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Conserved domains on  [gi|2065783947|gb|KAG7552438|]
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Zinc finger CCHC-type [Arabidopsis thaliana x Arabidopsis arenosa]

Protein Classification

retrotransposon gag family protein; reverse transcriptase family protein( domain architecture ID 13690324)

retrotransposon gag family protein that may also contain retropepsin-like aspartic protease and reverse transcriptase (RT) domains; reverse transcriptase family protein (RT) from retrotransposons catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements

Graphical summary

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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 ...
 687-778 2.23e-48

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: 168.93  E-value: 2.23e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 687 GFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNKVTRKNKYPLPRIDELLDQLGGAKWFSKIDLASGYHQIPIEPSDIR 766
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                          90
                  ....*....|..
gi 2065783947 767 KTAFRTRYGYYE 778
Cdd:cd01647    81 KTAFRTPFGLYE 92
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 185-280 4.88e-34

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: 125.52  E-value: 4.88e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 185 DIAIHFLEGDAHNWWLTVEKRKGDQIQTFANFEEEFNKKFFPPEAWDRLECAYLDLIQGNRTVREYDEEFNRLRRYVGRE 264
Cdd:pfam03732   1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                          90
                  ....*....|....*.
gi 2065783947 265 LEDEQSQVRRFIRGLR 280
Cdd:pfam03732  81 GRDEEALISAFLRGLR 96
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 446-576 1.90e-23

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 pfam08284:

Pssm-ID: 472175  Cd Length: 134  Bit Score: 96.35  E-value: 1.90e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 446 RVYELS-EDANNAGNFraITGTLCIGDVETHTLFDSGATHCFVSSEMVEKGGFKKEPNTEYGMVRAAGGQVMYPSGVVRE 524
Cdd:pfam08284   4 RVNHLSaEEAEASPDV--IQGTFLVNSIPATVLFDSGATHSFISHAFVGKLKLPVESLSNPLCIETPTGGSVTTNLICPS 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2065783947 525 ISVVVDGVNMPTDLIVVQLKKHDVILGMDWLGKYKAHIDCHRGRIQFEREEG 576
Cdd:pfam08284  82 CPIEIQGISFLADLILLDMKDLDVILGMDWLSKNKANIDCARRTVTLTKERE 133
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 369-415 2.55e-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: 56.35  E-value: 2.55e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2065783947 369 ACGRCGSKDHGIQNCPRMDSGQpkvlaeEPRACYHCGKAGHFKRECP 415
Cdd:PTZ00368   29 PCYKCGEPGHLSRECPSAPGGR------GERSCYNCGKTGHLSRECP 69
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 687-778 2.23e-48

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: 168.93  E-value: 2.23e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 687 GFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNKVTRKNKYPLPRIDELLDQLGGAKWFSKIDLASGYHQIPIEPSDIR 766
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                          90
                  ....*....|..
gi 2065783947 767 KTAFRTRYGYYE 778
Cdd:cd01647    81 KTAFRTPFGLYE 92
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 185-280 4.88e-34

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: 125.52  E-value: 4.88e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 185 DIAIHFLEGDAHNWWLTVEKRKGDQIQTFANFEEEFNKKFFPPEAWDRLECAYLDLIQGNRTVREYDEEFNRLRRYVGRE 264
Cdd:pfam03732   1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                          90
                  ....*....|....*.
gi 2065783947 265 LEDEQSQVRRFIRGLR 280
Cdd:pfam03732  81 GRDEEALISAFLRGLR 96
RVP_2 pfam08284
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 446-576 1.90e-23

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.


Pssm-ID: 400537  Cd Length: 134  Bit Score: 96.35  E-value: 1.90e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 446 RVYELS-EDANNAGNFraITGTLCIGDVETHTLFDSGATHCFVSSEMVEKGGFKKEPNTEYGMVRAAGGQVMYPSGVVRE 524
Cdd:pfam08284   4 RVNHLSaEEAEASPDV--IQGTFLVNSIPATVLFDSGATHSFISHAFVGKLKLPVESLSNPLCIETPTGGSVTTNLICPS 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2065783947 525 ISVVVDGVNMPTDLIVVQLKKHDVILGMDWLGKYKAHIDCHRGRIQFEREEG 576
Cdd:pfam08284  82 CPIEIQGISFLADLILLDMKDLDVILGMDWLSKNKANIDCARRTVTLTKERE 133
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 469-555 7.86e-19

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: 82.00  E-value: 7.86e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 469 IGDVETHTLFDSGATHCFVSSEMVEKGGFKKEPNTEYGMVRAAGGQVMYPSGVVREISVVVDGVNMPTDLIVVQLKKHDV 548
Cdd:cd00303     5 INGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDV 84


                  ....*..
gi 2065783947 549 ILGMDWL 555
Cdd:cd00303    85 ILGRPWL 91
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 703-773 5.50e-14

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: 71.18  E-value: 5.50e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 703 VKKKD-GSFRLC----IDYRGLNKVTRK-------NKYPLPRIDELLDQLGGAKWFSKIDLASGYHQIPIEPSDIRKTAF 770
Cdd:pfam00078   1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80


                  ...
gi 2065783947 771 RTR 773
Cdd:pfam00078  81 TTP 83
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
438-573 5.11e-11

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 61.50  E-value: 5.11e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 438 PKRQAIAPRVYELSEDANNAGNFRaITGTlcIGDVETHTLFDSGATHCFVSSEMVEKGGFKKEPNTEYGMVRAAGGQVMY 517
Cdd:COG3577    20 PGQAPVSTGGGEVVLKRDRDGHFV-VEGT--INGQPVRFLVDTGASTVVLSESDARRLGLDPEDLGRPVRVQTANGVVRA 96

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2065783947 518 PSGVVREISV---VVDGVNMptdLIVVQLKKHDVILGMDWLGKYKAHIDchRGRIQFER 573
Cdd:COG3577    97 ARVRLDSVRIggiTLRNVRA---VVLPGGELDDGLLGMSFLGRLDFEID--GDRLTLRP 150
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 369-415 2.55e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 56.35  E-value: 2.55e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2065783947 369 ACGRCGSKDHGIQNCPRMDSGQpkvlaeEPRACYHCGKAGHFKRECP 415
Cdd:PTZ00368   29 PCYKCGEPGHLSRECPSAPGGR------GERSCYNCGKTGHLSRECP 69
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 369-415 4.60e-07

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: 51.00  E-value: 4.60e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2065783947 369 ACGRCGSKDHGIQNCP------RMDSGQPKVLAEEPRACYHCGKAGHFKRECP 415
Cdd:COG5082    62 VCFNCGQNGHLRRDCPhsicynCSWDGHRSNHCPKPKKCYNCGETGHLSRDCN 114
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 399-416 5.61e-05

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: 40.59  E-value: 5.61e-05
                          10
                  ....*....|....*...
gi 2065783947 399 RACYHCGKAGHFKRECPK 416
Cdd:pfam00098   1 GKCYNCGEPGHIARDCPK 18
ZnF_C2HC smart00343
zinc finger;
401-416 1.28e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 39.35  E-value: 1.28e-04
                           10
                   ....*....|....*.
gi 2065783947  401 CYHCGKAGHFKRECPK 416
Cdd:smart00343   2 CYNCGKEGHIARDCPS 17
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 687-778 2.23e-48

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: 168.93  E-value: 2.23e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 687 GFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNKVTRKNKYPLPRIDELLDQLGGAKWFSKIDLASGYHQIPIEPSDIR 766
Cdd:cd01647     1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                          90
                  ....*....|..
gi 2065783947 767 KTAFRTRYGYYE 778
Cdd:cd01647    81 KTAFRTPFGLYE 92
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 185-280 4.88e-34

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: 125.52  E-value: 4.88e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 185 DIAIHFLEGDAHNWWLTVEKRKGDQIQTFANFEEEFNKKFFPPEAWDRLECAYLDLIQGNRTVREYDEEFNRLRRYVGRE 264
Cdd:pfam03732   1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                          90
                  ....*....|....*.
gi 2065783947 265 LEDEQSQVRRFIRGLR 280
Cdd:pfam03732  81 GRDEEALISAFLRGLR 96
RVP_2 pfam08284
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 446-576 1.90e-23

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.


Pssm-ID: 400537  Cd Length: 134  Bit Score: 96.35  E-value: 1.90e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 446 RVYELS-EDANNAGNFraITGTLCIGDVETHTLFDSGATHCFVSSEMVEKGGFKKEPNTEYGMVRAAGGQVMYPSGVVRE 524
Cdd:pfam08284   4 RVNHLSaEEAEASPDV--IQGTFLVNSIPATVLFDSGATHSFISHAFVGKLKLPVESLSNPLCIETPTGGSVTTNLICPS 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2065783947 525 ISVVVDGVNMPTDLIVVQLKKHDVILGMDWLGKYKAHIDCHRGRIQFEREEG 576
Cdd:pfam08284  82 CPIEIQGISFLADLILLDMKDLDVILGMDWLSKNKANIDCARRTVTLTKERE 133
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 469-555 7.86e-19

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: 82.00  E-value: 7.86e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 469 IGDVETHTLFDSGATHCFVSSEMVEKGGFKKEPNTEYGMVRAAGGQVMYPSGVVREISVVVDGVNMPTDLIVVQLKKHDV 548
Cdd:cd00303     5 INGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDV 84


                  ....*..
gi 2065783947 549 ILGMDWL 555
Cdd:cd00303    85 ILGRPWL 91
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 660-770 3.68e-18

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: 83.55  E-value: 3.68e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 660 PISKVPYRMAPAEMAEVKKQLEELLDKGFIRPSSSPWGAPVLFVKKKDG-SFRLCIDYRGLNKVTRKNKYPLPRIDELLD 738
Cdd:cd03715     1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2065783947 739 QLGGA-KWFSKIDLASGYHQIPIEPSDIRKTAF 770
Cdd:cd03715    81 LLPPKhQWYTVLDLANAFFSLPLAPDSQPLFAF 113
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 703-773 5.50e-14

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: 71.18  E-value: 5.50e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 703 VKKKD-GSFRLC----IDYRGLNKVTRK-------NKYPLPRIDELLDQLGGAKWFSKIDLASGYHQIPIEPSDIRKTAF 770
Cdd:pfam00078   1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80


                  ...
gi 2065783947 771 RTR 773
Cdd:pfam00078  81 TTP 83
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 670-770 9.64e-14

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: 70.77  E-value: 9.64e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 670 PAEMAEVKKQL-EELLDKGFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNKVTRKnkyplprIDELldQLG------- 741
Cdd:cd01645    10 TEEKLEALTELvTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQD-------MGAL--QPGlphpaal 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 2065783947 742 -GAKWFSKIDLASGYHQIPIEPSDIRKTAF 770
Cdd:cd01645    81 pKGWPLIVLDLKDCFFSIPLHPDDRERFAF 110
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 469-557 2.74e-11

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: 60.28  E-value: 2.74e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 469 IGDVETHTLFDSGATHCFVSSEMVEKGGFKKEPNTEYGMVRAAGGQVMYPSGVVREISV---VVDGVnmptDLIVVQLKK 545
Cdd:pfam13975   5 INGRPVRFLVDTGASVTVISEALAERLGLDRLVDAYPVTVRTANGTVRAARVRLDSVKIggiELRNV----PAVVLPGDL 80

                          90
                  ....*....|..
gi 2065783947 546 HDVILGMDWLGK 557
Cdd:pfam13975  81 DDVLLGMDFLKR 92
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
438-573 5.11e-11

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 61.50  E-value: 5.11e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 438 PKRQAIAPRVYELSEDANNAGNFRaITGTlcIGDVETHTLFDSGATHCFVSSEMVEKGGFKKEPNTEYGMVRAAGGQVMY 517
Cdd:COG3577    20 PGQAPVSTGGGEVVLKRDRDGHFV-VEGT--INGQPVRFLVDTGASTVVLSESDARRLGLDPEDLGRPVRVQTANGVVRA 96

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2065783947 518 PSGVVREISV---VVDGVNMptdLIVVQLKKHDVILGMDWLGKYKAHIDchRGRIQFER 573
Cdd:COG3577    97 ARVRLDSVRIggiTLRNVRA---VVLPGGELDDGLLGMSFLGRLDFEID--GDRLTLRP 150
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 466-554 9.26e-11

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: 58.84  E-value: 9.26e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 466 TLCIGDVETHTLFDSGATHCFVSSEMVEKGGFKKEPNTEYGMVRAAGGQVMYPSGVVREISV---VVDGVnmptDLIVVQ 542
Cdd:pfam13650   2 PVTINGKPVRFLVDTGASGTVISPSLAERLGLKVRGLAYTVRVSTAGGRVSAARVRLDSLRLgglTLENV----PALVLD 77

                          90
                  ....*....|...
gi 2065783947 543 LK-KHDVILGMDW 554
Cdd:pfam13650  78 LGdLIDGLLGMDF 90
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 369-415 2.55e-09

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 56.35  E-value: 2.55e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2065783947 369 ACGRCGSKDHGIQNCPRMDSGQpkvlaeEPRACYHCGKAGHFKRECP 415
Cdd:PTZ00368   29 PCYKCGEPGHLSRECPSAPGGR------GERSCYNCGKTGHLSRECP 69
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 347-415 1.42e-08

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 54.43  E-value: 1.42e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2065783947 347 AKRGECLTCGKNhGGI---CWKAIG-----ACGRCGSKDHGIQNCPrmdSGQPKVlaeEPRACYHCGKAGHFKRECP 415
Cdd:PTZ00368   25 AKARPCYKCGEP-GHLsreCPSAPGgrgerSCYNCGKTGHLSRECP---EAPPGS---GPRSCYNCGQTGHISRECP 94
Ty3_capsid pfam19259
Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the ...
 153-332 3.22e-08

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: 54.40  E-value: 3.22e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 153 FTGSSDPIVADEWRTRLKRNFNSTRCPEDYRKdiaIHF----LEGDAHNWWLTVEKRKGDQIQTFANFEEEFNKKFF-PP 227
Cdd:pfam19259  17 FRGRKDVLKLKSFISEIMLQMSMIFWPNDAER---IVFcarhLTGPAAQWFHDFVQEQGILDATFDTFIKAFKQHFYgKP 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 228 EAWDRLEcAYLDLIQGNRTVREYDEEFNRLRRYVGRELEDEQSQVRRFIRGLRVEIRNHCLIRTFNSVSELveraamIEI 307
Cdd:pfam19259  94 DINKLFN-DIVNLSEAKLGIERYNSHFNRLWDLLPPDFLSEKAAIMFYIRGLKPETYIIVRLAKPSTLKEA------MEI 166

                         170       180
                  ....*....|....*....|....*.
gi 2065783947 308 GIEEEKLMNREKF-PNRSSQPSKSAD 332
Cdd:pfam19259 167 AYETIPYTERFSPtFTQNSKTVLDAD 192
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 369-415 1.06e-07

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 51.73  E-value: 1.06e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2065783947 369 ACGRCGSKDHGIQNCPRMDSGqpkvlAEEPRACYHCGKAGHFKRECP 415
Cdd:PTZ00368   79 SCYNCGQTGHISRECPNRAKG-----GAARRACYNCGGEGHISRDCP 120
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 370-416 1.90e-07

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 50.96  E-value: 1.90e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2065783947 370 CGRCGSKDHGIQNCPRmdsgQPKVLAEEPRACYHCGKAGHFKRECPK 416
Cdd:PTZ00368    3 CYRCGGVGHQSRECPN----SAPAGAAKARPCYKCGEPGHLSRECPS 45
retropepsin_like_bacteria cd05483
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ...
 469-556 2.05e-07

Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria aspartate proteases is a subfamily of retropepsin-like protease family, which includes enzymes from retrovirus and retrotransposons. While fungal and mammalian pepsin-like aspartate proteases are bilobal proteins with structurally related N- and C-termini, this family of bacteria aspartate proteases is half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. 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 proteases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133150  Cd Length: 96  Bit Score: 49.55  E-value: 2.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 469 IGDVETHTLFDSGATHCFVSSEMVEKGGFKKEPNTEYgMVRAAGGQVMYPSGVVREISV---VVDGVnmptDLIVVQLKK 545
Cdd:cd05483     9 INGQPVRFLLDTGASTTVISEELAERLGLPLTLGGKV-TVQTANGRVRAARVRLDSLQIggiTLRNV----PAVVLPGDA 83

                          90
                  ....*....|...
gi 2065783947 546 H--DVILGMDWLG 556
Cdd:cd05483    84 LgvDGLLGMDFLR 96
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 369-415 4.60e-07

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: 51.00  E-value: 4.60e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2065783947 369 ACGRCGSKDHGIQNCP------RMDSGQPKVLAEEPRACYHCGKAGHFKRECP 415
Cdd:COG5082    62 VCFNCGQNGHLRRDCPhsicynCSWDGHRSNHCPKPKKCYNCGETGHLSRDCN 114
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 366-415 4.60e-07

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 49.81  E-value: 4.60e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2065783947 366 AIGACGRCGSKDHGIQNCPrmdsgQPKVLAEEPRACYHCGKAGHFKRECP 415
Cdd:PTZ00368  102 ARRACYNCGGEGHISRDCP-----NAGKRPGGDKTCYNCGQTGHLSRDCP 146
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 399-416 5.61e-05

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: 40.59  E-value: 5.61e-05
                          10
                  ....*....|....*...
gi 2065783947 399 RACYHCGKAGHFKRECPK 416
Cdd:pfam00098   1 GKCYNCGEPGHIARDCPK 18
ZnF_C2HC smart00343
zinc finger;
401-416 1.28e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 39.35  E-value: 1.28e-04
                           10
                   ....*....|....*.
gi 2065783947  401 CYHCGKAGHFKRECPK 416
Cdd:smart00343   2 CYNCGKEGHIARDCPS 17
RP_DDI cd05479
RP_DDI; retropepsin-like domain of DNA damage inducible protein; The family represents the ...
 469-571 3.46e-03

RP_DDI; retropepsin-like domain of DNA damage inducible protein; The family represents the retropepsin-like domain of DNA damage inducible protein. DNA damage inducible protein has a retropepsin-like domain and an amino-terminal ubiquitin-like domain and/or a UBA (ubiquitin-associated) domain. This CD represents the retropepsin-like domain of DDI.


Pssm-ID: 133146  Cd Length: 124  Bit Score: 38.30  E-value: 3.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065783947 469 IGDVETHTLFDSGATHCFVSSEMVEKGGFKKEPNTEY-GMVRAAGGQVMYpsGVVREISVVVDGVNMPTDLIVVQLKKHD 547
Cdd:cd05479    23 INGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFqGIAKGVGTQKIL--GRIHLAQVKIGNLFLPCSFTVLEDDDVD 100

                          90       100
                  ....*....|....*....|....
gi 2065783947 548 VILGMDWLGKYKAHIDCHRGRIQF 571
Cdd:cd05479   101 FLIGLDMLKRHQCVIDLKENVLRI 124
 
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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