Psyllid ID: psy7535

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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-------20
Protein Sequence
MHLKTSIPLLLPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSLQNIISSSPIALEIINLLHKIQCQVRPSHFNMREQVSLTRLRIGHTNLTHVHLMKREPPPECDTYNCRLTVKHLLKYCNKYQNIRSPNDLYACLLMFQILILGPNFNMNY
Secondary Structure (PSIPRED)
cccccccccccccccEEEcccccccccEEEEEEEcccEEEEEccccccccHHHHHHHHHHHHHHHHccccccccccEEEEccHHHHHHHHHHHccccHHHHHHHHHHHHccccccccccccccEEEEEEEcccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccHHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccEEEEEcccccccEEEEEEEcccEEEEEccccccHHHHHHHHHHHHHHHHHcccccccccccEEEEccHHHHHHHHHHcccccHHHHHHHHHHHHHcccccccccccccEEEEEEEEcccccccHHHHHcccccccccccccEEEEEEEEEEcHHHHHHcccccHHHHHHHHHHHHccccccccc
Coil and Loop (DISEMBL)
mhlktsiplllpnykqiftdasknehsvssafcceetkfsvkldpriSICNAELISIQYAISFIIsttplqvptpkfvlYSDSLSALQSLQNIISSSPIALEIINLLHKIqcqvrpshfnmreqVSLTRlrightnlthvhlmkrepppecdtyncrltVKHLLKYCNKyqnirspnDLYACLLMFQILIlgpnfnmny
Flexible Loop (DISEMBL)
mhlktsiplllpNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSLQNIISSSPIALEIINLLHKIQCQVRPSHFNMREQVSLTRLRIGHTNlthvhlmkrepppecdtYNCRLTVKHLLKYCNKYQNIRSPNDLYACLLMFQILILGPNFNMNY
Low Complexity Region (SEG)
MHLKTSIPLLLPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSLQNIISSSPIALEIINLLHKIQCQVRPSHFNMREQVSLTRLRIGHTNLTHVHLMKREPPPECDTYNCRLTVKHLLKYCNKYQNIRSPNDLYACLLMFQILILGPNFNMNY
Disordered region (IsUnstruct)
******IPLLLPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSLQNIISSSPIALEIINLLHKIQCQVRPSHFNMREQVSLTRLRIGHTNLTHVHLMKREPPPECDTYNCRLTVKHLLKYCNKYQNIRSPNDLYACLLMFQILILGPNF****
Disordered Region (DISOPRED)
****TSIPLLLPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSLQNIISSSPIALEIINLLHKIQCQVRPSHFNMREQVSLTRLRIGHTNLTHVHLMKREPPPECDTYNCRLTVKHLLKYCNKYQNIRSPNDL***LL***************
Disordered Region (DISEMBL)
MHLKTSIPLLLPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSLQNIISSSPIALEIINLLHKIQCQVRPSHFNMREQVSLTRLRIGHTNLTHVHLMKREPPPECDTYNCRLTVKHLLKYCNKYQNIRSPNDLYACLLMFQILILGPNFNMNY
Disordered Region (DISPRO)
**LKTSIPLLLPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSLQNIISSSPIALEIINLLHKIQCQVRPSHFNMREQVSLTRLRIGHTNLTHVHLMKREPPPECDTYNCRLTVKHLLKYCNKYQNIRSPNDLYACLLMFQILILGPNFN***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MHLKTSIPLLLPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSLQNIISSSPIALEIINLLHKIQCQVRPSHFNMREQVSLTRLRIGHTNLTHVHLMKREPPPECDTYNCRLTVKHLLKYCNKYQNIRSPNDLYACLLMFQILILGPNFNMNY
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

No hits with e-value below 0.001 by BLAST

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	199
443730613	233	hypothetical protein CAPTEDRAFT_206814 [	0.753	0.643	0.271	3e-08
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.552	0.090	0.327	7e-08
328720146	164	PREDICTED: hypothetical protein LOC10056	0.326	0.396	0.454	9e-08
328697220	1915	PREDICTED: hypothetical protein LOC10016	0.427	0.044	0.438	3e-07
328721829	152	PREDICTED: hypothetical protein LOC10057	0.316	0.414	0.417	7e-07
383864731	833	PREDICTED: protein toll-like [Megachile	0.316	0.075	0.428	2e-06
189242251	1808	PREDICTED: similar to pol-like protein [	0.301	0.033	0.45	3e-06
270015744	879	hypothetical protein TcasGA2_TC004345 [T	0.301	0.068	0.45	3e-06
328725948	118	PREDICTED: hypothetical protein LOC10057	0.346	0.584	0.438	3e-06
328697314	118	PREDICTED: hypothetical protein LOC10057	0.346	0.584	0.438	3e-06

>gi|443730613|gb|ELU16038.1| hypothetical protein CAPTEDRAFT_206814 [Capitella teleta]

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 58/214 (27%), Positives = 85/214 (39%), Gaps = 64/214 (29%)

Query: 10  LLPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFI----- 64
           L P++  I+TD SK+E  V+           V+L    SI +AEL++I   ++ +     
Sbjct: 9   LCPDHLPIYTDGSKSETRVACVATANRLLIQVRLPDSASIFSAELLAIYEVLTLLECAAP 68

Query: 65  -------------------------------------ISTTPLQVPTPKF-------VLY 80
                                                +S T   V  P F         Y
Sbjct: 69  QKYTILYNRGFDLVILWCPSHIGVVGNERADLLAKEALSFTACDVRIPAFDFNSVAYSFY 128

Query: 81  SDSLSALQSLQNIISSSPIALEIINLLHKIQCQVRP----SHFNMREQVSLTRLRIGHTN 136
            D   AL SL+             N LH +Q  ++     S  + R+++ L R RIGHT+
Sbjct: 129 RDKWQALWSLEQN-----------NKLHSVQPIIKKLTNSSREDRRKEIVLARARIGHTH 177

Query: 137 LTHVHLMKREPPPECDTYNCRLTVKHLLKYCNKY 170
           LTH +L++RE PP C    C LTVKH+L  C  +
Sbjct: 178 LTHGYLLRRELPPFCVHCQCPLTVKHILIECVDF 211

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 40/122 (32%), Positives = 64/122 (52%), Gaps = 12/122 (9%)

Query: 58   QYAISFIISTTPLQVPTPKFVLYSDSLSALQSLQNIISSSPIALEIINLLHKIQCQVR-- 115
            + A++  +S T  Q+P      YSD   ++ S       +    E  + L +I   VR  
Sbjct: 1076 KRALNHAVSGT--QIP------YSDLRQSIASATYREWQNRWEAETHSKLRQIVADVRWR 1127

Query: 116  --PSHFNMREQVSLTRLRIGHTNLTHVHLMKREPPPECDTYNCRLTVKHLLKYCNKYQNI 173
                    R   +++RLRIGHT +TH  ++KRE PP C+  + RLTV+H+L  C +YQ++
Sbjct: 1128 PTSKGLTRRGSTTMSRLRIGHTYITHSFVLKREEPPLCEYCDSRLTVEHILVDCPRYQDV 1187

Query: 174  RS 175
            R+
Sbjct: 1188 RA 1189

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|328720146|ref|XP_003246964.1| PREDICTED: hypothetical protein LOC100568990, partial [Acyrthosiphon pisum]

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 30/66 (45%), Positives = 40/66 (60%), Gaps = 1/66 (1%)

Query: 110 IQCQVRPSHFNMREQVSLTRLRIGHTNLTHVHLMKREPPPECDTYNCRLTVKHLLKYCNK 169
           IQ    P   N +E+  L RLRIGHT +TH HLM++  PP C+     LTVKH++  C K
Sbjct: 76  IQTWKNPG-LNRKEETILNRLRIGHTFITHRHLMEKNDPPICEMCGVDLTVKHIITECRK 134

Query: 170 YQNIRS 175
           Y ++R 
Sbjct: 135 YDDMRK 140

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 39/89 (43%), Positives = 50/89 (56%), Gaps = 4/89 (4%)

Query: 17   IFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPK 76
            I+TDAS  E  V  A  C+ET    KL  + SI  AE ++I  AI F IS    ++    
Sbjct: 956  IYTDASIIEGRVGMAIICDETTIQWKLSDKCSIYTAETLAILKAIEFTIS----EINDSN 1011

Query: 77   FVLYSDSLSALQSLQNIISSSPIALEIIN 105
              ++SDSLSAL SLQN+ S S I  +I N
Sbjct: 1012 ITIFSDSLSALTSLQNLYSPSDIVRKIQN 1040

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328721829|ref|XP_003247415.1| PREDICTED: hypothetical protein LOC100572018 [Acyrthosiphon pisum]

 Score = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 28/67 (41%), Positives = 43/67 (64%), Gaps = 4/67 (5%)

Query: 122 REQVSLTRLRIGHTNLTHVHLMKREPPPECDTYNCRLTVKHLLKYCNKYQNIR----SPN 177
           REQ  + R RIGH+N+TH +L+ +EP P CDT N  LT++H++  C K+ + R    +P+
Sbjct: 66  REQTIINRARIGHSNITHSYLITKEPRPNCDTCNTPLTIEHIIINCPKFASSRHLLKNPS 125

Query: 178 DLYACLL 184
            L   L+
Sbjct: 126 SLEEALI 132

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383864731|ref|XP_003707831.1| PREDICTED: protein toll-like [Megachile rotundata]

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/63 (42%), Positives = 37/63 (58%)

Query: 117 SHFNMREQVSLTRLRIGHTNLTHVHLMKREPPPECDTYNCRLTVKHLLKYCNKYQNIRSP 176
           S    R+QV +TR+ IGHT +TH +L+ +E PP CD     +TV HL+  C KY   R  
Sbjct: 90  SSLQRRDQVVITRITIGHTRITHQYLLTKEEPPICDLCKVSVTVDHLIIQCAKYAADRQK 149

