Psyllid ID: psy10407

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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
Protein Sequence
MVLPWYKAQNLLPGYNQLFVTMETHLLPDKVISGFTNYNFYRKDFLDGRISCGGVMLMIHKKYFSQPVPGSPVEMGCCTNSLHFKYIHCSLNEATDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSNDLGFKELGLTANIIINSTRKDKVLSRVMEYVKHGWPSVKNLSCDKKTFHTVVKISNK
Secondary Structure (PSIPRED)
ccccccccccccccHHHHHHHHHHccccccEEEccccccEEEEEcccccEEEEEEEccHHHHccccccccHHHHHHHHHHHHHcccccccEEEEcccHHHHHHHccccccccccHHHHHHHHHHHccEEEEEEEEccccccccccccccccccccccccccccHHHHHHHHHccHHHHHHHHHHHHcccccccccccccccEEEcccccc
Secondary Structure Prediction (SSPRO)
ccccccHHccccccccEEEEEEHHccccccEEEEccccccccccccccHEcHHHHHHHHHHccccccccccHEEHHHHHHcccEEEEccEEEEEcccccHHHHHcccccccHHHHHHHHHHHHHHHHcccEEEEEcccccccccHHcccccccccccccccccHHHHHHHHHccHHHHHHHHHHHcccccccccccccccccEEEEEccc
Coil and Loop (DISEMBL)
mvlpwykaqnllpgyNQLFVTMEthllpdkvisgftnynfyrkdfldgriscgGVMLMIHKKyfsqpvpgspvemgcctnslhFKYIHCSLNEATDNKALVTLFgedkavpmlssARLQRWSLILSNFdysikykkgtqipvadalsrlplsndlgfkelgLTANIIINSTRKDKVLSRVMEYVKhgwpsvknlscdkktfHTVVKISNK
Flexible Loop (DISEMBL)
MVLPWYKAQNLLPGYNQLFVTMETHLLPDKVISGFTNYNFYRKDFLDGRISCGGVMLMIHKKYFSQPVPGSPVEMGCCTNSLHFKYIHCSLNEATDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSNDLGFKelgltaniiinstrkdkVLSRVMEYVKhgwpsvknlscdkktfhtvvkisnk
Low Complexity Region (SEG)
MVLPWYKAQNLLPGYNQLFVTMETHLLPDKVISGFTNYNFYRKDFLDGRISCGGVMLMIHKKYFSQPVPGSPVEMGCCTNSLHFKYIHCSLNEATDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSNDLGFKELGLTANIIINSTRKDKVLSRVMEYVKHGWPSVKNLSCDKKTFHTVVKISNK
Disordered region (IsUnstruct)
**LPWYKAQNLLPGYNQLFVTMETHLLPDKVISGFTNYNFYRKDFLDGRISCGGVMLMIHKKYFSQPVPGSPVEMGCCTNSLHFKYIHCSLNEATDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSNDLGFKELGLTANIIINSTRKDKVLSRVMEYVKHGWPSVKNLSCDKKTFHTVVK****
Disordered Region (DISOPRED)
MVLPWYKAQNLLPGYNQLFVTMETHLLPDKVISGFTNYNFYRKDFLDGRISCGGVMLMIHKKYFSQPVPGSPVEMGCCTNSLHFKYIHCSLNEATDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSN**GFKELGLTANIIINSTRKDKVLSRVMEYVKHGWPS*****CDKKTFH*VVKI***
Disordered Region (DISEMBL)
MVLPWYKAQNLLPGYNQLFVTMETHLLPDKVISGFTNYNFYRKDFLDGRISCGGVMLMIHKKYFSQPVPGSPVEMGCCTNSLHFKYIHCSLNEATDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSNDLGFKELGLTANIIINSTRKDKVLSRVMEYVKHGWPSVKNLSCDKKTFHTVVKISNK
Disordered Region (DISPRO)
*VLPWYKAQNLLPGYNQLFVTMETHLLPDKVISGFTNYNFYRKDFLDGRISCGGVMLMIHKKYFSQPVPGSPVEMGCCTNSLHFKYIHCSLNEATDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSNDLGFKELGLTANIIINSTRKDKVLSRVMEYVKHGWPSVKNLSCDKKTFHTVVKISN*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVLPWYKAQNLLPGYNQLFVTMETHLLPDKVISGFTNYNFYRKDFLDGRISCGGVMLMIHKKYFSQPVPGSPVEMGCCTNSLHFKYIHCSLNEATDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSNDLGFKELGLTANIIINSTRKDKVLSRVMEYVKHGWPSVKNLSCDKKTFHTVVKISNK
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	210	2.2.26 [Sep-21-2011]
P04323	1058	Retrovirus-related Pol po	yes	N/A	0.180	0.035	0.526	0.0009

>sp|P04323|POL3_DROME Retrovirus-related Pol polyprotein from transposon 17.6 OS=Drosophila melanogaster GN=pol PE=4 SV=1

 Score = 43.9 bits (102), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 20/38 (52%), Positives = 27/38 (71%)

Query: 115 SARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLS 152
           +++L RW + LS FD+ IKY KG +  VADALSR+ L 
Sbjct: 590 NSKLTRWRVKLSEFDFDIKYIKGKENCVADALSRIKLE 627

Drosophila melanogaster (taxid: 7227)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 4EC: 9

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	210
326674110	1299	PREDICTED: uncharacterized protein K02A2	0.504	0.081	0.408	2e-16
326664467	1299	PREDICTED: uncharacterized protein K02A2	0.504	0.081	0.408	2e-16
326675162	1299	PREDICTED: uncharacterized protein K02A2	0.504	0.081	0.408	2e-16
125835738	1299	PREDICTED: uncharacterized protein K02A2	0.504	0.081	0.408	2e-16
326667102	1177	PREDICTED: uncharacterized protein K02A2	0.457	0.081	0.415	7e-16
291224973	1346	PREDICTED: polyprotein-like [Saccoglossu	0.457	0.071	0.409	3e-15
291224971	1173	PREDICTED: polyprotein-like [Saccoglossu	0.457	0.081	0.4	7e-15
340386408	702	PREDICTED: uncharacterized protein K02A2	0.452	0.135	0.405	1e-14
125843865	1312	PREDICTED: uncharacterized protein K02A2	0.457	0.073	0.435	3e-14
326670210	1312	PREDICTED: uncharacterized protein K02A2	0.457	0.073	0.425	8e-14

>gi|326674110|ref|XP_003200072.1| PREDICTED: uncharacterized protein K02A2.6-like [Danio rerio]

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 51/125 (40%), Positives = 75/125 (60%), Gaps = 19/125 (15%)

Query: 95  TDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSN- 153
           TD+K L+TLFGE K++P +++AR+QRW++ILS +DY I+Y    +   AD LSR+PL   
Sbjct: 783 TDHKPLLTLFGEHKSLPTMAAARIQRWAIILSAYDYHIEYCPSEKNSNADGLSRVPLPEM 842

Query: 154 -DLG---------------FKELGLTANIIINSTRKDKVLSRVMEYVKHGWPSVKNLSCD 197
            D G               F++  L A  +   TR+DKVLS+V++YV  GWP   N+  +
Sbjct: 843 TDGGTAALSEHIHALIAEHFEQAPLKAEHVSRVTRRDKVLSKVLKYVMEGWPM--NVDEN 900

Query: 198 KKTFH 202
            K +H
Sbjct: 901 LKAYH 905

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|326664467|ref|XP_003197819.1| PREDICTED: uncharacterized protein K02A2.6-like [Danio rerio]

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 51/125 (40%), Positives = 75/125 (60%), Gaps = 19/125 (15%)

Query: 95  TDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSN- 153
           TD+K L+TLFGE K++P +++AR+QRW++ILS +DY I+Y    +   AD LSR+PL   
Sbjct: 783 TDHKPLLTLFGEHKSLPTMAAARIQRWAIILSAYDYHIEYCPSEKNSNADGLSRVPLPEM 842

Query: 154 -DLG---------------FKELGLTANIIINSTRKDKVLSRVMEYVKHGWPSVKNLSCD 197
            D G               F++  L A  +   TR+DKVLS+V++YV  GWP   N+  +
Sbjct: 843 TDGGTAALSEHIHALIAEHFEQAPLKAEHVSRVTRRDKVLSKVLKYVMEGWPM--NVDEN 900

Query: 198 KKTFH 202
            K +H
Sbjct: 901 LKAYH 905

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|326675162|ref|XP_003200292.1| PREDICTED: uncharacterized protein K02A2.6 [Danio rerio]

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 51/125 (40%), Positives = 75/125 (60%), Gaps = 19/125 (15%)

Query: 95  TDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLS-- 152
           TD+K L+TLFGE K++P +++AR+QRW++ILS +DY I+Y    +   AD LSR+PL   
Sbjct: 783 TDHKPLLTLFGEHKSLPTMAAARIQRWAIILSAYDYHIEYCPSEKNSNADGLSRVPLPVM 842

Query: 153 NDLG---------------FKELGLTANIIINSTRKDKVLSRVMEYVKHGWPSVKNLSCD 197
            D G               F++  L A  +   TR+DKVLS+V++YV  GWP   N+  +
Sbjct: 843 TDGGTAALSEHIHALIAEHFEQAPLKAEHVSRVTRRDKVLSKVLKYVMEGWPM--NVDEN 900

Query: 198 KKTFH 202
            K +H
Sbjct: 901 LKAYH 905

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|125835738|ref|XP_001337220.1| PREDICTED: uncharacterized protein K02A2.6-like [Danio rerio]

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 51/125 (40%), Positives = 75/125 (60%), Gaps = 19/125 (15%)

Query: 95  TDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSN- 153
           TD+K L+TLFGE K++P +++AR+QRW++ILS +DY I+Y    +   AD LSR+PL   
Sbjct: 783 TDHKPLLTLFGEHKSLPTMAAARIQRWAIILSAYDYHIEYCPSEKNSNADGLSRVPLPEM 842

Query: 154 -DLG---------------FKELGLTANIIINSTRKDKVLSRVMEYVKHGWPSVKNLSCD 197
            D G               F++  L A  +   TR+DKVLS+V++YV  GWP   N+  +
Sbjct: 843 TDGGTAALSEHIHALIAEHFEQAPLKAEHVSRVTRRDKVLSKVLKYVMEGWPM--NVDEN 900

Query: 198 KKTFH 202
            K +H
Sbjct: 901 LKAYH 905

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|326667102|ref|XP_003198486.1| PREDICTED: uncharacterized protein K02A2.6-like [Danio rerio]

 Score = 89.7 bits (221), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 47/113 (41%), Positives = 67/113 (59%), Gaps = 17/113 (15%)

Query: 95  TDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSN- 153
           TD++ LVTLFGE K  PM+++AR+QRW++IL+ +DY I Y+K      AD LSR+PL   
Sbjct: 649 TDHRPLVTLFGEHKHFPMMAAARIQRWAIILAAYDYHICYRKAEMHGNADGLSRVPLPEI 708

Query: 154 -DLG---------------FKELGLTANIIINSTRKDKVLSRVMEYVKHGWPS 190
            D+G                 E  + A+ I  +TR+D  +S+V +YV  GWPS
Sbjct: 709 TDVGTEAMSAHINTLLSNHIHEAPINASQIARATRRDLHMSKVAQYVMEGWPS 761

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|291224973|ref|XP_002732476.1| PREDICTED: polyprotein-like [Saccoglossus kowalevskii]

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 45/110 (40%), Positives = 67/110 (60%), Gaps = 14/110 (12%)

Query: 95  TDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSND 154
           TD+K L+ L  EDKA+  L+SAR+QRW+L L+N+ Y ++YK G+ +  AD LSRLP+   
Sbjct: 803 TDHKPLLGLLKEDKAISQLASARIQRWALTLANYQYQLEYKPGSNMGNADGLSRLPIKEQ 862

Query: 155 LGF----KELGL----------TANIIINSTRKDKVLSRVMEYVKHGWPS 190
            G     +E+ L          TA ++ N T +D VLS ++++V  GWP 
Sbjct: 863 PGSVPVPEEVVLTLSTLDGSPVTAELVANWTARDPVLSHILKWVTQGWPE 912

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|291224971|ref|XP_002732475.1| PREDICTED: polyprotein-like [Saccoglossus kowalevskii]

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 44/110 (40%), Positives = 67/110 (60%), Gaps = 14/110 (12%)

Query: 95  TDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSND 154
           TD+K L+ L  +DKA+  L+SAR+QRW+L L+N+ Y ++YK G+ +  AD LSRLP+   
Sbjct: 630 TDHKPLLGLLKQDKAISQLASARIQRWALTLANYQYQLEYKPGSNMGNADGLSRLPIKEQ 689

