NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2065826704|gb|KAG7594102|]
View 

Integrase catalytic core [Arabidopsis thaliana x Arabidopsis arenosa]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1214-1390 5.43e-96

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: 307.21  E-value: 5.43e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1214 GFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNKVTVKNKYPLPRIDELLDQLRGARWFSKIDLASGYHQIPIEPSDVR 1293
Cdd:cd01647      1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1294 KTAFRTRYGHYEFVVMPFGLTNAPAAFMKMMNGIFREFLDEFVIIFIDDILVYSKDRETHQNHIRTVLERLREQKLFAKL 1373
Cdd:cd01647     81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                          170
                   ....*....|....*..
gi 2065826704 1374 SKCSFWQRSIGFLGHII 1390
Cdd:cd01647    161 EKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1485-1598 7.94e-54

Ty3/Gypsy 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 eukaryotes. 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. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


:

Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 184.23  E-value: 7.94e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1485 VYMDASIMGLGCVLMQR-----GRVIAYASRQLRKHEGNYPTHDLEMVAVVFALKIWRSYLYGAKVQIFTDHKSLKYIFT 1559
Cdd:cd09274      2 LETDASDYGIGAVLSQEdddgkERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLLT 81

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 2065826704 1560 QPDLNLRQRRWMELVADYDLDIAYHPGKANQVADALSRR 1598
Cdd:cd09274     82 QKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 753-848 2.64e-33

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


:

Pssm-ID: 367628  Cd Length: 97  Bit Score: 124.75  E-value: 2.64e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704  753 DIAIHFLEGDAHNWWLTVEKRKGDQIQSFADFEEEFNKKFFPPEAWDRLECAYLDLVQGNRTVREYDEEFNRLRRYVGRE 832
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                           90
                   ....*....|....*.
gi 2065826704  833 LEDEQAQVRRFIRGLR 848
Cdd:pfam03732   81 GRDEEALISAFLRGLR 96
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 235-327 1.18e-19

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


:

Pssm-ID: 367628  Cd Length: 97  Bit Score: 85.85  E-value: 1.18e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704  235 KLFSENLSGSALLWFTQLEPVTID---SFKELSSAFLKEYSMFMEKTTSDADLWNLTQGqNEPLRKYIAKFKEVIAKIP- 310
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIDafdSWDELKDAFLKRFFPSIRKDLLRNELRSLRQG-TESVREYVERFKRLARQLPh 79

                           90
                   ....*....|....*...
gi 2065826704  311 -GVSHTAALSALRNGLWH 327
Cdd:pfam03732   80 hGRDEEALISAFLRGLRP 97
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1685-1741 1.14e-17

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


:

Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 78.83  E-value: 1.14e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2065826704 1685 KELKEEILREAHQSrfSIHPGLHKMYHDLKRYYHWVGMKKDVARWVARCPTCQLVKA 1741
Cdd:pfam17921    3 KSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 919-983 2.58e-09

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: 57.89  E-value: 2.58e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2065826704  919 ECATCGKNHSgtcwRAVGACVRCGSKDHSIQNCPRMEQGTpkegvnEQRTCFYCGKAGHFKRECP 983
Cdd:PTZ00368    15 ECPNSAPAGA----AKARPCYKCGEPGHLSRECPSAPGGR------GERSCYNCGKTGHLSRECP 69
transpos_IS481 super family cl41329
IS481 family transposase; null
 1685-1871 6.66e-09

IS481 family transposase; null


The actual alignment was detected with superfamily member NF033577:

Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 59.53  E-value: 6.66e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1685 KELKEEILreaHQSRFSIHPGLHKmyHDLKRyyhWVGMKKDVARWVarcptcqlvKAESQVPSGLVQslpmpewkwdhvt 1764
Cdd:NF033577    83 YELERQGP---GVSRSTVHRILRR--HGLSR---LRALDRKTGKVK---------RYERAHPGELWH------------- 132

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1765 MDfVTGLPRSPAK-HDAVWVVVDRLTKSA-HFVAVSETDgaeRIAAKYIEEIVRLHGVPV-SIVSDRDTRFTSHFwKAFQ 1841
Cdd:NF033577   133 ID-IKKLGRIPDVgRLYLHTAIDDHSRFAyAELYPDETA---ETAADFLRRAFAEHGIPIrRVLTDNGSEFRSRA-HGFE 207

                          170       180       190
                   ....*....|....*....|....*....|...
gi 2065826704 1842 KAL---GTRVNMSTAYHPQTDGQSERTIRTLED 1871
Cdd:NF033577   208 LALaelGIEHRRTRPYHPQTNGKVERFHRTLKD 240
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 1033-1098 6.92e-05

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, 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: 133136  Cd Length: 92  Bit Score: 43.48  E-value: 6.92e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2065826704 1033 GGVETNTLFDSGATHCFVSPEMVTKGGFEKERNTEYGMVRAAGGQVMYPFGKY---KAHIDCHRGRIQF 1098
Cdd:cd00303      6 NGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVIlpvTIGIGGKTFTVDF 74
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 498-533 1.06e-03

Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin 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. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family).


The actual alignment was detected with superfamily member cd00303:

Pssm-ID: 472175  Cd Length: 92  Bit Score: 40.40  E-value: 1.06e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 2065826704  498 ITLDVANFEVtRCLIDTGSSVDLIFLSTLQRMGISK 533
Cdd:cd00303      1 LKGKINGVPV-RALVDSGASVNFISESLAKKLGLPP 35
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1214-1390 5.43e-96

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: 307.21  E-value: 5.43e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1214 GFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNKVTVKNKYPLPRIDELLDQLRGARWFSKIDLASGYHQIPIEPSDVR 1293
Cdd:cd01647      1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1294 KTAFRTRYGHYEFVVMPFGLTNAPAAFMKMMNGIFREFLDEFVIIFIDDILVYSKDRETHQNHIRTVLERLREQKLFAKL 1373
Cdd:cd01647     81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                          170
                   ....*....|....*..
gi 2065826704 1374 SKCSFWQRSIGFLGHII 1390
Cdd:cd01647    161 EKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1485-1598 7.94e-54

Ty3/Gypsy 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 eukaryotes. 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. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 184.23  E-value: 7.94e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1485 VYMDASIMGLGCVLMQR-----GRVIAYASRQLRKHEGNYPTHDLEMVAVVFALKIWRSYLYGAKVQIFTDHKSLKYIFT 1559
Cdd:cd09274      2 LETDASDYGIGAVLSQEdddgkERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLLT 81

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 2065826704 1560 QPDLNLRQRRWMELVADYDLDIAYHPGKANQVADALSRR 1598
Cdd:cd09274     82 QKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1230-1390 1.15e-44

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: 160.93  E-value: 1.15e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1230 VKKKD-GSFRLC----IDYRGLNKVTVK-------NKYPLPRIDELLDQLRGARWFSKIDLASGYHQIPIEPSDVRKTAF 1297
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1298 RTR-----------YGHYEFVVMPFGLTNAPAAFMKMMNGIFREFL---DEFVIIFIDDILVYSKDRETHQNHIRTVLER 1363
Cdd:pfam00078   81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRkraGLTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 2065826704 1364 LREQKLFAKLSKCSF--WQRSIGFLGHII 1390
Cdd:pfam00078  161 LKESGLKINPEKTQFflKSKEVKYLGVTL 189
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1480-1576 1.39e-37

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 137.26  E-value: 1.39e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1480 DEPYMVYMDASIMGLGCVLMQRG-----RVIAYASRQLRKHEGNYPTHDLEMVAVVFALKIWRSYLYGAKVQIFTDHKSL 1554
Cdd:pfam17917    3 SKPFILETDASDYGIGAVLSQKDedgkeRPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHKPL 82

                           90       100
                   ....*....|....*....|..
gi 2065826704 1555 KYIFTQPDLNLRQRRWMELVAD 1576
Cdd:pfam17917   83 KYLFTPKELNGRLARWALFLQE 104
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 753-848 2.64e-33

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 124.75  E-value: 2.64e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704  753 DIAIHFLEGDAHNWWLTVEKRKGDQIQSFADFEEEFNKKFFPPEAWDRLECAYLDLVQGNRTVREYDEEFNRLRRYVGRE 832
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                           90
                   ....*....|....*.
gi 2065826704  833 LEDEQAQVRRFIRGLR 848
Cdd:pfam03732   81 GRDEEALISAFLRGLR 96
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 235-327 1.18e-19

