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Conserved domains on  [gi|599352850|ref|XP_007391764|]
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uncharacterized protein PHACADRAFT_61321, partial [Phanerochaete carnosa HHB-10118-sp]

Protein Classification

CTD-interacting domain-containing protein( domain architecture ID 13015791)

CTD-interacting domain (CID)-containing protein similar to Caenorhabditis elegans polyadenylation and cleavage factor homolog 11 (Pcf11)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 26-152 1.91e-59

CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied protein is Saccharomyces cerevisiae Pcf11, also called protein 1 of CF I, an essential subunit of the cleavage factor IA (CFIA) complex which is required for polyadenylation-dependent pre-mRNA 3'-end processing and RNA polymerase (Pol) II (RNAP II) transcription termination. Human Pcf11, also referred to as pre-mRNA cleavage complex 2 protein Pcf11, has been shown to enhance degradation of RNAP II-associated nascent RNA and transcriptional termination. The family also includes plant PCFS4 (Pcf11-similar-4 protein or Polyadenylation and cleavage factor homolog 4) and Caenorhabditis elegans Polyadenylation and cleavage factor homolog 11. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Pcf11 CID preferentially interacts with CTD phosphorylated at Ser2. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


:

Pssm-ID: 340779  Cd Length: 127  Bit Score: 194.71  E-value: 1.91e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  26 RRDYVARLADLTVNSRPIIQTLSMIAQEYSRYADIVVSCIEQHIRRVPPWMKLPAFYLLDAISKNVYEPYARHFNSVVVK 105
Cdd:cd16982    1 VEEYRSALAELTFNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIVKNVGGPYTSLFSPNLVD 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 599352850 106 LFLDTYEQVDQSTRGKMEEMLLTWRTGAPNGRELFGPIAQVAIERQI 152
Cdd:cd16982   81 LFLDAYRLVDEKTRKKLEKLLNTWKTVFPNGKLLFPDEVLNKIERAL 127
PHA03369 super family cl25753
capsid maturational protease; Provisional
 156-310 1.04e-04

capsid maturational protease; Provisional


The actual alignment was detected with superfamily member PHA03369:

Pssm-ID: 223061 [Multi-domain]  Cd Length: 663  Bit Score: 45.38  E-value: 1.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850 156 EDSPVSAAQVLSELEFV--LSAKQRSLQTNPYDKQTQNHVSVLYQLRKLVQTGVSQEELAQILTQLRTMSPAQPSvhqhv 233
Cdd:PHA03369 286 GSSDESPEWKTFYEALAdqLNNLYKLLRTIYKHKDETVIEQYLIEGRKLFSTINGLKAHNEILKTASLTAPSRVL----- 360

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 599352850 234 APTPHVPQVPYQVPAPATQPPVQPAYPPVQPSYLPQPSYSAVYPPVKTE-AAPAPVPPTQPVASTSSAAGSSTASVVP 310
Cdd:PHA03369 361 AAAAKVAVIAAPQTHTGPADRQRPQRPDGIPYSVPARSPMTAYPPVPQFcGDPGLVSPYNPQSPGTSYGPEPVGPVPP 438
 
Name Accession Description Interval E-value
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 26-152 1.91e-59

CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied protein is Saccharomyces cerevisiae Pcf11, also called protein 1 of CF I, an essential subunit of the cleavage factor IA (CFIA) complex which is required for polyadenylation-dependent pre-mRNA 3'-end processing and RNA polymerase (Pol) II (RNAP II) transcription termination. Human Pcf11, also referred to as pre-mRNA cleavage complex 2 protein Pcf11, has been shown to enhance degradation of RNAP II-associated nascent RNA and transcriptional termination. The family also includes plant PCFS4 (Pcf11-similar-4 protein or Polyadenylation and cleavage factor homolog 4) and Caenorhabditis elegans Polyadenylation and cleavage factor homolog 11. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Pcf11 CID preferentially interacts with CTD phosphorylated at Ser2. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340779  Cd Length: 127  Bit Score: 194.71  E-value: 1.91e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  26 RRDYVARLADLTVNSRPIIQTLSMIAQEYSRYADIVVSCIEQHIRRVPPWMKLPAFYLLDAISKNVYEPYARHFNSVVVK 105
Cdd:cd16982    1 VEEYRSALAELTFNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIVKNVGGPYTSLFSPNLVD 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 599352850 106 LFLDTYEQVDQSTRGKMEEMLLTWRTGAPNGRELFGPIAQVAIERQI 152
Cdd:cd16982   81 LFLDAYRLVDEKTRKKLEKLLNTWKTVFPNGKLLFPDEVLNKIERAL 127
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
28-142 7.35e-23

domain present in proteins, which are involved in regulation of nuclear pre-mRNA;


