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Conserved domains on  [gi|28872819|ref|NP_057849|]
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Gag-Pol [Human immunodeficiency virus 1]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 605-821 3.13e-117

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


:

Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 365.84  E-value: 3.13e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  605 GPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGpeNPYNTPVFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 684
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  685 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPD 764
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 28872819  765 IVIYQYMDDLYVGSDLEiGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYEL 821
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 2-132 1.43e-69

gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell associated with the inner membrane of the mature immunodeficiency virus.


:

Pssm-ID: 249943  Cd Length: 140  Bit Score: 229.44  E-value: 1.43e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819      2 GARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNT 81
Cdd:pfam00540    1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819     82 VATLYCVHQRIEIKDTKEALDKIEEEQNKSKKK-------AQQAA--ADTGHSNQVSQNY 132
Cdd:pfam00540   81 VAVLYCVHQRIDVKDTKEALEKIEEEQNKSKKKktavppgAQQAAntGGTGNSSGVSQNY 140
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 276-349 1.96e-38

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: 138.00  E-value: 1.96e-38
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 28872819    276 MYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTA 349
Cdd:pfam19317    1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 493-586 1.65e-37

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: 136.34  E-value: 1.65e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819    493 LWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRW----KPKMIGGIGGFIKVRQYDQILIEICGHKAIGTV--LVG 566
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                           90       100
                   ....*....|....*....|.
gi 28872819    567 PT-PVNIIGRNLLTQIGCTLN 586
Cdd:pfam00077   81 PTcPVNIIGRDLLQQLGGRLT 101
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 905-1006 3.47e-36

Reverse transcriptase connection domain; This domain is known as the connection domain. This domain lies between the thumb and palm domains.


:

Pssm-ID: 462013  Cd Length: 102  Bit Score: 132.57  E-value: 3.47e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819    905 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 984
Cdd:pfam06815    1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                           90       100
                   ....*....|....*....|..
gi 28872819    985 WETWWTEYWQATWIPEWEFVNT 1006
Cdd:pfam06815   81 WETWWTEYWQATWIPEWEFVNT 102
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1024-1144 3.39e-34

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


:

Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 128.26  E-value: 3.39e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819   1024 AETFYVDGAANRETKLGKAGYVTNRGRQ--KVVTLTDTTNQKTELQAIYLALQD--SGLEVNIVTDSQYALGII------ 1093
Cdd:pfam00075    3 AVTVYTDGSCLGNPGPGGAGAVLYRGHEniSAPLPGRTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGItqwvhg 82

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 28872819   1094 ---QAQPDQSES-ELVNQIIEQL----IKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIR 1144
Cdd:pfam00075   83 wkkNGWPTTSEGkPVKNKDLWQLlkalCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 828-883 1.17e-19

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


:

Pssm-ID: 429135  Cd Length: 66  Bit Score: 83.91  E-value: 1.17e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 28872819    828 VQPIVLPEKDSWTVNDIQKLVGKLNWASQIY--PGIKVRQLCKLLRGTKALTEVIPLT 883
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLT 58
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1204-1292 2.28e-15

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


:

Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 73.12  E-value: 2.28e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819   1204 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFLLKLA---GRWPVKTIHTDNGSNFTGATVR 1274
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 28872819   1275 AACWWAGIKQEFGIPYNP 1292
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 1372-1415 1.14e-13

Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.


:

Pssm-ID: 425747  Cd Length: 45  Bit Score: 66.27  E-value: 1.14e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 28872819   1372 VYYRDSRNPLWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 1415
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 143-250 5.31e-13

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: 67.30  E-value: 5.31e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819    143 VHQAISPRTLNAWVKVVEEKAF-SPEVIPMFSALSEG--ATPQDLNTMLNTVGGHqAAMQMLKETINEEAAEWDRvHPVH 219
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPnSPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                           90       100       110
                   ....*....|....*....|....*....|....
gi 28872819    220 AGPIapgqmrEPRGSD-IAGTT--STLQEQIGWM 250
Cdd:pfam00607   79 AGPD------RGITLDmLTGTGqyATPQAQAQLP 106
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 1157-1191 2.22e-12

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.


