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Conserved domains on  [gi|9626966|ref|NP_056881|]
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Pr110 [Mouse mammary tumor virus]

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 ...
 284-409 3.96e-45

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: 158.21  E-value: 3.96e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966    284 VWEPLPLKTLKELQSAVRTMGPSAPYTLQVVD-MVASQWLTPSDWHQTARATLSPGDYVLWRTEYEEKSKEMVQK--AAG 360
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEaLASSNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRnqRAG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 9626966    361 KRKGkVSLDMLLGTGQFLSPSSQIKLSKDVLKDVTTNAVLAWRAIPPPG 409
Cdd:pfam00607  81 PDRG-ITLDMLTGTGQYATPQAQAQLPPEVLEQIKALALRAWKKLPPPG 128
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 751-849 2.08e-39

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


:

Pssm-ID: 425454  Cd Length: 101  Bit Score: 140.97  E-value: 2.08e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966    751 SDSRPMLHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQ-PLRWQHEDKSGIIHPFVI 829
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQiLILIGEDKFRGTVSPLIL 80

                          90       100
                  ....*....|....*....|
gi 9626966    830 PTLPFTLWGRDIMKDIKVRL 849
Cdd:pfam00077  81 PTCPVNIIGRDLLQQLGGRL 100
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 8-92 1.19e-38

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: 138.25  E-value: 1.19e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966      8 GQKLFVSVLQRLLSERGLHVKESSAIEFYQFLIKVSPWFPEEGGLNLQDWKRVGREMKRYAAEHGTDSIPKQAYPIWLQL 87
Cdd:pfam02337   1 SKQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEHGPKNIPVDTWPIWALI 80


                  ....*
gi 9626966     88 REILT 92
Cdd:pfam02337  81 RAVLD 85
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 619-741 1.00e-35

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


:

Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 131.64  E-value: 1.00e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966    619 TIHDLPRGTPGSAGLDLSSQKDLILSLeDGVSLVPTLVKGTLPEGTTGLIIGRSSNYKKGLEVLPGVIDSDFQGEIKVMV 698
Cdd:pfam00692   2 EAEIPTPGSPGDAGYDLYAPYDLTVKP-GGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 9626966    699 KAAKNA-VIIHKGERIAQ----LLLLPYLKLPNPVIKEERGSEGFGST 741
Cdd:pfam00692  81 FNLGKSdFTIKKGDRIAQlifePILHPELEPVETLDNTDRGDGGFGSS 128
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 409-482 1.19e-34

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: 126.44  E-value: 1.19e-34
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9626966    409 GVKKTVLAGLKQGNEESYETFISRLEEAVYRMMPRGEGSDILIKQLAWENANSLCQDLIRPIRKTGTIQDYIRA 482
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
550-584 2.04e-16

GAG-polyprotein viral zinc-finger;


:

Pssm-ID: 373297  Cd Length: 36  Bit Score: 73.36  E-value: 2.04e-16
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 9626966    550 PPGLCPRCKKGYHWKSECKSKFDKDGNPLPPLETN 584
Cdd:pfam14787   1 PPGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGN 35
AIR1 super family cl34894
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 525-567 1.89e-05

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


The actual alignment was detected with superfamily member COG5082:

Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 46.38  E-value: 1.89e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 9626966  525 PVCFSCGKTGHIRKDCkdekgskraPPGLCPRCKKGYHWKSEC 567
Cdd:COG5082  61 PVCFNCGQNGHLRRDC---------PHSICYNCSWDGHRSNHC 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 ...
 284-409 3.96e-45

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: 158.21  E-value: 3.96e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966    284 VWEPLPLKTLKELQSAVRTMGPSAPYTLQVVD-MVASQWLTPSDWHQTARATLSPGDYVLWRTEYEEKSKEMVQK--AAG 360
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEaLASSNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRnqRAG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 9626966    361 KRKGkVSLDMLLGTGQFLSPSSQIKLSKDVLKDVTTNAVLAWRAIPPPG 409
Cdd:pfam00607  81 PDRG-ITLDMLTGTGQYATPQAQAQLPPEVLEQIKALALRAWKKLPPPG 128
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 751-849 2.08e-39

