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Conserved domains on  [gi|2065821253|gb|KAG7588752|]
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Xylanase inhibitor C-terminal [Arabidopsis suecica]

Protein Classification

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 ...
 1521-1697 2.15e-97

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: 311.45  E-value: 2.15e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1521 GFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNRVTVKNKYPLPRIDELLDQLRGAKWFSKIDLASGYHQIPIDPLDIR 1600
Cdd:cd01647      1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1601 KTAFRTRYGHYEFVVMPFGLTNAPAAFMKMMNGVFQEFLDEFVIIFIDDILVYSKDWESHQDHLRAVLERLRKHELFAKL 1680
Cdd:cd01647     81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                          170
                   ....*....|....*..
gi 2065821253 1681 SKCSFWQRSIGFLGHIV 1697
Cdd:cd01647    161 EKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1791-1909 1.09e-53

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


:

Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 184.23  E-value: 1.09e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1791 TVYTDASITGLGCVLMQKGS-----VIAYASRQLRKHEGNYPTHDLEMAAVVFALKIWRSYLYGAKVQIFTDHKSLKYIF 1865
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDdgkerPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 2065821253 1866 TQPELNLRQRRWMEFVADYDLDIAYHPGKANQVADAltdlLSRI 1909
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADA----LSRL 120
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 2604-2788 1.30e-49

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 cd05489:

Pssm-ID: 472175 [Multi-domain]  Cd Length: 362  Bit Score: 181.78  E-value: 1.30e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2604 ASVVFDLGGRELWVDCDKDYvSSTYQSPRCNYAECSRAGSTSC-GTCFSPPKPGCR------------------------ 2658
Cdd:cd05489     10 VPLVLDLAGPLLWSTCDAGH-SSTYQTVPCSSSVCSLANRYHCpGTCGGAPGPGCGnntctahpynpvtgecatgdltqd 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2659 --------------------------------LASGTVGMAGMGGHNIGLPPQFAAAFSFSQKFAVYLTSGKG------- 2699
Cdd:cd05489     89 vlsanttdgsnpllvvifnfvfscapslllkgLPPGAQGVAGLGRSPLSLPAQLASAFGVARKFALCLPSSPGgpgvaif 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2700 -----------------LQTTPLLINP--------------------------------------VSTAS---------- 2714
Cdd:cd05489    169 gggpyylfpppidlsksLSYTPLLTNPrksgeyyigvtsiavnghavplnptlsandrlgpggvkLSTVVpytvlrsdiy 248

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2065821253 2715 -----AFSQAARNITRVASEKPFGDACFSTKNVGVKRLGYAVPEIQLLLHSNDVVWRIFRANSMVSVSDDVICLGFIDG 2788
Cdd:cd05489    249 raftqAFAKATARIPRVPAAAVFPELCYPASALGNTRLGYAVPAIDLVLDGGGVNWTIFGANSMVQVKGGVACLAFVDG 327
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 1019-1114 6.38e-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: 126.68  E-value: 6.38e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1019 DIAIHFLEGDAHNWWLTVEKRKGDQIQSFADFEEEFNKKFFPPEAWDRLECAYLDLVQGNRTVCEYDEEFNRLRRYVGRE 1098
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                           90
                   ....*....|....*.
gi 2065821253 1099 LEDEQAQVRRFIRGLR 1114
Cdd:pfam03732   81 GRDEEALISAFLRGLR 96
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 271-635 2.04e-33

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 cd05489:

Pssm-ID: 472175 [Multi-domain]  Cd Length: 362  Bit Score: 134.40  E-value: 2.04e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  271 TTVINQHIPLVpasvvFDLGGRELWVDCDKDYvSSTYQSPRCNYAECSRITNFifDCGATFllkrlasrtVGMAGMGRHN 350
Cdd:cd05489      3 ITPLKGAVPLV-----LDLAGPLLWSTCDAGH-SSTYQTVPCSSSVCSLANRY--HCPGTC---------GGAPGPGCGN 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  351 iglppqfaaafsfsqkfAVClipakrnqnqlresiygvgvidlqifyvGVRQTNSgeehhessvgvrnVNQKTNlpsstq 430
Cdd:cd05489     66 -----------------NTC----------------------------TAHPYNP-------------VTGECA------ 81

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  431 psstnehlssplpssstsvvenSGWTTTKTTSLPLTNLlvattpgahasapppaahvsllPDLAVVTtlaatlqITNFIF 510
Cdd:cd05489     82 ----------------------TGDLTQDVLSANTTDG----------------------SNPLLVV-------IFNFVF 110

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  511 DCGATFLLKGLASGTVGMAGMGRHNIGLPPQFATAFSFSRKLAVCLT----------FG--------------KGLQTMP 566
Cdd:cd05489    111 SCAPSLLLKGLPPGAQGVAGLGRSPLSLPAQLASAFGVARKFALCLPsspggpgvaiFGggpyylfpppidlsKSLSYTP 190

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  567 LLINP--------------------------------------VSTAS---------------VFSQAARIITRVASEKP 593
Cdd:cd05489    191 LLTNPrksgeyyigvtsiavnghavplnptlsandrlgpggvkLSTVVpytvlrsdiyraftqAFAKATARIPRVPAAAV 270

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|..
gi 2065821253  594 FGDACFSTKNVGVTRLGYAVPEIQLLLHSNDVVWRIFRANSM 635
Cdd:cd05489    271 FPELCYPASALGNTRLGYAVPAIDLVLDGGGVNWTIFGANSM 312
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 49-224 6.46e-33

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 cd05489:

Pssm-ID: 472175 [Multi-domain]  Cd Length: 362  Bit Score: 132.86  E-value: 6.46e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253   49 NQRTPLVPA-SVVFDLGGRELWVDCDKDYvSSTYQSPRCNYAECSRAGSTSC-STCFSPPRPG----------------- 109
Cdd:cd05489      1 YTITPLKGAvPLVLDLAGPLLWSTCDAGH-SSTYQTVPCSSSVCSLANRYHCpGTCGGAPGPGcgnntctahpynpvtge 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  110 ---------------------------------------YRLASGTVGMAGMGRHNIGLPPQLKSSM------------- 137
Cdd:cd05489     80 catgdltqdvlsanttdgsnpllvvifnfvfscapslllKGLPPGAQGVAGLGRSPLSLPAQLASAFgvarkfalclpss 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  138 -------------------AIKIIEKKQFQRLKIN--------------------------------------------- 153
Cdd:cd05489    160 pggpgvaifgggpyylfppPIDLSKSLSYTPLLTNprksgeyyigvtsiavnghavplnptlsandrlgpggvklstvvp 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  154 ------------------ATARnITRVASKKPFGDACFSTKNVGVTRLGYAAPEIQLLLCSNDVVWRIFRANSMVSVSDD 215
Cdd:cd05489    240 ytvlrsdiyraftqafakATAR-IPRVPAAAVFPELCYPASALGNTRLGYAVPAIDLVLDGGGVNWTIFGANSMVQVKGG 318


                   ....*....
gi 2065821253  216 VICLGFVDG 224
Cdd:cd05489    319 VACLAFVDG 327
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 1280-1410 1.74e-22

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: 95.58  E-value: 1.74e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1280 RVYELS-EEANNAGNFraITGTLSIGDVETHTLFDSGATHCFVSSEMVKKGGFIKERNTEYGMVRAAGGQAMYPSGIVRD 1358
Cdd:pfam08284    4 RVNHLSaEEAEASPDV--IQGTFLVNSIPATVLFDSGATHSFISHAFVGKLKLPVESLSNPLCIETPTGGSVTTNLICPS 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2065821253 1359 ISVVVIGVNMPTDLIVVQLKKHDVILGMDWLGKYKAHIDCHRGRIQFEREEG 1410
Cdd:pfam08284   82 CPIEIQGISFLADLILLDMKDLDVILGMDWLSKNKANIDCARRTVTLTKERE 133
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 720-790 7.75e-18

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 cd05489:

Pssm-ID: 472175 [Multi-domain]  Cd Length: 362  Bit Score: 88.18  E-value: 7.75e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  720 ITNFIFDCGATFLLKGLASGTVGMAGMGRHNIGLPPQFAAAFSFSQKFAVCLTSGKG----------------------- 776
Cdd:cd05489    105 IFNFVFSCAPSLLLKGLPPGAQGVAGLGRSPLSLPAQLASAFGVARKFALCLPSSPGgpgvaifgggpyylfpppidlsk 184

                           90
                   ....*....|....*
gi 2065821253  777 -LQTMPLLINPDRRG 790
Cdd:cd05489    185 sLSYTPLLTNPRKSG 199
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1948-2006 6.68e-17

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


:

Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 76.90  E-value: 6.68e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2065821253 1948 NDKELKEEILKEAHQSkfSIHPGSSKMYRDLKRYYHWVGMKKDVAAWVAKCSTCQLVKA 2006
Cdd:pfam17921    1 VPKSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
TAXi_N super family cl48255
Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly ...
 2420-2473 2.47e-11

Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylanase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


The actual alignment was detected with superfamily member pfam14543:

Pssm-ID: 464203 [Multi-domain]  Cd Length: 172  Bit Score: 64.60  E-value: 2.47e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2065821253 2420 QITNFIFDCGaTFLLKGLASGTVGMAGMGRHNIGLPPQFATAFSFSRKLAVCLT 2473
Cdd:pfam14543  107 SVPNFVFGCG-YNLLGGLPAGADGILGLGRGKLSLPSQLASQGIFGNKFSYCLS 159
transpos_IS481 super family cl41329
IS481 family transposase; null
 2026-2137 5.84e-09

IS481 family transposase; null


The actual alignment was detected with superfamily member NF033577:

Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 59.91  E-value: 5.84e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2026 DYVTMDfVTGLPTGIKSKHNAVWVVVDRLTKSAHFMA-ISETDgaeEIAAKYIDEIVQLHGVPV-SIVSDRDTRFTSHFw 2103
Cdd:NF033577   129 ELWHID-IKKLGRIPDVGRLYLHTAIDDHSRFAYAELyPDETA---ETAADFLRRAFAEHGIPIrRVLTDNGSEFRSRA- 203

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 2065821253 2104 KAFQKAL---GTRVNLSTAYHPQTDGQSERTIQTLED 2137
Cdd:NF033577   204 HGFELALaelGIEHRRTRPYHPQTNGKVERFHRTLKD 240
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 1185-1249 1.37e-07

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: 53.27  E-value: 1.37e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2065821253 1185 ECATCGKNH---SGTCWRavgacvcCGSKDHCIQNCPRMdQGTPKERvneqkTCFYCGKAGHFKRECP 1249
Cdd:PTZ00368    15 ECPNSAPAGaakARPCYK-------CGEPGHLSRECPSA-PGGRGER-----SCYNCGKTGHLSRECP 69
TAXi_C super family cl38456
Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly ...
 2497-2538 5.44e-07

Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylasnase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


The actual alignment was detected with superfamily member pfam14541:

Pssm-ID: 434029  Cd Length: 160  Bit Score: 51.89  E-value: 5.44e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 2065821253 2497 GTKISSVNPNTVLESSIYKAFTSEFIKQTAARNITRVASEKT 2538
Cdd:pfam14541   32 GTILDTGTPYTVLRPSVYRAVVQAFDKALAALGPRVVAPVAP 73
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1521-1697 2.15e-97

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: 311.45  E-value: 2.15e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1521 GFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNRVTVKNKYPLPRIDELLDQLRGAKWFSKIDLASGYHQIPIDPLDIR 1600
Cdd:cd01647      1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1601 KTAFRTRYGHYEFVVMPFGLTNAPAAFMKMMNGVFQEFLDEFVIIFIDDILVYSKDWESHQDHLRAVLERLRKHELFAKL 1680
Cdd:cd01647     81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                          170
                   ....*....|....*..
gi 2065821253 1681 SKCSFWQRSIGFLGHIV 1697
Cdd:cd01647    161 EKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1791-1909 1.09e-53

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


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 184.23  E-value: 1.09e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1791 TVYTDASITGLGCVLMQKGS-----VIAYASRQLRKHEGNYPTHDLEMAAVVFALKIWRSYLYGAKVQIFTDHKSLKYIF 1865
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDdgkerPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 2065821253 1866 TQPELNLRQRRWMEFVADYDLDIAYHPGKANQVADAltdlLSRI 1909
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADA----LSRL 120
xylanase_inhibitor_I_like cd05489
TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a ...
 2604-2788 1.30e-49

TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a member of potent TAXI-type inhibitors of fungal and bacterial family 11 xylanases. Plants developed a diverse battery of defense mechanisms in response to continual challenges by a broad spectrum of pathogenic microorganisms. Their defense arsenal includes inhibitors of cell wall-degrading enzymes, which hinder a possible invasion and colonization by antagonists. Xylanases of fungal and bacterial pathogens are the key enzymes in the degradation of xylan in the cell wall. Plants secrete proteins that inhibit these degradation glycosidases, including xylanase. Surprisingly, TAXI-I displays structural homology with the pepsin-like family of aspartic proteases but is proteolytically nonfunctional, because one or more residues of the essential catalytic triad are absent. The structure of the TAXI-inhibitor, Aspergillus niger xylanase I complex, illustrates the ability of tight binding and inhibition with subnanomolar affinity and indicates the importance of the C-terminal end for the differences in xylanase specificity among different TAXI-type inhibitors. This family also contains pepsin-like aspartic proteinases homologous to TAXI-I. Unlike TAXI-I, they have active site aspartates and are functionally active. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA).


Pssm-ID: 133156 [Multi-domain]  Cd Length: 362  Bit Score: 181.78  E-value: 1.30e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2604 ASVVFDLGGRELWVDCDKDYvSSTYQSPRCNYAECSRAGSTSC-GTCFSPPKPGCR------------------------ 2658
Cdd:cd05489     10 VPLVLDLAGPLLWSTCDAGH-SSTYQTVPCSSSVCSLANRYHCpGTCGGAPGPGCGnntctahpynpvtgecatgdltqd 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2659 --------------------------------LASGTVGMAGMGGHNIGLPPQFAAAFSFSQKFAVYLTSGKG------- 2699
Cdd:cd05489     89 vlsanttdgsnpllvvifnfvfscapslllkgLPPGAQGVAGLGRSPLSLPAQLASAFGVARKFALCLPSSPGgpgvaif 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2700 -----------------LQTTPLLINP--------------------------------------VSTAS---------- 2714
Cdd:cd05489    169 gggpyylfpppidlsksLSYTPLLTNPrksgeyyigvtsiavnghavplnptlsandrlgpggvkLSTVVpytvlrsdiy 248

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2065821253 2715 -----AFSQAARNITRVASEKPFGDACFSTKNVGVKRLGYAVPEIQLLLHSNDVVWRIFRANSMVSVSDDVICLGFIDG 2788
Cdd:cd05489    249 raftqAFAKATARIPRVPAAAVFPELCYPASALGNTRLGYAVPAIDLVLDGGGVNWTIFGANSMVQVKGGVACLAFVDG 327
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1537-1697 2.81e-44

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


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 159.78  E-value: 2.81e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1537 VKKKD-GSFRLC----IDYRGLNRVTVK-------NKYPLPRIDELLDQLRGAKWFSKIDLASGYHQIPIDPLDIRKTAF 1604
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1605 RTR-----------YGHYEFVVMPFGLTNAPAAFMKMMNGVFQEFL---DEFVIIFIDDILVYSKDWESHQDHLRAVLER 1670
Cdd:pfam00078   81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRkraGLTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 2065821253 1671 LRKHELFAKLSKCSF--WQRSIGFLGHIV 1697
Cdd:pfam00078  161 LKESGLKINPEKTQFflKSKEVKYLGVTL 189
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1787-1883 6.00e-40

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: 144.19  E-value: 6.00e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1787 GEPYTVYTDASITGLGCVLMQKGS-----VIAYASRQLRKHEGNYPTHDLEMAAVVFALKIWRSYLYGAKVQIFTDHKSL 1861
Cdd:pfam17917    3 SKPFILETDASDYGIGAVLSQKDEdgkerPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHKPL 82

                           90       100
                   ....*....|....*....|..
gi 2065821253 1862 KYIFTQPELNLRQRRWMEFVAD 1883
Cdd:pfam17917   83 KYLFTPKELNGRLARWALFLQE 104
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 1019-1114 6.38e-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: 126.68  E-value: 6.38e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1019 DIAIHFLEGDAHNWWLTVEKRKGDQIQSFADFEEEFNKKFFPPEAWDRLECAYLDLVQGNRTVCEYDEEFNRLRRYVGRE 1098
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                           90
                   ....*....|....*.
gi 2065821253 1099 LEDEQAQVRRFIRGLR 1114
Cdd:pfam03732   81 GRDEEALISAFLRGLR 96
xylanase_inhibitor_I_like cd05489
TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a ...
 271-635 2.04e-33

TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a member of potent TAXI-type inhibitors of fungal and bacterial family 11 xylanases. Plants developed a diverse battery of defense mechanisms in response to continual challenges by a broad spectrum of pathogenic microorganisms. Their defense arsenal includes inhibitors of cell wall-degrading enzymes, which hinder a possible invasion and colonization by antagonists. Xylanases of fungal and bacterial pathogens are the key enzymes in the degradation of xylan in the cell wall. Plants secrete proteins that inhibit these degradation glycosidases, including xylanase. Surprisingly, TAXI-I displays structural homology with the pepsin-like family of aspartic proteases but is proteolytically nonfunctional, because one or more residues of the essential catalytic triad are absent. The structure of the TAXI-inhibitor, Aspergillus niger xylanase I complex, illustrates the ability of tight binding and inhibition with subnanomolar affinity and indicates the importance of the C-terminal end for the differences in xylanase specificity among different TAXI-type inhibitors. This family also contains pepsin-like aspartic proteinases homologous to TAXI-I. Unlike TAXI-I, they have active site aspartates and are functionally active. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA).