:

Pssm-ID: 426567  Cd Length: 36  Bit Score: 62.39  E-value: 2.22e-12
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 28872819   1157 DEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQ 1191
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 349-429 9.74e-12

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: 64.44  E-value: 9.74e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819   349 ACQGVGGPGHKARvlaeamsQVTNSAtimmqrgnfRNQRKIVKCFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQM 423
Cdd:PTZ00368   79 SCYNCGQTGHISR-------ECPNRA---------KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLS 142


                  ....*.
gi 28872819   424 KDCTER 429
Cdd:PTZ00368  143 RDCPDK 148
Tra5 super family cl34487
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1259-1342 5.25e-09

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


The actual alignment was detected with superfamily member COG2801:

Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 59.40  E-value: 5.25e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819 1259 TIHTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKK--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 1335
Cdd:COG2801  211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                 ....*..
gi 28872819 1336 GGIGGYS 1342
Cdd:COG2801  291 SSLGYLT 297
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 605-821 3.13e-117

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 365.84  E-value: 3.13e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  605 GPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGpeNPYNTPVFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 684
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  685 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPD 764
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 28872819  765 IVIYQYMDDLYVGSDLEiGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYEL 821
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 2-132 1.43e-69

gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell associated with the inner membrane of the mature immunodeficiency virus.


Pssm-ID: 249943  Cd Length: 140  Bit Score: 229.44  E-value: 1.43e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819      2 GARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNT 81
Cdd:pfam00540    1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819     82 VATLYCVHQRIEIKDTKEALDKIEEEQNKSKKK-------AQQAA--ADTGHSNQVSQNY 132
Cdd:pfam00540   81 VAVLYCVHQRIDVKDTKEALEKIEEEQNKSKKKktavppgAQQAAntGGTGNSSGVSQNY 140
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 650-821 4.50e-46

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 164.01  E-value: 4.50e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819    650 IKKKDSTKWRKL----VDFRELNKRTQD-------FWEVQLGIPHPAG-LKKKKSVTVLDVGDAYFSVPLDEDFRKYTAF 717
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819    718 TIPSINN----ETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQnPDIVIYQYMDDLYVGSDlEIGQHRTKIEELR 793
Cdd:pfam00078   81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 28872819    794 QHLLRWGLTTPDKKHQ---KEPPFLWMGYEL 821
Cdd:pfam00078  159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 276-349 1.96e-38

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: 138.00  E-value: 1.96e-38
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 28872819    276 MYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTA 349
Cdd:pfam19317    1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 493-586 1.65e-37

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: 136.34  E-value: 1.65e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819    493 LWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRW----KPKMIGGIGGFIKVRQYDQILIEICGHKAIGTV--LVG 566
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                           90       100
                   ....*....|....*....|.
gi 28872819    567 PT-PVNIIGRNLLTQIGCTLN 586
Cdd:pfam00077   81 PTcPVNIIGRDLLQQLGGRLT 101
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 905-1006 3.47e-36

Reverse transcriptase connection domain; This domain is known as the connection domain. This domain lies between the thumb and palm domains.


Pssm-ID: 462013  Cd Length: 102  Bit Score: 132.57  E-value: 3.47e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819    905 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 984
Cdd:pfam06815    1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                           90       100
                   ....*....|....*....|..
gi 28872819    985 WETWWTEYWQATWIPEWEFVNT 1006
Cdd:pfam06815   81 WETWWTEYWQATWIPEWEFVNT 102
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1024-1144 3.39e-34

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 128.26  E-value: 3.39e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819   1024 AETFYVDGAANRETKLGKAGYVTNRGRQ--KVVTLTDTTNQKTELQAIYLALQD--SGLEVNIVTDSQYALGII------ 1093
Cdd:pfam00075    3 AVTVYTDGSCLGNPGPGGAGAVLYRGHEniSAPLPGRTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGItqwvhg 82

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 28872819   1094 ---QAQPDQSES-ELVNQIIEQL----IKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIR 1144
Cdd:pfam00075   83 wkkNGWPTTSEGkPVKNKDLWQLlkalCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 499-579 3.72e-26

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: 103.50  E-value: 3.72e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  499 VTIKIGGQLKEALLDTGADDTVLEEMSLPGRW----KPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGP--TPVNI 572
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80


                 ....*..
gi 28872819  573 IGRNLLT 579
Cdd:cd05482   81 WGRDILS 87
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 828-883 1.17e-19

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


Pssm-ID: 429135  Cd Length: 66  Bit Score: 83.91  E-value: 1.17e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 28872819    828 VQPIVLPEKDSWTVNDIQKLVGKLNWASQIY--PGIKVRQLCKLLRGTKALTEVIPLT 883
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLT 58
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1204-1292 2.28e-15

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 73.12  E-value: 2.28e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819   1204 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFLLKLA---GRWPVKTIHTDNGSNFTGATVR 1274
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 28872819   1275 AACWWAGIKQEFGIPYNP 1292
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 1372-1415 1.14e-13

Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.


