Psyllid ID: psy15450

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------66
Protein Sequence
MNIRKYVIRKNVDNENGTNVQEKVDIAQREVNRSGESLNTAGKNDNNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVFHGRRLVIVMSDFNNSDGEDITMSGDCPRDKRGIPPDPGKGSGNATQDDGDQYESAPEYAKQNCFLNEVKDKWPNAYLIFTDGSKTSESVASAFYDTQNKNSGTFKLQNFATIFTAEAFAILQALKYASSIKEKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTDALNPYPIPVQDVRAVTDMQHEIQWRENVMSQNNNKGLFYKNLFTITDKKPWFAKAIPLRKFIVTFNRLRSNHAICQAYLHKINIAPTNLCQECLEREDMAHIILCCPKYQVTLAIALVGSGQDARLVNGGRGFDPTQGFACVYYEIISKNGDFYQRADCALATNYGFHACSQLVYQPMVKKEYYIQNCRVCYSDGCNSIKQQYILNKDLPLYGNFFTAIWFLYLGVACCLAAGACVVIRTYFLYRKATKSDNCCSHSSYSPSHRSESICPY
Secondary Structure (PSIPRED)
cccccEEEEccccccccccHHHHHHHHHHHHHHcHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccEEEEEEEHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHccccEEEEEccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccHHHHHHcccccccccHHHHHHHHHHHHcccccEEEEEEEEccccccccccEEEEEEcccEEEEEcccccccccccccccccHHHHHHHHHHHHHHcccccccEEEEEEccHHHHHHHHcccccccccHHHHHHHHHHHHHHHHccccEEEEEEcccccccHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHEHHHHHccccccHHHHHcccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHHcccccHHHHHHHHccccccccccccccccccEEEEcccEEEEcccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHccccEEEEEEEEEEEcccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEEEccccccccccHHHHEHHHHHHcccccccccccccccccccHHHccccccccccHHHHHHHHHHHHHHHHHccccEEEEEEHHHHHccccHHHHHHHHHHccccHHHHHHHHHHHHccccEEEEEEccccccccccEcccccccccccccccccccccHHHcccccccccHHHHHHHHHcccccHccccccccccccccccHHHHHHHHcccccccccEEEccccHHccccHHHHHHHHccccccccccccccHEEEccccEEEEccccccEEEEEcccccHHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccEcccccccccccccccccccHHHHHHHHHHHHccccHHHHHHHHcccccccccccccccccccEEEEccccHHEEEEEEEccccccHHHEccccccccccccEEEEEEEEcccccHHHHHHHHHHHHccccHccHEEEcccccEEEEEEccEEEEcccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mnirkyvirknvdnengtnvqEKVDIAQREvnrsgeslntagkndnnilpmeqrgclegatgckdLLMLDKIITEDCKKKYKNLSVAWIDLLKaydncpheWMVKVIQMYKIDLKSATFCVFCVFHGRRLVIVMsdfnnsdgeditmsgdcprdkrgippdpgkgsgnatqddgdqyesapeyakqncflnevkdkwpnayliftdgsktseSVASAFYdtqnknsgtfklqnFATIFTAEAFAILQALKYASSIKEKEAGYCKVSIRESLWIFdtqnknsgtfklknFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKntsksngnpsHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETArgtdalnpypipvqdvravTDMQHEIQWRENVMsqnnnkglfyknlftitdkkpwfakaiplRKFIVTFNRLRSNHAICQAYLHKIniaptnlcqeclerEDMAHIILCCPKYQVTLAIALVGsgqdarlvnggrgfdptqgfACVYYEIISKngdfyqradcalatnygfhacsqlvyqpmvkkeyyiqNCRVCysdgcnsikqqyilnkdlplygnFFTAIWFLYLGVACCLAAGACVVIRTYFLYRkatksdnccshssyspshrsesicpy
Flexible Loop (DISEMBL)
mnirkyvirknvdnengtnvqekvdiaqrevnrsgeslntagkndnnilPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVFHGRRLVIVMsdfnnsdgeditmsgdcprdKRGIPPDPGKGSGNATQDDGDQYESAPEYAKQNCFLNEVKDKWPNAYLIFTDGSKTSESVASAFYDTQNKNSGTFKLQNFATIFTAEAFAILQALKYASSIKEKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKntsksngnpsHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETargtdalnpypipvQDVRAVTDMQHEIQWRenvmsqnnnKGLFYKNLFTITDKKPWFAKAIPLRKFIVTFNRLRSNHAICQAYLHKINIAPTNLCQECLEREDMAHIILCCPKYQVTLAIALVGSGQDARLVNGGRGFDPTQGFACVYYEIISKNGDFYQRADCALATNYGFHACSQLVYQPMVKKEYYIQNCRVCYSDGCNSIKQQYILNKDLPLYGNFFTAIWFLYLGVACCLAAGACVVIRTYFLYRKatksdnccshssyspshrsesicpy
Low Complexity Region (SEG)
MNIRKYVIRKNVDNENGTNVQEKVDIAQREVNRSGESLNTAGKNDNNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVFHGRRLVIVMSDFNNSDGEDITMSGDCPRDKRGIPPDPGKGSGNATQDDGDQYESAPEYAKQNCFLNEVKDKWPNAYLIFTDGSKTSESVASAFYDTQNKNSGTFKLQNfatiftaeafaiLQALKYASSIKEKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNfatiftaeafaiLQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTDALNPYPIPVQDVRAVTDMQHEIQWRENVMSQNNNKGLFYKNLFTITDKKPWFAKAIPLRKFIVTFNRLRSNHAICQAYLHKINIAPTNLCQECLEREDMAHIILCCPKYQVTLAIALVGSGQDARLVNGGRGFDPTQGFACVYYEIISKNGDFYQRADCALATNYGFHACSQLVYQPMVKKEYYIQNCRVCYSDGCNSIKQQYILNKDLPLYGNFFTAIWFLYlgvacclaagacvvIRTYFLYRKATKsdnccshssyspshrsesICPY
Disordered region (IsUnstruct)
****************************************************QRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVFHGRRLVIVMSDF**********************************************AKQNCFLNEVKDKWPNAYLIFTDGS*****VASAFYDTQNKNSGTFKLQNFATIFTAEAFAILQALKYASSIKEKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLE*************HLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTDALNPYPIPVQDVRAVTDMQHEIQWRENVMSQNNNKGLFYKNLFTITDKKPWFAKAIPLRKFIVTFNRLRSNHAICQAYLHKINIAPTNLCQECLEREDMAHIILCCPKYQVTLAIALVGSGQDARLVNGGRGFDPTQGFACVYYEIISKNGDFYQRADCALATNYGFHACSQLVYQPMVKKEYYIQNCRVCYSDGCNSIKQQYILNKDLPLYGNFFTAIWFLYLGVACCLAAGACVVIRTYFLYRKATK**********************
Disordered Region (DISOPRED)
***RKYVIRKNVDNEN*TNVQ**VDI*********ESLNTAGKNDNNILPMEQ********GCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVFHGRRLVIVMSDFNNS*****************IP**PG***********************NCFLNEVKDKWPNAYL******************************NFATIFTAEAFAILQALKYASSIKEKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTDALNPYPIPVQDVRAVTDMQHEIQWRENVMSQNNNKGLFYKNLFTITDKKPWFAKAIPLRKFIVTFNRLRSNHAICQAYLHKINIAPTNLCQECLEREDMAHIILCCPKYQVTLAIAL***GQD**LVNGGRGFDPTQGFACVYYEIISKNGDFYQRADCALATNYGFHACSQLVYQPMVKKEYYIQNCRVCYSDGCNSIKQQYILNKDLPLYGNFFTAIWFLYLGVACCLAAGACVVIRTYFLYRKATKSD*****************CP*
Disordered Region (DISEMBL)
MNIRKYVIRKNVDNENGTNVQEKVDIAQREVNRSGESLNTAGKNDNNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVFHGRRLVIVMSDFNNSDGEDITMSGDCPRDKRGIPPDPGKGSGNATQDDGDQYESAPEYAKQNCFLNEVKDKWPNAYLIFTDGSKTSESVASAFYDTQNKNSGTFKLQNFATIFTAEAFAILQALKYASSIKEKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTDALNPYPIPVQDVRAVTDMQHEIQWRENVMSQNNNKGLFYKNLFTITDKKPWFAKAIPLRKFIVTFNRLRSNHAICQAYLHKINIAPTNLCQECLEREDMAHIILCCPKYQVTLAIALVGSGQDARLVNGGRGFDPTQGFACVYYEIISKNGDFYQRADCALATNYGFHACSQLVYQPMVKKEYYIQNCRVCYSDGCNSIKQQYILNKDLPLYGNFFTAIWFLYLGVACCLAAGACVVIRTYFLYRKAT***********************
Disordered Region (DISPRO)
*NIRKYVIRKNVDNENGTNVQEKVDIAQREVNRSGESLNTAGKNDNNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVFHGRRLVIVMSDFNNSDGEDITMSGDCPRDKRGIPPDPGKGSGNATQDDGDQYESAPEYAKQNCFLNEVKDKWPNAYLIFTDGSKTSESVASAFYDTQNKNSGTFKLQNFATIFTAEAFAILQALKYASSIKEKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTDALNPYPIPVQDVRAVTDMQHEIQWRENVMSQNNNKGLFYKNLFTITDKKPWFAKAIPLRKFIVTFNRLRSNHAICQAYLHKINIAPTNLCQECLEREDMAHIILCCPKYQVTLAIALVGSGQDARLVNGGRGFDPTQGFACVYYEIISKNGDFYQRADCALATNYGFHACSQLVYQPMVKKEYYIQNCRVCYSDGCNSIKQQYILNKDLPLYGNFFTAIWFLYLGVACCLAAGACVVIRTYFLYRKATK**********************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MNIRKYVIRKNVDNENGTNVQEKVDIAQREVNRSGESLNTAGKNDNNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVFHGRRLVIVMSDFNNSDGEDITMSGDCPRDKRGIPPDPGKGSGNATQDDGDQYESAPEYAKQNCFLNEVKDKWPNAYLIFTDGSKTSESVASAFYDTQNKNSGTFKLQNFATIFTAEAFAILQALKYASSIKEKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTDALNPYPIPVQDVRAVTDMQHEIQWRENVMSQNNNKGLFYKNLFTITDKKPWFAKAIPLRKFIVTFNRLRSNHAICQAYLHKINIAPTNLCQECLEREDMAHIILCCPKYQVTLAIALVGSGQDARLVNGGRGFDPTQGFACVYYEIISKNGDFYQRADCALATNYGFHACSQLVYQPMVKKEYYIQNCRVCYSDGCNSIKQQYILNKDLPLYGNFFTAIWFLYLGVACCLAAGACVVIRTYFLYRKATKSDNCCSHSSYSPSHRSESICPY
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	659	2.2.26 [Sep-21-2011]
B4UMK8	183	Ribonuclease H OS=Anaerom	yes	N/A	0.132	0.475	0.37	8e-05
B8J731	183	Ribonuclease H OS=Anaerom	yes	N/A	0.132	0.475	0.36	0.0002
Q2IJL8	183	Ribonuclease H OS=Anaerom	yes	N/A	0.132	0.475	0.35	0.0009

>sp|B4UMK8|RNH_ANASK Ribonuclease H OS=Anaeromyxobacter sp. (strain K) GN=rnhA PE=3 SV=1

 Score = 49.7 bits (117), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 37/100 (37%), Positives = 56/100 (56%), Gaps = 13/100 (13%)

Query: 296 EAFAILQALKYVSSIKENEVIIITDSKSCLEKL---------KNTSKSNGNPSHLILDIF 346
           E  A+L+AL+ +   ++ EVI  +DS+  ++ L         K    ++G P  L  D+ 
Sbjct: 57  ELRAVLEALEGLPGGEQVEVI--SDSRYVVDALSRWIHGWRKKGWRTASGEPV-LNRDLI 113

Query: 347 KALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARG 386
           +AL   +   +SVR+ WVRGH G A NE VD+LA+  ARG
Sbjct: 114 EALD-ARASALSVRYTWVRGHDGHAVNEVVDQLAQAAARG 152

Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
Anaeromyxobacter sp. (strain K) (taxid: 447217)
EC: 3EC: .EC: 1EC: .EC: 2EC: 6EC: .EC: 4

>sp|B8J731|RNH_ANAD2 Ribonuclease H OS=Anaeromyxobacter dehalogenans (strain 2CP-1 / ATCC BAA-258) GN=rnhA PE=3 SV=1

 Score = 48.5 bits (114), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 36/100 (36%), Positives = 56/100 (56%), Gaps = 13/100 (13%)

Query: 296 EAFAILQALKYVSSIKENEVIIITDSKSCLEKL---------KNTSKSNGNPSHLILDIF 346
           E  A+L+AL+ +   ++ EVI  +DS+  ++ L         K    ++G P  L  D+ 
Sbjct: 57  ELRAVLEALEGLPGGEQVEVI--SDSRYVVDALSRWIHGWRKKGWRTASGEPV-LNRDLI 113

Query: 347 KALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARG 386
           +AL   +   ++VR+ WVRGH G A NE VD+LA+  ARG
Sbjct: 114 EALD-ARASALTVRYTWVRGHDGHAVNEVVDQLAQAAARG 152

Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.

Anaeromyxobacter dehalogenans (strain 2CP-1 / ATCC BAA-258) (taxid: 455488)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: 4

>sp|Q2IJL8|RNH_ANADE Ribonuclease H OS=Anaeromyxobacter dehalogenans (strain 2CP-C) GN=rnhA PE=3 SV=1

 Score = 46.2 bits (108), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 35/100 (35%), Positives = 54/100 (54%), Gaps = 13/100 (13%)

Query: 296 EAFAILQALKYVSSIKENEVIIITDSKSCLEKL---------KNTSKSNGNPSHLILDIF 346
           E  A+L+AL+ +       V +I+DS+  ++ L         K    ++G P  L  D+ 
Sbjct: 57  ELRAVLEALEGLPG--GEAVQVISDSRYVVDALSRWIHGWRRKGWRTASGEPV-LNRDLI 113

Query: 347 KALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARG 386
           +AL   +  ++SV + WVRGH G A NE VD+LA+  ARG
Sbjct: 114 EALD-ARARDLSVTYTWVRGHDGHAVNEVVDQLAQAAARG 152

Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.