Pssm-ID: 214731  Cd Length: 124  Bit Score: 94.27  E-value: 7.35e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850    28 DYVARLADLTvNSRPIIQTLSMIAQEYSRYADIVVSCIEQHIRRVPPWMKLPAFYLLDAISKNVYEPYARHFNSVVVKLF 107
Cdd:smart00582   1 AFEQKLESLN-NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVF 79

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 599352850   108 LDTYEQVD----QSTRGKMEEMLLTWRTgapngRELFGP 142
Cdd:smart00582  80 QDALRRVLgaapEELKKKIRRLLNIWEE-----RGIFPP 113
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 30-142 3.46e-16

CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. This domain is known as the CTD-interacting domain (CID).


Pssm-ID: 461442  Cd Length: 117  Bit Score: 74.94  E-value: 3.46e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850   30 VARLADLTvNSRPIIQTLSMIAQEYSRYADIVVSCIEQHIRRVPPWMKLPAFYLLDAISKNVY----EPYARHFNSVVVK 105
Cdd:pfam04818   4 EKKLSSLN-NSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRkkgkSEFADAFEPVLPE 82

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 599352850  106 LFLDTYEQVDQSTRGKMEEMLLTWRTgapngRELFGP 142
Cdd:pfam04818  83 AFASAYKKCDEKLKKKLERLLNIWEE-----RNVFSP 114
PHA03369 PHA03369
capsid maturational protease; Provisional
 156-310 1.04e-04

capsid maturational protease; Provisional


Pssm-ID: 223061 [Multi-domain]  Cd Length: 663  Bit Score: 45.38  E-value: 1.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850 156 EDSPVSAAQVLSELEFV--LSAKQRSLQTNPYDKQTQNHVSVLYQLRKLVQTGVSQEELAQILTQLRTMSPAQPSvhqhv 233
Cdd:PHA03369 286 GSSDESPEWKTFYEALAdqLNNLYKLLRTIYKHKDETVIEQYLIEGRKLFSTINGLKAHNEILKTASLTAPSRVL----- 360

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 599352850 234 APTPHVPQVPYQVPAPATQPPVQPAYPPVQPSYLPQPSYSAVYPPVKTE-AAPAPVPPTQPVASTSSAAGSSTASVVP 310
Cdd:PHA03369 361 AAAAKVAVIAAPQTHTGPADRQRPQRPDGIPYSVPARSPMTAYPPVPQFcGDPGLVSPYNPQSPGTSYGPEPVGPVPP 438
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 174-292 1.66e-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: 44.76  E-value: 1.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  174 SAKQRSLQTNPYDKQTQNHVSVLYQLrklvqtgvsqeelaqiltqlrtmSPAQPSVHQHVAPTPHVPQVPYQVPAPATQP 253
Cdd:pfam03154 161 SAQQQILQTQPPVLQAQSGAASPPSP-----------------------PPPGTTQAATAGPTPSAPSVPPQGSPATSQP 217

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 599352850  254 PVQPAY-----------PPVQPSYLPQPsysavYPPVktEAAPAPVPPTQ 292
Cdd:pfam03154 218 PNQTQStaaphtliqqtPTLHPQRLPSP-----HPPL--QPMTQPPPPSQ 260
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 222-293 1.11e-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: 1.11e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 599352850   222 MSPAQPSVHQH-VAPTP-HVPQVPYQVPAPATQPPVQPaypPVQPSYLPQPSYSavyPPVKTEAAPAPVPPTQP 293
Cdd:smart00818  61 LPAQQPVVPQQpLMPVPgQHSMTPTQHHQPNLPQPAQQ---PFQPQPLQPPQPQ---QPMQPQPPVHPIPPLPP 128
 
Name Accession Description Interval E-value
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 26-152 1.91e-59

CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied protein is Saccharomyces cerevisiae Pcf11, also called protein 1 of CF I, an essential subunit of the cleavage factor IA (CFIA) complex which is required for polyadenylation-dependent pre-mRNA 3'-end processing and RNA polymerase (Pol) II (RNAP II) transcription termination. Human Pcf11, also referred to as pre-mRNA cleavage complex 2 protein Pcf11, has been shown to enhance degradation of RNAP II-associated nascent RNA and transcriptional termination. The family also includes plant PCFS4 (Pcf11-similar-4 protein or Polyadenylation and cleavage factor homolog 4) and Caenorhabditis elegans Polyadenylation and cleavage factor homolog 11. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Pcf11 CID preferentially interacts with CTD phosphorylated at Ser2. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340779  Cd Length: 127  Bit Score: 194.71  E-value: 1.91e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  26 RRDYVARLADLTVNSRPIIQTLSMIAQEYSRYADIVVSCIEQHIRRVPPWMKLPAFYLLDAISKNVYEPYARHFNSVVVK 105
Cdd:cd16982    1 VEEYRSALAELTFNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIVKNVGGPYTSLFSPNLVD 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 599352850 106 LFLDTYEQVDQSTRGKMEEMLLTWRTGAPNGRELFGPIAQVAIERQI 152
Cdd:cd16982   81 LFLDAYRLVDEKTRKKLEKLLNTWKTVFPNGKLLFPDEVLNKIERAL 127
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
28-142 7.35e-23

domain present in proteins, which are involved in regulation of nuclear pre-mRNA;


Pssm-ID: 214731  Cd Length: 124  Bit Score: 94.27  E-value: 7.35e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850    28 DYVARLADLTvNSRPIIQTLSMIAQEYSRYADIVVSCIEQHIRRVPPWMKLPAFYLLDAISKNVYEPYARHFNSVVVKLF 107
Cdd:smart00582   1 AFEQKLESLN-NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVF 79

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 599352850   108 LDTYEQVD----QSTRGKMEEMLLTWRTgapngRELFGP 142
Cdd:smart00582  80 QDALRRVLgaapEELKKKIRRLLNIWEE-----RGIFPP 113
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 27-129 3.09e-19

CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several eukaryotic RNA-processing factors including yeast proteins, Pcf11 and Nrd1, and vertebrate proteins, CTD-associated factors 8 (SCAF8) and Regulation of nuclear pre-mRNA domain-containing proteins (such as RPRD1 and RPRD2). Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340766  Cd Length: 123  Bit Score: 83.72  E-value: 3.09e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  27 RDYVARLADLTVNSRPIIQTLSMIAQEYSRYADIVVSCIEQHIRRVPPWMKLPAFYLLDAISKNV---YEPYARHFNSVV 103
Cdd:cd03562    1 KAFNSKLEELSDLSQQSITTLTKWAIHHIKHSRPIVTVIEREIRKCKPNRKLTFLYLIDSIIRNSkrkGPEFTKDFSPVI 80

                         90       100
                 ....*....|....*....|....*.
gi 599352850 104 VKLFLDTYEQVDQSTRGKMEEMLLTW 129
Cdd:cd03562   81 VELFKHVYSETDEDCKKKLGRVLSIW 106
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 30-142 3.46e-16

CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. This domain is known as the CTD-interacting domain (CID).


Pssm-ID: 461442  Cd Length: 117  Bit Score: 74.94  E-value: 3.46e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850   30 VARLADLTvNSRPIIQTLSMIAQEYSRYADIVVSCIEQHIRRVPPWMKLPAFYLLDAISKNVY----EPYARHFNSVVVK 105
Cdd:pfam04818   4 EKKLSSLN-NSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRkkgkSEFADAFEPVLPE 82

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 599352850  106 LFLDTYEQVDQSTRGKMEEMLLTWRTgapngRELFGP 142
Cdd:pfam04818  83 AFASAYKKCDEKLKKKLERLLNIWEE-----RNVFSP 114
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 32-142 3.98e-06

