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Conserved domains on  [gi|2199033117|gb|ULR16446|]
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ORFIII [Banana streak CA virus]

Protein Classification

reverse transcriptase family protein( domain architecture ID 10443361)

reverse transcriptase family protein may be an RNA-directed DNA polymerase that catalyzes DNA replication from an RNA template of retrotransposons or retrons

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 ...
 1275-1458 5.02e-62

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: 209.76  E-value: 5.02e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1275 KVIRPSQSKHRTTAMIVesgtevdpvtgKEKRGKERLVFNYKRLNDNTEKDQYSLPGINTIIKRIGNAKIYSKFDLKSGF 1354
Cdd:cd01647      1 GIIEPSSSPYASPVVVV-----------KKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGY 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1355 HQVAMDPESIPWTAFWAIDGLYEWLVMPFGLKNAPAIFQRRMDNCFRGT-EKFIAVYIDDILVFSETVQQHKEHLKKFME 1433
Cdd:cd01647     70 HQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlGDFVEVYLDDILVYSKTEEEHLEHLREVLE 149

                          170       180
                   ....*....|....*....|....*
gi 2199033117 1434 ICERNGLVLSPTKMKIGTRQVDFLG 1458
Cdd:cd01647    150 RLREAGLKLNPEKCEFGVPEVEFLG 174
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1557-1685 2.79e-21

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


The actual alignment was detected with superfamily member cd09274:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 121  Bit Score: 91.01  E-value: 2.79e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1557 IIETDGCMEGWGGVCKWKEQSGQprwsEKICAYASGKFNPIK---STIDAEIQAVINSLDKFKiYYLDKKELIIRTDSKA 1633
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDDGK----ERPIAFFSRKLTPAErnySTTEKELLAIVWALKKFR-HYLLGRPFTVYTDHKA 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2199033117 1634 IVSFYKKSsDHKPSRVRWLAF-TDYitgtglDVKFEHIDGKDNVLADTLSRLV 1685
Cdd:cd09274     76 LKYLLTQK-DLNGRLARWLLLlSEF------DFEIEYRPGKENVVADALSRLP 121
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 1054-1154 2.85e-07

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 pfam00077:

Pssm-ID: 472175  Cd Length: 101  Bit Score: 50.44  E-value: 2.85e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1054 RCEVEIKEKKVvlNAILDTGATVCVADSRMIPAEMREQAKNrIIIRGVNGVTEVNEVTAIgRLWVGKQWFTLPQTF--IM 1131
Cdd:pfam00077    6 LLTVKIGGKYF--TALLDTGADDTVISQNDWPTNWPKQKAT-TNIQGIGGGINVRQSDQI-LILIGEDKFRGTVSPliLP 81

                           90       100
                   ....*....|....*....|...
gi 2199033117 1132 PTLGDgvhmIIGMNFIRTVGLRI 1154
Cdd:pfam00077   82 TCPVN----IIGRDLLQQLGGRL 100
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
898-1114 5.70e-06

Uncharacterized protein, contains DUF3084 domain [Function unknown];


:

Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 50.67  E-value: 5.70e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  898 TEEVKKTRVRIERVIdwKEIALRQHEVLKTsianEKQLSEENEglkeKIEELKKKELITVEEIS--EEEGAAMIEKIENL 975
Cdd:COG4372     51 REELEQAREELEQLE--EELEQARSELEQL----EEELEELNE----QLQAAQAELAQAQEELEslQEEAEELQEELEEL 120

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  976 EKENELLNAIIAKKEEEEVGYLNKIQELEERIRKLEQQMKYRDEEIQVILKQQREEKVNALEEVSVNALRPRNNHLNIRC 1055
Cdd:COG4372    121 QKERQDLEQQRKQLEAQIAELQSEIAEREEELKELEEQLESLQEELAALEQELQALSEAEAEQALDELLKEANRNAEKEE 200

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2199033117 1056 EVEIKEKK----------VVLNAILDTGATVCVADSRMIPAEMREQAKNRIIIRGVNGVTEVNEVTAIG 1114
Cdd:COG4372    201 ELAEAEKLieslprelaeELLEAKDSLEAKLGLALSALLDALELEEDKEELLEEVILKEIEELELAILV 269
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 736-753 1.52e-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: 40.20  E-value: 1.52e-04
                           10
                   ....*....|....*...
gi 2199033117  736 CRCYACGEEGHFASECTN 753
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
zf-GRF super family cl46396
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 1751-1784 7.07e-03

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


The actual alignment was detected with superfamily member pfam06839:

Pssm-ID: 480736  Cd Length: 45  Bit Score: 36.23  E-value: 7.07e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 2199033117 1751 CGCRKPAKLYTSR-TSRNPGREFYSC---ENKAC--FTWV 1784
Cdd:pfam06839    3 CPCGQRAVLLTVRkTGPNPGRQFYKCpvgREKQCgfFQWA 42
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1275-1458 5.02e-62