Query: 177 NDL 179
            D+
Sbjct: 150 YDI 152

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189242251|ref|XP_001808188.1| PREDICTED: similar to pol-like protein [Tribolium castaneum]

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/60 (45%), Positives = 39/60 (65%)

Query: 116  PSHFNMREQVSLTRLRIGHTNLTHVHLMKREPPPECDTYNCRLTVKHLLKYCNKYQNIRS 175
            PS+    E+V++ RLR+GHT LT  + +K+  PP C     RLTV+H+L  C KY +IR+
Sbjct: 1407 PSNLKRGEEVTINRLRLGHTRLTQEYHLKKVDPPTCCYCEGRLTVRHILLECPKYHDIRN 1466

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270015744|gb|EFA12192.1| hypothetical protein TcasGA2_TC004345 [Tribolium castaneum]

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/60 (45%), Positives = 39/60 (65%)

Query: 116 PSHFNMREQVSLTRLRIGHTNLTHVHLMKREPPPECDTYNCRLTVKHLLKYCNKYQNIRS 175
           PS+    E+V++ RLR+GHT LT  + +K+  PP C     RLTV+H+L  C KY +IR+
Sbjct: 478 PSNLKRGEEVTINRLRLGHTRLTQEYHLKKVDPPTCCYCEGRLTVRHILLECPKYHDIRN 537

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328725948|ref|XP_003248683.1| PREDICTED: hypothetical protein LOC100573436 [Acyrthosiphon pisum]

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 32/73 (43%), Positives = 41/73 (56%), Gaps = 4/73 (5%)

Query: 122 REQVSLTRLRIGHTNLTHVHLMKREPPPECDTYNCRLTVKHLLKYCNKYQNIRSPNDLYA 181
           +E+  L RLRIGHT +TH  LM RE PP C T    LTVKH++  C +Y   R+ + +  
Sbjct: 30  KEETVLNRLRIGHTRITHGFLMAREDPPICQTCETALTVKHIIADCLRYNQERADHTISN 89

Query: 182 CLLMFQILILGPN 194
            L       LGPN
Sbjct: 90  HLNT----ALGPN 98

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328697314|ref|XP_003240305.1| PREDICTED: hypothetical protein LOC100572200 [Acyrthosiphon pisum]

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 32/73 (43%), Positives = 41/73 (56%), Gaps = 4/73 (5%)

Query: 122 REQVSLTRLRIGHTNLTHVHLMKREPPPECDTYNCRLTVKHLLKYCNKYQNIRSPNDLYA 181
           +E+  L RLRIGHT +TH  LM RE PP C T    LTVKH++  C +Y   R+ + +  
Sbjct: 30  KEETVLNRLRIGHTRITHGFLMAREDPPICQTCETALTVKHIIADCLRYNQERADHTISN 89

Query: 182 CLLMFQILILGPN 194
            L       LGPN
Sbjct: 90  HLNT----ALGPN 98

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

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

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

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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	199
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	1e-17
pfam00075	126	pfam00075, RNase_H, RNase H	2e-05

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

 Score = 75.0 bits (185), Expect = 1e-17
 Identities = 36/113 (31%), Positives = 53/113 (46%), Gaps = 13/113 (11%)

Query: 16  QIFTDASKNEHSVSSAFCCEE---TKFSVKLDPRISICNAELISIQYAISFIISTTPLQV 72
            I+TD SK E    + F          S KL P  S+ +AEL++I  A+   +       
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALRE---GR 57

Query: 73  PTPKFVLYSDSLSALQSLQNIISSSPIALEI---INLLHKIQCQVR----PSH 118
              K  ++SDS +AL++L++  SSSP+ L I   I  L     +VR    P H
Sbjct: 58  RARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGH 110

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

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 24/104 (23%), Positives = 37/104 (35%), Gaps = 14/104 (13%)

Query: 12  PNYKQIFTDAS--KNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTP 69
           P    ++TD S   N     + +  +  K   K  P  +   AEL+++  A+        
Sbjct: 1   PEAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALE------- 53

Query: 70  LQVPTPKFVLYSDSL----SALQSLQNIISSSPIALEIINLLHK 109
             +   K  +Y+DS                S PI  EI  LL K
Sbjct: 54  -ALSGQKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQK 96

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	199
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.69
PRK06548	161	ribonuclease H; Provisional	99.67
PRK08719	147	ribonuclease H; Reviewed	99.63
PRK00203	150	rnhA ribonuclease H; Reviewed	99.62
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.57
PRK13907	128	rnhA ribonuclease H; Provisional	99.56
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.52
KOG3752|consensus	371		99.34
PRK07708	219	hypothetical protein; Validated	99.26
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.19
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	98.72
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	96.23
.; GO: 0004523 ribonuclease H activity" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF00336">PF00336	245	DNA_pol_viral_C: DNA polymerase (viral) C-terminal	95.71
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	91.99

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

Probab=99.69  E-value=1.2e-16  Score=121.78  Aligned_cols=100  Identities=27%  Similarity=0.328  Sum_probs=75.3

Q ss_pred             CceEEEEcCCCC--CCceEEEEEEc-CeeeEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHHH
Q psy7535          13 NYKQIFTDASKN--EHSVSSAFCCE-ETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS   89 (199)
Q Consensus        13 ~~~~IyTDgSk~--~~~~G~ai~~~-~~~~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~a   89 (199)
                      +++.||||||..  .+..|+|++.. +......++ ..|++.||+.||..||+.+  .      ...++|+|||++++++
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~--~------~~~v~I~tDS~~v~~~   72 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL--E------HRKVTIYTDSQYVLNA   72 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH--S------TSEEEEEES-HHHHHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh--h------cccccccccHHHHHHH
Confidence            678999999964  33346665443 434555566 9999999999999999944  4      2889999999999998


Q ss_pred             hhc-----CCC-C--c-HHHHHHHHHHhc---ceEEecCCCCcc
Q psy7535          90 LQN-----IIS-S--S-PIALEIINLLHK---IQCQVRPSHFNM  121 (199)
Q Consensus        90 I~n-----~~~-~--s-~i~~~I~~ll~~---I~l~WiP~h~nR  121 (199)
                      |..     ... .  . ++..+|.+++.+   |.|+|+|+|.+.
T Consensus        73 l~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~  116 (132)
T PF00075_consen   73 LNKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGV  116 (132)
T ss_dssp             HHTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSS
T ss_pred             HHHhccccccccccccccchhheeeccccceEEeeeeccCcCCC
Confidence            887     222 1  2 577788887754   999999999876

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 ....

>PRK06548 ribonuclease H; Provisional

Probab=99.67  E-value=8.1e-16  Score=123.80  Aligned_cols=103  Identities=19%  Similarity=0.115  Sum_probs=75.8

Q ss_pred             CCceEEEEcCCCCCC--ceEEEEEEcCeeeEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHHH
Q psy7535          12 PNYKQIFTDASKNEH--SVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS   89 (199)
Q Consensus        12 ~~~~~IyTDgSk~~~--~~G~ai~~~~~~~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~a   89 (199)
                      ++.+.||||||...+  ..|.|++..+......-....|+..||+.||+.||+.+..      ....+.|+|||+.++++
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~------~~~~v~I~TDS~yvi~~   76 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH------TDRPILILSDSKYVINS   76 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc------CCceEEEEeChHHHHHH
Confidence            455899999998544  5678877655432223335689999999999999986643      34579999999999999


Q ss_pred             hhc---------CCCC-------cHHHHHHHHHHhc--ceEEecCCCCc
Q psy7535          90 LQN---------IISS-------SPIALEIINLLHK--IQCQVRPSHFN  120 (199)
Q Consensus        90 I~n---------~~~~-------s~i~~~I~~ll~~--I~l~WiP~h~n  120 (199)
                      |..         ++.+       .++.++|.+++.+  |+|.|||+|.+
T Consensus        77 i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~v~~~wVkgHsg  125 (161)
T PRK06548         77 LTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSWVNAHTG  125 (161)
T ss_pred             HHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcCceEEEEEecCCC
Confidence            993         3221       1456666666655  99999999997

>PRK08719 ribonuclease H; Reviewed

Probab=99.63  E-value=3.3e-15  Score=118.51  Aligned_cols=100  Identities=16%  Similarity=0.197  Sum_probs=72.1

Q ss_pred             CCceEEEEcCCCCCCc-----eEEEEEE--cCee----eEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEE
Q psy7535          12 PNYKQIFTDASKNEHS-----VSSAFCC--EETK----FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLY   80 (199)
Q Consensus        12 ~~~~~IyTDgSk~~~~-----~G~ai~~--~~~~----~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~   80 (199)
                      ++.+.||||||..+++     .|+|++.  ++..    ....+....|+++||+.||+.||+.+.+.         ..|+
T Consensus         2 ~~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~---------~~i~   72 (147)
T PRK08719          2 RASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG---------DVIY   72 (147)
T ss_pred             CceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC---------CEEE
Confidence            4568999999996543     4777654  3221    33345556899999999999999998643         2799


Q ss_pred             cCcHHHHHHh--------hcCCCCc--------HHHHHHHHHHhc--ceEEecCCCCc
Q psy7535          81 SDSLSALQSL--------QNIISSS--------PIALEIINLLHK--IQCQVRPSHFN  120 (199)
Q Consensus        81 SDS~sal~aI--------~n~~~~s--------~i~~~I~~ll~~--I~l~WiP~h~n  120 (199)
                      |||+.++++|        +|.+..+        ++.+.|..+..+  |+|.|+|+|.+
T Consensus        73 tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~~~~VkgH~g  130 (147)
T PRK08719         73 SDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKVTAHSG  130 (147)
T ss_pred             echHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEEEEEecCCCC
Confidence            9999999999        4443311        345555555554  99999999987

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.62  E-value=5e-15  Score=117.26  Aligned_cols=101  Identities=14%  Similarity=0.084  Sum_probs=73.2

Q ss_pred             ceEEEEcCCCCCC--ceEEEEEE--cCeeeEE-ecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHH
Q psy7535          14 YKQIFTDASKNEH--SVSSAFCC--EETKFSV-KLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ   88 (199)
Q Consensus        14 ~~~IyTDgSk~~~--~~G~ai~~--~~~~~~~-~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~   88 (199)
                      ++.||||||...+  ..|+|++.  ++....+ +.....|+..||+.|++.||+.+.+       ...+.|+|||+.+++
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~-------~~~v~I~tDS~yvi~   75 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE-------PCEVTLYTDSQYVRQ   75 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC-------CCeEEEEECHHHHHH
Confidence            4889999998643  45666554  3333222 2345789999999999999998743       356999999999999


Q ss_pred             HhhcC---------CCC-------cHHHHHHHHHHhc--ceEEecCCCCcc
Q psy7535          89 SLQNI---------ISS-------SPIALEIINLLHK--IQCQVRPSHFNM  121 (199)
Q Consensus        89 aI~n~---------~~~-------s~i~~~I~~ll~~--I~l~WiP~h~nR  121 (199)
                      +|..+         ..+       .++.++|.+++..  |.|.|+|+|.++
T Consensus        76 ~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~wV~~H~~~  126 (150)
T PRK00203         76 GITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGH  126 (150)
T ss_pred             HHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEEEEecCCCCC
Confidence            99851         111       1356677766654  999999999973

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

Probab=99.57  E-value=3.6e-14  Score=113.27  Aligned_cols=104  Identities=17%  Similarity=0.137  Sum_probs=77.7

Q ss_pred             CceEEEEcCCCCCC-c-eEEEEEE--cCeeeEEecC-CCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHH
Q psy7535          13 NYKQIFTDASKNEH-S-VSSAFCC--EETKFSVKLD-PRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSAL   87 (199)
Q Consensus        13 ~~~~IyTDgSk~~~-~-~G~ai~~--~~~~~~~~l~-~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal   87 (199)
                      ..+.||||||...+ | .|+|++.  ++..+.+..+ ..+|+..||+.|++.||+.+.+.     +...+.|+|||+.++
T Consensus         2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~~-----~~~~v~l~tDS~yv~   76 (154)
T COG0328           2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKEL-----GACEVTLYTDSKYVV   76 (154)
T ss_pred             CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHhc-----CCceEEEEecHHHHH
Confidence            45789999998443 3 4555444  3333323322 38999999999999999999987     889999999999999


Q ss_pred             HHhhcCCC---------------Cc-HHHHHHHHHHhc---ceEEecCCCCcc
Q psy7535          88 QSLQNIIS---------------SS-PIALEIINLLHK---IQCQVRPSHFNM  121 (199)
Q Consensus        88 ~aI~n~~~---------------~s-~i~~~I~~ll~~---I~l~WiP~h~nR  121 (199)
                      ++|..+..               ++ ++.+++.++.++   |.+.|||+|.++
T Consensus        77 ~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~  129 (154)
T COG0328          77 EGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGH  129 (154)
T ss_pred             HHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCC
Confidence            99983311               01 356677777665   899999999984

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.56  E-value=3.4e-14  Score=109.06  Aligned_cols=105  Identities=12%  Similarity=0.161  Sum_probs=81.4

Q ss_pred             eEEEEcCCCCCC--ceEEEEEEcCee--eEEec-CCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHHH
Q psy7535          15 KQIFTDASKNEH--SVSSAFCCEETK--FSVKL-DPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS   89 (199)
Q Consensus        15 ~~IyTDgSk~~~--~~G~ai~~~~~~--~~~~l-~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~a   89 (199)
                      ++||||||...+  ..|+|++..+..  ...+. ...+|+..||+.|++.||+.+...     ....+.|+|||+.+++.
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~-----g~~~v~i~sDS~~vi~~   76 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEH-----NYNIVSFRTDSQLVERA   76 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhC-----CCCEEEEEechHHHHHH
Confidence            579999998543  577887665432  22222 356899999999999999999987     77789999999999999


Q ss_pred             hhcCCCCc----HHHHHHHHHHhc---ceEEecCCCCccchh
Q psy7535          90 LQNIISSS----PIALEIINLLHK---IQCQVRPSHFNMREQ  124 (199)
Q Consensus        90 I~n~~~~s----~i~~~I~~ll~~---I~l~WiP~h~nR~~~  124 (199)
                      +++.+.++    ++.+++..++.+   +.|.|+|.+.|+...
T Consensus        77 ~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad  118 (128)
T PRK13907         77 VEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVAD  118 (128)
T ss_pred             HhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCchhchhHH
Confidence            99865433    467777777765   778999999886543

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

Probab=99.52  E-value=1.9e-13  Score=100.29  Aligned_cols=100  Identities=18%  Similarity=0.292  Sum_probs=77.3

Q ss_pred             EEEEcCCCCCC--ceEEEEEEcCe--eeEEe---cCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHH
Q psy7535          16 QIFTDASKNEH--SVSSAFCCEET--KFSVK---LDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ   88 (199)
Q Consensus        16 ~IyTDgSk~~~--~~G~ai~~~~~--~~~~~---l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~   88 (199)
                      .+|||||...+  +.|+|++..+.  ...+.   .....|++.||+.|++.||+.+...     ...++.|+|||+.+++
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~-----~~~~i~i~~Ds~~~~~   75 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALEL-----GGKKVNIYTDSQYVIN   75 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhC-----CCceEEEEECHHHHHH
Confidence            48999999655  67777665443  22222   2257899999999999999999876     8899999999999999


Q ss_pred             HhhcCCC-----CcHHHHHHHHHHhc---ceEEecCCCCc
Q psy7535          89 SLQNIIS-----SSPIALEIINLLHK---IQCQVRPSHFN  120 (199)
Q Consensus        89 aI~n~~~-----~s~i~~~I~~ll~~---I~l~WiP~h~n  120 (199)
                      .+++...     ..++...+.+++.+   ++|.|+|+|.+
T Consensus        76 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~  115 (130)
T cd06222          76 ALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSG  115 (130)
T ss_pred             HhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCC
Confidence            9998754     12466677777743   99999999764

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

>KOG3752|consensus

Probab=99.34  E-value=6.2e-12  Score=111.85  Aligned_cols=118  Identities=20%  Similarity=0.122  Sum_probs=91.2

Q ss_pred             hhhhhcccCCCceEEEEcCCCCCC-----ceEEEEEEcCe---eeEEecC-CCcchhHHHHHHHHHHHHHHHhhCCCCCC
Q psy7535           3 LKTSIPLLLPNYKQIFTDASKNEH-----SVSSAFCCEET---KFSVKLD-PRISICNAELISIQYAISFIISTTPLQVP   73 (199)
Q Consensus         3 ~~~~i~~~~~~~~~IyTDgSk~~~-----~~G~ai~~~~~---~~~~~l~-~~~Si~tAEl~AI~~AL~~i~~~~~~~~~   73 (199)
                      |+.++..++.+.+.||||||...+     .+|.||+.++.   +.+..+. +..+++.||+.||.+||+-+.+.     +
T Consensus       201 ~k~~~d~e~~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~-----~  275 (371)
T KOG3752|consen  201 EKLENDREEIEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSK-----N  275 (371)
T ss_pred             hhcccccccccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhc-----C
Confidence            667777788888999999998553     58999988764   4777776 88999999999999999999887     7


Q ss_pred             CCcEEEEcCcHHHHHHhhcCCCC-----------cH----------HHHHHHHHHhc-----ceEEecCCCCc-cchhh
Q psy7535          74 TPKFVLYSDSLSALQSLQNIISS-----------SP----------IALEIINLLHK-----IQCQVRPSHFN-MREQV  125 (199)
Q Consensus        74 ~~~i~I~SDS~sal~aI~n~~~~-----------s~----------i~~~I~~ll~~-----I~l~WiP~h~n-R~~~~  125 (199)
                      ..++.|.|||+.++++|+.+...           ++          ...++-++.++     |.+.|+|+|.+ +.++.
T Consensus       276 ~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~  354 (371)
T KOG3752|consen  276 INKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEM  354 (371)
T ss_pred             CCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHH
Confidence            77999999999999999865320           12          12333343332     99999999987 44443

>PRK07708 hypothetical protein; Validated

Probab=99.26  E-value=8.2e-11  Score=99.11  Aligned_cols=111  Identities=12%  Similarity=0.049  Sum_probs=79.9

Q ss_pred             hcccCCCceEEEEcCCCCC--CceEEEEEE--cCeeeEE------ecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCC-
Q psy7535           7 IPLLLPNYKQIFTDASKNE--HSVSSAFCC--EETKFSV------KLDPRISICNAELISIQYAISFIISTTPLQVPTP-   75 (199)
Q Consensus         7 i~~~~~~~~~IyTDgSk~~--~~~G~ai~~--~~~~~~~------~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~-   75 (199)
                      |..+ |+...+|+|||...  ++.|+|++.  ++....+      .+....|+..||+.|++.||+.+.+.     +.+ 
T Consensus        67 ~~~e-p~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~-----g~~~  140 (219)
T PRK07708         67 VEEE-PHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEEL-----GVKH  140 (219)
T ss_pred             hccC-CCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHc-----CCCc
Confidence            3343 45689999999743  356666544  3222222      34556899999999999999999987     443 


Q ss_pred             -cEEEEcCcHHHHHHhhcCCC-Cc----HHHHHHHHHHhc----ceEEecCCCCccch
Q psy7535          76 -KFVLYSDSLSALQSLQNIIS-SS----PIALEIINLLHK----IQCQVRPSHFNMRE  123 (199)
Q Consensus        76 -~i~I~SDS~sal~aI~n~~~-~s----~i~~~I~~ll~~----I~l~WiP~h~nR~~  123 (199)
                       .+.|++||+.+++.+.+.+. .+    ++..++..++++    +.+.|+|...|+..
T Consensus       141 ~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~A  198 (219)
T PRK07708        141 EPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEA  198 (219)
T ss_pred             ceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHH
Confidence             48999999999999998754 23    356666666654    66789999888544

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.19  E-value=2.1e-10  Score=102.78  Aligned_cols=102  Identities=11%  Similarity=0.027  Sum_probs=77.4

Q ss_pred             ceEEEEcCCCCCC--ceEEEEEEcCe--e---eEEe-cCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHH
Q psy7535          14 YKQIFTDASKNEH--SVSSAFCCEET--K---FSVK-LDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLS   85 (199)
Q Consensus        14 ~~~IyTDgSk~~~--~~G~ai~~~~~--~---~~~~-l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~s   85 (199)
                      .+.||||||...+  ..|+|++..+.  .   ..++ ....+|+..||+.|++.||+++.+.     ....+.|++||+.
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~-----g~~~v~i~~DS~l   76 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAEL-----GATEVEVRMDSKL   76 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhC-----CCCeEEEEeCcHH
Confidence            3689999998654  46777655432  1   1222 2347888999999999999999988     7789999999999


Q ss_pred             HHHHhhcCCC-Cc----HHHHHHHHHHhc---ceEEecCCCCc
Q psy7535          86 ALQSLQNIIS-SS----PIALEIINLLHK---IQCQVRPSHFN  120 (199)
Q Consensus        86 al~aI~n~~~-~s----~i~~~I~~ll~~---I~l~WiP~h~n  120 (199)
                      +++.+.+.+. ++    .+..++.++.++   +++.|+|...|
T Consensus        77 vi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N  119 (372)
T PRK07238         77 VVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARN  119 (372)
T ss_pred             HHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCchhh
Confidence            9999987653 33    345567776665   99999998777

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

Probab=98.72  E-value=6.3e-08  Score=68.08  Aligned_cols=69  Identities=22%  Similarity=0.259  Sum_probs=55.1

Q ss_pred             hhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHHHhhcCCCC----cHHHHHHHHHHhc---ceEEecCCCCcc
Q psy7535          49 ICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSLQNIISS----SPIALEIINLLHK---IQCQVRPSHFNM  121 (199)
Q Consensus        49 i~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~aI~n~~~~----s~i~~~I~~ll~~---I~l~WiP~h~nR  121 (199)
                      +..||+.|++.||+++.+.     +..++.|.|||+.+++.|++....    ..++.+|+.++++   +.+.|+|...|+
T Consensus         1 ~~~aE~~al~~al~~a~~~-----g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~   75 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWEL-----GIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPREQNK   75 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCC-----T-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GGGSH
T ss_pred             CcHHHHHHHHHHHHHHHHC-----CCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChHHhH
Confidence            3689999999999999988     899999999999999999887432    2678889888886   999999987775


Q ss_pred             c
Q psy7535         122 R  122 (199)
Q Consensus       122 ~  122 (199)
                      .
T Consensus        76 ~   76 (87)
T PF13456_consen   76 V   76 (87)
T ss_dssp             H
T ss_pred             H
Confidence            3

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

Probab=96.23  E-value=0.0021  Score=45.96  Aligned_cols=29  Identities=21%  Similarity=0.264  Sum_probs=24.0

Q ss_pred             cCCCCCCCcccCC-ccccccchhhcccchh
Q psy7535         143 MKREPPPECDTYN-CRLTVKHLLKYCNKYQ  171 (199)
Q Consensus       143 ~~~~~~p~C~~Cg-~~~tv~Hil~~Cp~~~  171 (199)
                      .+...++.|..|+ ..||+.|+|++||...
T Consensus        54 r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~   83 (86)
T PF13966_consen   54 RGIQVDPICPLCGNEEETIEHLFFHCPFAR   83 (86)
T ss_pred             cCCccCCccccCCCccccccceeccCcCcc
Confidence            3456678999999 4899999999999754

>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein

Probab=95.71  E-value=0.024  Score=47.59  Aligned_cols=92  Identities=22%  Similarity=0.245  Sum_probs=62.4

Q ss_pred             CCceEEEEcCCCCCCceEEEEEEcCeeeEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHHHhh
Q psy7535          12 PNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSLQ   91 (199)
Q Consensus        12 ~~~~~IyTDgSk~~~~~G~ai~~~~~~~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~aI~   91 (199)
                      +-.-+||+|+.-    +|.|+.+......+....--.|++||+.|...|--++...          .|.|||-.++..  
T Consensus        92 ~~lc~VfaDATp----Tgwgi~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~~~r----------~l~tDnt~Vlsr--  155 (245)
T PF00336_consen   92 PGLCQVFADATP----TGWGISITGQRMRGTFSKPLPIHTAELLAACLARLMSGAR----------CLGTDNTVVLSR--  155 (245)
T ss_pred             CCCCceeccCCC----CcceeeecCceeeeeecccccchHHHHHHHHHHHhccCCc----------EEeecCcEEEec--
Confidence            334589999876    5555556666656666667789999999998887666432          499999877642  


Q ss_pred             cCCCCcH--HHHHHHHHHhcceEEecCCCCc
Q psy7535          92 NIISSSP--IALEIINLLHKIQCQVRPSHFN  120 (199)
Q Consensus        92 n~~~~s~--i~~~I~~ll~~I~l~WiP~h~n  120 (199)
                       .+.+=|  ++-....++..+.|..+|+..|
T Consensus       156 -kyts~PW~lac~A~wiLrgts~~yVPS~~N  185 (245)
T PF00336_consen  156 -KYTSFPWLLACAANWILRGTSFYYVPSKYN  185 (245)
T ss_pred             -ccccCcHHHHHHHHHhhcCceEEEeccccC
Confidence             222223  2333334455599999999888

The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity

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

Probab=91.99  E-value=0.54  Score=37.35  Aligned_cols=53  Identities=15%  Similarity=0.235  Sum_probs=36.1

Q ss_pred             CceEEEEcCCCCCCceEEEEEEcC---eeeEE-------ec-C-CCcchhHHHHHHHHHHHHHHHhh
Q psy7535          13 NYKQIFTDASKNEHSVSSAFCCEE---TKFSV-------KL-D-PRISICNAELISIQYAISFIIST   67 (199)
Q Consensus        13 ~~~~IyTDgSk~~~~~G~ai~~~~---~~~~~-------~l-~-~~~Si~tAEl~AI~~AL~~i~~~   67 (199)
                      -.+++|+|||+  .+.|+.++...   .....       +. | ...||=.-|+.|+..|.+++...
T Consensus        80 ~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~  144 (159)
T PF05380_consen   80 VELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTV  144 (159)
T ss_pred             eeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence            35789999995  55666654432   22111       12 2 35699999999999999998653

---

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	199
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.76
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.66
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.65
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.65
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.65
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.63
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.63
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.63
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.61
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.6
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.59
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.51
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.47
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.44
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.26
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.13
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	94.12
2zd1_B	428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	80.72

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

Probab=99.76  E-value=6.6e-18  Score=132.58  Aligned_cols=105  Identities=18%  Similarity=0.231  Sum_probs=84.5

Q ss_pred             CCceEEEEcCCCCCC-c----eEEEEEEcCee---eEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCc
Q psy7535          12 PNYKQIFTDASKNEH-S----VSSAFCCEETK---FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDS   83 (199)
Q Consensus        12 ~~~~~IyTDgSk~~~-~----~G~ai~~~~~~---~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS   83 (199)
                      .+.+.||||||...+ +    .|+|++..+..   .+..+++.+|++.||+.|++.||+.+.+.     ...++.|+|||
T Consensus         5 ~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~-----~~~~v~i~tDS   79 (154)
T 2qkb_A            5 GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQ-----NINKLVLYTNS   79 (154)
T ss_dssp             TTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHT-----TCCEEEEEESC
T ss_pred             CCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhC-----CCceEEEEECc
Confidence            467899999998543 2    78888775432   55667778999999999999999999886     67899999999


Q ss_pred             HHHHHHhhcCC---------------CC-cHHHHHHHHHHhc--ceEEecCCCCcc
Q psy7535          84 LSALQSLQNII---------------SS-SPIALEIINLLHK--IQCQVRPSHFNM  121 (199)
Q Consensus        84 ~sal~aI~n~~---------------~~-s~i~~~I~~ll~~--I~l~WiP~h~nR  121 (199)
                      +.+++.|.++.               .+ .++.++|..++.+  |.|.|||+|.++
T Consensus        80 ~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~~~v~~~~V~~H~g~  135 (154)
T 2qkb_A           80 MFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGF  135 (154)
T ss_dssp             HHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTTCEEEEEECCTTSSC
T ss_pred             HHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcCCceEEEEccCCCCC
Confidence            99999998731               11 2578888888776  999999999863

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

Probab=99.66  E-value=2.9e-16  Score=121.91  Aligned_cols=104  Identities=15%  Similarity=0.153  Sum_probs=76.6

Q ss_pred             CceEEEEcCCCCCC--ceEEEEEEc--CeeeEE-ecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHH
Q psy7535          13 NYKQIFTDASKNEH--SVSSAFCCE--ETKFSV-KLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSAL   87 (199)
Q Consensus        13 ~~~~IyTDgSk~~~--~~G~ai~~~--~~~~~~-~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal   87 (199)
                      +.+.||||||...+  ..|+|++..  +....+ ...+.+|+..||+.|++.||+.+.+       ..++.|+|||+.++
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~AL~~~~~-------~~~v~I~tDS~~vi   75 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDPATTNNRMELMAAIKGLEALKE-------PARVQLYSDSAYLV   75 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCSS-------CCEEEEEESCHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCCCCCcHHHHHHHHHHHHHHhcCc-------cCcEEEEeChHHHH
Confidence            56899999998554  467776553  322222 1224689999999999999999853       47899999999999


Q ss_pred             HHhhcCC----------------CC-cHHHHHHHHHHhc--ceEEecCCCCccch
Q psy7535          88 QSLQNII----------------SS-SPIALEIINLLHK--IQCQVRPSHFNMRE  123 (199)
Q Consensus        88 ~aI~n~~----------------~~-s~i~~~I~~ll~~--I~l~WiP~h~nR~~  123 (199)
                      +.|.+.+                .. .++.++|..++.+  |.|.|+|+|.+|..
T Consensus        76 ~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~~v~~~~V~gH~g~~~  130 (146)
T 3h08_A           76 NAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLHRVTFHKVKGHSDNPY  130 (146)
T ss_dssp             HHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHHSEEEEEECCC-CCSHH
T ss_pred             HHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhhCceEEEEcCCcCCcHh
Confidence            9998720                11 2577888887775  99999999998543

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

Probab=99.65  E-value=1.2e-16  Score=124.85  Aligned_cols=105  Identities=10%  Similarity=0.008  Sum_probs=77.2

Q ss_pred             CCCceEEEEcCCCCCCceEEEEEEc--Cee--eEE-ec--CC--CcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEc
Q psy7535          11 LPNYKQIFTDASKNEHSVSSAFCCE--ETK--FSV-KL--DP--RISICNAELISIQYAISFIISTTPLQVPTPKFVLYS   81 (199)
Q Consensus        11 ~~~~~~IyTDgSk~~~~~G~ai~~~--~~~--~~~-~l--~~--~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~S   81 (199)
                      .++.+.||||||...+..|+|++..  +..  .+. +.  +.  .+|++.||+.|++.||+++.+.     +. ++.|+|
T Consensus         3 ~~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~-----~~-~v~I~t   76 (147)
T 2kq2_A            3 DRTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQL-----GV-KIRILH   76 (147)
T ss_dssp             TTSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHH-----TC-CCCBSS
T ss_pred             CCCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHC-----CC-eEEEEE
Confidence            4677899999999877788886653  332  222 23  32  3699999999999999998876     45 899999


Q ss_pred             CcHHHHHHhhcCCC-CcHHHHHHHHHHh----cceEEecCCCCcc
Q psy7535          82 DSLSALQSLQNIIS-SSPIALEIINLLH----KIQCQVRPSHFNM  121 (199)
Q Consensus        82 DS~sal~aI~n~~~-~s~i~~~I~~ll~----~I~l~WiP~h~nR  121 (199)
                      ||+.+.+.+.+.+. +++......+++.    +|.|.|||+|.++
T Consensus        77 DS~~i~~w~~~~w~~~~~~~~~~~~l~~~l~~~v~~~wV~gH~g~  121 (147)
T 2kq2_A           77 DYAGIAFWATGEWKAKNEFTQAYAKLMNQYRGIYSFEKVKAHSGN  121 (147)
T ss_dssp             CCSTHHHHTTSSSSCCHHHHHHHHCGGGGGSTTCCBCCCCCCCCC
T ss_pred             CcHHHHHHHhCCCccCCcchHHHHHHHHHhcCCeeEEEecCcCCC
Confidence            99988887776554 3344444444433    4999999999974

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

Probab=99.65  E-value=3.1e-16  Score=123.43  Aligned_cols=103  Identities=17%  Similarity=0.099  Sum_probs=76.9

Q ss_pred             CceEEEEcCCCCCC--ceEEEEEEc--Ceee--EEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHH
Q psy7535          13 NYKQIFTDASKNEH--SVSSAFCCE--ETKF--SVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSA   86 (199)
Q Consensus        13 ~~~~IyTDgSk~~~--~~G~ai~~~--~~~~--~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sa   86 (199)
                      ..+.||||||...+  ..|+|++..  +...  +..+ +.+|++.||+.|++.||+.+.+       ..++.|+|||+.+
T Consensus         3 ~~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~-------~~~v~I~tDS~~v   74 (155)
T 1jl1_A            3 KQVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE-------HAEVILSTDSQYV   74 (155)
T ss_dssp             CCEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS-------CCEEEEEECCHHH
T ss_pred             ceEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc-------CCcEEEEeCHHHH
Confidence            35789999999654  367776553  3222  2223 4679999999999999998853       3689999999999


Q ss_pred             HHHhhcC--------C-------CC-cHHHHHHHHHHhc--ceEEecCCCCccch
Q psy7535          87 LQSLQNI--------I-------SS-SPIALEIINLLHK--IQCQVRPSHFNMRE  123 (199)
Q Consensus        87 l~aI~n~--------~-------~~-s~i~~~I~~ll~~--I~l~WiP~h~nR~~  123 (199)
                      +++|..+        +       .+ .++.++|..++.+  |.|.|||+|.+|..
T Consensus        75 i~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~  129 (155)
T 1jl1_A           75 RQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPE  129 (155)
T ss_dssp             HHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTCHH
T ss_pred             HHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHHccCceEEEEcCCCCCCHH
Confidence            9999861        1       12 2577788887775  99999999988543

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

Probab=99.65  E-value=5e-16  Score=122.69  Aligned_cols=103  Identities=17%  Similarity=0.084  Sum_probs=76.9

Q ss_pred             CceEEEEcCCCCCC--ceEEEEEEc--Cee--eEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHH
Q psy7535          13 NYKQIFTDASKNEH--SVSSAFCCE--ETK--FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSA   86 (199)
Q Consensus        13 ~~~~IyTDgSk~~~--~~G~ai~~~--~~~--~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sa   86 (199)
                      ..+.||||||...+  ..|+|++..  +..  .+..+ +.+|++.||+.|++.||+.+.+       ..++.|+|||+.+
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~-------~~~v~I~tDS~~v   76 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKE-------PCKIILTSDSQYM   76 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS-------CCEEEEEECCHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhcc-------CCeEEEEeCHHHH
Confidence            46899999998643  467776653  322  22223 4589999999999999998742       2789999999999


Q ss_pred             HHHhhc--------CC-------CCc-HHHHHHHHHHhc--ceEEecCCCCccch
Q psy7535          87 LQSLQN--------II-------SSS-PIALEIINLLHK--IQCQVRPSHFNMRE  123 (199)
Q Consensus        87 l~aI~n--------~~-------~~s-~i~~~I~~ll~~--I~l~WiP~h~nR~~  123 (199)
                      +++|.+        .+       .++ ++.++|..++.+  |.|.|||+|.+|..
T Consensus        77 i~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~  131 (158)
T 2e4l_A           77 RQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQLHQIDWRWVKGHAGHAE  131 (158)
T ss_dssp             HHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTTSEEEEEECCTTCCCHH
T ss_pred             HHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHccCcEEEEEccCCCCchh
Confidence            999988        21       122 577788888776  99999999988543

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

Probab=99.63  E-value=7.9e-16  Score=116.99  Aligned_cols=104  Identities=13%  Similarity=0.076  Sum_probs=77.8

Q ss_pred             CceEEEEcCCCCCC--ceEEEEEEcC--eee--EE-ecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCC----cEEEEc
Q psy7535          13 NYKQIFTDASKNEH--SVSSAFCCEE--TKF--SV-KLDPRISICNAELISIQYAISFIISTTPLQVPTP----KFVLYS   81 (199)
Q Consensus        13 ~~~~IyTDgSk~~~--~~G~ai~~~~--~~~--~~-~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~----~i~I~S   81 (199)
                      +.+.||||||...+  ..|+|++..+  ...  .+ +..+.+|++.||+.|++.||+++.+.     +..    ++.|+|
T Consensus         2 ~~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~-----~~~~~~~~v~i~t   76 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMF-----GDKLVDMEVEVRM   76 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEEEECHHHHHHHHHHHHHHHHGGG-----GGGGTTCEEEEEE
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCCCCchHHHHHHHHHHHHHHHHHc-----CCCCCCceEEEEe
Confidence            35789999998654  5677766543  221  22 22245899999999999999999876     455    899999


Q ss_pred             CcHHHHHHhhcCCC-Cc----HHHHHHHHH-Hhc---ceEEecCCCCcc
Q psy7535          82 DSLSALQSLQNIIS-SS----PIALEIINL-LHK---IQCQVRPSHFNM  121 (199)
Q Consensus        82 DS~sal~aI~n~~~-~s----~i~~~I~~l-l~~---I~l~WiP~h~nR  121 (199)
                      ||+.+++.+.+.+. ++    ++..+|..+ +.+   |.|.|+|...|.
T Consensus        77 DS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~~~N~  125 (140)
T 3u3g_D           77 DSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNA  125 (140)
T ss_dssp             SCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCGGGGH
T ss_pred             ChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCchhhH
Confidence            99999999998653 33    356677777 554   999999977663

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

Probab=99.63  E-value=1.2e-15  Score=116.68  Aligned_cols=103  Identities=12%  Similarity=0.046  Sum_probs=77.8

Q ss_pred             ceEEEEcCCCCCC--ceEEEEEEcC---ee--eEE-ecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHH
Q psy7535          14 YKQIFTDASKNEH--SVSSAFCCEE---TK--FSV-KLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLS   85 (199)
Q Consensus        14 ~~~IyTDgSk~~~--~~G~ai~~~~---~~--~~~-~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~s   85 (199)
                      .+.||||||...+  ..|+|++..+   ..  ..+ ...+.+|++.||+.|++.||+++.+.     +..++.|+|||+.
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~-----~~~~v~i~tDS~~   77 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKL-----GATEAAVLMDSKL   77 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHH-----TCSEEEEEESCHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCCCCchHHHHHHHHHHHHHHHHHC-----CCceEEEEeChHH
Confidence            4789999998654  4677765532   11  122 22247899999999999999999987     7789999999999


Q ss_pred             HHHHhhcCC-CCcH----HHHHHHHHHhc---ceEEecCCCCcc
Q psy7535          86 ALQSLQNII-SSSP----IALEIINLLHK---IQCQVRPSHFNM  121 (199)
Q Consensus        86 al~aI~n~~-~~s~----i~~~I~~ll~~---I~l~WiP~h~nR  121 (199)
                      +++.+.+.+ .+++    +..+|..++.+   |.|.|||...|.
T Consensus        78 vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~~~N~  121 (141)
T 3hst_B           78 VVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNT  121 (141)
T ss_dssp             HHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCGGGCH
T ss_pred             HHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCCcccH
Confidence            999999854 4443    45566666654   999999987773

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

Probab=99.63  E-value=1.5e-15  Score=119.30  Aligned_cols=102  Identities=19%  Similarity=0.183  Sum_probs=75.7

Q ss_pred             ccCCCceEEEEcCCCCCC--ceEEEEEEcCee-eEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHH
Q psy7535           9 LLLPNYKQIFTDASKNEH--SVSSAFCCEETK-FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLS   85 (199)
Q Consensus         9 ~~~~~~~~IyTDgSk~~~--~~G~ai~~~~~~-~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~s   85 (199)
                      .-.++.+.||||||...+  ..|+|++..+.. ..+.+ +.+|+..||+.|++.||+.+         ..++.|+|||+.
T Consensus         7 ~P~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~---------~~~v~i~tDS~~   76 (150)
T 3qio_A            7 EPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS---------GLEVNIVTDSQY   76 (150)
T ss_dssp             SCCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS---------CSEEEEEESCHH
T ss_pred             CCCCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC---------CCcEEEEeCcHH
Confidence            345667899999998543  367777665433 33333 57899999999999999974         367999999999


Q ss_pred             HHHHhhcCC-----------C----C-cHHHHHHHHHHhc---ceEEecCCCCc
Q psy7535          86 ALQSLQNII-----------S----S-SPIALEIINLLHK---IQCQVRPSHFN  120 (199)
Q Consensus        86 al~aI~n~~-----------~----~-s~i~~~I~~ll~~---I~l~WiP~h~n  120 (199)
                      ++++|.++.           .    + .++.+++.+++.+   |.|.|||+|.+
T Consensus        77 v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g  130 (150)
T 3qio_A           77 ALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKG  130 (150)
T ss_dssp             HHHHHHHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSC
T ss_pred             HHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCC
Confidence            999998751           1    1 2456666665543   99999999985

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

Probab=99.61  E-value=5.3e-16  Score=123.62  Aligned_cols=104  Identities=12%  Similarity=0.027  Sum_probs=77.5

Q ss_pred             CceEEEEcCCCCCC--ceEEEEEEcC--eeeEEe-cCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHH
Q psy7535          13 NYKQIFTDASKNEH--SVSSAFCCEE--TKFSVK-LDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSAL   87 (199)
Q Consensus        13 ~~~~IyTDgSk~~~--~~G~ai~~~~--~~~~~~-l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal   87 (199)
                      ..+.||||||...+  ..|+|++...  ....+. ....+|++.||+.|++.||+.+.+       ..++.|+|||+.++
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~-------~~~v~I~tDS~~vi   79 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE-------PCEVDLYTDSHYLK   79 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS-------CCEEEEECCCHHHH
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHhcc-------CCeEEEEeChHHHH
Confidence            46789999999654  4677877642  222221 124689999999999999998754       24899999999999


Q ss_pred             HHhhc----------CC------CCc-HHHHHHHHHHhc--ceEEecCCCCccch
Q psy7535          88 QSLQN----------II------SSS-PIALEIINLLHK--IQCQVRPSHFNMRE  123 (199)
Q Consensus        88 ~aI~n----------~~------~~s-~i~~~I~~ll~~--I~l~WiP~h~nR~~  123 (199)
                      +.|.+          +.      .++ ++.++|..++.+  |.|.|||+|.+|..
T Consensus        80 ~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~  134 (166)
T 1ril_A           80 KAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTGHPE  134 (166)
T ss_dssp             HHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCCCGGGSCTH
T ss_pred             HHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhcCeEEEEEeeCCCCchh
Confidence            99988          21      122 577888888776  99999999988543

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

Probab=99.60  E-value=3.1e-15  Score=119.47  Aligned_cols=99  Identities=20%  Similarity=0.185  Sum_probs=71.7

Q ss_pred             ceEEEEcCCCCC--CceEEEEEE--cCeee-EEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHH
Q psy7535          14 YKQIFTDASKNE--HSVSSAFCC--EETKF-SVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ   88 (199)
Q Consensus        14 ~~~IyTDgSk~~--~~~G~ai~~--~~~~~-~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~   88 (199)
                      .+.||||||...  +..|+|++.  .+... ...++..+|++.||+.|++.||+++  .      ..++.|+|||+.+++
T Consensus        23 ~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~--~------~~~v~I~tDS~~vi~   94 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA--E------GKKLNVYTDSRYAFA   94 (165)
T ss_dssp             SEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT--B------TSEEEEEECCHHHHH
T ss_pred             CEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc--c------CceEEEEEchHHHHh
Confidence            489999999953  335666433  33332 2256778899999999999999998  1      468999999999999


Q ss_pred             HhhcCCC----Cc-HHHHHHHHHHhc---ceEEecCCCCc
Q psy7535          89 SLQNIIS----SS-PIALEIINLLHK---IQCQVRPSHFN  120 (199)
Q Consensus        89 aI~n~~~----~s-~i~~~I~~ll~~---I~l~WiP~h~n  120 (199)
                      +|.....    ++ ++.+++...+.+   |.|+|||+|.+
T Consensus        95 ~iw~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g  134 (165)
T 3p1g_A           95 TAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQK  134 (165)
T ss_dssp             HHHSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCC
T ss_pred             hhhcccCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCC
Confidence            9943222    22 456666554433   99999999995

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

Probab=99.59  E-value=8e-15  Score=113.82  Aligned_cols=103  Identities=13%  Similarity=0.062  Sum_probs=78.4

Q ss_pred             eEEEEcCCCC--C-CceEE-EEEEcC--ee-eEEe--cC---CCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcC
Q psy7535          15 KQIFTDASKN--E-HSVSS-AFCCEE--TK-FSVK--LD---PRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSD   82 (199)
Q Consensus        15 ~~IyTDgSk~--~-~~~G~-ai~~~~--~~-~~~~--l~---~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SD   82 (199)
                      +.||||||..  + +..|+ |++..+  .. ..+.  +.   ..+|++.||+.|++.||+.+.+.     ...++.|+||
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~-----g~~~v~i~tD   76 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRL-----GISSPIIKGD   76 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHH-----TCCSCEEEES
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHc-----CCCEEEEEeC
Confidence            5799999986  3 35675 755432  22 2222  22   37899999999999999999988     7789999999


Q ss_pred             cHHHHHHhhcCCC-Cc----HHHHHHHHHHhc--ceEEecCCCCccc
Q psy7535          83 SLSALQSLQNIIS-SS----PIALEIINLLHK--IQCQVRPSHFNMR  122 (199)
Q Consensus        83 S~sal~aI~n~~~-~s----~i~~~I~~ll~~--I~l~WiP~h~nR~  122 (199)
                      |+.+++.+.+++. ++    ++.+++..++++  |.|.|+|++.|..
T Consensus        77 S~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~~v~~~~V~~~~N~~  123 (149)
T 2ehg_A           77 SQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPREENKE  123 (149)
T ss_dssp             CHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHHTCEEEECCGGGCHH
T ss_pred             hHHHHHHHhCccccCCHHHHHHHHHHHHHHhcCCEEEEEcCCcccHH
Confidence            9999999998743 22    567777777665  9999999988843

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

Probab=99.51  E-value=1.2e-13  Score=110.27  Aligned_cols=103  Identities=14%  Similarity=0.115  Sum_probs=74.4

Q ss_pred             CceEEEEcCCCCCC-c------eEEEEEEc--Ce--e--eEEecC-CCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEE
Q psy7535          13 NYKQIFTDASKNEH-S------VSSAFCCE--ET--K--FSVKLD-PRISICNAELISIQYAISFIISTTPLQVPTPKFV   78 (199)
Q Consensus        13 ~~~~IyTDgSk~~~-~------~G~ai~~~--~~--~--~~~~l~-~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~   78 (199)
                      ..+.||||||+..| +      .|+||+..  +.  .  ..+..+ +..+...||+.|+..||+.+.+.      +.++.
T Consensus         6 ~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~------~~~v~   79 (165)
T 2lsn_A            6 YEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKI------PGPVL   79 (165)
T ss_dssp             CSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHS------SSCEE
T ss_pred             ceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcC------CCeEE
Confidence            34689999998433 2      68887653  21  1  233343 56788899999999999988764      45799


Q ss_pred             EEcCcHHHHHHhhcC---------CC------Cc-HHHHHHHHHHhc---ceEEecCCCCcc
Q psy7535          79 LYSDSLSALQSLQNI---------IS------SS-PIALEIINLLHK---IQCQVRPSHFNM  121 (199)
Q Consensus        79 I~SDS~sal~aI~n~---------~~------~s-~i~~~I~~ll~~---I~l~WiP~h~nR  121 (199)
                      |+|||+.+++.|..+         ..      ++ ++.+++.+++.+   |.|.|||+|.+.
T Consensus        80 I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~  141 (165)
T 2lsn_A           80 VITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPT  141 (165)
T ss_dssp             EEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCS
T ss_pred             EEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCc
Confidence            999999999999642         11      22 567777776653   999999999863

>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=99.47  E-value=2.1e-13  Score=126.63  Aligned_cols=100  Identities=19%  Similarity=0.180  Sum_probs=77.4