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; Regulation of nuclear pre-mRNA domain-containing protein 1B (RPRD1B) is also called Cell cycle-related and expression-elevated protein in tumor (CREPT). RPRD1B is a CID (CTD-Interacting Domain) containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1B form homodimers and heterodimers with RPRD1A through their coiled-coil domains. Both RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. RPRD1B is highly expressed during tumorigenesis and in endometrial cancer, has been shown to promote tumor growth by accelerating the cell cycle. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340809  Cd Length: 129  Bit Score: 46.54  E-value: 3.98e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  32 RLADLTvNSRPIIQTLSMIAQEYSRYADIVVSCIEQHIRRVPPWMKLPAFYLLDAI---SKNVYEPYARHFNSVVVKLFL 108
Cdd:cd17012   10 KLSELS-NSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFLYLANDViqnSKRKGPEFTREFESVLVDAFS 88

                         90       100       110
                 ....*....|....*....|....*....|....
gi 599352850 109 DTYEQVDQSTRGKMEEMLLTWRTgapngRELFGP 142
Cdd:cd17012   89 HVAREADEGCKKPLERLLNIWQE-----RSVYGG 117
CID_RPRD1A cd17011
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; ...
 32-146 9.32e-06

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; Regulation of nuclear pre-mRNA domain-containing protein 1A (RPRD1A) is also called Cyclin-dependent kinase inhibitor 2B-related protein or p15INK4B-related protein (P15RS). RPRD1A is a CID (CTD-Interacting Domain) containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1A form homodimers and heterodimers with RPRD1B through their coiled-coil domains. Both RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340808  Cd Length: 128  Bit Score: 45.42  E-value: 9.32e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  32 RLADLTvNSRPIIQTLSMIAQEYSRYADIVVSCIEQHIRRVPPWMKLPAFYLLDAI---SKNVYEPYARHFNSVVVKLFL 108
Cdd:cd17011    9 KLSELS-NSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFLYLANDViqnSKRKGPEFTKDFAPVIVEAFK 87

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 599352850 109 DTYEQVDQSTRGKMEEMLLTWRTGAPNGRELFGPIAQV 146
Cdd:cd17011   88 HVSSETDESCKKHLGRVLSIWEERSVYENDVLEQLKQA 125
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 30-141 7.17e-05

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; This family is composed of Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A), 1B (RPRD1B), 2 (RPRD2), yeast Rtt103, and similar proteins. RPRD1A, RPRD1B, and RPRD2 are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. Yeast transcription termination factor Rtt103 is a CID containing protein that functions in DNA damage response. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340778  Cd Length: 125  Bit Score: 42.57  E-value: 7.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  30 VARLADLTvNSRPIIQTLSMIAQEYSRYADIVVSCIEQHIRRVPPWMKLPAFYL-----LDAISKNVYEpYARHFNSVVV 104
Cdd:cd16981    5 EKKLRSLN-NTQQSIQTLSLWCLFHKKHAKQIVKIWLKELKKAKPERKLTLLYLandvlQNSRRKGAPE-FVEAFKKVLP 82

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 599352850 105 KLFLDTYEQVDQSTRGKMEEMLLTWRTgapngRELFG 141
Cdd:cd16981   83 EALALVRSEGDESVRKKVLRVLNIWEE-----RNVFG 114
PHA03369 PHA03369
capsid maturational protease; Provisional
 156-310 1.04e-04

capsid maturational protease; Provisional


Pssm-ID: 223061 [Multi-domain]  Cd Length: 663  Bit Score: 45.38  E-value: 1.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850 156 EDSPVSAAQVLSELEFV--LSAKQRSLQTNPYDKQTQNHVSVLYQLRKLVQTGVSQEELAQILTQLRTMSPAQPSvhqhv 233
Cdd:PHA03369 286 GSSDESPEWKTFYEALAdqLNNLYKLLRTIYKHKDETVIEQYLIEGRKLFSTINGLKAHNEILKTASLTAPSRVL----- 360

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 599352850 234 APTPHVPQVPYQVPAPATQPPVQPAYPPVQPSYLPQPSYSAVYPPVKTE-AAPAPVPPTQPVASTSSAAGSSTASVVP 310
Cdd:PHA03369 361 AAAAKVAVIAAPQTHTGPADRQRPQRPDGIPYSVPARSPMTAYPPVPQFcGDPGLVSPYNPQSPGTSYGPEPVGPVPP 438
PHA02682 PHA02682
ORF080 virion core protein; Provisional
 181-291 1.16e-04