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 425454  Cd Length: 101  Bit Score: 140.97  E-value: 2.08e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966    751 SDSRPMLHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQ-PLRWQHEDKSGIIHPFVI 829
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQiLILIGEDKFRGTVSPLIL 80

                          90       100
                  ....*....|....*....|
gi 9626966    830 PTLPFTLWGRDIMKDIKVRL 849
Cdd:pfam00077  81 PTCPVNIIGRDLLQQLGGRL 100
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 8-92 1.19e-38

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: 138.25  E-value: 1.19e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966      8 GQKLFVSVLQRLLSERGLHVKESSAIEFYQFLIKVSPWFPEEGGLNLQDWKRVGREMKRYAAEHGTDSIPKQAYPIWLQL 87
Cdd:pfam02337   1 SKQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEHGPKNIPVDTWPIWALI 80


                  ....*
gi 9626966     88 REILT 92
Cdd:pfam02337  81 RAVLD 85
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 619-741 1.00e-35

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 131.64  E-value: 1.00e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966    619 TIHDLPRGTPGSAGLDLSSQKDLILSLeDGVSLVPTLVKGTLPEGTTGLIIGRSSNYKKGLEVLPGVIDSDFQGEIKVMV 698
Cdd:pfam00692   2 EAEIPTPGSPGDAGYDLYAPYDLTVKP-GGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 9626966    699 KAAKNA-VIIHKGERIAQ----LLLLPYLKLPNPVIKEERGSEGFGST 741
Cdd:pfam00692  81 FNLGKSdFTIKKGDRIAQlifePILHPELEPVETLDNTDRGDGGFGSS 128
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 409-482 1.19e-34

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: 126.44  E-value: 1.19e-34
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9626966    409 GVKKTVLAGLKQGNEESYETFISRLEEAVYRMMPRGEGSDILIKQLAWENANSLCQDLIRPIRKTGTIQDYIRA 482
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 757-842 2.71e-31

Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133149  Cd Length: 87  Bit Score: 117.37  E-value: 2.71e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966  757 LHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQ-PLRWQHEDKSGIIHPFVIPtLPFT 835
Cdd:cd05482   1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSSVlLLEIDGEGHLGTILVYVLS-LPVN 79


                ....*..
gi 9626966  836 LWGRDIM 842
Cdd:cd05482  80 LWGRDIL 86
dut TIGR00576
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ...
 611-741 7.07e-23

deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is in maintaining the levels of dUTP in the cell to prevent dUTP incorporation into DNA during DNA replication. Pol proteins in viruses are very similar to this protein family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Changed role from 132 to 123. RTD [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 273149 [Multi-domain]  Cd Length: 142  Bit Score: 95.38  E-value: 7.07e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966    611 LNPEAPpftihdLP-RGTPGSAGLDLSSQKDLILsLEDGVSLVPTLVKGTLPEGTTGLIIGRSSN-YKKGLEVL--PGVI 686
Cdd:TIGR00576   7 LSPNAP------LPtYATEGAAGYDLRAAEDVTI-PPGERALVPTGIAIELPDGYYGRVAPRSGLaLKHGVTIDnsPGVI 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 9626966    687 DSDFQGEIKV-MVKAAKNAVIIHKGERIAQLLLLPYLKLPNPVIKEE-----RGSEGFGST 741
Cdd:TIGR00576  80 DADYRGEIKViLINLGKEDFTVKKGDRIAQLVVEKIVTEVEFEEVEEldeteRGEGGFGST 140
Dut COG0756
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ...
 611-741 1.05e-22

dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP pyrophosphatase (dUTPase) is part of the Pathway/BioSystem: Thymidylate biosynthesis


Pssm-ID: 440519 [Multi-domain]  Cd Length: 143  Bit Score: 94.70  E-value: 1.05e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966  611 LNPEAPpftihdLPR-GTPGSAGLDLSSQKDLILSLEDG-VSLVPTLVKGTLPEGTTGLIIGRSSN-YKKGLEVL--PGV 685
Cdd:COG0756   7 LDEDAP------LPAyATPGSAGLDLRAALDEPVTLKPGeRALVPTGLAIALPPGYEAQVRPRSGLaLKHGITLLnsPGT 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9626966  686 IDSDFQGEIKV-MVKAAKNAVIIHKGERIAQllllpylklpnPVIKE---------------ERGSEGFGST 741
Cdd:COG0756  81 IDSDYRGEIKViLINLGDEPFTIERGDRIAQ-----------LVIAPvvqaefeeveeldetERGAGGFGST 141
dut PRK00601
dUTP diphosphatase;
621-741 3.19e-20

dUTP diphosphatase;


