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Conserved domains on  [gi|1370463219|ref|XP_024305043|]
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protein SCAF11 isoform X9 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK12678 super family cl36163
transcription termination factor Rho; Provisional
 706-957 6.43e-07

transcription termination factor Rho; Provisional


The actual alignment was detected with superfamily member PRK12678:

Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 54.14  E-value: 6.43e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  706 PSSDLADEKVETVSQPSESPKDTIDKTKKPRTRRSRFHSPSTTWSPNKDTPQEKKRPQSPSPRRETGKESRKSQSPSPKN 785
Cdd:PRK12678    68 ATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGE 147

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  786 ESARGRKKSRSQSPKKDIARERRQSQSRSPKRDTTRESRRSEslsprRETSRENKRSQPRVKDSSPGEKSRSQSRERESD 865
Cdd:PRK12678   148 GGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGE-----RGRREERGRDGDDRDRRDRREQGDRREERGRRD 222

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  866 RDGQRRERERrtrkwsrsrshsrspsrcrtkskSSSFGRIDRDSYSPRWKGRWANDGWRCPRGNDRYRKNDPEKQNENTR 945
Cdd:PRK12678   223 GGDRRGRRRR-----------------------RDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDG 279

                          250
                   ....*....|..
gi 1370463219  946 KEKNDIHLDADD 957
Cdd:PRK12678   280 GNEREPELREDD 291
RING_Ubox super family cl17238
RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger ...
 19-38 1.29e-04

RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type RING fingers are closely related to RING-HC fingers. In contrast, C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type RING fingers are more closely related to RING-H2 fingers. However, not all RING finger-containing proteins display regular RING finger features, and the RING finger family has turned out to be multifarious. The degenerate RING fingers of the Siz/PIAS RING (SP-RING) family proteins and sporulation protein RMD5, are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues. They bind only one Zn2+ ion. On the other hand, the RING fingers of the human APC11 and RBX1 proteins can bind a third Zn atom since they harbor four additional Zn ligands. U-box is a modified form of the RING finger domain that lacks metal chelating Cys and His residues. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. RING finger/U-box-containing proteins are a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enable efficient transfer of ubiquitin from E2 to the substrates.


The actual alignment was detected with superfamily member cd16636:

Pssm-ID: 473075 [Multi-domain]  Cd Length: 52  Bit Score: 40.90  E-value: 1.29e-04
                           10        20
                   ....*....|....*....|
gi 1370463219   19 FSRTLASCPIDRKPFQAVFK 38
Cdd:cd16636     33 WAETVTSCPIDRKPFQAVYK 52
 
Name Accession Description Interval E-value
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 706-957 6.43e-07

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 54.14  E-value: 6.43e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  706 PSSDLADEKVETVSQPSESPKDTIDKTKKPRTRRSRFHSPSTTWSPNKDTPQEKKRPQSPSPRRETGKESRKSQSPSPKN 785
Cdd:PRK12678    68 ATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGE 147

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  786 ESARGRKKSRSQSPKKDIARERRQSQSRSPKRDTTRESRRSEslsprRETSRENKRSQPRVKDSSPGEKSRSQSRERESD 865
Cdd:PRK12678   148 GGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGE-----RGRREERGRDGDDRDRRDRREQGDRREERGRRD 222

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  866 RDGQRRERERrtrkwsrsrshsrspsrcrtkskSSSFGRIDRDSYSPRWKGRWANDGWRCPRGNDRYRKNDPEKQNENTR 945
Cdd:PRK12678   223 GGDRRGRRRR-----------------------RDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDG 279

                          250
                   ....*....|..
gi 1370463219  946 KEKNDIHLDADD 957
Cdd:PRK12678   280 GNEREPELREDD 291
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 769-866 2.42e-06

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 51.82  E-value: 2.42e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  769 RETGKESRKSQSPSPKNESARGRKKSRSQSPKKDIARERRQSQSRSPKRDTTRESRRSESLSPRRETSRENKRSQP--RV 846
Cdd:TIGR01642    3 EEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPrrRS 82

