Psyllid ID: psy6532

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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-------
Protein Sequence
MLIRIYKSLIRSKLDYGCPVYNSASSNSLQILNPVQNLCLRLATGAFRSSPVVSLEAETGEPNLDIRRKILSSNYIAKTLSIENHPNIMRTLNPLYVRKYENSNMKPTIDGSKNEQGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFHENPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINNDVIHNELFFDEVKIIIKKKYTEEWNTKWVNISPNENKLRKIKNSILPSS
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHcHHHcccccccHHHHHHHHHHHHHHHHHHccccccccccHHHHcccccHHHHHHHHHHHHHHHHccccccccccccccHHHHHcccccccccccccccccccccEEEEEcccEEEEEEcccccccHHHHHHHHHHHHHHHHHHccccEEEEcccHHHHHHHHccccccHHHHHHHHHHHcccccEEEEEEcccccccccHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccccHHcHHHHHHHHHHHHHHccccccHHHHHHHHHHcccccccEEEEEccccccccEEEEEEEEcccEEEEEccccccHHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccc
Coil and Loop (DISEMBL)
MLIRIYKSLIRSkldygcpvynsassnslqilNPVQNLCLRLatgafrsspvvsleaetgepnlDIRRKILSSNYIAktlsienhpnimrtlnPLYVRKyensnmkptidgskneqgvgcaltipekdivkrfglnknaSIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFHENPLVKRVQEelsstespveflwcpshvgiagnetADEEAKQAinndvihnelfFDEVKIIIKKKYTeewntkwvnispnenklRKIKNSILPSS
Flexible Loop (DISEMBL)
MLIRIYKSLIRSKLDYGCPVYNSASSNSLQILNPVQNLCLRLATGafrsspvvsleaetgepnldiRRKILSSNYIAKtlsienhpnimrTLNPLYVRKYENSNMKptidgskneqGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFHENPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINndvihnelffDEVKIIIKKKyteewntkwvnispnenklrkiknsilpss
Low Complexity Region (SEG)
MLIRIYKSLIRSKLDYGCPVYNSASSNSLQILNPVQNLCLRLATGAFRSSPVVSLEAETGEPNLDIRRKILSSNYIAKTLSIENHPNIMRTLNPLYVRKYENSNMKPTIDGSKNEQGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFHENPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINNDVIHNELFFDEVKIIIKKKYTEEWNTKWVNISPNENKLRKIKNSILPSS
Disordered region (IsUnstruct)
**IRIYKSLIRSKLDYGCPVYNSASSNSLQILNPVQNLCLRLATGAFRSSPVVSLEAETGEPNLDIRRKILSSNYIAKTLSIENHPNIMRTLNPLYVRKYE***************GVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFHENPLVKRVQ********PVEFLWCPSHVGIAGNETADEEAKQAINNDVIHNELFFDEVKIIIKKKYTEEWNTKWVNIS*****************
Disordered Region (DISOPRED)
MLIRIYKSLIRSKLDYGCPVYNSASSNSLQILNPVQNLCLRLATGAFRSSPVVSLEAETGEPNLDIRRKILSSNYIAKTLSIENHPNIMRTLNPLYVRKYENSNMKPTIDGSKNEQGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFHENPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQ*********ELFFDEVKIIIKKKYTEEWNTKWVNISP*ENKLRKI*N**L***
Disordered Region (DISEMBL)
MLIRIYKSLIRSKLDYGCPVYNSASSNSLQILNPVQNLCLRLATGAFRSSPVVSLEAETGEPNLDIRRKILSSNYIAKTLSIENHPNIMRTLNPLYVRKYENSNMKPTIDGSKNEQGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFHENPLVKR**********PVEFLWCPSHVGIAGNETADEEAKQAINNDVIHNELFFDEVKIIIKKKYTEEWNTKWVNISPNENKLRKIKNSILPSS
Disordered Region (DISPRO)
MLIRIYKSLIRSKLDYGCPVYNSASSNSLQILNPVQNLCLRLATGAFRSSPVVSLEAETGEPNLDIRRKILSSNYIAKTLSIENHPNIMRTLNPLYVRKYENSNMKPTIDGSKNEQGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFHENPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINNDVIHNELFFDEVKIIIKKKYTEEWNTKWVNISPNE**************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLIRIYKSLIRSKLDYGCPVYNSASSNSLQILNPVQNLCLRLATGAFRSSPVVSLEAETGEPNLDIRRKILSSNYIAKTLSIENHPNIMRTLNPLYVRKYENSNMKPTIDGSKNEQGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFHENPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINNDVIHNELFFDEVKIIIKKKYTEEWNTKWVNISPNENKLRKIKNSILPSS
Positional Conservation
no confident homologs detected

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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	277	2.2.26 [Sep-21-2011]
Q77373	1435	Gag-Pol polyprotein OS=Hu	yes	N/A	0.382	0.073	0.339	0.0002
Q82851	1432	Gag-Pol polyprotein OS=Je	N/A	N/A	0.299	0.057	0.340	0.0007

>sp|Q77373|POL_HV1AN Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group O (isolate ANT70) GN=gag-pol PE=3 SV=3

 Score = 46.2 bits (108), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/115 (33%), Positives = 60/115 (52%), Gaps = 9/115 (7%)

Query: 109  IDGSKN-EQGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALII 167
            +DG+ N E  +G A  + E+   K   L++  +   AEL A+L +L   K+       I+
Sbjct: 1028 VDGAANRETKLGKAGYVTEQGKQKIIKLDETTNQ-KAELMAILLALQDSKET----VNIV 1082

Query: 168  TDSLSCLQAIMNM--FHENPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADE 220
            TDS   L  I +     E+P+V+++ EEL+  E  V   W P+H GI GNE  D+
Sbjct: 1083 TDSQYALGVISSQPTQSESPIVQQIIEELTKKEQ-VYLTWVPAHKGIGGNEKIDK 1136

Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the HIV genome, a 5 bp duplication of host DNA is produced at the ends of HIV-1 integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 1EC: .EC: 1EC: 3EC: .EC: 2

>sp|Q82851|POL_JEMBR Gag-Pol polyprotein OS=Jembrana disease virus GN=gag-pol PE=3 SV=1

 Score = 44.7 bits (104), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 42/91 (46%), Gaps = 8/91 (8%)

Query: 143  HAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMN---MFHENPLVKRVQEELSSTES 199
             AEL A+L +L    Q G  K  IITDS    + +      +    L K + EEL   E 
Sbjct: 997  QAELKAVLMAL----QDGPAKMNIITDSRYAFEGMREEPETWGREGLWKEIGEELRRKEY 1052

Query: 200  PVEFLWCPSHVGIAGNETADEEAKQAINNDV 230
             V   W P H GI GN   D+E ++A+   +
Sbjct: 1053 -VGVSWVPGHKGIGGNTEVDQEVQKALQGPI 1082

Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA.

Bos javanicus (taxid: 9906)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 2

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	277
328697366	891	PREDICTED: hypothetical protein LOC10057	0.967	0.300	0.367	2e-32
357621647	1133	putative pol-like protein [Danaus plexip	0.978	0.239	0.266	2e-26
328697220	1915	PREDICTED: hypothetical protein LOC10016	0.974	0.140	0.282	5e-22
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.563	0.127	0.380	6e-20
443699889	347	hypothetical protein CAPTEDRAFT_215477 [	0.718	0.573	0.337	4e-19
427791981	1060	Putative tick transposon, partial [Rhipi	0.303	0.079	0.523	9e-16
443700898	300	hypothetical protein CAPTEDRAFT_212630,	0.649	0.6	0.355	1e-15
443710566	377	hypothetical protein CAPTEDRAFT_186063 [	0.649	0.477	0.355	2e-15
427791063	1035	Putative tick transposon, partial [Rhipi	0.274	0.073	0.482	3e-15
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.606	0.423	0.359	1e-14

>gi|328697366|ref|XP_003240318.1| PREDICTED: hypothetical protein LOC100575042 [Acyrthosiphon pisum]

 Score =  145 bits (365), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 101/275 (36%), Positives = 144/275 (52%), Gaps = 7/275 (2%)

Query: 2   LIRIYKSLIRSKLDYGCPVYNSASSNSLQILNPVQNLCLRLATGAFRSSPVVSLEAETGE 61
           L+ IYKSLI SK+ YG  +YN+A  N L+IL+P+ N  +RLA GAFR+S   S+    GE
Sbjct: 47  LLSIYKSLILSKIKYGSQIYNTAKPNLLKILDPIHNEGIRLAIGAFRTSSTDSILNYAGE 106

Query: 62  PNLDIRRKILSSNYIAKTLSIENHPNIMRTLNPLYVRKYENSNMKPTIDGSKNEQGVGCA 121
             L ++R   +  YI K  S  N        +          + K  +D SK+E GVG A
Sbjct: 107 LPLQLQRDQDTLAYITKRKSTTNRIGYKAIFDNHAASPINMEHKKKPLDASKSEHGVGFA 166

Query: 122 LTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMF 181
           +   + D + +  L +  SIF AE +A+ + +     L T   L+I+DSLS L A  N  
Sbjct: 167 VV--KDDTIIQHKLPEITSIFSAENYAIFEGVKLANTLETNDILLISDSLSTLLAFKNTS 224

Query: 182 HENPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETAD---EEAKQAINNDVIHNELFFD 238
             N +   +Q  L  ++  + F+W PSH GI GNE AD   E+A Q I N  I+N    D
Sbjct: 225 PRNEITSNIQACLVQSKKNIVFMWVPSHTGIIGNEKADKHAEQATQTILNPTINNISSID 284

Query: 239 EVKIIIKKKYTEEWNTKWVNISPNENKLRKIKNSI 273
            +K  I +K    W   W +I+ + NKL+ IK +I
Sbjct: 285 -IKNSINQKILSSWQNYWNSITLS-NKLKNIKKTI 317

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  125 bits (314), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 94/353 (26%), Positives = 150/353 (42%), Gaps = 82/353 (23%)

Query: 5    IYKSLIRSKLDYGCPVYNSASSNSLQILNPVQNLCLRLATGAFRSSPVVSLEAETGEPNL 64
            +Y ++IRS  DYG  +      ++L IL+ +Q  CLR+  GA +SSP+ +L+ E GE  L
Sbjct: 689  LYNAIIRSHFDYGSFLLVPCIKSALSILDKIQAKCLRIICGAMKSSPINALQVECGEAPL 748

Query: 65   DIRRKILSSNYIAKTLSIENH--------------------------------------- 85
             +RR+ LS  +  K +   NH                                       
Sbjct: 749  HLRRQYLSDRFFLKVIQFSNHPLIPKLNSLSDLIPSNKYWSHKEYPCLLTSLVKFLRLPC 808

Query: 86   PNIMRTLNPLYVRKYENSNMKPTI---------------------------------DGS 112
            P +   + PL+   Y+  N  P I                                 D S
Sbjct: 809  PVLQNQMFPLFATPYDVLNFHPQILLEFGIDKGSAIANVQFQNYVKEHWSDWLCIYTDAS 868

Query: 113  K--NEQGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDS 170
            K  ++   G A+ IP+ +I+  F      SIF AE  A+L+++  ++      ++I +DS
Sbjct: 869  KMADQSNAGAAVWIPKYNIILNFKFPSEISIFTAESIAILEAVSFVESHKLNNSIIFSDS 928

Query: 171  LSCLQAIM-NMF---HENPLVKRVQEELSSTESP---VEFLWCPSHVGIAGNETADEEAK 223
             SCLQAI  N F   H  P + ++++ L   +S    V   W PSH GI GNET D  AK
Sbjct: 929  KSCLQAIARNPFISKHNYPYILKIKDILFRCQSSNIQVRLAWIPSHSGIHGNETVDYYAK 988

Query: 224  QAINNDVI-HNELFFDEVKIIIKKKYTEEWNTKWVNISPNENKLRKIKNSILP 275
             A N   + H  ++ +++  I K+++   W   W+  S ++ K      S++P
Sbjct: 989  DATNTGCMDHFGVYPNDLIPIAKQRFFSSWTQYWLKTSRSKGKYYADVQSLIP 1041

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328697220|ref|XP_001949504.2| PREDICTED: hypothetical protein LOC100162931 [Acyrthosiphon pisum]

 Score =  110 bits (276), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 94/333 (28%), Positives = 155/333 (46%), Gaps = 63/333 (18%)

Query: 2    LIRIYKSLIRSKLDYGCPVYNSASSNSLQILNPVQNLCLRLATGAFRSSPVVSLEAETGE 61
            L++I+++ I SKLDYG P+++SA    L+IL  + N  +RL+ GAFRSSP+ S+    G 
Sbjct: 801  LLKIHEAFILSKLDYGAPIFSSAKHTKLKILETIHNSGIRLSIGAFRSSPIKSILNIAGI 860

Query: 62   PNLDIRRKILSSNYIAK-TLSIENH-PNIMRTLNPLYVRKYENSNMKPT----------- 108
            P+L++R +  +    A+ + S +NH  +   T N  ++ KY+  N+ P            
Sbjct: 861  PSLEVRWREQTHKLAARISRSPQNHIHHPKHTFNHTFI-KYDLENIIPYEKPLCPPWQFS 919

Query: 109  --------------------------------------IDGSKNEQGVGCALTIPEKDIV 130
                                                   D S  E  VG A+   E  I 
Sbjct: 920  MNINIDLHQFPKNSTCPHIFKNAFRDICSHTHPQTHIYTDASIIEGRVGMAIICDETTI- 978

Query: 131  KRFGLNKNASIFHAELFALLQSL-LTIKQLGTCKALIITDSLSCLQAIMNMFHENPLVKR 189
             ++ L+   SI+ AE  A+L+++  TI ++      I +DSLS L ++ N++  + +V++
Sbjct: 979  -QWKLSDKCSIYTAETLAILKAIEFTISEINDSNITIFSDSLSALTSLQNLYSPSDIVRK 1037

Query: 190  VQEEL---SSTESPVEFLWCPSHVGIAGNETADEEAKQAIN--NDVIHNELFFDEVKIII 244
            +Q         +  + + W P H  I GNE AD  AK A +  N +      F+++K +I
Sbjct: 1038 IQNTHYIPKQQDKNITYSWVPGHCNIDGNELADSAAKLAHSSPNSLSLPIFSFNDIKRVI 1097

Query: 245  KKKYTEEWNTKWVNISPNENKLRKIKNSILPSS 277
            +K        +W  +S    KL +IK S LPSS
Sbjct: 1098 EKDTLLHCQKEWNEMS---TKLNEIKRSTLPSS 1127

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|125901787|gb|ABN58714.1| pol-like protein [Biomphalaria glabrata]

 Score =  103 bits (258), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 62/163 (38%), Positives = 92/163 (56%), Gaps = 7/163 (4%)

Query: 110  DGSKNEQGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITD 169
            DGSK E  V CA +   K I +R  L    SIF AEL A+L +L+ +K     K +I +D
Sbjct: 962  DGSKMEGKVACACSFRNKTISRR--LPDGCSIFTAELHAILLALMAVKASERSKFIICSD 1019

Query: 170  SLSCLQAIMNMFHENPLVKR---VQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAI 226
            S S LQA+  M  + PLV +   + + +++    V F+W PSHVGI GNE AD EAK+A+
Sbjct: 1020 SKSALQALGRMKTDIPLVHKSLKLLDLITADRRDVTFIWVPSHVGIEGNEAADREAKRAL 1079

Query: 227  NNDVIHNELFFDEVKIIIKKKYTEEWNTKWVNISPNENKLRKI 269
            N+ V   ++ + +++  I      EW  +W   +   +KLR+I
Sbjct: 1080 NHAVSGTQIPYSDLRQSIASATYREWQNRWE--AETHSKLRQI 1120

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|443699889|gb|ELT99143.1| hypothetical protein CAPTEDRAFT_215477 [Capitella teleta]

 Score =  101 bits (251), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 77/228 (33%), Positives = 115/228 (50%), Gaps = 29/228 (12%)

Query: 12  SKLDYGCPVYNSASSNSLQILNPVQN--------LCLRLATGAFRSSPVVSLEAETGEPN 63
           S+LDYG  VY SA    L+ L P+QN        +CL    GAFR+SP+ SL  E  E  
Sbjct: 47  SRLDYGALVYGSAQPLYLERLKPMQNQAEAQAKSICL----GAFRTSPITSLHVEANEMP 102

Query: 64  LDIRRKILSSNYIAKTLSIENHPNIMRTLNPLYVRKYENSNMKPTIDGSKNEQGVGCALT 123
           + IR + LS ++  +  +   +P      N    R Y N + + T+    N         
Sbjct: 103 MPIRHQFLSLHFALRVYANVANPANQCIFNHYNARFYINGSKRETMQSGFNR-------- 154

Query: 124 IPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTC-KALIITDSLSCLQAIMNMFH 182
                ++ +  L  +ASIF AEL A+ + L  ++   +  + LI+TDSLS LQA+ N   
Sbjct: 155 -----LLIQVRLPDSASIFSAELLAIYEVLTLLECAASYEQILIVTDSLSSLQALGNFNI 209

Query: 183 ENPLVKRVQEE---LSSTESPVEFLWCPSHVGIAGNETADEEAKQAIN 227
            +P V ++ E+   L +    +  LWCPSHVG+ GN  AD  AK+A++
Sbjct: 210 THPYVFKILEKYTILYNRGFDLVMLWCPSHVGVVGNARADLLAKKALS 257

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|427791981|gb|JAA61442.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score = 90.1 bits (222), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 44/84 (52%), Positives = 59/84 (70%)

Query: 2   LIRIYKSLIRSKLDYGCPVYNSASSNSLQILNPVQNLCLRLATGAFRSSPVVSLEAETGE 61
           L+ IY+SL+RSKLDYG  +Y SA  + L+ L+PV N  LRLATGA+R+SP+ SL AE+ E
Sbjct: 809 LLHIYRSLVRSKLDYGSIIYGSARDSYLKRLDPVHNKGLRLATGAYRTSPIPSLYAESNE 868

Query: 62  PNLDIRRKILSSNYIAKTLSIENH 85
           P+L+ RR  L   Y+ K  S  +H
Sbjct: 869 PSLEYRRTQLMFTYVLKVRSSPDH 892

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443700898|gb|ELT99633.1| hypothetical protein CAPTEDRAFT_212630, partial [Capitella teleta]

 Score = 89.4 bits (220), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/197 (35%), Positives = 99/197 (50%), Gaps = 17/197 (8%)

Query: 90  RTLNPLYVRKYENSNMKPT--------IDGSKNEQGVGCALTIPEKDIVKRFGLNKNASI 141
           +T NP Y  + E  N+            DGSK++  V C+ T     I  R  L  +ASI
Sbjct: 95  KTANPNYTLRNEFYNLMDKYPDHKVIFTDGSKSDSAVACSATADNLRIQIR--LPDSASI 152

Query: 142 FHAELFALLQ--SLLTIKQLGTCKALIITDSLSCLQAIMNMFHENPLVKRVQEELSSTES 199
           F AEL A+ Q  +LL        + LI TDSLS LQAI N   ++P V ++ ++ +    
Sbjct: 153 FSAELLAIYQVLTLLECSANDQQQFLIATDSLSSLQAIGNFNIKHPYVFKILQKCTLLHK 212

Query: 200 PVEFL---WCPSHVGIAGNETADEEAKQAINNDVIHNELFFDEVKIIIKKKYTEEWNTKW 256
              +L   WCPSHVG+ GNE AD  AK+A++       +   + K I  + Y E+W  +W
Sbjct: 213 KGIYLVMAWCPSHVGVMGNERADLLAKEALSFTTCTIRVPSSDFKPITHEFYKEKWQEQW 272

Query: 257 VNISPNENKLRKIKNSI 273
              S  ENKL  I+ +I
Sbjct: 273 S--SEQENKLYCIQPTI 287

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443710566|gb|ELU04776.1| hypothetical protein CAPTEDRAFT_186063 [Capitella teleta]

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/197 (35%), Positives = 98/197 (49%), Gaps = 17/197 (8%)

Query: 90  RTLNPLYVRKYENSNMKPT--------IDGSKNEQGVGCALTIPEKDIVKRFGLNKNASI 141
           +T NP Y  K E  N+            DGSK++  V C  T     I  R  L  +ASI
Sbjct: 164 KTANPNYTLKNEFYNLMDKYPDHKVIFTDGSKSDSAVACFATADNLSIQIR--LPDSASI 221

Query: 142 FHAELFALLQ--SLLTIKQLGTCKALIITDSLSCLQAIMNMFHENPLVKRVQEELSSTES 199
           F AEL A+ Q  +LL        + LI TDSLS LQAI N   ++P V ++ E+ +    
Sbjct: 222 FSAELLAIYQVLTLLECSANDQQQFLIATDSLSSLQAIGNFNIKHPYVFKILEKCTLLHK 281

Query: 200 PVEFL---WCPSHVGIAGNETADEEAKQAINNDVIHNELFFDEVKIIIKKKYTEEWNTKW 256
              +L   WCPSHVG+ GNE AD  AK+A++       +   + K I  + + E+W  +W
Sbjct: 282 KGIYLVMAWCPSHVGVMGNERADLLAKEALSFTTCTIRIPSSDFKPITHEFFKEKWQEQW 341

Query: 257 VNISPNENKLRKIKNSI 273
              S  ENKL  I+ ++
Sbjct: 342 S--SEQENKLYCIQPTL 356

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|427791063|gb|JAA60983.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score = 88.2 bits (217), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 41/85 (48%), Positives = 63/85 (74%)

Query: 2   LIRIYKSLIRSKLDYGCPVYNSASSNSLQILNPVQNLCLRLATGAFRSSPVVSLEAETGE 61
           L+ IYKSL+R++LDYG  VY+SA+ ++L+IL+P+ +L +RLATGAFR+SPV SL  E+ +
Sbjct: 621 LMDIYKSLVRTRLDYGSVVYHSAAPSALKILDPIHHLGIRLATGAFRTSPVQSLYVESNQ 680

Query: 62  PNLDIRRKILSSNYIAKTLSIENHP 86
            +L ++R  +S  Y  K  + + HP
Sbjct: 681 WSLHLQRSYMSFVYFLKVKAEKEHP 705

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443712830|gb|ELU05953.1| hypothetical protein CAPTEDRAFT_202466 [Capitella teleta]

 Score = 86.3 bits (212), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 64/178 (35%), Positives = 87/178 (48%), Gaps = 10/178 (5%)

Query: 97  VRKYENSNMKPTIDGSKNEQGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTI 156
           + KY   N+    DGSK+   V CA T     I  +FGL    SI+ AEL A+ Q+L+ I
Sbjct: 125 IDKYPGINI--YTDGSKSNDTVACAFTCSTYQI--QFGLPAQMSIYTAELIAIEQALIFI 180

Query: 157 KQLGTCKAL-IITDSLSCLQAIMNMFHENPLVKRV---QEELSSTESPVEFLWCPSHVGI 212
           + +       I +DSLS L A+ N    +P +  +   Q  L      V F+WCPSHVGI
Sbjct: 181 ETVKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKKVVFIWCPSHVGI 240

Query: 213 AGNETADEEAKQAINNDVIHNELFFDEVKIIIKKKYTEEWNTKWVNISPNENKLRKIK 270
            GNE AD +AKQA+   V    L   + K  I+      W  +W      +NKL  I+
Sbjct: 241 LGNEVADRQAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDG--ETDNKLHIIQ 296

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

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	277
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.617	0.351	0.289	4.5e-08

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

 Score = 151 (58.2 bits), Expect = 4.5e-08, P = 4.5e-08
 Identities = 55/190 (28%), Positives = 88/190 (46%)