Pssm-ID: 234802 [Multi-domain]  Cd Length: 150  Bit Score: 87.91  E-value: 3.19e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966   621 HDLP-RGTPGSAGLDLSSQKDLILSLEDG-VSLVPTLVKGTLPEGTTGLIIGRSS-NYKKGLEVL--PGVIDSDFQGEIK 695
Cdd:PRK00601  17 FPLPaYATEGSAGLDLRACLDEPVTLAPGeRALVPTGLAIHIPDGYEAQILPRSGlAHKHGIVLGnlPGTIDSDYRGELK 96

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 9626966   696 V-MVKAAKNAVIIHKGERIAQLLLLPYLKLPNPVIKE----ERGSEGFGST 741
Cdd:PRK00601  97 VsLWNRGQEPFTIEPGERIAQLVIVPVVQAEFEEVEEfdetERGAGGFGST 147
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 631-715 9.90e-19

Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface.


Pssm-ID: 143638 [Multi-domain]  Cd Length: 92  Bit Score: 81.77  E-value: 9.90e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966  631 AGLDL-SSQKDLILSLE-DGVSLVPTLVKGTLPEGTTGLIIGRSSNYKKGLEVL-PGVIDSDFQGEIKVMVKAAKNA-VI 706
Cdd:cd07557   1 AGYDLrLGEDFEGIVLPpGETVLVPTGEAIELPEGYVGLVFPRSSLARKGITVHnAGVIDPGYRGEITLELYNLGPEpVV 80


                ....*....
gi 9626966  707 IHKGERIAQ 715
Cdd:cd07557  81 IKKGDRIAQ 89
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
550-584 2.04e-16

GAG-polyprotein viral zinc-finger;


Pssm-ID: 373297  Cd Length: 36  Bit Score: 73.36  E-value: 2.04e-16
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 9626966    550 PPGLCPRCKKGYHWKSECKSKFDKDGNPLPPLETN 584
Cdd:pfam14787   1 PPGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGN 35
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 525-567 1.89e-05

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: 46.38  E-value: 1.89e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 9626966  525 PVCFSCGKTGHIRKDCkdekgskraPPGLCPRCKKGYHWKSEC 567
Cdd:COG5082  61 PVCFNCGQNGHLRRDC---------PHSICYNCSWDGHRSNHC 94
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 733-765 4.41e-04

Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, lambda type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409373  Cd Length: 105  Bit Score: 40.52  E-value: 4.41e-04
                        10        20        30
                ....*....|....*....|....*....|...
gi 9626966  733 RGSEGFGSTSHVHWVQEISDSRPMLHIYLNGRR 765
Cdd:cd04984  21 TGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHR 53
ZnF_C2HC smart00343
zinc finger;
526-541 5.71e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 37.81  E-value: 5.71e-04
                           10
                   ....*....|....*.
gi 9626966     526 VCFSCGKTGHIRKDCK 541
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 527-570 6.88e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.95  E-value: 6.88e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 9626966   527 CFSCGKTGHIRKDCKDEKGSKRAPPgLCPRCKKGYHWKSECKSK 570
Cdd:PTZ00368 106 CYNCGGEGHISRDCPNAGKRPGGDK-TCYNCGQTGHLSRDCPDK 148
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 525-541 1.50e-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: 36.74  E-value: 1.50e-03
                          10
                  ....*....|....*..
gi 9626966    525 PVCFSCGKTGHIRKDCK 541
Cdd:pfam00098   1 GKCYNCGEPGHIARDCP 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 ...
 284-409 3.96e-45