ORF080 virion core protein; Provisional


Pssm-ID: 177464 [Multi-domain]  Cd Length: 280  Bit Score: 44.47  E-value: 1.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850 181 QTNPYDKQTQNHVSVLYQLRKLVQTGVSQEELAQILTQLRTMSPAQPSVHQHVAPTPHVPQVPYQVPAPATQPPVQPAYP 260
Cdd:PHA02682  46 DVDPLDKYSVKEAGRYYQSRLKANSACMQRPSGQSPLAPSPACAAPAPACPACAPAAPAPAVTCPAPAPACPPATAPTCP 125

                         90       100       110
                 ....*....|....*....|....*....|.
gi 599352850 261 PVQPSYLPQPSYSAVyPPVKTEAAPAPVPPT 291
Cdd:PHA02682 126 PPAVCPAPARPAPAC-PPSTRQCPPAPPLPT 155
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 174-292 1.66e-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: 44.76  E-value: 1.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  174 SAKQRSLQTNPYDKQTQNHVSVLYQLrklvqtgvsqeelaqiltqlrtmSPAQPSVHQHVAPTPHVPQVPYQVPAPATQP 253
Cdd:pfam03154 161 SAQQQILQTQPPVLQAQSGAASPPSP-----------------------PPPGTTQAATAGPTPSAPSVPPQGSPATSQP 217

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 599352850  254 PVQPAY-----------PPVQPSYLPQPsysavYPPVktEAAPAPVPPTQ 292
Cdd:pfam03154 218 PNQTQStaaphtliqqtPTLHPQRLPSP-----HPPL--QPMTQPPPPSQ 260
PHA03247 PHA03247
large tegument protein UL36; Provisional
 200-293 2.07e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 44.54  E-value: 2.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  200 RKLVQTGVSQEELAQILTQLRTMSPAQPSVHQHVAPTPHVPQVPYQVPAPATQP-PVQPAYPPVQPSYLPQPSYSAVYP- 277
Cdd:PHA03247 2884 RRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPrPQPPLAPTTDPAGAGEPSGAVPQPw 2963

                          90       100       110
                  ....*....|....*....|....*....|..
gi 599352850  278 ----------------PVKTEAAPAPVPPTQP 293
Cdd:PHA03247 2964 lgalvpgrvavprfrvPQPAPSREAPASSTPP 2995
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 31-109 2.08e-04

CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; This subfamily includes SR-related and CTD-associated factors 8 (SCAF8) and 4 (SCAF4), and similar proteins. SCAF4 is also called Splicing factor arginine serine rich 15 (SFRS15). Members may play roles in mRNA processing. Both SCAF4 and SCAF8 contains a CTD-interacting domain (CID) at the amino terminus and a Ser/Arg-rich domain followed by an RNA recognition motif. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340780  Cd Length: 131  Bit Score: 41.44  E-value: 2.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  31 ARLADLTVNSRPI----IQTLSMIAQEYSRYADIVVSCIEQHIRRVPPWMKLPAFYLLDAI---SKNVY----EPYARHF 99
Cdd:cd16983    5 KELSSLLDSKPPVskskINAITKLAIKAIKFYKHVVQSVEKFIQKCKPEYKLPGLYVIDSIirqSRHQYgkekDVYAPRF 84

                         90
                 ....*....|
gi 599352850 100 NSVVVKLFLD 109
Cdd:cd16983   85 AKNLSKTFLN 94
VHS_ENTH_ANTH cd00197
VHS, ENTH and ANTH domain superfamily; This superfamily is composed of proteins containing a ...
 35-130 3.17e-04

VHS, ENTH and ANTH domain superfamily; This superfamily is composed of proteins containing a VHS, CID, ENTH, or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The CTD-Interacting Domain (CID) is present in several RNA-processing factors and binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase II (RNAP II or Pol II). The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-Terminal Homology (ANTH) domain. VHS, ENTH, and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH and ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the Trans-Golgi Network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding.