Query:    77 AKTLSIENHPNIMRTLNPLYVRKYENSNMKPTIDGSKNEQGVGCALTIPEKDIVKR---F 133
             A+T +IE H NI+    P  +  Y         DGS     VG A   P K ++ R    
Sbjct:   165 AET-AIETHRNILNRA-PRPIALYT--------DGSGINGRVGAAAICP-KYLISRSSYM 213

Query:   134 GLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFHENP--LVKRVQ 191
             G    ++++ AEL  +L +L+ I Q     A+I TD+ + LQA+ N   ++   +++ + 
Sbjct:   214 GQQSESTVYVAELQGILLALVIILQRQMQHAVIFTDNQATLQALRNPGSQSGQYILEAII 273

Query:   192 EELSSTESP---VEFLWCPSHVGIAGNETADEEAKQAINNDVIHNELFFDEVKIIIKKKY 248
               L+        V F W P+H G+ GNE AD  AK+A     I        ++  +K++ 
Sbjct:   274 MALNKGRKAGLNVHFRWIPAHRGVEGNEQADRRAKEATGWRRIRGHRGRMTIRSAVKRRA 333

Query:   249 TEEWNTKWVN 258
              E  N +W N
Sbjct:   334 HEVVNARWEN 343


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.316   0.132   0.378    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      277       277   0.00080  115 3  11 22  0.38    34
                                                     33  0.41    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  610 (65 KB)
  Total size of DFA:  201 KB (2114 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  24.32u 0.15s 24.47t   Elapsed:  00:00:02
  Total cpu time:  24.32u 0.15s 24.47t   Elapsed:  00:00:02
  Start:  Thu Aug 15 16:52:59 2013   End:  Thu Aug 15 16:53:01 2013

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	0.691
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	277
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	8e-29
pfam00075	126	pfam00075, RNase_H, RNase H	1e-15
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	1e-10
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	7e-07
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	9e-07
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	4e-05
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	7e-04
pfam13456	88	pfam13456, RVT_3, Reverse transcriptase-like	0.001

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

 Score =  106 bits (266), Expect = 8e-29
 Identities = 45/122 (36%), Positives = 63/122 (51%), Gaps = 6/122 (4%)

Query: 110 DGSKNEQGVGCALTIPEK-DIVKRFGLNKNASIFHAELFALLQSLLTIKQLG--TCKALI 166
           DGSK E   G    I  K  I + + L    S+F AEL A+L++L    + G    K  I
Sbjct: 5   DGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRARKITI 64

Query: 167 ITDSLSCLQAIMNMFHENPLVKRVQ---EELSSTESPVEFLWCPSHVGIAGNETADEEAK 223
            +DS + L+A+ +    +PLV R++    EL++    V   W P H GI GNE AD  AK
Sbjct: 65  FSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLAK 124

Query: 224 QA 225
           +A
Sbjct: 125 EA 126

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 = 71.5 bits (176), Expect = 1e-15
 Identities = 40/123 (32%), Positives = 53/123 (43%), Gaps = 10/123 (8%)

Query: 109 IDGSKNEQ-GVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALII 167
            DGS N   G G A  + +    +   L    +   AEL AL+++L   + L   K  I 
Sbjct: 8   TDGSCNGNPGPGGAGYVTDGGKQRSKPLP-GTTNQRAELLALIEAL---EALSGQKVNIY 63

Query: 168 TDSLSCLQAIMNMF---HE-NPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAK 223
           TDS   +  I N +    E  P+   + E L      V   W P H GI GNE AD+ AK
Sbjct: 64  TDSQYVIGGITNGWPTKSESKPIKNEIWELLQKKHK-VYIQWVPGHSGIPGNELADKLAK 122

Query: 224 QAI 226
           Q  
Sbjct: 123 QGA 125

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

 Score = 58.1 bits (141), Expect = 1e-10
 Identities = 38/149 (25%), Positives = 56/149 (37%), Gaps = 28/149 (18%)

Query: 104 NMKPTI--DG-SKNEQGV-GCA----LTIPEKDIVKRFGLNKNASIFHAELFALLQSLLT 155
             K  I  DG      G  G          EK++    G   N     AEL AL+++L  
Sbjct: 1   MKKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNR---AELRALIEALEA 57

Query: 156 IKQLGTCKALIITDSLSCLQAIMNMFHENP----------------LVKRVQEELSSTES 199
           +K+LG C+  + TDS   ++ I     +                  L + + E L   E 
Sbjct: 58  LKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHEL 117

Query: 200 PVEFLWCPSHVGIAGNETADEEAKQAINN 228
            V + W   H G   NE AD+ A++A   
Sbjct: 118 -VFWEWVKGHAGHPENERADQLAREAARA 145

Length = 154

>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 = 47.0 bits (112), Expect = 7e-07
 Identities = 35/126 (27%), Positives = 48/126 (38%), Gaps = 12/126 (9%)

Query: 109 IDGSKNEQG--VGCALTIPEKDIVKRFGL---NKNASIFHAELFALLQSLLTIKQLGTCK 163
            DGS        G    + + +    F        A+   AEL ALL++L     LG  K
Sbjct: 2   TDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLKK 61

Query: 164 ALIITDSLSCLQAI---MNMFHENPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADE 220
            +I TDS   +  I      + +N L+      L S    + F   P      GNE AD 
Sbjct: 62  LIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEVADR 117

Query: 221 EAKQAI 226
            AK+A 
Sbjct: 118 LAKEAA 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 = 47.1 bits (113), Expect = 9e-07
 Identities = 27/99 (27%), Positives = 42/99 (42%), Gaps = 20/99 (20%)

Query: 145 ELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFH---------------ENP-LVK 188
           EL A++++L  +K+   C  L+ TDS   +  I    H               +N  L +
Sbjct: 45  ELTAVIEALEALKE--PCPVLLYTDSQYVINGITKWIHGWKKNGWKTADGKPVKNVDLWQ 102

Query: 189 RVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAIN 227
            +   L+  +  V + W   H G  GNE ADE A  A +
Sbjct: 103 ELDALLAKHQ--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|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term repeat retroelements

 Score = 42.3 bits (100), Expect = 4e-05
 Identities = 34/141 (24%), Positives = 54/141 (38%), Gaps = 34/141 (24%)

Query: 109 IDGSKNEQGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKAL-II 167
            DGS   +  G A+     D+++   L    S   AEL AL+++L   K     K + I 
Sbjct: 4   TDGSSFVRKAGYAVVT-GPDVLEIATLPYGTSAQRAELIALIRALELAKG----KPVNIY 58

Query: 168 TDSLSCLQAIMNMFHE------------------NPLVKRVQEELSSTESPVEFLWCPSH 209
           TDS         + H                     L+ ++Q+ +   + PV  +   +H
Sbjct: 59  TDS----AYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPK-PVAVIHIRAH 113

Query: 210 VG-----IAGNETADEEAKQA 225
            G       GN  AD+ A+QA
Sbjct: 114 SGLPGPLALGNARADQAARQA 134

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|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 = 38.7 bits (91), Expect = 7e-04
 Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 21/104 (20%)

Query: 144 AELFALLQSLLTIKQL--GTCKALIITDS---LSCLQAIMNMFHEN--------P----- 185
           AEL A++ +L  IK++  G  K +I TDS   ++ +   +  + +N        P     
Sbjct: 46  AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105

Query: 186 LVKRVQEELSSTES---PVEFLWCPSHVGIAGNETADEEAKQAI 226
           L+K + + L   E     V+F   P H GI GNE AD  AK+  
Sbjct: 106 LIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGA 149

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|205634 pfam13456, RVT_3, Reverse transcriptase-like

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 26/93 (27%), Positives = 40/93 (43%), Gaps = 9/93 (9%)

Query: 140 SIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMN--MFHEN--PLVKRVQEELS 195
           S   AE  ALL+ L    +LG  + ++ +DS   +Q I            L++ +++ L 
Sbjct: 1   SPLEAEAEALLEGLQLALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLK 60

Query: 196 STESPVEFLWCPSHVGIAGNETADEEAKQAINN 228
             +S V      SHV    N  AD  AK A  +
Sbjct: 61  KFDS-VSV----SHVPRECNRVADALAKLASAS 88

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	277
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.92
PRK06548	161	ribonuclease H; Provisional	99.91
PRK08719	147	ribonuclease H; Reviewed	99.91
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.9
PRK00203	150	rnhA ribonuclease H; Reviewed	99.9
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.8
KOG3752|consensus	371		99.8
PRK13907	128	rnhA ribonuclease H; Provisional	99.79
PRK07708	219	hypothetical protein; Validated	99.76
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.61
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.36
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	82.18

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

Probab=99.92  E-value=1.4e-24  Score=175.04  Aligned_cols=125  Identities=27%  Similarity=0.323  Sum_probs=99.2

Q ss_pred             CCceeeecCCCCC--CCeeEEEEEcCCCeEE--eecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHh
Q psy6532         103 SNMKPTIDGSKNE--QGVGCALTIPEKDIVK--RFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIM  178 (277)
Q Consensus       103 ~~~~iytDGS~~~--~~~G~g~v~~~~~~~~--~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~  178 (277)
                      ..+.||||||+..  |..|+|+|+..+...+  +.... .+||++||+.|++.||+.+.+.+...|.|+|||++++++|+
T Consensus         2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~   80 (154)
T COG0328           2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGIT   80 (154)
T ss_pred             CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHH
Confidence            4578999999884  4589998886544333  33444 88999999999999999999988999999999999999999


Q ss_pred             ccCC---CCh-------------HHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy6532         179 NMFH---ENP-------------LVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINND  229 (277)
Q Consensus       179 ~~~~---~~~-------------~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~  229 (277)
                      .+..   .++             +.+++.+++. ....|.++|||||+|.++||+||+||+.|++..
T Consensus        81 ~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~-~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          81 RWIVKWKKNGWKTADKKPVKNKDLWEELDELLK-RHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             HHHhhccccCccccccCccccHHHHHHHHHHHh-hCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            4421   111             2444444444 355899999999999999999999999998766

>PRK06548 ribonuclease H; Provisional

Probab=99.91  E-value=8.3e-24  Score=173.16  Aligned_cols=122  Identities=24%  Similarity=0.293  Sum_probs=92.9

Q ss_pred             CCceeeecCCCCC--CCeeEEEEEcCCCeEEeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhcc
Q psy6532         103 SNMKPTIDGSKNE--QGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNM  180 (277)
Q Consensus       103 ~~~~iytDGS~~~--~~~G~g~v~~~~~~~~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~~  180 (277)
                      ..+.||||||+.+  +..|+|+++.+... . .+.....||+.|||.|++.||+.+.. ....|.|+|||++++++|+.|
T Consensus         4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~-~-~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W   80 (161)
T PRK06548          4 NEIIAATDGSSLANPGPSGWAWYVDENTW-D-SGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKW   80 (161)
T ss_pred             CEEEEEEeeccCCCCCceEEEEEEeCCcE-E-ccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHH
Confidence            4589999999884  44889988764322 2 22234689999999999999986653 345799999999999999942


Q ss_pred             ---------CCCC-------hHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy6532         181 ---------FHEN-------PLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINND  229 (277)
Q Consensus       181 ---------~~~~-------~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~  229 (277)
                               ...+       .++++|.+++.+  ..|+|.|||||+|++|||.||+||++|+...
T Consensus        81 ~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~--~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~  143 (161)
T PRK06548         81 VYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN--RNIRMSWVNAHTGHPLNEAADSLARQAANNF  143 (161)
T ss_pred             HHHHHHCCCcccCCCccccHHHHHHHHHHHhc--CceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence                     2111       244556565553  4799999999999999999999999999665

>PRK08719 ribonuclease H; Reviewed

Probab=99.91  E-value=9.4e-24  Score=171.16  Aligned_cols=119  Identities=28%  Similarity=0.375  Sum_probs=89.6