Anaeromyxobacter dehalogenans (strain 2CP-C) (taxid: 290397)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: 4

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	659
357621647	1133	putative pol-like protein [Danaus plexip	0.329	0.191	0.324	3e-22
307189101	246	hypothetical protein EAG_08495 [Camponot	0.321	0.861	0.308	4e-19
242022987	1168	reverse transcriptase, putative [Pedicul	0.113	0.064	0.506	2e-16
242014730	1168	reverse transcriptase, putative [Pedicul	0.113	0.064	0.506	2e-16
242019801	700	reverse transcriptase, putative [Pedicul	0.113	0.107	0.506	2e-16
242023142	399	reverse transcriptase, putative [Pedicul	0.113	0.187	0.506	3e-16
242004074	759	reverse transcriptase, putative [Pedicul	0.113	0.098	0.506	3e-16
242006068	887	reverse transcriptase, putative [Pedicul	0.113	0.084	0.493	8e-16
242017106	1168	reverse transcriptase, putative [Pedicul	0.113	0.064	0.493	1e-15
242014754	1168	reverse transcriptase, putative [Pedicul	0.113	0.064	0.493	1e-15

>gi|357621647|gb|EHJ73416.1| putative pol-like protein [Danaus plexippus]

 Score =  113 bits (283), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 71/219 (32%), Positives = 112/219 (51%), Gaps = 2/219 (0%)

Query: 284  FKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLIL 343
            FK  +  +IFTAE+ AIL+A+ +V S K N  II +DSKSCL+ +      + +    IL
Sbjct: 891  FKFPSEISIFTAESIAILEAVSFVESHKLNNSIIFSDSKSCLQAIARNPFISKHNYPYIL 950

Query: 344  DIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTDALNPYPIPVQDVRAV 403
             I   L   Q  NI VR  W+  H+GI GNE VD  AK+ A  T  ++ + +   D+  +
Sbjct: 951  KIKDILFRCQSSNIQVRLAWIPSHSGIHGNETVDYYAKD-ATNTGCMDHFGVYPNDLIPI 1009

Query: 404  TDMQHEIQWRENVMSQNNNKGLFYKNLFTITDKKPWFAKAIPLRKFIVTFN-RLRSNHAI 462
               +    W +  +  + +KG +Y ++ ++   +PWF     L K + +   RLR  HA 
Sbjct: 1010 AKQRFFSSWTQYWLKTSRSKGKYYADVQSLIPFRPWFCNFKNLHKRVSSIICRLRLGHAC 1069

Query: 463  CQAYLHKINIAPTNLCQECLEREDMAHIILCCPKYQVTL 501
               +L K+ I  ++LC+  L+     HI   CP+   +L
Sbjct: 1070 TPVHLAKLRIKDSSLCECGLDEGSPDHIFFTCPRLSSSL 1108

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307189101|gb|EFN73572.1| hypothetical protein EAG_08495 [Camponotus floridanus]

 Score =  103 bits (256), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 66/214 (30%), Positives = 108/214 (50%), Gaps = 2/214 (0%)

Query: 284 FKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLIL 343
           +KL  + +IF+AE  AI+ A+ Y+         I TDS+S +E L N    + + S+LIL
Sbjct: 22  YKLDRYFSIFSAECIAIMCAMDYILEEGIKRSAIFTDSRSMVETLSN-GLLDRDLSYLIL 80

Query: 344 DIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTDALNPYPIPVQDVRAV 403
            +   L      N+ V  +WV  H GI GNE  D LA E AR  ++++  P P  D+ ++
Sbjct: 81  ALKNKLRSAYVQNLDVVIVWVPSHVGILGNETADLLAGEAARQEESVDYLP-PHTDLYSL 139

Query: 404 TDMQHEIQWRENVMSQNNNKGLFYKNLFTITDKKPWFAKAIPLRKFIVTFNRLRSNHAIC 463
              ++     + +++Q+  +G  Y +L+    +KPWFA     R  I T  R+RSNH   
Sbjct: 140 VKEKYFSDIEKYLLAQSEIRGAQYFSLYPPFARKPWFAGLDLSRAEITTICRIRSNHYNL 199

Query: 464 QAYLHKINIAPTNLCQECLEREDMAHIILCCPKY 497
              L++  +     C   L  +D+ H++  CP +
Sbjct: 200 NFSLYRCGLVRRPDCLCGLPYQDINHVLWSCPMF 233

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242022987|ref|XP_002431918.1| reverse transcriptase, putative [Pediculus humanus corporis] gi|212517262|gb|EEB19180.1| reverse transcriptase, putative [Pediculus humanus corporis]

 Score = 94.0 bits (232), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 57/75 (76%)

Query: 46  NNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVK 105
           NNI P EQ GC +G+ GCK++L+++K+I    K+K KNLS+AWID  KA+D+ PHEW+++
Sbjct: 517 NNIFPPEQYGCRKGSYGCKEVLLINKLIMASAKQKRKNLSMAWIDYQKAFDSVPHEWIIE 576

Query: 106 VIQMYKIDLKSATFC 120
            +++YK+D K   FC
Sbjct: 577 ALKIYKVDPKITAFC 591

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242014730|ref|XP_002428038.1| reverse transcriptase, putative [Pediculus humanus corporis] gi|212512557|gb|EEB15300.1| reverse transcriptase, putative [Pediculus humanus corporis]

 Score = 94.0 bits (232), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 57/75 (76%)

Query: 46  NNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVK 105
           NNI P EQ GC +G+ GCK++L+++K+I    K+K KNLS+AWID  KA+D+ PHEW+++
Sbjct: 517 NNIFPPEQYGCRKGSYGCKEVLLINKLIMASAKQKRKNLSMAWIDYQKAFDSVPHEWIIE 576

Query: 106 VIQMYKIDLKSATFC 120
            +++YK+D K   FC
Sbjct: 577 ALKIYKVDPKITAFC 591

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242019801|ref|XP_002430347.1| reverse transcriptase, putative [Pediculus humanus corporis] gi|212515471|gb|EEB17609.1| reverse transcriptase, putative [Pediculus humanus corporis]

 Score = 94.0 bits (232), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 57/75 (76%)

Query: 46  NNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVK 105
           NNI P EQ GC +G+ GCK++L+++K+I    K+K KNLS+AWID  KA+D+ PHEW+++
Sbjct: 517 NNIFPPEQYGCRKGSYGCKEVLLINKLIMASAKQKRKNLSMAWIDYQKAFDSVPHEWIIE 576

Query: 106 VIQMYKIDLKSATFC 120
            +++YK+D    TFC
Sbjct: 577 ALKIYKVDPNITTFC 591

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242023142|ref|XP_002431995.1| reverse transcriptase, putative [Pediculus humanus corporis] gi|212517346|gb|EEB19257.1| reverse transcriptase, putative [Pediculus humanus corporis]

 Score = 93.6 bits (231), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 57/75 (76%)

Query: 46  NNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVK 105
           NNI P EQ GC +G+ GCK++L+++K+I    K+K KNLS+AWID  KA+D+ PHEW+++
Sbjct: 58  NNIFPPEQYGCRKGSYGCKEVLLINKLIMASAKQKRKNLSMAWIDYQKAFDSVPHEWIIE 117

Query: 106 VIQMYKIDLKSATFC 120
            +++YK+D K   FC
Sbjct: 118 ALKIYKVDPKITAFC 132

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242004074|ref|XP_002422963.1| reverse transcriptase, putative [Pediculus humanus corporis] gi|212505879|gb|EEB10225.1| reverse transcriptase, putative [Pediculus humanus corporis]

 Score = 93.6 bits (231), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 38/75 (50%), Positives = 57/75 (76%)

Query: 46  NNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVK 105
           NNI P EQ GC +G+ GCK++L+++K+I    K+K KNLS+AWID  KA+D+ PHEW+++
Sbjct: 108 NNIFPPEQYGCRKGSYGCKEVLLINKLIMASAKQKRKNLSMAWIDYQKAFDSVPHEWIIE 167

Query: 106 VIQMYKIDLKSATFC 120
            +++YK+D K   FC
Sbjct: 168 ALKIYKVDPKITAFC 182

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242006068|ref|XP_002423878.1| reverse transcriptase, putative [Pediculus humanus corporis] gi|212507124|gb|EEB11140.1| reverse transcriptase, putative [Pediculus humanus corporis]

 Score = 92.4 bits (228), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 37/75 (49%), Positives = 56/75 (74%)

Query: 46  NNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVK 105
           NNI P EQ GC +G+ GCK++L+++K+I    K+K KNLS+AWID  KA+D+ PHEW+++
Sbjct: 517 NNIFPPEQYGCRKGSYGCKEVLLINKLIMASAKQKRKNLSMAWIDYQKAFDSVPHEWIIE 576

Query: 106 VIQMYKIDLKSATFC 120
            +++YK+D     FC
Sbjct: 577 ALKIYKVDPNITAFC 591

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242017106|ref|XP_002429033.1| reverse transcriptase, putative [Pediculus humanus corporis] gi|212513888|gb|EEB16295.1| reverse transcriptase, putative [Pediculus humanus corporis]

 Score = 92.0 bits (227), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 37/75 (49%), Positives = 56/75 (74%)

Query: 46  NNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVK 105
           NNI P EQ GC +G+ GCK++L+++K+I    K+K KNLS+AWID  KA+D+ PHEW+++
Sbjct: 517 NNIFPPEQYGCRKGSYGCKEVLLINKLIMASAKQKRKNLSMAWIDYQKAFDSVPHEWIIE 576

Query: 106 VIQMYKIDLKSATFC 120
            +++YK+D     FC
Sbjct: 577 ALKIYKVDPNITAFC 591

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242014754|ref|XP_002428050.1| reverse transcriptase, putative [Pediculus humanus corporis] gi|212512569|gb|EEB15312.1| reverse transcriptase, putative [Pediculus humanus corporis]

 Score = 92.0 bits (227), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 37/75 (49%), Positives = 56/75 (74%)

Query: 46  NNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVK 105
           NNI P EQ GC +G+ GCK++L+++K+I    K+K KNLS+AWID  KA+D+ PHEW+++
Sbjct: 517 NNIFPPEQYGCRKGSYGCKEVLLINKLIMASAKQKRKNLSMAWIDYQKAFDSVPHEWIIE 576

Query: 106 VIQMYKIDLKSATFC 120
            +++YK+D     FC
Sbjct: 577 ALKIYKVDPNITAFC 591

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	659
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.289	0.393	0.246	1.5e-06

ASPGD|ASPL0000075333 AN10625 [Emericella nidulans (taxid:162425)]

 Score = 151 (58.2 bits), Expect = 1.5e-06, Sum P(2) = 1.5e-06
 Identities = 50/203 (24%), Positives = 94/203 (46%)

Query:   301 LQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVR 360
             L AL  +   +    +I TD+++ L+ L+N    +G   +++  I  AL+  ++  ++V 
Sbjct:   230 LLALVIILQRQMQHAVIFTDNQATLQALRNPGSQSGQ--YILEAIIMALNKGRKAGLNVH 287

Query:   361 FIWVRGHAGIAGNEAVDRLAKETARGTDALNPYPIPVQDVRAVTDMQHEI---QWRENVM 417
             F W+  H G+ GNE  DR AKE A G   +  +   +    AV    HE+   +W  +  
Sbjct:   288 FRWIPAHRGVEGNEQADRRAKE-ATGWRRIRGHRGRMTIRSAVKRRAHEVVNARWENDWK 346

Query:   418 SQNNNKGLFYKNLFTITDKKPWFAKAIPLRKFIVTFN-RLRSNHAICQAYLHKINI--AP 474
             S ++ + L+     T T  +        L + + T   ++R+     + YL++  +   P
Sbjct:   347 SCHHGRELYE---LTPTPTRKVLRVHQDLHRALSTIIVQMRTGKIGLRHYLYQRGVPDVP 403

Query:   475 TNLCQECLEREDMAHIILCCPKY 497
              + CQ     + + HI+L CP +
Sbjct:   404 NSDCQCGRATQSVRHILLACPTF 426

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.26	LOW CONFIDENCE prediction!
3rd Layer	3.1.26.4	LOW CONFIDENCE prediction!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	659
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	2e-27
pfam00075	126	pfam00075, RNase_H, RNase H	9e-15
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	3e-13
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	6e-12
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	1e-11
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	1e-09
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	4e-07
pfam13456	88	pfam13456, RVT_3, Reverse transcriptase-like	5e-06
PRK00203	150	PRK00203, rnhA, ribonuclease H; Reviewed	2e-05
cd01650	220	cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long term	7e-05
PRK06548	161	PRK06548, PRK06548, ribonuclease H; Provisional	3e-04
cd09277	133	cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI	3e-04

>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse transcriptases

 Score =  106 bits (268), Expect = 2e-27
 Identities = 49/185 (26%), Positives = 74/185 (40%), Gaps = 60/185 (32%)

Query: 203 IFTDGSKTSESVASAFYDTQNKNSGTFKLQNFATIFTAEAFAILQALKYASSIKEKEAGY 262
           I+TDGSK      + F                                            
Sbjct: 2   IYTDGSKLEGRTGAGF-------------------------------------------- 17

Query: 263 CKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKEN--EVIIITD 320
               +R+           S ++KL  + ++F AE  AIL+AL+          ++ I +D
Sbjct: 18  --AIVRKGTI--------SRSYKLGPYCSVFDAELLAILEALQLALREGRRARKITIFSD 67

Query: 321 SKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLA 380
           S++ L+ L++      + S L+L I KA+  L    + VR  WV GH+GI GNE  DRLA
Sbjct: 68  SQAALKALRSPR----SSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLA 123

Query: 381 KETAR 385
           KE A+
Sbjct: 124 KEAAK 128

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 128

>gnl|CDD|215695 pfam00075, RNase_H, RNase H

 Score = 70.8 bits (174), Expect = 9e-15
 Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 7/98 (7%)

Query: 288 NFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFK 347
              T   AE  A+++AL+ +S  K   V I TDS+  +  + N   +      +  +I++
Sbjct: 36  PGTTNQRAELLALIEALEALSGQK---VNIYTDSQYVIGGITNGWPTKSESKPIKNEIWE 92

Query: 348 ALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETAR 385
            L         V   WV GH+GI GNE  D+LAK+ A 
Sbjct: 93  LLQK----KHKVYIQWVPGHSGIPGNELADKLAKQGAS 126

RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. Length = 126

>gnl|CDD|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and more complex than their prokaryotic counterparts and unlike prokaryote, RNase H are essential in higher eukaryote

 Score = 67.2 bits (165), Expect = 3e-13
 Identities = 39/105 (37%), Positives = 59/105 (56%), Gaps = 14/105 (13%)

Query: 295 AEAFAILQALKYVSSIKEN--EVIIITDSK---SCLEK-----LKNTSK-SNGNP-SH-- 340
           AE  A++ AL+ +  + E   +++I TDS+   + + +      KN  K S G P ++  
Sbjct: 46  AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105

Query: 341 LILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETAR 385
           LI ++ K L  L+E  I V+F  V GH+GI GNE  DRLAK+ A 
Sbjct: 106 LIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGAD 150

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at the N-terminal called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. Length = 150

>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

 Score = 62.8 bits (153), Expect = 6e-12
 Identities = 35/95 (36%), Positives = 48/95 (50%), Gaps = 8/95 (8%)

Query: 290 ATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKAL 349
           AT   AE  A+L+AL+    +   ++II TDSK  ++ + + SK     + L+ DI   L
Sbjct: 37  ATNNEAELLALLEALELALDLGLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLL 96

Query: 350 SHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETA 384
           S      I +RF  V       GNE  DRLAKE A
Sbjct: 97  SKF----IDIRFEHVPRE----GNEVADRLAKEAA 123

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. 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. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 123

>gnl|CDD|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in prokaryotes

 Score = 62.1 bits (152), Expect = 1e-11
 Identities = 29/100 (29%), Positives = 46/100 (46%), Gaps = 21/100 (21%)

Query: 299 AILQALKYVSSIKEN-EVIIITDSKSCLE---------KLKNTSKSNGNP---SHLILDI 345
           A+++AL+   ++KE   V++ TDS+  +          K      ++G P     L  ++
Sbjct: 48  AVIEALE---ALKEPCPVLLYTDSQYVINGITKWIHGWKKNGWKTADGKPVKNVDLWQEL 104

Query: 346 FKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETAR 385
              L+  Q     V + WV+GHAG  GNE  D LA   A 
Sbjct: 105 DALLAKHQ-----VTWHWVKGHAGHPGNERADELANAAAD 139

Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability. Length = 139

>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and repair]

 Score = 57.4 bits (139), Expect = 1e-09
 Identities = 32/100 (32%), Positives = 51/100 (51%), Gaps = 10/100 (10%)

Query: 295 AEAFAILQALKYVSSIKENEVIIITDSKSCLE---------KLKNTSKSNGNPSHLILDI 345
           AE  A+++AL+ +  +   EV + TDSK  +E         K      ++  P     D+
Sbjct: 46  AELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPV-KNKDL 104

Query: 346 FKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETAR 385
           ++ L  L + +  V + WV+GHAG   NE  D+LA+E AR
Sbjct: 105 WEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAAR 144

Length = 154

>gnl|CDD|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term repeat retroelements

 Score = 49.2 bits (118), Expect = 4e-07
 Identities = 38/149 (25%), Positives = 54/149 (36%), Gaps = 35/149 (23%)

Query: 252 ASSIKEKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIK 311
            SS   K AGY  V+  + L I       S             AE  A+++AL+      
Sbjct: 6   GSSFVRK-AGYAVVTGPDVLEIATLPYGTSAQ----------RAELIALIRALELAKGKP 54

Query: 312 ENEVIIITDSK-----------SCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVR 360
            N   I TDS               E+   T K     + LIL + KA+   +     V 
Sbjct: 55  VN---IYTDSAYAFGILHALETIWKERGFLTGKPIAL-ASLILQLQKAIQRPKP----VA 106

Query: 361 FIWVRGHAG-----IAGNEAVDRLAKETA 384
            I +R H+G       GN   D+ A++ A
Sbjct: 107 VIHIRAHSGLPGPLALGNARADQAARQAA 135