Pssm-ID: 340764  Cd Length: 115  Bit Score: 40.49  E-value: 3.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  35 DLTVNSRPIIQTLSMIAQEYSRYADIVVSCIEQHIRRVPPWMKLPAFYLLDAISKNVYEPYARHF--NSVVVKLFLD--- 109
Cdd:cd00197   12 ENMGPDWPLIMEICDLINETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERFHQEVasNDFAVELLKFdks 91

                         90       100
                 ....*....|....*....|...
gi 599352850 110 --TYEQVDQSTRGKMEEMLLTWR 130
Cdd:cd00197   92 glLGDDVSTNVREKAIELVQLWA 114
PHA03247 PHA03247
large tegument protein UL36; Provisional
 217-294 1.07e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 42.23  E-value: 1.07e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 599352850  217 TQLRTMSPAQPSVHQHVAPTPHVPQVPYQVPAPATQPPVQPAyPPVQPSYLPQPsysAVYPPVKTEAAPAPVPPTQPV 294
Cdd:PHA03247 2879 ARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQ-PQPPPPPQPQP---PPPPPPRPQPPLAPTTDPAGA 2952
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 222-293 1.11e-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: 1.11e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 599352850   222 MSPAQPSVHQH-VAPTP-HVPQVPYQVPAPATQPPVQPaypPVQPSYLPQPSYSavyPPVKTEAAPAPVPPTQP 293
Cdd:smart00818  61 LPAQQPVVPQQpLMPVPgQHSMTPTQHHQPNLPQPAQQ---PFQPQPLQPPQPQ---QPMQPQPPVHPIPPLPP 128
PHA03247 PHA03247
large tegument protein UL36; Provisional
 219-293 1.64e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 41.85  E-value: 1.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  219 LRTMSPAQPSvhqhvAPTPHVPQVP--YQVPAPATQPPVQP-AYPPVQPSYLPQPSYSA---VYPPVKTEAAPAPVPPTQ 292
Cdd:PHA03247 2862 VRRRPPSRSP-----AAKPAAPARPpvRRLARPAVSRSTESfALPPDQPERPPQPQAPPppqPQPQPPPPPQPQPPPPPP 2936


                  .
gi 599352850  293 P 293
Cdd:PHA03247 2937 P 2937
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 215-293 1.79e-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: 39.39  E-value: 1.79e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850   215 ILTQLRTMSPAQP----SVHQHVAPTP-HVPQVPYQVPAPATQPPVQPayPPVQPSYLPQPSYSAVyPPVKTEAAPAPVP 289
Cdd:smart00818  60 VLPAQQPVVPQQPlmpvPGQHSMTPTQhHQPNLPQPAQQPFQPQPLQP--PQPQQPMQPQPPVHPI-PPLPPQPPLPPMF 136


                   ....
gi 599352850   290 PTQP 293
Cdd:smart00818 137 PMQP 140
PHA02030 PHA02030
hypothetical protein
 210-293 1.97e-03

hypothetical protein


Pssm-ID: 222843 [Multi-domain]  Cd Length: 336  Bit Score: 40.73  E-value: 1.97e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850 210 EELAQILTQLRTMSPAQPSVHQhVAPTPHVPQVPYQVPAPATQPPVQPAYPPV-QPSYLPQ-PSYSAVYPPVKTEAAPAP 287
Cdd:PHA02030 250 GEDLIIKPKSKAAGSNLPAVPN-VAADAGSAAAPAVPAAAAAVAQAAPSVPQVpNVAVLPDvPQVAPVAAPAAPEVPAVP 328


                 ....*.
gi 599352850 288 VPPTQP 293
Cdd:PHA02030 329 VVPAAP 334
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 211-294 2.73e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 40.56  E-value: 2.73e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850 211 ELAQILTQLRTMSPAQPSVHQHVAPTPHVPQvpyqvPAPATQPPVQPAYPPvqPSYLPQPSySAVYPPVKTEAAPAPVPP 290
Cdd:PRK14950 352 ELAVIEALLVPVPAPQPAKPTAAAPSPVRPT-----PAPSTRPKAAAAANI--PPKEPVRE-TATPPPVPPRPVAPPVPH 423


                 ....
gi 599352850 291 TQPV 294
Cdd:PRK14950 424 TPES 427
PHA03247 PHA03247
large tegument protein UL36; Provisional
 223-293 2.76e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 41.08  E-value: 2.76e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 599352850  223 SPAQPSVHQHVAPTPHVPQVPYQVPAPATQPPVQPAyPPVQPsyLPQPSysavyPPVKTEAAPAPVPPTQP 293
Cdd:PHA03247 2877 APARPPVRRLARPAVSRSTESFALPPDQPERPPQPQ-APPPP--QPQPQ-----PPPPPQPQPPPPPPPRP 2939
SAP130_C pfam16014
Histone deacetylase complex subunit SAP130 C-terminus;
226-294 2.94e-03