Q ss_pred             CCceeeecCCCCCC-----CeeEEEEEcC--CCeE--EeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHH
Q psy6532         103 SNMKPTIDGSKNEQ-----GVGCALTIPE--KDIV--KRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSC  173 (277)
Q Consensus       103 ~~~~iytDGS~~~~-----~~G~g~v~~~--~~~~--~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~a  173 (277)
                      ..+++|||||+.++     ..|+|+++.+  +...  ....+....||++||+.|+..||+.+.+.    ..|+|||+++
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yv   78 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYC   78 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHH
Confidence            46899999999743     2589987654  3332  34445556899999999999999998752    4899999999


Q ss_pred             HHHHh--------ccCC-CC--h-----HHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhc
Q psy6532         174 LQAIM--------NMFH-EN--P-----LVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAIN  227 (277)
Q Consensus       174 i~~l~--------~~~~-~~--~-----~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~  227 (277)
                      +++++        +.+. ..  +     +.+.|.+++.  ...|+|.|||||+|++|||.||+||++|++
T Consensus        79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~--~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA--RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC--CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            99994        3332 11  1     2344444433  467999999999999999999999999975

>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=99.90  E-value=9.7e-24  Score=167.58  Aligned_cols=118  Identities=31%  Similarity=0.382  Sum_probs=93.5

Q ss_pred             CCceeeecCCCCC--CCeeEEEEEcCCCeEEeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhc-
Q psy6532         103 SNMKPTIDGSKNE--QGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMN-  179 (277)
Q Consensus       103 ~~~~iytDGS~~~--~~~G~g~v~~~~~~~~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~-  179 (277)
                      ..+.+|||||+.+  +..|+|++++.+ ......++ ..|++.||+.|+..||+.+ .  ...+.|+|||+++++.+.. 
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~-~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v~~~l~~~   76 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGG-RNFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYVLNALNKW   76 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETT-EEEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHHHHHHHTH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECC-eEEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHHHHHHHHh
Confidence            4689999999764  336888866555 34444455 7899999999999999944 3  3899999999999998877 


Q ss_pred             ----cCCC---C-hHHHHHHHHHhcCCCCeEEEEecCCCCC-ccchHHHHHHHHhh
Q psy6532         180 ----MFHE---N-PLVKRVQEELSSTESPVEFLWCPSHVGI-AGNETADEEAKQAI  226 (277)
Q Consensus       180 ----~~~~---~-~~~~~i~~~l~~~~~~v~~~WvpgH~g~-~gNe~AD~lAk~a~  226 (277)
                          .+..   . ++..+|.+++. .+..|.|.|||||+|+ .|||.||+|||+|+
T Consensus        77 ~~~~~~~~~~~~~~i~~~i~~~~~-~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   77 LHGNGWKKTSNGRPIKNEIWELLS-RGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HHHTTSBSCTSSSBHTHHHHHHHH-HSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccchhheeeccc-cceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence                3321   2 46678888774 4889999999999999 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 ....

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.90  E-value=2.6e-23  Score=169.57  Aligned_cols=122  Identities=22%  Similarity=0.294  Sum_probs=93.5

Q ss_pred             CceeeecCCCCC--CCeeEEEEEcCCCeE-EeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhcc
Q psy6532         104 NMKPTIDGSKNE--QGVGCALTIPEKDIV-KRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNM  180 (277)
Q Consensus       104 ~~~iytDGS~~~--~~~G~g~v~~~~~~~-~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~~  180 (277)
                      .+.||||||+.+  +..|+|+|+..++.. ...+.....||++|||.|+..||+.+.+  ...+.|+|||++++++|.++
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w   80 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEW   80 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHH
Confidence            478999999874  348888887543322 2223334689999999999999998865  46799999999999999863


Q ss_pred             C---------CC--C-----hHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy6532         181 F---------HE--N-----PLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINND  229 (277)
Q Consensus       181 ~---------~~--~-----~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~  229 (277)
                      .         ..  .     .++++|.+++.  ...|.|.|||||+|++||+.||+||++|+...
T Consensus        81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~--~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~  143 (150)
T PRK00203         81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALK--RHQIKWHWVKGHAGHPENERCDELARAGAEEA  143 (150)
T ss_pred             HHHHHHcCCcccCCCccccHHHHHHHHHHhc--cCceEEEEecCCCCCHHHHHHHHHHHHHHHHh
Confidence            1         11  1     13455655544  36899999999999999999999999998765

>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=99.80  E-value=1.1e-18  Score=135.21  Aligned_cols=120  Identities=32%  Similarity=0.391  Sum_probs=95.3

Q ss_pred             eeeecCCCCCC--CeeEEEEEcCCC--eEEe-ecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhcc
Q psy6532         106 KPTIDGSKNEQ--GVGCALTIPEKD--IVKR-FGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNM  180 (277)
Q Consensus       106 ~iytDGS~~~~--~~G~g~v~~~~~--~~~~-~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~~  180 (277)
                      .+|||||...+  ++|+|+++.+..  .... .......+++++|+.|+..||+.+...+..++.|++||+.+++.+++.
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~   80 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGW   80 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcc
Confidence            48999998754  689998875533  2222 222257899999999999999999988899999999999999999987


Q ss_pred             CC-C----ChHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhh
Q psy6532         181 FH-E----NPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAI  226 (277)
Q Consensus       181 ~~-~----~~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~  226 (277)
                      .. .    ..+...+++++ +....++|.|||+|+|..+|+.||.|||.|+
T Consensus        81 ~~~~~~~~~~~~~~i~~~~-~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          81 YEGKPVKNVDLWQRLLALL-KRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             ccCCChhhHHHHHHHHHHH-hCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            64 1    12345555554 3577899999999999999999999999874

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.

>KOG3752|consensus

Probab=99.80  E-value=4.4e-19  Score=159.26  Aligned_cols=127  Identities=21%  Similarity=0.192  Sum_probs=102.1

Q ss_pred             CCCceeeecCCCCC-----CCeeEEEEEcCCCeE-EeecCC-CCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHH
Q psy6532         102 NSNMKPTIDGSKNE-----QGVGCALTIPEKDIV-KRFGLN-KNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCL  174 (277)
Q Consensus       102 ~~~~~iytDGS~~~-----~~~G~g~v~~~~~~~-~~~~~~-~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai  174 (277)
                      ...+++|||||+..     ..+|+|++..++... .+..+. ...|||.|||.|+..||+-+.+....+|+|.|||++++
T Consensus       210 ~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i  289 (371)
T KOG3752|consen  210 IEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFI  289 (371)
T ss_pred             ccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHH
Confidence            34488999999874     248999998776554 556665 78899999999999999999998888999999999999


Q ss_pred             HHHhccCC---CC--------h----------HHHHHHHHHhc-CCCCeEEEEecCCCCCccchHHHHHHHHhhcC
Q psy6532         175 QAIMNMFH---EN--------P----------LVKRVQEELSS-TESPVEFLWCPSHVGIAGNETADEEAKQAINN  228 (277)
Q Consensus       175 ~~l~~~~~---~~--------~----------~~~~i~~~l~~-~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  228 (277)
                      +.|+.|..   .+        +          ...++.++++. .+..|.+.||+||.|+.|||+||.||+++...
T Consensus       290 ~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~  365 (371)
T KOG3752|consen  290 NSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL  365 (371)
T ss_pred             HHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence            99986542   11        1          12344455554 57899999999999999999999999998544

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.79  E-value=2.1e-18  Score=136.80  Aligned_cols=118  Identities=25%  Similarity=0.253  Sum_probs=92.9

Q ss_pred             ceeeecCCCCC--CCeeEEEEEcCCCeE--EeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhcc
Q psy6532         105 MKPTIDGSKNE--QGVGCALTIPEKDIV--KRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNM  180 (277)
Q Consensus       105 ~~iytDGS~~~--~~~G~g~v~~~~~~~--~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~~  180 (277)
                      ++||||||+..  +..|+|+|+.+....  ..+. ....||++||+.|++.||+.+.+.+..++.|+|||+.+++++++.
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~-~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~   80 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLP-LGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE   80 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEec-ccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHH
Confidence            57999999874  458999988654322  2222 245799999999999999999998888999999999999999986


Q ss_pred             CCCC----hHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcC
Q psy6532         181 FHEN----PLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINN  228 (277)
Q Consensus       181 ~~~~----~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  228 (277)
                      +..+    ++..+++.++. ....+.|.|||.    +.|+.||.||++|...
T Consensus        81 ~~~~~~~~~l~~~~~~l~~-~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         81 YAKNKMFAPLLEEALQYIK-SFDLFFIKWIPS----SQNKVADELARKAILQ  127 (128)
T ss_pred             HhcChhHHHHHHHHHHHHh-cCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence            6432    34556666554 355778899994    6999999999999753

>PRK07708 hypothetical protein; Validated

Probab=99.76  E-value=1.3e-17  Score=143.55  Aligned_cols=127  Identities=19%  Similarity=0.170  Sum_probs=100.2

Q ss_pred             cCCCceeeecCCCC--CCCeeEEEEEcC--CCeEE----eecCCCCcchhHHHHHHHHHHHHHHhhhCCCc--eEEEeCC
Q psy6532         101 ENSNMKPTIDGSKN--EQGVGCALTIPE--KDIVK----RFGLNKNASIFHAELFALLQSLLTIKQLGTCK--ALIITDS  170 (277)
Q Consensus       101 e~~~~~iytDGS~~--~~~~G~g~v~~~--~~~~~----~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~--v~I~tDS  170 (277)
                      |++.+++|+|||+.  ++++|+|+|+..  +....    ...++...||+.||+.|++.||+.+.+.+.+.  |.|++||
T Consensus        70 ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DS  149 (219)
T PRK07708         70 EPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDS  149 (219)
T ss_pred             CCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEecc
Confidence            47789999999986  356899988753  33322    12455568999999999999999999987654  8999999


Q ss_pred             HHHHHHHhccCC-CCh----HHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcCCcc
Q psy6532         171 LSCLQAIMNMFH-ENP----LVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINNDVI  231 (277)
Q Consensus       171 ~~ai~~l~~~~~-~~~----~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~~~  231 (277)
                      +.+++++++.+. .++    +...+.+++++....+.|.|||    +..|+.||+||++|++..+.
T Consensus       150 qlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~~  211 (219)
T PRK07708        150 QVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTVI  211 (219)
T ss_pred             HHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCCC
Confidence            999999999774 332    4556666666666678899998    78999999999999987643

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.61  E-value=1e-14  Score=135.65  Aligned_cols=120  Identities=21%  Similarity=0.311  Sum_probs=93.8

Q ss_pred             CceeeecCCCCC--CCeeEEEEEcC--CC-eE--EeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHH
Q psy6532         104 NMKPTIDGSKNE--QGVGCALTIPE--KD-IV--KRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQA  176 (277)
Q Consensus       104 ~~~iytDGS~~~--~~~G~g~v~~~--~~-~~--~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~  176 (277)
                      .+.||||||+.+  +.+|+|+++.+  +. ..  ....++ ..||+.||+.|++.||+.+.+.+.+++.|++||+.+++.
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~   80 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQ   80 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHH
Confidence            468999999885  35899988754  33 22  222333 678999999999999999999988999999999999999


Q ss_pred             HhccCC-CCh----HHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy6532         177 IMNMFH-ENP----LVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINND  229 (277)
Q Consensus       177 l~~~~~-~~~----~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~  229 (277)
                      +++.+. .+.    +..+++.+++ ....++|.|||    +++|+.||.||+.|+...
T Consensus        81 i~~~~~~~~~~l~~~~~~i~~l~~-~f~~~~i~~v~----r~~N~~AD~LA~~a~~~~  133 (372)
T PRK07238         81 MSGRWKVKHPDMKPLAAQARELAS-QFGRVTYTWIP----RARNAHADRLANEAMDAA  133 (372)
T ss_pred             hCCCCccCChHHHHHHHHHHHHHh-cCCceEEEECC----chhhhHHHHHHHHHHHhh
Confidence            998764 333    3445556554 44679999999    589999999999997544

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

Probab=99.36  E-value=6.1e-12  Score=92.10  Aligned_cols=82  Identities=29%  Similarity=0.310  Sum_probs=66.5

