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Conserved domains on  [gi|268638308|ref|XP_002649209|]
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RanBP2-type zinc finger [Dictyostelium discoideum AX4]

Protein Classification

nucleoporin( domain architecture ID 10614059)

nucleoporin is a component of the nuclear pore complex (NPC) that mediates the selective trafficking of proteins and RNAs through the nuclear envelope

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 1529-1606 8.28e-09

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


:

Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 55.31  E-value: 8.28e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308  1529 FGSASSNSSSVFGQTTTKPSTGSSVFGQNS--------SSVFGQTTTPSSGTGVFGQNSSSvfGQTSTGTGVFGQNSSSI 1600
Cdd:pfam13634    3 FGAATSTSGGLFGNTSTTAASGGGLFGAAStatattsgGGLFGNSSSNAPSGGLFGATNTT--TQTATGGGLFGNNAATT 80


                   ....*.
gi 268638308  1601 FGQSNG 1606
Cdd:pfam13634   81 TSTTGG 86
KREPA super family cl49620
Kinetoplastid RNA Editing Protein A (KREPA); The KREPA 1-6 (TbMP81, 63, 42, 24, 19, and 18, ...
 2472-2535 2.53e-05

Kinetoplastid RNA Editing Protein A (KREPA); The KREPA 1-6 (TbMP81, 63, 42, 24, 19, and 18, respectively) proteins are components of the RNA editing complex of parasitic protozoans such as Trypanosoma and Leishmania species. These parasites have a uniquely organized mitochondrial genome, the kinetoplast. Most kinetoplast-transcribed mRNAs are cryptic and encode multiple subunits for the electron transport chain following maturation through a uridine insertion/deletion process called RNA editing. KREPAs participate in the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. The editosome, a high molecular mass enzyme complex, carries out the reaction with the help of critical enzymes and structural proteins. Five related editosome proteins KREPA1 (TbMP81), KREPA2 (TbMP63), KREPA3 (TbMP42), KREPA4 (TbMP24), KREPA5 (TbMP19), and KREPA6 (TbMP18) play critical roles in the structure and auxiliary functions of the editing process without any predicted catalytic function. The KREPA1, KREPA2, and KREPA3 proteins contain C2H2 zinc finger motifs and KREPA4 and KREPA6, contain RNA-binding domains but all have a conserved C-terminal sequences that resemble an oligonucleotide-binding (OB)-fold domain. Thus, this group of five proteins is likely to be involved in protein-protein and/or protein-RNA interactions. RNA editing is crucial for the parasite's survival in both its bloodstream and procyclic form life cycle stages which allows the parasite to adapt to its environment and maintain its viability.


The actual alignment was detected with superfamily member cd23959:

Pssm-ID: 483960 [Multi-domain]  Cd Length: 424  Bit Score: 49.87  E-value: 2.53e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 268638308 2472 TLLSSSFTPPSFAPPSFAPSSF-APSSFAPPSFAPPSFAPSSFAPSSFAPPSFAPP-KPENTSTPT 2535
Cdd:cd23959   180 GEVASPFASGTVSASPFATATDtAPSSGAPDGFPAEASAPSPFAAPASAASFPAAPvANGEAATPT 245
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 9-167 7.75e-04

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 44.33  E-value: 7.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308    9 IKRYKEQLKKPLFKNEALYQLTKLYLSleneinENELDECKDYFNQL-KQSGVLKESQKELKEITIDfqtiTKQYDLAEQ 87
Cdd:COG2956    96 EELLEKLLELDPDDAEALRLLAEIYEQ------EGDWEKAIEVLERLlKLGPENAHAYCELAELYLE----QGDYDEAIE 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308   88 SLQSAIKSYPDNLNFLLKNINLLSINKKY---YEFFKSIKDSKIKYQRDLKYLNFIIKQIDNV--AIKAIKESVEEIQAN 162
Cdd:COG2956   166 ALEKALKLDPDCARALLLLAELYLEQGDYeeaIAALERALEQDPDYLPALPRLAELYEKLGDPeeALELLRKALELDPSD 245


                  ....*
gi 268638308  163 TMLLN 167
Cdd:COG2956   246 DLLLA 250
PHA02682 super family cl31817
ORF080 virion core protein; Provisional
 2479-2595 8.00e-04

ORF080 virion core protein; Provisional


The actual alignment was detected with superfamily member PHA02682:

Pssm-ID: 177464 [Multi-domain]  Cd Length: 280  Bit Score: 44.47  E-value: 8.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308 2479 TPPSFAPPSFAPSSFAPSSfAPPSFAPPSFAPssfAPSSFAPPSFAPPKPENTSTPTSSIFGSfSSQPSGGGISAFGPVS 2558
Cdd:PHA02682   80 SPLAPSPACAAPAPACPAC-APAAPAPAVTCP---APAPACPPATAPTCPPPAVCPAPARPAP-ACPPSTRQCPPAPPLP 154

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 268638308 2559 SNSSSPfgsgfgsASIPSFGQSQVNPLTInPTSTSPT 2595
Cdd:PHA02682  155 TPKPAP-------AAKPIFLHNQLPPPDY-PAASCPT 183
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 1754-1831 8.28e-04

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


:

Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 41.06  E-value: 8.28e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308  1754 NNKPSSLFAPTAFGGNAPPTTSTAveSSKLFGGGGITFNAPNIFGNNSNPSNlfgsgNNNSSSLFGGNSTTNPPP----L 1829
Cdd:pfam13634   16 NTSTTAASGGGLFGAASTATATTS--GGGLFGNSSSNAPSGGLFGATNTTTQ-----TATGGGLFGNNAATTTSTtgggL 88


                   ..
gi 268638308  1830 FG 1831
Cdd:pfam13634   89 FG 90
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 2344-2426 6.20e-03

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


:

Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 38.37  E-value: 6.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308  2344 TAFGGNAPPTTStavdsskLFGGGGSNTITfnAPTLFGNNNNSNPS----NLFGSGNNN--SSSLFGGNSTTIQPSQ--S 2415
Cdd:pfam13634    1 GLFGAATSTSGG-------LFGNTSTTAAS--GGGLFGAASTATATtsggGLFGNSSSNapSGGLFGATNTTTQTATggG 71

                           90
                   ....*....|.
gi 268638308  2416 LFGTKSTETKS 2426
Cdd:pfam13634   72 LFGNNAATTTS 82
 
Name Accession Description Interval E-value
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 1529-1606 8.28e-09

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 55.31  E-value: 8.28e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308  1529 FGSASSNSSSVFGQTTTKPSTGSSVFGQNS--------SSVFGQTTTPSSGTGVFGQNSSSvfGQTSTGTGVFGQNSSSI 1600
Cdd:pfam13634    3 FGAATSTSGGLFGNTSTTAASGGGLFGAAStatattsgGGLFGNSSSNAPSGGLFGATNTT--TQTATGGGLFGNNAATT 80


                   ....*.
gi 268638308  1601 FGQSNG 1606
Cdd:pfam13634   81 TSTTGG 86
KREPA2 cd23959
Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of ...
 2472-2535 2.53e-05

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


Pssm-ID: 467780 [Multi-domain]  Cd Length: 424  Bit Score: 49.87  E-value: 2.53e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 268638308 2472 TLLSSSFTPPSFAPPSFAPSSF-APSSFAPPSFAPPSFAPSSFAPSSFAPPSFAPP-KPENTSTPT 2535
Cdd:cd23959   180 GEVASPFASGTVSASPFATATDtAPSSGAPDGFPAEASAPSPFAAPASAASFPAAPvANGEAATPT 245
PHA03377 PHA03377
EBNA-3C; Provisional
 2469-2537 3.64e-04

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 46.58  E-value: 3.64e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308 2469 PKVTllSSSFTPPSFAPPSFAPSSFAPSSFAPPSFAPPSFAPSSFAPSSFAPPSFAPPKP-ENTSTPTSS 2537
Cdd:PHA03377  553 PKVS--PSDRGPPKASPPVMAPPSTGPRVMATPSTGPRDMAPPSTGPRQQAKCKDGPPASgPHEKQPPSS 620
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 9-167 7.75e-04

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 44.33  E-value: 7.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308    9 IKRYKEQLKKPLFKNEALYQLTKLYLSleneinENELDECKDYFNQL-KQSGVLKESQKELKEITIDfqtiTKQYDLAEQ 87
Cdd:COG2956    96 EELLEKLLELDPDDAEALRLLAEIYEQ------EGDWEKAIEVLERLlKLGPENAHAYCELAELYLE----QGDYDEAIE 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308   88 SLQSAIKSYPDNLNFLLKNINLLSINKKY---YEFFKSIKDSKIKYQRDLKYLNFIIKQIDNV--AIKAIKESVEEIQAN 162
Cdd:COG2956   166 ALEKALKLDPDCARALLLLAELYLEQGDYeeaIAALERALEQDPDYLPALPRLAELYEKLGDPeeALELLRKALELDPSD 245