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: 158.21  E-value: 3.96e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966    284 VWEPLPLKTLKELQSAVRTMGPSAPYTLQVVD-MVASQWLTPSDWHQTARATLSPGDYVLWRTEYEEKSKEMVQK--AAG 360
Cdd:pfam00607   1 VWEPLDFKLLKELKKAVKQYGPNSPYTMQLLEaLASSNALTPYDWRTLAKAVLSPGQYLLWKAEWQELAQEQARRnqRAG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 9626966    361 KRKGkVSLDMLLGTGQFLSPSSQIKLSKDVLKDVTTNAVLAWRAIPPPG 409
Cdd:pfam00607  81 PDRG-ITLDMLTGTGQYATPQAQAQLPPEVLEQIKALALRAWKKLPPPG 128
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 751-849 2.08e-39

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 425454  Cd Length: 101  Bit Score: 140.97  E-value: 2.08e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966    751 SDSRPMLHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQ-PLRWQHEDKSGIIHPFVI 829
Cdd:pfam00077   1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWPKQKATTNIQGIGGGINVRQSDQiLILIGEDKFRGTVSPLIL 80

                          90       100
                  ....*....|....*....|
gi 9626966    830 PTLPFTLWGRDIMKDIKVRL 849
Cdd:pfam00077  81 PTCPVNIIGRDLLQQLGGRL 100
Gag_p10 pfam02337
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ...
 8-92 1.19e-38

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: 138.25  E-value: 1.19e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966      8 GQKLFVSVLQRLLSERGLHVKESSAIEFYQFLIKVSPWFPEEGGLNLQDWKRVGREMKRYAAEHGTDSIPKQAYPIWLQL 87
Cdd:pfam02337   1 SKQLFLTALQALLKERGLKVSKSSLIKFLQFVEEVCPWFPEEGTLNLETWKKVGRELKTQATEHGPKNIPVDTWPIWALI 80


                  ....*
gi 9626966     88 REILT 92
Cdd:pfam02337  81 RAVLD 85
dUTPase pfam00692
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
 619-741 1.00e-35

dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate.


Pssm-ID: 395562 [Multi-domain]  Cd Length: 129  Bit Score: 131.64  E-value: 1.00e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966    619 TIHDLPRGTPGSAGLDLSSQKDLILSLeDGVSLVPTLVKGTLPEGTTGLIIGRSSNYKKGLEVLPGVIDSDFQGEIKVMV 698
Cdd:pfam00692   2 EAEIPTPGSPGDAGYDLYAPYDLTVKP-GGTVLVPTDISIPLPDGTYGRIFPRSGLAAKGLIVVPGVIDSDYRGEVKVVL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 9626966    699 KAAKNA-VIIHKGERIAQ----LLLLPYLKLPNPVIKEERGSEGFGST 741
Cdd:pfam00692  81 FNLGKSdFTIKKGDRIAQlifePILHPELEPVETLDNTDRGDGGFGSS 128
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 409-482 1.19e-34

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: 126.44  E-value: 1.19e-34
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9626966    409 GVKKTVLAGLKQGNEESYETFISRLEEAVYRMMPRGEGSDILIKQLAWENANSLCQDLIRPIRKTGTIQDYIRA 482
Cdd:pfam19317   1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 757-842 2.71e-31

Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133149  Cd Length: 87  Bit Score: 117.37  E-value: 2.71e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966  757 LHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQ-PLRWQHEDKSGIIHPFVIPtLPFT 835
Cdd:cd05482   1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWPIQPAPSNLTGIGGAITPSQSSVlLLEIDGEGHLGTILVYVLS-LPVN 79


                ....*..
gi 9626966  836 LWGRDIM 842
Cdd:cd05482  80 LWGRDIL 86
dut TIGR00576
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ...
 611-741 7.07e-23

deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is in maintaining the levels of dUTP in the cell to prevent dUTP incorporation into DNA during DNA replication. Pol proteins in viruses are very similar to this protein family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Changed role from 132 to 123. RTD [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 273149 [Multi-domain]  Cd Length: 142  Bit Score: 95.38  E-value: 7.07e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966    611 LNPEAPpftihdLP-RGTPGSAGLDLSSQKDLILsLEDGVSLVPTLVKGTLPEGTTGLIIGRSSN-YKKGLEVL--PGVI 686
Cdd:TIGR00576   7 LSPNAP------LPtYATEGAAGYDLRAAEDVTI-PPGERALVPTGIAIELPDGYYGRVAPRSGLaLKHGVTIDnsPGVI 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 9626966    687 DSDFQGEIKV-MVKAAKNAVIIHKGERIAQLLLLPYLKLPNPVIKEE-----RGSEGFGST 741
Cdd:TIGR00576  80 DADYRGEIKViLINLGKEDFTVKKGDRIAQLVVEKIVTEVEFEEVEEldeteRGEGGFGST 140
Dut COG0756
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ...
 611-741 1.05e-22

dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP pyrophosphatase (dUTPase) is part of the Pathway/BioSystem: Thymidylate biosynthesis