Q ss_pred             hhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhccCCC----ChHHHHHHHHHhcCCCCeEEEEecCCCCCccch
Q psy6532         141 IFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFHE----NPLVKRVQEELSSTESPVEFLWCPSHVGIAGNE  216 (277)
Q Consensus       141 ~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~~~~~----~~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe  216 (277)
                      +.+||+.|+..||+++.+.+..++.|+|||+.+++.+++....    ..++.+|+.+++. ...+.|.|||    +++|.
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~-~~~~~~~~i~----r~~N~   75 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDR-FWNVSVSHIP----REQNK   75 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCC-CSCEEEEE------GGGSH
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhcc-ccceEEEEEC----hHHhH
Confidence            4689999999999999999999999999999999999987532    2356677776664 7789999999    99999


Q ss_pred             HHHHHHHHhhc
Q psy6532         217 TADEEAKQAIN  227 (277)
Q Consensus       217 ~AD~lAk~a~~  227 (277)
                      .||.|||.|.+
T Consensus        76 ~A~~LA~~a~~   86 (87)
T PF13456_consen   76 VADALAKFALS   86 (87)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhh
Confidence            99999999874

>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family

Probab=82.18  E-value=8  Score=31.42  Aligned_cols=55  Identities=16%  Similarity=0.186  Sum_probs=35.0

Q ss_pred             CCCceeeecCCCCCCCeeEEEEEcC---CCeEE----e-ecCC--CCcchhHHHHHHHHHHHHHHhh
Q psy6532         102 NSNMKPTIDGSKNEQGVGCALTIPE---KDIVK----R-FGLN--KNASIFHAELFALLQSLLTIKQ  158 (277)
Q Consensus       102 ~~~~~iytDGS~~~~~~G~g~v~~~---~~~~~----~-~~~~--~~~t~~~aEl~Ai~~aL~~a~~  158 (277)
                      ...+++|+|+|..  +.|+.+++..   +....    + .++.  ...|+-+-||.|+..|.+.+..
T Consensus        79 ~~~L~~F~DAS~~--aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~  143 (159)
T PF05380_consen   79 SVELHVFCDASES--AYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT  143 (159)
T ss_pred             ceeeeEeeccccc--ceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence            4568999999943  3455444322   22221    1 1222  2458999999999999998864

---

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	277
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	2e-10
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	3e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-07
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	4e-06
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	2e-05
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	7e-05
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	7e-04

>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 = 57.0 bits (138), Expect = 2e-10
 Identities = 22/126 (17%), Positives = 38/126 (30%), Gaps = 9/126 (7%)

Query: 110 DGS--KNEQGVGCALTIPEKDIVKRFGL-----NKNASIFHAELFALLQSLLTIKQLGTC 162
           DGS    +     A     K   +   +              E+ A L ++    QLG  
Sbjct: 12  DGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLG-V 70

Query: 163 KALIITDSLSCLQAIMNMFHEN-PLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEE 221
           K  I+ D           +       +   + ++       F    +H G   N+  D +
Sbjct: 71  KIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMNQYRGIYSFEKVKAHSGNEFNDYVDMK 130

Query: 222 AKQAIN 227
           AK A+ 
Sbjct: 131 AKSALG 136

>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 = 56.8 bits (137), Expect = 3e-10
 Identities = 31/138 (22%), Positives = 48/138 (34%), Gaps = 17/138 (12%)

Query: 109 IDGSKN-EQGVGCA--LTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKAL 165
            DGS   ++G   A      E +++    L    S   AEL AL Q+L   K     K  
Sbjct: 28  TDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQAL---KMAEGKKLN 84

Query: 166 IITDSLSCLQAIMNMFHENP-----LVKRVQEELSSTESPVEFLWCPSHVG-----IAGN 215
           + TDS                     +  + + L   +  +  + CP H         GN
Sbjct: 85  VYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKR-LSIIHCPGHQKGNSAEARGN 143

Query: 216 ETADEEAKQAINNDVIHN 233
             AD+ A++A    V+  
Sbjct: 144 RMADQAAREAAMKAVLET 161

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 51.8 bits (123), Expect = 1e-07
 Identities = 44/276 (15%), Positives = 85/276 (30%), Gaps = 58/276 (21%)

Query: 27  NSLQILNPVQNLCLRLATGAFRSSPVVSLEAETGEPNLDIRRKILSSNYIA-KTLSIENH 85
            +L  L P +N+ +    G+ ++     +  +     L  + +      I    L   N 
Sbjct: 142 QALLELRPAKNVLIDGVLGSGKTW----VALDVC---LSYKVQCKMDFKIFWLNLKNCNS 194

Query: 86  PN-IMRTLNPLYVRKYENSNMKPTIDGSKNEQGVGCALTIPE-KDIVKRFGLNKNASIFH 143
           P  ++  L  L  +   + N     D S N +     L I   +  ++R   +K     +
Sbjct: 195 PETVLEMLQKLLYQI--DPNWTSRSDHSSNIK-----LRIHSIQAELRRLLKSKP----Y 243

Query: 144 AELFALL-----QSLLTIKQLG-TCKALIITDSLSCLQAIMNMFHENPLVKRVQEELSST 197
                LL     Q+         +CK L+ T        +      +  +      L+  
Sbjct: 244 EN--CLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPD 301

Query: 198 ESP---VEFLWC-------------PSHVGIAGNETADEEAKQAINNDVIHNELFFDEVK 241
           E     +++L C             P  + I      D  A    +N      +  D++ 
Sbjct: 302 EVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT--WDN---WKHVNCDKLT 356

Query: 242 IIIKKKYTEEWNTKWVNISPNENKLRKIKNSILPSS 277
            II+             + P E +    + S+ P S
Sbjct: 357 TIIESSLN--------VLEPAEYRKMFDRLSVFPPS 384

>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 = 44.9 bits (107), Expect = 4e-06
 Identities = 27/99 (27%), Positives = 36/99 (36%), Gaps = 21/99 (21%)

Query: 144 AELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFH----------------ENPLV 187
            EL A+  +L         +  I+TDS   L  I    H                   LV
Sbjct: 52  TELQAIYLALQDSG----LEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLV 107

Query: 188 KRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAI 226
            ++ E+L   E  V   W P+H GI GNE  D+     I
Sbjct: 108 NQIIEQLIKKEK-VYLAWVPAHKGIGGNEQVDKLVSAGI 145

>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 Length = 555

 Score = 44.3 bits (105), Expect = 2e-05
 Identities = 27/89 (30%), Positives = 39/89 (43%), Gaps = 15/89 (16%)

Query: 144 AELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFH------ENPLVKRVQEELSST 197
           AEL A   +L         K  II DS    Q +M +        E+ +V ++ EE+   
Sbjct: 476 AELEAFAMAL----TDSGPKVNIIVDS----QYVMGIVASQPTESESKIVNQIIEEMIKK 527

Query: 198 ESPVEFLWCPSHVGIAGNETADEEAKQAI 226
           E+ +   W P+H GI GN+  D    Q I
Sbjct: 528 EA-IYVAWVPAHKGIGGNQEVDHLVSQGI 555

>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* ... Length = 557

 Score = 42.8 bits (101), Expect = 7e-05
 Identities = 27/79 (34%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 144 AELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNM--FHENPLVKRVQEELSSTESPV 201
            EL A+  +L    Q    +  I+TDS   L  I       E+ LV ++ E+L   E  V
Sbjct: 479 TELQAIYLAL----QDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEK-V 533

Query: 202 EFLWCPSHVGIAGNETADE 220
              W P+H GI GNE  D+
Sbjct: 534 YLAWVPAHKGIGGNEQVDK 552

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

 Score = 38.3 bits (90), Expect = 7e-04
 Identities = 19/101 (18%), Positives = 37/101 (36%), Gaps = 18/101 (17%)

Query: 144 AELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFH---------------ENP-LV 187
           AE+ A  +++   K     K ++ T+S+  +  I N                   N    
Sbjct: 53  AEIHAACKAIEQAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDF 112

Query: 188 KRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINN 228
             ++      +  ++++  P H G  GNE AD  A++    
Sbjct: 113 VALERLTQGMD--IQWMHVPGHSGFIGNEEADRLAREGAKQ 151

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	277
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.93
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.93
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.92
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.92
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.92
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.91
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.91
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.9
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.89
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.86
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.85
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.85
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.83
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.82
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.53
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.35

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

Probab=99.93  E-value=4.1e-26  Score=185.60  Aligned_cols=126  Identities=18%  Similarity=0.226  Sum_probs=100.5

Q ss_pred             CCCceeeecCCCCCCC-----eeEEEEEcCCCe-EEeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHH
Q psy6532         102 NSNMKPTIDGSKNEQG-----VGCALTIPEKDI-VKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQ  175 (277)
Q Consensus       102 ~~~~~iytDGS~~~~~-----~G~g~v~~~~~~-~~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~  175 (277)
                      ...+.||||||+.+++     +|+|+|+.+++. ..+..+...+||+.||+.|++.||+.+.+.+..+|.|+|||+++++
T Consensus         5 ~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~   84 (154)
T 2qkb_A            5 GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTIN   84 (154)
T ss_dssp             TTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHH
T ss_pred             CCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHh
Confidence            3458899999987432     799998765432 2344555568999999999999999999888899999999999999


Q ss_pred             HHhccC--------C-C-------ChHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy6532         176 AIMNMF--------H-E-------NPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINND  229 (277)
Q Consensus       176 ~l~~~~--------~-~-------~~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~  229 (277)
                      +|.++.        . .       ..++++|..++.  +..|.|.|||||+|+++||+||+||++|+..+
T Consensus        85 ~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~--~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           85 GITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ--GMDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             HHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT--TCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             hhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc--CCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            998742        1 1       125666666655  45799999999999999999999999998764

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

Probab=99.93  E-value=4.3e-26  Score=183.78  Aligned_cols=122  Identities=19%  Similarity=0.152  Sum_probs=95.7

Q ss_pred             CCceeeecCCCCCC--CeeEEEEEcCCCeEE--eecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHh
Q psy6532         103 SNMKPTIDGSKNEQ--GVGCALTIPEKDIVK--RFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIM  178 (277)
Q Consensus       103 ~~~~iytDGS~~~~--~~G~g~v~~~~~~~~--~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~  178 (277)
                      ..+.+|||||+..+  ..|+|+++..++...  +... +.+||+.||+.|++.||+.+.+  ..++.|+|||++++++|.
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~   79 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMN   79 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHH
Confidence            45899999998753  389998876554322  2222 3689999999999999999976  589999999999999998


Q ss_pred             c-cC--------C--------CChHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy6532         179 N-MF--------H--------ENPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINND  229 (277)
Q Consensus       179 ~-~~--------~--------~~~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~  229 (277)
                      + +.        .        ...+++++.+++.+  ..|.|.|||||+|+++||+||+|||+|+...
T Consensus        80 ~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~--~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~~  145 (146)
T 3h08_A           80 EGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTL--HRVTFHKVKGHSDNPYNSRADELARLAIKEN  145 (146)
T ss_dssp             SSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHH--SEEEEEECCC-CCSHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhh--CceEEEEcCCcCCcHhHHHHHHHHHHHHHhC
Confidence            8 31        0        12356677776664  4699999999999999999999999998754

>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=99.92  E-value=5.5e-26  Score=183.56  Aligned_cols=128  Identities=17%  Similarity=0.104  Sum_probs=100.1

Q ss_pred             CCCceeeecCCCCCCCeeEEEEEcC-CCeE-Eee-cC--CC--CcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHH
Q psy6532         102 NSNMKPTIDGSKNEQGVGCALTIPE-KDIV-KRF-GL--NK--NASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCL  174 (277)
Q Consensus       102 ~~~~~iytDGS~~~~~~G~g~v~~~-~~~~-~~~-~~--~~--~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai  174 (277)
                      ...+.+|||||+.++.+|+|+|+.+ +... ... +.  +.  ..||+.||+.|++.||+.+.+.+. +|.|+|||+.+.
T Consensus         4 ~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i~   82 (147)
T 2kq2_A            4 RTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGIA   82 (147)
T ss_dssp             TSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTHH
T ss_pred             CCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHHH
Confidence            4568999999999877999998764 4322 222 22  22  369999999999999999888777 999999999988


Q ss_pred             HHHhccCCC-ChHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcCCc
Q psy6532         175 QAIMNMFHE-NPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINNDV  230 (277)
Q Consensus       175 ~~l~~~~~~-~~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~~  230 (277)
                      +.+.+.+.. ++....+.+++++....|.|.|||||+|+++||+||+|||+|+....
T Consensus        83 ~w~~~~w~~~~~~~~~~~~l~~~l~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~  139 (147)
T 2kq2_A           83 FWATGEWKAKNEFTQAYAKLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAKSALGIRD  139 (147)
T ss_dssp             HHTTSSSSCCHHHHHHHHCGGGGGSTTCCBCCCCCCCCCHHHHHHHHHHHHHHTCCC
T ss_pred             HHHhCCCccCCcchHHHHHHHHHhcCCeeEEEecCcCCCcchHHHHHHHHHHHhccc
Confidence            888776653 34444555555443338999999999999999999999999998773

>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=99.92  E-value=1e-24  Score=176.64  Aligned_cols=120  Identities=24%  Similarity=0.293  Sum_probs=94.0

Q ss_pred             CCCceeeecCCCCC--CCeeEEEEEcCCCeEEeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhc
Q psy6532         102 NSNMKPTIDGSKNE--QGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMN  179 (277)
Q Consensus       102 ~~~~~iytDGS~~~--~~~G~g~v~~~~~~~~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~  179 (277)
                      ...+.+|||||+..  +..|+|+++.++.... ... ..+||+.||+.|++.||+.+    ..++.|+|||++++++|++
T Consensus        10 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~-~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i~~   83 (150)
T 3qio_A           10 VGAETFYVDGAANRETKLGKAGYVTNRGRQKV-VTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIITQ   83 (150)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEE-EEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHHHH
T ss_pred             CCCEEEEEccCCCCCCCCeEEEEEEEcCCEEE-EeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHHHH
Confidence            45689999999874  3488998887654332 223 46899999999999999985    4799999999999999987


Q ss_pred             cC---C-------------CChHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcC
Q psy6532         180 MF---H-------------ENPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINN  228 (277)
Q Consensus       180 ~~---~-------------~~~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  228 (277)
                      +.   .             ...+.+++.+++. ....|.|.|||||+|++|||+||+||++|+..
T Consensus        84 w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~-~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           84 WIHNWKKRGWKTADKKPVKNVDLVNQIIEQLI-KKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHCC------------CHHHHHHHHHHHT-TCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHhhcCcCcCcCcccccHHHHHHHHHHHh-hcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            62   0             1123445544443 46789999999999999999999999999875

>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=99.92  E-value=5.5e-25  Score=179.18  Aligned_cols=122  Identities=23%  Similarity=0.290  Sum_probs=95.8

Q ss_pred             CceeeecCCCCCC--CeeEEEEEcCCCeE--EeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhc
Q psy6532         104 NMKPTIDGSKNEQ--GVGCALTIPEKDIV--KRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMN  179 (277)
Q Consensus       104 ~~~iytDGS~~~~--~~G~g~v~~~~~~~--~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~  179 (277)
                      .+.+|||||+.++  ..|+|+|+.+++..  ..... +.+||+.||+.|++.||+.+.+  ..++.|+|||++++++|.+
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~--~~~v~I~tDS~~vi~~i~~   80 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQ   80 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHT
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc--CCcEEEEeCHHHHHHHHHH
Confidence            5789999999753  38999887643322  22223 3678999999999999999876  3799999999999999997


Q ss_pred             c--------CC-------C-ChHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcCCc
Q psy6532         180 M--------FH-------E-NPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINNDV  230 (277)
Q Consensus       180 ~--------~~-------~-~~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~~  230 (277)
                      |        +.       . ..+.++|.++++  ...|.|.|||||+|+++||.||+||++|+..+.
T Consensus        81 w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~--~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~  145 (155)
T 1jl1_A           81 WIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQIKWEWVKGHAGHPENERADELARAAAMNPT  145 (155)
T ss_dssp             THHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT--TCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHhhcccccccCCccCCHHHHHHHHHHHc--cCceEEEEcCCCCCCHHHHHHHHHHHHHHhccc
Confidence            3        11       1 135566666554  368999999999999999999999999998764

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

Probab=99.91  E-value=5.9e-25  Score=179.57  Aligned_cols=120  Identities=26%  Similarity=0.332  Sum_probs=94.6

Q ss_pred             CceeeecCCCCC--CCeeEEEEEcCCCeE--EeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhc
Q psy6532         104 NMKPTIDGSKNE--QGVGCALTIPEKDIV--KRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMN  179 (277)
Q Consensus       104 ~~~iytDGS~~~--~~~G~g~v~~~~~~~--~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~  179 (277)
                      .+.||||||+.+  +.+|+|+|+.+++..  ..... +.+||+.||+.|++.||+.+.+  ..+|.|+|||++++++|.+
T Consensus         6 ~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~~   82 (158)
T 2e4l_A            6 LIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKE--PCKIILTSDSQYMRQGIMT   82 (158)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEECCHHHHHHHHT
T ss_pred             eEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhcc--CCeEEEEeCHHHHHHHHHH
Confidence            478999999974  348999887544322  22223 3579999999999999999865  3899999999999999988


Q ss_pred             --------cCC-------CC-hHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcC
Q psy6532         180 --------MFH-------EN-PLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINN  228 (277)
Q Consensus       180 --------~~~-------~~-~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  228 (277)
                              .+.       .+ .+++++.++++  ...|.|.|||||+|+++||.||+||++|+..
T Consensus        83 w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~--~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A           83 WIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQ--LHQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             HHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHT--TSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHccccccCCCcccCHHHHHHHHHHHc--cCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence                    221       11 34566666665  3589999999999999999999999999987

>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=99.91  E-value=1.4e-24  Score=178.38  Aligned_cols=124  Identities=23%  Similarity=0.236  Sum_probs=94.9

Q ss_pred             CCCceeeecCCCC--CCCeeEEEEEcC-CCeEEeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHh
Q psy6532         102 NSNMKPTIDGSKN--EQGVGCALTIPE-KDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIM  178 (277)
Q Consensus       102 ~~~~~iytDGS~~--~~~~G~g~v~~~-~~~~~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~  178 (277)
                      ...+.+|||||+.  ++..|+|+++.. ++.....+....+||+.||+.|++.||+.+   ...++.|||||+++++.+-
T Consensus        21 ~~~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~iw   97 (165)
T 3p1g_A           21 DADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATAH   97 (165)
T ss_dssp             TCSEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHHH
T ss_pred             CCCEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhhh
Confidence            3458999999997  345888887654 443333345567899999999999999999   3689999999999999993


Q ss_pred             ccCC----CC-hHHHHHHHHHhcCCCCeEEEEecCCCC-----CccchHHHHHHHHhhcCC
Q psy6532         179 NMFH----EN-PLVKRVQEELSSTESPVEFLWCPSHVG-----IAGNETADEEAKQAINND  229 (277)
Q Consensus       179 ~~~~----~~-~~~~~i~~~l~~~~~~v~~~WvpgH~g-----~~gNe~AD~lAk~a~~~~  229 (277)
                      ....    .+ .+++++.+.+. .+..|.|.|||||+|     ++|||+||+|||+|+...
T Consensus        98 ~~~~g~~v~n~dl~~~l~~~l~-~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~  157 (165)
T 3p1g_A           98 VHSEGREIKNKNEILALLKALF-LPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKA  157 (165)
T ss_dssp             SCCCSCCCSSHHHHHHHHHHTT-SBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCcccCHHHHHHHHHHHh-cCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcC
Confidence            1111    12 23444444333 467899999999999     999999999999999876

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

Probab=99.90  E-value=2.5e-24  Score=177.20  Aligned_cols=124  Identities=21%  Similarity=0.213  Sum_probs=96.0

Q ss_pred             CCceeeecCCCCCC--CeeEEEEEcCCCeE-EeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhc
Q psy6532         103 SNMKPTIDGSKNEQ--GVGCALTIPEKDIV-KRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMN  179 (277)
Q Consensus       103 ~~~~iytDGS~~~~--~~G~g~v~~~~~~~-~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~  179 (277)
                      ..+.||||||+.++  ..|+|+|+.+++.. ...+....+||+.||+.|++.||+.+.+.  .+|.|+|||++++++|.+
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i~~   84 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAFTE   84 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHHHS
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHHhh
Confidence            45789999999853  48999987543322 11111236799999999999999988653  589999999999999998


Q ss_pred             -c--------C-CC------C-hHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcCCc
Q psy6532         180 -M--------F-HE------N-PLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINNDV  230 (277)
Q Consensus       180 -~--------~-~~------~-~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~~  230 (277)
                       |        + ..      + .++++|.+++..  ..|.|.|||||+|+++||.||+|||+|+....
T Consensus        85 ~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~--~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~  150 (166)
T 1ril_A           85 GWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP--HRVRFHFVKGHTGHPENERVDREARRQAQSQA  150 (166)
T ss_dssp             SHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTT--SEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             hHHHHHHhcccccccCCccCcHHHHHHHHHHHhc--CeEEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence             2        2 11      1 256667666653  58999999999999999999999999998874

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

Probab=99.89  E-value=1.2e-22  Score=166.72  Aligned_cols=124  Identities=19%  Similarity=0.165  Sum_probs=91.3

Q ss_pred             CCceeeecCCCCC--CC-----eeEEEEEcCCC----eEEeecC-CCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCC
Q psy6532         103 SNMKPTIDGSKNE--QG-----VGCALTIPEKD----IVKRFGL-NKNASIFHAELFALLQSLLTIKQLGTCKALIITDS  170 (277)
Q Consensus       103 ~~~~iytDGS~~~--~~-----~G~g~v~~~~~----~~~~~~~-~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS  170 (277)
                      ..+++|||||+..  ++     +|+|+|+..++    ....+.. ..+.+++.||+.|+..||+.+.+.+ .+|.|+|||
T Consensus         6 ~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~~-~~v~I~TDS   84 (165)
T 2lsn_A            6 YEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIP-GPVLVITDS   84 (165)
T ss_dssp             CSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHSS-SCEEEEESC
T ss_pred             ceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcCC-CeEEEEeCh
Confidence            4578999999873  22     79999874322    2223322 2467888999999999998877644 579999999


Q ss_pred             HHHHHHHhccC---------C------CC-hHHHHHHHHHhcCCCCeEEEEecCCCC------CccchHHHHHHHHhhcC
Q psy6532         171 LSCLQAIMNMF---------H------EN-PLVKRVQEELSSTESPVEFLWCPSHVG------IAGNETADEEAKQAINN  228 (277)
Q Consensus       171 ~~ai~~l~~~~---------~------~~-~~~~~i~~~l~~~~~~v~~~WvpgH~g------~~gNe~AD~lAk~a~~~  228 (277)
                      ++++++|..|.         .      .+ .+++++.+++.. ...|.|.|||||+|      .+|||+||+||++|+..
T Consensus        85 ~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~-~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~~  163 (165)
T 2lsn_A           85 FYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSM-KPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSYV  163 (165)
T ss_dssp             HHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHH-CTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhC-CCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhhhh
Confidence            99999997532         1      11 255666666654 45799999999999      46899999999999853

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

Probab=99.86  E-value=2.3e-21  Score=154.03  Aligned_cols=119  Identities=18%  Similarity=0.264  Sum_probs=93.6

Q ss_pred             CceeeecCCCCC--CCeeEEEEEcC--CCeEE--eecCCCCcchhHHHHHHHHHHHHHHhhhCCC----ceEEEeCCHHH
Q psy6532         104 NMKPTIDGSKNE--QGVGCALTIPE--KDIVK--RFGLNKNASIFHAELFALLQSLLTIKQLGTC----KALIITDSLSC  173 (277)
Q Consensus       104 ~~~iytDGS~~~--~~~G~g~v~~~--~~~~~--~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~----~v~I~tDS~~a  173 (277)
                      .+.+|||||+..  +.+|+|+++.+  +....  ...+ +.+||+.||+.|++.||+.+.+.+..    ++.|+|||+++
T Consensus         3 ~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~v   81 (140)
T 3u3g_D            3 KIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYI-GETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELI   81 (140)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEE-EEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHH
T ss_pred             eEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeC-CCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHH
Confidence            478999999874  34899988754  44332  2222 35799999999999999999987777    99999999999


Q ss_pred             HHHHhccCC-CCh----HHHHHHHH-HhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcC
Q psy6532         174 LQAIMNMFH-ENP----LVKRVQEE-LSSTESPVEFLWCPSHVGIAGNETADEEAKQAINN  228 (277)
Q Consensus       174 i~~l~~~~~-~~~----~~~~i~~~-l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  228 (277)
                      ++.+++++. .++    +..++.++ +.+ ...|.|.|||    +++||.||+|||+|+..
T Consensus        82 i~~i~~~~~~~~~~l~~~~~~i~~l~~~~-~~~v~~~~V~----~~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D           82 VRQMQGVYKVKEPTLKEKFAKIAHIKMER-VPNLVFVHIP----REKNARADELVNEAIDK  137 (140)
T ss_dssp             HHHHTTSSCCCCGGGHHHHHHHHHHHHHH-CTTCEEEECC----GGGGHHHHHHHHHHHHH
T ss_pred             HHHhCCCcccCCHHHHHHHHHHHHHhhcC-CCcEEEEEcC----chhhHHHHHHHHHHHHh
Confidence            999999764 332    34556666 553 3589999999    69999999999999864

>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=99.85  E-value=5e-21  Score=152.56  Aligned_cols=120  Identities=20%  Similarity=0.271  Sum_probs=93.8

Q ss_pred             CceeeecCCCCCC--CeeEEEEEcC---CCeEE--eecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHH
Q psy6532         104 NMKPTIDGSKNEQ--GVGCALTIPE---KDIVK--RFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQA  176 (277)
Q Consensus       104 ~~~iytDGS~~~~--~~G~g~v~~~---~~~~~--~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~  176 (277)
                      .+.+|||||+.++  .+|+|+++.+   +....  ...+ +.+||+.||+.|++.||+.+.+.+..++.|+|||+++++.
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~   81 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAI-GRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQ   81 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccC-CCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHH
Confidence            4789999998743  5899988754   22322  2222 3689999999999999999999888999999999999999


Q ss_pred             HhccCC-CChH----HHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy6532         177 IMNMFH-ENPL----VKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINND  229 (277)
Q Consensus       177 l~~~~~-~~~~----~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~  229 (277)
                      +++.+. .++.    ..++++++. ....|.|.|||    .++|+.||+||++|+...
T Consensus        82 i~~~~~~~~~~l~~~~~~i~~l~~-~~~~v~~~~V~----~~~N~~AD~LA~~a~~~~  134 (141)
T 3hst_B           82 MSGRWKVKHPDLLKLYVQAQALAS-QFRRINYEWVP----RARNTYADRLANDAMDAA  134 (141)
T ss_dssp             HTTSSCCCSHHHHHHHHHHHHHHT-TSSEEEEEECC----GGGCHHHHHHHHHHHHHH
T ss_pred             HhCCcccCCHHHHHHHHHHHHHHh-cCCeEEEEEcC----CcccHHHHHHHHHHHHHh
Confidence            998653 4442    234444443 45789999999    589999999999998765

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

Probab=99.85  E-value=1.1e-20  Score=152.38  Aligned_cols=119  Identities=19%  Similarity=0.267  Sum_probs=94.5

Q ss_pred             ceeeecCCCC--C-CCeeE-EEEEcC-CCeEEee--cCC---CCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHH
Q psy6532         105 MKPTIDGSKN--E-QGVGC-ALTIPE-KDIVKRF--GLN---KNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCL  174 (277)
Q Consensus       105 ~~iytDGS~~--~-~~~G~-g~v~~~-~~~~~~~--~~~---~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai  174 (277)
                      +.+|||||+.  + +.+|+ |+++.+ |.....+  ..+   +..||+.||+.|++.||+.+.+.+..++.|+|||++++
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi   81 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVI   81 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHH
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHH
Confidence            5799999987  2 45885 987764 4443222  222   37899999999999999999998889999999999999


Q ss_pred             HHHhccCCC-C----hHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy6532         175 QAIMNMFHE-N----PLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINND  229 (277)
Q Consensus       175 ~~l~~~~~~-~----~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~  229 (277)
                      +.+++++.. +    .+.+++..++++.  .|.|.|||+    ++|+.||+||++|+...
T Consensus        82 ~~i~~~w~~~~~~~~~l~~~i~~l~~~~--~v~~~~V~~----~~N~~AD~LA~~a~~~~  135 (149)
T 2ehg_A           82 KQMNGEYKVKAKRIIPLYEKAIELKKKL--NATLIWVPR----EENKEADRLSRVAYELV  135 (149)
T ss_dssp             HHHTTSSCCCCTTHHHHHHHHHHHHHHH--TCEEEECCG----GGCHHHHHHHHHHHHHH
T ss_pred             HHHhCccccCCHHHHHHHHHHHHHHhcC--CEEEEEcCC----cccHHHHHHHHHHHHhh
Confidence            999998642 2    2456666666654  599999997    69999999999999766

>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=99.83  E-value=1.3e-20  Score=182.28  Aligned_cols=118  Identities=25%  Similarity=0.276  Sum_probs=95.9

Q ss_pred             CCCceeeecCCCCCC--CeeEEEEEcCCCeEEeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhc
Q psy6532         102 NSNMKPTIDGSKNEQ--GVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMN  179 (277)
Q Consensus       102 ~~~~~iytDGS~~~~--~~G~g~v~~~~~~~~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~  179 (277)
                      ...+.+|||||+..+  ..|+|+++..++.. .... ..+||+.||+.|++.||+.    +..++.|+|||++|++++++
T Consensus       434 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~-~~~~-~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~  507 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDK-VKKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVAS  507 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEE-EEEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHT
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCCEe-eccC-CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhc
Confidence            456899999998743  37899988766533 2222 3679999999999999988    56899999999999999998


Q ss_pred             cCC--CChHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhh
Q psy6532         180 MFH--ENPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAI  226 (277)
Q Consensus       180 ~~~--~~~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~  226 (277)
                      +..  ..++.+++.+++.+ ...|.|.|||||+|++|||+||+||++|+
T Consensus       508 ~~~~~~~~l~~~~~~~~~~-~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          508 QPTESESKIVNQIIEEMIK-KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             CCSEESCHHHHHHHHHHHH-CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             ccccccHHHHHHHHHHhcc-CCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            763  45677777666553 57799999999999999999999999885

>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=99.82  E-value=1.2e-20  Score=182.65  Aligned_cols=117  Identities=25%  Similarity=0.278  Sum_probs=92.7

Q ss_pred             CCCceeeecCCCCC--CCeeEEEEEcCCCeEEeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhc
Q psy6532         102 NSNMKPTIDGSKNE--QGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMN  179 (277)
Q Consensus       102 ~~~~~iytDGS~~~--~~~G~g~v~~~~~~~~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~  179 (277)
                      ...+.+|||||+..  +..|+|+++..++.... +. ..+||+.||+.|++.||+.+    ..++.|+|||++|++++++
T Consensus       437 ~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~-~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~  510 (557)
T 2zd1_A          437 VGAETFYVDGAANRETKLGKAGYVTNKGRQKVV-PL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQA  510 (557)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEETTSCEEEE-EE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTT
T ss_pred             CCCEEEEEccCCCCCCCceEEEEEEECCcEEEe-cC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhc
Confidence            45689999999864  33788988876553322 22 46899999999999999998    5799999999999999999


Q ss_pred             cCCC--ChHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHh
Q psy6532         180 MFHE--NPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQA  225 (277)
Q Consensus       180 ~~~~--~~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a  225 (277)
                      +...  ..+.+++.+.+.+ ...|.|.|||||+|++|||+||+||++|
T Consensus       511 ~~~~~~~~l~~~~~~~l~~-~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          511 QPDKSESELVNQIIEQLIK-KEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             CCSEESSHHHHHHHHHHHH-CSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             CCccCCHHHHHHHHHHHhc-CCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            7753  4567776655544 3579999999999999999999999986

>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=99.53  E-value=4.5e-15  Score=118.49  Aligned_cols=116  Identities=14%  Similarity=0.038  Sum_probs=84.6

Q ss_pred             CCCceeeecCCCCC--CCeeEEEEEcC-CCeEEeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHh
Q psy6532         102 NSNMKPTIDGSKNE--QGVGCALTIPE-KDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIM  178 (277)
Q Consensus       102 ~~~~~iytDGS~~~--~~~G~g~v~~~-~~~~~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~  178 (277)
                      ..-+.+|||||+..  +.+|+|+|+.. +........-..+||+.||+.|++.||+.+.+.+. ++.|+|||+++++.+.
T Consensus         9 ~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~~   87 (142)
T 1zbf_A            9 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWVK   87 (142)
T ss_dssp             CCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHHH
T ss_pred             CCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccCCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHHH
Confidence            34578999999874  34899998863 44333222122579999999999999999998776 9999999999999999


Q ss_pred             ccCCC--------C-hHHHHHHHH---HhcCCCCeEEEEecCCCCCccchHHHH
Q psy6532         179 NMFHE--------N-PLVKRVQEE---LSSTESPVEFLWCPSHVGIAGNETADE  220 (277)
Q Consensus       179 ~~~~~--------~-~~~~~i~~~---l~~~~~~v~~~WvpgH~g~~gNe~AD~  220 (277)
                      +.+..        + .+.+.+.++   ++.  ..++...++-|++..||..||.
T Consensus        88 ~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~--~~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A           88 DKKAKSTLVRNEETALIWKLVDEAEEWLNT--HTYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             HTCCCCCCCCSTTTHHHHHHHHHHHHHHHH--CCCCCCEEECCHHHHCSCTTCC
T ss_pred             cCCccCCCCCCcccHHHHHHHHHHHHHHhh--CCCceeEEEeccCccCcCcccc
Confidence            87621        1 134444433   333  4456667888888999999884

>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=99.35  E-value=7.7e-13  Score=103.93  Aligned_cols=79  Identities=13%  Similarity=0.053  Sum_probs=59.9

Q ss_pred             cCCCceeeecCCCCC--CCeeEEEEEcC-CCeEE-eecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHH
Q psy6532         101 ENSNMKPTIDGSKNE--QGVGCALTIPE-KDIVK-RFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQA  176 (277)
Q Consensus       101 e~~~~~iytDGS~~~--~~~G~g~v~~~-~~~~~-~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~  176 (277)
                      |.....+|||||+..  +..|+|.|+.. +.... ...+ ..+||++||++|++.||+.+.+.+.. +.|+|||++|++.
T Consensus         2 ep~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~-~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~w   79 (134)
T 4htu_A            2 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKW   79 (134)
T ss_dssp             CCCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHH
T ss_pred             CccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCC-CCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHH
Confidence            455678999999874  34888655544 44332 2233 36899999999999999999886544 8999999999999


Q ss_pred             HhccC
Q psy6532         177 IMNMF  181 (277)
Q Consensus       177 l~~~~  181 (277)
                      +.++.
T Consensus        80 i~~~~   84 (134)
T 4htu_A           80 VKDKK   84 (134)
T ss_dssp             HHHTC
T ss_pred             HHcCC
Confidence            98754

---

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	277
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	4e-09
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	2e-05
d1s1ta1	110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	3e-05
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	8e-05

>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 = 51.8 bits (123), Expect = 4e-09
 Identities = 30/120 (25%), Positives = 45/120 (37%), Gaps = 7/120 (5%)