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 85.85  E-value: 1.18e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704  235 KLFSENLSGSALLWFTQLEPVTID---SFKELSSAFLKEYSMFMEKTTSDADLWNLTQGqNEPLRKYIAKFKEVIAKIP- 310
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIDafdSWDELKDAFLKRFFPSIRKDLLRNELRSLRQG-TESVREYVERFKRLARQLPh 79

                           90
                   ....*....|....*...
gi 2065826704  311 -GVSHTAALSALRNGLWH 327
Cdd:pfam03732   80 hGRDEEALISAFLRGLRP 97
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1685-1741 1.14e-17

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 78.83  E-value: 1.14e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2065826704 1685 KELKEEILREAHQSrfSIHPGLHKMYHDLKRYYHWVGMKKDVARWVARCPTCQLVKA 1741
Cdd:pfam17921    3 KSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 919-983 2.58e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 57.89  E-value: 2.58e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2065826704  919 ECATCGKNHSgtcwRAVGACVRCGSKDHSIQNCPRMEQGTpkegvnEQRTCFYCGKAGHFKRECP 983
Cdd:PTZ00368    15 ECPNSAPAGA----AKARPCYKCGEPGHLSRECPSAPGGR------GERSCYNCGKTGHLSRECP 69
transpos_IS481 NF033577
IS481 family transposase; null
 1685-1871 6.66e-09

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 59.53  E-value: 6.66e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1685 KELKEEILreaHQSRFSIHPGLHKmyHDLKRyyhWVGMKKDVARWVarcptcqlvKAESQVPSGLVQslpmpewkwdhvt 1764
Cdd:NF033577    83 YELERQGP---GVSRSTVHRILRR--HGLSR---LRALDRKTGKVK---------RYERAHPGELWH------------- 132

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1765 MDfVTGLPRSPAK-HDAVWVVVDRLTKSA-HFVAVSETDgaeRIAAKYIEEIVRLHGVPV-SIVSDRDTRFTSHFwKAFQ 1841
Cdd:NF033577   133 ID-IKKLGRIPDVgRLYLHTAIDDHSRFAyAELYPDETA---ETAADFLRRAFAEHGIPIrRVLTDNGSEFRSRA-HGFE 207

                          170       180       190
                   ....*....|....*....|....*....|...
gi 2065826704 1842 KAL---GTRVNMSTAYHPQTDGQSERTIRTLED 1871
Cdd:NF033577   208 LALaelGIEHRRTRPYHPQTNGKVERFHRTLKD 240
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1756-1856 6.28e-06

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: 46.54  E-value: 6.28e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1756 PEWKWdhvTMDFVTGlpRSPAKHDAVW--VVVDRLTKSAHFVAVSETDGAERIAAKYIEEIVRLHGVPVSIVSDRDTRFT 1833
Cdd:pfam00665    1 PNQLW---QGDFTYI--RIPGGGGKLYllVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYT 75

                           90       100
                   ....*....|....*....|...
gi 2065826704 1834 SHFWKAFQKALGTRVNMSTAYHP 1856
Cdd:pfam00665   76 SKAFREFLKDLGIKPSFSRPGNP 98
ZnF_C2HC smart00343
zinc finger;
968-984 6.90e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 41.66  E-value: 6.90e-05
                            10
                    ....*....|....*..
gi 2065826704   968 TCFYCGKAGHFKRECPK 984
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 1033-1098 6.92e-05

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, 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: 133136  Cd Length: 92  Bit Score: 43.48  E-value: 6.92e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2065826704 1033 GGVETNTLFDSGATHCFVSPEMVTKGGFEKERNTEYGMVRAAGGQVMYPFGKY---KAHIDCHRGRIQF 1098
Cdd:cd00303      6 NGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVIlpvTIGIGGKTFTVDF 74
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 967-984 1.21e-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: 40.97  E-value: 1.21e-04
                           10
                   ....*....|....*...
gi 2065826704  967 RTCFYCGKAGHFKRECPK 984
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1685-1918 1.30e-04