Pssm-ID: 133156 [Multi-domain]  Cd Length: 362  Bit Score: 134.40  E-value: 2.04e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  271 TTVINQHIPLVpasvvFDLGGRELWVDCDKDYvSSTYQSPRCNYAECSRITNFifDCGATFllkrlasrtVGMAGMGRHN 350
Cdd:cd05489      3 ITPLKGAVPLV-----LDLAGPLLWSTCDAGH-SSTYQTVPCSSSVCSLANRY--HCPGTC---------GGAPGPGCGN 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  351 iglppqfaaafsfsqkfAVClipakrnqnqlresiygvgvidlqifyvGVRQTNSgeehhessvgvrnVNQKTNlpsstq 430
Cdd:cd05489     66 -----------------NTC----------------------------TAHPYNP-------------VTGECA------ 81

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  431 psstnehlssplpssstsvvenSGWTTTKTTSLPLTNLlvattpgahasapppaahvsllPDLAVVTtlaatlqITNFIF 510
Cdd:cd05489     82 ----------------------TGDLTQDVLSANTTDG----------------------SNPLLVV-------IFNFVF 110

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  511 DCGATFLLKGLASGTVGMAGMGRHNIGLPPQFATAFSFSRKLAVCLT----------FG--------------KGLQTMP 566
Cdd:cd05489    111 SCAPSLLLKGLPPGAQGVAGLGRSPLSLPAQLASAFGVARKFALCLPsspggpgvaiFGggpyylfpppidlsKSLSYTP 190

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  567 LLINP--------------------------------------VSTAS---------------VFSQAARIITRVASEKP 593
Cdd:cd05489    191 LLTNPrksgeyyigvtsiavnghavplnptlsandrlgpggvkLSTVVpytvlrsdiyraftqAFAKATARIPRVPAAAV 270

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|..
gi 2065821253  594 FGDACFSTKNVGVTRLGYAVPEIQLLLHSNDVVWRIFRANSM 635
Cdd:cd05489    271 FPELCYPASALGNTRLGYAVPAIDLVLDGGGVNWTIFGANSM 312
xylanase_inhibitor_I_like cd05489
TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a ...
 49-224 6.46e-33

TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a member of potent TAXI-type inhibitors of fungal and bacterial family 11 xylanases. Plants developed a diverse battery of defense mechanisms in response to continual challenges by a broad spectrum of pathogenic microorganisms. Their defense arsenal includes inhibitors of cell wall-degrading enzymes, which hinder a possible invasion and colonization by antagonists. Xylanases of fungal and bacterial pathogens are the key enzymes in the degradation of xylan in the cell wall. Plants secrete proteins that inhibit these degradation glycosidases, including xylanase. Surprisingly, TAXI-I displays structural homology with the pepsin-like family of aspartic proteases but is proteolytically nonfunctional, because one or more residues of the essential catalytic triad are absent. The structure of the TAXI-inhibitor, Aspergillus niger xylanase I complex, illustrates the ability of tight binding and inhibition with subnanomolar affinity and indicates the importance of the C-terminal end for the differences in xylanase specificity among different TAXI-type inhibitors. This family also contains pepsin-like aspartic proteinases homologous to TAXI-I. Unlike TAXI-I, they have active site aspartates and are functionally active. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA).


Pssm-ID: 133156 [Multi-domain]  Cd Length: 362  Bit Score: 132.86  E-value: 6.46e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253   49 NQRTPLVPA-SVVFDLGGRELWVDCDKDYvSSTYQSPRCNYAECSRAGSTSC-STCFSPPRPG----------------- 109
Cdd:cd05489      1 YTITPLKGAvPLVLDLAGPLLWSTCDAGH-SSTYQTVPCSSSVCSLANRYHCpGTCGGAPGPGcgnntctahpynpvtge 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  110 ---------------------------------------YRLASGTVGMAGMGRHNIGLPPQLKSSM------------- 137
Cdd:cd05489     80 catgdltqdvlsanttdgsnpllvvifnfvfscapslllKGLPPGAQGVAGLGRSPLSLPAQLASAFgvarkfalclpss 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  138 -------------------AIKIIEKKQFQRLKIN--------------------------------------------- 153
Cdd:cd05489    160 pggpgvaifgggpyylfppPIDLSKSLSYTPLLTNprksgeyyigvtsiavnghavplnptlsandrlgpggvklstvvp 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  154 ------------------ATARnITRVASKKPFGDACFSTKNVGVTRLGYAAPEIQLLLCSNDVVWRIFRANSMVSVSDD 215
Cdd:cd05489    240 ytvlrsdiyraftqafakATAR-IPRVPAAAVFPELCYPASALGNTRLGYAVPAIDLVLDGGGVNWTIFGANSMVQVKGG 318


                   ....*....
gi 2065821253  216 VICLGFVDG 224
Cdd:cd05489    319 VACLAFVDG 327
RVP_2 pfam08284
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 1280-1410 1.74e-22

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: 95.58  E-value: 1.74e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1280 RVYELS-EEANNAGNFraITGTLSIGDVETHTLFDSGATHCFVSSEMVKKGGFIKERNTEYGMVRAAGGQAMYPSGIVRD 1358
Cdd:pfam08284    4 RVNHLSaEEAEASPDV--IQGTFLVNSIPATVLFDSGATHSFISHAFVGKLKLPVESLSNPLCIETPTGGSVTTNLICPS 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2065821253 1359 ISVVVIGVNMPTDLIVVQLKKHDVILGMDWLGKYKAHIDCHRGRIQFEREEG 1410
Cdd:pfam08284   82 CPIEIQGISFLADLILLDMKDLDVILGMDWLSKNKANIDCARRTVTLTKERE 133
TAXi_N pfam14543
Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly ...
 270-371 1.73e-20

Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylanase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 464203 [Multi-domain]  Cd Length: 172  Bit Score: 91.18  E-value: 1.73e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  270 YTTVINQHIPLVPASVVFDLGGRELWVDCD-----------KDYVSSTYQSPRCNYAECS-------------------- 318
Cdd:pfam14543    1 YLVTISIGTPPVPFFLVVDTGSDLTWVQCDpccysqpdplfDPYKSSTYKPVPCSSPLCSlialsspgpccsnntcdyev 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2065821253  319 --------------------------RITNFIFDCGaTFLLKRLASRTVGMAGMGRHNIGLPPQFAAAFSFSQKFAVCL 371
Cdd:pfam14543   81 sygdgsstsgvlatdtltlnstggsvSVPNFVFGCG-YNLLGGLPAGADGILGLGRGKLSLPSQLASQGIFGNKFSYCL 158
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 1300-1389 5.78e-18

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: 80.84  E-value: 5.78e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1300 TLSIGDVETHTLFDSGATHCFVSSEMVKKGGFIKERNTEYGMVRAAGGQAMYPSGIVRDISVVVIGVNMPTDLIVVQLKK 1379
Cdd:cd00303      2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLS 81

                           90
                   ....*....|
gi 2065821253 1380 HDVILGMDWL 1389
Cdd:cd00303     82 YDVILGRPWL 91
xylanase_inhibitor_I_like cd05489
TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a ...
 720-790 7.75e-18

TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a member of potent TAXI-type inhibitors of fungal and bacterial family 11 xylanases. Plants developed a diverse battery of defense mechanisms in response to continual challenges by a broad spectrum of pathogenic microorganisms. Their defense arsenal includes inhibitors of cell wall-degrading enzymes, which hinder a possible invasion and colonization by antagonists. Xylanases of fungal and bacterial pathogens are the key enzymes in the degradation of xylan in the cell wall. Plants secrete proteins that inhibit these degradation glycosidases, including xylanase. Surprisingly, TAXI-I displays structural homology with the pepsin-like family of aspartic proteases but is proteolytically nonfunctional, because one or more residues of the essential catalytic triad are absent. The structure of the TAXI-inhibitor, Aspergillus niger xylanase I complex, illustrates the ability of tight binding and inhibition with subnanomolar affinity and indicates the importance of the C-terminal end for the differences in xylanase specificity among different TAXI-type inhibitors. This family also contains pepsin-like aspartic proteinases homologous to TAXI-I. Unlike TAXI-I, they have active site aspartates and are functionally active. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA).


Pssm-ID: 133156 [Multi-domain]  Cd Length: 362  Bit Score: 88.18  E-value: 7.75e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  720 ITNFIFDCGATFLLKGLASGTVGMAGMGRHNIGLPPQFAAAFSFSQKFAVCLTSGKG----------------------- 776
Cdd:cd05489    105 IFNFVFSCAPSLLLKGLPPGAQGVAGLGRSPLSLPAQLASAFGVARKFALCLPSSPGgpgvaifgggpyylfpppidlsk 184

                           90
                   ....*....|....*
gi 2065821253  777 -LQTMPLLINPDRRG 790
Cdd:cd05489    185 sLSYTPLLTNPRKSG 199
TAXi_C pfam14541
Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly ...
 2670-2788 2.80e-17

Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylasnase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 434029  Cd Length: 160  Bit Score: 81.55  E-value: 2.80e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2670 GGHNIGLPPqfaAAFSFSQKFA--VYLTSGkglqtTPL--LINPVSTA--SAFS-QAARNITR-VASEKPFgDACFSTKN 2741
Cdd:pfam14541   12 NGKRLPLPP---GLLDIDRTGSggTILDTG-----TPYtvLRPSVYRAvvQAFDkALAALGPRvVAPVAPF-DLCYNSTG 82

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2065821253 2742 VGVKRLGYAVPEIQLLLHSNdVVWRIFRANSMVSVSDDVICLGFIDG 2788
Cdd:pfam14541   83 LGSTRLGPAVPPITLVFEGG-ADWTIFGANSMVQVDGGVACLGFVDG 128
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1948-2006 6.68e-17

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


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 76.90  E-value: 6.68e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2065821253 1948 NDKELKEEILKEAHQSkfSIHPGSSKMYRDLKRYYHWVGMKKDVAAWVAKCSTCQLVKA 2006
Cdd:pfam17921    1 VPKSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
TAXi_C pfam14541
Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly ...
 153-224 2.46e-15

Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylasnase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 434029  Cd Length: 160  Bit Score: 75.78  E-value: 2.46e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2065821253  153 NATARNITR-VASKKPFgDACFSTKNVGVTRLGYAAPEIQLLLcSNDVVWRIFRANSMVSVSDDVICLGFVDG 224
Cdd:pfam14541   58 KALAALGPRvVAPVAPF-DLCYNSTGLGSTRLGPAVPPITLVF-EGGADWTIFGANSMVQVDGGVACLGFVDG 128
TAXi_N pfam14543
Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly ...
 719-773 6.92e-13

Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylanase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 464203 [Multi-domain]  Cd Length: 172  Bit Score: 69.23  E-value: 6.92e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2065821253  719 QITNFIFDCGaTFLLKGLASGTVGMAGMGRHNIGLPPQFAAAFSFSQKFAVCLTS 773
Cdd:pfam14543  107 SVPNFVFGCG-YNLLGGLPAGADGILGLGRGKLSLPSQLASQGIFGNKFSYCLSS 160
TAXi_N pfam14543
Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly ...
 2420-2473 2.47e-11

Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylanase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 464203 [Multi-domain]  Cd Length: 172  Bit Score: 64.60  E-value: 2.47e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2065821253 2420 QITNFIFDCGaTFLLKGLASGTVGMAGMGRHNIGLPPQFATAFSFSRKLAVCLT 2473
Cdd:pfam14543  107 SVPNFVFGCG-YNLLGGLPAGADGILGLGRGKLSLPSQLASQGIFGNKFSYCLS 159
transpos_IS481 NF033577
IS481 family transposase; null
 2026-2137 5.84e-09

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 59.91  E-value: 5.84e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2026 DYVTMDfVTGLPTGIKSKHNAVWVVVDRLTKSAHFMA-ISETDgaeEIAAKYIDEIVQLHGVPV-SIVSDRDTRFTSHFw 2103
Cdd:NF033577   129 ELWHID-IKKLGRIPDVGRLYLHTAIDDHSRFAYAELyPDETA---ETAADFLRRAFAEHGIPIrRVLTDNGSEFRSRA- 203

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 2065821253 2104 KAFQKAL---GTRVNLSTAYHPQTDGQSERTIQTLED 2137
Cdd:NF033577   204 HGFELALaelGIEHRRTRPYHPQTNGKVERFHRTLKD 240
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
1272-1407 5.92e-09

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 57.27  E-value: 5.92e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1272 PKRQAIAPRVYELSEEANNAGNFRAitgTLSIGDVETHTLFDSGATHCFVSSEMVKKGGFIKERNTEYGMVRAAGGQAMY 1351
Cdd:COG3577     20 PGQAPVSTGGGEVVLKRDRDGHFVV---EGTINGQPVRFLVDTGASTVVLSESDARRLGLDPEDLGRPVRVQTANGVVRA 96

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2065821253 1352 PSG----------IVRDISVVVIGVNMPTdlivvqlkkhDVILGMDWLGKYKAHIDchRGRIQFER 1407
Cdd:COG3577     97 ARVrldsvriggiTLRNVRAVVLPGGELD----------DGLLGMSFLGRLDFEID--GDRLTLRP 150
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 1185-1249 1.37e-07

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 53.27  E-value: 1.37e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2065821253 1185 ECATCGKNH---SGTCWRavgacvcCGSKDHCIQNCPRMdQGTPKERvneqkTCFYCGKAGHFKRECP 1249
Cdd:PTZ00368    15 ECPNSAPAGaakARPCYK-------CGEPGHLSRECPSA-PGGRGER-----SCYNCGKTGHLSRECP 69
TAXi_C pfam14541
Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly ...
 2497-2538 5.44e-07

Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylasnase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 434029  Cd Length: 160  Bit Score: 51.89  E-value: 5.44e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 2065821253 2497 GTKISSVNPNTVLESSIYKAFTSEFIKQTAARNITRVASEKT 2538
Cdd:pfam14541   32 GTILDTGTPYTVLRPSVYRAVVQAFDKALAALGPRVVAPVAP 73
ZnF_C2HC smart00343
zinc finger;
1234-1250 1.84e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.50  E-value: 1.84e-04
                            10
                    ....*....|....*..
gi 2065821253  1234 TCFYCGKAGHFKRECPK 1250
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 2021-2122 2.26e-04

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


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 42.69  E-value: 2.26e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2021 PEWKWdyvTMDFVTGlptGIKSKHNAVW--VVVDRLTKSAHFMAISETDGAEEIAAKYIDEIVQLHGVPVSIVSDRDTRF 2098
Cdd:pfam00665    1 PNQLW---QGDFTYI---RIPGGGGKLYllVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEY 74

                           90       100
                   ....*....|....*....|....
gi 2065821253 2099 TSHFWKAFQKALGTRVNLSTAYHP 2122
Cdd:pfam00665   75 TSKAFREFLKDLGIKPSFSRPGNP 98
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 1233-1250 3.23e-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: 39.82  E-value: 3.23e-04
                           10
                   ....*....|....*...
gi 2065821253 1233 KTCFYCGKAGHFKRECPK 1250
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 1203-1249 3.65e-04

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


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 44.07  E-value: 3.65e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2065821253 1203 ACVCCGSKDHCIQNCP------RMDQGTPKERVNEQKTCFYCGKAGHFKRECP 1249
Cdd:COG5082     62 VCFNCGQNGHLRRDCPhsicynCSWDGHRSNHCPKPKKCYNCGETGHLSRDCN 114
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1949-2184 4.24e-04

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 45.14  E-value: 4.24e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1949 DKELKEEILKEAHQSKFSihpGSSKMYRDLKRYYHWVG-------MKKD--VAAWVAKCSTCQLVKAEHKVPSGLVQNLP 2019
Cdd:COG2801     70 DAELLERIKEIFAESPRY---GYRRITAELRREGIAVNrkrvrrlMRELglQARRRRKKKYTTYSGHGGPIAPNLLFTAT 146

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2020 MPEWKWdyvTMDFvtglpTGIKSKHNAVW--VVVDRLTKSAHFMAISETDGAEeIAAKYIDEIVQLHGV--PVSIVSDRD 2095
Cdd:COG2801    147 APNQVW---VTDI-----TYIPTAEGWLYlaAVIDLFSREIVGWSVSDSMDAE-LVVDALEMAIERRGPpkPLILHSDNG 217

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2096 TRFTSHFWKAFQKALGTRVNLSTAYHPQTDGQSERTIQTLE------------DMLRACVLDWggnwekylrlVEFaYNN 2163
Cdd:COG2801    218 SQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKyellyrrrfeslEEAREAIEEY----------IEF-YNH 286

                          250       260
                   ....*....|....*....|...
gi 2065821253 2164 S-YQASIG-MSPYEALYGRACRT 2184
Cdd:COG2801    287 ErPHSSLGyLTPAEYEKQLAAAA 309
 
Name Accession Description Interval E-value
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1521-1697 2.15e-97

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: 311.45  E-value: 2.15e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1521 GFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNRVTVKNKYPLPRIDELLDQLRGAKWFSKIDLASGYHQIPIDPLDIR 1600
Cdd:cd01647      1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1601 KTAFRTRYGHYEFVVMPFGLTNAPAAFMKMMNGVFQEFLDEFVIIFIDDILVYSKDWESHQDHLRAVLERLRKHELFAKL 1680
Cdd:cd01647     81 KTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNP 160

                          170
                   ....*....|....*..
gi 2065821253 1681 SKCSFWQRSIGFLGHIV 1697
Cdd:cd01647    161 EKCEFGVPEVEFLGHIV 177
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1791-1909 1.09e-53

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


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 184.23  E-value: 1.09e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1791 TVYTDASITGLGCVLMQKGS-----VIAYASRQLRKHEGNYPTHDLEMAAVVFALKIWRSYLYGAKVQIFTDHKSLKYIF 1865
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDdgkerPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 2065821253 1866 TQPELNLRQRRWMEFVADYDLDIAYHPGKANQVADAltdlLSRI 1909
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADA----LSRL 120
xylanase_inhibitor_I_like cd05489
TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a ...
 2604-2788 1.30e-49

TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a member of potent TAXI-type inhibitors of fungal and bacterial family 11 xylanases. Plants developed a diverse battery of defense mechanisms in response to continual challenges by a broad spectrum of pathogenic microorganisms. Their defense arsenal includes inhibitors of cell wall-degrading enzymes, which hinder a possible invasion and colonization by antagonists. Xylanases of fungal and bacterial pathogens are the key enzymes in the degradation of xylan in the cell wall. Plants secrete proteins that inhibit these degradation glycosidases, including xylanase. Surprisingly, TAXI-I displays structural homology with the pepsin-like family of aspartic proteases but is proteolytically nonfunctional, because one or more residues of the essential catalytic triad are absent. The structure of the TAXI-inhibitor, Aspergillus niger xylanase I complex, illustrates the ability of tight binding and inhibition with subnanomolar affinity and indicates the importance of the C-terminal end for the differences in xylanase specificity among different TAXI-type inhibitors. This family also contains pepsin-like aspartic proteinases homologous to TAXI-I. Unlike TAXI-I, they have active site aspartates and are functionally active. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA).