Query: 109 IDGSKNEQGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIIT 168
            DGS N Q               +    +  +   AEL A   +L         K  II 
Sbjct: 12  TDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTDSG----PKVNIIV 67

Query: 169 DSLSCLQAIMNMFHE--NPLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAI 226
           DS   +  + +   E  + +V ++ EE+   E  +   W P+H GI GN+  D    Q I
Sbjct: 68  DSQYVMGIVASQPTESESKIVNQIIEEMIKKE-AIYVAWVPAHKGIGGNQEVDHLVSQGI 126

>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 = 41.5 bits (96), Expect = 2e-05
 Identities = 28/137 (20%), Positives = 44/137 (32%), Gaps = 20/137 (14%)

Query: 110 DGS-KNEQGVG--CALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALI 166
           DG+     G G   AL           G     +    EL A ++ L  +K+   C+  +
Sbjct: 9   DGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE--PCEVDL 66

Query: 167 ITDSLSCLQAIMNMFHENPLVKR---------------VQEELSSTESPVEFLWCPSHVG 211
            TDS    +A    + E    +                    L+     V F +   H G
Sbjct: 67  YTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTG 126

Query: 212 IAGNETADEEAKQAINN 228
              NE  D EA++   +
Sbjct: 127 HPENERVDREARRQAQS 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 = 40.4 bits (94), Expect = 3e-05
 Identities = 27/103 (26%), Positives = 43/103 (41%), Gaps = 9/103 (8%)

Query: 110 DGS-KNEQGVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIIT 168
           DG+   E  +G A  +  +   K   L  + +    EL A+  +L    Q    +  I+T
Sbjct: 14  DGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLAL----QDSGLEVNIVT 68

Query: 169 DSLSCLQAIMNMFHEN--PLVKRVQEELSSTESPVEFLWCPSH 209
           DS   L  I     ++   LV ++ E+L   E  V   W P+H
Sbjct: 69  DSQYALGIIQAQPDQSESELVNQIIEQLIKKEK-VYLAWVPAH 110

>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 = 40.0 bits (92), Expect = 8e-05
 Identities = 11/37 (29%), Positives = 18/37 (48%)

Query: 200 PVEFLWCPSHVGIAGNETADEEAKQAINNDVIHNELF 236
            +++ W   H G   NE ADE A+ A  N  + +  +
Sbjct: 113 QIKWEWVKGHAGHPENERADELARAAAMNPTLEDTGY 149

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	277
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.93
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.91
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.9
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.79
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.67

>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=99.93  E-value=9.8e-26  Score=175.52  Aligned_cols=116  Identities=24%  Similarity=0.282  Sum_probs=89.5

Q ss_pred             CCceeeecCCCCC-C-CeeEEEEEcCCCeEEeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhcc
Q psy6532         103 SNMKPTIDGSKNE-Q-GVGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNM  180 (277)
Q Consensus       103 ~~~~iytDGS~~~-~-~~G~g~v~~~~~~~~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~~  180 (277)
                      ...++|||||+.. + ..|+|++++.+..... .+ ...||+.||+.||..||+.    ....+.|+|||+++++.+.++
T Consensus         6 ~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~-~~-~~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v~~~~~~~   79 (126)
T d1mu2a1           6 GAETFYTDGSCNRQSKEGKAGYVTDRGKDKVK-KL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQ   79 (126)
T ss_dssp             TCEEEEEEEEECTTTCCEEEEEEETTSCEEEE-EE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTC
T ss_pred             CCcEEEEcCCCCCCCCcEEEEEEecCCCEEEE-ec-CCCcchHHHHHHHHHHhcc----CCcceEEEechHHHHHHHhcC
Confidence            4468999999764 3 3777887777655432 22 2579999999999999875    357899999999999999997


Q ss_pred             CC--CChHHH-HHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhh
Q psy6532         181 FH--ENPLVK-RVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAI  226 (277)
Q Consensus       181 ~~--~~~~~~-~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~  226 (277)
                      +.  .+.... .+..+.+  ...|.|.|||||+|++|||+||+||++|+
T Consensus        80 ~~~~~~~~~~~~~~~~~~--~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          80 PTESESKIVNQIIEEMIK--KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             CSEESCHHHHHHHHHHHH--CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             CccccchHHHHHHHHhhh--cceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            75  333333 3444333  45899999999999999999999999984

>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=99.91  E-value=2.4e-25  Score=177.63  Aligned_cols=123  Identities=20%  Similarity=0.198  Sum_probs=92.7

Q ss_pred             CCceeeecCCCCCC--CeeEEEEEcC-CCeEEeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhc
Q psy6532         103 SNMKPTIDGSKNEQ--GVGCALTIPE-KDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMN  179 (277)
Q Consensus       103 ~~~~iytDGS~~~~--~~G~g~v~~~-~~~~~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~  179 (277)
                      ..++||||||+.++  ..|+|+|+.. +...........+||+.||+.|+..||+++..  ...+.|+|||+++++.+..
T Consensus         2 ~~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~--~~~i~i~tds~~~~~~~~~   79 (147)
T d1rila_           2 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYLKKAFTE   79 (147)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHHHHHHHS
T ss_pred             CEEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhccC--CceEEEecchhhhhccccc
Confidence            46899999998853  3788988754 33222222234579999999999999987653  5689999999999998865


Q ss_pred             cCC----------C--C-----hHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy6532         180 MFH----------E--N-----PLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINND  229 (277)
Q Consensus       180 ~~~----------~--~-----~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~  229 (277)
                      ...          .  .     .+++++..++.  ...|+|.|||||+|++|||+||+||++|+...
T Consensus        80 ~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~--~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_          80 GWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA--PHRVRFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             SHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT--TSEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             cchhhhhhccccccccccchhHHHHHHHHHHhh--hcccceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence            321          0  1     13455555433  56799999999999999999999999999875

>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=99.90  E-value=1.7e-24  Score=173.07  Aligned_cols=124  Identities=23%  Similarity=0.278  Sum_probs=92.9

Q ss_pred             CceeeecCCCCCC--CeeEEEEEcCCCeEE-eecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhcc
Q psy6532         104 NMKPTIDGSKNEQ--GVGCALTIPEKDIVK-RFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNM  180 (277)
Q Consensus       104 ~~~iytDGS~~~~--~~G~g~v~~~~~~~~-~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~~  180 (277)
                      .|.||||||+.++  .+|+|+|+..++... .....+..|++.||+.|+..|++++..  ...+.++|||++++..+..+
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~~--~~~i~i~tds~~~i~~~~~~   79 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQW   79 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHTT
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhcc--cceEEEeecceeeEEcccch
Confidence            5789999998753  389998876544332 222224678999999999999988654  56789999999999988754


Q ss_pred             CC---------C--C-----hHHHHHHHHHhcCCCCeEEEEecCCCCCccchHHHHHHHHhhcCCcc
Q psy6532         181 FH---------E--N-----PLVKRVQEELSSTESPVEFLWCPSHVGIAGNETADEEAKQAINNDVI  231 (277)
Q Consensus       181 ~~---------~--~-----~~~~~i~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~~~  231 (277)
                      ..         .  .     .+..++..++  ....|.|+|||||+|++|||+||+|||+|+..++.
T Consensus        80 ~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~--~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~  144 (152)
T d1jl1a_          80 IHNWKKRGWKTADKKPVKNVDLWQRLDAAL--GQHQIKWEWVKGHAGHPENERADELARAAAMNPTL  144 (152)
T ss_dssp             HHHHHHTTTBCTTSCBCTTHHHHHHHHHHT--TTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             hhHhHhccchhcccCeeecHHHHHHHHHHh--hcceeEEEEecccCCCccHHHHHHHHHHHHhCCCC
Confidence            31         1  1     1334444433  34689999999999999999999999999987743

>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=99.79  E-value=2.8e-19  Score=135.18  Aligned_cols=101  Identities=23%  Similarity=0.247  Sum_probs=77.2

Q ss_pred             CCCceeeecCCCCC-CC-eeEEEEEcCCCeEEeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhc
Q psy6532         102 NSNMKPTIDGSKNE-QG-VGCALTIPEKDIVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMN  179 (277)
Q Consensus       102 ~~~~~iytDGS~~~-~~-~G~g~v~~~~~~~~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~  179 (277)
                      ....++|||||+.. ++ .|+|++..++..... .+ ..+||+.|||.|++.||+.    ...++.|+|||+++++++++
T Consensus         6 ~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~-~~-~~~TNn~aEl~Avi~aL~~----~~~~v~I~TDS~yvi~~i~~   79 (110)
T d1s1ta1           6 VGAETFYVDGAANRETKLGKAGYVTNRGRQKVV-TL-TDTTNQKTELQAIYLALQD----SGLEVNIVTDSQYALGIIQA   79 (110)
T ss_dssp             TTSEEEEEEEEEETTTTEEEEEEEETTSCEEEE-EE-SSCCHHHHHHHHHHHHHHH----SCSEEEEEECCHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEE-ec-ccCcHHHHHHHHHHHHHHh----CCCeEEEEEehHHHHHHHhc
Confidence            34578999999764 33 677777776654322 22 2579999999999999974    45789999999999999999


Q ss_pred             cCC--CChHHHHHHHHHhcCCCCeEEEEecCC
Q psy6532         180 MFH--ENPLVKRVQEELSSTESPVEFLWCPSH  209 (277)
Q Consensus       180 ~~~--~~~~~~~i~~~l~~~~~~v~~~WvpgH  209 (277)
                      +..  ...+.+++.+.+.+ ...|.|.|||||
T Consensus        80 ~~~~~~~~l~~~il~~l~~-~~~v~i~WVpgH  110 (110)
T d1s1ta1          80 QPDQSESELVNQIIEQLIK-KEKVYLAWVPAH  110 (110)
T ss_dssp             CCSEESCHHHHHHHHHHHH-CSEEEEEECCSS
T ss_pred             CccccchHHHHHHHHHHhc-CCceEEEEeCCC
Confidence            775  45567777666554 468999999999

>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=99.67  E-value=1.4e-17  Score=128.53  Aligned_cols=111  Identities=14%  Similarity=0.052  Sum_probs=82.9

Q ss_pred             eeeecCCCCC--CCeeEEEEEcCCC-eEEeecCCCCcchhHHHHHHHHHHHHHHhhhCCCceEEEeCCHHHHHHHhccCC
Q psy6532         106 KPTIDGSKNE--QGVGCALTIPEKD-IVKRFGLNKNASIFHAELFALLQSLLTIKQLGTCKALIITDSLSCLQAIMNMFH  182 (277)
Q Consensus       106 ~iytDGS~~~--~~~G~g~v~~~~~-~~~~~~~~~~~t~~~aEl~Ai~~aL~~a~~~~~~~v~I~tDS~~ai~~l~~~~~  182 (277)
                      .||||||+.+  |.+|+|+|+...+ .....+.-+.+||++||+.|++.||+.+.+.+ .++.|+|||+++++.+.++..
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~~   84 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKKA   84 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTCC
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCce
Confidence            4899999884  4488888876543 33332222478999999999999999998755 679999999999999987652


Q ss_pred             C--------C-hHHHHHHH---HHhcCCCCeEEEEecCCCCCccchHHH
Q psy6532         183 E--------N-PLVKRVQE---ELSSTESPVEFLWCPSHVGIAGNETAD  219 (277)
Q Consensus       183 ~--------~-~~~~~i~~---~l~~~~~~v~~~WvpgH~g~~gNe~AD  219 (277)
                      .        + .+.+.+.+   .++  ...+.+.|++.|+...||..||
T Consensus        85 kt~~~~~vkN~~l~~~i~~a~~~lk--~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          85 KSTLVRNEETALIWKLVDEAEEWLN--THTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CCCCCCSTTTHHHHHHHHHHHHHHH--HCCCCCCEEECCHHHHCSCTTC
T ss_pred             ecCcCCCcccHHHHHHHHHHHHHHH--hCCcCceeEEecCcccccCCCC
Confidence            1        1 13333433   333  4568889999999999999988