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 46.30  E-value: 1.30e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1685 KELKEEILREAHQSRFSihpGLHKMYHDLKRYYHWVGMKKdVAR------WVARCP----TCQLVKAESQVPSGLVQSLP 1754
Cdd:COG2801     71 AELLERIKEIFAESPRY---GYRRITAELRREGIAVNRKR-VRRlmrelgLQARRRrkkkYTTYSGHGGPIAPNLLFTAT 146

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1755 MPEWKWdhvTMDFvtglprspaKHDAVW-------VVVDRLTKSAHFVAVSETDGAERiAAKYIEEIVRLHGV--PVSIV 1825
Cdd:COG2801    147 APNQVW---VTDI---------TYIPTAegwlylaAVIDLFSREIVGWSVSDSMDAEL-VVDALEMAIERRGPpkPLILH 213

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1826 SDRDTRFTSHFWKAFQKALGTRVNMSTAYHPQTDGQSERTIRTLE------------DMLRACTLDWggswekhltlVEF 1893
Cdd:COG2801    214 SDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKyellyrrrfeslEEAREAIEEY----------IEF 283

                          250       260
                   ....*....|....*....|....*..
gi 2065826704 1894 aYNNS-YQASIG-MSPYEALYGRACRT 1918
Cdd:COG2801    284 -YNHErPHSSLGyLTPAEYEKQLAAAA 309
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 904-983 1.46e-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: 44.84  E-value: 1.46e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704  904 KFDKVEDSKLDAKRNE---CATCGKN-H-SGTCWRAVgaCVRCGSKDHSIQNCPrmeqgtpkegvnEQRTCFYCGKAGHF 978
Cdd:COG5082     44 RYEDRSVEDVSAIREEnpvCFNCGQNgHlRRDCPHSI--CYNCSWDGHRSNHCP------------KPKKCYNCGETGHL 109


                   ....*
gi 2065826704  979 KRECP 983
Cdd:COG5082    110 SRDCN 114
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 1033-1084 4.82e-04

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: 41.12  E-value: 4.82e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2065826704 1033 GGVETNTLFDSGATHCFVSPEMVTKGGFEKERNTEYGMVRAAGGQVMYPFGK 1084
Cdd:pfam13650    6 NGKPVRFLVDTGASGTVISPSLAERLGLKVRGLAYTVRVSTAGGRVSAARVR 57
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 498-533 1.06e-03

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, 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: 133136  Cd Length: 92  Bit Score: 40.40  E-value: 1.06e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 2065826704  498 ITLDVANFEVtRCLIDTGSSVDLIFLSTLQRMGISK 533
Cdd:cd00303      1 LKGKINGVPV-RALVDSGASVNFISESLAKKLGLPP 35
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1214-1390 5.43e-96

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: 307.21  E-value: 5.43e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1214 GFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNKVTVKNKYPLPRIDELLDQLRGARWFSKIDLASGYHQIPIEPSDVR 1293
Cdd:cd01647      1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1294 KTAFRTRYGHYEFVVMPFGLTNAPAAFMKMMNGIFREFLDEFVIIFIDDILVYSKDRETHQNHIRTVLERLREQKLFAKL 1373
Cdd:cd01647     81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                          170
                   ....*....|....*..
gi 2065826704 1374 SKCSFWQRSIGFLGHII 1390
Cdd:cd01647    161 EKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1485-1598 7.94e-54

Ty3/Gypsy 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 eukaryotes. 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. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 184.23  E-value: 7.94e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1485 VYMDASIMGLGCVLMQR-----GRVIAYASRQLRKHEGNYPTHDLEMVAVVFALKIWRSYLYGAKVQIFTDHKSLKYIFT 1559
Cdd:cd09274      2 LETDASDYGIGAVLSQEdddgkERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLLT 81

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 2065826704 1560 QPDLNLRQRRWMELVADYDLDIAYHPGKANQVADALSRR 1598
Cdd:cd09274     82 QKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRL 120
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1230-1390 1.15e-44

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: 160.93  E-value: 1.15e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1230 VKKKD-GSFRLC----IDYRGLNKVTVK-------NKYPLPRIDELLDQLRGARWFSKIDLASGYHQIPIEPSDVRKTAF 1297
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1298 RTR-----------YGHYEFVVMPFGLTNAPAAFMKMMNGIFREFL---DEFVIIFIDDILVYSKDRETHQNHIRTVLER 1363
Cdd:pfam00078   81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRkraGLTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 2065826704 1364 LREQKLFAKLSKCSF--WQRSIGFLGHII 1390
Cdd:pfam00078  161 LKESGLKINPEKTQFflKSKEVKYLGVTL 189
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1480-1576 1.39e-37