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: 209.76  E-value: 5.02e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1275 KVIRPSQSKHRTTAMIVesgtevdpvtgKEKRGKERLVFNYKRLNDNTEKDQYSLPGINTIIKRIGNAKIYSKFDLKSGF 1354
Cdd:cd01647      1 GIIEPSSSPYASPVVVV-----------KKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGY 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1355 HQVAMDPESIPWTAFWAIDGLYEWLVMPFGLKNAPAIFQRRMDNCFRGT-EKFIAVYIDDILVFSETVQQHKEHLKKFME 1433
Cdd:cd01647     70 HQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlGDFVEVYLDDILVYSKTEEEHLEHLREVLE 149

                          170       180
                   ....*....|....*....|....*
gi 2199033117 1434 ICERNGLVLSPTKMKIGTRQVDFLG 1458
Cdd:cd01647    150 RLREAGLKLNPEKCEFGVPEVEFLG 174
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1303-1461 1.04e-35

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: 134.74  E-value: 1.04e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1303 KEKRGKERLV----FNYKRLNDNTEK-------DQYSLPGINTIIKRIGNAKIYSKFDLKSGFHQVAMDPESIPWTAF-- 1369
Cdd:pfam00078    3 KKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFtt 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1370 ---------WAIDGLYEWLVMPFGLKNAPAIFQRRMDNCFRG----TEKFIAVYIDDILVFSETVQQHKEHLKKFMEICE 1436
Cdd:pfam00078   83 ppininwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPlrkrAGLTLVRYADDILIFSKSEEEHQEALEEVLEWLK 162

                          170       180
                   ....*....|....*....|....*..
gi 2199033117 1437 RNGLVLSPTKMKI--GTRQVDFLGATI 1461
Cdd:pfam00078  163 ESGLKINPEKTQFflKSKEVKYLGVTL 189
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1557-1685 2.79e-21

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: 91.01  E-value: 2.79e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1557 IIETDGCMEGWGGVCKWKEQSGQprwsEKICAYASGKFNPIK---STIDAEIQAVINSLDKFKiYYLDKKELIIRTDSKA 1633
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDDGK----ERPIAFFSRKLTPAErnySTTEKELLAIVWALKKFR-HYLLGRPFTVYTDHKA 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2199033117 1634 IVSFYKKSsDHKPSRVRWLAF-TDYitgtglDVKFEHIDGKDNVLADTLSRLV 1685
Cdd:cd09274     76 LKYLLTQK-DLNGRLARWLLLlSEF------DFEIEYRPGKENVVADALSRLP 121
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1556-1654 3.16e-13

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: 67.54  E-value: 3.16e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1556 MIIETDGCMEGWGGVCKWKEQSGQprwsEKICAYASGKFNPIK---STIDAEIQAVINSLDKFKiYYLDKKELIIRTDSK 1632
Cdd:pfam17917    6 FILETDASDYGIGAVLSQKDEDGK----ERPIAYASRKLTPAErnySTTEKELLAIVWALKKFR-HYLLGRKFTVYTDHK 80

                           90       100
                   ....*....|....*....|...
gi 2199033117 1633 AIVSFykKSSDHKPSRV-RWLAF 1654
Cdd:pfam17917   81 PLKYL--FTPKELNGRLaRWALF 101
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 1054-1154 2.85e-07

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


Pssm-ID: 425454  Cd Length: 101  Bit Score: 50.44  E-value: 2.85e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1054 RCEVEIKEKKVvlNAILDTGATVCVADSRMIPAEMREQAKNrIIIRGVNGVTEVNEVTAIgRLWVGKQWFTLPQTF--IM 1131
Cdd:pfam00077    6 LLTVKIGGKYF--TALLDTGADDTVISQNDWPTNWPKQKAT-TNIQGIGGGINVRQSDQI-LILIGEDKFRGTVSPliLP 81

                           90       100
                   ....*....|....*....|...
gi 2199033117 1132 PTLGDgvhmIIGMNFIRTVGLRI 1154
Cdd:pfam00077   82 TCPVN----IIGRDLLQQLGGRL 100
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
898-1114 5.70e-06

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 50.67  E-value: 5.70e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  898 TEEVKKTRVRIERVIdwKEIALRQHEVLKTsianEKQLSEENEglkeKIEELKKKELITVEEIS--EEEGAAMIEKIENL 975
Cdd:COG4372     51 REELEQAREELEQLE--EELEQARSELEQL----EEELEELNE----QLQAAQAELAQAQEELEslQEEAEELQEELEEL 120

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  976 EKENELLNAIIAKKEEEEVGYLNKIQELEERIRKLEQQMKYRDEEIQVILKQQREEKVNALEEVSVNALRPRNNHLNIRC 1055
Cdd:COG4372    121 QKERQDLEQQRKQLEAQIAELQSEIAEREEELKELEEQLESLQEELAALEQELQALSEAEAEQALDELLKEANRNAEKEE 200

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2199033117 1056 EVEIKEKK----------VVLNAILDTGATVCVADSRMIPAEMREQAKNRIIIRGVNGVTEVNEVTAIG 1114
Cdd:COG4372    201 ELAEAEKLieslprelaeELLEAKDSLEAKLGLALSALLDALELEEDKEELLEEVILKEIEELELAILV 269
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
1044-1161 1.13e-05

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 47.25  E-value: 1.13e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1044 LRPRNNHLNIrcEVEIKEKKVvlNAILDTGATVCVadsrmIPAEMREQAK-------NRIIIRGVNGVTEVNEVTaIGRL 1116
Cdd:COG3577     35 KRDRDGHFVV--EGTINGQPV--RFLVDTGASTVV-----LSESDARRLGldpedlgRPVRVQTANGVVRAARVR-LDSV 104

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2199033117 1117 WVGKqwFTLPQT--FIMPTlGDGVHMIIGMNFIRTVGLRIENGEVTI 1161
Cdd:COG3577    105 RIGG--ITLRNVraVVLPG-GELDDGLLGMSFLGRLDFEIDGDRLTL 148
retropepsin_like_bacteria cd05483
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ...
 1056-1148 2.67e-05

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: 44.54  E-value: 2.67e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1056 EVEIKEKKVvlNAILDTGATVCVadsrmIPAEMREQAK------NRIIIRGVNGVTEVNEVTaIGRLWVGKQWFTLPQTF 1129
Cdd:cd05483      6 PVTINGQPV--RFLLDTGASTTV-----ISEELAERLGlpltlgGKVTVQTANGRVRAARVR-LDSLQIGGITLRNVPAV 77

                           90
                   ....*....|....*....
gi 2199033117 1130 IMPTLGDGVHMIIGMNFIR 1148
Cdd:cd05483     78 VLPGDALGVDGLLGMDFLR 96
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 736-753 1.52e-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: 40.20  E-value: 1.52e-04
                           10
                   ....*....|....*...
gi 2199033117  736 CRCYACGEEGHFASECTN 753
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
897-1063 1.65e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 46.60  E-value: 1.65e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  897 NTEEVKKTrvrIERVIDWKEIALRQHEVLKTSIANEKQLSEENEGLKEKIEELKKKELITVEEISEE--EGAAMIEKIEN 974
Cdd:PRK03918   166 NLGEVIKE---IKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPELREELEKLEKEvkELEELKEEIEE 242

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  975 LEKENELLNAIIAKKEEEEVGYLNKIQELEERIRKLEQQMKyRDEEIQ------VILKQQREEKVNALEEVSVNALRPRN 1048
Cdd:PRK03918   243 LEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVK-ELKELKekaeeyIKLSEFYEEYLDELREIEKRLSRLEE 321

                          170
                   ....*....|....*
gi 2199033117 1049 NHLNIRCEVEIKEKK 1063
Cdd:PRK03918   322 EINGIEERIKELEEK 336
ZnF_C2HC smart00343
zinc finger;
737-753 6.07e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.58  E-value: 6.07e-04
                            10
                    ....*....|....*..
gi 2199033117   737 RCYACGEEGHFASECTN 753
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
Caldesmon pfam02029
Caldesmon;
895-1038 2.58e-03

Caldesmon;


Pssm-ID: 460421 [Multi-domain]  Cd Length: 495  Bit Score: 42.55  E-value: 2.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  895 DINTEEVKKTRVRIERVIDWKEIALRQHEVLktsIANEKQLSEENEGLKEKIEELKKKELITVEEISEEEGAAMIE---K 971
Cdd:pfam02029  173 NFAKEEVKDEKIKKEKKVKYESKVFLDQKRG---HPEVKSQNGEEEVTKLKVTTKRRQGGLSQSQEREEEAEVFLEaeqK 249

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2199033117  972 IENL-----EKENELLNAIIAKKEEEEVgylnkiqELEERIRKLEQQMKYRDEEIQViLKQQREEKVNALEE 1038
Cdd:pfam02029  250 LEELrrrrqEKESEEFEKLRQKQQEAEL-------ELEELKKKREERRKLLEEEEQR-RKQEEAERKLREEE 313
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 1751-1784 7.07e-03

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 36.23  E-value: 7.07e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 2199033117 1751 CGCRKPAKLYTSR-TSRNPGREFYSC---ENKAC--FTWV 1784
Cdd:pfam06839    3 CPCGQRAVLLTVRkTGPNPGRQFYKCpvgREKQCgfFQWA 42
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1275-1458 5.02e-62

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: 209.76  E-value: 5.02e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1275 KVIRPSQSKHRTTAMIVesgtevdpvtgKEKRGKERLVFNYKRLNDNTEKDQYSLPGINTIIKRIGNAKIYSKFDLKSGF 1354
Cdd:cd01647      1 GIIEPSSSPYASPVVVV-----------KKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGY 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1355 HQVAMDPESIPWTAFWAIDGLYEWLVMPFGLKNAPAIFQRRMDNCFRGT-EKFIAVYIDDILVFSETVQQHKEHLKKFME 1433
Cdd:cd01647     70 HQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLlGDFVEVYLDDILVYSKTEEEHLEHLREVLE 149

                          170       180
                   ....*....|....*....|....*
gi 2199033117 1434 ICERNGLVLSPTKMKIGTRQVDFLG 1458
Cdd:cd01647    150 RLREAGLKLNPEKCEFGVPEVEFLG 174
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1303-1461 1.04e-35

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: 134.74  E-value: 1.04e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1303 KEKRGKERLV----FNYKRLNDNTEK-------DQYSLPGINTIIKRIGNAKIYSKFDLKSGFHQVAMDPESIPWTAF-- 1369
Cdd:pfam00078    3 KKGKGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAFtt 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1370 ---------WAIDGLYEWLVMPFGLKNAPAIFQRRMDNCFRG----TEKFIAVYIDDILVFSETVQQHKEHLKKFMEICE 1436
Cdd:pfam00078   83 ppininwngELSGGRYEWKGLPQGLVLSPALFQLFMNELLRPlrkrAGLTLVRYADDILIFSKSEEEHQEALEEVLEWLK 162

                          170       180
                   ....*....|....*....|....*..
gi 2199033117 1437 RNGLVLSPTKMKI--GTRQVDFLGATI 1461
Cdd:pfam00078  163 ESGLKINPEKTQFflKSKEVKYLGVTL 189
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1557-1685 2.79e-21

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: 91.01  E-value: 2.79e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1557 IIETDGCMEGWGGVCKWKEQSGQprwsEKICAYASGKFNPIK---STIDAEIQAVINSLDKFKiYYLDKKELIIRTDSKA 1633
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDDGK----ERPIAFFSRKLTPAErnySTTEKELLAIVWALKKFR-HYLLGRPFTVYTDHKA 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2199033117 1634 IVSFYKKSsDHKPSRVRWLAF-TDYitgtglDVKFEHIDGKDNVLADTLSRLV 1685
Cdd:cd09274     76 LKYLLTQK-DLNGRLARWLLLlSEF------DFEIEYRPGKENVVADALSRLP 121
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 1262-1458 3.67e-19

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: 87.79  E-value: 3.67e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1262 EAMAKHVKKLLELKVIRPSQSKHRTTamivesgteVDPVtgKEKRGKE-RLVFNYKRLNDNTEKDQYSLPGINTIIKRIG 1340
Cdd:cd03715     15 EGITPHIQELLEAGILVPCQSPWNTP---------ILPV--KKPGGNDyRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLP 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1341 NA-KIYSKFDLKSGFHQVAMDPESIPWTAFWAIDGLYEWLVMPFGLKNAPAIF----QRRMDNCFRGTEKFIAV-YIDDI 1414
Cdd:cd03715     84 PKhQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFhealARDLAPFPLEHEGTILLqYVDDL 163

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 2199033117 1415 LVFSETVQQHKEHLKKFMEICERNGLVLSPTKMKIGTRQVDFLG 1458
Cdd:cd03715    164 LLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLG 207
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 1262-1461 1.24e-13

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: 71.93  E-value: 1.24e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1262 EAMAKHVKKLLELKVIRPSQSKHRTTAMIVesgtevdpvtgKEKRGKERLVFNYKRLNDNTEKD---QYSLPGINTIIKR 1338
Cdd:cd01645     15 EALTELVTEQLKEGHIEPSTSPWNTPVFVI-----------KKKSGKWRLLHDLRAVNAQTQDMgalQPGLPHPAALPKG 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1339 ignakiYSK--FDLKSGFHQVAMDPESIPWTAFW--AIDGL-----YEWLVMPFGLKNAPAIFQRRMDNC---FRgtEKF 1406
Cdd:cd01645     84 ------WPLivLDLKDCFFSIPLHPDDRERFAFTvpSINNKgpakrYQWKVLPQGMKNSPTICQSFVAQAlepFR--KQY 155

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2199033117 1407 ----IAVYIDDILVFSETVQQHKEHLKKFMEICERNGLVLSPTKMKIGTrQVDFLGATI 1461
Cdd:cd01645    156 pdivIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEP-PFQYLGYEL 213
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1556-1654 3.16e-13

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: 67.54  E-value: 3.16e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1556 MIIETDGCMEGWGGVCKWKEQSGQprwsEKICAYASGKFNPIK---STIDAEIQAVINSLDKFKiYYLDKKELIIRTDSK 1632
Cdd:pfam17917    6 FILETDASDYGIGAVLSQKDEDGK----ERPIAYASRKLTPAErnySTTEKELLAIVWALKKFR-HYLLGRKFTVYTDHK 80

                           90       100
                   ....*....|....*....|...
gi 2199033117 1633 AIVSFykKSSDHKPSRV-RWLAF 1654
Cdd:pfam17917   81 PLKYL--FTPKELNGRLaRWALF 101
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 1348-1461 3.31e-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: 67.75  E-value: 3.31e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1348 FDLKSGFHQVAMDPESIPWTAFWAIDGLYEWLVMPFGLKNAPAIFQRRMDNCF---RGTEKFIAVYIDDILVFSETvQQH 1424
Cdd:cd03714      1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLaplRLLGVRIFSYLDDLLIIASS-IKT 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2199033117 1425 KEHLKK--FMEICERNGLVLSPTKMKIG-TRQVDFLGATI 1461
Cdd:cd03714     80 SEAVLRhlRATLLANLGFTLNLEKSKLGpTQRITFLGLEL 119
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
1534-1627 2.05e-11

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 62.13  E-value: 2.05e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1534 VDKIKDLVKNLPELELPPNNAMMIIETDGCMEGWGGVCKWKEQSGQprwsEKICAYASGKFNPIK---STIDAEIQAVIN 1610
Cdd:pfam17919    9 FEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDDGG----ERPIAYASRKLSPAErnySTTEKELLAIVF 84

                           90
                   ....*....|....*..
gi 2199033117 1611 SLDKFKiYYLDKKELII 1627
Cdd:pfam17919   85 ALKKFR-HYLLGRKFTV 100
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 1348-1461 8.36e-08

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: 51.97  E-value: 8.36e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1348 FDLKSGFHQVAMdpesipwtafwaidglyewlvmPFGLKNAPAIFQRRMDN-----CFRGTEKFIAVYIDDILVFSETVQ 1422
Cdd:cd00304      1 FDVKSFFTSIPL----------------------PQGSPLSPALANLYMEKleapiLKQLLDITLIRYVDDLVVIAKSEQ 58

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2199033117 1423 QhKEHLKKFMEICERNGLVLSPTKMK--IGTRQVDFLGATI 1461
Cdd:cd00304     59 Q-AVKKRELEEFLARLGLNLSDEKTQftEKEKKFKFLGILV 98
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 1054-1154 2.85e-07

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


Pssm-ID: 425454  Cd Length: 101  Bit Score: 50.44  E-value: 2.85e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1054 RCEVEIKEKKVvlNAILDTGATVCVADSRMIPAEMREQAKNrIIIRGVNGVTEVNEVTAIgRLWVGKQWFTLPQTF--IM 1131
Cdd:pfam00077    6 LLTVKIGGKYF--TALLDTGADDTVISQNDWPTNWPKQKAT-TNIQGIGGGINVRQSDQI-LILIGEDKFRGTVSPliLP 81

                           90       100
                   ....*....|....*....|...
gi 2199033117 1132 PTLGDgvhmIIGMNFIRTVGLRI 1154
Cdd:pfam00077   82 TCPVN----IIGRDLLQQLGGRL 100
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 1056-1146 4.20e-06

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: 46.51  E-value: 4.20e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1056 EVEIKEKKVvlNAILDTGATVCVadsrmIPAEMREQAK-------NRIIIRGVNGVTEVNEVTaIGRLWVGKQWFTLPQT 1128
Cdd:pfam13650    2 PVTINGKPV--RFLVDTGASGTV-----ISPSLAERLGlkvrglaYTVRVSTAGGRVSAARVR-LDSLRLGGLTLENVPA 73

                           90
                   ....*....|....*...
gi 2199033117 1129 FIMPtLGDGVHMIIGMNF 1146
Cdd:pfam13650   74 LVLD-LGDLIDGLLGMDF 90
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
898-1114 5.70e-06

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 50.67  E-value: 5.70e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  898 TEEVKKTRVRIERVIdwKEIALRQHEVLKTsianEKQLSEENEglkeKIEELKKKELITVEEIS--EEEGAAMIEKIENL 975
Cdd:COG4372     51 REELEQAREELEQLE--EELEQARSELEQL----EEELEELNE----QLQAAQAELAQAQEELEslQEEAEELQEELEEL 120

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  976 EKENELLNAIIAKKEEEEVGYLNKIQELEERIRKLEQQMKYRDEEIQVILKQQREEKVNALEEVSVNALRPRNNHLNIRC 1055
Cdd:COG4372    121 QKERQDLEQQRKQLEAQIAELQSEIAEREEELKELEEQLESLQEELAALEQELQALSEAEAEQALDELLKEANRNAEKEE 200

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2199033117 1056 EVEIKEKK----------VVLNAILDTGATVCVADSRMIPAEMREQAKNRIIIRGVNGVTEVNEVTAIG 1114
Cdd:COG4372    201 ELAEAEKLieslprelaeELLEAKDSLEAKLGLALSALLDALELEEDKEELLEEVILKEIEELELAILV 269
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1557-1684 8.29e-06

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: 46.89  E-value: 8.29e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1557 IIETDGCMEGWGGVCKWKEQSGQprWSEKicayasgkfnPIKSTIDA-EIQAVINSLDKFKiYYLDKKELIIRTDSKAIV 1635
Cdd:cd09275      1 VLFTDASLSGWGAYLLNSRAHGP--WSAD----------ERNKHINLlELKAVLLALQHFA-AELKNRKILIRTDNTTAV 67

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2199033117 1636 SFYKKSSDHKPSRVRWLA--FTDYITGTGLDVKFEHIDGKDNVLADTLSRL 1684
Cdd:cd09275     68 AYINKQGGTSSPPLLALArqILLWCEQRNIWLRASHIPGVLNTEADRLSRL 118
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
1044-1161 1.13e-05

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 47.25  E-value: 1.13e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1044 LRPRNNHLNIrcEVEIKEKKVvlNAILDTGATVCVadsrmIPAEMREQAK-------NRIIIRGVNGVTEVNEVTaIGRL 1116
Cdd:COG3577     35 KRDRDGHFVV--EGTINGQPV--RFLVDTGASTVV-----LSESDARRLGldpedlgRPVRVQTANGVVRAARVR-LDSV 104

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2199033117 1117 WVGKqwFTLPQT--FIMPTlGDGVHMIIGMNFIRTVGLRIENGEVTI 1161
Cdd:COG3577    105 RIGG--ITLRNVraVVLPG-GELDDGLLGMSFLGRLDFEIDGDRLTL 148
retropepsin_like_bacteria cd05483
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ...
 1056-1148 2.67e-05

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: 44.54  E-value: 2.67e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1056 EVEIKEKKVvlNAILDTGATVCVadsrmIPAEMREQAK------NRIIIRGVNGVTEVNEVTaIGRLWVGKQWFTLPQTF 1129
Cdd:cd05483      6 PVTINGQPV--RFLLDTGASTTV-----ISEELAERLGlpltlgGKVTVQTANGRVRAARVR-LDSLQIGGITLRNVPAV 77

                           90
                   ....*....|....*....
gi 2199033117 1130 IMPTLGDGVHMIIGMNFIR 1148
Cdd:cd05483     78 VLPGDALGVDGLLGMDFLR 96
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 1056-1148 4.21e-05

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: 43.72  E-value: 4.21e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1056 EVEIKEKKVvlNAILDTGATVCVadsrmIPAEM-------REQAKNRIIIRGVNGVTEVNEVTaIGRLWVGKQWFTLPQT 1128
Cdd:pfam13975    2 DVTINGRPV--RFLVDTGASVTV-----ISEALaerlgldRLVDAYPVTVRTANGTVRAARVR-LDSVKIGGIELRNVPA 73

                           90       100
                   ....*....|....*....|
gi 2199033117 1129 FIMPtlGDGVHMIIGMNFIR 1148
Cdd:pfam13975   74 VVLP--GDLDDVLLGMDFLK 91
RT_pepA17 cd01644
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ...
 1307-1444 5.40e-05

RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.


Pssm-ID: 238822  Cd Length: 213  Bit Score: 46.53  E-value: 5.40e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1307 GKERLVFN----YK--RLNDNTEKDQYSLPGINTIIKRIGNAKIYSKFDLKSGFHQVAMDPESIPWTAF-WAIDG----- 1374
Cdd:cd01644     17 TKLRVVFDasarYNgvSLNDMLLKGPDLLNSLFGVLLRFRQGKIAVSADIEKMFHQVKVRPEDRDVLRFlWRKDGdepkp 96

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2199033117 1375 -LYEWLVMPFGLKNAPAIFQRRM-----DNCFRGTEKFIA--VYIDDILVFSETVQQHKEHLKKFMEICERNGLVLSP 1444
Cdd:cd01644     97 iEYRMTVVPFGAASAPFLANRALkqhaeDHPHEAAAKIIKrnFYVDDILVSTDTLNEAVNVAKRLIALLKKGGFNLRK 174
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 736-753 1.52e-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: 40.20  E-value: 1.52e-04
                           10
                   ....*....|....*...
gi 2199033117  736 CRCYACGEEGHFASECTN 753
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
897-1063 1.65e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 46.60  E-value: 1.65e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  897 NTEEVKKTrvrIERVIDWKEIALRQHEVLKTSIANEKQLSEENEGLKEKIEELKKKELITVEEISEE--EGAAMIEKIEN 974
Cdd:PRK03918   166 NLGEVIKE---IKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPELREELEKLEKEvkELEELKEEIEE 242

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  975 LEKENELLNAIIAKKEEEEVGYLNKIQELEERIRKLEQQMKyRDEEIQ------VILKQQREEKVNALEEVSVNALRPRN 1048
Cdd:PRK03918   243 LEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVK-ELKELKekaeeyIKLSEFYEEYLDELREIEKRLSRLEE 321

                          170
                   ....*....|....*
gi 2199033117 1049 NHLNIRCEVEIKEKK 1063
Cdd:PRK03918   322 EINGIEERIKELEEK 336
PTZ00121 PTZ00121
MAEBL; Provisional
 899-1039 4.26e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.52  E-value: 4.26e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  899 EEVKKTRVRiERVIDWKEIALRQHEVLKTS----IANEKQLSEENEGLKEKIEELKKKELITVEEI-------------- 960
Cdd:PTZ00121  1561 EEKKKAEEA-KKAEEDKNMALRKAEEAKKAeearIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELkkaeeekkkveqlk 1639

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  961 -SEEEGAAMIEKIENLEKENELLNAIIAKKEEEEVGYLNKIQELEERIRKLEQQMKYRDEEIQVI--LKQQREEKVNALE 1037
Cdd:PTZ00121  1640 kKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAeeLKKKEAEEKKKAE 1719


                   ..
gi 2199033117 1038 EV 1039
Cdd:PTZ00121  1720 EL 1721
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
856-1063 4.92e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 45.05  E-value: 4.92e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  856 ESHRTICRACGSEAVHKHRIDCLKCdmticlmcqpwfYkdinTEEVKKTRVRIERVIDWKEIALRQHEVLKTSIANEKQL 935
Cdd:PRK03918   432 KKAKGKCPVCGRELTEEHRKELLEE------------Y----TAELKRIEKELKEIEEKERKLRKELRELEKVLKKESEL 495

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  936 SEENEglkekieelkkkELITVEEISEEEGAAMIEKIENLEKENELLNAIIAKKEEEEVGY---LNKIQELEERIRKLEQ 1012
Cdd:PRK03918   496 IKLKE------------LAEQLKELEEKLKKYNLEELEKKAEEYEKLKEKLIKLKGEIKSLkkeLEKLEELKKKLAELEK 563

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2199033117 1013 QMKYRDEEIQVILKQQREEKVNALEEVS--VNALRPRNNH----LNIRCEVEIKEKK 1063
Cdd:PRK03918   564 KLDELEEELAELLKELEELGFESVEELEerLKELEPFYNEylelKDAEKELEREEKE 620
ZnF_C2HC smart00343
zinc finger;
737-753 6.07e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.58  E-value: 6.07e-04
                            10
                    ....*....|....*..
gi 2199033117   737 RCYACGEEGHFASECTN 753
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1558-1683 7.42e-04

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


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 41.15  E-value: 7.42e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1558 IETDGCME------GWGGVCKwkeqSGQPRWsekICAYASGkfNPIKSTIDAEIQAVINSLDKFKIYYLdkKELIIRTDS 1631
Cdd:cd06222      1 INVDGSCRgnpgpaGIGGVLR----DHEGGW---LGGFALK--IGAPTALEAELLALLLALELALDLGY--LKVIIESDS 69

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2199033117 1632 KAIVSFYKKSSDHKPSRVRWLAFTDYITGTGLDVKFEHIDGKDNVLADTLSR 1683
Cdd:cd06222     70 KYVVDLINSGSFKWSPNILLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
HEC1 COG5185
Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell ...
 895-1101 8.74e-04

Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 444066 [Multi-domain]  Cd Length: 594  Bit Score: 44.18  E-value: 8.74e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  895 DINTEEVKKTRVRIERVIDWKEIALRQHEVLKTSIA-NEKQLSEENEGLKEKIEELKKKELITVEEISEEEGAAMIEKIE 973
Cdd:COG5185    264 DLRLEKLGENAESSKRLNENANNLIKQFENTKEKIAeYTKSIDIKKATESLEEQLAAAEAEQELEESKRETETGIQNLTA 343

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  974 NLEKENELLNAIIA--KKEEEEVGYLNKIQELEERIRKLEQQMKYRDEEIQVILKQQREEKVNALEEVSVNALRPRNNHL 1051
Cdd:COG5185    344 EIEQGQESLTENLEaiKEEIENIVGEVELSKSSEELDSFKDTIESTKESLDEIPQNQRGYAQEILATLEDTLKAADRQIE 423

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2199033117 1052 NIRCEVEIKEKKVVLNAILDTGATVCVADSR---MIPAEMREQAKNRIIIRGV 1101
Cdd:COG5185    424 ELQRQIEQATSSNEEVSKLLNELISELNKVMreaDEESQSRLEEAYDEINRSV 476
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 1057-1148 9.27e-04

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: 40.01  E-value: 9.27e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1057 VEIKEKKVVLNAILDTGATVCVADSRMIPA--EMREQAKNRIIIRGVNG-VTEVNEVTAIGRLWVGKQWFTLpqTF-IMP 1132
Cdd:cd00303      1 LKGKINGVPVRALVDSGASVNFISESLAKKlgLPPRLLPTPLKVKGANGsSVKTLGVILPVTIGIGGKTFTV--DFyVLD 78

                           90
                   ....*....|....*.
gi 2199033117 1133 TLgdGVHMIIGMNFIR 1148
Cdd:cd00303     79 LL--SYDVILGRPWLE 92
DR0291 COG1579
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ...
 972-1038 9.88e-04

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];


Pssm-ID: 441187 [Multi-domain]  Cd Length: 236  Bit Score: 42.60  E-value: 9.88e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2199033117  972 IENLEKENELLNAIIAKKEEEEVGYLNKIQELEERIRKLEQQMKYRDEEIQViLKQQREEKVNALEE 1038
Cdd:COG1579     91 YEALQKEIESLKRRISDLEDEILELMERIEELEEELAELEAELAELEAELEE-KKAELDEELAELEA 156
COG2433 COG2433
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
894-1038 1.11e-03

Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];


Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 43.69  E-value: 1.11e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  894 KDINTEEVKKtrvrieRVIDWKEIAlrqhEVLKTSIanEKQLSEENEGLKEKIEELKKKELITVEEISEEEgaamiEKIE 973
Cdd:COG2433    361 PDVDRDEVKA------RVIRGLSIE----EALEELI--EKELPEEEPEAEREKEHEERELTEEEEEIRRLE-----EQVE 423

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2199033117  974 NLEKENELLNaiiakkeeeevgylNKIQELEERIRKLEQQMKY-RDEEIQVILKqqrEEKVNALEE 1038
Cdd:COG2433    424 RLEAEVEELE--------------AELEEKDERIERLERELSEaRSEERREIRK---DREISRLDR 472
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
 1064-1148 1.42e-03

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


Pssm-ID: 133159  Cd Length: 86  Bit Score: 39.24  E-value: 1.42e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1064 VVLNAILDTGATVCVADSRMIPaeMREQAKNRIIIRGVNGVTEVNEVTAIGRLWVGKQwfTLPQTF-IMPTLGDGvhmII 1142
Cdd:cd06095      8 VPIVFLVDTGATHSVLKSDLGP--KQELSTTSVLIRGVSGQSQQPVTTYRTLVDLGGH--TVSHSFlVVPNCPDP---LL 80


                   ....*.
gi 2199033117 1143 GMNFIR 1148
Cdd:cd06095     81 GRDLLS 86
Caldesmon pfam02029
Caldesmon;
895-1038 2.58e-03

Caldesmon;


Pssm-ID: 460421 [Multi-domain]  Cd Length: 495  Bit Score: 42.55  E-value: 2.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  895 DINTEEVKKTRVRIERVIDWKEIALRQHEVLktsIANEKQLSEENEGLKEKIEELKKKELITVEEISEEEGAAMIE---K 971
Cdd:pfam02029  173 NFAKEEVKDEKIKKEKKVKYESKVFLDQKRG---HPEVKSQNGEEEVTKLKVTTKRRQGGLSQSQEREEEAEVFLEaeqK 249

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2199033117  972 IENL-----EKENELLNAIIAKKEEEEVgylnkiqELEERIRKLEQQMKYRDEEIQViLKQQREEKVNALEE 1038
Cdd:pfam02029  250 LEELrrrrqEKESEEFEKLRQKQQEAEL-------ELEELKKKREERRKLLEEEEQR-RKQEEAERKLREEE 313
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 1603-1684 2.98e-03

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


Pssm-ID: 260012 [Multi-domain]  Cd Length: 145  Bit Score: 39.86  E-value: 2.98e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117 1603 AEIQAVINSLDKFKIYylDKKELIIRTDSK-AIVSFYKKSSDHKPSRVR------------WLAFTDYITGTGLDVKFEH 1669
Cdd:cd09280     46 AELLAVIHALEQAPEE--GIRKLEIRTDSKyAINCITKWIPKWKKNGWKtskgkpvknqdlIKELDKLLRKRGIKVKFEH 123

                           90
                   ....*....|....*....
gi 2199033117 1670 IDG----KDNVLADTLSRL 1684
Cdd:cd09280    124 VKGhsgdPGNEEADRLARE 142
PRK12704 PRK12704
phosphodiesterase; Provisional
 891-1040 5.08e-03

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 41.69  E-value: 5.08e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  891 WFYKDINTEEVKKTRVRIERVIDWKEIALRQHEVLKTSIANEKQLSEENEGLKEKIEELkkkelitvEEISEEEgAAMIE 970
Cdd:PRK12704    23 FVRKKIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERR--------NELQKLE-KRLLQ 93

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2199033117  971 KIENLEKENELLNaiiaKKEEEevgylnkIQELEERIRKLEQQMKYRDEEIQVILKQQREEkvnaLEEVS 1040
Cdd:PRK12704    94 KEENLDRKLELLE----KREEE-------LEKKEKELEQKQQELEKKEEELEELIEEQLQE----LERIS 148
PhaF COG3937
Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport ...
 959-1015 5.26e-03

Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms];


Pssm-ID: 443138 [Multi-domain]  Cd Length: 103  Bit Score: 38.24  E-value: 5.26e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2199033117  959 EISEEEGAAMIEK-IENLEKENELLNAIIAKKEEEEVGYLN-----KIQELEERIRKLEQQMK 1015
Cdd:COG3937     35 ELTEEEAKKFVDElVEKGEEEKEELEEKIEEQVEEALEKLGlatkeEVDELEERIDRLEKQLR 97
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 1751-1784 7.07e-03

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 36.23  E-value: 7.07e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 2199033117 1751 CGCRKPAKLYTSR-TSRNPGREFYSC---ENKAC--FTWV 1784
Cdd:pfam06839    3 CPCGQRAVLLTVRkTGPNPGRQFYKCpvgREKQCgfFQWA 42
 
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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