Query: 155 LGF----KELGL----------TANIIINSTRKDKVLSRVMEYVKHGWPS 190
            G     +E+ L          TA ++ N T +D VLS ++++V  GWP 
Sbjct: 690 PGSVPVPEEVVLTLSTLDGSPVTAELVANWTARDPVLSHILKWVTQGWPE 739

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|340386408|ref|XP_003391700.1| PREDICTED: uncharacterized protein K02A2.6-like, partial [Amphimedon queenslandica]

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 45/111 (40%), Positives = 66/111 (59%), Gaps = 16/111 (14%)

Query: 95  TDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSN- 153
           +D++ L  LF E + VP ++S+R+QRW+L LS ++YSI Y+ G+++  ADALSRLPL++ 
Sbjct: 464 SDHQPLKYLFSESRPVPAMASSRIQRWALTLSAYEYSIHYRPGSRLGNADALSRLPLTDQ 523

Query: 154 --DLGFKELG-------------LTANIIINSTRKDKVLSRVMEYVKHGWP 189
             D     LG             ++A  I   T KD  LSRV  ++ HGWP
Sbjct: 524 PQDKDIPPLGDVNLLVQQLSHCIVSATQIAQWTDKDSTLSRVHHFILHGWP 574

Source: Amphimedon queenslandica

Species: Amphimedon queenslandica

Genus: Amphimedon

Family: Niphatidae

Order: Haplosclerida

Class: Demospongiae

Phylum: Porifera

Superkingdom: Eukaryota

>gi|125843865|ref|XP_001343884.1| PREDICTED: uncharacterized protein K02A2.6-like [Danio rerio]

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 47/108 (43%), Positives = 63/108 (58%), Gaps = 12/108 (11%)

Query: 95  TDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSN- 153
           TD++ LV +F  +K VP++++ARLQRW+L L   DYSI++K       AD LSRLP  N 
Sbjct: 796 TDHQPLVAIFSPNKCVPVMAAARLQRWALFLGGHDYSIEFKGTKHHGNADGLSRLPHENA 855

Query: 154 DLGFKE-----------LGLTANIIINSTRKDKVLSRVMEYVKHGWPS 190
           D G  E           L +T+  I N TR+D VLS+V E    GWP+
Sbjct: 856 DEGTDETNMFHIVQMEPLPVTSAQIQNETRRDPVLSKVFELTMKGWPA 903

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|326670210|ref|XP_003199161.1| PREDICTED: uncharacterized protein K02A2.6-like [Danio rerio]

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 63/108 (58%), Gaps = 12/108 (11%)

Query: 95  TDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPLSN- 153
           TD++ LV +F  +K VP++++ARLQRW+L L   DYSI++K       AD LSRLP  N 
Sbjct: 796 TDHQPLVAIFSPNKCVPVMAAARLQRWALFLGGHDYSIEFKGTKHHGNADGLSRLPHENA 855

Query: 154 DLGFKE-----------LGLTANIIINSTRKDKVLSRVMEYVKHGWPS 190
           D G  E           L +T+  I N TR+D VLS+V +    GWP+
Sbjct: 856 DEGTDETDMFHIVQMEPLPVTSAQIQNETRRDPVLSKVFDLTMKGWPA 903

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

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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

No EC number assignment, probably not an enzyme!

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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	210
cd09274	121	cd09274, RNase_HI_RT_Ty3, Ty3/Gypsy family of RNas	7e-17

>gnl|CDD|187698 cd09274, RNase_HI_RT_Ty3, Ty3/Gypsy family of RNase HI in long-term repeat retroelements

 Score = 72.9 bits (180), Expect = 7e-17
 Identities = 25/57 (43%), Positives = 34/57 (59%), Gaps = 5/57 (8%)

Query: 95  TDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPL 151
           TD+K+L  L  +        + RL RW L+L  FD+ I+Y+ G +  VADALSRLP 
Sbjct: 70  TDHKSLKYLLTKKDL-----NPRLARWLLLLQEFDFEIEYRPGKENVVADALSRLPE 121

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one 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. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 121

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	210
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	98.63
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	97.51
PRK13907	128	rnhA ribonuclease H; Provisional	97.42
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	97.31
PRK00203	150	rnhA ribonuclease H; Reviewed	97.18
PRK07708	219	hypothetical protein; Validated	96.71
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	96.66
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	96.27
PRK08719	147	ribonuclease H; Reviewed	96.17
PRK06548	161	ribonuclease H; Provisional	95.68
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	93.0

>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=98.63  E-value=6.3e-08  Score=71.11  Aligned_cols=108  Identities=12%  Similarity=-0.053  Sum_probs=76.6

Q ss_pred             EEEecCCCC------ceeEEEEeecc--cccccc--CCCchhhHHHHHHHhhhee---ccc-eEEEeecchhhHhhhccc
Q psy10407         42 RKDFLDGRI------SCGGVMLMIHK--KYFSQP--VPGSPVEMGCCTNSLHFKY---IHC-SLNEATDNKALVTLFGED  107 (210)
Q Consensus        42 ~l~tDAS~~------~~GavL~q~~~--~~~s~~--~~y~~~ekellaiv~~~~y---l~g-~f~v~TDh~~L~~l~~~~  107 (210)
                      .++||+|..      |+|+++.+...  .+.+..  ..++..+.|+.|++....+   ..+ ++.++||++.+...++..
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            378898877      89999988765  222222  3567889999999987633   344 899999999999999865


Q ss_pred             CcCCCccc-hhccchhhhh-ccccceeeeecC----CCCCCccccCCC
Q psy10407        108 KAVPMLSS-ARLQRWSLIL-SNFDYSIKYKKG----TQIPVADALSRL  149 (210)
Q Consensus       108 ~~~~~~~~-~rl~rw~~~L-~~f~~~I~y~~G----k~n~~aD~LSR~  149 (210)
                      ........ .....+...+ ...++.+.|++|    ..|..||.|+|.
T Consensus        81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~  128 (130)
T cd06222          81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKE  128 (130)
T ss_pred             ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHh
Confidence            42111122 2233334444 566799999999    999999999875

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.

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

Probab=97.51  E-value=5.5e-05  Score=52.91  Aligned_cols=77  Identities=17%  Similarity=0.113  Sum_probs=55.1

Q ss_pred             hhHHHHHHHhhh--eeccc--eEEEeecchhhHhhhcccCcCCCccchhccchhhhhcccc-ceeeeecCCCCCCccccC
Q psy10407         73 VEMGCCTNSLHF--KYIHC--SLNEATDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFD-YSIKYKKGTQIPVADALS  147 (210)
Q Consensus        73 ~ekellaiv~~~--~yl~g--~f~v~TDh~~L~~l~~~~~~~~~~~~~rl~rw~~~L~~f~-~~I~y~~Gk~n~~aD~LS  147 (210)
                      .+-|++|+.+..  ..-.|  ++.+.||++.+...++.+...+......+......+..|+ +.+.|++...|..||.|+
T Consensus         2 ~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~A~~LA   81 (87)
T PF13456_consen    2 LEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPREQNKVADALA   81 (87)
T ss_dssp             HHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GGGSHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChHHhHHHHHHH
Confidence            467899998876  44456  8999999999999998775443334444555566677766 889999999999999998


Q ss_pred             CC
Q psy10407        148 RL  149 (210)
Q Consensus       148 R~  149 (210)
                      |.
T Consensus        82 ~~   83 (87)
T PF13456_consen   82 KF   83 (87)
T ss_dssp             HH
T ss_pred             HH
Confidence            64

>PRK13907 rnhA ribonuclease H; Provisional

Probab=97.42  E-value=0.00027  Score=53.82  Aligned_cols=109  Identities=18%  Similarity=0.103  Sum_probs=66.4

Q ss_pred             eEEEecCCC------CceeEEEEeecc--ccccccCCCchhhHHHHHHHhhheec--cc--eEEEeecchhhHhhhcccC
Q psy10407         41 YRKDFLDGR------ISCGGVMLMIHK--KYFSQPVPGSPVEMGCCTNSLHFKYI--HC--SLNEATDNKALVTLFGEDK  108 (210)
Q Consensus        41 ~~l~tDAS~------~~~GavL~q~~~--~~~s~~~~y~~~ekellaiv~~~~yl--~g--~f~v~TDh~~L~~l~~~~~  108 (210)
                      +.++||+|-      .|+|+|+--...  .+.......+..+-|+.|++....+.  .|  ++.++||.+-+...++..-
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~   81 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEY   81 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHH
Confidence            578999554      366777732222  11111122456678888988876333  23  7899999999998887533


Q ss_pred             cCCCccchhccchhhhhccccce-eeeecCCCCCCccccCCC
Q psy10407        109 AVPMLSSARLQRWSLILSNFDYS-IKYKKGTQIPVADALSRL  149 (210)
Q Consensus       109 ~~~~~~~~rl~rw~~~L~~f~~~-I~y~~Gk~n~~aD~LSR~  149 (210)
                      ........-+..-...+..|... +.|+++..|..||.|.|.
T Consensus        82 ~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~~  123 (128)
T PRK13907         82 AKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARK  123 (128)
T ss_pred             hcChhHHHHHHHHHHHHhcCCceEEEEcCchhchhHHHHHHH
Confidence            10000111122223335677644 589999999999999874

>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=97.31  E-value=0.00035  Score=52.82  Aligned_cols=107  Identities=12%  Similarity=0.061  Sum_probs=64.8

Q ss_pred             CceEEEecCCCC------ceeEEEEeeccccccccCCCchhhHHHHHHHhhheeccc-eEEEeecchhhHhhhcc-----
Q psy10407         39 NFYRKDFLDGRI------SCGGVMLMIHKKYFSQPVPGSPVEMGCCTNSLHFKYIHC-SLNEATDNKALVTLFGE-----  106 (210)
Q Consensus        39 ~~~~l~tDAS~~------~~GavL~q~~~~~~s~~~~y~~~ekellaiv~~~~yl~g-~f~v~TDh~~L~~l~~~-----  106 (210)
                      +.+.++||+|-.      |.|.++ ...+.+...-...+..+-|+.|+..++..+.. +++|+||.+.+...+..     
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~-~~~~~~~~~~~~~s~~~aEl~Ai~~AL~~~~~~~v~I~tDS~~v~~~l~~~~~~~   80 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVV-WGGRNFSFRLGGQSNNRAELQAIIEALKALEHRKVTIYTDSQYVLNALNKWLHGN   80 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEE-ETTEEEEEEEESECHHHHHHHHHHHHHHTHSTSEEEEEES-HHHHHHHHTHHHHT
T ss_pred             CcEEEEEeCCccCCCCceEEEEEE-ECCeEEEecccccchhhhheehHHHHHHHhhcccccccccHHHHHHHHHHhcccc
Confidence            468899999933      556644 43331111111556888999999998854455 99999999999984444     


Q ss_pred             cCcCCCccch-hccc--hhhhhccccceeeeecCCCCC-----CccccCC
Q psy10407        107 DKAVPMLSSA-RLQR--WSLILSNFDYSIKYKKGTQIP-----VADALSR  148 (210)
Q Consensus       107 ~~~~~~~~~~-rl~r--w~~~L~~f~~~I~y~~Gk~n~-----~aD~LSR  148 (210)
                      ....  .... .+..  |.+....-.+.+.|+||..+.     .||-|.|
T Consensus        81 ~~~~--~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk  128 (132)
T PF00075_consen   81 GWKK--TSNGRPIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAK  128 (132)
T ss_dssp             TSBS--CTSSSBHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHH
T ss_pred             cccc--ccccccchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHH
Confidence            2211  1112 1222  222234566889999998654     5776654

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=97.18  E-value=0.00087  Score=52.76  Aligned_cols=109  Identities=13%  Similarity=0.046  Sum_probs=63.8

Q ss_pred             eEEEecCCC------CceeEEEEeecc--ccccccCCCchhhHHHHHHHhhheeccc--eEEEeecchhhHhhhcc----
Q psy10407         41 YRKDFLDGR------ISCGGVMLMIHK--KYFSQPVPGSPVEMGCCTNSLHFKYIHC--SLNEATDNKALVTLFGE----  106 (210)
Q Consensus        41 ~~l~tDAS~------~~~GavL~q~~~--~~~s~~~~y~~~ekellaiv~~~~yl~g--~f~v~TDh~~L~~l~~~----  106 (210)
                      +.++||.|.      .|+|+++.....  .+......-+...-|+.|++.++.++..  .+.|+||.+.+..-++.    
T Consensus         4 v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~~~~v~I~tDS~yvi~~i~~w~~~   83 (150)
T PRK00203          4 VEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKEPCEVTLYTDSQYVRQGITEWIHG   83 (150)
T ss_pred             EEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCCCCeEEEEECHHHHHHHHHHHHHH
Confidence            789999775      466667754333  2222222334566899999998855544  89999998766554442    