                  ....*
gi 268638308  163 TMLLN 167
Cdd:COG2956   246 DLLLA 250
PHA02682 PHA02682
ORF080 virion core protein; Provisional
 2479-2595 8.00e-04

ORF080 virion core protein; Provisional


Pssm-ID: 177464 [Multi-domain]  Cd Length: 280  Bit Score: 44.47  E-value: 8.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308 2479 TPPSFAPPSFAPSSFAPSSfAPPSFAPPSFAPssfAPSSFAPPSFAPPKPENTSTPTSSIFGSfSSQPSGGGISAFGPVS 2558
Cdd:PHA02682   80 SPLAPSPACAAPAPACPAC-APAAPAPAVTCP---APAPACPPATAPTCPPPAVCPAPARPAP-ACPPSTRQCPPAPPLP 154

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 268638308 2559 SNSSSPfgsgfgsASIPSFGQSQVNPLTInPTSTSPT 2595
Cdd:PHA02682  155 TPKPAP-------AAKPIFLHNQLPPPDY-PAASCPT 183
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 1754-1831 8.28e-04

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 41.06  E-value: 8.28e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308  1754 NNKPSSLFAPTAFGGNAPPTTSTAveSSKLFGGGGITFNAPNIFGNNSNPSNlfgsgNNNSSSLFGGNSTTNPPP----L 1829
Cdd:pfam13634   16 NTSTTAASGGGLFGAASTATATTS--GGGLFGNSSSNAPSGGLFGATNTTTQ-----TATGGGLFGNNAATTTSTtgggL 88


                   ..
gi 268638308  1830 FG 1831
Cdd:pfam13634   89 FG 90
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2469-2564 5.00e-03

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: 42.83  E-value: 5.00e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308  2469 PKVTLLSSS--FTPPSFAPPSF--APSSFAPSSFAPPSFAPPSFAPSS-FAPSSFAPPSFAPPKPENTSTPTSSIFGSFS 2543
Cdd:pfam03154  413 PPLQLMPQSqqLPPPPAQPPVLtqSQSLPPPAASHPPTSGLHQVPSQSpFPQHPFVPGGPPPITPPSGPPTSTSSAMPGI 492

                           90       100
                   ....*....|....*....|.
gi 268638308  2544 SQPSGGGISAFGPVSSNSSSP 2564
Cdd:pfam03154  493 QPPSSASVSSSGPVPAAVSCP 513
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 2344-2426 6.20e-03

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 38.37  E-value: 6.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308  2344 TAFGGNAPPTTStavdsskLFGGGGSNTITfnAPTLFGNNNNSNPS----NLFGSGNNN--SSSLFGGNSTTIQPSQ--S 2415
Cdd:pfam13634    1 GLFGAATSTSGG-------LFGNTSTTAAS--GGGLFGAASTATATtsggGLFGNSSSNapSGGLFGATNTTTQTATggG 71

                           90
                   ....*....|.
gi 268638308  2416 LFGTKSTETKS 2426
Cdd:pfam13634   72 LFGNNAATTTS 82
 
Name Accession Description Interval E-value
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 1529-1606 8.28e-09

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 55.31  E-value: 8.28e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308  1529 FGSASSNSSSVFGQTTTKPSTGSSVFGQNS--------SSVFGQTTTPSSGTGVFGQNSSSvfGQTSTGTGVFGQNSSSI 1600
Cdd:pfam13634    3 FGAATSTSGGLFGNTSTTAASGGGLFGAAStatattsgGGLFGNSSSNAPSGGLFGATNTT--TQTATGGGLFGNNAATT 80


                   ....*.
gi 268638308  1601 FGQSNG 1606
Cdd:pfam13634   81 TSTTGG 86
KREPA2 cd23959
Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of ...
 2472-2535 2.53e-05

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


Pssm-ID: 467780 [Multi-domain]  Cd Length: 424  Bit Score: 49.87  E-value: 2.53e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 268638308 2472 TLLSSSFTPPSFAPPSFAPSSF-APSSFAPPSFAPPSFAPSSFAPSSFAPPSFAPP-KPENTSTPT 2535
Cdd:cd23959   180 GEVASPFASGTVSASPFATATDtAPSSGAPDGFPAEASAPSPFAAPASAASFPAAPvANGEAATPT 245
KREPA2 cd23959
Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of ...
 2469-2555 4.13e-05

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


Pssm-ID: 467780 [Multi-domain]  Cd Length: 424  Bit Score: 49.10  E-value: 4.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308 2469 PKVTLLSSSFTP----PSFAPPSFAPSSFAPSSFAPPSFAPPSFAPSSFAPSSFAPPSFAPPKPENTSTPTSSIFGSFSS 2544
Cdd:cd23959   138 PKAEPQTAPVTPfgqlPMFGQHPPPAKPLPAAAAAQQSSASPGEVASPFASGTVSASPFATATDTAPSSGAPDGFPAEAS 217

                          90
                  ....*....|.
gi 268638308 2545 QPSGGGISAFG 2555
Cdd:cd23959   218 APSPFAAPASA 228
KREPA2 cd23959
Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of ...
 2469-2546 7.11e-05

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


Pssm-ID: 467780 [Multi-domain]  Cd Length: 424  Bit Score: 48.33  E-value: 7.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308 2469 PKVTLLSSSFTPPSFAPPSFAPSSFAPSSFAPPSFA------PPSFAPSSFAPSSFAPPSFAPPKPENtSTPTSSIFGSF 2542
Cdd:cd23959   162 PAKPLPAAAAAQQSSASPGEVASPFASGTVSASPFAtatdtaPSSGAPDGFPAEASAPSPFAAPASAA-SFPAAPVANGE 240


                  ....
gi 268638308 2543 SSQP 2546
Cdd:cd23959   241 AATP 244
PHA03377 PHA03377
EBNA-3C; Provisional
 2469-2537 3.64e-04

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 46.58  E-value: 3.64e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308 2469 PKVTllSSSFTPPSFAPPSFAPSSFAPSSFAPPSFAPPSFAPSSFAPSSFAPPSFAPPKP-ENTSTPTSS 2537
Cdd:PHA03377  553 PKVS--PSDRGPPKASPPVMAPPSTGPRVMATPSTGPRDMAPPSTGPRQQAKCKDGPPASgPHEKQPPSS 620
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 1477-1594 7.01e-04

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 41.06  E-value: 7.01e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308  1477 NKPKPTFLFGTSSTTsnpaqtttpttstptpsssifgqPPTSSSVFGSKPTvfGSASSNSSSVFGQTTTKPSTGSSvFGQ 1556
Cdd:pfam13634    6 ATSTSGGLFGNTSTT-----------------------AASGGGLFGAAST--ATATTSGGGLFGNSSSNAPSGGL-FGA 59

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 268638308  1557 NSssvfgQTTTPSSGTGVFGQNSSSvfGQTSTGTGVFG 1594
Cdd:pfam13634   60 TN-----TTTQTATGGGLFGNNAAT--TTSTTGGGLFG 90
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 9-167 7.75e-04

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 44.33  E-value: 7.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308    9 IKRYKEQLKKPLFKNEALYQLTKLYLSleneinENELDECKDYFNQL-KQSGVLKESQKELKEITIDfqtiTKQYDLAEQ 87
Cdd:COG2956    96 EELLEKLLELDPDDAEALRLLAEIYEQ------EGDWEKAIEVLERLlKLGPENAHAYCELAELYLE----QGDYDEAIE 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308   88 SLQSAIKSYPDNLNFLLKNINLLSINKKY---YEFFKSIKDSKIKYQRDLKYLNFIIKQIDNV--AIKAIKESVEEIQAN 162
Cdd:COG2956   166 ALEKALKLDPDCARALLLLAELYLEQGDYeeaIAALERALEQDPDYLPALPRLAELYEKLGDPeeALELLRKALELDPSD 245


                  ....*
gi 268638308  163 TMLLN 167
Cdd:COG2956   246 DLLLA 250
PHA02682 PHA02682
ORF080 virion core protein; Provisional
 2479-2595 8.00e-04

ORF080 virion core protein; Provisional


Pssm-ID: 177464 [Multi-domain]  Cd Length: 280  Bit Score: 44.47  E-value: 8.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308 2479 TPPSFAPPSFAPSSFAPSSfAPPSFAPPSFAPssfAPSSFAPPSFAPPKPENTSTPTSSIFGSfSSQPSGGGISAFGPVS 2558
Cdd:PHA02682   80 SPLAPSPACAAPAPACPAC-APAAPAPAVTCP---APAPACPPATAPTCPPPAVCPAPARPAP-ACPPSTRQCPPAPPLP 154

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 268638308 2559 SNSSSPfgsgfgsASIPSFGQSQVNPLTInPTSTSPT 2595
Cdd:PHA02682  155 TPKPAP-------AAKPIFLHNQLPPPDY-PAASCPT 183
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 1754-1831 8.28e-04

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 41.06  E-value: 8.28e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308  1754 NNKPSSLFAPTAFGGNAPPTTSTAveSSKLFGGGGITFNAPNIFGNNSNPSNlfgsgNNNSSSLFGGNSTTNPPP----L 1829
Cdd:pfam13634   16 NTSTTAASGGGLFGAASTATATTS--GGGLFGNSSSNAPSGGLFGATNTTTQ-----TATGGGLFGNNAATTTSTtgggL 88


                   ..
gi 268638308  1830 FG 1831
Cdd:pfam13634   89 FG 90
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 1764-1834 1.14e-03

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 40.68  E-value: 1.14e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308  1764 TAFGGNAPPTTStavesskLFGGGGITFNAP-NIFGNNSNPSN------LFGSGNNN--SSSLFGGNSTTNPPP----LF 1830
Cdd:pfam13634    1 GLFGAATSTSGG-------LFGNTSTTAASGgGLFGAASTATAttsgggLFGNSSSNapSGGLFGATNTTTQTAtgggLF 73


                   ....
gi 268638308  1831 GNKS 1834
Cdd:pfam13634   74 GNNA 77
PHA03377 PHA03377
EBNA-3C; Provisional
 2484-2526 2.43e-03

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 43.89  E-value: 2.43e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 268638308 2484 APPSFAPSSFAPSSFAPPSFAPPSFAPSSFAPSSFAPPSFAPP 2526
Cdd:PHA03377  551 TPPKVSPSDRGPPKASPPVMAPPSTGPRVMATPSTGPRDMAPP 593
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2469-2564 5.00e-03

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: 42.83  E-value: 5.00e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308  2469 PKVTLLSSS--FTPPSFAPPSF--APSSFAPSSFAPPSFAPPSFAPSS-FAPSSFAPPSFAPPKPENTSTPTSSIFGSFS 2543
Cdd:pfam03154  413 PPLQLMPQSqqLPPPPAQPPVLtqSQSLPPPAASHPPTSGLHQVPSQSpFPQHPFVPGGPPPITPPSGPPTSTSSAMPGI 492

                           90       100
                   ....*....|....*....|.
gi 268638308  2544 SQPSGGGISAFGPVSSNSSSP 2564
Cdd:pfam03154  493 QPPSSASVSSSGPVPAAVSCP 513
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 2477-2597 5.54e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 42.85  E-value: 5.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308 2477 SFTPPSFAPPSFAPSSFA--------PSSFAPPSFAPPSFAPSSFAPSSFAPPSFAPPKPENTSTPTSSIF--GSFSSQP 2546
Cdd:PHA03307  143 SPGPPPAASPPAAGASPAavasdaasSRQAALPLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPIsaSASSPAP 222

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 268638308 2547 SGGGISAFGPVSSNSSSPFGSGFGSASipsfGQSQVNPLTINPTSTSPTAV 2597
Cdd:PHA03307  223 APGRSAADDAGASSSDSSSSESSGCGW----GPENECPLPRPAPITLPTRI 269
Nucleoporin_FG pfam13634
Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in ...
 2344-2426 6.20e-03

Nucleoporin FG repeat region; This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.


Pssm-ID: 463941 [Multi-domain]  Cd Length: 90  Bit Score: 38.37  E-value: 6.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 268638308  2344 TAFGGNAPPTTStavdsskLFGGGGSNTITfnAPTLFGNNNNSNPS----NLFGSGNNN--SSSLFGGNSTTIQPSQ--S 2415
Cdd:pfam13634    1 GLFGAATSTSGG-------LFGNTSTTAAS--GGGLFGAASTATATtsggGLFGNSSSNapSGGLFGATNTTTQTATggG 71

                           90
                   ....*....|.
gi 268638308  2416 LFGTKSTETKS 2426
Cdd:pfam13634   72 LFGNNAATTTS 82
 
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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