                           90       100
                   ....*....|....*....|
gi 1370463219  847 KDSSPGEKSRSQSRERESDR 866
Cdd:TIGR01642   83 RSVRSIEQHRRRLRDRSPSN 102
mRING-HC-C3HC3D_SCAF11 cd16636
Modified RING finger, HC subclass (C3HC3D-type), found in SR-related and CTD-associated factor ...
 19-38 1.29e-04

Modified RING finger, HC subclass (C3HC3D-type), found in SR-related and CTD-associated factor 11 (SCAF11) and similar proteins; SCAF11, also known as CTD-associated SR protein 11 (CASP11), renal carcinoma antigen NY-REN-40, SC35-interacting protein 1 (Sip1), Serine/arginine-rich splicing factor 2 (SRSF2)-interacting protein, or splicing regulatory protein 129 (SRrp129), is a novel arginine-serine-rich (RS) domain-containing protein essential for pre-mRNA splicing. It functions as an auxiliary splice factor interacting with the spliceosomal component SC35, promoting RNAPII elongation. In addition to SR proteins, such as SC35, ASF/SF2, SRp75, and SRp20, SCAF11 also associates with U1-70K and U2AF65, proteins associated with 5' and 3' splice sites, respectively. SCAF11 contains an N-terminal modified C3HC3D-type RING-HC finger, an internal serine-arginine rich domain (SR domain), and a C-terminal SRI domain.


Pssm-ID: 438298 [Multi-domain]  Cd Length: 52  Bit Score: 40.90  E-value: 1.29e-04
                           10        20
                   ....*....|....*....|
gi 1370463219   19 FSRTLASCPIDRKPFQAVFK 38
Cdd:cd16636     33 WAETVTSCPIDRKPFQAVYK 52
RSRP pfam17069
Arginine/Serine-Rich protein 1; RSRP1 is an eukaryotic protein family. Its function is unknown.
 703-862 5.07e-04

Arginine/Serine-Rich protein 1; RSRP1 is an eukaryotic protein family. Its function is unknown.


Pssm-ID: 293674 [Multi-domain]  Cd Length: 299  Bit Score: 44.00  E-value: 5.07e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  703 NNMPSSDLADEKVETVSQPSESPKDTIDKTKKPRTRRSRFHSPSTTWSPNKDTPQEKK-RPQSPSPRRETGKESRKSQSP 781
Cdd:pfam17069    6 NDMWPGSPQEKKSPSTSSSGSSSRLSSRSRSRSSSRSSRSHSRSSSRFSSRSRSRPRRsRSRSRSRRRHQRKYRRYSRSY 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  782 SPKNESARGRKksrsqspkkdIARERRQSQSRSPKRDTTRESRRSESLSPRRET------SRENKRSQPRVKDSSPGEKS 855
Cdd:pfam17069   86 SRSRSRSRRRR----------YYRRSRYRYSRRYYRSPSRSRSRSRSRSRGRSYyaiwrgSRYYGFGRTVYPERSPRWRS 155


                   ....*..
gi 1370463219  856 RSQSRER 862
Cdd:pfam17069  156 RSRTRSR 162
 
Name Accession Description Interval E-value
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 706-957 6.43e-07

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 54.14  E-value: 6.43e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  706 PSSDLADEKVETVSQPSESPKDTIDKTKKPRTRRSRFHSPSTTWSPNKDTPQEKKRPQSPSPRRETGKESRKSQSPSPKN 785
Cdd:PRK12678    68 ATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGE 147

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  786 ESARGRKKSRSQSPKKDIARERRQSQSRSPKRDTTRESRRSEslsprRETSRENKRSQPRVKDSSPGEKSRSQSRERESD 865
Cdd:PRK12678   148 GGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGE-----RGRREERGRDGDDRDRRDRREQGDRREERGRRD 222

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  866 RDGQRRERERrtrkwsrsrshsrspsrcrtkskSSSFGRIDRDSYSPRWKGRWANDGWRCPRGNDRYRKNDPEKQNENTR 945
Cdd:PRK12678   223 GGDRRGRRRR-----------------------RDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDG 279

                          250
                   ....*....|..
gi 1370463219  946 KEKNDIHLDADD 957
Cdd:PRK12678   280 GNEREPELREDD 291
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 769-866 2.42e-06

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 51.82  E-value: 2.42e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  769 RETGKESRKSQSPSPKNESARGRKKSRSQSPKKDIARERRQSQSRSPKRDTTRESRRSESLSPRRETSRENKRSQP--RV 846
Cdd:TIGR01642    3 EEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPrrRS 82

                           90       100
                   ....*....|....*....|
gi 1370463219  847 KDSSPGEKSRSQSRERESDR 866
Cdd:TIGR01642   83 RSVRSIEQHRRRLRDRSPSN 102
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 769-867 3.52e-06

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 51.46  E-value: 3.52e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  769 RETGKESRKSQSPSPKNESARGRKKSRSQSPKKDIARERRQSQSRSPKRDTTRESR--------RSESLSPRRETSRENK 840
Cdd:TIGR01622    7 RERLRDSSSAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRsrrpnrryRPREKRRRRGDSYRRR 86

                           90       100
                   ....*....|....*....|....*..
gi 1370463219  841 RSQPRVKDSSPGEKSRSQSRERESDRD 867
Cdd:TIGR01622   87 RDDRRSRREKPRARDGTPEPLTEDERD 113
mRING-HC-C3HC3D_SCAF11 cd16636
Modified RING finger, HC subclass (C3HC3D-type), found in SR-related and CTD-associated factor ...
 19-38 1.29e-04

Modified RING finger, HC subclass (C3HC3D-type), found in SR-related and CTD-associated factor 11 (SCAF11) and similar proteins; SCAF11, also known as CTD-associated SR protein 11 (CASP11), renal carcinoma antigen NY-REN-40, SC35-interacting protein 1 (Sip1), Serine/arginine-rich splicing factor 2 (SRSF2)-interacting protein, or splicing regulatory protein 129 (SRrp129), is a novel arginine-serine-rich (RS) domain-containing protein essential for pre-mRNA splicing. It functions as an auxiliary splice factor interacting with the spliceosomal component SC35, promoting RNAPII elongation. In addition to SR proteins, such as SC35, ASF/SF2, SRp75, and SRp20, SCAF11 also associates with U1-70K and U2AF65, proteins associated with 5' and 3' splice sites, respectively. SCAF11 contains an N-terminal modified C3HC3D-type RING-HC finger, an internal serine-arginine rich domain (SR domain), and a C-terminal SRI domain.


Pssm-ID: 438298 [Multi-domain]  Cd Length: 52  Bit Score: 40.90  E-value: 1.29e-04
                           10        20
                   ....*....|....*....|
gi 1370463219   19 FSRTLASCPIDRKPFQAVFK 38
Cdd:cd16636     33 WAETVTSCPIDRKPFQAVYK 52
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 719-862 2.68e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 45.55  E-value: 2.68e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  719 SQPSESPKDTIDKTKKPRTRRSRFHSPSTTWSPNKDTPQEKKRPQSPSPRRETGKESRKSQSPSPKNESARGRKKSRSQS 798
Cdd:PHA03307   242 SESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSS 321

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1370463219  799 PKKDIARERRQSQSR-----SPKRDTTReSRRSESLSPRRETSRENKRSQPRVKDSSPGEKSRSQSRER 862
Cdd:PHA03307   322 RESSSSSTSSSSESSrgaavSPGPSPSR-SPSPSRPPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRR 389
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 786-867 3.59e-04

