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Conserved domains on  [gi|916339485|gb|AKZ17466|]
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nonstructural polyprotein [Sindbis virus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_C9 super family cl03324
Peptidase family C9;
972-1179 1.33e-120

Peptidase family C9;


The actual alignment was detected with superfamily member pfam01707:

Pssm-ID: 279970  Cd Length: 202  Bit Score: 378.15  E-value: 1.33e-120
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   972 DPWIKQLTNIPKGNFQATIEDWEAEHKGIIAAINSPTPRANPFSCKTNVCWAKALEPILATAGIVLTGCQWSELFPQFAD 1051
Cdd:pfam01707    1 DPWIKQLTNIPKGNFQATIEEWEAEHKGIMAAINSPTPRADPFQNKANVCWAKSLVPILATAGIVLTGCQWSEIIPAFKE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485  1052 DKPHSAIYALDVICIKFFGMDLTSGLFSKQSIPLTYhpADSarpvaHWDNSPGTRKYGYDHAIAAELSRRFPVfqLAGK- 1130
Cdd:pfam01707   81 DKAYSPIVALNEICTKFYGVDLDSGLFSKPSVSLYY--ADN-----HWDNRPGGRMYGFNHAIAAELERRFPF--LKGKw 151

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 916339485  1131 --GTQLDLQTGRTRVISAQHNLVPVNRNLPHALVPEYKEKQPGPVEKFLNQ 1179
Cdd:pfam01707  152 niGKQLDLQTRRIRVISAQHNLIPVNRRLPHALVAEYKEVKGGRVEWLVNK 202
Macro_X_Nsp3-like cd21557
X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The ...
 1363-1490 1.66e-43

X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The X-domain, also called Mac1, is the macrodomain found in riboviral non-structural protein 3 (Nsp3), including the Nsp3 of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) as well as SARS-CoV-2, and other coronaviruses (alpha-, beta-, gamma-, and deltacoronavirus), among others. The SARS-CoV-2 Nsp3 Mac1 is highly conserved among all CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. It appears to counter host-mediated antiviral ADP-ribosylation, a post-translational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Assays show that the de-MARylating activity leads to a rapid loss of substrate, and that Mac1 could not hydrolyze poly-ADP-ribose; thus, Mac1 is a MAR-hydrolase (mono-ADP ribosylhydrolase). Mac1 was originally named ADP-ribose-1"-phosphatase (ADRP) based on data demonstrating that it could remove the phosphate group from ADP-ribose-1"-phosphate; however, activity was modest and was unclear why this would impact a virus infection. This family also includes the X-domain of Avian infectious bronchitis virus (IBV) strain Beaudette coronavirus that does not bind ADP-ribose; the triple glycine sequence found in the X-domains of SARS-CoV and human coronavirus 229E (HCoV229E), which are involved in ADP-ribose binding, is not conserved in the IBV X-domain. SARS-CoVs have two other macrodomains referred to as the SUD-N (N-terminal subdomain, or Mac2) and SUD-M (middle SUD subdomain, or Mac3) of the SARS-unique domain (SUD), which also do not bind ADP-ribose; these bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). SARS-CoV SUD-N and SUD-M are not included in this group.


:

Pssm-ID: 438957  Cd Length: 127  Bit Score: 154.64  E-value: 1.66e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1363 EEAVVNAANPLGRPGEGVCRAIYKRWPTSF--------TDSATETGTARMTVC--LGKKVIHAVGPDFRKHPeaeALKLL 1432
Cdd:cd21557     1 EDVVVNAANENLKHGGGVAGAIYKATGGAFqkesdyikKNGPLKVGTAVLLPGhgLAKNIIHVVGPRKRKGQ---DDQLL 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 916339485 1433 QNAYHAVADlvnehNIKSVAIPLLSTGIYaagKDRLEVSLNCLTTALDRTDADVTIYC 1490
Cdd:cd21557    78 AAAYKAVNK-----EYGSVLTPLLSAGIF---GVPPEQSLNALLDAVDTTDADVTVYC 127
Vmethyltransf pfam01660
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ...
 26-373 2.81e-41

Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily.


:

Pssm-ID: 396298  Cd Length: 308  Bit Score: 155.15  E-value: 2.81e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485    26 QFEVVAQQVTPNDHANARAFSHLASKLIELEVPTTATILDIGSAPARRMFSEHQY-HCVCPMRSPEDPDRMMKYASkLAE 104
Cdd:pfam01660   17 GIEFSPYSVTPHSHPAAKALENLLLEVLPSYLPNPSTVLDIKGSKLRHLKRGNPNvHCCNPILDPRDVARYPEAFS-LEK 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   105 KACKITNKNLHEKIKDLRtvldtPDAETPSLCFHNDvtcnmraeySVMqDVYINAPGTIYHQAMKGVRTLYWIGFDTTQF 184
Cdd:pfam01660   96 SLGNGEDLRPTNTFEDCR-----VLAPTTSYAFMHD---------SLH-DWSPEELADLFLRKPKLERLYATLVFPPELL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   185 MFSAmAGSYPAYNTNWADEKvlearniglcstklsegrtgklsimrkkelkpgsRVYFSVGSTL---YpEHRASLQSWHL 261
Cdd:pfam01660  161 FGDK-ESLYPELYTFWYKGD----------------------------------RFHFYPDGHLggsY-THPLNLLSWLT 204

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   262 PSVFHLNGKQSYTcrCDTVVSCEGYVVKKITISPGITGETVGYavthnsegfllCKVTDTVkGERVSFPvCTYIPATICD 341
Cdd:pfam01660  205 TSKIHLPGGFTYT--VERLESRGAHHLFKITRGDGLTPKVIVP-----------DSRTFGP-FEAVLLP-KIFVPRVLNY 269

                          330       340       350
                   ....*....|....*....|....*....|..
gi 916339485   342 QmTGIMATDISPDDAQKLLVGLNQRIVINGRT 373
Cdd:pfam01660  270 I-RGKPIPLTVVNKLFSYLRSLKKRVVINGMA 300
Viral_helicase1 super family cl26263
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 726-959 5.67e-14

Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.


The actual alignment was detected with superfamily member pfam01443:

Pssm-ID: 366646 [Multi-domain]  Cd Length: 227  Bit Score: 73.18  E-value: 5.67e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   726 GTPGSGKSAIIKSTVtarDLVTSGKKENC--REIEADVLRLRGmqitsKTVDSV-MLNGCHKAvEVLYVDEAFACHAGAL 802
Cdd:pfam01443    5 GVPGCGKSTLIRKLL---RTSRVIRPTAElrTEGKPDLPNLNV-----RTVDTFlMALLKPTG-KILILDEYTLLPPGYI 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   803 LALIAIVRPrKKVVLCGDPMQCGFFNmmqlkvhfnhPEKDICTKTFYKYISRRCTQPVTAIVSTLHYD--GKMKTTNPCK 880
Cdd:pfam01443   76 LLLAAISGA-KLVILFGDPLQIPYHS----------RAPSFLIPHFPSSLSHRVGRRTTYLLPSLRAPilSAKGFEVVVE 144

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 916339485   881 KNIEIDITGATKPKPGDIILTCFRGWVKQLqidypGHEVMTAAASQGLTRKGVYAVRQKVNENPLYAITSEHVNVLLTR 959
Cdd:pfam01443  145 RSGEYKVDYDPNGVLVLVYLTFTQALKESL-----GVRVTTVHEVQGLTFDSVTLVLDTDTDLLIISDSPEHLYVALTR 218
Tam super family cl30593
Trans-aconitate methyltransferase [Energy production and conversion];
1174-1272 8.06e-05

Trans-aconitate methyltransferase [Energy production and conversion];


The actual alignment was detected with superfamily member COG4106:

Pssm-ID: 443282 [Multi-domain]  Cd Length: 100  Bit Score: 43.27  E-value: 8.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1174 EKFLNQFKHHSVLVV--SEEKIEAPRKR---IEWIApigiagADknynlAFGFPPQARYDLVFInigtkyrNHHFQQCED 1248
Cdd:COG4106    17 ALLAERFPGARVTGVdlSPEMLARARARlpnVRFVV------AD-----LRDLDPPEPFDLVVS-------NAALHWLPD 78

                          90       100
                  ....*....|....*....|....
gi 916339485 1249 HAATLKTLSRsalnCLNPGGTLVV 1272
Cdd:COG4106    79 HAALLARLAA----ALAPGGVLAV 98
 
Name Accession Description Interval E-value
Peptidase_C9 pfam01707
Peptidase family C9;
972-1179 1.33e-120

Peptidase family C9;


Pssm-ID: 279970  Cd Length: 202  Bit Score: 378.15  E-value: 1.33e-120
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   972 DPWIKQLTNIPKGNFQATIEDWEAEHKGIIAAINSPTPRANPFSCKTNVCWAKALEPILATAGIVLTGCQWSELFPQFAD 1051
Cdd:pfam01707    1 DPWIKQLTNIPKGNFQATIEEWEAEHKGIMAAINSPTPRADPFQNKANVCWAKSLVPILATAGIVLTGCQWSEIIPAFKE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485  1052 DKPHSAIYALDVICIKFFGMDLTSGLFSKQSIPLTYhpADSarpvaHWDNSPGTRKYGYDHAIAAELSRRFPVfqLAGK- 1130
Cdd:pfam01707   81 DKAYSPIVALNEICTKFYGVDLDSGLFSKPSVSLYY--ADN-----HWDNRPGGRMYGFNHAIAAELERRFPF--LKGKw 151

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 916339485  1131 --GTQLDLQTGRTRVISAQHNLVPVNRNLPHALVPEYKEKQPGPVEKFLNQ 1179
Cdd:pfam01707  152 niGKQLDLQTRRIRVISAQHNLIPVNRRLPHALVAEYKEVKGGRVEWLVNK 202
Macro_X_Nsp3-like cd21557
X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The ...
 1363-1490 1.66e-43

X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The X-domain, also called Mac1, is the macrodomain found in riboviral non-structural protein 3 (Nsp3), including the Nsp3 of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) as well as SARS-CoV-2, and other coronaviruses (alpha-, beta-, gamma-, and deltacoronavirus), among others. The SARS-CoV-2 Nsp3 Mac1 is highly conserved among all CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. It appears to counter host-mediated antiviral ADP-ribosylation, a post-translational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Assays show that the de-MARylating activity leads to a rapid loss of substrate, and that Mac1 could not hydrolyze poly-ADP-ribose; thus, Mac1 is a MAR-hydrolase (mono-ADP ribosylhydrolase). Mac1 was originally named ADP-ribose-1"-phosphatase (ADRP) based on data demonstrating that it could remove the phosphate group from ADP-ribose-1"-phosphate; however, activity was modest and was unclear why this would impact a virus infection. This family also includes the X-domain of Avian infectious bronchitis virus (IBV) strain Beaudette coronavirus that does not bind ADP-ribose; the triple glycine sequence found in the X-domains of SARS-CoV and human coronavirus 229E (HCoV229E), which are involved in ADP-ribose binding, is not conserved in the IBV X-domain. SARS-CoVs have two other macrodomains referred to as the SUD-N (N-terminal subdomain, or Mac2) and SUD-M (middle SUD subdomain, or Mac3) of the SARS-unique domain (SUD), which also do not bind ADP-ribose; these bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). SARS-CoV SUD-N and SUD-M are not included in this group.


Pssm-ID: 438957  Cd Length: 127  Bit Score: 154.64  E-value: 1.66e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1363 EEAVVNAANPLGRPGEGVCRAIYKRWPTSF--------TDSATETGTARMTVC--LGKKVIHAVGPDFRKHPeaeALKLL 1432
Cdd:cd21557     1 EDVVVNAANENLKHGGGVAGAIYKATGGAFqkesdyikKNGPLKVGTAVLLPGhgLAKNIIHVVGPRKRKGQ---DDQLL 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 916339485 1433 QNAYHAVADlvnehNIKSVAIPLLSTGIYaagKDRLEVSLNCLTTALDRTDADVTIYC 1490
Cdd:cd21557    78 AAAYKAVNK-----EYGSVLTPLLSAGIF---GVPPEQSLNALLDAVDTTDADVTVYC 127
Vmethyltransf pfam01660
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ...
 26-373 2.81e-41

Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily.


Pssm-ID: 396298  Cd Length: 308  Bit Score: 155.15  E-value: 2.81e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485    26 QFEVVAQQVTPNDHANARAFSHLASKLIELEVPTTATILDIGSAPARRMFSEHQY-HCVCPMRSPEDPDRMMKYASkLAE 104
Cdd:pfam01660   17 GIEFSPYSVTPHSHPAAKALENLLLEVLPSYLPNPSTVLDIKGSKLRHLKRGNPNvHCCNPILDPRDVARYPEAFS-LEK 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   105 KACKITNKNLHEKIKDLRtvldtPDAETPSLCFHNDvtcnmraeySVMqDVYINAPGTIYHQAMKGVRTLYWIGFDTTQF 184
Cdd:pfam01660   96 SLGNGEDLRPTNTFEDCR-----VLAPTTSYAFMHD---------SLH-DWSPEELADLFLRKPKLERLYATLVFPPELL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   185 MFSAmAGSYPAYNTNWADEKvlearniglcstklsegrtgklsimrkkelkpgsRVYFSVGSTL---YpEHRASLQSWHL 261
Cdd:pfam01660  161 FGDK-ESLYPELYTFWYKGD----------------------------------RFHFYPDGHLggsY-THPLNLLSWLT 204

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   262 PSVFHLNGKQSYTcrCDTVVSCEGYVVKKITISPGITGETVGYavthnsegfllCKVTDTVkGERVSFPvCTYIPATICD 341
Cdd:pfam01660  205 TSKIHLPGGFTYT--VERLESRGAHHLFKITRGDGLTPKVIVP-----------DSRTFGP-FEAVLLP-KIFVPRVLNY 269

                          330       340       350
                   ....*....|....*....|....*....|..
gi 916339485   342 QmTGIMATDISPDDAQKLLVGLNQRIVINGRT 373
Cdd:pfam01660  270 I-RGKPIPLTVVNKLFSYLRSLKKRVVINGMA 300
A1pp smart00506
Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by ...
 1351-1472 1.62e-34

Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson _ Fuji).


Pssm-ID: 214701  Cd Length: 133  Bit Score: 129.35  E-value: 1.62e-34
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   1351 YRTKRENIADCQEEAVVNAANPLGRPGEGVCRAIYKRWP-----TSFTDSA---TETGTARMT---VCLGKKVIHAVGPD 1419
Cdd:smart00506    2 LKVVKGDITKPRADAIVNAANSDGAHGGGVAGAIARAAGkalskEEVRKLAggeCPVGTAVVTeggNLPAKYVIHAVGPR 81

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|...
gi 916339485   1420 FRKHPEaEALKLLQNAYHAVADLVNEHNIKSVAIPLLSTGIYAAGKDRLEVSL 1472
Cdd:smart00506   82 ASGHSK-EGFELLENAYRNCLELAIELGITSVALPLIGTGIYGVPKDRSAQAL 133
YmdB COG2110
O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ...
 1355-1504 6.11e-25

O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441713  Cd Length: 168  Bit Score: 103.33  E-value: 6.11e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1355 RENIADCQEEAVVNAANPLGRPGEGVCRAIYKRW-PTSFTDSAT-------ETGTARMTVCLG---KKVIHAVGPDFRKH 1423
Cdd:COG2110     5 QGDITELDVDAIVNAANSSLLGGGGVAGAIHRAAgPELLEECRRlckqggcPTGEAVITPAGNlpaKYVIHTVGPVWRGG 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1424 PEAEAlKLLQNAYHAVADLVNEHNIKSVAIPLLSTGIYAAGKDR-LEVSLNCLTTALDRTDA--DVTIYCLDKKWKERID 1500
Cdd:COG2110    85 GPSEE-ELLASCYRNSLELAEELGIRSIAFPAIGTGVGGFPWEEaAPIAVETLRDFLEEHPSleEVRFVLFDEEDYEAYR 163


                  ....
gi 916339485 1501 AALQ 1504
Cdd:COG2110   164 RALA 167
Macro pfam01661
Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ...
 1367-1461 1.33e-20

Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent: in certain cases it is believed to bind non-covalently; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site.


Pssm-ID: 460286  Cd Length: 116  Bit Score: 88.78  E-value: 1.33e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485  1367 VNAANPLGRPGEGVCRAIYKRWPTSFTDSATE-------TGTARMT---VCLGKKVIHAVGPDFRKHPEAEALKLLQNAY 1436
Cdd:pfam01661    1 VNAANSRLLGGGGVAGAIHRAAGPELLEECRElkkggcpTGEAVVTpggNLPAKYVIHTVGPTWRHGGSHGEEELLESCY 80

                           90       100
                   ....*....|....*....|....*
gi 916339485  1437 HAVADLVNEHNIKSVAIPLLSTGIY 1461
Cdd:pfam01661   81 RNALALAEELGIKSIAFPAISTGIY 105
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 726-959 5.67e-14

Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.


Pssm-ID: 366646 [Multi-domain]  Cd Length: 227  Bit Score: 73.18  E-value: 5.67e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   726 GTPGSGKSAIIKSTVtarDLVTSGKKENC--REIEADVLRLRGmqitsKTVDSV-MLNGCHKAvEVLYVDEAFACHAGAL 802
Cdd:pfam01443    5 GVPGCGKSTLIRKLL---RTSRVIRPTAElrTEGKPDLPNLNV-----RTVDTFlMALLKPTG-KILILDEYTLLPPGYI 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   803 LALIAIVRPrKKVVLCGDPMQCGFFNmmqlkvhfnhPEKDICTKTFYKYISRRCTQPVTAIVSTLHYD--GKMKTTNPCK 880
Cdd:pfam01443   76 LLLAAISGA-KLVILFGDPLQIPYHS----------RAPSFLIPHFPSSLSHRVGRRTTYLLPSLRAPilSAKGFEVVVE 144

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 916339485   881 KNIEIDITGATKPKPGDIILTCFRGWVKQLqidypGHEVMTAAASQGLTRKGVYAVRQKVNENPLYAITSEHVNVLLTR 959
Cdd:pfam01443  145 RSGEYKVDYDPNGVLVLVYLTFTQALKESL-----GVRVTTVHEVQGLTFDSVTLVLDTDTDLLIISDSPEHLYVALTR 218
PRK00431 PRK00431
ADP-ribose-binding protein;
1364-1461 2.80e-12

ADP-ribose-binding protein;


Pssm-ID: 234759  Cd Length: 177  Bit Score: 67.17  E-value: 2.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1364 EAVVNAANPLGRPGEGVCRAIYK-----------RWPTSF----TDSATETGTARMTVclgKKVIHAVGPDFRKhPEAEA 1428
Cdd:PRK00431   18 DAIVNAANSSLLGGGGVDGAIHRaagpeileecrELRQQQgpcpTGEAVITSAGRLPA---KYVIHTVGPVWRG-GEDNE 93

                          90       100       110
                  ....*....|....*....|....*....|...
gi 916339485 1429 LKLLQNAYHAVADLVNEHNIKSVAIPLLSTGIY 1461
Cdd:PRK00431   94 AELLASAYRNSLRLAAELGLRSIAFPAISTGVY 126
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 724-823 1.08e-06

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 49.16  E-value: 1.08e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485  724 VIGTPGSGKSAIIKSTVTARDLVTSGKKencreieadVLrlrgmqITSKTvdsvmlngcHKAVE---VLYVDEAfaCHAG 800
Cdd:cd17934     4 IQGPPGTGKTTTIAAIVLQLLKGLRGKR---------VL------VTAQS---------NVAVDnvdVVIIDEA--SQIT 57

                          90       100
                  ....*....|....*....|...
gi 916339485  801 ALLALIAIVRPrKKVVLCGDPMQ 823
Cdd:cd17934    58 EPELLIALIRA-KKVVLVGDPKQ 79
Tam COG4106
Trans-aconitate methyltransferase [Energy production and conversion];
1174-1272 8.06e-05

Trans-aconitate methyltransferase [Energy production and conversion];


Pssm-ID: 443282 [Multi-domain]  Cd Length: 100  Bit Score: 43.27  E-value: 8.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1174 EKFLNQFKHHSVLVV--SEEKIEAPRKR---IEWIApigiagADknynlAFGFPPQARYDLVFInigtkyrNHHFQQCED 1248
Cdd:COG4106    17 ALLAERFPGARVTGVdlSPEMLARARARlpnVRFVV------AD-----LRDLDPPEPFDLVVS-------NAALHWLPD 78

                          90       100
                  ....*....|....*....|....
gi 916339485 1249 HAATLKTLSRsalnCLNPGGTLVV 1272
Cdd:COG4106    79 HAALLARLAA----ALAPGGVLAV 98
 
Name Accession Description Interval E-value
Peptidase_C9 pfam01707
Peptidase family C9;
972-1179 1.33e-120

Peptidase family C9;


Pssm-ID: 279970  Cd Length: 202  Bit Score: 378.15  E-value: 1.33e-120
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   972 DPWIKQLTNIPKGNFQATIEDWEAEHKGIIAAINSPTPRANPFSCKTNVCWAKALEPILATAGIVLTGCQWSELFPQFAD 1051
Cdd:pfam01707    1 DPWIKQLTNIPKGNFQATIEEWEAEHKGIMAAINSPTPRADPFQNKANVCWAKSLVPILATAGIVLTGCQWSEIIPAFKE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485  1052 DKPHSAIYALDVICIKFFGMDLTSGLFSKQSIPLTYhpADSarpvaHWDNSPGTRKYGYDHAIAAELSRRFPVfqLAGK- 1130
Cdd:pfam01707   81 DKAYSPIVALNEICTKFYGVDLDSGLFSKPSVSLYY--ADN-----HWDNRPGGRMYGFNHAIAAELERRFPF--LKGKw 151

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 916339485  1131 --GTQLDLQTGRTRVISAQHNLVPVNRNLPHALVPEYKEKQPGPVEKFLNQ 1179
Cdd:pfam01707  152 niGKQLDLQTRRIRVISAQHNLIPVNRRLPHALVAEYKEVKGGRVEWLVNK 202
Macro_X_Nsp3-like cd21557
X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The ...
 1363-1490 1.66e-43

X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The X-domain, also called Mac1, is the macrodomain found in riboviral non-structural protein 3 (Nsp3), including the Nsp3 of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) as well as SARS-CoV-2, and other coronaviruses (alpha-, beta-, gamma-, and deltacoronavirus), among others. The SARS-CoV-2 Nsp3 Mac1 is highly conserved among all CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. It appears to counter host-mediated antiviral ADP-ribosylation, a post-translational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Assays show that the de-MARylating activity leads to a rapid loss of substrate, and that Mac1 could not hydrolyze poly-ADP-ribose; thus, Mac1 is a MAR-hydrolase (mono-ADP ribosylhydrolase). Mac1 was originally named ADP-ribose-1"-phosphatase (ADRP) based on data demonstrating that it could remove the phosphate group from ADP-ribose-1"-phosphate; however, activity was modest and was unclear why this would impact a virus infection. This family also includes the X-domain of Avian infectious bronchitis virus (IBV) strain Beaudette coronavirus that does not bind ADP-ribose; the triple glycine sequence found in the X-domains of SARS-CoV and human coronavirus 229E (HCoV229E), which are involved in ADP-ribose binding, is not conserved in the IBV X-domain. SARS-CoVs have two other macrodomains referred to as the SUD-N (N-terminal subdomain, or Mac2) and SUD-M (middle SUD subdomain, or Mac3) of the SARS-unique domain (SUD), which also do not bind ADP-ribose; these bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). SARS-CoV SUD-N and SUD-M are not included in this group.


Pssm-ID: 438957  Cd Length: 127  Bit Score: 154.64  E-value: 1.66e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1363 EEAVVNAANPLGRPGEGVCRAIYKRWPTSF--------TDSATETGTARMTVC--LGKKVIHAVGPDFRKHPeaeALKLL 1432
Cdd:cd21557     1 EDVVVNAANENLKHGGGVAGAIYKATGGAFqkesdyikKNGPLKVGTAVLLPGhgLAKNIIHVVGPRKRKGQ---DDQLL 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 916339485 1433 QNAYHAVADlvnehNIKSVAIPLLSTGIYaagKDRLEVSLNCLTTALDRTDADVTIYC 1490
Cdd:cd21557    78 AAAYKAVNK-----EYGSVLTPLLSAGIF---GVPPEQSLNALLDAVDTTDADVTVYC 127
Vmethyltransf pfam01660
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ...
 26-373 2.81e-41

Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily.


Pssm-ID: 396298  Cd Length: 308  Bit Score: 155.15  E-value: 2.81e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485    26 QFEVVAQQVTPNDHANARAFSHLASKLIELEVPTTATILDIGSAPARRMFSEHQY-HCVCPMRSPEDPDRMMKYASkLAE 104
Cdd:pfam01660   17 GIEFSPYSVTPHSHPAAKALENLLLEVLPSYLPNPSTVLDIKGSKLRHLKRGNPNvHCCNPILDPRDVARYPEAFS-LEK 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   105 KACKITNKNLHEKIKDLRtvldtPDAETPSLCFHNDvtcnmraeySVMqDVYINAPGTIYHQAMKGVRTLYWIGFDTTQF 184
Cdd:pfam01660   96 SLGNGEDLRPTNTFEDCR-----VLAPTTSYAFMHD---------SLH-DWSPEELADLFLRKPKLERLYATLVFPPELL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   185 MFSAmAGSYPAYNTNWADEKvlearniglcstklsegrtgklsimrkkelkpgsRVYFSVGSTL---YpEHRASLQSWHL 261
Cdd:pfam01660  161 FGDK-ESLYPELYTFWYKGD----------------------------------RFHFYPDGHLggsY-THPLNLLSWLT 204

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   262 PSVFHLNGKQSYTcrCDTVVSCEGYVVKKITISPGITGETVGYavthnsegfllCKVTDTVkGERVSFPvCTYIPATICD 341
Cdd:pfam01660  205 TSKIHLPGGFTYT--VERLESRGAHHLFKITRGDGLTPKVIVP-----------DSRTFGP-FEAVLLP-KIFVPRVLNY 269

                          330       340       350
                   ....*....|....*....|....*....|..
gi 916339485   342 QmTGIMATDISPDDAQKLLVGLNQRIVINGRT 373
Cdd:pfam01660  270 I-RGKPIPLTVVNKLFSYLRSLKKRVVINGMA 300
A1pp smart00506
Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by ...
 1351-1472 1.62e-34

Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson _ Fuji).


Pssm-ID: 214701  Cd Length: 133  Bit Score: 129.35  E-value: 1.62e-34
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   1351 YRTKRENIADCQEEAVVNAANPLGRPGEGVCRAIYKRWP-----TSFTDSA---TETGTARMT---VCLGKKVIHAVGPD 1419
Cdd:smart00506    2 LKVVKGDITKPRADAIVNAANSDGAHGGGVAGAIARAAGkalskEEVRKLAggeCPVGTAVVTeggNLPAKYVIHAVGPR 81

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|...
gi 916339485   1420 FRKHPEaEALKLLQNAYHAVADLVNEHNIKSVAIPLLSTGIYAAGKDRLEVSL 1472
Cdd:smart00506   82 ASGHSK-EGFELLENAYRNCLELAIELGITSVALPLIGTGIYGVPKDRSAQAL 133
YmdB COG2110
O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ...
 1355-1504 6.11e-25

O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441713  Cd Length: 168  Bit Score: 103.33  E-value: 6.11e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1355 RENIADCQEEAVVNAANPLGRPGEGVCRAIYKRW-PTSFTDSAT-------ETGTARMTVCLG---KKVIHAVGPDFRKH 1423
Cdd:COG2110     5 QGDITELDVDAIVNAANSSLLGGGGVAGAIHRAAgPELLEECRRlckqggcPTGEAVITPAGNlpaKYVIHTVGPVWRGG 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1424 PEAEAlKLLQNAYHAVADLVNEHNIKSVAIPLLSTGIYAAGKDR-LEVSLNCLTTALDRTDA--DVTIYCLDKKWKERID 1500
Cdd:COG2110    85 GPSEE-ELLASCYRNSLELAEELGIRSIAFPAIGTGVGGFPWEEaAPIAVETLRDFLEEHPSleEVRFVLFDEEDYEAYR 163


                  ....
gi 916339485 1501 AALQ 1504
Cdd:COG2110   164 RALA 167
Macro_OAADPr_deacetylase cd02908
macrodomain, O-acetyl-ADP-ribose (OAADPr) family; Macrodomains are found in a variety of ...
 1355-1491 5.57e-21

macrodomain, O-acetyl-ADP-ribose (OAADPr) family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. This family includes eukaryotic macrodomain proteins such as human MacroD1 and MacroD2, and bacterial proteins such as Escherichia coli YmdB; these have been shown to be O-acetyl-ADP-ribose (OAADPr) deacetylases that efficiently catalyze the hydrolysis of OAADPr to produce ADP-ribose and free acetate. OAADPr is a sirtuin reaction product generated from the NAD+-dependent protein deacetylation reactions and has been implicated as a signaling molecule. By acting on mono-ADP-ribosylated substrates, OAADPr deacetylases may reverse cellular ADP-ribosylation.


Pssm-ID: 438955  Cd Length: 166  Bit Score: 91.81  E-value: 5.57e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1355 RENIADCQEEAVVNAANP--LGrpGEGVCRAIY-----------KRWPtsftdSATETGTARMTvcLG-----KKVIHAV 1416
Cdd:cd02908     6 RGDITKLEVDAIVNAANSslLG--GGGVDGAIHraagpelleecRKLG-----GVCPTGEAKIT--PGynlpaKYVIHTV 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 916339485 1417 GPDFRKHPEAEAlKLLQNAYHAVADLVNEHNIKSVAIPLLSTGIYAAGKDR-LEVSLNCLTTALDRTDA-DVTIYCL 1491
Cdd:cd02908    77 GPIGEGGVEEEP-ELLASCYRSSLELALENGLKSIAFPCISTGIYGYPNEEaAEIALNTVREWLEEHDKiDRIIFVV 152
Macro pfam01661
Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ...
 1367-1461 1.33e-20

Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent: in certain cases it is believed to bind non-covalently; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site.


Pssm-ID: 460286  Cd Length: 116  Bit Score: 88.78  E-value: 1.33e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485  1367 VNAANPLGRPGEGVCRAIYKRWPTSFTDSATE-------TGTARMT---VCLGKKVIHAVGPDFRKHPEAEALKLLQNAY 1436
Cdd:pfam01661    1 VNAANSRLLGGGGVAGAIHRAAGPELLEECRElkkggcpTGEAVVTpggNLPAKYVIHTVGPTWRHGGSHGEEELLESCY 80

                           90       100
                   ....*....|....*....|....*
gi 916339485  1437 HAVADLVNEHNIKSVAIPLLSTGIY 1461
Cdd:pfam01661   81 RNALALAEELGIKSIAFPAISTGIY 105
Macro_Af1521_BAL-like cd02907
macrodomain, Af1521-like family; Macrodomains are found in a variety of proteins with diverse ...
 1354-1461 9.78e-17

macrodomain, Af1521-like family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. The macrodomains in this family show similarity to Af1521, a protein from Archaeoglobus fulgidus containing a stand-alone macrodomain. Af1521 binds ADP-ribose and exhibits phosphatase activity toward ADP-ribose-1"-monophosphate (Appr-1"-p). Also included in this family are the N-terminal (or first) macrodomains of BAL (B-aggressive lymphoma) proteins which contain multiple macrodomains, such as the first macrodomain of mono-ADP-ribosyltransferase PARP14 (PARP-14, also known as ADP-ribosyltransferase diphtheria toxin-like 8, ATRD8, B aggressive lymphoma protein 2, or BAL2). Most BAL proteins also contain a C-terminal PARP active site and are also named as PARPs. Human BAL1 (or PARP-9) was originally identified as a risk-related gene in diffuse large B-cell lymphoma that promotes malignant B-cell migration. Some BAL family proteins exhibit PARP activity. Poly (ADP-ribosyl)ation is an immediate DNA-damage-dependent post-translational modification of histones and other nuclear proteins. BAL proteins may also function as transcriptional repressors.


Pssm-ID: 394877 [Multi-domain]  Cd Length: 158  Bit Score: 79.46  E-value: 9.78e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1354 KRENIADCQEEAVVNAANPLGRPGEGVCRAIYKRWPTSFTD---------SATETGTARMT-----VClgKKVIHAVGPD 1419
Cdd:cd02907     7 YKGDITKEKVDAIVNAANERLKHGGGVAGAISKAGGPEIQEecdkyikknGKLRVGEVVVTsagklPC--KYVIHAVGPR 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 916339485 1420 FRKHPEAEALKLLQNAYHAVADLVNEHNIKSVAIPLLSTGIY 1461
Cdd:cd02907    85 WSGGSKEECEDLLYKAVLNSLEEAEELKATSIAIPAISSGIF 126
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 726-959 5.67e-14

Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.


Pssm-ID: 366646 [Multi-domain]  Cd Length: 227  Bit Score: 73.18  E-value: 5.67e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   726 GTPGSGKSAIIKSTVtarDLVTSGKKENC--REIEADVLRLRGmqitsKTVDSV-MLNGCHKAvEVLYVDEAFACHAGAL 802
Cdd:pfam01443    5 GVPGCGKSTLIRKLL---RTSRVIRPTAElrTEGKPDLPNLNV-----RTVDTFlMALLKPTG-KILILDEYTLLPPGYI 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485   803 LALIAIVRPrKKVVLCGDPMQCGFFNmmqlkvhfnhPEKDICTKTFYKYISRRCTQPVTAIVSTLHYD--GKMKTTNPCK 880
Cdd:pfam01443   76 LLLAAISGA-KLVILFGDPLQIPYHS----------RAPSFLIPHFPSSLSHRVGRRTTYLLPSLRAPilSAKGFEVVVE 144

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 916339485   881 KNIEIDITGATKPKPGDIILTCFRGWVKQLqidypGHEVMTAAASQGLTRKGVYAVRQKVNENPLYAITSEHVNVLLTR 959
Cdd:pfam01443  145 RSGEYKVDYDPNGVLVLVYLTFTQALKESL-----GVRVTTVHEVQGLTFDSVTLVLDTDTDLLIISDSPEHLYVALTR 218
PRK00431 PRK00431
ADP-ribose-binding protein;
1364-1461 2.80e-12

ADP-ribose-binding protein;


Pssm-ID: 234759  Cd Length: 177  Bit Score: 67.17  E-value: 2.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1364 EAVVNAANPLGRPGEGVCRAIYK-----------RWPTSF----TDSATETGTARMTVclgKKVIHAVGPDFRKhPEAEA 1428
Cdd:PRK00431   18 DAIVNAANSSLLGGGGVDGAIHRaagpeileecrELRQQQgpcpTGEAVITSAGRLPA---KYVIHTVGPVWRG-GEDNE 93

                          90       100       110
                  ....*....|....*....|....*....|...
gi 916339485 1429 LKLLQNAYHAVADLVNEHNIKSVAIPLLSTGIY 1461
Cdd:PRK00431   94 AELLASAYRNSLRLAAELGLRSIAFPAISTGVY 126
Macro_SF cd02749
macrodomain superfamily; Macrodomains are found in a variety of proteins with diverse cellular ...
 1365-1461 6.36e-11

macrodomain superfamily; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Macrodomains include the yeast macrodomain Poa1 which is a phosphatase of ADP-ribose-1"-phosphate, a by-product of tRNA splicing. Some macrodomains have ADPr-unrelated binding partners such as the coronavirus SUD-N (N-terminal subdomain) and SUD-M (middle subdomain) of the SARS-unique domain (SUD) which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). Macrodomains regulate a wide variety of cellular and organismal processes, including DNA damage repair, signal transduction, and immune response.