Q ss_pred             ------cC-cCCCccchhc-cchhhhhccccceeeeecCCC----CCCccccCCC
Q psy10407        107 ------DK-AVPMLSSARL-QRWSLILSNFDYSIKYKKGTQ----IPVADALSRL  149 (210)
Q Consensus       107 ------~~-~~~~~~~~rl-~rw~~~L~~f~~~I~y~~Gk~----n~~aD~LSR~  149 (210)
                            +. ......+..+ .+-...+....+.+.++||..    |..||.|.|.
T Consensus        84 Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~wV~~H~~~~~N~~AD~lA~~  138 (150)
T PRK00203         84 WKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELARA  138 (150)
T ss_pred             HHHcCCcccCCCccccHHHHHHHHHHhccCceEEEEecCCCCCHHHHHHHHHHHH
Confidence                  00 0000111111 112223455678889999754    7778888764

>PRK07708 hypothetical protein; Validated

Probab=96.71  E-value=0.0054  Score=51.57  Aligned_cols=109  Identities=14%  Similarity=0.084  Sum_probs=70.1

Q ss_pred             ceEEEecCCC------CceeEEEEeecc--cc--c-cccCC--CchhhHHHHHHHhhheecc--c----eEEEeecchhh
Q psy10407         40 FYRKDFLDGR------ISCGGVMLMIHK--KY--F-SQPVP--GSPVEMGCCTNSLHFKYIH--C----SLNEATDNKAL  100 (210)
Q Consensus        40 ~~~l~tDAS~------~~~GavL~q~~~--~~--~-s~~~~--y~~~ekellaiv~~~~yl~--g----~f~v~TDh~~L  100 (210)
                      ...+++|.|-      .|+|+|+.....  .+  . +..+.  .+..+-|+.|++.++.++.  |    ++++++|.+-+
T Consensus        73 ~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlV  152 (219)
T PRK07708         73 EILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVV  152 (219)
T ss_pred             cEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHH
Confidence            5899999654      577888875433  11  1 11222  2455668888877653322  3    48999999999


Q ss_pred             HhhhcccCcCCCccchhccchhh----hhcccc--ceeeeecCCCCCCccccCCCCC
Q psy10407        101 VTLFGEDKAVPMLSSARLQRWSL----ILSNFD--YSIKYKKGTQIPVADALSRLPL  151 (210)
Q Consensus       101 ~~l~~~~~~~~~~~~~rl~rw~~----~L~~f~--~~I~y~~Gk~n~~aD~LSR~p~  151 (210)
                      ...++..-..   .+..+.+|..    .+.+|.  +.+.+++.+.|..||.|.+.-.
T Consensus       153 i~qi~g~wk~---~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~Al  206 (219)
T PRK07708        153 LNQLAGEWPC---YDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQAL  206 (219)
T ss_pred             HHHhCCCcee---CChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHHHH
Confidence            9888754211   2344555543    445565  5678999999999999987543

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

Probab=96.66  E-value=0.0019  Score=51.42  Aligned_cols=111  Identities=12%  Similarity=-0.074  Sum_probs=69.2

Q ss_pred             CceEEEecCC------CCceeEEEEeeccc--cccccCCCchhhHHHHHHHhhheecc--c--eEEEeecchhhHhhhcc
Q psy10407         39 NFYRKDFLDG------RISCGGVMLMIHKK--YFSQPVPGSPVEMGCCTNSLHFKYIH--C--SLNEATDNKALVTLFGE  106 (210)
Q Consensus        39 ~~~~l~tDAS------~~~~GavL~q~~~~--~~s~~~~y~~~ekellaiv~~~~yl~--g--~f~v~TDh~~L~~l~~~  106 (210)
                      +.+.|+||.+      .-|+|+||......  +.-.+..=+-.+.|+.|++.++.++.  |  .++|+||.+-+..-++.
T Consensus         2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~   81 (154)
T COG0328           2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITR   81 (154)
T ss_pred             CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHH
Confidence            3567889955      34677888744442  22233333466799999999986666  6  89999999988776652


Q ss_pred             cCcCCCccchh------------ccchhhhhccc-cceeeeecCC----CCCCccccCCC
Q psy10407        107 DKAVPMLSSAR------------LQRWSLILSNF-DYSIKYKKGT----QIPVADALSRL  149 (210)
Q Consensus       107 ~~~~~~~~~~r------------l~rw~~~L~~f-~~~I~y~~Gk----~n~~aD~LSR~  149 (210)
                      -.........+            ..+-.+.+.++ .+.+.+++|.    .|-.||.|.|.
T Consensus        82 w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~  141 (154)
T COG0328          82 WIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLARE  141 (154)
T ss_pred             HHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHH
Confidence            11000001111            22223456778 7899999974    56677777664

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=96.27  E-value=0.0081  Score=53.96  Aligned_cols=107  Identities=11%  Similarity=0.006  Sum_probs=68.9

Q ss_pred             ceEEEecCCCC------ceeEEEEeeccc-----cccccCCCchhhHHHHHHHhhheec--cc--eEEEeecchhhHhhh
Q psy10407         40 FYRKDFLDGRI------SCGGVMLMIHKK-----YFSQPVPGSPVEMGCCTNSLHFKYI--HC--SLNEATDNKALVTLF  104 (210)
Q Consensus        40 ~~~l~tDAS~~------~~GavL~q~~~~-----~~s~~~~y~~~ekellaiv~~~~yl--~g--~f~v~TDh~~L~~l~  104 (210)
                      .+.|+||+|..      |+|.++......     +...-...+..+-|+.|++..+.++  .|  .++++||.+.+...+
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i   81 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQM   81 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHh
Confidence            36799996654      677777654321     1111123345567888888876222  24  899999999999888


Q ss_pred             cccCcCCCccchhccch----hhhhcccc-ceeeeecCCCCCCccccCCC
Q psy10407        105 GEDKAVPMLSSARLQRW----SLILSNFD-YSIKYKKGTQIPVADALSRL  149 (210)
Q Consensus       105 ~~~~~~~~~~~~rl~rw----~~~L~~f~-~~I~y~~Gk~n~~aD~LSR~  149 (210)
                      +..-..   .+..+...    ...++.|+ +++.|+++..|..||.|.+.
T Consensus        82 ~~~~~~---~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~  128 (372)
T PRK07238         82 SGRWKV---KHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANE  128 (372)
T ss_pred             CCCCcc---CChHHHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHH
Confidence            753211   22333332    23345655 77999999999999999874

>PRK08719 ribonuclease H; Reviewed

Probab=96.17  E-value=0.01  Score=46.78  Aligned_cols=111  Identities=14%  Similarity=-0.023  Sum_probs=65.1

Q ss_pred             CceEEEecCCC---------CceeEEEEeecc-cc--ccccC--CCchhhHHHHHHHhhheeccceEEEeecchhhHhhh
Q psy10407         39 NFYRKDFLDGR---------ISCGGVMLMIHK-KY--FSQPV--PGSPVEMGCCTNSLHFKYIHCSLNEATDNKALVTLF  104 (210)
Q Consensus        39 ~~~~l~tDAS~---------~~~GavL~q~~~-~~--~s~~~--~y~~~ekellaiv~~~~yl~g~f~v~TDh~~L~~l~  104 (210)
                      .++.+|||.|.         -|+|.++..... .+  .+...  .-+..+.|+.|++.++.++..+.+|+||.+-+..-+
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~~~i~tDS~yvi~~i   82 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDGDVIYSDSDYCVRGF   82 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCCCEEEechHHHHHHH
Confidence            46889999655         277777654432 11  11112  234667899999998866655448999997776554


Q ss_pred             cc-------c---Cc-CCCccchhccchhh-hhccccceeeeecC----CCCCCccccCCC
Q psy10407        105 GE-------D---KA-VPMLSSARLQRWSL-ILSNFDYSIKYKKG----TQIPVADALSRL  149 (210)
Q Consensus       105 ~~-------~---~~-~~~~~~~rl~rw~~-~L~~f~~~I~y~~G----k~n~~aD~LSR~  149 (210)
                      +.       +   +. .....+.-+-+.+. .++.-++++.+.+|    ..|..||.|.|.
T Consensus        83 ~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~~~~VkgH~g~~~Ne~aD~lA~~  143 (147)
T PRK08719         83 NEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKVTAHSGIEGNEAADMLAQA  143 (147)
T ss_pred             HHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEEEEEecCCCCChhHHHHHHHHHH
Confidence            21       1   00 00012222222233 23445688999999    558888887654

>PRK06548 ribonuclease H; Provisional

Probab=95.68  E-value=0.037  Score=44.40  Aligned_cols=109  Identities=7%  Similarity=-0.082  Sum_probs=62.7

Q ss_pred             ceEEEecCCCCc------eeEEEEeeccccccccCCCchhhHHHHHHHhhheecc--c-eEEEeecchhhHhhhcc----
Q psy10407         40 FYRKDFLDGRIS------CGGVMLMIHKKYFSQPVPGSPVEMGCCTNSLHFKYIH--C-SLNEATDNKALVTLFGE----  106 (210)
Q Consensus        40 ~~~l~tDAS~~~------~GavL~q~~~~~~s~~~~y~~~ekellaiv~~~~yl~--g-~f~v~TDh~~L~~l~~~----  106 (210)
                      .+.|+||+|..|      +|+++.. ...+...+..-+-...|+.|++.++..+.  + +++|+||.+-+...++.    
T Consensus         5 ~~~IytDGa~~gnpg~~G~g~~~~~-~~~~~g~~~~~TNnraEl~Aii~aL~~~~~~~~~v~I~TDS~yvi~~i~~W~~~   83 (161)
T PRK06548          5 EIIAATDGSSLANPGPSGWAWYVDE-NTWDSGGWDIATNNIAELTAVRELLIATRHTDRPILILSDSKYVINSLTKWVYS   83 (161)
T ss_pred             EEEEEEeeccCCCCCceEEEEEEeC-CcEEccCCCCCCHHHHHHHHHHHHHHhhhcCCceEEEEeChHHHHHHHHHHHHH
Confidence            488999966552      3334321 11111112223355689999988774332  3 79999999998887762    


Q ss_pred             ------cC-cCCCccchhccch-hhhhccccceeeeecCCC----CCCccccCCC
Q psy10407        107 ------DK-AVPMLSSARLQRW-SLILSNFDYSIKYKKGTQ----IPVADALSRL  149 (210)
Q Consensus       107 ------~~-~~~~~~~~rl~rw-~~~L~~f~~~I~y~~Gk~----n~~aD~LSR~  149 (210)
                            ++ ..+...|.-+-+- ...++...+++.+++|..    |..||.|.|.
T Consensus        84 Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~v~~~wVkgHsg~~gNe~aD~LA~~  138 (161)
T PRK06548         84 WKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSWVNAHTGHPLNEAADSLARQ  138 (161)
T ss_pred             HHHCCCcccCCCccccHHHHHHHHHHHhcCceEEEEEecCCCCHHHHHHHHHHHH
Confidence                  00 0010122222222 223445678899998854    7778888765

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

Probab=93.00  E-value=0.43  Score=37.83  Aligned_cols=71  Identities=7%  Similarity=-0.071  Sum_probs=42.7

Q ss_pred             hHHHHHHHHHHHhcCCC-C--cccccC----CCCceEEEecCCCCceeEEEEeecc--------cccccc-----CCCch
Q psy10407         13 PGYNQLFVTMETHLLPD-K--VISGFT----NYNFYRKDFLDGRISCGGVMLMIHK--------KYFSQP-----VPGSP   72 (210)
Q Consensus        13 ~~~~~aF~~lK~~l~~~-p--vl~~~~----~~~~~~l~tDAS~~~~GavL~q~~~--------~~~s~~-----~~y~~   72 (210)
                      ....+.+..+.+.+.+. +  +-...+    ..-.+.+.||||..|.|||++=...        -..++.     .+-++
T Consensus        47 ~el~~~w~~~~~~l~~~~~i~iPR~i~~~~~~~~~L~~F~DAS~~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tI  126 (159)
T PF05380_consen   47 DELRKEWKKWLKELESLSPIRIPRCIPISDYRSVELHVFCDASESAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTI  126 (159)
T ss_pred             HHHHHHHHHHHHHHhhcccccCCcccccccccceeeeEeecccccceeeEeEeeeccCCceeeeeeeecccccCCCCCcH
Confidence            35566677776666542 2  111111    1236889999999999999764331        122221     12367