Pssm-ID: 425747  Cd Length: 45  Bit Score: 66.27  E-value: 1.14e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 28872819   1372 VYYRDSRNPLWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 1415
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 143-250 5.31e-13

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: 67.30  E-value: 5.31e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819    143 VHQAISPRTLNAWVKVVEEKAF-SPEVIPMFSALSEG--ATPQDLNTMLNTVGGHqAAMQMLKETINEEAAEWDRvHPVH 219
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPnSPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                           90       100       110
                   ....*....|....*....|....*....|....
gi 28872819    220 AGPIapgqmrEPRGSD-IAGTT--STLQEQIGWM 250
Cdd:pfam00607   79 AGPD------RGITLDmLTGTGqyATPQAQAQLP 106
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1028-1143 1.79e-12

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 66.02  E-value: 1.79e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819 1028 YVDGAANRETKLGKAGYV---TNRGRQKVVTLTDTTNQKTELQAIYLALQ----DSGLEVNIVTDSQYALGIIQAQPDQS 1100
Cdd:COG0328    6 YTDGACRGNPGPGGWGAViryGGEEKELSGGLGDTTNNRAELTALIAALEalkeLGPCEVEIYTDSQYVVNQITGWIHGW 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 28872819 1101 ES---------ELVNQIIEqLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGI 1143
Cdd:COG0328   86 KKngwkpvknpDLWQRLDE-LLARHKVTFEWVKGHAGHPGNERADALANKAL 136
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 1157-1191 2.22e-12

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.


Pssm-ID: 426567  Cd Length: 36  Bit Score: 62.39  E-value: 2.22e-12
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 28872819   1157 DEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQ 1191
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 1026-1144 6.18e-12

non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260008 [Multi-domain]  Cd Length: 131  Bit Score: 64.16  E-value: 6.18e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819 1026 TFYVDGAANrETKLGkAGYVTNRGRQKVVTLTDTTNQKT----ELQAIYLALQ------DSGLEVNIVTDSQYALGIIQ- 1094
Cdd:cd09276    1 VIYTDGSKL-EGSVG-AGFVIYRGGEVISRSYRLGTHASvfdaELEAILEALElalataRRARKVTIFTDSQSALQALRn 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 28872819 1095 --AQPDQSESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDKLVSAGIR 1144
Cdd:cd09276   79 prRSSGQVILIRILRLLRLLKAKGvKVRLRWVPGHVGIEGNEAADRLAKEAAS 131
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 349-429 9.74e-12

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 64.44  E-value: 9.74e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819   349 ACQGVGGPGHKARvlaeamsQVTNSAtimmqrgnfRNQRKIVKCFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQM 423
Cdd:PTZ00368   79 SCYNCGQTGHISR-------ECPNRA---------KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLS 142


                  ....*.
gi 28872819   424 KDCTER 429
Cdd:PTZ00368  143 RDCPDK 148
transpos_IS481 NF033577
IS481 family transposase; null
 1202-1306 8.99e-11

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 64.53  E-value: 8.99e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  1202 DCSPGIWQLDCTHL-----EGKV-ILVAVHVASGYIEAEVIPAETGQETAYFLLKL-AGRW-PVKTIHTDNGSNFTGAT- 1272
Cdd:NF033577  125 AHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAfAEHGiPIRRVLTDNGSEFRSRAh 204

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 28872819  1273 -VRAACWWAGIKQEFGIPYNPQSQGVVESMNKELK 1306
Cdd:NF033577  205 gFELALAELGIEHRRTRPYHPQTNGKVERFHRTLK 239
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1259-1342 5.25e-09

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 59.40  E-value: 5.25e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819 1259 TIHTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKK--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 1335
Cdd:COG2801  211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                 ....*..
gi 28872819 1336 GGIGGYS 1342
Cdd:COG2801  291 SSLGYLT 297
transpos_IS3 NF033516
IS3 family transposase;
1260-1306 7.61e-08

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 56.42  E-value: 7.61e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 28872819  1260 IHTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELK 1306
Cdd:NF033516  279 LHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 391-429 5.62e-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: 45.61  E-value: 5.62e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 28872819  391 KCFNCGKEGHTARNC----------------RAPRKKGCWKCGKEGHQMKDCTER 429
Cdd:COG5082   62 VCFNCGQNGHLRRDCphsicyncswdghrsnHCPKPKKCYNCGETGHLSRDCNPS 116
ZnF_C2HC smart00343
zinc finger;
391-406 6.53e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.89  E-value: 6.53e-05
                            10
                    ....*....|....*.
gi 28872819     391 KCFNCGKEGHTARNCR 406
Cdd:smart00343    1 KCYNCGKEGHIARDCP 16
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
1205-1305 1.41e-04

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 45.64  E-value: 1.41e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819 1205 PGIWQLDCthLEGK----VILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWP---VKTIHTDNGSNFTGatvraac 1277
Cdd:COG2826  172 PGHWEGDL--IIGKrgksALLTLVERKSRFVILLKLPDKTAESVADALIRLLRKLPaflRKSITTDNGKEFAD------- 242

