein PspC, ...
 838-979 3.59e-03

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


Pssm-ID: 468202 [Multi-domain]  Cd Length: 557  Bit Score: 41.29  E-value: 3.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  838 DEPTPSPQAYGGTPNPQTPGYPDPSSPQVNPQynPQTPGTPAMYNTDQFSPYAAPSPQ-GSYQPSPSPQSYH-QVAPSPA 915
Cdd:NF033839  370 EKPKPEVKPQPETPKPEVKPQPEKPKPEVKPQ--PEKPKPEVKPQPEKPKPEVKPQPEkPKPEVKPQPEKPKpEVKPQPE 447

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  916 GYQNTHSPASYHPTPSPMAYQASPSPgPVGYSPMTP----GAPSPGGYNPHTPG--SGIEQNSSDWVTTD 979
Cdd:NF033839  448 KPKPEVKPQPETPKPEVKPQPEKPKP-EVKPQPEKPkpdnSKPQADDKKPSTPNnlSKDKQPSNQASTNE 516
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 839-945 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 328927069  839 EPTPSPQAYGG--TPNPQTPGYPDPSSPqvnPQYNPQTPGTPAMYNTDQfSPYAAPSPQGSYQPSPSPQSYHQVAPSPAG 916
Cdd:PRK07764  407 AAAPAPAAAAPaaAAAPAPAAAPQPAPA---PAPAPAPPSPAGNAPAGG-APSPPPAAAPSAQPAPAPAAAPEPTAAPAP 482

                          90       100
                  ....*....|....*....|....*....
gi 328927069  917 YQNTHSPASYHPTPSPmayQASPSPGPVG 945
Cdd:PRK07764  483 APPAAPAPAAAPAAPA---APAAPAGADD 508
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 840-957 4.35e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.12  E-value: 4.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  840 PTPSPQAYGGTPNPQTPgypDPSSPQVNPQYNPQTPGTPAmyntdqfSPYAAPSPQGSYQPSPSPQSYHQVAPSPAGYQN 919
Cdd:PRK07764  404 AAPAAAPAPAAAAPAAA---AAPAPAAAPQPAPAPAPAPA-------PPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAA 473

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 328927069  920 THSPASyhPTPSPMAYQASPSPGPVgysPMTPGAPSPG 957
Cdd:PRK07764  474 PEPTAA--PAPAPPAAPAPAAAPAA---PAAPAAPAGA 506
dnaA PRK14086
chromosomal replication initiator protein DnaA;
819-967 4.83e-03

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 40.96  E-value: 4.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  819 PNNPNTPSRAEEeyeyafddeptPSPQAYGGTPNPQTPGYPDPSSPQVNPQYnPQTPGTPAMY--NTDQFSPYAAPSPQG 896
Cdd:PRK14086   96 APPPPHARRTSE-----------PELPRPGRRPYEGYGGPRADDRPPGLPRQ-DQLPTARPAYpaYQQRPEPGAWPRAAD 163

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  897 SYQPSPSPQSYhqvaPSPAGYQnthSPASYHPTPSPMAY---QASPSPGPVGYSPMTPGA--------------PSPGGY 959
Cdd:PRK14086  164 DYGWQQQRLGF----PPRAPYA---SPASYAPEQERDREpydAGRPEYDQRRRDYDHPRPdwdrprrdrtdrpePPPGAG 236


                  ....*...
gi 328927069  960 NPHTPGSG 967
Cdd:PRK14086  237 HVHRGGPG 244
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 777-915 5.61e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 40.74  E-value: 5.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 328927069  777 GSRTPMYGSQTPLQDGSRTPHYGSQTPLHDGSRTPAQSGAWDPNNPNTPSRAEEEYEyafddeptPSPQAYGGTPNPQTP 856
Cdd:PRK07764  674 GGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASA--------PSPAADDPVPLPPEP 745

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 328927069  857 GYPDPSSPQVNPQYNPQTPGTPAmyntdqfspyAAPSPQGSYQPSPSPQSYHQVAPSPA 915
Cdd:PRK07764  746 DDPPDPAGAPAQPPPPPAPAPAA----------APAAAPPPSPPSEEEEMAEDDAPSMD 794
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 592-623 7.67e-03

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


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 35.06  E-value: 7.67e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 328927069   592 VKDIVKVIDGPHSGREGEIRHLFRSFAFLHCK 623
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH