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Conserved domains on  [gi|1230880955|gb|AST51857|]
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gag protein (endogenous virus) [Ovis aries]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 270-393 8.58e-49

gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


:

Pssm-ID: 459864  Cd Length: 128  Bit Score: 166.30  E-value: 8.58e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1230880955 270 YYESLPFKQLKELKIACSQYGPTAPFTIAMIENL-GTQALPPNDWKQTARACLSGGDYLLWKSEFFEQCARIADVNRQQG 348
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALaSSNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRNQRAG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1230880955 349 --IQTSYEMLIGEGPYQATDTQLNFLPGAYAQISNAARQAWKKLPSS 393
Cdd:pfam00607  81 pdRGITLDMLTGTGQYATPQAQAQLPPEVLEQIKALALRAWKKLPPP 127
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 6-90 1.82e-44

Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10.


:

Pssm-ID: 426727  Cd Length: 85  Bit Score: 152.89  E-value: 1.82e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1230880955   6 SRQLFVHMLSVMLKHRGITVSKPKLINFLSFIEEVCPWFPREGTVNLETWKKVGEQIRTHYTLHGPEKIPVETLSFWTLI 85
Cdd:pfam02337   1 SKQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEHGPKNIPVDTWPIWALI 80


                  ....*
gi 1230880955  86 RDCLD 90
Cdd:pfam02337  81 RAVLD 85
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 394-467 8.60e-37

Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


:

Pssm-ID: 466038  Cd Length: 74  Bit Score: 131.45  E-value: 8.60e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1230880955 394 STKTEDLSKVRQGPDEPYQDFVARLLDTIGKIMSDEKAGMVLAKQLAFENANSACQAALRPYRKKGDLSDFIRI 467
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
536-571 3.59e-16

GAG-polyprotein viral zinc-finger;


:

Pssm-ID: 373297  Cd Length: 36  Bit Score: 72.20  E-value: 3.59e-16
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1230880955 536 TPNLCPRCKKGKHWARDCRSKTDVQGNPLPPVSGNW 571
Cdd:pfam14787   1 PPGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGNG 36
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 508-554 4.04e-06

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: 46.72  E-value: 4.04e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1230880955 508 SGNSGCFVCGQPGHRAAVCPQKQQSPvnTPNLCPRCKKGKHWARDCR 554
Cdd:PTZ00368   50 RGERSCYNCGKTGHLSRECPEAPPGS--GPRSCYNCGQTGHISRECP 94
 
Name Accession Description Interval E-value
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 270-393 8.58e-49

gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 459864  Cd Length: 128  Bit Score: 166.30  E-value: 8.58e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1230880955 270 YYESLPFKQLKELKIACSQYGPTAPFTIAMIENL-GTQALPPNDWKQTARACLSGGDYLLWKSEFFEQCARIADVNRQQG 348
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALaSSNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRNQRAG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1230880955 349 --IQTSYEMLIGEGPYQATDTQLNFLPGAYAQISNAARQAWKKLPSS 393
Cdd:pfam00607  81 pdRGITLDMLTGTGQYATPQAQAQLPPEVLEQIKALALRAWKKLPPP 127
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 6-90 1.82e-44

Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10.


Pssm-ID: 426727  Cd Length: 85  Bit Score: 152.89  E-value: 1.82e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1230880955   6 SRQLFVHMLSVMLKHRGITVSKPKLINFLSFIEEVCPWFPREGTVNLETWKKVGEQIRTHYTLHGPEKIPVETLSFWTLI 85
Cdd:pfam02337   1 SKQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEHGPKNIPVDTWPIWALI 80


                  ....*
gi 1230880955  86 RDCLD 90
Cdd:pfam02337  81 RAVLD 85
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 394-467 8.60e-37

Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 466038  Cd Length: 74  Bit Score: 131.45  E-value: 8.60e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1230880955 394 STKTEDLSKVRQGPDEPYQDFVARLLDTIGKIMSDEKAGMVLAKQLAFENANSACQAALRPYRKKGDLSDFIRI 467
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
536-571 3.59e-16

GAG-polyprotein viral zinc-finger;


Pssm-ID: 373297  Cd Length: 36  Bit Score: 72.20  E-value: 3.59e-16
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1230880955 536 TPNLCPRCKKGKHWARDCRSKTDVQGNPLPPVSGNW 571
Cdd:pfam14787   1 PPGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGNG 36
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 508-554 4.04e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 46.72  E-value: 4.04e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1230880955 508 SGNSGCFVCGQPGHRAAVCPQKQQSPvnTPNLCPRCKKGKHWARDCR 554
Cdd:PTZ00368   50 RGERSCYNCGKTGHLSRECPEAPPGS--GPRSCYNCGQTGHISRECP 94
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 506-560 3.37e-04