Q ss_pred             CCceEEEEcCCCCCC-c-eEEEEEEcCee-eEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHH
Q psy7535          12 PNYKQIFTDASKNEH-S-VSSAFCCEETK-FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ   88 (199)
Q Consensus        12 ~~~~~IyTDgSk~~~-~-~G~ai~~~~~~-~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~   88 (199)
                      ++...||||||...+ + .|+|++..+.. ..+. ...+|++.||+.|++.||+.+         ..++.|+|||+.+++
T Consensus       437 ~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~~-~~~~TNn~aEl~Ai~~aL~~~---------~~~v~I~tDS~~vi~  506 (557)
T 2zd1_A          437 VGAETFYVDGAANRETKLGKAGYVTNKGRQKVVP-LTNTTNQKTELQAIYLALQDS---------GLEVNIVTDSQYALG  506 (557)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEETTSCEEEEE-ECSCCHHHHHHHHHHHHHHHS---------CSEEEEEECCHHHHH
T ss_pred             CCCEEEEEccCCCCCCCceEEEEEEECCcEEEec-CCCCCHHHHHHHHHHHHHHhC---------CCcEEEEeChHHHHH
Confidence            456899999998543 3 56776664433 3333 357899999999999999987         357999999999999


Q ss_pred             HhhcCCCC--cHHHHHHHHHHhc---ceEEecCCCCcc
Q psy7535          89 SLQNIISS--SPIALEIINLLHK---IQCQVRPSHFNM  121 (199)
Q Consensus        89 aI~n~~~~--s~i~~~I~~ll~~---I~l~WiP~h~nR  121 (199)
                      +|+++..+  .++..++.+.+.+   |.|.|+|+|.++
T Consensus       507 ~i~~~~~~~~~~l~~~~~~~l~~~~~v~~~wV~~H~g~  544 (557)
T 2zd1_A          507 IIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGI  544 (557)
T ss_dssp             HHTTCCSEESSHHHHHHHHHHHHCSEEEEEECCSSSCC
T ss_pred             HHhcCCccCCHHHHHHHHHHHhcCCCEEEEEcCCCCCC
Confidence            99998765  4777777655543   999999999863

>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=99.44  E-value=4.1e-13  Score=124.61  Aligned_cols=101  Identities=24%  Similarity=0.256  Sum_probs=77.5

Q ss_pred             CCceEEEEcCCCCCC--ceEEEEEEcCeeeEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHHH
Q psy7535          12 PNYKQIFTDASKNEH--SVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS   89 (199)
Q Consensus        12 ~~~~~IyTDgSk~~~--~~G~ai~~~~~~~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~a   89 (199)
                      ++...||||||...+  ..|+|++.............+|++.||+.|++.||+.         ...++.|+|||+.++++
T Consensus       434 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~TNn~aEl~A~i~aL~~---------~~~~v~I~tDS~~v~~~  504 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTD---------SGPKVNIIVDSQYVMGI  504 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEESSCCHHHHHHHHHHHHHHT---------SCSEEEEEESCHHHHHH
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCCEeeccCCCCCHHHHHHHHHHHHHHc---------CCCeEEEEEehHHHHHH
Confidence            567899999998644  2677776654332222235789999999999999987         24689999999999999


Q ss_pred             hhcCCC--CcHHHHHHHHHHhc---ceEEecCCCCcc
Q psy7535          90 LQNIIS--SSPIALEIINLLHK---IQCQVRPSHFNM  121 (199)
Q Consensus        90 I~n~~~--~s~i~~~I~~ll~~---I~l~WiP~h~nR  121 (199)
                      |+++..  ..++.+++.+++.+   |.|.|+|+|.++
T Consensus       505 i~~~~~~~~~~l~~~~~~~~~~~~~v~~~wV~~H~g~  541 (555)
T 1mu2_A          505 VASQPTESESKIVNQIIEEMIKKEAIYVAWVPAHKGI  541 (555)
T ss_dssp             HHTCCSEESCHHHHHHHHHHHHCSEEEEEECCSSSCC
T ss_pred             HhcccccccHHHHHHHHHHhccCCcEEEEEEECCCCC
Confidence            998654  34777777776543   999999999874

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

Probab=99.26  E-value=2.3e-11  Score=94.90  Aligned_cols=77  Identities=12%  Similarity=0.119  Sum_probs=59.3

Q ss_pred             CCceEEEEcCCCCCC--ceEEEEEEcC-e-eeEEecC-CCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHH
Q psy7535          12 PNYKQIFTDASKNEH--SVSSAFCCEE-T-KFSVKLD-PRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSA   86 (199)
Q Consensus        12 ~~~~~IyTDgSk~~~--~~G~ai~~~~-~-~~~~~l~-~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sa   86 (199)
                      ++...||||||...+  ..|+|++... . ......+ ..+|+..||+.|++.||+++.+.     .. ++.|+|||+.+
T Consensus         9 ~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~~~TNN~aEl~A~i~aL~~~~~~-----~~-~v~i~tDS~~v   82 (142)
T 1zbf_A            9 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKER-----NS-RKPIYSNSQTA   82 (142)
T ss_dssp             CCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHT-----TC-CCCEEESCHHH
T ss_pred             CCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccCCcCcHHHHHHHHHHHHHHHHhC-----CC-eEEEEEehHHH
Confidence            456789999998544  4678877642 2 2222222 36899999999999999999886     44 89999999999


Q ss_pred             HHHhhcCC
Q psy7535          87 LQSLQNII   94 (199)
Q Consensus        87 l~aI~n~~   94 (199)
                      ++.+++.+
T Consensus        83 i~w~~~~~   90 (142)
T 1zbf_A           83 IKWVKDKK   90 (142)
T ss_dssp             HHHHHHTC
T ss_pred             HHHHHcCC
Confidence            99999876

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

Probab=99.13  E-value=4e-11  Score=92.74  Aligned_cols=77  Identities=12%  Similarity=0.139  Sum_probs=56.4

Q ss_pred             CCceEEEEcCCCCCC-c-eEE-EEEEcCee-eEEe-cCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHH
Q psy7535          12 PNYKQIFTDASKNEH-S-VSS-AFCCEETK-FSVK-LDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSA   86 (199)
Q Consensus        12 ~~~~~IyTDgSk~~~-~-~G~-ai~~~~~~-~~~~-l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sa   86 (199)
                      |+...||||||...+ | .|. ||+..+.. .... -.+.+|+..||++|++.||+.+.+.     ... +.|+|||+.+
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~~~tTNN~aEl~A~i~aL~~l~~~-----~~~-v~i~tDSqyV   76 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKER-----NSR-KPIYSNSQTA   76 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEEEEECHHHHHHHHHHHHHHHHHHT-----TCC-CCEEESCHHH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCCCCCchHHHHHHHHHHHHHHHHhC-----CCC-EEEEcchHHH
Confidence            567789999998443 3 566 34443322 2221 1247899999999999999999875     333 7999999999


Q ss_pred             HHHhhcCC
Q psy7535          87 LQSLQNII   94 (199)
Q Consensus        87 l~aI~n~~   94 (199)
                      ++.|++..
T Consensus        77 i~wi~~~~   84 (134)
T 4htu_A           77 IKWVKDKK   84 (134)
T ss_dssp             HHHHHHTC
T ss_pred             HHHHHcCC
Confidence            99998753

>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=94.12  E-value=0.012  Score=52.82  Aligned_cols=73  Identities=12%  Similarity=0.068  Sum_probs=48.5

Q ss_pred             ceEEEEcCCCCCCceEEEEEEcC----ee----eEEecC---CCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcC
Q psy7535          14 YKQIFTDASKNEHSVSSAFCCEE----TK----FSVKLD---PRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSD   82 (199)
Q Consensus        14 ~~~IyTDgSk~~~~~G~ai~~~~----~~----~~~~l~---~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SD   82 (199)
                      ...+|||||.  .++|+ |+...    ..    .+-++.   ...|++..|+.||..|++.....    -....+.|+||
T Consensus       346 ~~~l~~DAS~--~~~ga-vL~q~~~~~~~~i~y~Sk~l~~~e~~ys~~ekEllAi~~a~~~~~~y----l~g~~~~v~tD  418 (455)
T 1rw3_A          346 PFELFVDEKQ--GYAKG-VLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKL----TMGQPLVIKAP  418 (455)
T ss_dssp             TTSCEEEEEE--CSSSB-EECCBCTTTTCCCCCCCBCSCSSCSSSCCSSHHHHHHHHHHHHHHGG----GCSSCEEEECS
T ss_pred             cEEEEEeccC--Cccee-EEEEecCCcEEEEEEEcccCCccccccchHHHHHHHHHHHHHHHHHH----cCCCcEEEEec
Confidence            4579999985  33443 33321    11    122332   46789999999999999998764    24568999999


Q ss_pred             cHHHHHHhhcCC
Q psy7535          83 SLSALQSLQNII   94 (199)
Q Consensus        83 S~sal~aI~n~~   94 (199)
                      +. ++.-+.++.
T Consensus       419 h~-~~~~l~~~~  429 (455)
T 1rw3_A          419 HA-VEALVKQPP  429 (455)
T ss_dssp             SC-TTTTSSSTT
T ss_pred             Ch-HHHHhCCCc
Confidence            96 666665543

>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=80.72  E-value=1.8  Score=38.31  Aligned_cols=74  Identities=4%  Similarity=-0.220  Sum_probs=43.5

Q ss_pred             CCceEEEEcCCCCCCceEEEEEEcCe-e----eEEecCCCcchhHHHHHH-HHHHHHHHHhhCCCCCCCCcEEEEcCcHH
Q psy7535          12 PNYKQIFTDASKNEHSVSSAFCCEET-K----FSVKLDPRISICNAELIS-IQYAISFIISTTPLQVPTPKFVLYSDSLS   85 (199)
Q Consensus        12 ~~~~~IyTDgSk~~~~~G~ai~~~~~-~----~~~~l~~~~Si~tAEl~A-I~~AL~~i~~~~~~~~~~~~i~I~SDS~s   85 (199)
                      .....+|||||..  +...|++..+. .    ..+.-....+.+.-|++| |..||+...... -+..+..++++||.+.
T Consensus       322 ~~~~~l~~das~~--g~~g~vl~q~~~~~~~s~~~~~~~~y~~~~~e~la~vv~al~~~r~yl-~G~~~~~~i~~td~~~  398 (428)
T 2zd1_B          322 SKDLIAEIQKQGQ--GQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVI-WGKTPKFKLPIQKETW  398 (428)
T ss_dssp             TSCCEEEEEEEET--TEEEEEEESSTTCEEEEEEEECCSSCTTCHHHHHHHHHHHHHHHHHHH-HSSCCEEEESSCHHHH
T ss_pred             CCCEEEEEecCCC--CcEEEEEecCCCceeeecccchhhhcccchHHHHHHHHHHhhccceEE-ECCCCcEECCccHHHH
Confidence            3456999999962  23223333222 1    233323445666777778 999998754320 0234566788899987


Q ss_pred             HHH
Q psy7535          86 ALQ   88 (199)
Q Consensus        86 al~   88 (199)
                      ..-
T Consensus       399 ~~~  401 (428)
T 2zd1_B          399 ETW  401 (428)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

---

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	199
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.76
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.73
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.57
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.57
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.28

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

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

Probab=99.76  E-value=1.5e-18  Score=128.39  Aligned_cols=99  Identities=20%  Similarity=0.219  Sum_probs=74.0

Q ss_pred             CCCceEEEEcCCCC-CCce-EEEEEEcCeeeEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHH
Q psy7535          11 LPNYKQIFTDASKN-EHSV-SSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ   88 (199)
Q Consensus        11 ~~~~~~IyTDgSk~-~~~~-G~ai~~~~~~~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~   88 (199)
                      .++...+|||||+. +++. |+|++..+...........|+..||+.||+.||+.         ...++.|+|||+.+++
T Consensus         5 i~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~~~~TNn~aEl~Avi~aL~~---------~~~~v~I~TDS~yvi~   75 (110)
T d1s1ta1           5 IVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD---------SGLEVNIVTDSQYALG   75 (110)
T ss_dssp             CTTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEESSCCHHHHHHHHHHHHHHH---------SCSEEEEEECCHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEecccCcHHHHHHHHHHHHHHh---------CCCeEEEEEehHHHHH
Confidence            34567899999974 4444 45566655443333345679999999999999863         3457999999999999


Q ss_pred             HhhcCCC--CcHHHHHHHHHHhc---ceEEecCCC
Q psy7535          89 SLQNIIS--SSPIALEIINLLHK---IQCQVRPSH  118 (199)
Q Consensus        89 aI~n~~~--~s~i~~~I~~ll~~---I~l~WiP~h  118 (199)
                      ++.....  ..++..+|.+++.+   |.+.|+|+|
T Consensus        76 ~i~~~~~~~~~~l~~~il~~l~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          76 IIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH  110 (110)
T ss_dssp             HHHHCCSEESCHHHHHHHHHHHHCSEEEEEECCSS
T ss_pred             HHhcCccccchHHHHHHHHHHhcCCceEEEEeCCC
Confidence            9998765  34677777666553   999999998

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

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

Probab=99.73  E-value=1.4e-17  Score=124.85  Aligned_cols=101  Identities=22%  Similarity=0.243  Sum_probs=74.8

Q ss_pred             CCceEEEEcCCCCC-Cc-eEEEEEEcCeeeEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHHH
Q psy7535          12 PNYKQIFTDASKNE-HS-VSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS   89 (199)
Q Consensus        12 ~~~~~IyTDgSk~~-~~-~G~ai~~~~~~~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~a   89 (199)
                      ++...||||||+.. ++ .|+|++.......+...+..|++.||+.||++||+.         ...++.|+|||+.+++.
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~~~tnn~AEl~Ai~~al~~---------~~~~i~I~tDS~~v~~~   75 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTD---------SGPKVNIIVDSQYVMGI   75 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEESSCCHHHHHHHHHHHHHHT---------SCSEEEEEESCHHHHHH
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecCCCcchHHHHHHHHHHhcc---------CCcceEEEechHHHHHH
Confidence            55678999999743 34 456666666554444445679999999999999873         35679999999999999


Q ss_pred             hhcCCCC--cH-HHHHHHHHHhc--ceEEecCCCCcc
Q psy7535          90 LQNIISS--SP-IALEIINLLHK--IQCQVRPSHFNM  121 (199)
Q Consensus        90 I~n~~~~--s~-i~~~I~~ll~~--I~l~WiP~h~nR  121 (199)
                      +.+....  +. ..+.+..+..+  |.|.|+|+|.++
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~~wV~gH~g~  112 (126)
T d1mu2a1          76 VASQPTESESKIVNQIIEEMIKKEAIYVAWVPAHKGI  112 (126)
T ss_dssp             HHTCCSEESCHHHHHHHHHHHHCSEEEEEECCSSSCC
T ss_pred             HhcCCccccchHHHHHHHHhhhcceeEEEEEeCCCCC
Confidence            9987652  23 44445555554  999999999974

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

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

Probab=99.57  E-value=9.9e-16  Score=117.00  Aligned_cols=102  Identities=11%  Similarity=0.023  Sum_probs=73.1

Q ss_pred             CceEEEEcCCCCCC--ceEEEEEEc--Cee-eEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHH
Q psy7535          13 NYKQIFTDASKNEH--SVSSAFCCE--ETK-FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSAL   87 (199)
Q Consensus        13 ~~~~IyTDgSk~~~--~~G~ai~~~--~~~-~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal   87 (199)
                      ..+.||||||...|  ..|+|++..  +.. ........+|+.+||+.||+.||+++.       ....+.|+|||+.++
T Consensus         2 ~~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~-------~~~~i~i~tds~~~~   74 (147)
T d1rila_           2 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALK-------EPCEVDLYTDSHYLK   74 (147)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCC-------SCCEEEEECCCHHHH
T ss_pred             CEEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhcc-------CCceEEEecchhhhh
Confidence            46899999998654  356776553  222 222333557999999999999998753       456789999999999


Q ss_pred             HHhhcCCC----------------Cc-HHHHHHHHHHhc--ceEEecCCCCcc
Q psy7535          88 QSLQNIIS----------------SS-PIALEIINLLHK--IQCQVRPSHFNM  121 (199)
Q Consensus        88 ~aI~n~~~----------------~s-~i~~~I~~ll~~--I~l~WiP~h~nR  121 (199)
                      +.+.....                .+ ++.+++..+..+  |.|+|||+|.++
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~~~~v~~~wVkgHsg~  127 (147)
T d1rila_          75 KAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTGH  127 (147)
T ss_dssp             HHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCCCGGGSC
T ss_pred             ccccccchhhhhhccccccccccchhHHHHHHHHHHhhhcccceEEccCCCCC
Confidence            88865321                11 356667666655  999999999884

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

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

Probab=99.57  E-value=4.6e-15  Score=113.01  Aligned_cols=101  Identities=16%  Similarity=0.098  Sum_probs=72.9

Q ss_pred             ceEEEEcCCCCCC--ceEEEEEE--cCeeeEEec-CCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHH
Q psy7535          14 YKQIFTDASKNEH--SVSSAFCC--EETKFSVKL-DPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ   88 (199)
Q Consensus        14 ~~~IyTDgSk~~~--~~G~ai~~--~~~~~~~~l-~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~   88 (199)
                      .+.||||||..++  ..|+|++.  .+....+.. .+..|+.+||++||+.||+.+.       ....+.|+|||+.++.
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~-------~~~~i~i~tds~~~i~   74 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALK-------EHAEVILSTDSQYVRQ   74 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCC-------SCCEEEEEECCHHHHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhc-------ccceEEEeecceeeEE
Confidence            4789999998654  46777654  444433333 3567899999999999998764       4567899999999988


Q ss_pred             HhhcCCC---------------C-cHHHHHHHHHHhc--ceEEecCCCCcc
Q psy7535          89 SLQNIIS---------------S-SPIALEIINLLHK--IQCQVRPSHFNM  121 (199)
Q Consensus        89 aI~n~~~---------------~-s~i~~~I~~ll~~--I~l~WiP~h~nR  121 (199)
                      .+.....               . .++.+.|..+..+  |.|+|||+|.++
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~~~~V~~~wV~gH~g~  125 (152)
T d1jl1a_          75 GITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGH  125 (152)
T ss_dssp             HHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTC
T ss_pred             cccchhhHhHhccchhcccCeeecHHHHHHHHHHhhcceeEEEEecccCCC
Confidence            7754321               1 1356666666665  999999999984

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

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

Probab=99.28  E-value=4.2e-12  Score=96.12  Aligned_cols=73  Identities=14%  Similarity=0.140  Sum_probs=55.9

Q ss_pred             EEEEcCCCCCC--ceEEEEEEcCee--eEEecC-CCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHHHh
Q psy7535          16 QIFTDASKNEH--SVSSAFCCEETK--FSVKLD-PRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSL   90 (199)
Q Consensus        16 ~IyTDgSk~~~--~~G~ai~~~~~~--~~~~l~-~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~aI   90 (199)
                      .||||||...|  ..|.|+|.....  ..++-+ +..|+..||+.|++.||+++.+.     + .++.|+|||+.++..+
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~-----~-~~i~I~tDS~yvi~wv   79 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKER-----N-SRKPIYSNSQTAIKWV   79 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHT-----T-CCCCEEESCHHHHHHH
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcC-----C-ceEEEEeccHHHHHHH
Confidence            48999998544  367776665432  222222 57899999999999999999875     3 5689999999999999


Q ss_pred             hcCC
Q psy7535          91 QNII   94 (199)
Q Consensus        91 ~n~~   94 (199)
                      ++.+
T Consensus        80 ~~~~   83 (132)
T d1zbfa1          80 KDKK   83 (132)
T ss_dssp             HHTC
T ss_pred             HhCc
Confidence            8765