Pssm-ID: 394871  Cd Length: 121  Bit Score: 61.65  E-value: 6.36e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1365 AVVNAANPLGRPGEGVCRAIYKRWPTSFTDSATE--------TGTARMT---VCLGKKVIHAVGPDFRKHPEAEalKLLQ 1433
Cdd:cd02749     2 AIVNPANNDLYLGGGVAKAISKKAGGDLQEECEErkkngylkVGEVAVTkggNLPARYIIHVVGPVASSKKKTY--EPLK 79

                          90       100
                  ....*....|....*....|....*...
gi 916339485 1434 NAYHAVADLVNEHNIKSVAIPLLSTGIY 1461
Cdd:cd02749    80 KCVKNCLSLADEKGLKSVAFPAIGTGIA 107
Macro_Ttha0132-like cd03330
Macrodomain, uncharacterized family similar to Thermus thermophilus hypothetical protein ...
 1352-1460 4.81e-09

Macrodomain, uncharacterized family similar to Thermus thermophilus hypothetical protein Ttha0132; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Macrodomains include the yeast macrodomain Poa1 which is a phosphatase of ADP-ribose-1"-phosphate, a by-product of tRNA splicing. Some macrodomains have ADPr-unrelated binding partners such as the coronavirus SUD-N (N-terminal subdomain) and SUD-M (middle subdomain) of the SARS-unique domain (SUD) which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). Macrodomains regulate a wide variety of cellular and organismal processes, including DNA damage repair, signal transduction, and immune response. This family is composed of uncharacterized proteins containing a stand-alone macrodomain, similar to Thermus thermophilus hypothetical protein Ttha0132.


Pssm-ID: 394879  Cd Length: 147  Bit Score: 56.67  E-value: 4.81e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1352 RTKRENIADCQEEAVVNAANPLGRPGEGVCRAIYKRWPTSFTD-----------SATETGTARMTVclgKKVIHA--VGP 1418
Cdd:cd03330     3 IVVQGDITEQDADAIVNAANRRLLMGSGVAGAIKRKGGEEIEReamrkgpirvgEAVETGAGKLPA---KYVIHAavMGM 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 916339485 1419 DFRKHPEAealklLQNAYHAVADLVNEHNIKSVAIPLLSTGI 1460
Cdd:cd03330    80 PGRSSEES-----IRDATRNALAKAEELGLESVAFPAIGTGV 116
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 724-823 1.08e-06

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 49.16  E-value: 1.08e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485  724 VIGTPGSGKSAIIKSTVTARDLVTSGKKencreieadVLrlrgmqITSKTvdsvmlngcHKAVE---VLYVDEAfaCHAG 800
Cdd:cd17934     4 IQGPPGTGKTTTIAAIVLQLLKGLRGKR---------VL------VTAQS---------NVAVDnvdVVIIDEA--SQIT 57

                          90       100
                  ....*....|....*....|...
gi 916339485  801 ALLALIAIVRPrKKVVLCGDPMQ 823
Cdd:cd17934    58 EPELLIALIRA-KKVVLVGDPKQ 79
PRK04143 PRK04143
protein-ADP-ribose hydrolase;
1398-1461 3.05e-05

protein-ADP-ribose hydrolase;


Pssm-ID: 235225  Cd Length: 264  Bit Score: 47.67  E-value: 3.05e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 916339485 1398 ETGTARMT--VCL-GKKVIHAVGPDFRKHPEAEALK-LLQNAYHAVADLVNEHNIKSVAIPLLSTGIY 1461
Cdd:PRK04143  147 ATGQAKITraYNLpAKYVIHTVGPIIRKQPVSPIRAdLLASCYRSCLKLAEKAGLKSIAFCCISTGVF 214
Tam COG4106
Trans-aconitate methyltransferase [Energy production and conversion];
1174-1272 8.06e-05

Trans-aconitate methyltransferase [Energy production and conversion];


Pssm-ID: 443282 [Multi-domain]  Cd Length: 100  Bit Score: 43.27  E-value: 8.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 916339485 1174 EKFLNQFKHHSVLVV--SEEKIEAPRKR---IEWIApigiagADknynlAFGFPPQARYDLVFInigtkyrNHHFQQCED 1248
Cdd:COG4106    17 ALLAERFPGARVTGVdlSPEMLARARARlpnVRFVV------AD-----LRDLDPPEPFDLVVS-------NAALHWLPD 78

                          90       100
                  ....*....|....*....|....
gi 916339485 1249 HAATLKTLSRsalnCLNPGGTLVV 1272
Cdd:COG4106    79 HAALLARLAA----ALAPGGVLAV 98
Macro_GDAP2-like cd02905
macrodomain, GDAP2-like family; Macrodomains are found in a variety of proteins with diverse ...
 1399-1458 3.06e-04

macrodomain, GDAP2-like family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. This family contains proteins similar to human GDAP2, the ganglioside induced differentiation associated protein 2, whose gene is expressed at a higher level in differentiated Neuro2a cells compared with non-differentiated cells. GDAP2 contains an N-terminal macrodomain and a C-terminal Sec14p-like lipid binding domain. It is specifically expressed in brain and testis.


Pssm-ID: 394876  Cd Length: 169  Bit Score: 43.38  E-value: 3.06e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 916339485 1399 TGTARMTVC---LGKKVIHAVGPDFR-KHPEAeALKLLQNAYHAVADLVNEHNIKSVAIPLLST 1458
Cdd:cd02905    56 TGEAKLTKGynlPARYVIHTVGPRYNeKYRTA-AESALYSCYRNVLQLAKEHKLRSVAFPVIHS 118
 
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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