Pssm-ID: 440519 [Multi-domain]  Cd Length: 143  Bit Score: 94.70  E-value: 1.05e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966  611 LNPEAPpftihdLPR-GTPGSAGLDLSSQKDLILSLEDG-VSLVPTLVKGTLPEGTTGLIIGRSSN-YKKGLEVL--PGV 685
Cdd:COG0756   7 LDEDAP------LPAyATPGSAGLDLRAALDEPVTLKPGeRALVPTGLAIALPPGYEAQVRPRSGLaLKHGITLLnsPGT 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9626966  686 IDSDFQGEIKV-MVKAAKNAVIIHKGERIAQllllpylklpnPVIKE---------------ERGSEGFGST 741
Cdd:COG0756  81 IDSDYRGEIKViLINLGDEPFTIERGDRIAQ-----------LVIAPvvqaefeeveeldetERGAGGFGST 141
dut PRK00601
dUTP diphosphatase;
621-741 3.19e-20

dUTP diphosphatase;


Pssm-ID: 234802 [Multi-domain]  Cd Length: 150  Bit Score: 87.91  E-value: 3.19e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966   621 HDLP-RGTPGSAGLDLSSQKDLILSLEDG-VSLVPTLVKGTLPEGTTGLIIGRSS-NYKKGLEVL--PGVIDSDFQGEIK 695
Cdd:PRK00601  17 FPLPaYATEGSAGLDLRACLDEPVTLAPGeRALVPTGLAIHIPDGYEAQILPRSGlAHKHGIVLGnlPGTIDSDYRGELK 96

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 9626966   696 V-MVKAAKNAVIIHKGERIAQLLLLPYLKLPNPVIKE----ERGSEGFGST 741
Cdd:PRK00601  97 VsLWNRGQEPFTIEPGERIAQLVIVPVVQAEFEEVEEfdetERGAGGFGST 147
trimeric_dUTPase cd07557
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ...
 631-715 9.90e-19

Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface.


Pssm-ID: 143638 [Multi-domain]  Cd Length: 92  Bit Score: 81.77  E-value: 9.90e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966  631 AGLDL-SSQKDLILSLE-DGVSLVPTLVKGTLPEGTTGLIIGRSSNYKKGLEVL-PGVIDSDFQGEIKVMVKAAKNA-VI 706
Cdd:cd07557   1 AGYDLrLGEDFEGIVLPpGETVLVPTGEAIELPEGYVGLVFPRSSLARKGITVHnAGVIDPGYRGEITLELYNLGPEpVV 80


                ....*....
gi 9626966  707 IHKGERIAQ 715
Cdd:cd07557  81 IKKGDRIAQ 89
zf-CCHC_5 pfam14787
GAG-polyprotein viral zinc-finger;
550-584 2.04e-16

GAG-polyprotein viral zinc-finger;


Pssm-ID: 373297  Cd Length: 36  Bit Score: 73.36  E-value: 2.04e-16
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 9626966    550 PPGLCPRCKKGYHWKSECKSKFDKDGNPLPPLETN 584
Cdd:pfam14787   1 PPGLCPRCKKGKHWARDCHSKFDKNGNPLSPNEGN 35
PLN02547 PLN02547
dUTP pyrophosphatase
 623-741 1.17e-13

dUTP pyrophosphatase


Pssm-ID: 215302  Cd Length: 157  Bit Score: 69.44  E-value: 1.17e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966   623 LP-RGTPGSAGLDLSSQKDLILSLEdGVSLVPTLVKGTLPEGTTGLIIGRSS-NYKKGLEVLPGVIDSDFQGEIKVMV-K 699
Cdd:PLN02547  28 LPsRGSALAAGYDLSSAYDTVVPAR-GKALVPTDLSIAIPEGTYARIAPRSGlAWKHSIDVGAGVIDADYRGPVGVILfN 106