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 135

>gnl|CDD|205634 pfam13456, RVT_3, Reverse transcriptase-like

 Score = 44.9 bits (107), Expect = 5e-06
 Identities = 21/91 (23%), Positives = 43/91 (47%), Gaps = 8/91 (8%)

Query: 291 TIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALS 350
           +   AEA A+L+ L+    +    +I+ +DS+  +++++   ++    + L+ +I K L 
Sbjct: 1   SPLEAEAEALLEGLQLALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLK 60

Query: 351 HLQEWNISVRFIWVRGHAGIAGNEAVDRLAK 381
                ++SV  +  R       N   D LAK
Sbjct: 61  KF--DSVSVSHVP-R-----ECNRVADALAK 83

This domain is found in plants and appears to be part of a retrotransposon. Length = 88

>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed

 Score = 44.8 bits (107), Expect = 2e-05
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 358 SVRFIWVRGHAGIAGNEAVDRLAKETA 384
            +++ WV+GHAG   NE  D LA+  A
Sbjct: 114 QIKWHWVKGHAGHPENERCDELARAGA 140

Length = 150

>gnl|CDD|238827 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT)

 Score = 44.2 bits (105), Expect = 7e-05
 Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 45  DNNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMV 104
           + NILP  Q G   G     D ++L + + E  K+K K+L + ++D  KA+D+  HE+++
Sbjct: 45  EENILP-NQFGFRPGR-STTDAILLLREVIEKAKEKKKSLVLVFLDFEKAFDSVDHEFLL 102

Query: 105 KVI 107
           K +
Sbjct: 103 KAL 105

This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities. Length = 220

>gnl|CDD|75628 PRK06548, PRK06548, ribonuclease H; Provisional

 Score = 41.7 bits (97), Expect = 3e-04
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 15/122 (12%)

Query: 272 WIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLE----- 326
           W  D    +SG +   + AT   AE  A+ + L   +   +  ++I++DSK  +      
Sbjct: 25  WYVDENTWDSGGW---DIATNNIAELTAVRELL-IATRHTDRPILILSDSKYVINSLTKW 80

Query: 327 ----KLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKE 382
               K++   K++G P  L  +I + +  L E N ++R  WV  H G   NEA D LA++
Sbjct: 81  VYSWKMRKWRKADGKPV-LNQEIIQEIDSLME-NRNIRMSWVNAHTGHPLNEAADSLARQ 138

Query: 383 TA 384
            A
Sbjct: 139 AA 140

Length = 161

>gnl|CDD|187701 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus

 Score = 40.9 bits (97), Expect = 3e-04
 Identities = 11/27 (40%), Positives = 17/27 (62%)

Query: 356 NISVRFIWVRGHAGIAGNEAVDRLAKE 382
            I + F+ V+ H+G   NE  D+LAK+
Sbjct: 105 KIKISFVKVKAHSGDKYNELADKLAKK 131

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 involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability. Some bacteria distinguished from other bacterial RNase HI in the presence of a hybrid binding domain (HBD) at the N-terminus which is commonly present at the N-termini of eukaryotic RNase HI. It has been reported that this domain is required for dimerization and processivity of RNase HI upon binding to RNA-DNA hybrids. Length = 133

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	659
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.88
PRK06548	161	ribonuclease H; Provisional	99.86
PRK08719	147	ribonuclease H; Reviewed	99.84
PRK00203	150	rnhA ribonuclease H; Reviewed	99.83
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.75
KOG3752|consensus	371		99.68
PRK13907	128	rnhA ribonuclease H; Provisional	99.6
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.6
PRK07708	219	hypothetical protein; Validated	99.37
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.33
cd01651	226	RT_G2_intron RT_G2_intron: Reverse transcriptases	99.33
cd03487	214	RT_Bac_retron_II RT_Bac_retron_II: Reverse transcr	99.22
cd01650	220	RT_nLTR_like RT_nLTR: Non-LTR (long terminal repea	99.2
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	98.98
PF00078	214	RVT_1: Reverse transcriptase (RNA-dependent DNA po	98.89
cd01709	346	RT_like_1 RT_like_1: A subfamily of reverse transc	98.02
cd01646	158	RT_Bac_retron_I RT_Bac_retron_I: Reverse transcrip	97.9
KOG4768|consensus	796		97.65
cd01648	119	TERT TERT: Telomerase reverse transcriptase (TERT)	96.39
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	94.79
COG3344	328	Retron-type reverse transcriptase [DNA replication	94.7
KOG1005|consensus	888		93.25

>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]

Probab=99.88  E-value=9.5e-23  Score=192.92  Aligned_cols=134  Identities=25%  Similarity=0.288  Sum_probs=109.3

Q ss_pred             HHHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHH
Q psy15450        245 ILQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKS  323 (659)
Q Consensus       245 ~l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~  323 (659)
                      .+.||+||+|.+ ||+.|+|+|+.-....       ...+.... .+||++||+.|++.||+.+...+...|.|+|||+|
T Consensus         3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~-------~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~y   74 (154)
T COG0328           3 KVEIFTDGACLGNPGPGGWGAVLRYGDGE-------KELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKY   74 (154)
T ss_pred             ceEEEecCccCCCCCCceEEEEEEcCCce-------EEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHH
Confidence            467999999985 6766777666521111       11223333 89999999999999999999888899999999999


Q ss_pred             HHHHHhcC---------CcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhccC
Q psy15450        324 CLEKLKNT---------SKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGT  387 (659)
Q Consensus       324 ai~~I~~~---------~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~  387 (659)
                      |+++|+.|         ++++++|+ .+.++|+.+.++..+...|.+.|||||+|.++||+||+||+.+++..
T Consensus        75 v~~~i~~w~~~w~~~~w~~~~~~pv-kn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          75 VVEGITRWIVKWKKNGWKTADKKPV-KNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             HHHHHHHHHhhccccCccccccCcc-ccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            99999964         34556677 68999999999987666999999999999999999999999998864

>PRK06548 ribonuclease H; Provisional

Probab=99.86  E-value=2e-21  Score=186.67  Aligned_cols=128  Identities=27%  Similarity=0.386  Sum_probs=101.7

Q ss_pred             HHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHH
Q psy15450        246 LQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSC  324 (659)
Q Consensus       246 l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~a  324 (659)
                      +.|||||++.+ ||+.|.|+++.... +         .. .....+||++|||.|++.||+.+.. ....+.|+|||+|+
T Consensus         6 ~~IytDGa~~gnpg~~G~g~~~~~~~-~---------~~-g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yv   73 (161)
T PRK06548          6 IIAATDGSSLANPGPSGWAWYVDENT-W---------DS-GGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYV   73 (161)
T ss_pred             EEEEEeeccCCCCCceEEEEEEeCCc-E---------Ec-cCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHH
Confidence            67999999885 55666665543211 0         11 1124689999999999999987643 33579999999999


Q ss_pred             HHHHhc---------CCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhccC
Q psy15450        325 LEKLKN---------TSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGT  387 (659)
Q Consensus       325 i~~I~~---------~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~  387 (659)
                      +++|+.         |++++|+|+ .+++||+.+..+.++ ..|+|.|||||+|++|||.||+||++|+...
T Consensus        74 i~~i~~W~~~Wk~~gWk~s~G~pV-~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~  143 (161)
T PRK06548         74 INSLTKWVYSWKMRKWRKADGKPV-LNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNF  143 (161)
T ss_pred             HHHHHHHHHHHHHCCCcccCCCcc-ccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence            999995         466788887 689999999998764 5899999999999999999999999998753

>PRK08719 ribonuclease H; Reviewed

Probab=99.84  E-value=9.6e-21  Score=180.11  Aligned_cols=129  Identities=23%  Similarity=0.342  Sum_probs=98.9

Q ss_pred             HHhhhhhcccCCC----ccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcCh
Q psy15450        246 LQALKYASSIKEK----EAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDS  321 (659)
Q Consensus       246 l~iytDGS~~~~g----~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDS  321 (659)
                      +.||||||+.+++    .+|+|+++....     +.........+...+||++|||.|++.||+.+...    ..|+|||
T Consensus         5 ~~iYtDGs~~~n~~~~~~~G~G~vv~~~~-----~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS   75 (147)
T PRK08719          5 YSIYIDGAAPNNQHGCVRGGIGLVVYDEA-----GEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDS   75 (147)
T ss_pred             EEEEEecccCCCCCCCCCcEEEEEEEeCC-----CCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEech
Confidence            5699999997543    356666543221     11111223335556899999999999999998653    3899999


Q ss_pred             HHHHHHHhc---------CCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhc
Q psy15450        322 KSCLEKLKN---------TSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETAR  385 (659)
Q Consensus       322 q~ai~~I~~---------~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~  385 (659)
                      +|++++|+.         |++++|.++ .+.++|+.+..+.. ...|.|.|||||+|++|||.||+||++|++
T Consensus        76 ~yvi~~i~~~~~~W~~~~w~~s~g~~v-~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         76 DYCVRGFNEWLDTWKQKGWRKSDKKPV-ANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             HHHHHHHHHHHHHHHhCCcccCCCccc-ccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            999999954         345666776 47899999998865 577999999999999999999999999875

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.83  E-value=2.6e-20  Score=177.83  Aligned_cols=131  Identities=21%  Similarity=0.298  Sum_probs=101.1

Q ss_pred             HHhhhhhcccCC-CccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHH
Q psy15450        246 LQALKYASSIKE-KEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSC  324 (659)
Q Consensus       246 l~iytDGS~~~~-g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~a  324 (659)
                      +.||||||+.++ +..|.|++....+..      . ..... ....||++|||.|++.||+.+..  ...+.|||||+|+
T Consensus         4 v~iytDGs~~~n~~~~g~g~v~~~~~~~------~-~~~~~-~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yv   73 (150)
T PRK00203          4 VEIYTDGACLGNPGPGGWGAILRYKGHE------K-ELSGG-EALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYV   73 (150)
T ss_pred             EEEEEEecccCCCCceEEEEEEEECCee------E-EEecC-CCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHH
Confidence            578999999864 555666555432211      1 11111 24689999999999999998865  4689999999999


Q ss_pred             HHHHhcC---------CcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhccCC
Q psy15450        325 LEKLKNT---------SKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTD  388 (659)
Q Consensus       325 i~~I~~~---------~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~~  388 (659)
                      ++.|+.|         .+++|+++ .+.++|+.+.++.. ...|.|.|||||+|++||+.||+||++|+....
T Consensus        74 i~~i~~w~~~Wk~~~~~~~~g~~v-~n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~  144 (150)
T PRK00203         74 RQGITEWIHGWKKNGWKTADKKPV-KNVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAGAEEAT  144 (150)
T ss_pred             HHHHHHHHHHHHHcCCcccCCCcc-ccHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence            9999963         44567776 47888888888764 478999999999999999999999999987643

>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site

Probab=99.75  E-value=3.5e-18  Score=158.19  Aligned_cols=121  Identities=35%  Similarity=0.425  Sum_probs=87.1

Q ss_pred             HHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHH
Q psy15450        246 LQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSC  324 (659)
Q Consensus       246 l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~a  324 (659)
                      +.+|||||+.. ++..|+|++. ..+      +   .....++ ..|+++|||.||..||+.+ .  ...++|||||+++
T Consensus         4 ~~iytDgS~~~~~~~~~~g~v~-~~~------~---~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v   69 (132)
T PF00075_consen    4 IIIYTDGSCRPNPGKGGAGYVV-WGG------R---NFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYV   69 (132)
T ss_dssp             EEEEEEEEECTTTTEEEEEEEE-ETT------E---EEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHH
T ss_pred             EEEEEeCCccCCCCceEEEEEE-ECC------e---EEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHH
Confidence            56899999875 4444555533 222      1   2233344 7899999999999999944 3  3999999999999


Q ss_pred             HHHHhcC-----CcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCc-cchhhhhhHHHHHh
Q psy15450        325 LEKLKNT-----SKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGI-AGNEAVDRLAKETA  384 (659)
Q Consensus       325 i~~I~~~-----~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi-~GNE~AD~LAk~aa  384 (659)
                      ++.+..+     +.......++..+|++.+    .++..|.|.|||||+|+ .|||.||+|||.|+
T Consensus        70 ~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   70 LNALNKWLHGNGWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HHHHHTHHHHTTSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhccccccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence            9988883     222111112445565555    34789999999999999 69999999999987

This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....

>KOG3752|consensus

Probab=99.68  E-value=5.7e-17  Score=170.55  Aligned_cols=145  Identities=28%  Similarity=0.229  Sum_probs=114.0

Q ss_pred             ehhhhHHHHHhhhhhcccCCCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEE
Q psy15450        238 FTAEAFAILQALKYASSIKEKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVII  317 (659)
Q Consensus       238 F~~e~~g~l~iytDGS~~~~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I  317 (659)
                      -+.|..+.+.+|||||+..+|..++.   ++.++++++++..+......++.+|||+|||.|+..||+.+.+....+++|
T Consensus       205 ~d~e~~~~~vvytDGS~~~ng~~~~~---AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I  281 (371)
T KOG3752|consen  205 NDREEIEIQVVYTDGSSSGNGRKSSR---AGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVI  281 (371)
T ss_pred             cccccccceEEEecCccccCCCCCCc---ceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEE
Confidence            34445556889999999998876543   233466777777766555555899999999999999999998877789999


Q ss_pred             EcChHHHHHHHhcC---------CcCCCCC-----cccHHHHHHHHHHHHhc--CCeeeEEEeecCCCccchhhhhhHHH
Q psy15450        318 ITDSKSCLEKLKNT---------SKSNGNP-----SHLILDIFKALSHLQEW--NISVRFIWVRGHAGIAGNEAVDRLAK  381 (659)
Q Consensus       318 ~TDSq~ai~~I~~~---------~~~~g~~-----~~~~~~i~~~l~~l~~~--~~~V~~~WVPgH~gi~GNE~AD~LAk  381 (659)
                      .|||++++++|+.|         ..+++.+     + .+.+....+.+|.+.  +.+|.+.|||||.|+.|||.||.||+
T Consensus       282 ~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v-~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lAR  360 (371)
T KOG3752|consen  282 RTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYV-KNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALAR  360 (371)
T ss_pred             EechHHHHHHHHHHHhhhccCccccccCCCccceee-ecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHh
Confidence            99999999999986         3344444     3 356666667776543  48999999999999999999999999


Q ss_pred             HHhcc
Q psy15450        382 ETARG  386 (659)
Q Consensus       382 ~aa~~  386 (659)
                      +++..
T Consensus       361 kgs~~  365 (371)
T KOG3752|consen  361 KGSTL  365 (371)
T ss_pred             hhhhh
Confidence            98654

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.60  E-value=2.5e-15  Score=139.43  Aligned_cols=125  Identities=17%  Similarity=0.129  Sum_probs=98.0

Q ss_pred             HHHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHH
Q psy15450        245 ILQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKS  323 (659)
Q Consensus       245 ~l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~  323 (659)
                      |++||+|||+.. +|..|+|+|+........       .... .+..||+.||+.|++.||+.+...+..++.|+|||++
T Consensus         1 ~~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~-------~~~~-~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~   72 (128)
T PRK13907          1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQ-------LSLP-LGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQL   72 (128)
T ss_pred             CEEEEEeeCCCCCCCccEEEEEEEECCeeEE-------EEec-ccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHH
Confidence            467899999875 678888888764332111       1112 2457999999999999999999988889999999999


Q ss_pred             HHHHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhc
Q psy15450        324 CLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETAR  385 (659)
Q Consensus       324 ai~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~  385 (659)
                      +++.+++.+..+    ..+..+++.+..+..+...+.+.|||+    +.|+.||.||+.|..
T Consensus        73 vi~~~~~~~~~~----~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~  126 (128)
T PRK13907         73 VERAVEKEYAKN----KMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAIL  126 (128)
T ss_pred             HHHHHhHHHhcC----hhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence            999999975433    246777777777766667788899996    589999999999875

>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner

Probab=99.60  E-value=9.7e-15  Score=130.99  Aligned_cols=129  Identities=29%  Similarity=0.289  Sum_probs=97.9

Q ss_pred             HhhhhhcccCC-CccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHHH
Q psy15450        247 QALKYASSIKE-KEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCL  325 (659)
Q Consensus       247 ~iytDGS~~~~-g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~ai  325 (659)
                      ++|+|||.... +..|+|++....+......      ........+++.+|+.|+..||+.+...+..++.|+|||+.++
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~------~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~   74 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLS------GGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVI   74 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEe------ccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHH
Confidence            36899998754 6778887776533211111      1111157899999999999999999887889999999999999


Q ss_pred             HHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHh
Q psy15450        326 EKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETA  384 (659)
Q Consensus       326 ~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa  384 (659)
                      +.++++.....   .....++..+..+..+...+.|.|||+|+++.+|+.||.||+.++
T Consensus        75 ~~~~~~~~~~~---~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          75 NALTGWYEGKP---VKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             HHhhccccCCC---hhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            99998743121   235555556665555678999999999999999999999999873

One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.

>PRK07708 hypothetical protein; Validated

Probab=99.37  E-value=1.1e-12  Score=132.78  Aligned_cols=133  Identities=14%  Similarity=0.072  Sum_probs=94.1

Q ss_pred             HHHhhhhhccc-CCCccceEEEEecc-ceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCC--eEEEEcC
Q psy15450        245 ILQALKYASSI-KEKEAGYCKVSIRE-SLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKEN--EVIIITD  320 (659)
Q Consensus       245 ~l~iytDGS~~-~~g~~G~g~v~~~~-~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~--~i~I~TD  320 (659)
                      .+.+|+|||+. +++.+|+|+++... +....    .......++...||+.||+.|++.||+.+...+..  .|.|++|
T Consensus        73 ~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~----~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~D  148 (219)
T PRK07708         73 EILVYFDGGFDKETKLAGLGIVIYYKQGNKRY----RIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGD  148 (219)
T ss_pred             cEEEEEeeccCCCCCCcEEEEEEEECCCCEEE----EEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEec
Confidence            58999999986 47788888887532 11100    00111245556899999999999999999988754  4899999


Q ss_pred             hHHHHHHHhcCCcCCCCCcccHHHHHHHHHHHHhc-CCeeeEEEeecCCCccchhhhhhHHHHHhccCC
Q psy15450        321 SKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEW-NISVRFIWVRGHAGIAGNEAVDRLAKETARGTD  388 (659)
Q Consensus       321 Sq~ai~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~-~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~~  388 (659)
                      |+++++.+++.|.....   ....+.+.+..+..+ ...+.+.|||    ...|+.||+||+.|+....
T Consensus       149 SqlVi~qi~g~wk~~~~---~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~  210 (219)
T PRK07708        149 SQVVLNQLAGEWPCYDE---HLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTV  210 (219)
T ss_pred             cHHHHHHhCCCceeCCh---hHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCC
Confidence            99999999997655432   233444444443332 2347788987    5679999999999998643

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.33  E-value=5.9e-12  Score=137.48  Aligned_cols=129  Identities=21%  Similarity=0.173  Sum_probs=97.8

Q ss_pred             HHhhhhhcccC-CCccceEEEEeccc-eeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHH
Q psy15450        246 LQALKYASSIK-EKEAGYCKVSIRES-LWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKS  323 (659)
Q Consensus       246 l~iytDGS~~~-~g~~G~g~v~~~~~-~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~  323 (659)
                      +.||+||++.+ +|.+|+|+++...+ ....     ......++ ..||+.||+.|++.||+.+.+.+...+.|++||++
T Consensus         3 ~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~-----~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~l   76 (372)
T PRK07238          3 VVVEADGGSRGNPGPAGYGAVVWDADRGEVL-----AERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKL   76 (372)
T ss_pred             EEEEecCCCCCCCCceEEEEEEEeCCCCcEE-----EEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHH
Confidence            46899999875 57788888876532 1110     01122333 68999999999999999999988899999999999


Q ss_pred             HHHHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhccC
Q psy15450        324 CLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGT  387 (659)
Q Consensus       324 ai~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~  387 (659)
                      +++.+++.+....   +....++..+..+..+...+.+.|||+    .+|+.||.||+.|+...
T Consensus        77 vi~~i~~~~~~~~---~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~~  133 (372)
T PRK07238         77 VVEQMSGRWKVKH---PDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDAA  133 (372)
T ss_pred             HHHHhCCCCccCC---hHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHhh
Confidence            9999998654221   234555666666666678899999995    78999999999998753

>cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin

Probab=99.33  E-value=3e-12  Score=128.76  Aligned_cols=99  Identities=19%  Similarity=0.155  Sum_probs=80.1

Q ss_pred             CCCCCCccccCCCCCHHHHHHHHHHHHHHHHhcCcceeEEEEecchhcCCCCHHHHHHHHHHcCCChhhHHHHhhhcccc
Q psy15450         48 ILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVFHG  127 (659)
Q Consensus        48 ~l~~~Q~GFr~gr~st~~~l~~~~~~i~~~~~~~~~~~~v~lD~~KAFDsV~h~~L~~kL~~~Gi~~~li~~I~s~yl~~  127 (659)
                      .+++.|||||+++ |+.+++..+...     ......+++.+|+++|||+|+|+.|++.|...|.++.++.|+.+ |...
T Consensus        40 ~~~~~~~g~~~~r-s~~~~i~~i~~~-----~~~~~~~~~~~Di~~~Fdsi~~~~l~~~l~~~~~~~~~~~~i~~-~~~~  112 (226)
T cd01651          40 RFSDCSYGFRPGR-SAHDALKAIRRN-----VKGGYTWVIEGDIKGFFDNIDHDLLLKILKRRIGDKRVLRLIRK-WLKA  112 (226)
T ss_pred             ccccCCCCCCCCC-CHHHHHHHHHHH-----hcCCCeEEEEccHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHH-HHhc
Confidence            3677999999999 999998766554     34566889999999999999999999999999999999999998 4332


Q ss_pred             eEEEEEecccccCCCCCccccCCCCccccccCCCCCCCCCCcccCCCCccccccchh
Q psy15450        128 RRLVIVMSDFNNSDGEDITMSGDCPRDKRGIPPDPGKGSGNATQDDGDQYESAPEYA  184 (659)
Q Consensus       128 r~~~v~~~~~~~~~g~~~~~~s~~~~i~~GVpQ~~~~~~~~~~~~~G~~L~~~P~l~  184 (659)
                      ...                ..+.......||||             |+++  ||.|+
T Consensus       113 ~~~----------------~~~~~~~~~~Glpq-------------G~~l--Sp~L~  138 (226)
T cd01651         113 GVL----------------EDGKLVETEKGTPQ-------------GGVI--SPLLA  138 (226)
T ss_pred             eEc----------------cCCeEeCCCCCcCC-------------CccH--HHHHH
Confidence            111                12234456899999             9999  99983

RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).

>cd03487 RT_Bac_retron_II RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons

Probab=99.22  E-value=1.6e-11  Score=123.88  Aligned_cols=70  Identities=11%  Similarity=-0.024  Sum_probs=58.5

Q ss_pred             ccccCCCCCCCCccccCCCCCHHHHHHHHHHHHHHHHhcCcceeEEEEecchhcCCCCHHHHHHHHHHcCCC-hhhHHHH
Q psy15450         42 GKNDNNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKID-LKSATFC  120 (659)
Q Consensus        42 ~le~~~~l~~~Q~GFr~gr~st~~~l~~~~~~i~~~~~~~~~~~~v~lD~~KAFDsV~h~~L~~kL~~~Gi~-~~li~~I  120 (659)
                      +|..+-.+++.|+|||+|| ||.+++..          .....+++.+||++|||+|+|+.|+.+|...|.+ +.+..|+
T Consensus        26 ~l~~~~~~~~~~~g~~~gr-s~~~~~~~----------~~~~~~v~~~Di~~fFdsI~~~~L~~~l~~~~~~~~~~~~~l   94 (214)
T cd03487          26 NLLSKLPVHDAAHGFVKGR-SIITNAKP----------HCGAKYVLKLDIKDFFPSITFERVRGVFRSLGYFSPDVATIL   94 (214)
T ss_pred             HHhccCCCCcceeeecCCC-CHHHHHHH----------hcCCCEEEEeehhhhcccCCHHHHHHHHHHcCCCCHHHHHHH
Confidence            3334556889999999999 99887642          2345788999999999999999999999999999 8888888


Q ss_pred             hh
Q psy15450        121 VF  122 (659)
Q Consensus       121 ~s  122 (659)
                      ..
T Consensus        95 ~~   96 (214)
T cd03487          95 AK   96 (214)
T ss_pred             HH
Confidence            77

The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.

>cd01650 RT_nLTR_like RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT)

Probab=99.20  E-value=2e-11  Score=122.49  Aligned_cols=59  Identities=29%  Similarity=0.483  Sum_probs=55.5

Q ss_pred             CCCCCCccccCCCCCHHHHHHHHHHHHHHHHhcCcceeEEEEecchhcCCCCHHHHHHHH
Q psy15450         48 ILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVI  107 (659)
Q Consensus        48 ~l~~~Q~GFr~gr~st~~~l~~~~~~i~~~~~~~~~~~~v~lD~~KAFDsV~h~~L~~kL  107 (659)
                      .+.+.|+||++|+ |+.+++..+.+.++...+++....++++|++||||+|+|+.|+..|
T Consensus        47 ~~~~~q~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~Di~~aFdsi~~~~l~~~l  105 (220)
T cd01650          47 NILPNQFGFRPGR-STTDAILLLREVIEKAKEKKKSLVLVFLDFEKAFDSVDHEFLLKAL  105 (220)
T ss_pred             cCCcccccccCCC-hHHHHHHHHHHHHHHHHHcCCceEEEEEEHHhhcCcCCHHHHHHHh
Confidence            3458999999999 9999999999999999988999999999999999999999999999

This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.

>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B

Probab=98.98  E-value=2.6e-09  Score=91.16  Aligned_cols=86  Identities=22%  Similarity=0.281  Sum_probs=67.8

Q ss_pred             HHHHHHHHHHHHHHHchhcCCCeEEEEcChHHHHHHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCcc
Q psy15450        292 IFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIA  371 (659)
Q Consensus       292 ~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~ai~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~  371 (659)
                      +..||+.|+..||+.+...+..++.|+|||+.+++.|++......    ....+...+..+.+....+.|.|||    .+
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~----~~~~~~~~i~~~~~~~~~~~~~~i~----r~   72 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRS----ELRPLIQDIRSLLDRFWNVSVSHIP----RE   72 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---S----CCHHHHHHHHHHHCCCSCEEEEE------GG
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccc----cccccchhhhhhhccccceEEEEEC----hH
Confidence            468999999999999999999999999999999999998633332    3456666666666677889999999    88


Q ss_pred             chhhhhhHHHHHhc
Q psy15450        372 GNEAVDRLAKETAR  385 (659)
Q Consensus       372 GNE~AD~LAk~aa~  385 (659)
                      +|..||.|||.|..
T Consensus        73 ~N~~A~~LA~~a~~   86 (87)
T PF13456_consen   73 QNKVADALAKFALS   86 (87)
T ss_dssp             GSHHHHHHHHHHHH
T ss_pred             HhHHHHHHHHHHhh
Confidence            99999999999863

>PF00078 RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR000477 The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons

Probab=98.89  E-value=6.4e-11  Score=117.33  Aligned_cols=111  Identities=21%  Similarity=0.327  Sum_probs=82.1

Q ss_pred             CCCCCCCCccccCCCCCHHHHHHHHHHHHHHHHhcCcceeEEEEecchhcCCCCHHHHHHHHHHcCCChhhHHHHhhhcc
Q psy15450         46 NNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVF  125 (659)
Q Consensus        46 ~~~l~~~Q~GFr~gr~st~~~l~~~~~~i~~~~~~~~~~~~v~lD~~KAFDsV~h~~L~~kL~~~Gi~~~li~~I~s~yl  125 (659)
                      +..+++.|+||++++ ||.+        .+...+.+....++++|+++|||+|+|+.|...|..++.+..++.||.+ ++
T Consensus        35 ~~~~~~~~~~~~~~~-~~~~--------~~~~~~~~~~~~~~~~Di~~~f~sI~~~~l~~~l~~~~~~~~~~~~i~~-~~  104 (214)
T PF00078_consen   35 EPIFSPSQFGFRPGR-SCHD--------IKKLNRFKGYLYFLKLDISKAFDSIPHHRLLRKLKRFGVPKKLIRLIQN-LL  104 (214)
T ss_dssp             ---HHHTTSSCSHGC-CCHH--------HHHHHC-CGSSEEEEEECCCCGGGSBBHTTTGGGGEEEEECCSCHHHHH-HH
T ss_pred             cccCCCCCCCCcccc-cccc--------cccccccccccccceeccccccccceeeecccccccccccccccccccc-cc
Confidence            466888999999999 8887        3444566777999999999999999999999999999999999999999 55


Q ss_pred             cceEEEEEecccccCCCCCccccCCCCccccccCCCCCCCCCCcccCCCCccccccchhhhhhh-hhhhcc
Q psy15450        126 HGRRLVIVMSDFNNSDGEDITMSGDCPRDKRGIPPDPGKGSGNATQDDGDQYESAPEYAKQNCF-LNEVKD  195 (659)
Q Consensus       126 ~~r~~~v~~~~~~~~~g~~~~~~s~~~~i~~GVpQ~~~~~~~~~~~~~G~~L~~~P~l~~~~~~-ln~I~d  195 (659)
                      ..+...+.      .+    +.. .......||||             |+++  ||.++   .. +..+..
T Consensus       105 ~~~~~~~~------~~----~~~-~~~~~~~glpq-------------G~~~--S~~l~---~~~l~~l~~  146 (214)
T PF00078_consen  105 SDRTAKVY------LD----GDL-SPYFQKRGLPQ-------------GSPL--SPLLF---NIYLDDLDR  146 (214)
T ss_dssp             HHHHH-EE------CG----CSS-SEEEEESBS-T-------------TSTC--HHHHH---HHHHHHHHH
T ss_pred             cccccccc------cc----ccc-ccccccccccc-------------cccc--cchhh---ccccccccc
Confidence            55544441      11    112 34456799999             9999  99983   33 555443

The enzyme catalysing polymerisation is an RNA-directed DNA-polymerase, or reverse trancriptase (RT) (2.7.7.49 from EC). Reverse transcriptase occurs in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Retroviral reverse transcriptase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases and whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases [].; GO: 0003723 RNA binding, 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 1MU2_B 3RWE_C 3DU6_B 3DU5_A 3KYL_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B ....

>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs)

Probab=98.02  E-value=2.4e-05  Score=83.54  Aligned_cols=85  Identities=19%  Similarity=0.282  Sum_probs=65.6

Q ss_pred             HHHHHHHHhcCcceeEEEEecchhcCCCCHHHHHHHHHHcCCChhhHHHHhhhcccceEEEEEecccccCCCCCccccCC
Q psy15450         71 KIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVFHGRRLVIVMSDFNNSDGEDITMSGD  150 (659)
Q Consensus        71 ~~~i~~~~~~~~~~~~v~lD~~KAFDsV~h~~L~~kL~~~Gi~~~li~~I~s~yl~~r~~~v~~~~~~~~~g~~~~~~s~  150 (659)
                      ..+++..  .+....++=.||++=||+|+|+.|+..|..+|++.+++.+|+. |+..--...       -+|..    +.
T Consensus        11 e~~i~~~--l~G~~~vvd~Dik~fFdsIpH~~Lm~vL~~~~~~~~wL~li~r-~L~APl~~~-------~dg~~----~~   76 (346)
T cd01709          11 EILINTA--LYGEVTVVQSDFKWFGPSLPHSTILAVLKFFGVPEKWLDFFKK-FLEAPLRFV-------ADGPD----AP   76 (346)
T ss_pred             HHHHHHh--hcCCEEEEEeehHhhCCCCCHHHHHHHHHHhCCCHHHHHHHHH-HHhCceeec-------CCCCc----cc
Confidence            3444443  3567899999999999999999999999999999999999999 887644432       11111    22


Q ss_pred             CCccccccCCCCCCCCCCcccCCCCccccccchh
Q psy15450        151 CPRDKRGIPPDPGKGSGNATQDDGDQYESAPEYA  184 (659)
Q Consensus       151 ~~~i~~GVpQ~~~~~~~~~~~~~G~~L~~~P~l~  184 (659)
                      ...-++|+||             |.++  ||.|.
T Consensus        77 ~r~r~rGtPq-------------Ggvi--SplLa   95 (346)
T cd01709          77 PRIRKRGTPM-------------SHAL--SDVFG   95 (346)
T ss_pred             ccccCCccCC-------------Cchh--hHHHH
Confidence            3344699999             9999  99995

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.

>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons

Probab=97.90  E-value=2.9e-06  Score=81.65  Aligned_cols=65  Identities=11%  Similarity=0.011  Sum_probs=49.2

Q ss_pred             EecchhcCCCCHHHHHHHHHHcCCChhhHHHHhhhcccceEEEEEecccccCCCCCccccCCCCccccccCCCCCCCCCC
Q psy15450         89 IDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVFHGRRLVIVMSDFNNSDGEDITMSGDCPRDKRGIPPDPGKGSGN  168 (659)
Q Consensus        89 lD~~KAFDsV~h~~L~~kL~~~Gi~~~li~~I~s~yl~~r~~~v~~~~~~~~~g~~~~~~s~~~~i~~GVpQ~~~~~~~~  168 (659)
                      +||+|+||+|+|+.|..+|...+.+...+.+++. +....   .            ....+.......||||        
T Consensus         1 lDi~~fF~sI~~~~l~~~l~~~~~~~~~~~~~~~-~~~~~---~------------~~~~~~~~~~~~Glpq--------   56 (158)
T cd01646           1 LDISNFYDSIYTHSLPWALHGKIKAKQLLKLLRL-LGNLL---D------------LLLLSSQYGQTNGLPI--------   56 (158)
T ss_pred             CchhhccCcchHHHHHHHHHhhhhhHhhhhhHHH-HHHHH---H------------HHHHhccCCCCceEcc--------
Confidence            6999999999999999999999999999988743 22110   0            0112223445789999        


Q ss_pred             cccCCCCccccccchh
Q psy15450        169 ATQDDGDQYESAPEYA  184 (659)
Q Consensus       169 ~~~~~G~~L~~~P~l~  184 (659)
                           |+++  ||.|.
T Consensus        57 -----G~~l--S~~L~   65 (158)
T cd01646          57 -----GPLT--SRFLA   65 (158)
T ss_pred             -----Ccch--HHHHH
Confidence                 9999  99994

The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.

>KOG4768|consensus

Probab=97.65  E-value=5e-05  Score=84.88  Aligned_cols=114  Identities=17%  Similarity=0.141  Sum_probs=79.3

Q ss_pred             HHHHhhhcccccccccccCCCCCCCCccccCCCCCHHHHHHHHHHHHHHHHhcCcceeEEEEecchhcCCCCHHHHHHHH
Q psy15450         28 QREVNRSGESLNTAGKNDNNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVI  107 (659)
Q Consensus        28 ~~~~~~~~~~l~~~~le~~~~l~~~Q~GFr~gr~st~~~l~~~~~~i~~~~~~~~~~~~v~lD~~KAFDsV~h~~L~~kL  107 (659)
                      -.|+.|.+-.     .+-++..+-.-+|||||+ ||.++++.....+.      ...+.+-.|+.|-||+|+|+.|+..|
T Consensus       316 vQe~mRm~Le-----iiy~~~fst~shgfRpgl-Sc~tAi~~~~n~f~------gcnw~ie~DLkkcfdtIphd~LI~eL  383 (796)
T KOG4768|consen  316 VQECMRMGLE-----IIYGGEFSTVSHGFRPGL-SCKTAILKTHNLFR------GCNWFIEVDLKKCFDTIPHDELIIEL  383 (796)
T ss_pred             HHHHHHHHHH-----HHhcceeeeeecccCCCc-hhhHHHHHHHHHhh------ccceEEechHHHHhccccHHHHHHHH
Confidence            3466665422     223566777889999999 99999988776554      33566778999999999999999999


Q ss_pred             HHcCCChhhHHHHhhhcccceEEEEEecccccCCCCCccccCCCCccccccCCCCCCCCCCcccCCCCccccccchh
Q psy15450        108 QMYKIDLKSATFCVFCVFHGRRLVIVMSDFNNSDGEDITMSGDCPRDKRGIPPDPGKGSGNATQDDGDQYESAPEYA  184 (659)
Q Consensus       108 ~~~Gi~~~li~~I~s~yl~~r~~~v~~~~~~~~~g~~~~~~s~~~~i~~GVpQ~~~~~~~~~~~~~G~~L~~~P~l~  184 (659)
                      ++.=-+..+++++.. .+.+-+.-.        +    +....+   --|.||             |++.  +|.|.
T Consensus       384 ~~rIkdk~fidL~~k-ll~AGy~te--------n----~ry~~~---~lGtpq-------------gsvv--spil~  429 (796)
T KOG4768|consen  384 QKRIKDKGFIDLNYK-LLRAGYTTE--------N----ARYHVE---FLGTPQ-------------GSVV--SPILC  429 (796)
T ss_pred             HHHHhhhhHHHHHHH-HHhcCcccc--------c----cceecc---cccccc-------------cccC--CchhH
Confidence            887555666666655 333222211        1    111122   379999             9999  99984

>cd01648 TERT TERT: Telomerase reverse transcriptase (TERT)

Probab=96.39  E-value=0.00095  Score=61.30  Aligned_cols=12  Identities=42%  Similarity=0.822  Sum_probs=11.1

Q ss_pred             EecchhcCCCCH
Q psy15450         89 IDLLKAYDNCPH  100 (659)
Q Consensus        89 lD~~KAFDsV~h  100 (659)
                      .|+++|||+|+|
T Consensus         1 ~d~~~~~~~~~~   12 (119)
T cd01648           1 TDIKKCYDSIPQ   12 (119)
T ss_pred             CChHHhccchhh
Confidence            389999999999

Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at

>PF13966 zf-RVT: zinc-binding in reverse transcriptase

Probab=94.79  E-value=0.017  Score=49.90  Aligned_cols=42  Identities=24%  Similarity=0.445  Sum_probs=32.8

Q ss_pred             cccCCcchhccccccCCCCCCCccCCC-cccCcccccccCcCc
Q psy15450        456 LRSNHAICQAYLHKINIAPTNLCQECL-EREDMAHIILCCPKY  497 (659)
Q Consensus       456 lrTGHg~~~~yL~r~~~~~s~~C~cc~-~~et~~Hil~~Cp~~  497 (659)
                      +..+--..++-|.+.+...++.|..|+ +.||++|+|+.||.-
T Consensus        40 ~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a   82 (86)
T PF13966_consen   40 ALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFA   82 (86)
T ss_pred             eccccchhhhhhhccCCccCCccccCCCccccccceeccCcCc
Confidence            333444556678888888889999776 599999999999974

>COG3344 Retron-type reverse transcriptase [DNA replication, recombination, and repair]

Probab=94.70  E-value=0.067  Score=57.63  Aligned_cols=104  Identities=16%  Similarity=0.151  Sum_probs=69.8

Q ss_pred             CCCCCCCCccccCCCCCHHHHHHHHHHHHHHHHhcCcceeEEEEecchhcCCCCHHHHHHHHHHcCCChhhHH-HHhhhc
Q psy15450         46 NNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSAT-FCVFCV  124 (659)
Q Consensus        46 ~~~l~~~Q~GFr~gr~st~~~l~~~~~~i~~~~~~~~~~~~v~lD~~KAFDsV~h~~L~~kL~~~Gi~~~li~-~I~s~y  124 (659)
                      ....++.=+||++++ ++.+.+.............. ...++..|+.+=||+++|..++..+... +.+..+. ++...+
T Consensus       145 ~~~f~~~s~Gf~~~~-~~~~a~~~~~~~~~~~~~~~-~~~~~~~di~~~fd~~~h~~ll~~~~~~-i~~~~~~~~~~r~~  221 (328)
T COG3344         145 ENIFSPLSYGFRPGP-SASNAIAYAFDLPQGKICSP-NGWVYDRDIKKCFDSINHKLLLYALDVT-ISDKLVLLLLGRIL  221 (328)
T ss_pred             HhccccCCCCCCCCh-hHHHHHHHHHhhhccCCCCC-ceEEEeehHHHHhcccCHHHHHHHhHhh-hcchHHHHHHHHHH
Confidence            355677889999999 88888776654444322211 2477889999999999999999999985 5433333 443323


Q ss_pred             ccceEEEEEecccccCCCCCccccCCCCccccccCCCCCCCCCCcccCCCCccccccch
Q psy15450        125 FHGRRLVIVMSDFNNSDGEDITMSGDCPRDKRGIPPDPGKGSGNATQDDGDQYESAPEY  183 (659)
Q Consensus       125 l~~r~~~v~~~~~~~~~g~~~~~~s~~~~i~~GVpQ~~~~~~~~~~~~~G~~L~~~P~l  183 (659)
                      ....-...                ........|+||             |.++  +|.+
T Consensus       222 ~~~~~~~~----------------~~~~~~~~~~~q-------------~~~v--s~~l  249 (328)
T COG3344         222 IAGYKTKF----------------NLKKSKEKGTPQ-------------GGLV--SPIL  249 (328)
T ss_pred             Hcccceee----------------cccccccccCCC-------------CCcc--Cchh
Confidence            33322222                112223699999             9999  9998

>KOG1005|consensus

Probab=93.25  E-value=0.22  Score=58.77  Aligned_cols=27  Identities=22%  Similarity=0.452  Sum_probs=25.0

Q ss_pred             CcceeEEEEecchhcCCCCHHHHHHHH
Q psy15450         81 YKNLSVAWIDLLKAYDNCPHEWMVKVI  107 (659)
Q Consensus        81 ~~~~~~v~lD~~KAFDsV~h~~L~~kL  107 (659)
                      ++.++.+-+|++||||+|+|+.|+..+
T Consensus       516 ~~~LYfvk~DV~~cfDtIpqd~l~~II  542 (888)
T KOG1005|consen  516 NQKLYFVKADVSKCFDTIPQDELISII  542 (888)
T ss_pred             cCceEEEEEEhhhhhccCchHHHHHHH
Confidence            347999999999999999999999988

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	659
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	3e-13
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	5e-12
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	1e-11
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	1e-08
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	2e-07
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	1e-06
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	4e-06
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	6e-06

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A Length = 147

 Score = 66.6 bits (163), Expect = 3e-13
 Identities = 19/96 (19%), Positives = 29/96 (30%), Gaps = 7/96 (7%)

Query: 293 FTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALSHL 352
              E  A L A+K  S     ++ I+ D            K+    +     +       
Sbjct: 51  VAGEIAAALYAVKKASQ-LGVKIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMNQYRG- 108

Query: 353 QEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTD 388
                   F  V+ H+G   N+ VD  AK      D
Sbjct: 109 -----IYSFEKVKAHSGNEFNDYVDMKAKSALGIRD 139

>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A Length = 165

 Score = 63.7 bits (155), Expect = 5e-12
 Identities = 25/102 (24%), Positives = 36/102 (35%), Gaps = 11/102 (10%)

Query: 295 AEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQE 354
           AE  A+ QALK     +  ++ + TDS+         S+  G       +I   L  L  
Sbjct: 66  AELIALTQALKM---AEGKKLNVYTDSRYAFATAHVHSE--GREIKNKNEILALLKALFL 120

Query: 355 WNISVRFIWVRGH-----AGIAGNEAVDRLAKETARGTDALN 391
               +  I   GH     A   GN   D+ A+E A       
Sbjct: 121 -PKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLET 161

>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A* Length = 154

 Score = 62.2 bits (152), Expect = 1e-11
 Identities = 27/102 (26%), Positives = 50/102 (49%), Gaps = 15/102 (14%)

Query: 295 AEAFAILQALKYVSSIKENEVIIITDS---KSCLE------KLKNTSKSNGNPSHLIL-- 343
           AE  A  +A++   +   N++++ T+S    + +       K      S G     ++  
Sbjct: 53  AEIHAACKAIEQAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKE---VINK 109

Query: 344 DIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETAR 385
           + F AL  L +  + ++++ V GH+G  GNE  DRLA+E A+
Sbjct: 110 EDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREGAK 150

>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A Length = 150

 Score = 53.3 bits (129), Expect = 1e-08
 Identities = 29/103 (28%), Positives = 41/103 (39%), Gaps = 20/103 (19%)

Query: 295 AEAFAILQALKYVSSIKENEVIIITDSK-------SCLE--KLKNTSKSNGNP---SHLI 342
            E  AI  AL+        EV I+TDS+         +   K +    ++  P     L+
Sbjct: 52  TELQAIYLALQDSGL----EVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLV 107

Query: 343 LDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETAR 385
             I + L   ++    V   WV  H GI GNE VD+L     R
Sbjct: 108 NQIIEQLIKKEK----VYLAWVPAHKGIGGNEQVDKLVSAGIR 146

>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ... Length = 155

 Score = 49.8 bits (120), Expect = 2e-07
 Identities = 28/104 (26%), Positives = 47/104 (45%), Gaps = 23/104 (22%)

Query: 299 AILQALKYVSSIKEN-EVIIITDS---KSCLEKLKNTSKSNG----------NPSHLILD 344
           A + AL+   ++KE+ EVI+ TDS   +  + +  +  K  G          N      D
Sbjct: 51  AAIVALE---ALKEHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNV-----D 102

Query: 345 IFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTD 388
           +++ L      +  +++ WV+GHAG   NE  D LA+  A    
Sbjct: 103 LWQRLDAALGQH-QIKWEWVKGHAGHPENERADELARAAAMNPT 145

>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A Length = 158

 Score = 47.9 bits (115), Expect = 1e-06
 Identities = 27/106 (25%), Positives = 47/106 (44%), Gaps = 23/106 (21%)

Query: 299 AILQALKYVSSIKEN-EVIIITDSK---SCLEKLKNTSKSNG----------NPSHLILD 344
           A + AL+   ++KE  ++I+ +DS+     +    +  K  G          N      D
Sbjct: 53  APIVALE---ALKEPCKIILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNV-----D 104

Query: 345 IFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTDAL 390
           ++K L    + +  + + WV+GHAG A NE  D+LA+  A      
Sbjct: 105 LWKRLDKAAQLH-QIDWRWVKGHAGHAENERCDQLARAAAEANPTQ 149

>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A Length = 166

 Score = 46.4 bits (111), Expect = 4e-06
 Identities = 15/36 (41%), Positives = 19/36 (52%)

Query: 359 VRFIWVRGHAGIAGNEAVDRLAKETARGTDALNPYP 394
           VRF +V+GH G   NE VDR A+  A+        P
Sbjct: 121 VRFHFVKGHTGHPENERVDREARRQAQSQAKTPCPP 156

>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum} Length = 146

 Score = 45.6 bits (109), Expect = 6e-06
 Identities = 9/27 (33%), Positives = 13/27 (48%)

Query: 359 VRFIWVRGHAGIAGNEAVDRLAKETAR 385
           V F  V+GH+    N   D LA+   +
Sbjct: 117 VTFHKVKGHSDNPYNSRADELARLAIK 143

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	659
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.87
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.86
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.85
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.84
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.83
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.83
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.83
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.83
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.76
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.72
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.72
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.71
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.66
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.65
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.4
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.28
3kyl_A	596	Telomerase reverse transcriptase; reverse transcri	97.61

>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A*

Probab=99.87  E-value=2e-22  Score=191.49  Aligned_cols=135  Identities=23%  Similarity=0.277  Sum_probs=106.1

Q ss_pred             HHHHHhhhhhcccCCCc----cceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEE
Q psy15450        243 FAILQALKYASSIKEKE----AGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIII  318 (659)
Q Consensus       243 ~g~l~iytDGS~~~~g~----~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~  318 (659)
                      .+.+.+|||||+.+++.    +|+|+++...       ... .....+.+.+||++|||.|++.||+.+...+..++.|+
T Consensus         5 ~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~-------~~~-~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~   76 (154)
T 2qkb_A            5 GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPG-------HPL-NVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLY   76 (154)
T ss_dssp             TTEEEEEEEEEEETTTSSSCEEEEEEECSTT-------CTT-CEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCeEEEEEccCcCCCCCCCCcEEEEEEEECC-------Cce-eEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEE
Confidence            35678999999986653    4555554321       111 12334555789999999999999999988778999999


Q ss_pred             cChHHHHHHHhcC---------CcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhccC
Q psy15450        319 TDSKSCLEKLKNT---------SKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGT  387 (659)
Q Consensus       319 TDSq~ai~~I~~~---------~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~  387 (659)
                      |||+++++.|+.|         ++++|.++ .+.++++.+..+.. +..|.|.|||||+|++|||.||+||++|+..+
T Consensus        77 tDS~~vi~~i~~~~~~w~~~~w~~~~~~~~-~n~~l~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           77 TNSMFTINGITNWVQGWKKNGWKTSAGKEV-INKEDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             ESCHHHHHHHHTHHHHHHTTTSBCTTSSBC-TTHHHHHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             ECcHHHHhhhhhhHHHHHhccccccCCCcc-ccHHHHHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            9999999999974         34556665 46788888888765 57799999999999999999999999998754

>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} SCOP: c.55.3.1 PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A

Probab=99.86  E-value=2.7e-22  Score=190.17  Aligned_cols=130  Identities=24%  Similarity=0.198  Sum_probs=96.6

Q ss_pred             hhHHHHHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEc
Q psy15450        241 EAFAILQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIIT  319 (659)
Q Consensus       241 e~~g~l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~T  319 (659)
                      +..+.+.+|+|||+.+ +|..|+|++.......        .  .. .+.+||++||+.|++.||+.+    ..++.|+|
T Consensus         8 P~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~--------~--~~-~~~~Tnn~aEl~A~i~AL~~~----~~~v~i~t   72 (150)
T 3qio_A            8 PIVGAETFYVDGAANRETKLGKAGYVTNRGRQK--------V--VT-LTDTTNQKTELQAIYLALQDS----GLEVNIVT   72 (150)
T ss_dssp             CCTTCEEEEEEEEECTTTCCEEEEEEETTSCEE--------E--EE-ESSCCHHHHHHHHHHHHHHHS----CSEEEEEE
T ss_pred             CCCCCEEEEEccCCCCCCCCeEEEEEEEcCCEE--------E--Ee-CCCCCHHHHHHHHHHHHHHhC----CCcEEEEe
Confidence            3456789999999976 4555666555432110        1  11 247899999999999999986    48999999


Q ss_pred             ChHHHHHHHhcC---------CcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhcc
Q psy15450        320 DSKSCLEKLKNT---------SKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARG  386 (659)
Q Consensus       320 DSq~ai~~I~~~---------~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~  386 (659)
                      ||+|+++.|+.|         ++++|+++ .+.++++.+..+..+...|.|.|||||+|++|||+||+||++|++.
T Consensus        73 DS~~v~~~i~~w~~~W~~~gw~~~~g~~v-~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           73 DSQYALGIITQWIHNWKKRGWKTADKKPV-KNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             SCHHHHHHHHHHHHHHCC-------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             CcHHHHHHHHHHHHHHhhcCcCcCcCccc-ccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            999999999985         33555565 4678888776655568899999999999999999999999999875

>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum}

Probab=99.85  E-value=9.1e-22  Score=185.19  Aligned_cols=129  Identities=16%  Similarity=0.169  Sum_probs=98.1

Q ss_pred             HHhhhhhcccCC-CccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHH
Q psy15450        246 LQALKYASSIKE-KEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSC  324 (659)
Q Consensus       246 l~iytDGS~~~~-g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~a  324 (659)
                      +.+|||||+..+ |..|+|+++...+..       ......+ +.+||++|||.|++.||+.+.+  ..++.|+|||+|+
T Consensus         5 i~iytDGs~~~n~g~~g~G~v~~~~~~~-------~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~v   74 (146)
T 3h08_A            5 ITIYTDGAASGNPGKGGWGALLMYGSSR-------KEISGYD-PATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYL   74 (146)
T ss_dssp             EEEEEEEEESSTTEEEEEEEEEEETTEE-------EEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHH
T ss_pred             EEEEEecCCCCCCCceEEEEEEEECCee-------EEeecCC-CCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHH
Confidence            579999999864 566777766543311       1112222 3689999999999999999976  5899999999999


Q ss_pred             HHHHhc-C---------CcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhcc
Q psy15450        325 LEKLKN-T---------SKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARG  386 (659)
Q Consensus       325 i~~I~~-~---------~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~  386 (659)
                      ++.|+. |         ++++|.++ .+.++++.+..+.. ...|.|.|||||+|+++||.||+||++|+..
T Consensus        75 i~~i~~~w~~~W~~~~w~~~~~~~v-~n~~l~~~~~~~~~-~~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A           75 VNAMNEGWLKRWVKNGWKTAAKKPV-ENIDLWQEILKLTT-LHRVTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             HHHHHSSHHHHHHHTTCC----CCC-TTHHHHHHHHHHHH-HSEEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCccCCCCCc-CCHHHHHHHHHHHh-hCceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence            999987 3         34556665 46788888887765 4679999999999999999999999999874

>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A 4e89_A

Probab=99.84  E-value=2.2e-21  Score=186.64  Aligned_cols=130  Identities=22%  Similarity=0.120  Sum_probs=102.6

Q ss_pred             HHHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHH
Q psy15450        245 ILQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKS  323 (659)
Q Consensus       245 ~l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~  323 (659)
                      .+.+|+|||+.+ +|..|+|+++...+..      .. .. .....+||++||+.|++.||+.+.   ..++.|||||+|
T Consensus        23 ~i~iytDGs~~~npG~~g~G~vi~~~~~~------~~-~~-~~~~~~Tnn~aEl~Ai~~AL~~~~---~~~v~I~tDS~~   91 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQRRAGAAVTTETEV------IW-AR-ALPAGTSAQRAELIALTQALKMAE---GKKLNVYTDSRY   91 (165)
T ss_dssp             SEEEEEEEEEEEETTEEEEEEEEECSSCE------EE-EE-EECTTCCHHHHHHHHHHHHHHHTB---TSEEEEEECCHH
T ss_pred             CEEEEEEcccCCCCCceEEEEEEEECCEE------EE-Ee-cCCCCCcHHHHHHHHHHHHHHHcc---CceEEEEEchHH
Confidence            478999999985 6777777766543311      11 11 345578999999999999999982   689999999999


Q ss_pred             HHHHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCC-----ccchhhhhhHHHHHhccCC
Q psy15450        324 CLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAG-----IAGNEAVDRLAKETARGTD  388 (659)
Q Consensus       324 ai~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~g-----i~GNE~AD~LAk~aa~~~~  388 (659)
                      +++.|  |..++|+++ .+.++|+.+.....++..|.|.|||||+|     ++|||+||+||++|+....
T Consensus        92 vi~~i--w~~~~g~~v-~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~~  158 (165)
T 3p1g_A           92 AFATA--HVHSEGREI-KNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAV  158 (165)
T ss_dssp             HHHHH--HSCCCSCCC-SSHHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhh--hcccCCCcc-cCHHHHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcCC
Confidence            99999  556777777 46787776644334678999999999999     9999999999999998643

>2lsn_A Reverse transcriptase; RNAse H, viral protein; NMR {Simian foamy virus}

Probab=99.83  E-value=3.5e-21  Score=185.20  Aligned_cols=135  Identities=21%  Similarity=0.121  Sum_probs=100.5

Q ss_pred             HHhhhhhcccCC-Cc-----cceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEc
Q psy15450        246 LQALKYASSIKE-KE-----AGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIIT  319 (659)
Q Consensus       246 l~iytDGS~~~~-g~-----~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~T  319 (659)
                      +.+||||||.+| |+     +|+|+++...+.    ............+..++++||+.|+..||+.+.+. +.+|.|+|
T Consensus         8 vviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~----~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~-~~~v~I~T   82 (165)
T 2lsn_A            8 GVFYTDGSAIKSPDPTKSNNAGMGIVHATYKP----EYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKI-PGPVLVIT   82 (165)
T ss_dssp             EEEEEEEEEEECSSCTTCEEEEEEEEEECCSS----SCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHS-SSCEEEEE
T ss_pred             EEEEEcCCCCCCCCCCCCCcEEEEEEEEECCC----ccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcC-CCeEEEEe
Confidence            568999999864 44     566666542221    00000011112346789999999999999887654 36799999


Q ss_pred             ChHHHHHHHhcC---------CcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCC------ccchhhhhhHHHHHh
Q psy15450        320 DSKSCLEKLKNT---------SKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAG------IAGNEAVDRLAKETA  384 (659)
Q Consensus       320 DSq~ai~~I~~~---------~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~g------i~GNE~AD~LAk~aa  384 (659)
                      ||+|++++|+.|         ++++|+|+ .+.++|+.+.++......|.|.|||||+|      .+|||+||+||++|+
T Consensus        83 DS~Yvi~~it~w~~~Wk~ngw~~~~~~pV-kN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA  161 (165)
T 2lsn_A           83 DSFYVAESANKELPYWKSNGFVNNKKKPL-KHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGS  161 (165)
T ss_dssp             SCHHHHHHHHTHHHHHHHTTSCSCSSSCC-SSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHhhhhhhhhhheeccccccCCCcc-cCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhh
Confidence            999999999864         56677777 47899999888766678899999999999      468999999999998


Q ss_pred             cc
Q psy15450        385 RG  386 (659)
Q Consensus       385 ~~  386 (659)
                      ..
T Consensus       162 ~~  163 (165)
T 2lsn_A          162 YV  163 (165)
T ss_dssp             HH
T ss_pred             hh
Confidence            64

>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ...

Probab=99.83  E-value=3.9e-21  Score=183.02  Aligned_cols=131  Identities=22%  Similarity=0.296  Sum_probs=103.0

Q ss_pred             HHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHH
Q psy15450        246 LQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSC  324 (659)
Q Consensus       246 l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~a  324 (659)
                      +.+|||||+.+ +|..|+|+++...+...       .....+ +.+||++||+.|++.||+.+..  ..++.|+|||+++
T Consensus         5 ~~iytDGs~~~n~~~~G~G~v~~~~~~~~-------~~~~~~-~~~tn~~aEl~A~~~aL~~~~~--~~~v~I~tDS~~v   74 (155)
T 1jl1_A            5 VEIFTAGSALGNPGPGGYGAILRYRGREK-------TFSAGY-TRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYV   74 (155)
T ss_dssp             EEEEEEEEESSTTEEEEEEEEEEETTEEE-------EEEEEE-EEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHH
T ss_pred             EEEEEccccCCCCCceEEEEEEEECCeEE-------EEecCC-CCCcHHHHHHHHHHHHHHHhCc--CCcEEEEeCHHHH
Confidence            56899999986 45667777765433111       111122 3679999999999999999976  4899999999999


Q ss_pred             HHHHhcC---------CcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhccCC
Q psy15450        325 LEKLKNT---------SKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTD  388 (659)
Q Consensus       325 i~~I~~~---------~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~~  388 (659)
                      ++.|+.|         .+++|.++ .+.++++.+..+.. ...|.|.|||||+|++|||.||+||++|+..+.
T Consensus        75 i~~i~~w~~~W~~n~~~~~~g~~v-~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~  145 (155)
T 1jl1_A           75 RQGITQWIHNWKKRGWKTADKKPV-KNVDLWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAAAMNPT  145 (155)
T ss_dssp             HHHHHTTHHHHHHTTTBCTTSCBC-TTHHHHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHhhcccccccCCcc-CCHHHHHHHHHHHc-cCceEEEEcCCCCCCHHHHHHHHHHHHHHhccc
Confidence            9999973         44556666 46788888888765 578999999999999999999999999998754

>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A

Probab=99.83  E-value=5.2e-21  Score=182.76  Aligned_cols=129  Identities=24%  Similarity=0.310  Sum_probs=101.6

Q ss_pred             HHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHH
Q psy15450        246 LQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSC  324 (659)
Q Consensus       246 l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~a  324 (659)
                      +.+|||||+.+ +|..|+|+++...+...       .....+ +.+||++|||.|++.||+.+..  ..++.|+|||+++
T Consensus         7 i~iytDGs~~~n~g~~G~G~v~~~~~~~~-------~~~~~~-~~~tn~~aEl~A~~~AL~~~~~--~~~v~I~tDS~~v   76 (158)
T 2e4l_A            7 IHIFTDGSCLGNPGPGGYGIVMNYKGHTK-------EMSDGF-SLTTNNRMELLAPIVALEALKE--PCKIILTSDSQYM   76 (158)
T ss_dssp             EEEEEEEEESSSSEEEEEEEEEEETTEEE-------EEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEECCHHH
T ss_pred             EEEEEcccccCCCCcEEEEEEEEECCEEE-------EEecCc-CCCccHHHHHHHHHHHHHHhcc--CCeEEEEeCHHHH
Confidence            67999999985 45667777765433111       111122 2589999999999999999865  3899999999999


Q ss_pred             HHHHhc---------CCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhcc
Q psy15450        325 LEKLKN---------TSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARG  386 (659)
Q Consensus       325 i~~I~~---------~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~  386 (659)
                      ++.|+.         |.+++|.++ .+.++++.+..+.. ...|.|.|||||+|+++||.||+||++|+..
T Consensus        77 i~~i~~w~~~W~~n~~~~~~g~~v-~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A           77 RQGIMTWIHGWKKKGWMTSNRTPV-KNVDLWKRLDKAAQ-LHQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             HHHHHTHHHHHHHTTTBCTTSSBC-TTHHHHHHHHHHHT-TSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHccccccCCCcc-cCHHHHHHHHHHHc-cCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            999998         344556666 46788888888765 4799999999999999999999999999987

>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A

Probab=99.83  E-value=2.8e-21  Score=186.15  Aligned_cols=135  Identities=23%  Similarity=0.213  Sum_probs=104.3

Q ss_pred             hHHHHHhhhhhcccCC-CccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcC
Q psy15450        242 AFAILQALKYASSIKE-KEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITD  320 (659)
Q Consensus       242 ~~g~l~iytDGS~~~~-g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TD  320 (659)
                      +-..+.+|||||+.++ |..|+|+++...+..      .. ..... ..+||++|||.|++.||+.+..  ..+|.|+||
T Consensus         5 ~m~~i~iytDGs~~~n~g~~G~G~v~~~~~~~------~~-~~~~~-~~~Tnn~aEl~Ai~~AL~~~~~--~~~v~I~tD   74 (166)
T 1ril_A            5 PRKRVALFTDGACLGNPGPGGWAALLRFHAHE------KL-LSGGE-ACTTNNRMELKAAIEGLKALKE--PCEVDLYTD   74 (166)
T ss_dssp             -CCCCCEEEEEEESSTTEEEEEEEEECBTTBC------CE-ECCEE-EEECHHHHHHHHHHHHHHSCCS--CCEEEEECC
T ss_pred             CCccEEEEECccccCCCCCEEEEEEEEECCEE------EE-EecCC-CCCcHHHHHHHHHHHHHHHhcc--CCeEEEEeC
Confidence            3346789999999864 566666666432211      11 11111 3689999999999999999866  369999999


Q ss_pred             hHHHHHHHhc----------CCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhccCC
Q psy15450        321 SKSCLEKLKN----------TSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTD  388 (659)
Q Consensus       321 Sq~ai~~I~~----------~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~~  388 (659)
                      |+|+++.|+.          |++++|.++ .+.++++.+..+.. ...|.|.|||||+|+++|+.||+||++|+....
T Consensus        75 S~~vi~~i~~~w~~~W~~~~w~~~~g~~v-~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~  150 (166)
T 1ril_A           75 SHYLKKAFTEGWLEGWRKRGWRTAEGKPV-KNRDLWEALLLAMA-PHRVRFHFVKGHTGHPENERVDREARRQAQSQA  150 (166)
T ss_dssp             CHHHHHHHHSSHHHHHHHTTSBCTTSSBC-TTHHHHHHHHHHHT-TSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             hHHHHHHHhhhHHHHHHhcccccccCCcc-CcHHHHHHHHHHHh-cCeEEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence            9999999998          455666666 46788888888765 469999999999999999999999999998754

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A

Probab=99.76  E-value=6.7e-20  Score=173.07  Aligned_cols=132  Identities=17%  Similarity=0.104  Sum_probs=94.4

Q ss_pred             HHHHhhhhhcccCCCccceEEEEeccceeeeCCCccccc-cccCC--CCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcC
Q psy15450        244 AILQALKYASSIKEKEAGYCKVSIRESLWIFDTQNKNSG-TFKLK--NFATIFTAEAFAILQALKYVSSIKENEVIIITD  320 (659)
Q Consensus       244 g~l~iytDGS~~~~g~~G~g~v~~~~~~~~~~~~~~~~~-~~~l~--~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TD  320 (659)
                      +.+.+|||||+.+ |.+|+|+++...+....    . .. ....+  ..+||++||+.|++.||+.+.+.+. +|.|+||
T Consensus         5 ~~i~iytDGs~~~-g~~G~G~vi~~~g~~~~----~-~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tD   77 (147)
T 2kq2_A            5 TEYDVYTDGSYVN-GQYAWAYAFVKDGKVHY----E-DADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHD   77 (147)
T ss_dssp             SCCEEECCCCCBT-TBCEEEEEEEETTEEEE----E-EEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSC
T ss_pred             CeEEEEECCCCCC-CCcEEEEEEEECCEEEE----E-EeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEEC
Confidence            3467999999988 88899888764332110    0 00 11111  1469999999999999998877666 9999999


Q ss_pred             hHHHHHHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhccCC
Q psy15450        321 SKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTD  388 (659)
Q Consensus       321 Sq~ai~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~~  388 (659)
                      |+.+.+.+.+.|..+.   .....+.+.+.++..   .|.|.|||||+|++|||.||+||++|+....
T Consensus        78 S~~i~~w~~~~w~~~~---~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~  139 (147)
T 2kq2_A           78 YAGIAFWATGEWKAKN---EFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALGIRD  139 (147)
T ss_dssp             CSTHHHHTTSSSSCCH---HHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHTCCC
T ss_pred             cHHHHHHHhCCCccCC---cchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHhccc
Confidence            9988887776544331   112233333333321   7999999999999999999999999998643

>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A

Probab=99.72  E-value=5.9e-18  Score=159.45  Aligned_cols=129  Identities=15%  Similarity=0.117  Sum_probs=98.9

Q ss_pred             HHHhhhhhccc--CCCccce-EEEEeccceeeeCCCccccccccC---CCCCcHHHHHHHHHHHHHHHchhcCCCeEEEE
Q psy15450        245 ILQALKYASSI--KEKEAGY-CKVSIRESLWIFDTQNKNSGTFKL---KNFATIFTAEAFAILQALKYVSSIKENEVIII  318 (659)
Q Consensus       245 ~l~iytDGS~~--~~g~~G~-g~v~~~~~~~~~~~~~~~~~~~~l---~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~  318 (659)
                      ++++|+|||+.  ++|.+|+ |+++...+..+      ......+   ...+||++||+.|++.||+.+...+..++.|+
T Consensus         1 m~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~------~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~   74 (149)
T 2ehg_A            1 MIIGYFDGLCEPKNPGGIATFGFVIYLDNRKI------EGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIK   74 (149)
T ss_dssp             CCEEEEEEEEESSSSSSEEEEEEEEECSSCEE------EEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEE
T ss_pred             CEEEEEeeccCCCCCChheEEEEEEEECCEEE------EEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEE
Confidence            35789999997  3577776 77765433221      1111122   24789999999999999999998888899999


Q ss_pred             cChHHHHHHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhccC
Q psy15450        319 TDSKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGT  387 (659)
Q Consensus       319 TDSq~ai~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~  387 (659)
                      |||+++++.+++++..+.   +.+.++++.+..+..+. .|.|.|||+    ++|+.||+||++|+...
T Consensus        75 tDS~~vi~~i~~~w~~~~---~~~~~l~~~i~~l~~~~-~v~~~~V~~----~~N~~AD~LA~~a~~~~  135 (149)
T 2ehg_A           75 GDSQLVIKQMNGEYKVKA---KRIIPLYEKAIELKKKL-NATLIWVPR----EENKEADRLSRVAYELV  135 (149)
T ss_dssp             ESCHHHHHHHTTSSCCCC---TTHHHHHHHHHHHHHHH-TCEEEECCG----GGCHHHHHHHHHHHHHH
T ss_pred             eChHHHHHHHhCccccCC---HHHHHHHHHHHHHHhcC-CEEEEEcCC----cccHHHHHHHHHHHHhh
Confidence            999999999999865442   24677777777776544 699999998    58999999999999853

>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain, fusion protein, maltose binding protein, HYDR; HET: MLR TAR; 2.25A {Mycobacterium tuberculosis}

Probab=99.72  E-value=1e-17  Score=155.59  Aligned_cols=129  Identities=20%  Similarity=0.201  Sum_probs=97.9

Q ss_pred             HHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHH
Q psy15450        246 LQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSC  324 (659)
Q Consensus       246 l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~a  324 (659)
                      +++|||||+.+ +|.+|+|+++...+.    +.........+ +.+||++||+.|++.||+.+...+..++.|+|||+++
T Consensus         4 ~~iy~DGs~~~~~g~~g~G~v~~~~~~----~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~v   78 (141)
T 3hst_B            4 VVIEADGGSRGNPGPAGYGAVVWTADH----STVLAESKQAI-GRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLV   78 (141)
T ss_dssp             EEEEEEEEESSSSEEEEEEEEEEETTS----CSEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHH
T ss_pred             EEEEEecCCCCCCCCcEEEEEEEeCCC----CcEEEeeeccC-CCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHH
Confidence            57999999875 567788877764320    00011112222 3689999999999999999998888999999999999


Q ss_pred             HHHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhcc
Q psy15450        325 LEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARG  386 (659)
Q Consensus       325 i~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~  386 (659)
                      ++.+++.|....   +.+..+++.+..+..+...|.|.|||    .++|+.||+||++|+..
T Consensus        79 v~~i~~~~~~~~---~~l~~~~~~i~~l~~~~~~v~~~~V~----~~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B           79 VEQMSGRWKVKH---PDLLKLYVQAQALASQFRRINYEWVP----RARNTYADRLANDAMDA  133 (141)
T ss_dssp             HHHHTTSSCCCS---HHHHHHHHHHHHHHTTSSEEEEEECC----GGGCHHHHHHHHHHHHH
T ss_pred             HHHHhCCcccCC---HHHHHHHHHHHHHHhcCCeEEEEEcC----CcccHHHHHHHHHHHHH
Confidence            999998643321   23556666677776667899999999    48999999999999875

>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism}

Probab=99.71  E-value=8.2e-18  Score=155.60  Aligned_cols=128  Identities=18%  Similarity=0.163  Sum_probs=95.6

Q ss_pred             HHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCC----eEEEEcC
Q psy15450        246 LQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKEN----EVIIITD  320 (659)
Q Consensus       246 l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~----~i~I~TD  320 (659)
                      +++|||||+.+ +|.+|+|+++...+...     .......+ +.+||++||+.|++.||+.+...+..    ++.|+||
T Consensus         4 ~~iy~DGs~~~n~g~~G~G~v~~~~~g~~-----~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tD   77 (140)
T 3u3g_D            4 IIIYTDGGARGNPGPAGIGVVITDEKGNT-----LHESSAYI-GETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMD   77 (140)
T ss_dssp             EEEEEEEEESSTTEEEEEEEEEECTTSCE-----EEEEEEEE-EEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEES
T ss_pred             EEEEEecCCCCCCCCcEEEEEEEeCCCCE-----EEEEEeeC-CCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeC
Confidence            57999999985 56778887775422111     11112222 25799999999999999999887666    9999999


Q ss_pred             hHHHHHHHhcCCcCCCCCcccHHHHHHHHHHH-HhcCCeeeEEEeecCCCccchhhhhhHHHHHhcc
Q psy15450        321 SKSCLEKLKNTSKSNGNPSHLILDIFKALSHL-QEWNISVRFIWVRGHAGIAGNEAVDRLAKETARG  386 (659)
Q Consensus       321 Sq~ai~~I~~~~~~~g~~~~~~~~i~~~l~~l-~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~  386 (659)
                      |+++++.+++++....   +.+..+++.+..+ ..+...|.|.|||    .++|+.||+||++|+..
T Consensus        78 S~~vi~~i~~~~~~~~---~~l~~~~~~i~~l~~~~~~~v~~~~V~----~~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D           78 SELIVRQMQGVYKVKE---PTLKEKFAKIAHIKMERVPNLVFVHIP----REKNARADELVNEAIDK  137 (140)
T ss_dssp             CHHHHHHHTTSSCCCC---GGGHHHHHHHHHHHHHHCTTCEEEECC----GGGGHHHHHHHHHHHHH
T ss_pred             hHHHHHHhCCCcccCC---HHHHHHHHHHHHHhhcCCCcEEEEEcC----chhhHHHHHHHHHHHHh
Confidence            9999999999764321   2345556666666 5555789999999    58999999999999864

>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B

Probab=99.66  E-value=6.3e-17  Score=183.60  Aligned_cols=121  Identities=21%  Similarity=0.153  Sum_probs=90.5

Q ss_pred             HHHHHhhhhhcccCCCc-cceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcCh
Q psy15450        243 FAILQALKYASSIKEKE-AGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDS  321 (659)
Q Consensus       243 ~g~l~iytDGS~~~~g~-~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDS  321 (659)
                      .+.+.+|+|||+.++++ .|+|++....+..          ... ...+||++||+.|++.||+.    +...+.|+|||
T Consensus       434 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~----------~~~-~~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS  498 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDK----------VKK-LEQTTNQQAELEAFAMALTD----SGPKVNIIVDS  498 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEE----------EEE-ESSCCHHHHHHHHHHHHHHT----SCSEEEEEESC
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCCEe----------ecc-CCCCCHHHHHHHHHHHHHHc----CCCeEEEEEeh
Confidence            45688999999987554 4555555422111          111 23689999999999999998    46899999999


Q ss_pred             HHHHHHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHh
Q psy15450        322 KSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETA  384 (659)
Q Consensus       322 q~ai~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa  384 (659)
                      +||++.|++|.+..+      .++++.+.++...+..|.|.|||||+|++|||.||+||++|+
T Consensus       499 ~~v~~~i~~~~~~~~------~~l~~~~~~~~~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          499 QYVMGIVASQPTESE------SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             HHHHHHHHTCCSEES------CHHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHHHHHHhccccccc------HHHHHHHHHHhccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            999999999865433      233333333333468899999999999999999999999874

>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...

Probab=99.65  E-value=7.4e-17  Score=183.10  Aligned_cols=120  Identities=26%  Similarity=0.236  Sum_probs=87.0

Q ss_pred             HHHHHhhhhhcccCCC-ccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcCh
Q psy15450        243 FAILQALKYASSIKEK-EAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDS  321 (659)
Q Consensus       243 ~g~l~iytDGS~~~~g-~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDS  321 (659)
                      .+.+.+|+|||+.+++ ..|+|++...+..       .. .  . ...+||++||+.|++.||+.+    ..++.|+|||
T Consensus       437 ~~~~~iytDGs~~~n~g~~g~g~v~~~~~~-------~~-~--~-~~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS  501 (557)
T 2zd1_A          437 VGAETFYVDGAANRETKLGKAGYVTNKGRQ-------KV-V--P-LTNTTNQKTELQAIYLALQDS----GLEVNIVTDS  501 (557)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEETTSCE-------EE-E--E-ECSCCHHHHHHHHHHHHHHHS----CSEEEEEECC
T ss_pred             CCCEEEEEccCCCCCCCceEEEEEEECCcE-------EE-e--c-CCCCCHHHHHHHHHHHHHHhC----CCcEEEEeCh
Confidence            3468999999997654 4555555432211       10 1  1 246899999999999999998    5899999999


Q ss_pred             HHHHHHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHH
Q psy15450        322 KSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKET  383 (659)
Q Consensus       322 q~ai~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~a  383 (659)
                      ++|++.|++|...+++  ++..++.+.   + .+...|.|.|||||+|++|||+||+||++|
T Consensus       502 ~~vi~~i~~~~~~~~~--~l~~~~~~~---l-~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          502 QYALGIIQAQPDKSES--ELVNQIIEQ---L-IKKEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             HHHHHHHTTCCSEESS--HHHHHHHHH---H-HHCSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             HHHHHHHhcCCccCCH--HHHHHHHHH---H-hcCCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            9999999998655322  233333333   2 235789999999999999999999999986

>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE motif, hydrolase; 1.50A {Bacillus halodurans} SCOP: c.55.3.1 PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A 2g8f_A 2g8v_A 2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A* 2r7y_A*

Probab=99.40  E-value=5.3e-14  Score=131.85  Aligned_cols=125  Identities=14%  Similarity=0.086  Sum_probs=94.2

Q ss_pred             HHHHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChH
Q psy15450        244 AILQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSK  322 (659)
Q Consensus       244 g~l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq  322 (659)
                      +.+.||+||||.+ +|.+|.|+++...+..+.       ....+ +.+||++||+.|++.||+.+.+.+. ++.|+|||+
T Consensus        10 ~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~-------~~~~~-~~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~   80 (142)
T 1zbf_A           10 IWESLSVDVGSQGNPGIVEYKGVDTKTGEVLF-------EREPI-PIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQ   80 (142)
T ss_dssp             CSSSEEEEEEECSSSEEEEEEEEETTTCCEEE-------ECCCE-EEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCH
T ss_pred             CeEEEEEeeccCCCCCCeEEEEEEEeCCEEEE-------Eeccc-CCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehH
Confidence            5788999999875 677788888763332111       11122 2589999999999999999988766 999999999


Q ss_pred             HHHHHHhcCC--cCCCCCcccHHHHHHHHHHHHh--cCCeeeEEEeecCCCccchhhhhh
Q psy15450        323 SCLEKLKNTS--KSNGNPSHLILDIFKALSHLQE--WNISVRFIWVRGHAGIAGNEAVDR  378 (659)
Q Consensus       323 ~ai~~I~~~~--~~~g~~~~~~~~i~~~l~~l~~--~~~~V~~~WVPgH~gi~GNE~AD~  378 (659)
                      ++++.+++.+  +..++++ .+.++|+.++.+..  +...+....|.-|++.-||.-||.
T Consensus        81 ~vi~w~~~~~~k~~~~~~v-~n~dLw~~l~~~~~w~~~~~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A           81 TAIKWVKDKKAKSTLVRNE-ETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             HHHHHHHHTCCCCCCCCST-TTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTCC
T ss_pred             HHHHHHHcCCccCCCCCCc-ccHHHHHHHHHHHHHHhhCCCceeEEEeccCccCcCcccc
Confidence            9999999874  3334555 57888888776522  245677778888999999999984

>4htu_A Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine, W-C base PAIR, wobble base PAIR, D helix; HET: DNA UCL; 1.49A {Bacillus halodurans} PDB: 3d0p_A* 4hue_A* 4huf_A* 4hug_A* 1zbf_A 1zbi_A 2g8u_A 3uld_A* 3ey1_A* 3twh_A* 2g8f_A 2g8v_A 2g8w_A 2g8i_A 2g8h_A 2g8k_A 3i8d_A* 2r7y_A* 1zbl_A

Probab=99.28  E-value=1.7e-12  Score=119.88  Aligned_cols=98  Identities=14%  Similarity=0.082  Sum_probs=73.8

Q ss_pred             HHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHH
Q psy15450        246 LQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSC  324 (659)
Q Consensus       246 l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~a  324 (659)
                      ..||+||+|.+ ||+.|.|+|+...+..      ... ...+ +.+|||+||+.|++.||+.+.+.+.. +.|+|||+||
T Consensus         6 ~~iytDGac~GNPGp~G~ggV~~~~g~~------~~~-~g~~-~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyV   76 (134)
T 4htu_A            6 ESLSVDVGSQGNPGIVEYKGVDTKTGEV------LFE-REPI-PIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTA   76 (134)
T ss_dssp             SSEEEEEEEETTTEEEEEEEEETTTCCE------EEE-EEEE-EEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHH
T ss_pred             eEEEEeeccCCCCCCeEEEEEEEECCEE------EEE-ecCC-CCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHH
Confidence            56899999875 6777776776543211      111 1122 36899999999999999999876533 8999999999