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 44.88  E-value: 3.59e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  786 ESARGRKKSRSQSPKKDIARERRQSQSRSPKRDTTRESRRSESLSPRRETSRENKRS-QPRVKDSSPGEKSRSQSRERES 864
Cdd:TIGR01642    4 EPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSrSPRSLRYSSVRRSRDRPRRRSR 83


                   ...
gi 1370463219  865 DRD 867
Cdd:TIGR01642   84 SVR 86
RSRP pfam17069
Arginine/Serine-Rich protein 1; RSRP1 is an eukaryotic protein family. Its function is unknown.
 703-862 5.07e-04

Arginine/Serine-Rich protein 1; RSRP1 is an eukaryotic protein family. Its function is unknown.


Pssm-ID: 293674 [Multi-domain]  Cd Length: 299  Bit Score: 44.00  E-value: 5.07e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  703 NNMPSSDLADEKVETVSQPSESPKDTIDKTKKPRTRRSRFHSPSTTWSPNKDTPQEKK-RPQSPSPRRETGKESRKSQSP 781
Cdd:pfam17069    6 NDMWPGSPQEKKSPSTSSSGSSSRLSSRSRSRSSSRSSRSHSRSSSRFSSRSRSRPRRsRSRSRSRRRHQRKYRRYSRSY 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  782 SPKNESARGRKksrsqspkkdIARERRQSQSRSPKRDTTRESRRSESLSPRRET------SRENKRSQPRVKDSSPGEKS 855
Cdd:pfam17069   86 SRSRSRSRRRR----------YYRRSRYRYSRRYYRSPSRSRSRSRSRSRGRSYyaiwrgSRYYGFGRTVYPERSPRWRS 155


                   ....*..
gi 1370463219  856 RSQSRER 862
Cdd:pfam17069  156 RSRTRSR 162
PRP38_assoc pfam12871
Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region ...
 798-869 5.18e-04

Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known.


Pssm-ID: 463734 [Multi-domain]  Cd Length: 98  Bit Score: 40.53  E-value: 5.18e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1370463219  798 SPKKDIARERRQSQSRSPKRDTTRESRRSESLSPRRETSRENKRSQPRVKDSSPGEKSRSQSRERESDRDGQ 869
Cdd:pfam12871   25 SDESERASLSRKRRSRSRRRSSTRDRSRSRSRSRSRDRRSRGTRDRRRDRDRDRYRSLRSRSRDRSRDRDRD 96
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 753-842 6.53e-04

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 44.11  E-value: 6.53e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  753 KDTPQEKKRPQSPSPRRETGKESRKSQSPSPKNESARGRKKSRSQSPKKDIARERRQSQSRSPKRD-----TTRESRRSE 827
Cdd:TIGR01642   17 RDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSrsvrsIEQHRRRLR 96

                           90
                   ....*....|....*
gi 1370463219  828 SLSPRRETSRENKRS 842
Cdd:TIGR01642   97 DRSPSNQWRKDDKKR 111
RSRP pfam17069
Arginine/Serine-Rich protein 1; RSRP1 is an eukaryotic protein family. Its function is unknown.
 755-917 8.23e-04

Arginine/Serine-Rich protein 1; RSRP1 is an eukaryotic protein family. Its function is unknown.


Pssm-ID: 293674 [Multi-domain]  Cd Length: 299  Bit Score: 43.23  E-value: 8.23e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  755 TPQEKKRPQSPSPRRETGKESRKSQSPSPKNESARGRKKSRSQSPKKDIAReRRQSQSRSPKRDTTRESRRSESLSPRRE 834
Cdd:pfam17069   12 SPQEKKSPSTSSSGSSSRLSSRSRSRSSSRSSRSHSRSSSRFSSRSRSRPR-RSRSRSRSRRRHQRKYRRYSRSYSRSRS 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  835 TSReNKRSQPRVKDSSPGEKSRSQSREResdrdgqrrererrtrKWSRSRSHSRSPSRCRTKSKSSSFGRIDRDSYSPRW 914
Cdd:pfam17069   91 RSR-RRRYYRRSRYRYSRRYYRSPSRSR----------------SRSRSRSRGRSYYAIWRGSRYYGFGRTVYPERSPRW 153