Q ss_pred             hhHHHHHHHhh
Q psy10407         73 VEMGCCTNSLH   83 (210)
Q Consensus        73 ~ekellaiv~~   83 (210)
                      ..+|++|++..
T Consensus       127 PRlEL~a~~l~  137 (159)
T PF05380_consen  127 PRLELLAALLG  137 (159)
T ss_pred             HHHHHHHHHHH
Confidence            78999998763

---

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	210
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	99.83
2zd1_B	428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	99.66
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.62
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.53
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	98.1
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	97.95
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	97.72
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	97.6
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	97.51
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	97.51
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	97.46
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	97.44
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	97.44
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	97.17
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	97.1
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	96.14
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	96.08
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	93.64
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	80.91
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	80.36

>1rw3_A POL polyprotein; RNA and DNA dependent DNA polymerase, reverse transcriptase, transferase, replication; 3.00A {Moloney murine leukemia virus} SCOP: e.8.1.2

Probab=99.83  E-value=4.4e-22  Score=180.96  Aligned_cols=123  Identities=13%  Similarity=0.024  Sum_probs=103.0

Q ss_pred             cCCCChHHHHHHHHHHHhcCCCCcccccCCCCceEEEecCCCCceeEEEEeecc-----------ccccccCCCchhhHH
Q psy10407          8 AQNLLPGYNQLFVTMETHLLPDKVISGFTNYNFYRKDFLDGRISCGGVMLMIHK-----------KYFSQPVPGSPVEMG   76 (210)
Q Consensus         8 ~~~~~~~~~~aF~~lK~~l~~~pvl~~~~~~~~~~l~tDAS~~~~GavL~q~~~-----------~~~s~~~~y~~~eke   76 (210)
                      ...|.+.+++||++||+.|+++|+|..|+++.+|.|+||||+.|+||||+|..+           .+.+.|.+|+++|+|
T Consensus       314 ~~~W~~~~~~af~~lK~~l~~~pvL~~p~~~~~~~l~~DAS~~~~gavL~q~~~~~~~~i~y~Sk~l~~~e~~ys~~ekE  393 (455)
T 1rw3_A          314 LFNWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRM  393 (455)
T ss_dssp             --CCCCCCSSSCCHHHHHTCSSCCSCCSSSCCTTSCEEEEEECSSSBEECCBCTTTTCCCCCCCBCSCSSCSSSCCSSHH
T ss_pred             CcCchHHHHHHHHHHHHHhhcCcccccCCCCCcEEEEEeccCCcceeEEEEecCCcEEEEEEEcccCCccccccchHHHH
Confidence            456778889999999999999999999999999999999999999999999853           444567899999999


Q ss_pred             HHHHHhh---h-eeccc-eEEEeecchhhHhhhcccCcCCCccchhccchhhhhc-ccccee
Q psy10407         77 CCTNSLH---F-KYIHC-SLNEATDNKALVTLFGEDKAVPMLSSARLQRWSLILS-NFDYSI  132 (210)
Q Consensus        77 llaiv~~---~-~yl~g-~f~v~TDh~~L~~l~~~~~~~~~~~~~rl~rw~~~L~-~f~~~I  132 (210)
                      ++|++++   | +|+.| +|+|+|||+ +.+++.++. ..-..++|++||+.+|+ .||+++
T Consensus       394 llAi~~a~~~~~~yl~g~~~~v~tDh~-~~~~l~~~~-~~~~~~~Rl~rW~~~L~e~~~i~~  453 (455)
T 1rw3_A          394 VAAIAVLTKDAGKLTMGQPLVIKAPHA-VEALVKQPP-DRWLSNARMTHYQALLLDTDRVQF  453 (455)
T ss_dssp             HHHHHHHHHHHHGGGCSSCEEEECSSC-TTTTSSSTT-TTTCCCCCCSCCCCCCCCCCSSSS
T ss_pred             HHHHHHHHHHHHHHcCCCcEEEEecCh-HHHHhCCCc-cccccchHHHHHHHHhCcCCCeEe
Confidence            9999885   4 99999 999999998 555555443 12236899999999999 577654

>2zd1_B P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} SCOP: e.8.1.2 PDB: 2ykm_B* 2ykn_B* 2ze2_B* 3bgr_B* 3ig1_B* 3irx_B* 3is9_B* 3qo9_B* 3v4i_B* 3v6d_B* 3v81_B* 3klf_B* 3kk1_B* 3kjv_B* 3kk2_B* 3kk3_B* 2be2_B* 1n5y_B* 1bqm_B* 1n6q_B* ...

Probab=99.66  E-value=6.2e-17  Score=146.36  Aligned_cols=97  Identities=6%  Similarity=-0.221  Sum_probs=85.7

Q ss_pred             cCCCChHHHHHHHHHHHhcCCCCcccccCCCCceEEEecCCCC-ceeEEEEeecc------ccccccCCCchhhHHHHH-
Q psy10407          8 AQNLLPGYNQLFVTMETHLLPDKVISGFTNYNFYRKDFLDGRI-SCGGVMLMIHK------KYFSQPVPGSPVEMGCCT-   79 (210)
Q Consensus         8 ~~~~~~~~~~aF~~lK~~l~~~pvl~~~~~~~~~~l~tDAS~~-~~GavL~q~~~------~~~s~~~~y~~~ekella-   79 (210)
                      +..|.+.+++||++||++|+++|+|.+||+++||.++||||+. ++|+||.|...      .|. ++.||.++|+|+|| 
T Consensus       292 ~~~Wt~~~~~af~~lK~~L~~~p~l~~pd~~~~~~l~~das~~g~~g~vl~q~~~~~~~s~~~~-~~~~y~~~~~e~la~  370 (428)
T 2zd1_B          292 VIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYA-RMRGAHTNDVKQLTE  370 (428)
T ss_dssp             EECCCHHHHHHHHHHHHHTTSCCTTCCCCTTSCCEEEEEEEETTEEEEEEESSTTCEEEEEEEE-CCSSCTTCHHHHHHH
T ss_pred             eecCCHHHHHHHHHHHHHHhcchhccccCCCCCEEEEEecCCCCcEEEEEecCCCceeeecccc-hhhhcccchHHHHHH
Confidence            4789999999999999999999999999999999999999996 55999999753      444 78999999999999 


Q ss_pred             HHhh---h-eeccc----eEEEeecchhhHhhhc
Q psy10407         80 NSLH---F-KYIHC----SLNEATDNKALVTLFG  105 (210)
Q Consensus        80 iv~~---~-~yl~g----~f~v~TDh~~L~~l~~  105 (210)
                      ++++   | +||.|    .|+++|||+.+.++..
T Consensus       371 vv~al~~~r~yl~G~~~~~~i~~td~~~~~~~~~  404 (428)
T 2zd1_B          371 AVQKITTESIVIWGKTPKFKLPIQKETWETWWTE  404 (428)
T ss_dssp             HHHHHHHHHHHHHSSCCEEEESSCHHHHHHHHHH
T ss_pred             HHHHhhccceEEECCCCcEECCccHHHHHHHHHh
Confidence            8874   5 99988    3678899999999854

>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=99.62  E-value=1.6e-16  Score=147.81  Aligned_cols=131  Identities=8%  Similarity=-0.089  Sum_probs=104.0

Q ss_pred             ccCCCChHHHHHHHHHHHhcCCCCcccccCCCCceEEEecCCCCc-eeEEEEeecc----ccccccCCCchhhHHHHH-H
Q psy10407          7 KAQNLLPGYNQLFVTMETHLLPDKVISGFTNYNFYRKDFLDGRIS-CGGVMLMIHK----KYFSQPVPGSPVEMGCCT-N   80 (210)
Q Consensus         7 ~~~~~~~~~~~aF~~lK~~l~~~pvl~~~~~~~~~~l~tDAS~~~-~GavL~q~~~----~~~s~~~~y~~~ekella-i   80 (210)
                      .+..|.+.+++||++||++|+++|+|.+|++++||.++||||+.| +||||.|..+    +|++++++|...|+|+|| +
T Consensus       291 ~~~~wt~~~~~af~~lK~~L~~~p~L~~p~~~~~~~l~~das~~ga~g~vl~Q~~~~~~~~~~s~~~~~~~~~~~~la~~  370 (555)
T 1mu2_A          291 EEVQWTELAEAELEENRIILSQEQEGHYYQEEKELEATVQKDQDNQWTYKIHQEEKILKVGKYAKVKNTHTNGIRLLAQV  370 (555)
T ss_dssp             CBCCCCHHHHHHHHHHHHHHSCCEEEECBCTTSCCEEEEEECSSSCEEEEEEETTEEEEEEEECCC--CEECHHHHHHHH
T ss_pred             CcccCCHHHHHHHHHHHHHHhhCccccccCCCCCEEEEEecCCCCcEEEEEeeCCcceeeeeccccccccCCHHHHHHHH
Confidence            467899999999999999999999999999999999999999996 9999999766    688999999999999988 6


Q ss_pred             Hhh---h-eeccc-e--EEEe----------ecchhhHhhhcccCcCCCccchhccchhhhhccccceeeeecCCCCCCc
Q psy10407         81 SLH---F-KYIHC-S--LNEA----------TDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVA  143 (210)
Q Consensus        81 v~~---~-~yl~g-~--f~v~----------TDh~~L~~l~~~~~~~~~~~~~rl~rw~~~L~~f~~~I~y~~Gk~n~~a  143 (210)
                      +++   | +|+.| .  |.+.          |||.++.++.....    ..+.++.||.     |++...+.+|......
T Consensus       371 v~~l~~~~~~l~g~~~~~~v~~~~~~w~~~~td~~~l~~~p~~~~----~~~~~~~~~~-----~~~~~~p~~~~~~iyt  441 (555)
T 1mu2_A          371 VQKIGKEALVIWGRIPKFHLPVEREIWEQWWDNYWQVTWIPDWDF----VSTPPLVRLA-----FNLVGDPIPGAETFYT  441 (555)
T ss_dssp             HHHHHHHHHHHHSSCCEEEESBCHHHHHHHHHHCSSBCCCCSEEE----CCCSSCBCCC-----CCEESSCCTTCEEEEE
T ss_pred             HHHhchhheeeeCCCeeEECCccHHHHHHhhhccchhhcCCcHHh----ccCCcccccc-----cccCCCCCCCceEEEE
Confidence            663   4 99999 4  8888          99999988765332    2467888886     5555545554444444


Q ss_pred             ccc
Q psy10407        144 DAL  146 (210)
Q Consensus       144 D~L  146 (210)
                      |.=
T Consensus       442 DGs  444 (555)
T 1mu2_A          442 DGS  444 (555)
T ss_dssp             EEE
T ss_pred             ccc
Confidence            443

>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=99.53  E-value=1e-14  Score=135.66  Aligned_cols=98  Identities=4%  Similarity=-0.209  Sum_probs=86.7

Q ss_pred             cCCCChHHHHHHHHHHHhcCCCCcccccCCCCceEEEecCCCCc-eeEEEEeecc-----ccccccCCCchhhHHHHH-H
Q psy10407          8 AQNLLPGYNQLFVTMETHLLPDKVISGFTNYNFYRKDFLDGRIS-CGGVMLMIHK-----KYFSQPVPGSPVEMGCCT-N   80 (210)
Q Consensus         8 ~~~~~~~~~~aF~~lK~~l~~~pvl~~~~~~~~~~l~tDAS~~~-~GavL~q~~~-----~~~s~~~~y~~~ekella-i   80 (210)
                      +..|.+.+++||++||++|+++|+|.+|++++||.|+||||+.| +|+||.|...     ..+.++.+|.++|+|++| +
T Consensus       294 ~~~Wt~~~~~af~~lK~~L~~~p~L~~pd~~~~~~l~~das~~g~~g~vl~q~~~~~~~~~~~~~~~~y~~~e~e~la~v  373 (557)
T 2zd1_A          294 VIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEA  373 (557)
T ss_dssp             EECCCHHHHHHHHHHHHHTSSCCCBCCCCTTSCCEEEEEEEETTEEEEEEEEETTEEEEEEEEECCSCSEECHHHHHHHH
T ss_pred             ceecCHHHHHHHHHHHHHHhCccceeecCCCCCEEEEEecCCCCcEEEEEecCCCceeeeeecccccccCCChHHHHHHH
Confidence            57899999999999999999999999999999999999999987 5999999765     334479999999999999 8