Pssm-ID: 133156 [Multi-domain]  Cd Length: 362  Bit Score: 181.78  E-value: 1.30e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2604 ASVVFDLGGRELWVDCDKDYvSSTYQSPRCNYAECSRAGSTSC-GTCFSPPKPGCR------------------------ 2658
Cdd:cd05489     10 VPLVLDLAGPLLWSTCDAGH-SSTYQTVPCSSSVCSLANRYHCpGTCGGAPGPGCGnntctahpynpvtgecatgdltqd 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2659 --------------------------------LASGTVGMAGMGGHNIGLPPQFAAAFSFSQKFAVYLTSGKG------- 2699
Cdd:cd05489     89 vlsanttdgsnpllvvifnfvfscapslllkgLPPGAQGVAGLGRSPLSLPAQLASAFGVARKFALCLPSSPGgpgvaif 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2700 -----------------LQTTPLLINP--------------------------------------VSTAS---------- 2714
Cdd:cd05489    169 gggpyylfpppidlsksLSYTPLLTNPrksgeyyigvtsiavnghavplnptlsandrlgpggvkLSTVVpytvlrsdiy 248

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2065821253 2715 -----AFSQAARNITRVASEKPFGDACFSTKNVGVKRLGYAVPEIQLLLHSNDVVWRIFRANSMVSVSDDVICLGFIDG 2788
Cdd:cd05489    249 raftqAFAKATARIPRVPAAAVFPELCYPASALGNTRLGYAVPAIDLVLDGGGVNWTIFGANSMVQVKGGVACLAFVDG 327
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1537-1697 2.81e-44

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


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 159.78  E-value: 2.81e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1537 VKKKD-GSFRLC----IDYRGLNRVTVK-------NKYPLPRIDELLDQLRGAKWFSKIDLASGYHQIPIDPLDIRKTAF 1604
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1605 RTR-----------YGHYEFVVMPFGLTNAPAAFMKMMNGVFQEFL---DEFVIIFIDDILVYSKDWESHQDHLRAVLER 1670
Cdd:pfam00078   81 TTPpininwngelsGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRkraGLTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 2065821253 1671 LRKHELFAKLSKCSF--WQRSIGFLGHIV 1697
Cdd:pfam00078  161 LKESGLKINPEKTQFflKSKEVKYLGVTL 189
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 1787-1883 6.00e-40

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: 144.19  E-value: 6.00e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1787 GEPYTVYTDASITGLGCVLMQKGS-----VIAYASRQLRKHEGNYPTHDLEMAAVVFALKIWRSYLYGAKVQIFTDHKSL 1861
Cdd:pfam17917    3 SKPFILETDASDYGIGAVLSQKDEdgkerPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHKPL 82

                           90       100
                   ....*....|....*....|..
gi 2065821253 1862 KYIFTQPELNLRQRRWMEFVAD 1883
Cdd:pfam17917   83 KYLFTPKELNGRLARWALFLQE 104
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
1760-1854 2.43e-35

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 130.70  E-value: 2.43e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1760 WSEECEKSFSELKAMLTSASVLVLLEEGEPYTVYTDASITGLGCVLMQKGS-----VIAYASRQLRKHEGNYPTHDLEMA 1834
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDdggerPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 2065821253 1835 AVVFALKIWRSYLYGAKVQI 1854
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 1019-1114 6.38e-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: 126.68  E-value: 6.38e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1019 DIAIHFLEGDAHNWWLTVEKRKGDQIQSFADFEEEFNKKFFPPEAWDRLECAYLDLVQGNRTVCEYDEEFNRLRRYVGRE 1098
Cdd:pfam03732    1 KLAVHSLRGAALTWWKSLVARSIDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHH 80

                           90
                   ....*....|....*.
gi 2065821253 1099 LEDEQAQVRRFIRGLR 1114
Cdd:pfam03732   81 GRDEEALISAFLRGLR 96
xylanase_inhibitor_I_like cd05489
TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a ...
 271-635 2.04e-33

TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a member of potent TAXI-type inhibitors of fungal and bacterial family 11 xylanases. Plants developed a diverse battery of defense mechanisms in response to continual challenges by a broad spectrum of pathogenic microorganisms. Their defense arsenal includes inhibitors of cell wall-degrading enzymes, which hinder a possible invasion and colonization by antagonists. Xylanases of fungal and bacterial pathogens are the key enzymes in the degradation of xylan in the cell wall. Plants secrete proteins that inhibit these degradation glycosidases, including xylanase. Surprisingly, TAXI-I displays structural homology with the pepsin-like family of aspartic proteases but is proteolytically nonfunctional, because one or more residues of the essential catalytic triad are absent. The structure of the TAXI-inhibitor, Aspergillus niger xylanase I complex, illustrates the ability of tight binding and inhibition with subnanomolar affinity and indicates the importance of the C-terminal end for the differences in xylanase specificity among different TAXI-type inhibitors. This family also contains pepsin-like aspartic proteinases homologous to TAXI-I. Unlike TAXI-I, they have active site aspartates and are functionally active. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA).


Pssm-ID: 133156 [Multi-domain]  Cd Length: 362  Bit Score: 134.40  E-value: 2.04e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  271 TTVINQHIPLVpasvvFDLGGRELWVDCDKDYvSSTYQSPRCNYAECSRITNFifDCGATFllkrlasrtVGMAGMGRHN 350
Cdd:cd05489      3 ITPLKGAVPLV-----LDLAGPLLWSTCDAGH-SSTYQTVPCSSSVCSLANRY--HCPGTC---------GGAPGPGCGN 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  351 iglppqfaaafsfsqkfAVClipakrnqnqlresiygvgvidlqifyvGVRQTNSgeehhessvgvrnVNQKTNlpsstq 430
Cdd:cd05489     66 -----------------NTC----------------------------TAHPYNP-------------VTGECA------ 81

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  431 psstnehlssplpssstsvvenSGWTTTKTTSLPLTNLlvattpgahasapppaahvsllPDLAVVTtlaatlqITNFIF 510
Cdd:cd05489     82 ----------------------TGDLTQDVLSANTTDG----------------------SNPLLVV-------IFNFVF 110

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  511 DCGATFLLKGLASGTVGMAGMGRHNIGLPPQFATAFSFSRKLAVCLT----------FG--------------KGLQTMP 566
Cdd:cd05489    111 SCAPSLLLKGLPPGAQGVAGLGRSPLSLPAQLASAFGVARKFALCLPsspggpgvaiFGggpyylfpppidlsKSLSYTP 190

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  567 LLINP--------------------------------------VSTAS---------------VFSQAARIITRVASEKP 593
Cdd:cd05489    191 LLTNPrksgeyyigvtsiavnghavplnptlsandrlgpggvkLSTVVpytvlrsdiyraftqAFAKATARIPRVPAAAV 270

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|..
gi 2065821253  594 FGDACFSTKNVGVTRLGYAVPEIQLLLHSNDVVWRIFRANSM 635
Cdd:cd05489    271 FPELCYPASALGNTRLGYAVPAIDLVLDGGGVNWTIFGANSM 312
xylanase_inhibitor_I_like cd05489
TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a ...
 49-224 6.46e-33

TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a member of potent TAXI-type inhibitors of fungal and bacterial family 11 xylanases. Plants developed a diverse battery of defense mechanisms in response to continual challenges by a broad spectrum of pathogenic microorganisms. Their defense arsenal includes inhibitors of cell wall-degrading enzymes, which hinder a possible invasion and colonization by antagonists. Xylanases of fungal and bacterial pathogens are the key enzymes in the degradation of xylan in the cell wall. Plants secrete proteins that inhibit these degradation glycosidases, including xylanase. Surprisingly, TAXI-I displays structural homology with the pepsin-like family of aspartic proteases but is proteolytically nonfunctional, because one or more residues of the essential catalytic triad are absent. The structure of the TAXI-inhibitor, Aspergillus niger xylanase I complex, illustrates the ability of tight binding and inhibition with subnanomolar affinity and indicates the importance of the C-terminal end for the differences in xylanase specificity among different TAXI-type inhibitors. This family also contains pepsin-like aspartic proteinases homologous to TAXI-I. Unlike TAXI-I, they have active site aspartates and are functionally active. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA).


Pssm-ID: 133156 [Multi-domain]  Cd Length: 362  Bit Score: 132.86  E-value: 6.46e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253   49 NQRTPLVPA-SVVFDLGGRELWVDCDKDYvSSTYQSPRCNYAECSRAGSTSC-STCFSPPRPG----------------- 109
Cdd:cd05489      1 YTITPLKGAvPLVLDLAGPLLWSTCDAGH-SSTYQTVPCSSSVCSLANRYHCpGTCGGAPGPGcgnntctahpynpvtge 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  110 ---------------------------------------YRLASGTVGMAGMGRHNIGLPPQLKSSM------------- 137
Cdd:cd05489     80 catgdltqdvlsanttdgsnpllvvifnfvfscapslllKGLPPGAQGVAGLGRSPLSLPAQLASAFgvarkfalclpss 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  138 -------------------AIKIIEKKQFQRLKIN--------------------------------------------- 153
Cdd:cd05489    160 pggpgvaifgggpyylfppPIDLSKSLSYTPLLTNprksgeyyigvtsiavnghavplnptlsandrlgpggvklstvvp 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  154 ------------------ATARnITRVASKKPFGDACFSTKNVGVTRLGYAAPEIQLLLCSNDVVWRIFRANSMVSVSDD 215
Cdd:cd05489    240 ytvlrsdiyraftqafakATAR-IPRVPAAAVFPELCYPASALGNTRLGYAVPAIDLVLDGGGVNWTIFGANSMVQVKGG 318


                   ....*....
gi 2065821253  216 VICLGFVDG 224
Cdd:cd05489    319 VACLAFVDG 327
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 1494-1694 6.92e-27

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: 110.90  E-value: 6.92e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1494 PISKAPYRMAPAEMAELKKQLEELLDKGFIRPSSSPWGAPVLFVKKKDG-SFRLCIDYRGLNRVTVKNKYPLPRIDELLD 1572
Cdd:cd03715      1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1573 QL-RGAKWFSKIDLASGYHQIPIDPLDIRKTAFRTRYGHYEFVVMPFGLTNAPAAFmkmmNGVFQEFLDEF--------V 1643
Cdd:cd03715     81 LLpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLF----HEALARDLAPFplehegtiL 156

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2065821253 1644 IIFIDDILVYSKDWESHQDHLRAVLERLRKHELFAKLSKCSFWQRSIGFLG 1694
Cdd:cd03715    157 LQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLG 207
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 1510-1697 9.75e-24

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: 101.59  E-value: 9.75e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1510 LKKQLEELLDKGFIRPSSSPWGAPVLFVKKKDGSFRLCIDYRGLNRVT-----VKNKYPLPridellDQLRGAKWFSKID 1584
Cdd:cd01645     17 LTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTqdmgaLQPGLPHP------AALPKGWPLIVLD 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1585 LASGYHQIPIDPLDIRKTAF-------RTRYGHYEFVVMPFGLTNAPAAFMKMMNGVFQEFLDEF----VIIFIDDILVY 1653
Cdd:cd01645     91 LKDCFFSIPLHPDDRERFAFtvpsinnKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYpdivIYHYMDDILIA 170

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 2065821253 1654 SKDWESHQDHLRAVLERLRKHELFAKLSKcsfWQRSIGF--LGHIV 1697
Cdd:cd01645    171 SDLEGQLREIYEELRQTLLRWGLTIPPEK---VQKEPPFqyLGYEL 213
RVP_2 pfam08284
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
 1280-1410 1.74e-22

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: 95.58  E-value: 1.74e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1280 RVYELS-EEANNAGNFraITGTLSIGDVETHTLFDSGATHCFVSSEMVKKGGFIKERNTEYGMVRAAGGQAMYPSGIVRD 1358
Cdd:pfam08284    4 RVNHLSaEEAEASPDV--IQGTFLVNSIPATVLFDSGATHSFISHAFVGKLKLPVESLSNPLCIETPTGGSVTTNLICPS 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2065821253 1359 ISVVVIGVNMPTDLIVVQLKKHDVILGMDWLGKYKAHIDCHRGRIQFEREEG 1410
Cdd:pfam08284   82 CPIEIQGISFLADLILLDMKDLDVILGMDWLSKNKANIDCARRTVTLTKERE 133
TAXi_N pfam14543
Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly ...
 270-371 1.73e-20

Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylanase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 464203 [Multi-domain]  Cd Length: 172  Bit Score: 91.18  E-value: 1.73e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  270 YTTVINQHIPLVPASVVFDLGGRELWVDCD-----------KDYVSSTYQSPRCNYAECS-------------------- 318
Cdd:pfam14543    1 YLVTISIGTPPVPFFLVVDTGSDLTWVQCDpccysqpdplfDPYKSSTYKPVPCSSPLCSlialsspgpccsnntcdyev 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2065821253  319 --------------------------RITNFIFDCGaTFLLKRLASRTVGMAGMGRHNIGLPPQFAAAFSFSQKFAVCL 371
Cdd:pfam14543   81 sygdgsstsgvlatdtltlnstggsvSVPNFVFGCG-YNLLGGLPAGADGILGLGRGKLSLPSQLASQGIFGNKFSYCL 158
retropepsin_like cd00303
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ...
 1300-1389 5.78e-18

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: 80.84  E-value: 5.78e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1300 TLSIGDVETHTLFDSGATHCFVSSEMVKKGGFIKERNTEYGMVRAAGGQAMYPSGIVRDISVVVIGVNMPTDLIVVQLKK 1379
Cdd:cd00303      2 KGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLS 81

                           90
                   ....*....|
gi 2065821253 1380 HDVILGMDWL 1389
Cdd:cd00303     82 YDVILGRPWL 91
xylanase_inhibitor_I_like cd05489
TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a ...
 720-790 7.75e-18

TAXI-I inhibits degradation of xylan in the cell wall; Xylanase inhibitor-I (TAXI-I) is a member of potent TAXI-type inhibitors of fungal and bacterial family 11 xylanases. Plants developed a diverse battery of defense mechanisms in response to continual challenges by a broad spectrum of pathogenic microorganisms. Their defense arsenal includes inhibitors of cell wall-degrading enzymes, which hinder a possible invasion and colonization by antagonists. Xylanases of fungal and bacterial pathogens are the key enzymes in the degradation of xylan in the cell wall. Plants secrete proteins that inhibit these degradation glycosidases, including xylanase. Surprisingly, TAXI-I displays structural homology with the pepsin-like family of aspartic proteases but is proteolytically nonfunctional, because one or more residues of the essential catalytic triad are absent. The structure of the TAXI-inhibitor, Aspergillus niger xylanase I complex, illustrates the ability of tight binding and inhibition with subnanomolar affinity and indicates the importance of the C-terminal end for the differences in xylanase specificity among different TAXI-type inhibitors. This family also contains pepsin-like aspartic proteinases homologous to TAXI-I. Unlike TAXI-I, they have active site aspartates and are functionally active. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA).


Pssm-ID: 133156 [Multi-domain]  Cd Length: 362  Bit Score: 88.18  E-value: 7.75e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  720 ITNFIFDCGATFLLKGLASGTVGMAGMGRHNIGLPPQFAAAFSFSQKFAVCLTSGKG----------------------- 776
Cdd:cd05489    105 IFNFVFSCAPSLLLKGLPPGAQGVAGLGRSPLSLPAQLASAFGVARKFALCLPSSPGgpgvaifgggpyylfpppidlsk 184

                           90
                   ....*....|....*
gi 2065821253  777 -LQTMPLLINPDRRG 790
Cdd:cd05489    185 sLSYTPLLTNPRKSG 199
TAXi_C pfam14541
Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly ...
 2670-2788 2.80e-17

Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylasnase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 434029  Cd Length: 160  Bit Score: 81.55  E-value: 2.80e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2670 GGHNIGLPPqfaAAFSFSQKFA--VYLTSGkglqtTPL--LINPVSTA--SAFS-QAARNITR-VASEKPFgDACFSTKN 2741
Cdd:pfam14541   12 NGKRLPLPP---GLLDIDRTGSggTILDTG-----TPYtvLRPSVYRAvvQAFDkALAALGPRvVAPVAPF-DLCYNSTG 82

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2065821253 2742 VGVKRLGYAVPEIQLLLHSNdVVWRIFRANSMVSVSDDVICLGFIDG 2788
Cdd:pfam14541   83 LGSTRLGPAVPPITLVFEGG-ADWTIFGANSMVQVDGGVACLGFVDG 128
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 1948-2006 6.68e-17

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


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 76.90  E-value: 6.68e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2065821253 1948 NDKELKEEILKEAHQSkfSIHPGSSKMYRDLKRYYHWVGMKKDVAAWVAKCSTCQLVKA 2006
Cdd:pfam17921    1 VPKSLRKEILKEAHDS--GGHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKP 57
TAXi_N pfam14543
Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly ...
 2591-2696 2.27e-16

Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylanase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 464203 [Multi-domain]  Cd Length: 172  Bit Score: 79.24  E-value: 2.27e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2591 YTTVINQRIHLVPASVVFDLGGRELWVDCD-----------KDYVSSTYQSPRCNYAECSRAGSTSCGTCfSPPKP---- 2655
Cdd:pfam14543    1 YLVTISIGTPPVPFFLVVDTGSDLTWVQCDpccysqpdplfDPYKSSTYKPVPCSSPLCSLIALSSPGPC-CSNNTcdye 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2656 ----------------------------------GC------RLASGTVGMAGMGGHNIGLPPQFAAAFSFSQKFAVYLT 2695
Cdd:pfam14543   80 vsygdgsstsgvlatdtltlnstggsvsvpnfvfGCgynllgGLPAGADGILGLGRGKLSLPSQLASQGIFGNKFSYCLS 159


                   .
gi 2065821253 2696 S 2696
Cdd:pfam14543  160 S 160
TAXi_C pfam14541
Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly ...
 153-224 2.46e-15

Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylasnase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 434029  Cd Length: 160  Bit Score: 75.78  E-value: 2.46e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2065821253  153 NATARNITR-VASKKPFgDACFSTKNVGVTRLGYAAPEIQLLLcSNDVVWRIFRANSMVSVSDDVICLGFVDG 224
Cdd:pfam14541   58 KALAALGPRvVAPVAPF-DLCYNSTGLGSTRLGPAVPPITLVF-EGGADWTIFGANSMVQVDGGVACLGFVDG 128
TAXi_N pfam14543
Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly ...
 44-140 6.96e-15

Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylanase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 464203 [Multi-domain]  Cd Length: 172  Bit Score: 75.00  E-value: 6.96e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253   44 YTTVINQRTPLVPASVVFDLGGRELWVDCD-----------KDYVSSTYQSPRCNYAECSR------AGSTSCSTC---- 102
Cdd:pfam14543    1 YLVTISIGTPPVPFFLVVDTGSDLTWVQCDpccysqpdplfDPYKSSTYKPVPCSSPLCSLialsspGPCCSNNTCdyev 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2065821253  103 ------------------FSPPRPGYR---------------LASGTVGMAGMGRHNIGLPPQLKSSMAIK 140
Cdd:pfam14543   81 sygdgsstsgvlatdtltLNSTGGSVSvpnfvfgcgynllggLPAGADGILGLGRGKLSLPSQLASQGIFG 151
TAXi_N pfam14543
Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly ...
 719-773 6.92e-13

Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylanase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 464203 [Multi-domain]  Cd Length: 172  Bit Score: 69.23  E-value: 6.92e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2065821253  719 QITNFIFDCGaTFLLKGLASGTVGMAGMGRHNIGLPPQFAAAFSFSQKFAVCLTS 773
Cdd:pfam14543  107 SVPNFVFGCG-YNLLGGLPAGADGILGLGRGKLSLPSQLASQGIFGNKFSYCLSS 160
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 1583-1694 3.74e-12

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: 65.44  E-value: 3.74e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1583 IDLASGYHQIPIDPLDIRKTAFRTRYGHYEFVVMPFGLTNAPAAFMKMMNGVFQEFLDEFVIIF--IDDILVYSKDwesh 1660
Cdd:cd03714      1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFsyLDDLLIIASS---- 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2065821253 1661 QDHLRAVLERLRKHELFA---KLSKC-SFW--QRSIGFLG 1694
Cdd:cd03714     77 IKTSEAVLRHLRATLLANlgfTLNLEkSKLgpTQRITFLG 116
TAXi_N pfam14543
Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly ...
 2420-2473 2.47e-11

Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylanase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 464203 [Multi-domain]  Cd Length: 172  Bit Score: 64.60  E-value: 2.47e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2065821253 2420 QITNFIFDCGaTFLLKGLASGTVGMAGMGRHNIGLPPQFATAFSFSRKLAVCLT 2473
Cdd:pfam14543  107 SVPNFVFGCG-YNLLGGLPAGADGILGLGRGKLSLPSQLASQGIFGNKFSYCLS 159
TAXi_N pfam14543
Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly ...
 504-557 2.47e-11

Xylanase inhibitor N-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylanase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 464203 [Multi-domain]  Cd Length: 172  Bit Score: 64.60  E-value: 2.47e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2065821253  504 QITNFIFDCGaTFLLKGLASGTVGMAGMGRHNIGLPPQFATAFSFSRKLAVCLT 557
Cdd:pfam14543  107 SVPNFVFGCG-YNLLGGLPAGADGILGLGRGKLSLPSQLASQGIFGNKFSYCLS 159
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
 1300-1391 9.63e-10

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: 57.59  E-value: 9.63e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1300 TLSIGDVETHTLFDSGATHCFVSSEMVKKGGFIKERNTEYGMVRAAGGQAMYPSGIVRDISVVVIGVNMpTDLIVVQLKK 1379
Cdd:pfam13975    2 DVTINGRPVRFLVDTGASVTVISEALAERLGLDRLVDAYPVTVRTANGTVRAARVRLDSVKIGGIELRN-VPAVVLPGDL 80

                           90
                   ....*....|..
gi 2065821253 1380 HDVILGMDWLGK 1391
Cdd:pfam13975   81 DDVLLGMDFLKR 92
TAXi_C pfam14541
Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly ...
 580-637 1.09e-09

Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylasnase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 434029  Cd Length: 160  Bit Score: 59.60  E-value: 1.09e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2065821253  580 QAARIITR-VASEKPFgDACFSTKNVGVTRLGYAVPEIQLLLHSNdVVWRIFRANSMQK 637
Cdd:pfam14541   59 ALAALGPRvVAPVAPF-DLCYNSTGLGSTRLGPAVPPITLVFEGG-ADWTIFGANSMVQ 115
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 1583-1697 1.41e-09

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


Pssm-ID: 238185 [Multi-domain]  Cd Length: 98  Bit Score: 57.36  E-value: 1.41e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1583 IDLASGYHQIPidpldirktafrtryghyefvvMPFGLTNAPAAFMKMMNGVFQEF----LDEFVIIFIDDILVYSKDwE 1658
Cdd:cd00304      1 FDVKSFFTSIP----------------------LPQGSPLSPALANLYMEKLEAPIlkqlLDITLIRYVDDLVVIAKS-E 57

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2065821253 1659 SHQDHLRAVLERLRKHELFAKLSKCSF--WQRSIGFLGHIV 1697
Cdd:cd00304     58 QQAVKKRELEEFLARLGLNLSDEKTQFteKEKKFKFLGILV 98
transpos_IS481 NF033577
IS481 family transposase; null
 2026-2137 5.84e-09

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 59.91  E-value: 5.84e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2026 DYVTMDfVTGLPTGIKSKHNAVWVVVDRLTKSAHFMA-ISETDgaeEIAAKYIDEIVQLHGVPV-SIVSDRDTRFTSHFw 2103
Cdd:NF033577   129 ELWHID-IKKLGRIPDVGRLYLHTAIDDHSRFAYAELyPDETA---ETAADFLRRAFAEHGIPIrRVLTDNGSEFRSRA- 203

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 2065821253 2104 KAFQKAL---GTRVNLSTAYHPQTDGQSERTIQTLED 2137
Cdd:NF033577   204 HGFELALaelGIEHRRTRPYHPQTNGKVERFHRTLKD 240
COG3577 COG3577
Predicted aspartyl protease [General function prediction only];
1272-1407 5.92e-09

Predicted aspartyl protease [General function prediction only];


Pssm-ID: 442797  Cd Length: 152  Bit Score: 57.27  E-value: 5.92e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1272 PKRQAIAPRVYELSEEANNAGNFRAitgTLSIGDVETHTLFDSGATHCFVSSEMVKKGGFIKERNTEYGMVRAAGGQAMY 1351
Cdd:COG3577     20 PGQAPVSTGGGEVVLKRDRDGHFVV---EGTINGQPVRFLVDTGASTVVLSESDARRLGLDPEDLGRPVRVQTANGVVRA 96

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2065821253 1352 PSG----------IVRDISVVVIGVNMPTdlivvqlkkhDVILGMDWLGKYKAHIDchRGRIQFER 1407
Cdd:COG3577     97 ARVrldsvriggiTLRNVRAVVLPGGELD----------DGLLGMSFLGRLDFEID--GDRLTLRP 150
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 1791-1911 2.06e-08

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


Pssm-ID: 260007  Cd Length: 120  Bit Score: 54.60  E-value: 2.06e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1791 TVYTDASITGLGCVLmQKGSVIAYASrqlrKHEGNYPTHDLEMAAVVFALKIWRSYLYGAKVQIFTDHKS-LKYIFTQ-- 1867
Cdd:cd09275      1 VLFTDASLSGWGAYL-LNSRAHGPWS----ADERNKHINLLELKAVLLALQHFAAELKNRKILIRTDNTTaVAYINKQgg 75

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 2065821253 1868 ---PELNLRQRRWMEFVADYDLDI-AYH-PGKANQVADAltdlLSRIRL 1911
Cdd:cd09275     76 tssPPLLALARQILLWCEQRNIWLrASHiPGVLNTEADR----LSRLGL 120
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 1185-1249 1.37e-07

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 53.27  E-value: 1.37e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2065821253 1185 ECATCGKNH---SGTCWRavgacvcCGSKDHCIQNCPRMdQGTPKERvneqkTCFYCGKAGHFKRECP 1249
Cdd:PTZ00368    15 ECPNSAPAGaakARPCYK-------CGEPGHLSRECPSA-PGGRGER-----SCYNCGKTGHLSRECP 69
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 1300-1388 1.38e-07

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: 51.52  E-value: 1.38e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1300 TLSIGDVETHTLFDSGATHCFVSSEMVKKGGFIKERNTEYGMVRAAGGQAMYPSGIVRDISV---VVIGVnmptDLIVVQ 1376
Cdd:pfam13650    2 PVTINGKPVRFLVDTGASGTVISPSLAERLGLKVRGLAYTVRVSTAGGRVSAARVRLDSLRLgglTLENV----PALVLD 77

                           90
                   ....*....|...
gi 2065821253 1377 LK-KHDVILGMDW 1388
Cdd:pfam13650   78 LGdLIDGLLGMDF 90
TAXi_C pfam14541
Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly ...
 2497-2538 5.44e-07

Xylanase inhibitor C-terminal; The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylasnase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.


Pssm-ID: 434029  Cd Length: 160  Bit Score: 51.89  E-value: 5.44e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 2065821253 2497 GTKISSVNPNTVLESSIYKAFTSEFIKQTAARNITRVASEKT 2538
Cdd:pfam14541   32 GTILDTGTPYTVLRPSVYRAVVQAFDKALAALGPRVVAPVAP 73
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 1182-1249 7.49e-07

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 50.96  E-value: 7.49e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2065821253 1182 KRGECATCGK-NH-SGTCWRAVG-----ACVCCGSKDHCIQNCPRMDQGTpkervnEQKTCFYCGKAGHFKRECP 1249
Cdd:PTZ00368    26 KARPCYKCGEpGHlSRECPSAPGgrgerSCYNCGKTGHLSRECPEAPPGS------GPRSCYNCGQTGHISRECP 94
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 1186-1249 2.39e-06

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 49.81  E-value: 2.39e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2065821253 1186 CATCG-KNH-SGTC------WRAVGACVCCGSKDHCIQNCPrmdqgTPKERVNEQKTCFYCGKAGHFKRECP 1249
Cdd:PTZ00368    80 CYNCGqTGHiSRECpnrakgGAARRACYNCGGEGHISRDCP-----NAGKRPGGDKTCYNCGQTGHLSRDCP 146
Ty3_capsid pfam19259
Ty3 transposon capsid-like protein; This entry corresponds to the capsid protein found in the ...
 987-1136 5.83e-06

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


Pssm-ID: 437091 [Multi-domain]  Cd Length: 197  Bit Score: 49.39  E-value: 5.83e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253  987 FTGSSDPIVADEWRTRLKRNFNSTRCPEDYRKdiaIHF----LEGDAHNWWLTVEKRKGDQIQSFADFEEEFNKKFF-PP 1061
Cdd:pfam19259   17 FRGRKDVLKLKSFISEIMLQMSMIFWPNDAER---IVFcarhLTGPAAQWFHDFVQEQGILDATFDTFIKAFKQHFYgKP 93

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2065821253 1062 EAWDRLEcAYLDLVQGNRTVCEYDEEFNRLRRYVGRELEDEQAQVRRFIRGLRIEIRNHCLIRTFTSVSELVERA 1136
Cdd:pfam19259   94 DINKLFN-DIVNLSEAKLGIERYNSHFNRLWDLLPPDFLSEKAAIMFYIRGLKPETYIIVRLAKPSTLKEAMEIA 167
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 1186-1258 1.24e-05

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 47.49  E-value: 1.24e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1186 CATCGK-NH-SGTCWRAVG-----ACVCCGSKDHCIQNCPRMDQGTPKERvneqkTCFYCGKAGHFKRECPklEAERQAG 1258
Cdd:PTZ00368    55 CYNCGKtGHlSRECPEAPPgsgprSCYNCGQTGHISRECPNRAKGGAARR-----ACYNCGGEGHISRDCP--NAGKRPG 127
retropepsin_like_bacteria cd05483
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ...
 1303-1390 2.07e-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: 45.31  E-value: 2.07e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1303 IGDVETHTLFDSGATHCFVSSEMVKKGGfIKERNTEYGMVRAAGGQAMYPSGIVRDISvvvIGVNMPTDLIVV----QLK 1378
Cdd:cd05483      9 INGQPVRFLLDTGASTTVISEELAERLG-LPLTLGGKVTVQTANGRVRAARVRLDSLQ---IGGITLRNVPAVvlpgDAL 84

                           90
                   ....*....|..
gi 2065821253 1379 KHDVILGMDWLG 1390
Cdd:cd05483     85 GVDGLLGMDFLR 96
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 1204-1250 1.12e-04

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 44.80  E-value: 1.12e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2065821253 1204 CVCCGSKDHCIQNCPRMDQGTPKERvneqKTCFYCGKAGHFKRECPK 1250
Cdd:PTZ00368     3 CYRCGGVGHQSRECPNSAPAGAAKA----RPCYKCGEPGHLSRECPS 45
ZnF_C2HC smart00343
zinc finger;
1234-1250 1.84e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.50  E-value: 1.84e-04
                            10
                    ....*....|....*..
gi 2065821253  1234 TCFYCGKAGHFKRECPK 1250
Cdd:smart00343    1 KCYNCGKEGHIARDCPS 17
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 2021-2122 2.26e-04

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


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 42.69  E-value: 2.26e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2021 PEWKWdyvTMDFVTGlptGIKSKHNAVW--VVVDRLTKSAHFMAISETDGAEEIAAKYIDEIVQLHGVPVSIVSDRDTRF 2098
Cdd:pfam00665    1 PNQLW---QGDFTYI---RIPGGGGKLYllVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEY 74

                           90       100
                   ....*....|....*....|....
gi 2065821253 2099 TSHFWKAFQKALGTRVNLSTAYHP 2122
Cdd:pfam00665   75 TSKAFREFLKDLGIKPSFSRPGNP 98
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 1233-1250 3.23e-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: 39.82  E-value: 3.23e-04
                           10
                   ....*....|....*...
gi 2065821253 1233 KTCFYCGKAGHFKRECPK 1250
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 1203-1249 3.65e-04

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


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 44.07  E-value: 3.65e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2065821253 1203 ACVCCGSKDHCIQNCP------RMDQGTPKERVNEQKTCFYCGKAGHFKRECP 1249
Cdd:COG5082     62 VCFNCGQNGHLRRDCPhsicynCSWDGHRSNHCPKPKKCYNCGETGHLSRDCN 114
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1949-2184 4.24e-04

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 45.14  E-value: 4.24e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1949 DKELKEEILKEAHQSKFSihpGSSKMYRDLKRYYHWVG-------MKKD--VAAWVAKCSTCQLVKAEHKVPSGLVQNLP 2019
Cdd:COG2801     70 DAELLERIKEIFAESPRY---GYRRITAELRREGIAVNrkrvrrlMRELglQARRRRKKKYTTYSGHGGPIAPNLLFTAT 146

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2020 MPEWKWdyvTMDFvtglpTGIKSKHNAVW--VVVDRLTKSAHFMAISETDGAEeIAAKYIDEIVQLHGV--PVSIVSDRD 2095
Cdd:COG2801    147 APNQVW---VTDI-----TYIPTAEGWLYlaAVIDLFSREIVGWSVSDSMDAE-LVVDALEMAIERRGPpkPLILHSDNG 217

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2096 TRFTSHFWKAFQKALGTRVNLSTAYHPQTDGQSERTIQTLE------------DMLRACVLDWggnwekylrlVEFaYNN 2163
Cdd:COG2801    218 SQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKyellyrrrfeslEEAREAIEEY----------IEF-YNH 286

                          250       260
                   ....*....|....*....|...
gi 2065821253 2164 S-YQASIG-MSPYEALYGRACRT 2184
Cdd:COG2801    287 ErPHSSLGyLTPAEYEKQLAAAA 309
pepsin_retropepsin_like cd05470
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 52-121 1.78e-03

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


Pssm-ID: 133137 [Multi-domain]  Cd Length: 109  Bit Score: 40.44  E-value: 1.78e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253   52 TPLVPASVVFDLGGRELWVDCDKdyvsstyqSPRCNYAECSRAGSTSCSTCFSPPRPGYRLASGTVGMAG 121
Cdd:cd05470      7 TPPQTFNVLLDTGSSNLWVPSVD--------CQSLAIYSHSSYDDPSASSTYSDNGCTFSITYGTGSLSG 68
cnd41_like cd05472
Chloroplast Nucleoids DNA-binding Protease, catalyzes the degradation of ribulose-1, ...
 2415-2527 2.99e-03

Chloroplast Nucleoids DNA-binding Protease, catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase; Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco. Antisense tobacco with reduced amount of CND41 maintained green leaves and constant protein levels, especially Rubisco. CND41 has DNA-binding as well as aspartic protease activities. The pepsin-like aspartic protease domain is located at the C-terminus of the protein. The enzyme is characterized by having two aspartic protease catalytic site motifs, the Asp-Thr-Gly-Ser in the N-terminal and Asp-Ser-Gly-Ser in the C-terminal region. Aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA).


Pssm-ID: 133139 [Multi-domain]  Cd Length: 299  Bit Score: 42.26  E-value: 2.99e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 2415 LAAALQITNFIFDCGATFllKGLASGTVGMAGMGRHNIGLPPQfaTAFSFSRKLAVCL-----------TFGK------G 2477
Cdd:cd05472     57 LGSSDVVPGFAFGCGHDN--EGLFGGAAGLLGLGRGKLSLPSQ--TASSYGGVFSYCLpdrsssssgylSFGAaasvpaG 132

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2065821253 2478 LQTMPLLIN---------------------HVSTASVFSQGTKISSVNPNTVLESSIYKAFTSEFIKQTAA 2527
Cdd:cd05472    133 ASFTPMLSNprvptfyyvgltgisvggrrlPIPPASFGAGGVIIDSGTVITRLPPSAYAALRDAFRAAMAA 203
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1792-1902 6.49e-03

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: 38.83  E-value: 6.49e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2065821253 1792 VYTDASitglgCVLMQKGSVIAYAsrqLRKHEGNY--------PTHD---LEMAAVVFALKIWRSYLYgAKVQIFTDHKS 1860
Cdd:cd06222      1 INVDGS-----CRGNPGPAGIGGV---LRDHEGGWlggfalkiGAPTaleAELLALLLALELALDLGY-LKVIIESDSKY 71

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2065821253 1861 L---------KYIFTQPELNLRQRRWMEFvadYDLDIAYHPGKANQVADAL 1902
Cdd:cd06222     72 VvdlinsgsfKWSPNILLIEDILLLLSRF---WSVKISHVPREGNQVADAL 119
 
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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