Histone deacetylase complex subunit SAP130 C-terminus;


Pssm-ID: 464973 [Multi-domain]  Cd Length: 371  Bit Score: 40.30  E-value: 2.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  226 QPSVHQHVAP--TPHVPQVPYQV---PAPATQPPVQ-----------PAYPPVQPSYL--PQPSYSAVYPPVKTEAAPAP 287
Cdd:pfam16014  23 KPDIHVAVAPpvTVAVEALPGQNseqQTASASPPSQhpaqaiptilaPAAPPSQPSVVlsTLPAAMAVTPPIPASMANVV 102


                  ....*..
gi 599352850  288 VPPTQPV 294
Cdd:pfam16014 103 APPTQPA 109
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 135-294 3.11e-03

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 40.84  E-value: 3.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  135 NGRELFGPIAQVAIER---QIWGGEDSPVSAAQVLSELEFVLSAKQRSLQTNP---------------------YDKQTQ 190
Cdd:PRK10263  312 NGAPITEPVAVAAAATtatQSWAAPVEPVTQTPPVASVDVPPAQPTVAWQPVPgpqtgepviapapegypqqsqYAQPAV 391

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  191 NHVSVLYQLRKLVQTGVSQEELAQILTQLRTMSPAQPSVHQHVAPTPHVPQVPYQVPAPATQPPVQPayppvQPSYLPQP 270
Cdd:PRK10263  392 QYNEPLQQPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQQSTFAP-----QSTYQTEQ 466

                         170       180
                  ....*....|....*....|....
gi 599352850  271 SYSAVYPPVKTEAAPAPVPPTQPV 294
Cdd:PRK10263  467 TYQQPAAQEPLYQQPQPVEQQPVV 490
PRK11633 PRK11633
cell division protein DedD; Provisional
 217-294 4.74e-03

cell division protein DedD; Provisional


Pssm-ID: 236940 [Multi-domain]  Cd Length: 226  Bit Score: 38.83  E-value: 4.74e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 599352850 217 TQLRTMSPAQPSVHQHVAPTPHVPQVPyqvpapaTQPPVQPAYPPVQPSYLPQPSysavyPPVKTEAAPAPVPPTQPV 294
Cdd:PRK11633  73 EAVRAGDAAAPSLDPATVAPPNTPVEP-------EPAPVEPPKPKPVEKPKPKPK-----PQQKVEAPPAPKPEPKPV 138
PRK07994 PRK07994
DNA polymerase III subunits gamma and tau; Validated
 204-294 5.73e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236138 [Multi-domain]  Cd Length: 647  Bit Score: 39.85  E-value: 5.73e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850 204 QTGVSQEELAQILTQLRTMSPAQPsvhqhVAPTPHVPQVPYQVPAPATQPPVQPAYPPVQPSYLPQPSYSAVYPPVKTEA 283
Cdd:PRK07994 367 EPEVPPQSAAPAASAQATAAPTAA-----VAPPQAPAVPPPPASAPQQAPAVPLPETTSQLLAARQQLQRAQGATKAKKS 441

                         90
                 ....*....|.
gi 599352850 284 APAPVPPTQPV 294
Cdd:PRK07994 442 EPAAASRARPV 452
Cuticle_3 pfam11018
Pupal cuticle protein C1; Insect cuticles are composite structures whose mechanical properties ...
 213-293 8.45e-03

Pupal cuticle protein C1; Insect cuticles are composite structures whose mechanical properties are optimized for biological function. The major components are the chitin filament system and the cuticular proteins, and the cuticle's properties are determined largely by the interactions between these two sets of molecules. The proteins can be ordered by species.


Pssm-ID: 431611 [Multi-domain]  Cd Length: 182  Bit Score: 37.83  E-value: 8.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599352850  213 AQILTQLRTMSPAQPSVHQ-HVAPTPHVPQVPYQVPAPATQPPVQPAYPPVQPSYLPQPSYSAVYPPVKT--EAAPAPVP 289
Cdd:pfam11018  56 APVVTKSAYAAPAPVVTTYaHAAPAPVVAKTVYAAPAVVVYAAPAPVVAKTVTYAAPAVHYAAPAPVVAKtvYAAPAVQH 135


                  ....
gi 599352850  290 PTQP 293
Cdd:pfam11018 136 YAAP 139
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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