                         90       100       110
                 ....*....|....*....|....*....|....
gi 28872819 1278 wWAGIKQEFGI------PYNPQSQGVVESMNKEL 1305
Cdd:COG2826  243 -HKEIEAALGIkvyfadPYSPWQRGTNENTNGLL 275
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 390-405 4.22e-04

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


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 38.66  E-value: 4.22e-04
                           10
                   ....*....|....*.
gi 28872819    390 VKCFNCGKEGHTARNC 405
Cdd:pfam00098    1 GKCYNCGEPGHIARDC 16
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 605-821 3.13e-117

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 365.84  E-value: 3.13e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  605 GPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGpeNPYNTPVFAIKKKDStKWRKLVDFRELNKRTQDFWEVQLGIPHP 684
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPST--SPWNTPVFVIKKKSG-KWRLLHDLRAVNAQTQDMGALQPGLPHP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  685 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPD 764
Cdd:cd01645   78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 28872819  765 IVIYQYMDDLYVGSDLEiGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYEL 821
Cdd:cd01645  158 IVIYHYMDDILIASDLE-GQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
Gag_p17 pfam00540
gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell ...
 2-132 1.43e-69

gag gene protein p17 (matrix protein); The matrix protein forms an icosahedral shell associated with the inner membrane of the mature immunodeficiency virus.


Pssm-ID: 249943  Cd Length: 140  Bit Score: 229.44  E-value: 1.43e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819      2 GARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNT 81
Cdd:pfam00540    1 GARASVLSGGELDKWEKIRLRPGGKKKYKLKHLVWASRELERFAVNPGLLETSEGCRKILGQLQPSLQTGSEGLRSLYNT 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819     82 VATLYCVHQRIEIKDTKEALDKIEEEQNKSKKK-------AQQAA--ADTGHSNQVSQNY 132
Cdd:pfam00540   81 VAVLYCVHQRIDVKDTKEALEKIEEEQNKSKKKktavppgAQQAAntGGTGNSSGVSQNY 140
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 650-821 4.50e-46

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 164.01  E-value: 4.50e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819    650 IKKKDSTKWRKL----VDFRELNKRTQD-------FWEVQLGIPHPAG-LKKKKSVTVLDVGDAYFSVPLDEDFRKYTAF 717
Cdd:pfam00078    1 IPKKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819    718 TIPSINN----ETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQnPDIVIYQYMDDLYVGSDlEIGQHRTKIEELR 793
Cdd:pfam00078   81 TTPPINInwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKR-AGLTLVRYADDILIFSK-SEEEHQEALEEVL 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 28872819    794 QHLLRWGLTTPDKKHQ---KEPPFLWMGYEL 821
Cdd:pfam00078  159 EWLKESGLKINPEKTQfflKSKEVKYLGVTL 189
Gag_p24_C pfam19317
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 276-349 1.96e-38

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: 138.00  E-value: 1.96e-38
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 28872819    276 MYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTA 349
Cdd:pfam19317    1 GYKPTSLADIRQGPKEPYQDFVARLYDALRKEMPDGKAKDVITKQLAYENANPECQDLLKPLGKTGTLSDMIRA 74
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 493-586 1.65e-37

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: 136.34  E-value: 1.65e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819    493 LWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRW----KPKMIGGIGGFIKVRQYDQILIEICGHKAIGTV--LVG 566
Cdd:pfam00077    1 AEQRPLLTVKIGGKYFTALLDTGADDTVISQNDWPTNWpkqkATTNIQGIGGGINVRQSDQILILIGEDKFRGTVspLIL 80

                           90       100
                   ....*....|....*....|.
gi 28872819    567 PT-PVNIIGRNLLTQIGCTLN 586
Cdd:pfam00077   81 PTcPVNIIGRDLLQQLGGRLT 101
RVT_connect pfam06815
Reverse transcriptase connection domain; This domain is known as the connection domain. This ...
 905-1006 3.47e-36

Reverse transcriptase connection domain; This domain is known as the connection domain. This domain lies between the thumb and palm domains.


Pssm-ID: 462013  Cd Length: 102  Bit Score: 132.57  E-value: 3.47e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819    905 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 984
Cdd:pfam06815    1 YYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET 80

                           90       100
                   ....*....|....*....|..
gi 28872819    985 WETWWTEYWQATWIPEWEFVNT 1006
Cdd:pfam06815   81 WETWWTEYWQATWIPEWEFVNT 102
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1024-1144 3.39e-34

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 128.26  E-value: 3.39e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819   1024 AETFYVDGAANRETKLGKAGYVTNRGRQ--KVVTLTDTTNQKTELQAIYLALQD--SGLEVNIVTDSQYALGII------ 1093
Cdd:pfam00075    3 AVTVYTDGSCLGNPGPGGAGAVLYRGHEniSAPLPGRTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGGItqwvhg 82

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 28872819   1094 ---QAQPDQSES-ELVNQIIEQL----IKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIR 1144
Cdd:pfam00075   83 wkkNGWPTTSEGkPVKNKDLWQLlkalCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 606-809 1.98e-31

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.