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 137.26  E-value: 1.39e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1480 DEPYMVYMDASIMGLGCVLMQRG-----RVIAYASRQLRKHEGNYPTHDLEMVAVVFALKIWRSYLYGAKVQIFTDHKSL 1554
Cdd:pfam17917    3 SKPFILETDASDYGIGAVLSQKDedgkeRPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHKPL 82

                           90       100
                   ....*....|....*....|..
gi 2065826704 1555 KYIFTQPDLNLRQRRWMELVAD 1576
Cdd:pfam17917   83 KYLFTPKELNGRLARWALFLQE 104
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
1453-1547 3.88e-36

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 133.01  E-value: 3.88e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1453 WSEECEKSFSELKSMLTSAPVLTLPEVDEPYMVYMDASIMGLGCVLMQRG-----RVIAYASRQLRKHEGNYPTHDLEMV 1527
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDddggeRPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 2065826704 1528 AVVFALKIWRSYLYGAKVQI 1547
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 753-848 2.64e-33

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 124.75  E-value: 2.64e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704  753 DIAIHFLEGDAHNWWLTVEKRKGDQIQSFADFEEEFNKKFFPPEAWDRLECAYLDLVQGNRTVREYDEEFNRLRRYVGRE 832
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                           90
                   ....*....|....*.
gi 2065826704  833 LEDEQAQVRRFIRGLR 848
Cdd:pfam03732   81 GRDEEALISAFLRGLR 96
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 1187-1390 6.10e-29

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: 116.29  E-value: 6.10e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1187 PISKAPYRMAPAEMAELKKQLEELLDKGFIRPSSSPWGAPVLFVKKKDG-SFRLCIDYRGLNKVTVKNKYPLPRIDELLD 1265
Cdd:cd03715      1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1266 QL-RGARWFSKIDLASGYHQIPIEPSDVRKTAFRTRYGHYEFVVMPFGLTNAPAAFmkmmNGIFREFLDEF--------V 1336
Cdd:cd03715     81 LLpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLF----HEALARDLAPFplehegtiL 156

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2065826704 1337 IIFIDDILVYSKDRETHQNHIRTVLERLREQKLFAKLSKCSFWQRSIGFLGHII 1390
Cdd:cd03715    157 LQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 1203-1363 5.64e-23

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: 99.28  E-value: 5.64e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1203 LKKQLEELLDKGFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNKVTVK---------NKYPLPRIDELLdqlrgarwf 1273
Cdd:cd01645     17 LTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDmgalqpglpHPAALPKGWPLI--------- 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1274 sKIDLASGYHQIPIEPSDVRKTAF-------RTRYGHYEFVVMPFGLTNAPAAFMKMMNGIFREFLDEF----VIIFIDD 1342
Cdd:cd01645     88 -VLDLKDCFFSIPLHPDDRERFAFtvpsinnKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYpdivIYHYMDD 166

                          170       180
                   ....*....|....*....|....
gi 2065826704 1343 ILVYSKDRETHQN---HIRTVLER 1363
Cdd:cd01645    167 ILIASDLEGQLREiyeELRQTLLR 190
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 235-327 1.18e-19

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.


Pssm-ID: 367628  Cd Length: 97  Bit Score: 85.85  E-value: 1.18e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704  235 KLFSENLSGSALLWFTQLEPVTID---SFKELSSAFLKEYSMFMEKTTSDADLWNLTQGqNEPLRKYIAKFKEVIAKIP- 310
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIDafdSWDELKDAFLKRFFPSIRKDLLRNELRSLRQG-TESVREYVERFKRLARQLPh 79

                           90
                   ....*....|....*...
gi 2065826704  311 -GVSHTAALSALRNGLWH 327
Cdd:pfam03732   80 hGRDEEALISAFLRGLRP 97
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1685-1741 1.14e-17

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 78.83  E-value: 1.14e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2065826704 1685 KELKEEILREAHQSrfSIHPGLHKMYHDLKRYYHWVGMKKDVARWVARCPTCQLVKA 1741
Cdd:pfam17921    3 KSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 1276-1387 8.97e-13