Q ss_pred             Hhh---h-eeccc---eEEE-eecchhhHhhhc
Q psy10407         81 SLH---F-KYIHC---SLNE-ATDNKALVTLFG  105 (210)
Q Consensus        81 v~~---~-~yl~g---~f~v-~TDh~~L~~l~~  105 (210)
                      +++   | +|+.|   .|.+ +|||+.+.++..
T Consensus       374 v~~l~~~~~~l~g~~p~~~vp~~~~~~~~~~~~  406 (557)
T 2zd1_A          374 VQKITTESIVIWGKTPKFKLPIQKETWETWWTE  406 (557)
T ss_dssp             HHHHHHHHHHHHSSCCEEEESBCHHHHHHHHHH
T ss_pred             HHHhhhhheEEeCCCCCEECCCcHHHHHHHhhh
Confidence            774   5 99999   5777 899999888754

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

Probab=98.10  E-value=9.2e-07  Score=67.99  Aligned_cols=109  Identities=11%  Similarity=0.027  Sum_probs=72.6

Q ss_pred             eEEEecCCCC-------ce-eEEEEeecccc--cccc-----CCCchhhHHHHHHHhhheec--cc--eEEEeecchhhH
Q psy10407         41 YRKDFLDGRI-------SC-GGVMLMIHKKY--FSQP-----VPGSPVEMGCCTNSLHFKYI--HC--SLNEATDNKALV  101 (210)
Q Consensus        41 ~~l~tDAS~~-------~~-GavL~q~~~~~--~s~~-----~~y~~~ekellaiv~~~~yl--~g--~f~v~TDh~~L~  101 (210)
                      +.++||.|..       |+ |+++...++.+  .+..     ...+..+-|+.|++.++..+  .|  +++|+||++.+.
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            4689996654       54 87887633321  1111     13457779999999876222  34  899999999999


Q ss_pred             hhhcccCcCCC-ccchhccchhhhhccccceeeeecCCCCCCccccCCC
Q psy10407        102 TLFGEDKAVPM-LSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRL  149 (210)
Q Consensus       102 ~l~~~~~~~~~-~~~~rl~rw~~~L~~f~~~I~y~~Gk~n~~aD~LSR~  149 (210)
                      ..++..-..+. ....-+.+....+..|++.+.|++|..|..||.|.|.
T Consensus        82 ~~i~~~w~~~~~~~~~l~~~i~~l~~~~~v~~~~V~~~~N~~AD~LA~~  130 (149)
T 2ehg_A           82 KQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPREENKEADRLSRV  130 (149)
T ss_dssp             HHHTTSSCCCCTTHHHHHHHHHHHHHHHTCEEEECCGGGCHHHHHHHHH
T ss_pred             HHHhCccccCCHHHHHHHHHHHHHHhcCCEEEEEcCCcccHHHHHHHHH
Confidence            98876421111 1112234445556778899999999999999999874

>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=97.95  E-value=2.3e-06  Score=64.68  Aligned_cols=108  Identities=12%  Similarity=-0.010  Sum_probs=71.4

Q ss_pred             CceEEEecCCCC------ceeEEEEeecc-----ccccccCCCchhhHHHHHHHhhheec--cc--eEEEeecchhhHhh
Q psy10407         39 NFYRKDFLDGRI------SCGGVMLMIHK-----KYFSQPVPGSPVEMGCCTNSLHFKYI--HC--SLNEATDNKALVTL  103 (210)
Q Consensus        39 ~~~~l~tDAS~~------~~GavL~q~~~-----~~~s~~~~y~~~ekellaiv~~~~yl--~g--~f~v~TDh~~L~~l  103 (210)
                      .++.|+||.|..      |+|+++.....     .+......-+..+-|+.|++.++.++  .|  +++|+||.+.+...
T Consensus         2 ~~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~   81 (141)
T 3hst_B            2 VKVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQ   81 (141)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHH
T ss_pred             cEEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCCCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHH
Confidence            468999997754      77777765431     11111112346678999998876222  34  89999999999998


Q ss_pred             hcccCcCCCccchhccchh----hhhccc-cceeeeecCCCCCCccccCCC
Q psy10407        104 FGEDKAVPMLSSARLQRWS----LILSNF-DYSIKYKKGTQIPVADALSRL  149 (210)
Q Consensus       104 ~~~~~~~~~~~~~rl~rw~----~~L~~f-~~~I~y~~Gk~n~~aD~LSR~  149 (210)
                      ++..-..   .+..+.++.    ..+..| .+++.|+++..|..||.|.|.
T Consensus        82 i~~~~~~---~~~~l~~~~~~i~~l~~~~~~v~~~~V~~~~N~~AD~LA~~  129 (141)
T 3hst_B           82 MSGRWKV---KHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLAND  129 (141)
T ss_dssp             HTTSSCC---CSHHHHHHHHHHHHHHTTSSEEEEEECCGGGCHHHHHHHHH
T ss_pred             HhCCccc---CCHHHHHHHHHHHHHHhcCCeEEEEEcCCcccHHHHHHHHH
Confidence            8863211   233333332    333444 688999999999999999764

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

Probab=97.72  E-value=1.1e-05  Score=60.57  Aligned_cols=107  Identities=10%  Similarity=-0.055  Sum_probs=69.2

Q ss_pred             ceEEEecCCC------CceeEEEEeecc----ccccccCCCchhhHHHHHHHhhheec--c-----c-eEEEeecchhhH
Q psy10407         40 FYRKDFLDGR------ISCGGVMLMIHK----KYFSQPVPGSPVEMGCCTNSLHFKYI--H-----C-SLNEATDNKALV  101 (210)
Q Consensus        40 ~~~l~tDAS~------~~~GavL~q~~~----~~~s~~~~y~~~ekellaiv~~~~yl--~-----g-~f~v~TDh~~L~  101 (210)
                      .+.++||.|.      .|+|+++.....    .+......-+..+-|+.|++.++.++  .     + +++|+||.+.+.
T Consensus         3 ~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~vi   82 (140)
T 3u3g_D            3 KIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIV   82 (140)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEEEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHHH
T ss_pred             eEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCCCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHHH
Confidence            5789999775      477887765322    11111112246678999998865211  1     2 799999999999


Q ss_pred             hhhcccCcCCCccchhcc----chhhh-hccc-cceeeeecCCCCCCccccCCC
Q psy10407        102 TLFGEDKAVPMLSSARLQ----RWSLI-LSNF-DYSIKYKKGTQIPVADALSRL  149 (210)
Q Consensus       102 ~l~~~~~~~~~~~~~rl~----rw~~~-L~~f-~~~I~y~~Gk~n~~aD~LSR~  149 (210)
                      ..++..-..   .+..+.    +.... +..| .+++.|+++..|..||.|.+.
T Consensus        83 ~~i~~~~~~---~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~~~N~~AD~LA~~  133 (140)
T 3u3g_D           83 RQMQGVYKV---KEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNE  133 (140)
T ss_dssp             HHHTTSSCC---CCGGGHHHHHHHHHHHHHHCTTCEEEECCGGGGHHHHHHHHH
T ss_pred             HHhCCCccc---CCHHHHHHHHHHHHHhhcCCCcEEEEEcCchhhHHHHHHHHH
Confidence            988863211   222222    22233 4565 799999999999999998763

>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=97.60  E-value=9.2e-05  Score=58.33  Aligned_cols=114  Identities=15%  Similarity=-0.009  Sum_probs=70.5

Q ss_pred             ccCCCCceEEEecCCCC------ceeEEEEeecccc--ccccCCCchhhHHHHHHHhhheeccc-eEEEeecchhhHhhh
Q psy10407         34 GFTNYNFYRKDFLDGRI------SCGGVMLMIHKKY--FSQPVPGSPVEMGCCTNSLHFKYIHC-SLNEATDNKALVTLF  104 (210)
Q Consensus        34 ~~~~~~~~~l~tDAS~~------~~GavL~q~~~~~--~s~~~~y~~~ekellaiv~~~~yl~g-~f~v~TDh~~L~~l~  104 (210)
                      .|.++..+.++||.|..      |+|+++......+  ......-+...-|+.|++.++.++.+ +++|+||.+-+...+
T Consensus        17 ~P~~~~~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~~~v~I~tDS~~vi~~i   96 (165)
T 3p1g_A           17 QPIPDADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFATA   96 (165)
T ss_dssp             SCCTTCSEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHTBTSEEEEEECCHHHHHHH
T ss_pred             CCCCCCCEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHccCceEEEEEchHHHHhhh
Confidence            45555579999997764      4677776644321  11112224567899999998855556 999999998777655


Q ss_pred             cccCcCCCccchhccchhhh---h-ccccceeeeecCCC---------CCCccccCCC
Q psy10407        105 GEDKAVPMLSSARLQRWSLI---L-SNFDYSIKYKKGTQ---------IPVADALSRL  149 (210)
Q Consensus       105 ~~~~~~~~~~~~rl~rw~~~---L-~~f~~~I~y~~Gk~---------n~~aD~LSR~  149 (210)
                      -.....+...+..  -|...   + ...++.+.+++|..         |-.||.|.|.
T Consensus        97 w~~~~g~~v~n~d--l~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~  152 (165)
T 3p1g_A           97 HVHSEGREIKNKN--EILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAARE  152 (165)
T ss_dssp             HSCCCSCCCSSHH--HHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHH
T ss_pred             hcccCCCcccCHH--HHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHH
Confidence            2111111112222  14333   2 44578899999976         6778887653

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

Probab=97.51  E-value=2e-05  Score=61.98  Aligned_cols=112  Identities=12%  Similarity=0.018  Sum_probs=68.3

Q ss_pred             CceEEEecCCCC------ceeEEEEeecc--ccccccCCCchhhHHHHHHHhhheec-cc-eEEEeecchhhHhhhccc-
Q psy10407         39 NFYRKDFLDGRI------SCGGVMLMIHK--KYFSQPVPGSPVEMGCCTNSLHFKYI-HC-SLNEATDNKALVTLFGED-  107 (210)
Q Consensus        39 ~~~~l~tDAS~~------~~GavL~q~~~--~~~s~~~~y~~~ekellaiv~~~~yl-~g-~f~v~TDh~~L~~l~~~~-  107 (210)
                      ..+.++||.|..      |+|+++.....  .+......-+..+-|+.|++.++.++ .. +++|+||.+.+...++.. 
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~~~~v~I~tDS~~vi~~i~~~w   86 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCEVDLYTDSHYLKKAFTEGW   86 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCSCCEEEEECCCHHHHHHHHSSH
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHhccCCeEEEEeChHHHHHHHhhhH
Confidence            468899997764      56677654322  11111112235678999999988444 34 999999999887666551 


Q ss_pred             ----------CcC-CCccchh-ccchhhhhccccceeeeecCC----CCCCccccCCCC
Q psy10407        108 ----------KAV-PMLSSAR-LQRWSLILSNFDYSIKYKKGT----QIPVADALSRLP  150 (210)
Q Consensus       108 ----------~~~-~~~~~~r-l~rw~~~L~~f~~~I~y~~Gk----~n~~aD~LSR~p  150 (210)
                                ... ....+.. ..+....+..+++.+.+++|.    .|..||.|.|.-
T Consensus        87 ~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LAk~a  145 (166)
T 1ril_A           87 LEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQ  145 (166)
T ss_dssp             HHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCCCGGGSCTHHHHHHHHHHHH
T ss_pred             HHHHHhcccccccCCccCcHHHHHHHHHHHhcCeEEEEEeeCCCCchhHHHHHHHHHHH
Confidence                      000 0011222 222233456678899999964    788899988644

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

Probab=97.51  E-value=4.3e-05  Score=59.52  Aligned_cols=111  Identities=11%  Similarity=0.025  Sum_probs=68.3

Q ss_pred             CceEEEecCCCC------ceeEEEEeecc--ccccccCCCchhhHHHHHHHhhheec-cc-eEEEeecchhhHhhhcc--
Q psy10407         39 NFYRKDFLDGRI------SCGGVMLMIHK--KYFSQPVPGSPVEMGCCTNSLHFKYI-HC-SLNEATDNKALVTLFGE--  106 (210)
Q Consensus        39 ~~~~l~tDAS~~------~~GavL~q~~~--~~~s~~~~y~~~ekellaiv~~~~yl-~g-~f~v~TDh~~L~~l~~~--  106 (210)
                      ..+.++||.|..      |+|+++.....  .+......-+..+-|+.|++.++.++ .+ +++|+||.+.+...++.  
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~tn~~aEl~A~~~AL~~~~~~~~v~I~tDS~~vi~~i~~w~   84 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGFSLTTNNRMELLAPIVALEALKEPCKIILTSDSQYMRQGIMTWI   84 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCSSCCEEEEEECCHHHHHHHHTHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCcCCCccHHHHHHHHHHHHHHhccCCeEEEEeCHHHHHHHHHHHH
Confidence            468899997764      67777764322  11111112235678999999987333 34 99999999888776654  


Q ss_pred             ------c--CcC-CCccchhc-cchhhhhccccceeeeecCC----CCCCccccCCC
Q psy10407        107 ------D--KAV-PMLSSARL-QRWSLILSNFDYSIKYKKGT----QIPVADALSRL  149 (210)
Q Consensus       107 ------~--~~~-~~~~~~rl-~rw~~~L~~f~~~I~y~~Gk----~n~~aD~LSR~  149 (210)
                            .  ... ....+..+ .+-...+..+++.+.+++|.    .|..||.|.|.
T Consensus        85 ~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LAk~  141 (158)
T 2e4l_A           85 HGWKKKGWMTSNRTPVKNVDLWKRLDKAAQLHQIDWRWVKGHAGHAENERCDQLARA  141 (158)
T ss_dssp             HHHHHTTTBCTTSSBCTTHHHHHHHHHHHTTSEEEEEECCTTCCCHHHHHHHHHHHH
T ss_pred             HHHHHccccccCCCcccCHHHHHHHHHHHccCcEEEEEccCCCCchhHHHHHHHHHH
Confidence                  1  000 00122222 22234456678999999975    67788888764

>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=97.46  E-value=5.9e-05  Score=58.47  Aligned_cols=110  Identities=14%  Similarity=0.120  Sum_probs=67.7

Q ss_pred             ceEEEecCCCC------ceeEEEEeecc--ccccccCCCchhhHHHHHHHhhheec-cc-eEEEeecchhhHhhhcc---
Q psy10407         40 FYRKDFLDGRI------SCGGVMLMIHK--KYFSQPVPGSPVEMGCCTNSLHFKYI-HC-SLNEATDNKALVTLFGE---  106 (210)
Q Consensus        40 ~~~l~tDAS~~------~~GavL~q~~~--~~~s~~~~y~~~ekellaiv~~~~yl-~g-~f~v~TDh~~L~~l~~~---  106 (210)
                      .+.++||.|..      |+|+++.....  .+......-+..+-|+.|++.++.++ .. +++|+||.+.+...++.   
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL~~~~~~~~v~I~tDS~~vi~~i~~w~~   83 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAEVILSTDSQYVRQGITQWIH   83 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCSCCEEEEEECCHHHHHHHHTTHH
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEecCCCCCcHHHHHHHHHHHHHHHhCcCCcEEEEeCHHHHHHHHHHHHH
Confidence            57899997664      56777765332  11111112235678999999988443 34 99999999988877764   


Q ss_pred             -----c--Cc-CCCccchhc-cchhhhhccccceeeeecCC----CCCCccccCCC
Q psy10407        107 -----D--KA-VPMLSSARL-QRWSLILSNFDYSIKYKKGT----QIPVADALSRL  149 (210)
Q Consensus       107 -----~--~~-~~~~~~~rl-~rw~~~L~~f~~~I~y~~Gk----~n~~aD~LSR~  149 (210)
                           .  .. .....+..+ .+....+..+++.+.|++|.    .|..||.|.|.
T Consensus        84 ~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~  139 (155)
T 1jl1_A           84 NWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARA  139 (155)
T ss_dssp             HHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTCHHHHHHHHHHHH
T ss_pred             HHhhcccccccCCccCCHHHHHHHHHHHccCceEEEEcCCCCCCHHHHHHHHHHHH
Confidence                 1  00 000112222 22233455678899999975    68889988764

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

Probab=97.44  E-value=4.6e-05  Score=58.88  Aligned_cols=112  Identities=10%  Similarity=-0.071  Sum_probs=66.9

Q ss_pred             CCceEEEecCCCC---------ceeEEEEeeccccccccC--CCchhhHHHHHHHhhheec--cc--eEEEeecchhhHh
Q psy10407         38 YNFYRKDFLDGRI---------SCGGVMLMIHKKYFSQPV--PGSPVEMGCCTNSLHFKYI--HC--SLNEATDNKALVT  102 (210)
Q Consensus        38 ~~~~~l~tDAS~~---------~~GavL~q~~~~~~s~~~--~y~~~ekellaiv~~~~yl--~g--~f~v~TDh~~L~~  102 (210)
                      ...+.++||.|..         |+|.++......-.+..+  .-+..+-|+.|++.++.++  .|  +++|+||.+.+..
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            3568899997643         455555422111112222  2346678999999987333  34  8999999988876


Q ss_pred             hhcc----------cCcCC-Cccchh-ccchhhhhccccceeeeecCCC----CCCccccCCC
Q psy10407        103 LFGE----------DKAVP-MLSSAR-LQRWSLILSNFDYSIKYKKGTQ----IPVADALSRL  149 (210)
Q Consensus       103 l~~~----------~~~~~-~~~~~r-l~rw~~~L~~f~~~I~y~~Gk~----n~~aD~LSR~  149 (210)
                      .++.          +.... ...+.. +.+-...+..+++.+.+++|..    |..||.|.|.
T Consensus        85 ~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~~~v~~~~V~~H~g~~~N~~AD~LA~~  147 (154)
T 2qkb_A           85 GITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLARE  147 (154)
T ss_dssp             HHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTTCEEEEEECCTTSSCHHHHHHHHHHHH
T ss_pred             hhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcCCceEEEEccCCCCCHhHHHHHHHHHH
Confidence            6653          11000 011222 1222333567889999999965    8889988763

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

Probab=97.44  E-value=3.1e-05  Score=59.24  Aligned_cols=110  Identities=14%  Similarity=0.042  Sum_probs=65.9

Q ss_pred             CceEEEecCCC------CceeEEEEeecc--ccccccCCCchhhHHHHHHHhhheecc-c-eEEEeecchhhHhhhccc-
Q psy10407         39 NFYRKDFLDGR------ISCGGVMLMIHK--KYFSQPVPGSPVEMGCCTNSLHFKYIH-C-SLNEATDNKALVTLFGED-  107 (210)
Q Consensus        39 ~~~~l~tDAS~------~~~GavL~q~~~--~~~s~~~~y~~~ekellaiv~~~~yl~-g-~f~v~TDh~~L~~l~~~~-  107 (210)
                      ..+.++||.|.      .|+|+++.....  .+......-+..+-|+.|++.++.++. . +++|+||.+.+...++.. 
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~AL~~~~~~~~v~I~tDS~~vi~~i~~~w   82 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDPATTNNRMELMAAIKGLEALKEPARVQLYSDSAYLVNAMNEGW   82 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCSSCCEEEEEESCHHHHHHHHSSH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCCCCCcHHHHHHHHHHHHHHhcCccCcEEEEeChHHHHHHHHHHH
Confidence            56899999773      356676654322  111111122355689999999884333 5 999999999887766641 


Q ss_pred             -----------CcCCCccchhc-cchhhhhccccceeeeecCC----CCCCccccCC
Q psy10407        108 -----------KAVPMLSSARL-QRWSLILSNFDYSIKYKKGT----QIPVADALSR  148 (210)
Q Consensus       108 -----------~~~~~~~~~rl-~rw~~~L~~f~~~I~y~~Gk----~n~~aD~LSR  148 (210)
                                 .......+..+ .+-...+..+++.+.+++|.    .|..||.|.|
T Consensus        83 ~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~~v~~~~V~gH~g~~~N~~AD~LA~  139 (146)
T 3h08_A           83 LKRWVKNGWKTAAKKPVENIDLWQEILKLTTLHRVTFHKVKGHSDNPYNSRADELAR  139 (146)
T ss_dssp             HHHHHHTTCC----CCCTTHHHHHHHHHHHHHSEEEEEECCC-CCSHHHHHHHHHHH
T ss_pred             HHHHHHCCCccCCCCCcCCHHHHHHHHHHHhhCceEEEEcCCcCCcHhHHHHHHHHH
Confidence                       00000112222 22233456678889999964    5777888765

>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=97.17  E-value=7.8e-05  Score=57.37  Aligned_cols=108  Identities=9%  Similarity=-0.112  Sum_probs=66.3

Q ss_pred             CCceEEEecCCC----CceeEEEEeecc--cccc-cc--C---CCchhhHHHHHHHhhheec--cc-eEEEeecchhhHh
Q psy10407         38 YNFYRKDFLDGR----ISCGGVMLMIHK--KYFS-QP--V---PGSPVEMGCCTNSLHFKYI--HC-SLNEATDNKALVT  102 (210)
Q Consensus        38 ~~~~~l~tDAS~----~~~GavL~q~~~--~~~s-~~--~---~y~~~ekellaiv~~~~yl--~g-~f~v~TDh~~L~~  102 (210)
                      ...+.++||.|.    .|+|+++.+...  .+.. ..  .   .-...+-|+.|++.++.+.  .| +++|+||.+.+..
T Consensus         4 ~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~~v~I~tDS~~i~~   83 (147)
T 2kq2_A            4 RTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGVKIRILHDYAGIAF   83 (147)
T ss_dssp             TSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTCCCCBSSCCSTHHH
T ss_pred             CCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCCeEEEEECcHHHHH
Confidence            356889999875    688888876433  1111 11  0   1245678999999877332  36 8999999998876


Q ss_pred             hhcccCcCCCccchhccchhh---hhccccceeeeecCC----CCCCccccCCC
Q psy10407        103 LFGEDKAVPMLSSARLQRWSL---ILSNFDYSIKYKKGT----QIPVADALSRL  149 (210)
Q Consensus       103 l~~~~~~~~~~~~~rl~rw~~---~L~~f~~~I~y~~Gk----~n~~aD~LSR~  149 (210)
                      .+...-..   .++....+..   .|.. ++.+.++||.    .|..||.|.|.
T Consensus        84 w~~~~w~~---~~~~~~~~~~l~~~l~~-~v~~~wV~gH~g~~~Ne~AD~LA~~  133 (147)
T 2kq2_A           84 WATGEWKA---KNEFTQAYAKLMNQYRG-IYSFEKVKAHSGNEFNDYVDMKAKS  133 (147)
T ss_dssp             HTTSSSSC---CHHHHHHHHCGGGGGST-TCCBCCCCCCCCCHHHHHHHHHHHH
T ss_pred             HHhCCCcc---CCcchHHHHHHHHHhcC-CeeEEEecCcCCCcchHHHHHHHHH
Confidence            55431100   1222222222   2333 6888888985    48889988764

>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=97.10  E-value=0.00024  Score=54.95  Aligned_cols=111  Identities=10%  Similarity=-0.066  Sum_probs=65.8

Q ss_pred             CceEEEecCCC------CceeEEEEeeccccccccCCCchhhHHHHHHHhhheeccc-eEEEeecchhhHhhhccc----
Q psy10407         39 NFYRKDFLDGR------ISCGGVMLMIHKKYFSQPVPGSPVEMGCCTNSLHFKYIHC-SLNEATDNKALVTLFGED----  107 (210)
Q Consensus        39 ~~~~l~tDAS~------~~~GavL~q~~~~~~s~~~~y~~~ekellaiv~~~~yl~g-~f~v~TDh~~L~~l~~~~----  107 (210)
                      ..+.++||.|.      .|+|+++........+ ...-+...-|+.|++.++..+ + +++|+||.+.+...++.-    
T Consensus        11 ~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~-~~~~Tnn~aEl~A~i~AL~~~-~~~v~i~tDS~~v~~~i~~w~~~W   88 (150)
T 3qio_A           11 GAETFYVDGAANRETKLGKAGYVTNRGRQKVVT-LTDTTNQKTELQAIYLALQDS-GLEVNIVTDSQYALGIITQWIHNW   88 (150)
T ss_dssp             TCEEEEEEEEECTTTCCEEEEEEETTSCEEEEE-ESSCCHHHHHHHHHHHHHHHS-CSEEEEEESCHHHHHHHHHHHHHH
T ss_pred             CCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEe-CCCCCHHHHHHHHHHHHHHhC-CCcEEEEeCcHHHHHHHHHHHHHH
Confidence            35889999774      3566666432221111 122345568999999988443 7 999999988777655431    


Q ss_pred             -------CcCCCccchhccch-hhhh-ccccceeeeecCCC----CCCccccCCCCC
Q psy10407        108 -------KAVPMLSSARLQRW-SLIL-SNFDYSIKYKKGTQ----IPVADALSRLPL  151 (210)
Q Consensus       108 -------~~~~~~~~~rl~rw-~~~L-~~f~~~I~y~~Gk~----n~~aD~LSR~p~  151 (210)
                             ...+...+..+.+- ...+ ...++.+.+++|..    |..||.|.|.-.
T Consensus        89 ~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~  145 (150)
T 3qio_A           89 KKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGI  145 (150)
T ss_dssp             CC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTT
T ss_pred             hhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHH
Confidence                   00000112222111 1123 34568899999987    999999987543

>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=96.14  E-value=0.0071  Score=55.81  Aligned_cols=106  Identities=10%  Similarity=-0.039  Sum_probs=66.0

Q ss_pred             CceEEEecCCC------CceeEEEEeeccccccccCCCchhhHHHHHHHhhheeccc-eEEEeecchhhHhhhcccCcCC
Q psy10407         39 NFYRKDFLDGR------ISCGGVMLMIHKKYFSQPVPGSPVEMGCCTNSLHFKYIHC-SLNEATDNKALVTLFGEDKAVP  111 (210)
Q Consensus        39 ~~~~l~tDAS~------~~~GavL~q~~~~~~s~~~~y~~~ekellaiv~~~~yl~g-~f~v~TDh~~L~~l~~~~~~~~  111 (210)
                      ..+.++||.|.      .|+|+++........ ....-+..+-|+.|++.++..+ + ++.|+||.+.+...++....  
T Consensus       438 ~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~-~~~~~TNn~aEl~Ai~~aL~~~-~~~v~I~tDS~~vi~~i~~~~~--  513 (557)
T 2zd1_A          438 GAETFYVDGAANRETKLGKAGYVTNKGRQKVV-PLTNTTNQKTELQAIYLALQDS-GLEVNIVTDSQYALGIIQAQPD--  513 (557)
T ss_dssp             TSCEEEEEEEECTTTCCEEEEEEETTSCEEEE-EECSCCHHHHHHHHHHHHHHHS-CSEEEEEECCHHHHHHHTTCCS--
T ss_pred             CCEEEEEccCCCCCCCceEEEEEEECCcEEEe-cCCCCCHHHHHHHHHHHHHHhC-CCcEEEEeChHHHHHHHhcCCc--
Confidence            35899999764      345555542111111 1223346678999999988444 7 99999999988888775331  


Q ss_pred             Cccchhcc-chh-hhhccccceeeeecCC----CCCCccccCCC
Q psy10407        112 MLSSARLQ-RWS-LILSNFDYSIKYKKGT----QIPVADALSRL  149 (210)
Q Consensus       112 ~~~~~rl~-rw~-~~L~~f~~~I~y~~Gk----~n~~aD~LSR~  149 (210)
                       ..+..+. +.. ......++.+.|++|.    .|..||.|.+.
T Consensus       514 -~~~~~l~~~~~~~l~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~  556 (557)
T 2zd1_A          514 -KSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA  556 (557)
T ss_dssp             -EESSHHHHHHHHHHHHCSEEEEEECCSSSCCTTCCGGGGCC--
T ss_pred             -cCCHHHHHHHHHHHhcCCCEEEEEcCCCCCChhHHHHHHHHhc
Confidence             1122222 222 2233457889999995    59999999874

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

Probab=96.08  E-value=0.0046  Score=48.52  Aligned_cols=111  Identities=14%  Similarity=-0.077  Sum_probs=57.7

Q ss_pred             CCceEEEecCCC-----------CceeEEEEeecc------ccccccCCCchhhHHHHHHHhhh--eeccc-eEEEeecc
Q psy10407         38 YNFYRKDFLDGR-----------ISCGGVMLMIHK------KYFSQPVPGSPVEMGCCTNSLHF--KYIHC-SLNEATDN   97 (210)
Q Consensus        38 ~~~~~l~tDAS~-----------~~~GavL~q~~~------~~~s~~~~y~~~ekellaiv~~~--~yl~g-~f~v~TDh   97 (210)
                      ..+.++|||-|.           .|+|.++.....      .+...+-+-....-|+.|+....  ..-.+ +++|+||.
T Consensus         5 ~~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~~~~v~I~TDS   84 (165)
T 2lsn_A            5 QYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIPGPVLVITDS   84 (165)
T ss_dssp             CCSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHSSSCEEEEESC
T ss_pred             CceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcCCCeEEEEeCh
Confidence            356899999663           467777754332      11111111112223444554443  12245 89999999


Q ss_pred             hhhHhhhcc----------cCc-CCCccchhcc-chhhhhccc-cceeeeecCCC----------CCCccccCC
Q psy10407         98 KALVTLFGE----------DKA-VPMLSSARLQ-RWSLILSNF-DYSIKYKKGTQ----------IPVADALSR  148 (210)
Q Consensus        98 ~~L~~l~~~----------~~~-~~~~~~~rl~-rw~~~L~~f-~~~I~y~~Gk~----------n~~aD~LSR  148 (210)
                      +-+...++.          ++. .+-..+.-+- +-...+..+ ++++.|++|..          |..||.|.|
T Consensus        85 ~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~  158 (165)
T 2lsn_A           85 FYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLAT  158 (165)
T ss_dssp             HHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHH
Confidence            887765542          110 0111222221 112234433 68899999864          667887755

>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=93.64  E-value=0.044  Score=50.41  Aligned_cols=106  Identities=8%  Similarity=-0.075  Sum_probs=64.7

Q ss_pred             CceEEEecCCC------CceeEEEEeeccccccccCCCchhhHHHHHHHhhheeccc-eEEEeecchhhHhhhcccCcCC
Q psy10407         39 NFYRKDFLDGR------ISCGGVMLMIHKKYFSQPVPGSPVEMGCCTNSLHFKYIHC-SLNEATDNKALVTLFGEDKAVP  111 (210)
Q Consensus        39 ~~~~l~tDAS~------~~~GavL~q~~~~~~s~~~~y~~~ekellaiv~~~~yl~g-~f~v~TDh~~L~~l~~~~~~~~  111 (210)
                      ....++||.|.      .|+|+++...... ......-+..+-|+.|++.++.. .+ ++.|+||.+-+...++.-..  
T Consensus       435 ~~~~iytDGs~~~n~g~~g~G~v~~~~~~~-~~~~~~~TNn~aEl~A~i~aL~~-~~~~v~I~tDS~~v~~~i~~~~~--  510 (555)
T 1mu2_A          435 GAETFYTDGSCNRQSKEGKAGYVTDRGKDK-VKKLEQTTNQQAELEAFAMALTD-SGPKVNIIVDSQYVMGIVASQPT--  510 (555)
T ss_dssp             TCEEEEEEEEECTTTCCEEEEEEETTSCEE-EEEESSCCHHHHHHHHHHHHHHT-SCSEEEEEESCHHHHHHHHTCCS--
T ss_pred             CceEEEEcccccCCCCCceEEEEEEeCCEe-eccCCCCCHHHHHHHHHHHHHHc-CCCeEEEEEehHHHHHHHhcccc--
Confidence            45899999763      2455555432211 11111233556899999998844 45 99999999988877764221  


Q ss_pred             Cccchhccch-hhh-hccccceeeeecCC----CCCCccccCCC
Q psy10407        112 MLSSARLQRW-SLI-LSNFDYSIKYKKGT----QIPVADALSRL  149 (210)
Q Consensus       112 ~~~~~rl~rw-~~~-L~~f~~~I~y~~Gk----~n~~aD~LSR~  149 (210)
                       ..+..+.+- ... ....++.+.|++|.    .|..||.|.+.
T Consensus       511 -~~~~~l~~~~~~~~~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~  553 (555)
T 1mu2_A          511 -ESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQ  553 (555)
T ss_dssp             -EESCHHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHHT
T ss_pred             -cccHHHHHHHHHHhccCCcEEEEEEECCCCChhHHHHHHHHHh
Confidence             122222221 122 23456889999994    58889988764

>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=80.91  E-value=0.42  Score=36.25  Aligned_cols=69  Identities=9%  Similarity=0.032  Sum_probs=44.4

Q ss_pred             CceEEEecCCCC------ceeEEEEeecccc-ccccC-CCchhhHHHHHHHhhheec--cc-eEEEeecchhhHhhhccc
Q psy10407         39 NFYRKDFLDGRI------SCGGVMLMIHKKY-FSQPV-PGSPVEMGCCTNSLHFKYI--HC-SLNEATDNKALVTLFGED  107 (210)
Q Consensus        39 ~~~~l~tDAS~~------~~GavL~q~~~~~-~s~~~-~y~~~ekellaiv~~~~yl--~g-~f~v~TDh~~L~~l~~~~  107 (210)
                      ..+.|+||.|..      |+|+++......+ .+... .-+..+.|+.|++.++.++  .| ++.|+||.+-+...++..
T Consensus        10 ~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~~~TNN~aEl~A~i~aL~~~~~~~~~v~i~tDS~~vi~w~~~~   89 (142)
T 1zbf_A           10 IWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKDK   89 (142)
T ss_dssp             CSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTTCCCCEEESCHHHHHHHHHT
T ss_pred             CeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccCCcCcHHHHHHHHHHHHHHHHhCCCeEEEEEehHHHHHHHHcC
Confidence            457899996543      6778876322211 11111 2246678999999877333  35 899999999888766644

>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=80.36  E-value=0.37  Score=36.38  Aligned_cols=66  Identities=8%  Similarity=-0.049  Sum_probs=42.0

Q ss_pred             eEEEecCCC------CceeEEEEeecc--ccccccCCCchhhHHHHHHHhhheec--cc-eEEEeecchhhHhhhcc
Q psy10407         41 YRKDFLDGR------ISCGGVMLMIHK--KYFSQPVPGSPVEMGCCTNSLHFKYI--HC-SLNEATDNKALVTLFGE  106 (210)
Q Consensus        41 ~~l~tDAS~------~~~GavL~q~~~--~~~s~~~~y~~~ekellaiv~~~~yl--~g-~f~v~TDh~~L~~l~~~  106 (210)
                      ..|+||.|.      .|+|||+.....  ......-.-.-.+.|++|++.++..+  .| .++|+||.+-+...+..
T Consensus         6 ~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~~~tTNN~aEl~A~i~aL~~l~~~~~~v~i~tDSqyVi~wi~~   82 (134)
T 4htu_A            6 ESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKD   82 (134)
T ss_dssp             SSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEEEEECHHHHHHHHHHHHHHHHHHTTCCCCEEESCHHHHHHHHH
T ss_pred             eEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCCCCCchHHHHHHHHHHHHHHHHhCCCCEEEEcchHHHHHHHHc
Confidence            468999654      356777755222  11111112235668999999987444  36 78999999988776653

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	210
d2zd1b1	424	HIV-1 reverse transcriptase {Human immunodeficienc	98.93
d1mu2a2	427	HIV-1 reverse transcriptase {Human immunodeficienc	98.26
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	97.09
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	96.61
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	96.42
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	95.0
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	92.25

>d2zd1b1 e.8.1.2 (B:5-428) HIV-1 reverse transcriptase {Human immunodeficiency virus type 1 [TaxId: 11676]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Reverse transcriptase
domain: HIV-1 reverse transcriptase
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=98.93  E-value=5.8e-10  Score=98.49  Aligned_cols=122  Identities=5%  Similarity=-0.058  Sum_probs=88.6

Q ss_pred             cccCCCChHHHHHHHHHHHhcCCCCcccccCCCCceEEEecCCCCceeEEEEee-cc-----ccccccCCC--chhhHHH
Q psy10407          6 YKAQNLLPGYNQLFVTMETHLLPDKVISGFTNYNFYRKDFLDGRISCGGVMLMI-HK-----KYFSQPVPG--SPVEMGC   77 (210)
Q Consensus         6 ~~~~~~~~~~~~aF~~lK~~l~~~pvl~~~~~~~~~~l~tDAS~~~~GavL~q~-~~-----~~~s~~~~y--~~~ekel   77 (210)
                      .....|.+.+++||++||++|+++|+|++||+++||.++||||..|.|+...|. ..     +++++..+-  +..+.-.
T Consensus       286 ~~~~~Wt~e~~~af~~lK~~l~~~p~L~~~Dp~kp~~~~~das~~g~~~~~~~q~~~~~~~~~~~~~~~~~~~n~~~~~~  365 (424)
T d2zd1b1         286 TEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLT  365 (424)
T ss_dssp             TCEECCCHHHHHHHHHHHHHTTSCCTTCCCCTTSCCEEEEEEEETTEEEEEEESSTTCEEEEEEEECCSSCTTCHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHHHhcccccccCCCCCCCEEEEEecCCCCceEEEEEcCCCcccceEEeccccccccCHHHHHH
Confidence            445679999999999999999999999999999999999999977776554433 32     555553322  2333222


Q ss_pred             HHHHh----hh-eeccc-eEEEeecchhhHhhhcccCcCCCccchhccchhhhhccccceeeeecCCCCCCccccCCC
Q psy10407         78 CTNSL----HF-KYIHC-SLNEATDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRL  149 (210)
Q Consensus        78 laiv~----~~-~yl~g-~f~v~TDh~~L~~l~~~~~~~~~~~~~rl~rw~~~L~~f~~~I~y~~Gk~n~~aD~LSR~  149 (210)
                      +++..    .+ ++..+ .|.                     ...+..+|.....+| +.+.|+|+-+++.++.|+|.
T Consensus       366 ~~~~k~~~e~~~~~g~~p~~~---------------------~p~~~~~w~~~~~~~-~~~~~~p~~~~~~~~~l~~~  421 (424)
T d2zd1b1         366 EAVQKITTESIVIWGKTPKFK---------------------LPIQKETWETWWTEY-WQATWIPEWEFVNTPPLVKL  421 (424)
T ss_dssp             HHHHHHHHHHHHHHSSCCEEE---------------------ESSCHHHHHHHHHHH-CCCSSCCEEEECCSCCTTTG
T ss_pred             HHHHHHHHHHHHHhCcCccEE---------------------CCccHHHHHHHHHhh-cccccCCCceeccCcHHHHH
Confidence            23322    22 44333 332                     344666899999999 99999999999999999996

>d1mu2a2 e.8.1.2 (A:3-429) HIV-1 reverse transcriptase {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Reverse transcriptase
domain: HIV-1 reverse transcriptase
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=98.26  E-value=6.4e-07  Score=78.67  Aligned_cols=74  Identities=3%  Similarity=-0.149  Sum_probs=60.4

Q ss_pred             ccCCCChHHHHHHHHHHHhcCCCCcccccCCCCceEEEecCCCCc-eeEEEEeecc----ccccccCCCchhhHHHHHH
Q psy10407          7 KAQNLLPGYNQLFVTMETHLLPDKVISGFTNYNFYRKDFLDGRIS-CGGVMLMIHK----KYFSQPVPGSPVEMGCCTN   80 (210)
Q Consensus         7 ~~~~~~~~~~~aF~~lK~~l~~~pvl~~~~~~~~~~l~tDAS~~~-~GavL~q~~~----~~~s~~~~y~~~ekellai   80 (210)
                      ....|.+.+++||+++|++|+++|+|++||+++|+.+++|++..| +|+++.|...    ....+..++.+.+.|++|.
T Consensus       289 ~~~~Wt~e~q~afe~lK~~L~~~~~l~~~dp~kpl~~~i~~~~~~~~~~~~~q~~~~l~~~~~~~~~~~~~~~~~~l~~  367 (427)
T d1mu2a2         289 EEVQWTELAEAELEENRIILSQEQEGHYYQEEKELEATVQKDQDNQWTYKIHQEEKILKVGKYAKVKNTHTNGIRLLAQ  367 (427)
T ss_dssp             CBCCCCHHHHHHHHHHHHHHSCCEEEECBCTTSCCEEEEEECSSSCEEEEEEETTEEEEEEEECCC--CEECHHHHHHH
T ss_pred             CCccCCHHHHHHHHHHHHHhccCcccccCCCCCCEEEEEEcCCCCcEEEEEEccCCceeeeeecccccccCCHHHHHHH
Confidence            456799999999999999999999999999999999999999655 5677777655    4556677888888887764

>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=97.09  E-value=0.00027  Score=50.83  Aligned_cols=106  Identities=8%  Similarity=-0.070  Sum_probs=63.1

Q ss_pred             eEEEecCCCC---c--eeEEEEeeccccccccCCCchhhHHHHHHHhhheeccc-eEEEeecchhhHhhhcccCcCCCcc
Q psy10407         41 YRKDFLDGRI---S--CGGVMLMIHKKYFSQPVPGSPVEMGCCTNSLHFKYIHC-SLNEATDNKALVTLFGEDKAVPMLS  114 (210)
Q Consensus        41 ~~l~tDAS~~---~--~GavL~q~~~~~~s~~~~y~~~ekellaiv~~~~yl~g-~f~v~TDh~~L~~l~~~~~~~~~~~  114 (210)
                      ..+|||.|..   +  -+++.....+........-+...-|+.|++.+..+ .+ ++.|+||.+.+...++...... ..
T Consensus         8 ~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~~~tnn~AEl~Ai~~al~~-~~~~i~I~tDS~~v~~~~~~~~~~~-~~   85 (126)
T d1mu2a1           8 ETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTD-SGPKVNIIVDSQYVMGIVASQPTES-ES   85 (126)
T ss_dssp             EEEEEEEEECTTTCCEEEEEEETTSCEEEEEESSCCHHHHHHHHHHHHHHT-SCSEEEEEESCHHHHHHHHTCCSEE-SC
T ss_pred             cEEEEcCCCCCCCCcEEEEEEecCCCEEEEecCCCcchHHHHHHHHHHhcc-CCcceEEEechHHHHHHHhcCCccc-cc
Confidence            4799997632   2  22333333221111111224556899999887743 35 9999999999988887644211 11


Q ss_pred             chhccchhhhhccccceeeeecCCC----CCCccccCC
Q psy10407        115 SARLQRWSLILSNFDYSIKYKKGTQ----IPVADALSR  148 (210)
Q Consensus       115 ~~rl~rw~~~L~~f~~~I~y~~Gk~----n~~aD~LSR  148 (210)
                      ..............++.+.|+||..    |-.||.|.+
T Consensus        86 ~~~~~~~~~~~~~~~v~~~wV~gH~g~~gNe~AD~LA~  123 (126)
T d1mu2a1          86 KIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVS  123 (126)
T ss_dssp             HHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHH
T ss_pred             hHHHHHHHHhhhcceeEEEEEeCCCCCcchHHHHHHHH
Confidence            1222223444566778899999965    777887754

>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=96.61  E-value=0.0004  Score=50.94  Aligned_cols=110  Identities=12%  Similarity=0.048  Sum_probs=63.2

Q ss_pred             ceEEEecCCC------CceeEEEEeecc--ccccccCCCchhhHHHHHHHhhheeccc--eEEEeecchhhHhhhcccC-
Q psy10407         40 FYRKDFLDGR------ISCGGVMLMIHK--KYFSQPVPGSPVEMGCCTNSLHFKYIHC--SLNEATDNKALVTLFGEDK-  108 (210)
Q Consensus        40 ~~~l~tDAS~------~~~GavL~q~~~--~~~s~~~~y~~~ekellaiv~~~~yl~g--~f~v~TDh~~L~~l~~~~~-  108 (210)
                      .+.||||.|.      .|+|+++.....  .+......-+...-|+.|++.+..++..  .+.++||.+.....++... 
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~~~~~i~i~tds~~~i~~~~~~~~   81 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAEVILSTDSQYVRQGITQWIH   81 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCSCCEEEEEECCHHHHHHHHTTHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhcccceEEEeecceeeEEcccchhh
Confidence            5789999663      367887765543  1211111112445789999988744444  7889999887766554221 


Q ss_pred             --------cCCC--ccch-hccchhhhhccccceeeeecCCC----CCCccccCCC
Q psy10407        109 --------AVPM--LSSA-RLQRWSLILSNFDYSIKYKKGTQ----IPVADALSRL  149 (210)
Q Consensus       109 --------~~~~--~~~~-rl~rw~~~L~~f~~~I~y~~Gk~----n~~aD~LSR~  149 (210)
                              ....  ..+. ........+..+++.+.++||..    |-.||.|.+.
T Consensus        82 ~~~~~~~~~~~~~~~~n~~~~~~i~~~~~~~~V~~~wV~gH~g~~gNe~AD~LAk~  137 (152)
T d1jl1a_          82 NWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARA  137 (152)
T ss_dssp             HHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTCHHHHHHHHHHHH
T ss_pred             HhHhccchhcccCeeecHHHHHHHHHHhhcceeEEEEecccCCCccHHHHHHHHHH
Confidence                    0000  0000 11112233466688899999853    5668888653

>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=96.42  E-value=0.00016  Score=53.29  Aligned_cols=110  Identities=13%  Similarity=0.034  Sum_probs=62.1

Q ss_pred             CceEEEecCCCC------ceeEEEEeecc-ccccccCCC-chhhHHHHHHHhhheeccc--eEEEeecchhhHhhhcccC
Q psy10407         39 NFYRKDFLDGRI------SCGGVMLMIHK-KYFSQPVPG-SPVEMGCCTNSLHFKYIHC--SLNEATDNKALVTLFGEDK  108 (210)
Q Consensus        39 ~~~~l~tDAS~~------~~GavL~q~~~-~~~s~~~~y-~~~ekellaiv~~~~yl~g--~f~v~TDh~~L~~l~~~~~  108 (210)
                      +.+.||||.|..      |+|+++..... ...+..... +...-|+.|++.++.+...  .+.++||...+...+....
T Consensus         2 ~~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~~~~i~i~tds~~~~~~~~~~~   81 (147)
T d1rila_           2 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCEVDLYTDSHYLKKAFTEGW   81 (147)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCSCCEEEEECCCHHHHHHHHSSH
T ss_pred             CEEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhccCCceEEEecchhhhhccccccc
Confidence            357899996533      45666543332 111111111 2344699999998855554  8999999998876553210


Q ss_pred             --------cCC----Cccchh-ccchhhhhccccceeeeecCC----CCCCccccCC
Q psy10407        109 --------AVP----MLSSAR-LQRWSLILSNFDYSIKYKKGT----QIPVADALSR  148 (210)
Q Consensus       109 --------~~~----~~~~~r-l~rw~~~L~~f~~~I~y~~Gk----~n~~aD~LSR  148 (210)
                              ...    ...+.- ..+-...+..+++++.|+||.    .|-.||.|.|
T Consensus        82 ~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~~~~v~~~wVkgHsg~~gNe~AD~LAk  138 (147)
T d1rila_          82 LEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREAR  138 (147)
T ss_dssp             HHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCCCGGGSCTHHHHHHHHHH
T ss_pred             hhhhhhccccccccccchhHHHHHHHHHHhhhcccceEEccCCCCCcchHHHHHHHH
Confidence                    000    001110 112223456778888999884    4556887765

>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=95.00  E-value=0.016  Score=40.52  Aligned_cols=62  Identities=8%  Similarity=-0.006  Sum_probs=40.1

Q ss_pred             chhhHHHHHHHhhheeccceEEEeecchhhHhhhcccCcCCCccchhccchh---hhhccc-cceeeeecC
Q psy10407         71 SPVEMGCCTNSLHFKYIHCSLNEATDNKALVTLFGEDKAVPMLSSARLQRWS---LILSNF-DYSIKYKKG  137 (210)
Q Consensus        71 ~~~ekellaiv~~~~yl~g~f~v~TDh~~L~~l~~~~~~~~~~~~~rl~rw~---~~L~~f-~~~I~y~~G  137 (210)
                      +...-|+.|++.++.....++.|+||.+-+...++...     ......-|.   ..|..+ .+.|.+.||
T Consensus        44 TNn~aEl~Avi~aL~~~~~~v~I~TDS~yvi~~i~~~~-----~~~~~~l~~~il~~l~~~~~v~i~WVpg  109 (110)
T d1s1ta1          44 TNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQP-----DQSESELVNQIIEQLIKKEKVYLAWVPA  109 (110)
T ss_dssp             CHHHHHHHHHHHHHHHSCSEEEEEECCHHHHHHHHHCC-----SEESCHHHHHHHHHHHHCSEEEEEECCS
T ss_pred             cHHHHHHHHHHHHHHhCCCeEEEEEehHHHHHHHhcCc-----cccchHHHHHHHHHHhcCCceEEEEeCC
Confidence            45568999999988433239999999999988887654     222222232   223333 366777776

>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=92.25  E-value=0.037  Score=40.08  Aligned_cols=65  Identities=8%  Similarity=-0.012  Sum_probs=43.0

Q ss_pred             EEEecCCCC------ceeEEEEeecc-ccccc-cCCCchhhHHHHHHHhhheecc--c-eEEEeecchhhHhhhcc
Q psy10407         42 RKDFLDGRI------SCGGVMLMIHK-KYFSQ-PVPGSPVEMGCCTNSLHFKYIH--C-SLNEATDNKALVTLFGE  106 (210)
Q Consensus        42 ~l~tDAS~~------~~GavL~q~~~-~~~s~-~~~y~~~ekellaiv~~~~yl~--g-~f~v~TDh~~L~~l~~~  106 (210)
                      .|+||.|..      |+|+|+..... .+.+. .-+-+-.+.|++|++.++.++.  + ++.|+||.+-+...+..
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~~~~i~I~tDS~yvi~wv~~   81 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTAIKWVKD   81 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTTCCCCEEESCHHHHHHHHH
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcCCceEEEEeccHHHHHHHHh
Confidence            378996665      47777755443 22222 1122355689999999885553  5 89999999988776643