                   ...
gi 1370463219  915 KGR 917
Cdd:pfam17069  154 RSR 156
PRK13863 PRK13863
T-DNA border endonuclease VirD2;
676-868 8.27e-04

T-DNA border endonuclease VirD2;


Pssm-ID: 237533 [Multi-domain]  Cd Length: 446  Bit Score: 43.78  E-value: 8.27e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  676 QNESEVEPSVNADLKQMNENSVTHCSENNMPSSDLADEKVETVSQPSESPKDTIDKTKKPRtRRSRFHSPSTtwSPNKDT 755
Cdd:PRK13863   254 QNESEVRLQEPAGSSIKADARIRVSLESERRAQPSASKIPVADDFGIETSYVAEGDVRKLE-GNSGTPRLAT--EVATHT 330

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  756 PQEkkrpQSPSPRRETGKESRKSQSPSPKNESARGRKKSRSQSP--KKDIARERRQSQSRSPKRDTTRESRRSESLSP-- 831
Cdd:PRK13863   331 TSE----RQQRRKRPRDDEGEPSGAKRTRLNGIAVGPEANAGEQdgRDDPITSPAQPPRSNPLADPVRASIATDSLPAta 406

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1370463219  832 RRETSRENKRSQPRVKDSSPGEKSRSQSRERESDRDG 868
Cdd:PRK13863   407 DRQQQREPSSKRPRDDDGEPSIRKRARDGRSQDGREG 443
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 793-866 8.75e-04

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 43.75  E-value: 8.75e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  793 KSRSQSPKKDiaRERRQSQSRSPKRDTTRESRRSESLSPRRETSRENKR-------SQPRVKDSSPGEKSRSQSRERESD 865
Cdd:TIGR01622    1 RYRDRERERL--RDSSSAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRhrdrdyyRGRERRSRSRRPNRRYRPREKRRR 78


                   .
gi 1370463219  866 R 866
Cdd:TIGR01622   79 R 79
DMP1 pfam07263
Dentin matrix protein 1 (DMP1); This family consists of several mammalian dentin matrix ...
 626-864 1.05e-03

Dentin matrix protein 1 (DMP1); This family consists of several mammalian dentin matrix protein 1 (DMP1) sequences. The dentin matrix acidic phosphoprotein 1 (DMP1) gene has been mapped to human chromosome 4q21. DMP1 is a bone and teeth specific protein initially identified from mineralized dentin. DMP1 is primarily localized in the nuclear compartment of undifferentiated osteoblasts. In the nucleus, DMP1 acts as a transcriptional component for activation of osteoblast-specific genes like osteocalcin. During the early phase of osteoblast maturation, Ca(2+) surges into the nucleus from the cytoplasm, triggering the phosphorylation of DMP1 by a nuclear isoform of casein kinase II. This phosphorylated DMP1 is then exported out into the extracellular matrix, where it regulates nucleation of hydroxyapatite. DMP1 is a unique molecule that initiates osteoblast differentiation by transcription in the nucleus and orchestrates mineralized matrix formation extracellularly, at later stages of osteoblast maturation. The DMP1 gene has been found to be ectopically expressed in lung cancer although the reason for this is unknown.