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: 66.98  E-value: 8.97e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1276 IDLASGYHQIPIEPSDVRKTAFRTRYGHYEFVVMPFGLTNAPAAFMKMMNGIFREFLDEFVIIF--IDDILVYSKDrETH 1353
Cdd:cd03714      1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFsyLDDLLIIASS-IKT 79

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 2065826704 1354 QNHIRTVLERLREQKLFAKLSKC-SFW--QRSIGFLG 1387
Cdd:cd03714     80 SEAVLRHLRATLLANLGFTLNLEkSKLgpTQRITFLG 116
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 1276-1390 1.12e-09

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: 57.36  E-value: 1.12e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1276 IDLASGYHQIPiepsdvrktafrtryghyefvvMPFGLTNAPAAFMKMMNGIFREF----LDEFVIIFIDDILVYSKDrE 1351
Cdd:cd00304      1 FDVKSFFTSIP----------------------LPQGSPLSPALANLYMEKLEAPIlkqlLDITLIRYVDDLVVIAKS-E 57

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2065826704 1352 THQNHIRTVLERLREQKLFAKLSKCSF--WQRSIGFLGHII 1390
Cdd:cd00304     58 QQAVKKRELEEFLARLGLNLSDEKTQFteKEKKFKFLGILV 98
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 919-983 2.58e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 57.89  E-value: 2.58e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2065826704  919 ECATCGKNHSgtcwRAVGACVRCGSKDHSIQNCPRMEQGTpkegvnEQRTCFYCGKAGHFKRECP 983
Cdd:PTZ00368    15 ECPNSAPAGA----AKARPCYKCGEPGHLSRECPSAPGGR------GERSCYNCGKTGHLSRECP 69
transpos_IS481 NF033577
IS481 family transposase; null
 1685-1871 6.66e-09

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 59.53  E-value: 6.66e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1685 KELKEEILreaHQSRFSIHPGLHKmyHDLKRyyhWVGMKKDVARWVarcptcqlvKAESQVPSGLVQslpmpewkwdhvt 1764
Cdd:NF033577    83 YELERQGP---GVSRSTVHRILRR--HGLSR---LRALDRKTGKVK---------RYERAHPGELWH------------- 132

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1765 MDfVTGLPRSPAK-HDAVWVVVDRLTKSA-HFVAVSETDgaeRIAAKYIEEIVRLHGVPV-SIVSDRDTRFTSHFwKAFQ 1841
Cdd:NF033577   133 ID-IKKLGRIPDVgRLYLHTAIDDHSRFAyAELYPDETA---ETAADFLRRAFAEHGIPIrRVLTDNGSEFRSRA-HGFE 207

                          170       180       190
                   ....*....|....*....|....*....|...
gi 2065826704 1842 KAL---GTRVNMSTAYHPQTDGQSERTIRTLED 1871
Cdd:NF033577   208 LALaelGIEHRRTRPYHPQTNGKVERFHRTLKD 240
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 915-998 1.27e-08

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 55.97  E-value: 1.27e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704  915 AKRNECATCGK-NH-SGTCWRAVG-----ACVRCGSKDHSIQNCPRMEQGTpkegvnEQRTCFYCGKAGHFKRECPklev 987
Cdd:PTZ00368    25 AKARPCYKCGEpGHlSRECPSAPGgrgerSCYNCGKTGHLSRECPEAPPGS------GPRSCYNCGQTGHISRECP---- 94

                           90
                   ....*....|.
gi 2065826704  988 ERQAGQRVNRS 998
Cdd:PTZ00368    95 NRAKGGAARRA 105
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1486-1598 8.81e-08

DIRS1 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 eukaryotes. 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. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260007  Cd Length: 120  Bit Score: 52.67  E-value: 8.81e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1486 YMDASIMGLGCVLmQRGRVIAYASrqlrKHEGNYPTHDLEMVAVVFALKIWRSYLYGAKVQIFTDHKS-LKYIFTQ---- 1560
Cdd:cd09275      3 FTDASLSGWGAYL-LNSRAHGPWS----ADERNKHINLLELKAVLLALQHFAAELKNRKILIRTDNTTaVAYINKQggts 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2065826704 1561 -PDLNLRQRRWMELVADYDLDI-AYH-PGKANQVADALSRR 1598
Cdd:cd09275     78 sPPLLALARQILLWCEQRNIWLrASHiPGVLNTEADRLSRL 118
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 938-984 3.30e-07