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 9626966   700 AAKNAVIIHKGERIAQLLLLPYLKLPNPVIKE----ERGSEGFGST 741
Cdd:PLN02547 107 HSDVDFEVKVGDRIAQLILEKIVTPEVVEVEDldatVRGAGGFGST 152
PHA03094 PHA03094
dUTPase; Provisional
 625-741 7.01e-11

dUTPase; Provisional


Pssm-ID: 165376 [Multi-domain]  Cd Length: 144  Bit Score: 60.93  E-value: 7.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966   625 RGTPGSAGLDLSSQKDLILSLEDGVsLVPTLVKGTLPEGTTGLIIGRSS-NYKKGLEVLPGVIDSDFQGEIKVM-VKAAK 702
Cdd:PHA03094  20 RSSPKSAGYDLYSAYDYTVPPKERI-LVKTDISLSIPKFCYGRIAPRSGlSLNYGIDIGGGVIDEDYRGNIGVIfINNGK 98

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 9626966   703 NAVIIHKGERIAQLLLLPYLKLPNPVIKE----ERGSEGFGST 741
Cdd:PHA03094  99 CTFNIKTGDRIAQIIFERIEYPELKEVQSldstDRGDQGFGSS 141
PHA02703 PHA02703
ORF007 dUTPase; Provisional
 625-741 3.56e-10

ORF007 dUTPase; Provisional


Pssm-ID: 165079  Cd Length: 165  Bit Score: 59.61  E-value: 3.56e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966   625 RGTPGSAGLDLSSQKDLILSlEDGVSLVPTLVKGTLPEGTTGLIIGRSS-NYKKGLEVLPGVIDSDFQGEIKVMV-KAAK 702
Cdd:PHA02703  28 RGSPGAAGLDLCSACDCIVP-AGCRCVVFTDLLIKLPDGCYGRIAPRSGlAVKHFIDVGAGVIDADYRGNVGVVLfNFGH 106

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 9626966   703 NAVIIHKGERIAQLLLLPYLKLPNPVIK----EERGSEGFGST 741
Cdd:PHA02703 107 NDFEVKKGDRIAQLICERAAFPAVEEVAclddTDRGAGGFGST 149
dut PRK13956
dUTP diphosphatase;
623-743 2.51e-07

dUTP diphosphatase;


Pssm-ID: 184417 [Multi-domain]  Cd Length: 147  Bit Score: 50.95  E-value: 2.51e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966   623 LP-RGTPGSAGLDLSSQKDLILSLEDgVSLVPTLVKGTLPEGTTGLIIGRSSN-YKKGLEVLP--GVIDSDF------QG 692
Cdd:PRK13956  18 LPkRETAHAAGYDLKVAERTVIAPGE-IKLVPTGVKAYMQPGEVLYLYDRSSNpRKKGLVLINsvGVIDGDYygnpanEG 96

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 9626966   693 EIKVMVKAAKN-AVIIHKGERIAQLLLLPYLKLPNPVIKEERgSEGFGSTSH 743
Cdd:PRK13956  97 HIFAQMKNITDqEVVLEVGERIVQGVFMPFLIADGDQADGER-TGGFGSTGK 147
PTZ00143 PTZ00143
deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional
 628-742 1.52e-05

deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional


Pssm-ID: 240288 [Multi-domain]  Cd Length: 155  Bit Score: 45.88  E-value: 1.52e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966   628 PGSAGLDLSSQKDLILSLED------GVSLVPTLVKGTLPEG--TTGLIIGRSSNYKKGLEVLP--GVIDSDFQGEIKVM 697
Cdd:PTZ00143  24 EGDSGLDLFIVKDQTIKPGEtafiklGIKAAAFQKDEDGSDGknVSWLLFPRSSISKTPLRLANsiGLIDAGYRGELIAA 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 9626966   698 VKAAKN-AVIIHKGERIAQLLLLPYLKLPNPVIKE----ERGSEGFGSTS 742
Cdd:PTZ00143 104 VDNIKDePYTIKKGDRLVQLVSFDGEPITFELVDEldetTRGEGGFGSTG 153
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 525-567 1.89e-05

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: 46.38  E-value: 1.89e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 9626966  525 PVCFSCGKTGHIRKDCkdekgskraPPGLCPRCKKGYHWKSEC 567
Cdd:COG5082  61 PVCFNCGQNGHLRRDC---------PHSICYNCSWDGHRSNHC 94
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 733-765 4.41e-04

Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, lambda type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409373  Cd Length: 105  Bit Score: 40.52  E-value: 4.41e-04
                        10        20        30
                ....*....|....*....|....*....|...
gi 9626966  733 RGSEGFGSTSHVHWVQEISDSRPMLHIYLNGRR 765
Cdd:cd04984  21 TGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHR 53
ZnF_C2HC smart00343
zinc finger;
526-541 5.71e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 37.81  E-value: 5.71e-04
                           10
                   ....*....|....*.
gi 9626966     526 VCFSCGKTGHIRKDCK 541
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 526-569 6.33e-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: 41.76  E-value: 6.33e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 9626966  526 VCFSCGKTGHIRKDCkDEKGSKRAPpglCPRCKKGYHWKSECKS 569
Cdd:COG5082  99 KCYNCGETGHLSRDC-NPSKDQQKS---CFDCNSTRHSSEDCPS 138
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 527-570 6.88e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 40.95  E-value: 6.88e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 9626966   527 CFSCGKTGHIRKDCKDEKGSKRAPPgLCPRCKKGYHWKSECKSK 570
Cdd:PTZ00368 106 CYNCGGEGHISRDCPNAGKRPGGDK-TCYNCGQTGHLSRDCPDK 148
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 525-541 1.50e-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: 36.74  E-value: 1.50e-03
                          10
                  ....*....|....*..
gi 9626966    525 PVCFSCGKTGHIRKDCK 541
Cdd:pfam00098   1 GKCYNCGEPGHIARDCP 17
dCTP_deam TIGR02274
deoxycytidine triphosphate deaminase; Members of this family include the Escherichia coli ...
 651-715 1.64e-03

deoxycytidine triphosphate deaminase; Members of this family include the Escherichia coli monofunctional deoxycytidine triphosphate deaminase (dCTP deaminase) and a Methanocaldococcus jannaschii bifunctional dCTP deaminase (3.5.4.13)/dUTP diphosphatase (EC 3.6.1.23), which has the EC number 3.5.4.30 for the overall operation. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 274062  Cd Length: 179  Bit Score: 40.38  E-value: 1.64e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9626966    651 LVPTLVKGTLPEGTTGLIIGRSSNYKKGL--EVLPGVIDSDFQGEIKV-MVKAAKNAVIIHKGERIAQ 715
Cdd:TIGR02274  80 LATTLEYVKLPDDVVGFLEGRSSLARLGLfiHVTAGRIDPGFEGNITLeLFNAGKLPVKLRPGMRIAQ 147
CE4_SpCDA1 cd10980
Putative catalytic domain of Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and ...
 248-355 7.78e-03

Putative catalytic domain of Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins; This family is represented by Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), encoded by the cda1 gene. The general function of chitin deacetylase (CDA) is the synthesis of chitosan from chitin, a polymer of N-acetyl glucosamine, to build up the proper ascospore wall. The actual function of SpCDA1 might be involved in allantoin hydrolysis. It is likely an ortholog to bacterial PuuE allantoinase, whereas it is more distantly related to the CDAs found in other fungi, such as Saccharomyces cerevisiae and Mucor rouxii. Those CDAs are similar with rizobial NodB protein and are not included in this family.


Pssm-ID: 200602 [Multi-domain]  Cd Length: 297  Bit Score: 39.45  E-value: 7.78e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9626966  248 PPVGFAGAMAEAREKGDLTFTF-----PVVFMGESDEDDTPVWEPLPLKTLKELQSAVRTMgpsaPYTLQVVDM---VAS 319
Cdd:cd10980 142 APRGWYYGRASLRSRSLVAQVYkelglPLLWYSDAYNDDLPYWVPYPGGSKPEDDKGLLIV----PYTLDTNDYknaGYQ 217

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 9626966  320 QWLTPSDWHQTARATLSpgdyVLWRtEYEEKSKEMV 355
Cdd:cd10980 218 GFINSDDFYTYLRDAFD----VLYE-EGLEGAPKMM 248
 
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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