Q ss_pred             HHHHhcC--CcCCCCCcccHHHHHHHHHHHH
Q psy15450        325 LEKLKNT--SKSNGNPSHLILDIFKALSHLQ  353 (659)
Q Consensus       325 i~~I~~~--~~~~g~~~~~~~~i~~~l~~l~  353 (659)
                      ++.|.++  +++.++|+ .+.++|+.++.+.
T Consensus        77 i~wi~~~~~kt~~~~~v-kN~dLw~~ld~~~  106 (134)
T 4htu_A           77 IKWVKDKKAKSTLVRNE-ETALIWKLVDEAE  106 (134)
T ss_dssp             HHHHHHTCCCCCCCCSS-TTHHHHHHHHHHH
T ss_pred             HHHHHcCCcccCCCCCc-cCHHHHHHHHHHH
Confidence            9999975  56677777 6899999988664

>3kyl_A Telomerase reverse transcriptase; reverse transcriptase; 2.70A {Tribolium castaneum} PDB: 3du5_A 3du6_A

Probab=97.61  E-value=5.2e-05  Score=83.07  Aligned_cols=84  Identities=17%  Similarity=0.169  Sum_probs=59.9

Q ss_pred             CcceeEEEEecchhcCCCCHHHHHHHHHHcCC---ChhhHHHHhhhcccceEEEEEecccccCCCCCccccCCCCccccc
Q psy15450         81 YKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKI---DLKSATFCVFCVFHGRRLVIVMSDFNNSDGEDITMSGDCPRDKRG  157 (659)
Q Consensus        81 ~~~~~~v~lD~~KAFDsV~h~~L~~kL~~~Gi---~~~li~~I~s~yl~~r~~~v~~~~~~~~~g~~~~~~s~~~~i~~G  157 (659)
                      ...-++|=+|+++-||+|+|+.|+.+|...+.   ...+++||+. .+..-. +.       .+|.       ....+.|
T Consensus       242 ~G~~yVVDaDIkkFFDnINHdkLLk~L~~~i~~IlDk~Il~LIkk-~Lka~L-V~-------igGk-------~y~qekG  305 (596)
T 3kyl_A          242 QGQIYGIKVDIRDAYGNVKIPVLCKLIQSIPTHLLDSEKKNFIVD-HISNQF-VA-------FRRK-------IYKWNHG  305 (596)
T ss_dssp             CSCCEEEEEEESSTTTTCCHHHHHHHHTTSCTTTSCHHHHHHHHH-HHHCEE-EE-------SSSS-------EEEECSS
T ss_pred             CCCeEEEeeEHHhhCCCCCHHHHHHHHHhhccccccHHHHHHHHH-HHhhCe-EE-------ECCE-------EEecCCc
Confidence            44467899999999999999999999999875   5778888887 444322 11       1111       1223689


Q ss_pred             cCCCCCCCCCCcccCCCCccccccchhhhhhhhhhhcccC
Q psy15450        158 IPPDPGKGSGNATQDDGDQYESAPEYAKQNCFLNEVKDKW  197 (659)
Q Consensus       158 VpQ~~~~~~~~~~~~~G~~L~~~P~l~~~~~~ln~I~d~l  197 (659)
                      +||             |+++  ||+|.  +.+|+.+.+.+
T Consensus       306 TPQ-------------GGVI--SPLLA--NIYLheLDkel  328 (596)
T 3kyl_A          306 LLQ-------------GDPL--SGCLC--ELYMAFMDRLY  328 (596)
T ss_dssp             SCB-------------TCTT--HHHHH--HHHHHHHHHHH
T ss_pred             ccC-------------Ccch--hHHHH--HHHHHHHHHHH
Confidence            999             9999  99993  33366665544

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	659
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	6e-07
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	3e-05
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	4e-05
d1s1ta1	110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	1e-04

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]} Length = 126

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 2 [TaxId: 11709]

 Score = 46.8 bits (110), Expect = 6e-07
 Identities = 20/92 (21%), Positives = 31/92 (33%), Gaps = 10/92 (10%)

Query: 291 TIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALS 350
           T   AE  A   AL            II DS+  +  + +    + +           + 
Sbjct: 43  TNQQAELEAFAMALTDSGPKV----NIIVDSQYVMGIVASQPTESESKIV------NQII 92

Query: 351 HLQEWNISVRFIWVRGHAGIAGNEAVDRLAKE 382
                  ++   WV  H GI GN+ VD L  +
Sbjct: 93  EEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQ 124

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]} Length = 152

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Escherichia coli [TaxId: 562]

 Score = 42.3 bits (98), Expect = 3e-05
 Identities = 19/90 (21%), Positives = 37/90 (41%), Gaps = 1/90 (1%)

Query: 297 AFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWN 356
           A   L+    V    +++ +    ++      K   K+        +D+++ L      +
Sbjct: 53  ALEALKEHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQH 112

Query: 357 ISVRFIWVRGHAGIAGNEAVDRLAKETARG 386
             +++ WV+GHAG   NE  D LA+  A  
Sbjct: 113 Q-IKWEWVKGHAGHPENERADELARAAAMN 141

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]} Length = 147

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Thermus thermophilus [TaxId: 274]

 Score = 41.9 bits (97), Expect = 4e-05
 Identities = 15/36 (41%), Positives = 19/36 (52%)

Query: 351 HLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARG 386
            L      VRF +V+GH G   NE VDR A+  A+ 
Sbjct: 108 LLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQS 143

>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]} Length = 110

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 1 [TaxId: 11676]

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 10/79 (12%)

Query: 289 FATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKA 348
             T    E  AI  AL+        EV I+TDS+  L  +   ++ + + S L+  I + 
Sbjct: 42  DTTNQKTELQAIYLALQDSGL----EVNIVTDSQYALGII--QAQPDQSESELVNQIIEQ 95

Query: 349 LSHLQEWNISVRFIWVRGH 367
           L   ++    V   WV  H
Sbjct: 96  LIKKEK----VYLAWVPAH 110

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	659
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.84
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.84
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.82
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.62
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.57

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=99.84  E-value=1.5e-21  Score=177.27  Aligned_cols=121  Identities=21%  Similarity=0.187  Sum_probs=88.8

Q ss_pred             HHHHhhhhhcccCCCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHH
Q psy15450        244 AILQALKYASSIKEKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKS  323 (659)
Q Consensus       244 g~l~iytDGS~~~~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~  323 (659)
                      +.+.+|||||+..++..|++++....+....         ..+ +..||++|||.||++||+..    ...+.|+|||++
T Consensus         6 ~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~---------~~~-~~~tnn~AEl~Ai~~al~~~----~~~i~I~tDS~~   71 (126)
T d1mu2a1           6 GAETFYTDGSCNRQSKEGKAGYVTDRGKDKV---------KKL-EQTTNQQAELEAFAMALTDS----GPKVNIIVDSQY   71 (126)
T ss_dssp             TCEEEEEEEEECTTTCCEEEEEEETTSCEEE---------EEE-SSCCHHHHHHHHHHHHHHTS----CSEEEEEESCHH
T ss_pred             CCcEEEEcCCCCCCCCcEEEEEEecCCCEEE---------Eec-CCCcchHHHHHHHHHHhccC----CcceEEEechHH
Confidence            3457999999987666555554443332111         112 35799999999999999864    578999999999


Q ss_pred             HHHHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHh
Q psy15450        324 CLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETA  384 (659)
Q Consensus       324 ai~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa  384 (659)
                      +++.++++++....     ...++.+..+. +...|.|.|||||+|++|||.||+||++|+
T Consensus        72 v~~~~~~~~~~~~~-----~~~~~~~~~~~-~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          72 VMGIVASQPTESES-----KIVNQIIEEMI-KKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             HHHHHHTCCSEESC-----HHHHHHHHHHH-HCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHHHHhcCCccccc-----hHHHHHHHHhh-hcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            99999997554321     22333444443 357899999999999999999999999874

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Thermus thermophilus [TaxId: 274]

Probab=99.84  E-value=1.2e-21  Score=182.21  Aligned_cols=130  Identities=23%  Similarity=0.251  Sum_probs=99.9

Q ss_pred             HHhhhhhcccCC-CccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHH
Q psy15450        246 LQALKYASSIKE-KEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSC  324 (659)
Q Consensus       246 l~iytDGS~~~~-g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~a  324 (659)
                      +.||||||+.+| |..|.|+++...+..       .... .....+||++||+.|++.||+.+..  ...+.|+|||+++
T Consensus         4 i~iytDGs~~~N~g~~G~g~vi~~~~~~-------~~~~-~~~~~~Tnn~aEl~Ai~~AL~~~~~--~~~i~i~tds~~~   73 (147)
T d1rila_           4 VALFTDGACLGNPGPGGWAALLRFHAHE-------KLLS-GGEACTTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYL   73 (147)
T ss_dssp             CCEEEEEEESSTTEEEEEEEEECBTTBC-------CEEC-CEEEEECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHH
T ss_pred             EEEEEccCCCCCCCccEEEEEEEECCcc-------eEEe-cccccccHHHHHHHHHHHHhhhccC--CceEEEecchhhh
Confidence            579999999875 455666655432211       1111 1123579999999999999998754  5789999999999


Q ss_pred             HHHHhcC----------CcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhccC
Q psy15450        325 LEKLKNT----------SKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGT  387 (659)
Q Consensus       325 i~~I~~~----------~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~  387 (659)
                      ++.++.+          .+..++++ .+.++|+.+..+.. ...|.|.|||||+|++|||.||+||++|+...
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~v-~n~dL~~~l~~~~~-~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_          74 KKAFTEGWLEGWRKRGWRTAEGKPV-KNRDLWEALLLAMA-PHRVRFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             HHHHHSSHHHHHHHTTSBCTTSSBC-TTHHHHHHHHHHHT-TSEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             hccccccchhhhhhccccccccccc-hhHHHHHHHHHHhh-hcccceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence            9998763          34566666 47888888887754 67899999999999999999999999999864

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Escherichia coli [TaxId: 562]

Probab=99.82  E-value=8.5e-21  Score=176.62  Aligned_cols=131  Identities=22%  Similarity=0.285  Sum_probs=99.5

Q ss_pred             HHhhhhhcccCC-CccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHH
Q psy15450        246 LQALKYASSIKE-KEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSC  324 (659)
Q Consensus       246 l~iytDGS~~~~-g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~a  324 (659)
                      ++||||||+.++ |.+|+|+++...+....       .... .+.+||++||+.|++.||+.+..  ...+.|+|||+++
T Consensus         3 I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~-------~~~~-~~~~tnn~aE~~Ai~~Al~~~~~--~~~i~i~tds~~~   72 (152)
T d1jl1a_           3 VEIFTAGSALGNPGPGGYGAILRYRGREKT-------FSAG-YTRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYV   72 (152)
T ss_dssp             EEEEEEEEESSTTEEEEEEEEEEETTEEEE-------EEEE-EEEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHH
T ss_pred             EEEEEeCCCCCCCCcEEEEEEEEECCeEEE-------eccc-cCcccHHHHHHhhhhhhhhhhcc--cceEEEeecceee
Confidence            579999999864 56777776644332111       1111 23679999999999999998754  5789999999999


Q ss_pred             HHHHhcC---------CcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhccCC
Q psy15450        325 LEKLKNT---------SKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTD  388 (659)
Q Consensus       325 i~~I~~~---------~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~~  388 (659)
                      +..++.+         +...++++ .+.++++.+..+.. ...|.|.|||||+|++|||.||+|||+|+..+.
T Consensus        73 i~~~~~~~~~~~~~~~~~~~~~~~-~n~~~~~~i~~~~~-~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~  143 (152)
T d1jl1a_          73 RQGITQWIHNWKKRGWKTADKKPV-KNVDLWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAAAMNPT  143 (152)
T ss_dssp             HHHHHTTHHHHHHTTTBCTTSCBC-TTHHHHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCC
T ss_pred             EEcccchhhHhHhccchhcccCee-ecHHHHHHHHHHhh-cceeEEEEecccCCCccHHHHHHHHHHHHhCCC
Confidence            9999864         33445554 45667777777643 578999999999999999999999999998654

>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=99.62  E-value=2.1e-16  Score=139.85  Aligned_cols=102  Identities=20%  Similarity=0.136  Sum_probs=71.3

Q ss_pred             HHhhhhhcccCCCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHHH
Q psy15450        246 LQALKYASSIKEKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCL  325 (659)
Q Consensus       246 l~iytDGS~~~~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~ai  325 (659)
                      ..+|||||+.++++.|++++....+...         ...+ ..+|||+|||.||+.||+..    ..++.|||||+|++
T Consensus         9 ~t~ytDGs~~~n~~~g~~g~~~~~~~~~---------~~~~-~~~TNn~aEl~Avi~aL~~~----~~~v~I~TDS~yvi   74 (110)
T d1s1ta1           9 ETFYVDGAANRETKLGKAGYVTNRGRQK---------VVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYAL   74 (110)
T ss_dssp             EEEEEEEEEETTTTEEEEEEEETTSCEE---------EEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHH
T ss_pred             cEEEEeCCCCCCCCCcEEEEEEecCCeE---------EEec-ccCcHHHHHHHHHHHHHHhC----CCeEEEEEehHHHH
Confidence            4589999998776655554443322111         1112 35799999999999999864    57899999999999


Q ss_pred             HHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecC
Q psy15450        326 EKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGH  367 (659)
Q Consensus       326 ~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH  367 (659)
                      ++++.++...      ...+|+.+..+..+...|.+.|||||
T Consensus        75 ~~i~~~~~~~------~~~l~~~il~~l~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          75 GIIQAQPDQS------ESELVNQIIEQLIKKEKVYLAWVPAH  110 (110)
T ss_dssp             HHHHHCCSEE------SCHHHHHHHHHHHHCSEEEEEECCSS
T ss_pred             HHHhcCcccc------chHHHHHHHHHHhcCCceEEEEeCCC
Confidence            9999975433      22334333333344688999999999

>d1zbfa1 c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: BH0863-like Ribonuclease H
species: Bacillus halodurans [TaxId: 86665]

Probab=99.57  E-value=5e-16  Score=140.63  Aligned_cols=120  Identities=15%  Similarity=0.111  Sum_probs=91.4

Q ss_pred             hhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHHHH
Q psy15450        248 ALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLE  326 (659)
Q Consensus       248 iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~ai~  326 (659)
                      ||+||||.+ ||+.|.|+|+...+....       .+..+ +.+||++|||.|++.||+.+...+ .++.|||||+|+++
T Consensus         7 Iy~DGa~~GNPGp~g~g~v~~~~~~~~~-------~sg~~-~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~   77 (132)
T d1zbfa1           7 LSVDVGSQGNPGIVEYKGVDTKTGEVLF-------EREPI-PIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIK   77 (132)
T ss_dssp             EEEEEEECSSSEEEEEEEEETTTCCEEE-------ECCCE-EEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHH
T ss_pred             EEEeecCCCCCchheEEEEEEcCCEEEE-------EEcCc-CccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHH
Confidence            799999875 778888877754332211       11112 468999999999999999997754 57999999999999


Q ss_pred             HHhcC--CcCCCCCcccHHHHHHHHHHHHh--cCCeeeEEEeecCCCccchhhhh
Q psy15450        327 KLKNT--SKSNGNPSHLILDIFKALSHLQE--WNISVRFIWVRGHAGIAGNEAVD  377 (659)
Q Consensus       327 ~I~~~--~~~~g~~~~~~~~i~~~l~~l~~--~~~~V~~~WVPgH~gi~GNE~AD  377 (659)
                      .+.++  ++..+.++ .++++|+.++++..  +.+.+.+.|++.|+..-||..||
T Consensus        78 wv~~~~~kt~~~~~v-kN~~l~~~i~~a~~~lk~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          78 WVKDKKAKSTLVRNE-ETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             HHHHTCCCCCCCCST-TTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             HHHhCceecCcCCCc-ccHHHHHHHHHHHHHHHhCCcCceeEEecCcccccCCCC
Confidence            99886  34455555 57888887766421  35779999999999999999998