Pssm-ID: 239685 [Multi-domain]  Cd Length: 210  Bit Score: 122.84  E-value: 1.98e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  606 PKVKQWPLTEEKIKALVEICTEMEKEGKIskIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDfweVQLGIPHPA 685
Cdd:cd03715    2 VNQKQYPLPREAREGITPHIQELLEAGIL--VPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLP---IHPAVPNPY 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  686 GL-----KKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPsinnetpGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRK 760
Cdd:cd03715   77 TLlsllpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWE-------GQQYTFTRLPQGFKNSPTLFHEALARDLAPFPL 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 28872819  761 QNPDIVIYQYMDDLYVGSDLEIGQHRTkIEELRQHLLRWGLTTPDKKHQ 809
Cdd:cd03715  150 EHEGTILLQYVDDLLLAADSEEDCLKG-TDALLTHLGELGYKVSPKKAQ 197
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 642-815 7.11e-28

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 111.53  E-value: 7.11e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  642 PYNTPVFAIKKKDStKWRKLVDFRELNKRT-QDFWEvqlgIPHPAG----LKKKKSVTVLDVGDAYFSVPLDEDFRKYTA 716
Cdd:cd01647    9 PYASPVVVVKKKDG-KLRLCVDYRKLNKVTiKDRYP----LPTIDElleeLAGAKVFSKLDLRSGYHQIPLAEESRPKTA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  717 FTipsinneTPGIRYQYNVLPQGWKGSPAIFQSSMTKIlepFRKQNPDIVIyQYMDDLYVGSDlEIGQHRTKIEELRQHL 796
Cdd:cd01647   84 FR-------TPFGLYEYTRMPFGLKNAPATFQRLMNKI---LGDLLGDFVE-VYLDDILVYSK-TEEEHLEHLREVLERL 151

                        170       180
                 ....*....|....*....|..
gi 28872819  797 LRWGLTTPDKK---HQKEPPFL 815
Cdd:cd01647  152 REAGLKLNPEKcefGVPEVEFL 173
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
 499-579 3.72e-26

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: 103.50  E-value: 3.72e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  499 VTIKIGGQLKEALLDTGADDTVLEEMSLPGRW----KPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGP--TPVNI 572
Cdd:cd05482    1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80


                 ....*..
gi 28872819  573 IGRNLLT 579
Cdd:cd05482   81 WGRDILS 87
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 828-883 1.17e-19

Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle.


Pssm-ID: 429135  Cd Length: 66  Bit Score: 83.91  E-value: 1.17e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 28872819    828 VQPIVLPEKDSWTVNDIQKLVGKLNWASQIY--PGIKVRQLCKLLRGTKALTEVIPLT 883
Cdd:pfam06817    1 PQKLQLRKDHLKTLNDFQKLLGDINWIRPYLgiTTYDLKPLFSLLRGDSDLTSPRTLT 58
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 736-821 1.55e-19

RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.


Pssm-ID: 238185 [Multi-domain]  Cd Length: 98  Bit Score: 84.71  E-value: 1.55e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  736 LPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEigQHRTKIEELRQHLLRWGLTTPDKKHQ---KEP 812
Cdd:cd00304   12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE--QQAVKKRELEEFLARLGLNLSDEKTQfteKEK 89


                 ....*....
gi 28872819  813 PFLWMGYEL 821
Cdd:cd00304   90 KFKFLGILV 98
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1204-1292 2.28e-15

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 73.12  E-value: 2.28e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819   1204 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFLLKLA---GRWPVKTIHTDNGSNFTGATVR 1274
Cdd:pfam00665    1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 28872819   1275 AACWWAGIKQEFGIPYNP 1292
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 1372-1415 1.14e-13

Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.


Pssm-ID: 425747  Cd Length: 45  Bit Score: 66.27  E-value: 1.14e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 28872819   1372 VYYRDSRNPLWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 1415
Cdd:pfam00552    1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Gag_p24 pfam00607
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ...
 143-250 5.31e-13

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: 67.30  E-value: 5.31e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819    143 VHQAISPRTLNAWVKVVEEKAF-SPEVIPMFSALSEG--ATPQDLNTMLNTVGGHqAAMQMLKETINEEAAEWDRvHPVH 219
Cdd:pfam00607    1 VWEPLDFKLLKELKKAVKQYGPnSPYTMQLLEALASSnaLTPYDWRTLAKAVLSP-GQYLLWKAEWQELAQEQAR-RNQR 78

                           90       100       110
                   ....*....|....*....|....*....|....
gi 28872819    220 AGPIapgqmrEPRGSD-IAGTT--STLQEQIGWM 250
Cdd:pfam00607   79 AGPD------RGITLDmLTGTGqyATPQAQAQLP 106
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1028-1143 1.79e-12

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 66.02  E-value: 1.79e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819 1028 YVDGAANRETKLGKAGYV---TNRGRQKVVTLTDTTNQKTELQAIYLALQ----DSGLEVNIVTDSQYALGIIQAQPDQS 1100
Cdd:COG0328    6 YTDGACRGNPGPGGWGAViryGGEEKELSGGLGDTTNNRAELTALIAALEalkeLGPCEVEIYTDSQYVVNQITGWIHGW 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 28872819 1101 ES---------ELVNQIIEqLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGI 1143
Cdd:COG0328   86 KKngwkpvknpDLWQRLDE-LLARHKVTFEWVKGHAGHPGNERADALANKAL 136
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 1157-1191 2.22e-12

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.


Pssm-ID: 426567  Cd Length: 36  Bit Score: 62.39  E-value: 2.22e-12
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 28872819   1157 DEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQ 1191
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 1026-1144 6.18e-12

non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260008 [Multi-domain]  Cd Length: 131  Bit Score: 64.16  E-value: 6.18e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819 1026 TFYVDGAANrETKLGkAGYVTNRGRQKVVTLTDTTNQKT----ELQAIYLALQ------DSGLEVNIVTDSQYALGIIQ- 1094
Cdd:cd09276    1 VIYTDGSKL-EGSVG-AGFVIYRGGEVISRSYRLGTHASvfdaELEAILEALElalataRRARKVTIFTDSQSALQALRn 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 28872819 1095 --AQPDQSESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDKLVSAGIR 1144
Cdd:cd09276   79 prRSSGQVILIRILRLLRLLKAKGvKVRLRWVPGHVGIEGNEAADRLAKEAAS 131
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 349-429 9.74e-12

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 64.44  E-value: 9.74e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819   349 ACQGVGGPGHKARvlaeamsQVTNSAtimmqrgnfRNQRKIVKCFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQM 423
Cdd:PTZ00368   79 SCYNCGQTGHISR-------ECPNRA---------KGGAARRACYNCGGEGHISRDCPNAGKRPggdktCYNCGQTGHLS 142


                  ....*.
gi 28872819   424 KDCTER 429
Cdd:PTZ00368  143 RDCPDK 148
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1026-1139 5.06e-11

Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260005 [Multi-domain]  Cd Length: 131  Bit Score: 61.59  E-value: 5.06e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819 1026 TFYVDGAAnreTKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD-SGLEVNIVTDSQYALGIIQA--------- 1095
Cdd:cd09273    1 TVFTDGSS---FKAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELaKGKPVNIYTDSAYAVHALHLletigierg 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 28872819 1096 -QPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIG-----GNEQVDKLV 1139
Cdd:cd09273   78 fLKSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPgplaeGNAQADAAA 127
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 348-430 5.52e-11

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 62.13  E-value: 5.52e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819   348 TACQGVGGPGHKARvlaeamsQVTNSATIMMQRGnfrnqrkiVKCFNCGKEGHTARNCRAPRKKG----CWKCGKEGHQM 423
Cdd:PTZ00368    1 MVCYRCGGVGHQSR-------ECPNSAPAGAAKA--------RPCYKCGEPGHLSRECPSAPGGRgersCYNCGKTGHLS 65


                  ....*..
gi 28872819   424 KDCTERQ 430
Cdd:PTZ00368   66 RECPEAP 72
transpos_IS481 NF033577
IS481 family transposase; null
 1202-1306 8.99e-11

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 64.53  E-value: 8.99e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  1202 DCSPGIWQLDCTHL-----EGKV-ILVAVHVASGYIEAEVIPAETGQETAYFLLKL-AGRW-PVKTIHTDNGSNFTGAT- 1272
Cdd:NF033577  125 AHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAfAEHGiPIRRVLTDNGSEFRSRAh 204

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 28872819  1273 -VRAACWWAGIKQEFGIPYNPQSQGVVESMNKELK 1306
Cdd:NF033577  205 gFELALAELGIEHRRTRPYHPQTNGKVERFHRTLK 239
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 1028-1144 2.73e-10

Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at their N-termini called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos.


Pssm-ID: 260012 [Multi-domain]  Cd Length: 145  Bit Score: 59.89  E-value: 2.73e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819 1028 YVDGAA-NRETKLGKAGYV------TNRGRQKVVTLTDTTNQKTELQAIYLALQ----DSGLEVNIVTDSQYALGII--- 1093
Cdd:cd09280    3 YTDGSClNNGKPGARAGIGvyfgpgDPRNVSEPLPGRKQTNNRAELLAVIHALEqapeEGIRKLEIRTDSKYAINCItkw 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28872819 1094 ------QAQPDQSESELVNQ-IIEQLIK-----KEKVYLAWVPAHKGIGGNEQVDKLVSAGIR 1144
Cdd:cd09280   83 ipkwkkNGWKTSKGKPVKNQdLIKELDKllrkrGIKVKFEHVKGHSGDPGNEEADRLAREGAD 145
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 349-426 2.62e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 57.12  E-value: 2.62e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819   349 ACQGVGGPGHKARVLAEAmsqvtnsatimmqrgnfRNQRKIVKCFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQM 423
Cdd:PTZ00368   54 SCYNCGKTGHLSRECPEA-----------------PPGSGPRSCYNCGQTGHISRECPNRAKGGaarraCYNCGGEGHIS 116


                  ...
gi 28872819   424 KDC 426
Cdd:PTZ00368  117 RDC 119
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1259-1342 5.25e-09

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 59.40  E-value: 5.25e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819 1259 TIHTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKK--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 1335
Cdd:COG2801  211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                 ....*..
gi 28872819 1336 GGIGGYS 1342
Cdd:COG2801  291 SSLGYLT 297
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 1028-1144 2.83e-08

RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability.


Pssm-ID: 260010 [Multi-domain]  Cd Length: 139  Bit Score: 54.03  E-value: 2.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819 1028 YVDGAANRETklGKAGY-VTNRGRQKVVTLT----DTTNQKTELQAIYLALQ--DSGLEVNIVTDSQYAL-GIIQAQPD- 1098
Cdd:cd09278    5 YTDGACLGNP--GPGGWaAVIRYGDHEKELSggepGTTNNRMELTAAIEALEalKEPCPVTIYTDSQYVInGITKWIKGw 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 28872819 1099 ------QSESELV-N----QIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIR 1144
Cdd:cd09278   83 kkngwkTADGKPVkNrdlwQELDALLAGHKVTWEWVKGHAGHPGNERADRLANKAAD 139
transpos_IS3 NF033516
IS3 family transposase;
1260-1306 7.61e-08

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 56.42  E-value: 7.61e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 28872819  1260 IHTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELK 1306
Cdd:NF033516  279 LHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 499-579 2.82e-06

Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family includes aspartate proteases from retroelements with LTR (long terminal repeats) including the RTVL_H family of human endogenous retrovirus-like elements. 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: 133159  Cd Length: 86  Bit Score: 46.56  E-value: 2.82e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  499 VTIKIGGQLKEALLDTGADDTVLEEMSLPGRW---KPKMIGGIGGFIK--VRQYDQiLIEICGHKAIGTVLVGPT-PVNI 572
Cdd:cd06095    1 VTITVEGVPIVFLVDTGATHSVLKSDLGPKQElstTSVLIRGVSGQSQqpVTTYRT-LVDLGGHTVSHSFLVVPNcPDPL 79


                 ....*..
gi 28872819  573 IGRNLLT 579
Cdd:cd06095   80 LGRDLLS 86
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 696-812 6.01e-06

RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.


Pssm-ID: 239684 [Multi-domain]  Cd Length: 119  Bit Score: 46.95  E-value: 6.01e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  696 LDVGDAYFSVPLDEDFRKYTAFtIPSinnetpGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNpdIVIYQYMDD-L 774
Cdd:cd03714    1 VDLKDAYFHIPILPRSRDLLGF-AWQ------GETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLG--VRIFSYLDDlL 71

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 28872819  775 YVGSDLEIGQHRtkieeLRQHLLRW----GLTTPDKKHQKEP 812
Cdd:cd03714   72 IIASSIKTSEAV-----LRHLRATLlanlGFTLNLEKSKLGP 108
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1028-1138 3.73e-05

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 44.61  E-value: 3.73e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819 1028 YVDGAANRETKLGKAGYVtNRGRQKVVTLTDT------TNQKTELQAIYLALQ----DSGLEVNIVTDSQYALGIIQAQP 1097
Cdd:cd06222    2 NVDGSCRGNPGPAGIGGV-LRDHEGGWLGGFAlkigapTALEAELLALLLALElaldLGYLKVIIESDSKYVVDLINSGS 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 28872819 1098 DQSES--ELVNQIIEQLIKKEKVYLAWVPAHkgigGNEQVDKL 1138
Cdd:cd06222   81 FKWSPniLLIEDILLLLSRFWSVKISHVPRE----GNQVADAL 119
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 391-429 5.62e-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: 45.61  E-value: 5.62e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 28872819  391 KCFNCGKEGHTARNC----------------RAPRKKGCWKCGKEGHQMKDCTER 429
Cdd:COG5082   62 VCFNCGQNGHLRRDCphsicyncswdghrsnHCPKPKKCYNCGETGHLSRDCNPS 116
ZnF_C2HC smart00343
zinc finger;
391-406 6.53e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.89  E-value: 6.53e-05
                            10
                    ....*....|....*.
gi 28872819     391 KCFNCGKEGHTARNCR 406
Cdd:smart00343    1 KCYNCGKEGHIARDCP 16
ZnF_C2HC smart00343
zinc finger;
412-428 7.06e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.89  E-value: 7.06e-05
                            10
                    ....*....|....*..
gi 28872819     412 GCWKCGKEGHQMKDCTE 428
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
1205-1305 1.41e-04

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 45.64  E-value: 1.41e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819 1205 PGIWQLDCthLEGK----VILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWP---VKTIHTDNGSNFTGatvraac 1277
Cdd:COG2826  172 PGHWEGDL--IIGKrgksALLTLVERKSRFVILLKLPDKTAESVADALIRLLRKLPaflRKSITTDNGKEFAD------- 242

                         90       100       110
                 ....*....|....*....|....*....|....
gi 28872819 1278 wWAGIKQEFGI------PYNPQSQGVVESMNKEL 1305
Cdd:COG2826  243 -HKEIEAALGIkvyfadPYSPWQRGTNENTNGLL 275
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 349-443 2.34e-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: 43.69  E-value: 2.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819  349 ACQGVGGPGHKAR----VLAEAMSQVTNSATIMMQRgnfrnqrkiVKCFNCGKEGHTARNC--RAPRKKGCWKCGKEGHQ 422
Cdd:COG5082   62 VCFNCGQNGHLRRdcphSICYNCSWDGHRSNHCPKP---------KKCYNCGETGHLSRDCnpSKDQQKSCFDCNSTRHS 132

                         90       100
                 ....*....|....*....|...
gi 28872819  423 MKDCTE--RQANFLREDLAFLQG 443
Cdd:COG5082  133 SEDCPSiwKHYVLNNGDGHPIKK 155
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 390-405 4.22e-04

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


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 38.66  E-value: 4.22e-04
                           10
                   ....*....|....*.
gi 28872819    390 VKCFNCGKEGHTARNC 405
Cdd:pfam00098    1 GKCYNCGEPGHIARDC 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 411-428 9.14e-04

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


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 37.89  E-value: 9.14e-04
                           10
                   ....*....|....*...
gi 28872819    411 KGCWKCGKEGHQMKDCTE 428
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
zf-CCHC_6 pfam15288
Zinc knuckle; This Zinc knuckle is found in FAM90A mammalian proteins.
 390-414 2.37e-03

Zinc knuckle; This Zinc knuckle is found in FAM90A mammalian proteins.


Pssm-ID: 464616 [Multi-domain]  Cd Length: 42  Bit Score: 36.98  E-value: 2.37e-03
                           10        20
                   ....*....|....*....|....*
gi 28872819    390 VKCFNCGKEGHTARNCRAPRKkgCW 414
Cdd:pfam15288    2 VKCKNCGAFGHTARSKRCPIK--CW 24
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 1028-1144 3.95e-03

RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties.


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 38.99  E-value: 3.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819 1028 YVDGAANRETKLGKAGYV----TNRGRQKVVTLT-DTTNQKTELQAIYLALQ---DSGLE-VNIVTDSQYALGIIQAQPD 1098
Cdd:cd09279    4 YFDGASRGNPGPAGAGVViyspGGEVLELSERLGfPATNNEAEYEALIAGLElalELGAEkLEIYGDSQLVVNQLNGEYK 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 28872819 1099 QSE---SELVNQIIEQLIKKEKVYLAWVPAHKgiggNEQVDKLVSAGIR 1144
Cdd:cd09279   84 VKNerlKPLLEKVLELLAKFELVELKWIPREQ----NKEADALANQALD 128
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 499-577 6.16e-03

Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix.


Pssm-ID: 433378  Cd Length: 90  Bit Score: 37.26  E-value: 6.16e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28872819    499 VTIKIGGQLKEALLDTGADDTVL-----EEMSLPGRWK--PKMIGGIGGFIKVRQYDQILIEICGHKAIG-TVLV---GP 567
Cdd:pfam13650    1 VPVTINGKPVRFLVDTGASGTVIspslaERLGLKVRGLayTVRVSTAGGRVSAARVRLDSLRLGGLTLENvPALVldlGD 80

                           90
                   ....*....|
gi 28872819    568 TPVNIIGRNL 577
Cdd:pfam13650   81 LIDGLLGMDF 90
 
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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