Pssm-ID: 462128 [Multi-domain]  Cd Length: 519  Bit Score: 43.38  E-value: 1.05e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  626 EKSLEEKNES-LTEHPRSTELPKTHI-EQIQKHFSEDNNEMIPMECDSfCSDQNESEVEPSVNADLKQMNENSVTHCSEN 703
Cdd:pfam07263  247 QASTQDSGDSqSVEYPSRKFFRKSRIsEEDDRGELDDSNTMEEVKSDS-TESTSSKEAGLSQSREDSKSESQEDSEESQS 325

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  704 NMPSSDLADEKVETVSQPSESPKDTIDKTKKPRTRRSRFHSPSTTWSPNKDTP-QEKKRPQSPSPRRETGKESRKSQSPS 782
Cdd:pfam07263  326 QEDSQNSQDPSSESSQEADLPSQESSSESQEEVVSESRGDNPDNTSSSEEDQEdSDSSEEDSLSTFSSSESESREEQADS 405

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  783 PKNESARGRKKSRSQSPKKDIA-RERRQSQSRSpkrdttRESRRSESLSPRRETSRENKRSqprvkDSSPGEKSRSQSRE 861
Cdd:pfam07263  406 ESNESLRSSEESPESSEDENSSsQEGLQSHSAS------TESQSEESQSEQDSQSEEDDES-----DSQDSSRSKEDSNS 474


                   ...
gi 1370463219  862 RES 864
Cdd:pfam07263  475 TES 477
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 753-862 1.24e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 42.96  E-value: 1.24e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  753 KDTPQEKKRPQSPSPRRETGKESRKSQSPSpknesaRGRKKSRSQSPKKDIARERRQSQSRSPKRDTTRES--RRSESLS 830
Cdd:TIGR01642    5 PDREREKSRGRDRDRSSERPRRRSRDRSRF------RDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSsvRRSRDRP 78

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1370463219  831 PRRETSRE-NKRSQPRVKDSSPGEKSRSQSRER 862
Cdd:TIGR01642   79 RRRSRSVRsIEQHRRRLRDRSPSNQWRKDDKKR 111
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 736-867 5.02e-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: 41.29  E-value: 5.02e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  736 RTRRSRfHSPSTTWSpnkdtpQEKKRPQSPSPR--------RETGKESRKSQSPSPKNESARGRKKSRSQ------SPKK 801
Cdd:pfam03154    6 RTRRSR-GSMSTLRS------GRKKQTASPDGRasptnedlRSSGRNSPSAASTSSNDSKAESMKKSSKKikeeapSPLK 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  802 DIARERRQ--SQSRSPKRDTTRESRRSESLSPRRETSRENKRSQPRV---------KDSSPGEKSRSQS----RERESDR 866
Cdd:pfam03154   79 SAKRQREKgaSDTEEPERATAKKSKTQEISRPNSPSEGEGESSDGRSvndegssdpKDIDQDNRSTSPSipspQDNESDS 158


                   .
gi 1370463219  867 D 867
Cdd:pfam03154  159 D 159
PLN02543 PLN02543
pfkB-type carbohydrate kinase family protein
 721-839 5.25e-03

pfkB-type carbohydrate kinase family protein


Pssm-ID: 215299  Cd Length: 496  Bit Score: 41.05  E-value: 5.25e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  721 PSESPKDTIDKTKKPRTRRSRFHSPSttwsPNKDTPQEKKRPQSPSPRRETGKESRKSQSPSPkneSARGRKKSRSQSPK 800
Cdd:PLN02543     8 PHLHHSYSSLDRREKTCLRSSQKTRR----FPKPKASLHPSIKRSRPGRCSTNGAAVPESPKP---SRRGRKKKPTSSPP 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1370463219  801 KDIARERrqsqsRSPKRDTTRESRRSESLSPRRETSREN 839
Cdd:PLN02543    81 KAKTTRR-----RTKKTDQELDPEGAEEDQEAAEDGEDY 114
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 739-826 9.04e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 40.26  E-value: 9.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370463219  739 RSRFHSPSTTWSPNKDTPQEKKRPQSPSPRRETGKESRKSQSPSPKNESARGRkksrsqspkkdIARERRQSQSRSPKRD 818
Cdd:TIGR01642   35 RDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRS-----------IEQHRRRLRDRSPSNQ 103


                   ....*...
gi 1370463219  819 TTRESRRS 826
Cdd:TIGR01642  104 WRKDDKKR 111
 
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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