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: 42.15  E-value: 3.37e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1230880955 506 QKSGNSGCFVCGQPGHRAAVCPQKQQSPVNTPN----------LCPRCKKGKHWARDCRSKTDVQ 560
Cdd:COG5082    56 IREENPVCFNCGQNGHLRRDCPHSICYNCSWDGhrsnhcpkpkKCYNCGETGHLSRDCNPSKDQQ 120
ZnF_C2HC smart00343
zinc finger;
512-528 4.07e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.11  E-value: 4.07e-03
                           10
                   ....*....|....*..
gi 1230880955  512 GCFVCGQPGHRAAVCPQ 528
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
ZnF_C2HC smart00343
zinc finger;
540-555 6.45e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 34.34  E-value: 6.45e-03
                           10
                   ....*....|....*.
gi 1230880955  540 CPRCKKGKHWARDCRS 555
Cdd:smart00343   2 CYNCGKEGHIARDCPS 17
 
Name Accession Description Interval E-value
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 270-393 8.58e-49

gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 459864  Cd Length: 128  Bit Score: 166.30  E-value: 8.58e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1230880955 270 YYESLPFKQLKELKIACSQYGPTAPFTIAMIENL-GTQALPPNDWKQTARACLSGGDYLLWKSEFFEQCARIADVNRQQG 348
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEALaSSNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRNQRAG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1230880955 349 --IQTSYEMLIGEGPYQATDTQLNFLPGAYAQISNAARQAWKKLPSS 393
Cdd:pfam00607  81 pdRGITLDMLTGTGQYATPQAQAQLPPEVLEQIKALALRAWKKLPPP 127
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 6-90 1.82e-44

Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10.


Pssm-ID: 426727  Cd Length: 85  Bit Score: 152.89  E-value: 1.82e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1230880955   6 SRQLFVHMLSVMLKHRGITVSKPKLINFLSFIEEVCPWFPREGTVNLETWKKVGEQIRTHYTLHGPEKIPVETLSFWTLI 85
Cdd:pfam02337   1 SKQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEHGPKNIPVDTWPIWALI 80


                  ....*
gi 1230880955  86 RDCLD 90
Cdd:pfam02337  81 RAVLD 85
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 394-467 8.60e-37

Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.


Pssm-ID: 466038  Cd Length: 74  Bit Score: 131.45  E-value: 8.60e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1230880955 394 STKTEDLSKVRQGPDEPYQDFVARLLDTIGKIMSDEKAGMVLAKQLAFENANSACQAALRPYRKKGDLSDFIRI 467
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
536-571 3.59e-16

GAG-polyprotein viral zinc-finger;


Pssm-ID: 373297  Cd Length: 36  Bit Score: 72.20  E-value: 3.59e-16
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1230880955 536 TPNLCPRCKKGKHWARDCRSKTDVQGNPLPPVSGNW 571
Cdd:pfam14787   1 PPGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGNG 36
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 508-554 4.04e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 46.72  E-value: 4.04e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1230880955 508 SGNSGCFVCGQPGHRAAVCPQKQQSPvnTPNLCPRCKKGKHWARDCR 554
Cdd:PTZ00368   50 RGERSCYNCGKTGHLSRECPEAPPGS--GPRSCYNCGQTGHISRECP 94
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 506-583 5.54e-05

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 43.64  E-value: 5.54e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1230880955 506 QKSGNSGCFVCGQPGHRAAVCPQKQQSPVNTPNlCPRCKKGKHWARDCrsktdvqgnPLPPvsgnwvrGQPLAPKQCY 583
Cdd:PTZ00368   73 PGSGPRSCYNCGQTGHISRECPNRAKGGAARRA-CYNCGGEGHISRDC---------PNAG-------KRPGGDKTCY 133
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 513-553 1.36e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 42.49  E-value: 1.36e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1230880955 513 CFVCGQPGHRAAVCPQKQQSPVNTPNLCPRCKKGKHWARDC 553
Cdd:PTZ00368    3 CYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSREC 43
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 513-553 2.70e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 41.72  E-value: 2.70e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1230880955 513 CFVCGQPGHRAAVCPQKQQSPVNTPnlCPRCKKGKHWARDC 553
Cdd:PTZ00368   30 CYKCGEPGHLSRECPSAPGGRGERS--CYNCGKTGHLSREC 68
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 506-560 3.37e-04

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: 42.15  E-value: 3.37e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1230880955 506 QKSGNSGCFVCGQPGHRAAVCPQKQQSPVNTPN----------LCPRCKKGKHWARDCRSKTDVQ 560
Cdd:COG5082    56 IREENPVCFNCGQNGHLRRDCPHSICYNCSWDGhrsnhcpkpkKCYNCGETGHLSRDCNPSKDQQ 120
ZnF_C2HC smart00343
zinc finger;
512-528 4.07e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 35.11  E-value: 4.07e-03
                           10
                   ....*....|....*..
gi 1230880955  512 GCFVCGQPGHRAAVCPQ 528
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
ZnF_C2HC smart00343
zinc finger;
540-555 6.45e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 34.34  E-value: 6.45e-03
                           10
                   ....*....|....*.
gi 1230880955  540 CPRCKKGKHWARDCRS 555
Cdd:smart00343   2 CYNCGKEGHIARDCPS 17
 
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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