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 51.73  E-value: 3.30e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2065826704  938 CVRCGSKDHSIQNCPRmeqgTPKEGVNEQRTCFYCGKAGHFKRECPK 984
Cdd:PTZ00368     3 CYRCGGVGHQSRECPN----SAPAGAAKARPCYKCGEPGHLSRECPS 45
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 920-983 1.61e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 49.81  E-value: 1.61e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2065826704  920 CATCG-KNH-SGTC------WRAVGACVRCGSKDHSIQNCPRmEQGTPKEGvneqRTCFYCGKAGHFKRECP 983
Cdd:PTZ00368    80 CYNCGqTGHiSRECpnrakgGAARRACYNCGGEGHISRDCPN-AGKRPGGD----KTCYNCGQTGHLSRDCP 146
Ty3_capsid pfam19259
Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the ...
 721-870 5.66e-06

Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the Ty3 transposons of yeast as well as other transposable elements.


Pssm-ID: 437091 [Multi-domain]  Cd Length: 197  Bit Score: 49.39  E-value: 5.66e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704  721 FTGSSDPIVADEWRTRLKRNFNSTRCPEDYRKdiaIHF----LEGDAHNWWLTVEKRKGDQIQSFADFEEEFNKKFF-PP 795
Cdd:pfam19259   17 FRGRKDVLKLKSFISEIMLQMSMIFWPNDAER---IVFcarhLTGPAAQWFHDFVQEQGILDATFDTFIKAFKQHFYgKP 93

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2065826704  796 EAWDRLEcAYLDLVQGNRTVREYDEEFNRLRRYVGRELEDEQAQVRRFIRGLRVEIRNHCLIRTFTSVSELVERA 870
Cdd:pfam19259   94 DINKLFN-DIVNLSEAKLGIERYNSHFNRLWDLLPPDFLSEKAAIMFYIRGLKPETYIIVRLAKPSTLKEAMEIA 167
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1756-1856 6.28e-06

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: 46.54  E-value: 6.28e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1756 PEWKWdhvTMDFVTGlpRSPAKHDAVW--VVVDRLTKSAHFVAVSETDGAERIAAKYIEEIVRLHGVPVSIVSDRDTRFT 1833
Cdd:pfam00665    1 PNQLW---QGDFTYI--RIPGGGGKLYllVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYT 75

                           90       100
                   ....*....|....*....|...
gi 2065826704 1834 SHFWKAFQKALGTRVNMSTAYHP 1856
Cdd:pfam00665   76 SKAFREFLKDLGIKPSFSRPGNP 98
ZnF_C2HC smart00343
zinc finger;
968-984 6.90e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 41.66  E-value: 6.90e-05
                            10
                    ....*....|....*..
gi 2065826704   968 TCFYCGKAGHFKRECPK 984
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 1033-1098 6.92e-05

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, 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: 133136  Cd Length: 92  Bit Score: 43.48  E-value: 6.92e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2065826704 1033 GGVETNTLFDSGATHCFVSPEMVTKGGFEKERNTEYGMVRAAGGQVMYPFGKY---KAHIDCHRGRIQF 1098
Cdd:cd00303      6 NGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVIlpvTIGIGGKTFTVDF 74
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 967-984 1.21e-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: 40.97  E-value: 1.21e-04
                           10
                   ....*....|....*...
gi 2065826704  967 RTCFYCGKAGHFKRECPK 984
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1685-1918 1.30e-04

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 46.30  E-value: 1.30e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1685 KELKEEILREAHQSRFSihpGLHKMYHDLKRYYHWVGMKKdVAR------WVARCP----TCQLVKAESQVPSGLVQSLP 1754
Cdd:COG2801     71 AELLERIKEIFAESPRY---GYRRITAELRREGIAVNRKR-VRRlmrelgLQARRRrkkkYTTYSGHGGPIAPNLLFTAT 146

