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Conserved domains on  [gi|663515921|gb|AIF06387|]
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nucleic acid binding OB-fold tRNA/helicase-type protein [uncultured marine group II/III euryarchaeote KM3_191_F05]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 115-184 1.08e-23

universal minicircle sequence binding protein (UMSBP); Provisional


The actual alignment was detected with superfamily member PTZ00368:

Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 91.02  E-value: 1.08e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663515921 115 KCFNCGKPGHISRDCPEGGGGKPGGGKCFNCGKPGHISRDCPEGGGGKPGGGKCFNCGKPGHISRNCPDR 184
Cdd:PTZ00368  79 SCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCPDK 148
RPA_2b-aaRSs_OBF_like super family cl09930
Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with ...
 3-76 1.67e-17

Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism. This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B, of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases.


The actual alignment was detected with superfamily member PRK06461:

Pssm-ID: 471953 [Multi-domain]  Cd Length: 129  Bit Score: 74.69  E-value: 1.67e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 663515921   3 VKVLSMDEPRDIESGG---RVCEGLVGDETGTIVMSFWNEECDQVAVDATIWLKDARATLVRGSLRLSLGKFGSLGK 76
Cdd:PRK06461  21 VRVLEVGEPKVIQTKGgprTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISE 97
 
Name Accession Description Interval E-value
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 115-184 1.08e-23

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 91.02  E-value: 1.08e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663515921 115 KCFNCGKPGHISRDCPEGGGGKPGGGKCFNCGKPGHISRDCPEGGGGKPGGGKCFNCGKPGHISRNCPDR 184
Cdd:PTZ00368  79 SCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCPDK 148
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 3-76 1.67e-17

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 74.69  E-value: 1.67e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 663515921   3 VKVLSMDEPRDIESGG---RVCEGLVGDETGTIVMSFWNEECDQVAVDATIWLKDARATLVRGSLRLSLGKFGSLGK 76
Cdd:PRK06461  21 VRVLEVGEPKVIQTKGgprTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISE 97
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 3-74 4.46e-15

SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM.


Pssm-ID: 239937 [Multi-domain]  Cd Length: 82  Bit Score: 66.88  E-value: 4.46e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 663515921   3 VKVLSMDEPRDIE---SGGRVCEGLVGDETGTIVMSFWNEEC-DQVAVDATIWLKDARATLVRGSLRLSLGKFGSL 74
Cdd:cd04491    4 GKVLSISEPREFTrdgSEGKVQSGLVGDETGTIRFTLWDEKAaDDLEPGDVVRIENAYVREFNGRLELSVGKNSEI 79
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 115-185 7.17e-14

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 66.41  E-value: 7.17e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 663515921 115 KCFNCGKPGHISRDCPEggggkpggGKCFNCGKPGHISRDCPEggggkpgGGKCFNCGKPGHISRNCPDRG 185
Cdd:COG5082   62 VCFNCGQNGHLRRDCPH--------SICYNCSWDGHRSNHCPK-------PKKCYNCGETGHLSRDCNPSK 117
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
3-98 5.71e-11

ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 59.69  E-value: 5.71e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663515921   3 VKVLSMDEPRDIE----SGGRVCEGLVGDETGTIVMSFWNEECD-QVAVDATIWLKDARATLVRGSLRLSLGKFGSLGKP 77
Cdd:COG1599   38 GRVLEIGEERTFDrkdgSEGRVQSGVIGDETGRIRFTLWDDKADlELEEGDVVRIENAYVREFNGGPELNLGERTTIEKL 117

                         90       100
                 ....*....|....*....|.
gi 663515921  78 GREVgSVRDDLNLSDLAYAMP 98
Cdd:COG1599  118 DEDV-EVIPDEERTPIGDIEP 137
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 115-131 1.97e-04

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 37.12  E-value: 1.97e-04
                          10
                  ....*....|....*..
gi 663515921  115 KCFNCGKPGHISRDCPE 131
Cdd:pfam00098   2 KCYNCGEPGHIARDCPK 18
ZnF_C2HC smart00343
zinc finger;
115-131 3.24e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 36.65  E-value: 3.24e-04
                           10
                   ....*....|....*..
gi 663515921   115 KCFNCGKPGHISRDCPE 131
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
 
Name Accession Description Interval E-value
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 115-184 1.08e-23

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 91.02  E-value: 1.08e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663515921 115 KCFNCGKPGHISRDCPEGGGGKPGGGKCFNCGKPGHISRDCPEGGGGKPGGGKCFNCGKPGHISRNCPDR 184
Cdd:PTZ00368  79 SCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCPDK 148
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 116-182 3.41e-22

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 87.17  E-value: 3.41e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 663515921 116 CFNCGKPGHISRDCPEgGGGKPGGGKCFNCGKPGHISRDCPEGGGGKPGGGKCFNCGKPGHISRNCP 182
Cdd:PTZ00368  55 CYNCGKTGHLSRECPE-APPGSGPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCP 120
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 116-184 1.07e-20

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 83.32  E-value: 1.07e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 663515921 116 CFNCGKPGHISRDCPeGGGGKPGGGKCFNCGKPGHISRDCPEgGGGKPGGGKCFNCGKPGHISRNCPDR 184
Cdd:PTZ00368  30 CYKCGEPGHLSRECP-SAPGGRGERSCYNCGKTGHLSRECPE-APPGSGPRSCYNCGQTGHISRECPNR 96
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 116-184 1.03e-17

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 75.61  E-value: 1.03e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663515921 116 CFNCGKPGHISRDCPEGGGGKPGGGK-CFNCGKPGHISRDCPeGGGGKPGGGKCFNCGKPGHISRNCPDR 184
Cdd:PTZ00368   3 CYRCGGVGHQSRECPNSAPAGAAKARpCYKCGEPGHLSRECP-SAPGGRGERSCYNCGKTGHLSRECPEA 71
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 3-76 1.67e-17

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 74.69  E-value: 1.67e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 663515921   3 VKVLSMDEPRDIESGG---RVCEGLVGDETGTIVMSFWNEECDQVAVDATIWLKDARATLVRGSLRLSLGKFGSLGK 76
Cdd:PRK06461  21 VRVLEVGEPKVIQTKGgprTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISE 97
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 3-74 4.46e-15

SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM.


Pssm-ID: 239937 [Multi-domain]  Cd Length: 82  Bit Score: 66.88  E-value: 4.46e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 663515921   3 VKVLSMDEPRDIE---SGGRVCEGLVGDETGTIVMSFWNEEC-DQVAVDATIWLKDARATLVRGSLRLSLGKFGSL 74
Cdd:cd04491    4 GKVLSISEPREFTrdgSEGKVQSGLVGDETGTIRFTLWDEKAaDDLEPGDVVRIENAYVREFNGRLELSVGKNSEI 79
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 115-185 7.17e-14

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 66.41  E-value: 7.17e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 663515921 115 KCFNCGKPGHISRDCPEggggkpggGKCFNCGKPGHISRDCPEggggkpgGGKCFNCGKPGHISRNCPDRG 185
Cdd:COG5082   62 VCFNCGQNGHLRRDCPH--------SICYNCSWDGHRSNHCPK-------PKKCYNCGETGHLSRDCNPSK 117
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
3-98 5.71e-11

ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 59.69  E-value: 5.71e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663515921   3 VKVLSMDEPRDIE----SGGRVCEGLVGDETGTIVMSFWNEECD-QVAVDATIWLKDARATLVRGSLRLSLGKFGSLGKP 77
Cdd:COG1599   38 GRVLEIGEERTFDrkdgSEGRVQSGVIGDETGRIRFTLWDDKADlELEEGDVVRIENAYVREFNGGPELNLGERTTIEKL 117

                         90       100
                 ....*....|....*....|.
gi 663515921  78 GREVgSVRDDLNLSDLAYAMP 98
Cdd:COG1599  118 DEDV-EVIPDEERTPIGDIEP 137
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 115-181 2.18e-09

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 54.47  E-value: 2.18e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 663515921 115 KCFNCGKPGHISRDCPEgggGKPGGGKCFNCGKPGHISRDCPE--------GGGGKPGGGKCFNCGKPGHISRNC 181
Cdd:COG5082   99 KCYNCGETGHLSRDCNP---SKDQQKSCFDCNSTRHSSEDCPSiwkhyvlnNGDGHPIKKFCYSCGSAGHFGDDC 170
PRK06386 PRK06386
replication factor A; Reviewed
 1-98 7.97e-06

replication factor A; Reviewed


Pssm-ID: 235790 [Multi-domain]  Cd Length: 358  Bit Score: 44.89  E-value: 7.97e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663515921   1 MAVKVLSMDEpRDIES--GGRVC-EGLVGDETGTIVMSFWnEECDQVAVDATIWLKDARATLVRGSLRLSL-GKFGSLGK 76
Cdd:PRK06386  17 LKVKVLSLNK-RTIKNdrGETIYyYGIIGDETGTVPFTAW-EFPDAVKSGDVIEIKYCYSKEYNGKIRIYFdSRSEVMLK 94

                         90       100
                 ....*....|....*....|....
gi 663515921  77 PGR--EVGSVRDDLNLSDLAYAMP 98
Cdd:PRK06386  95 PDEniEVKRTYKLVKIRDLSLVTP 118
PRK14699 PRK14699
replication factor A; Provisional
 4-81 6.16e-05

replication factor A; Provisional


Pssm-ID: 173162 [Multi-domain]  Cd Length: 484  Bit Score: 42.68  E-value: 6.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663515921   4 KVLSMDEPRDIE----SGGRVCEGLVGDETGTIVMSFWNEEC---DQVAVDATIWLKDA--RATLVRGSLRLSLGKFGSL 74
Cdd:PRK14699 294 RVLDISEVRTFEkkdgSPGRVGNLLLGDSTGKIRLTLWDEKTnflDEIDFDETVEVLNAysRENTFSQQVELNLGARGII 373


                 ....*..
gi 663515921  75 GKPGREV 81
Cdd:PRK14699 374 QKSEKKV 380
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 115-131 1.97e-04

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 37.12  E-value: 1.97e-04
                          10
                  ....*....|....*..
gi 663515921  115 KCFNCGKPGHISRDCPE 131
Cdd:pfam00098   2 KCYNCGEPGHIARDCPK 18
ZnF_C2HC smart00343
zinc finger;
115-131 3.24e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 36.65  E-value: 3.24e-04
                           10
                   ....*....|....*..
gi 663515921   115 KCFNCGKPGHISRDCPE 131
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 142-157 4.23e-04

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 36.35  E-value: 4.23e-04
                          10
                  ....*....|....*.
gi 663515921  142 CFNCGKPGHISRDCPE 157
Cdd:pfam00098   3 CYNCGEPGHIARDCPK 18
PRK14699 PRK14699
replication factor A; Provisional
 4-57 5.15e-04

replication factor A; Provisional


Pssm-ID: 173162 [Multi-domain]  Cd Length: 484  Bit Score: 39.98  E-value: 5.15e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 663515921   4 KVLSMDEPRDIE----SGGRVCEGLVGDETGTIVMSFWNEECD---QVAVDATIWLKDARA 57
Cdd:PRK14699 184 KVLEISEIRTFQrkdgTSGKVGNLLLGDETGTLRVTLWDDKTDflnQIEYGDTVELINAYA 244
ZnF_C2HC smart00343
zinc finger;
142-157 6.22e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.88  E-value: 6.22e-04
                           10
                   ....*....|....*.
gi 663515921   142 CFNCGKPGHISRDCPE 157
Cdd:smart00343   2 CYNCGKEGHIARDCPS 17
PRK12366 PRK12366
replication factor A; Reviewed
 3-85 1.25e-03

replication factor A; Reviewed


Pssm-ID: 237078 [Multi-domain]  Cd Length: 637  Bit Score: 38.88  E-value: 1.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663515921   3 VKVLSMDEPRDIE----SGGRVCEGLVGDETGTIVMSFWNEECD-QVAVDATIWLKDARATLVRGSLRLSLGKFGSLGKP 77
Cdd:PRK12366 415 ARVVEDYPVNEFErsdgSKGKVRNIELADGTGSIRLTLWDDDAEiEIKEGDAIKILHPYVKENGDYLDLSIGRYGRIEIN 494

                         90
                 ....*....|
gi 663515921  78 --GREVGSVR 85
Cdd:PRK12366 495 peGEIIKSNR 504
ZnF_C2HC smart00343
zinc finger;
168-182 2.62e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 33.96  E-value: 2.62e-03
                           10
                   ....*....|....*
gi 663515921   168 CFNCGKPGHISRNCP 182
Cdd:smart00343   2 CYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 168-182 2.72e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 34.04  E-value: 2.72e-03
                          10
                  ....*....|....*
gi 663515921  168 CFNCGKPGHISRNCP 182
Cdd:pfam00098   3 CYNCGEPGHIARDCP 17
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 116-179 3.48e-03

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 36.75  E-value: 3.48e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 663515921 116 CFNCGKPGHISRDCPE--------GGGGKPGGGKCFNCGKPGHISRDCPEGGGGKPGggkcFNCGKPGHISR 179
Cdd:COG5082  123 CFDCNSTRHSSEDCPSiwkhyvlnNGDGHPIKKFCYSCGSAGHFGDDCKEPRSSRVP----YVCGKKGYVSF 190
PRK07211 PRK07211
single-stranded DNA binding protein;
12-94 3.65e-03

single-stranded DNA binding protein;


Pssm-ID: 180887 [Multi-domain]  Cd Length: 485  Bit Score: 37.43  E-value: 3.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663515921  12 RDIESGGRVCEGLVGDETGTIVMSFWNEECDQV-AVDA--TIWLKDARATLVRGSLRLSLGKFGSLGKPGREVGSVRDDL 88
Cdd:PRK07211 191 RDDGSEGRVSNLTVGDETGRVRVTLWDDRADLAeELDAgeSVEIVDGYVRERDGSLELHVGDRGAVEEVDEDVEYVPDTT 270


                 ....*.
gi 663515921  89 NLSDLA 94
Cdd:PRK07211 271 PIESLE 276
 
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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