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1755 MPEWKWdhvTMDFvtglprspaKHDAVW-------VVVDRLTKSAHFVAVSETDGAERiAAKYIEEIVRLHGV--PVSIV 1825
Cdd:COG2801    147 APNQVW---VTDI---------TYIPTAegwlylaAVIDLFSREIVGWSVSDSMDAEL-VVDALEMAIERRGPpkPLILH 213

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1826 SDRDTRFTSHFWKAFQKALGTRVNMSTAYHPQTDGQSERTIRTLE------------DMLRACTLDWggswekhltlVEF 1893
Cdd:COG2801    214 SDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKyellyrrrfeslEEAREAIEEY----------IEF 283

                          250       260
                   ....*....|....*....|....*..
gi 2065826704 1894 aYNNS-YQASIG-MSPYEALYGRACRT 1918
Cdd:COG2801    284 -YNHErPHSSLGyLTPAEYEKQLAAAA 309
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 904-983 1.46e-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: 44.84  E-value: 1.46e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704  904 KFDKVEDSKLDAKRNE---CATCGKN-H-SGTCWRAVgaCVRCGSKDHSIQNCPrmeqgtpkegvnEQRTCFYCGKAGHF 978
Cdd:COG5082     44 RYEDRSVEDVSAIREEnpvCFNCGQNgHlRRDCPHSI--CYNCSWDGHRSNHCP------------KPKKCYNCGETGHL 109


                   ....*
gi 2065826704  979 KRECP 983
Cdd:COG5082    110 SRDCN 114
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 1033-1084 4.82e-04

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: 41.12  E-value: 4.82e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2065826704 1033 GGVETNTLFDSGATHCFVSPEMVTKGGFEKERNTEYGMVRAAGGQVMYPFGK 1084
Cdd:pfam13650    6 NGKPVRFLVDTGASGTVISPSLAERLGLKVRGLAYTVRVSTAGGRVSAARVR 57
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 937-984 8.65e-04

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


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 42.53  E-value: 8.65e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2065826704  937 ACVRCGSKDHSIQNCPrmeqgtpkegvneQRTCFYCGKAGHFKRECPK 984
Cdd:COG5082     62 VCFNCGQNGHLRRDCP-------------HSICYNCSWDGHRSNHCPK 96
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 498-533 1.06e-03

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, 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: 133136  Cd Length: 92  Bit Score: 40.40  E-value: 1.06e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 2065826704  498 ITLDVANFEVtRCLIDTGSSVDLIFLSTLQRMGISK 533
Cdd:cd00303      1 LKGKINGVPV-RALVDSGASVNFISESLAKKLGLPP 35
zf-H2C2 pfam09337
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ...
 1703-1737 2.10e-03

H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters.


Pssm-ID: 430537  Cd Length: 39  Bit Score: 37.69  E-value: 2.10e-03
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2065826704 1703 HPGLHKMYHDLKRYYHWVGMKKDVARWVARCPTCQ 1737
Cdd:pfam09337    5 HLGINKLTALLARKYHWLGIKETVSEVISSCVACQ 39
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 1034-1090 5.85e-03

gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins.


Pssm-ID: 464060  Cd Length: 92  Bit Score: 37.94  E-value: 5.85e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2065826704 1034 GVETNTLFDSGATHCFVSPEMVTKGGFEKERNTEYGMVRAAGGQVMypfgKYKAHID 1090
Cdd:pfam13975    7 GRPVRFLVDTGASVTVISEALAERLGLDRLVDAYPVTVRTANGTVR----AARVRLD 59
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
1762-1869 6.55e-03

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 41.02  E-value: 6.55e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065826704 1762 HVTMDFVTGlprsPAKHDAVWVVVDRLTKsahFVAVSETDG--AERIAAKYIEEIVRL-HGVPVSIVSDRDTRFTSHfwK 1838
Cdd:COG2826    174 HWEGDLIIG----KRGKSALLTLVERKSR---FVILLKLPDktAESVADALIRLLRKLpAFLRKSITTDNGKEFADH--K 244

                           90       100       110
                   ....*....|....*....|....*....|.
gi 2065826704 1839 AFQKALGTRVNMSTAYHPQTDGQSERTIRTL 1869
Cdd:COG2826    245 EIEAALGIKVYFADPYSPWQRGTNENTNGLL 275
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH