Psyllid ID: psy3161

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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
EGKKSDIAPVVFQQKFSEVINTKYANHTICYTDGSKSPDATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANWNNVPNTNKLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHTRLTHNHLFTKSDPPICQCGAPLSVRHLLSCPRHGHIRASLRPPPSLGDDEEGVNSLFSYLQKLNIYHLI
Secondary Structure (PSIPRED)
ccccccccHHHHHHHHHHHHHHHccccEEEEcccccccccEEEEEEEccEEEEEEccccccHHHHHHHHHHHHHHHHHHcccccEEEEHHHHHHHHHHHHccccccccccccccccccccccccccccccEEEEEEHHcccccccccccccccccccccccccccHHHHccccccHHHHHHccccccccccHHHHHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHHHHHHHHcccccEEEEccccccccEEEEEEEcccEEEEEccccccHHHHHHHHHHHHHHHHHccccccEEEEEccHHHHHHHHHHccccccccHHHccccccccccccccccccEEEEEEEEcccccccHHHHHccccccccccccEEEEEEEEEcHHHHHHHHHcccccHccccHHHHHHHHHHHHHcccHccc
Coil and Loop (DISEMBL)
egkksdiapvVFQQKFSEVINTKYanhticytdgskspdatgcafsigdmvrstslnpinsIFSAELIAIFLCLEAilespsdqfliVSDSRSAIAALAnwnnvpntnklksirpnikhwntstqdRRIKEVILTRMRightrlthnhlftksdppicqcgaplsvrhllscprhghiraslrpppslgddeegVNSLFSYLQKLNIYHLI
Flexible Loop (DISEMBL)
egkksdiapvvFQQKFSEVINTKYANHTICYTDGSKSPDATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALanwnnvpntnklksirpnikhwntstqdrrikEVILTRMRIGHtrlthnhlftksdPPICQCGAPLSVRHLLSCPRHGHIRASLRPPPSLGDDEEGVNSLFSylqklniyhli
Low Complexity Region (SEG)
EGKKSDIAPVVFQQKFSEVINTKYANHTICYTDGSKSPDATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANWNNVPNTNKLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHTRLTHNHLFTKSDPPICQCGAPLSVRHLLSCPRHGHIRASLRPPPSLGDDEEGVNSLFSYLQKLNIYHLI
Disordered region (IsUnstruct)
*******APVVFQQKFSEVINTKYANHTICYTDGSKSPDATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANWNNVPNTNKLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHTRLTHNHLFTKSDPPICQCGAPLSVRHLLSCPRHGHI*****************NSLFSYLQKLNIYH**
Disordered Region (DISOPRED)
*********VVFQQKFSEVINTKYANHTICYTDGSKSPDATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANWNNVPNTNKLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHTRLTHNHLFTKSDPPICQCGAPLSVRHLLSCPRHGHIRASLRPPPSLGDDEEGVNSLFSYLQKLNIYHLI
Disordered Region (DISEMBL)
EGKKSDIAPVVFQQKFSEVINTKYANHTICYTDGSKSPDATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANWNNVPNTNKLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHTRLTHNHLFTKSDPPICQCGAPLSVRHLLSCPRHGHIRASLRPPPSLGDDEEGVNSLFSYLQKLNIYHLI
Disordered Region (DISPRO)
****SDIAPVVFQQKFSEVINTKYANHTICYTDGSKSPDATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANWNNVPNTNKLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHTRLTHNHLFTKSDPPICQCGAPLSVRHLLSCPRHGHIRASLRPPPSLGDDEEGVNSLFSYLQKLNIYHLI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
EGKKSDIAPVVFQQKFSEVINTKYANHTICYTDGSKSPDATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANWNNVPNTNKLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHTRLTHNHLFTKSDPPICQCGAPLSVRHLLSCPRHGHIRASLRPPPSLGDDEEGVNSLFSYLQKLNIYHLI
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	211
443730613	233	hypothetical protein CAPTEDRAFT_206814 [	0.682	0.618	0.302	2e-12
328721829	152	PREDICTED: hypothetical protein LOC10057	0.554	0.769	0.319	2e-10
427791807	1212	Putative tick transposon, partial [Rhipi	0.407	0.070	0.419	3e-10
427791321	1210	Putative tick transposon, partial [Rhipi	0.407	0.071	0.419	3e-10
328720146	164	PREDICTED: hypothetical protein LOC10056	0.383	0.493	0.404	7e-10
270015744	879	hypothetical protein TcasGA2_TC004345 [T	0.412	0.098	0.423	1e-09
427791063	1035	Putative tick transposon, partial [Rhipi	0.336	0.068	0.434	2e-09
189242251	1808	PREDICTED: similar to pol-like protein [	0.549	0.064	0.362	2e-09
270002674	321	hypothetical protein TcasGA2_TC005227 [T	0.412	0.271	0.423	2e-09
328696858	206	PREDICTED: hypothetical protein LOC10056	0.488	0.5	0.345	1e-08

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

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/195 (30%), Positives = 84/195 (43%), Gaps = 51/195 (26%)

Query: 26  NHTICYTDGSKSPDATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQF 85
           +H   YTDGSKS     C  +   ++    L    SIFSAEL+AI+  L  +LE  + Q 
Sbjct: 12  DHLPIYTDGSKSETRVACVATANRLLIQVRLPDSASIFSAELLAIYEVL-TLLECAAPQK 70

Query: 86  LIVSDSR----------SAIAALAN----------------------------------- 100
             +  +R          S I  + N                                   
Sbjct: 71  YTILYNRGFDLVILWCPSHIGVVGNERADLLAKEALSFTACDVRIPAFDFNSVAYSFYRD 130

Query: 101 -WN---NVPNTNKLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHTRLTHNHLFTKSDPP 156
            W    ++   NKL S++P IK    S+++ R KE++L R RIGHT LTH +L  +  PP
Sbjct: 131 KWQALWSLEQNNKLHSVQPIIKKLTNSSREDRRKEIVLARARIGHTHLTHGYLLRRELPP 190

Query: 157 IC-QCGAPLSVRHLL 170
            C  C  PL+V+H+L
Sbjct: 191 FCVHCQCPLTVKHIL 205

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 39/122 (31%), Positives = 69/122 (56%), Gaps = 5/122 (4%)

Query: 86  LIVSDSRSAIAALAN-WNNVPNTNKLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHTRL 144
           LI    +S +A+  N W+++  +NKL+ ++  +  W  S    R ++ I+ R RIGH+ +
Sbjct: 22  LINEAQKSILASWQNHWDDILTSNKLRIVKKTVSKWTYSENASRREQTIINRARIGHSNI 81

Query: 145 THNHLFTKSDPPICQ-CGAPLSVRH-LLSCPRHGHIRASLRPPPSLGDDEEGVNS--LFS 200
           TH++L TK   P C  C  PL++ H +++CP+    R  L+ P SL +    VN+  +F+
Sbjct: 82  THSYLITKEPRPNCDTCNTPLTIEHIIINCPKFASSRHLLKNPSSLEEALIQVNTGNIFN 141

Query: 201 YL 202
           + 
Sbjct: 142 FF 143

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427791807|gb|JAA61355.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 39/93 (41%), Positives = 53/93 (56%), Gaps = 7/93 (7%)

Query: 88   VSDSRSAI--AALANWNNVPNT---NKLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHT 142
            + DS+  I  A LA W    ++   NKL  ++P +  W       R  EVIL R+RIGHT
Sbjct: 1072 LKDSQRTIRLALLAKWQQQWDSCTSNKLHLVKPTLGEWKNCRHQERFIEVILCRLRIGHT 1131

Query: 143  RLTHNHLFTKSDPPICQ-CGAPLSVRH-LLSCP 173
             LTHN L TK + P+C+ C  PL++ H L+ CP
Sbjct: 1132 HLTHNFLLTKEEQPMCEKCQEPLTLIHILILCP 1164

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427791321|gb|JAA61112.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 39/93 (41%), Positives = 53/93 (56%), Gaps = 7/93 (7%)

Query: 88   VSDSRSAI--AALANWNNVPNT---NKLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHT 142
            + DS+  I  A LA W    ++   NKL  ++P +  W       R  EVIL R+RIGHT
Sbjct: 1069 LKDSQRTIRLALLAKWQQQWDSCTSNKLHLVKPTLGEWKNCRHQERFIEVILCRLRIGHT 1128

Query: 143  RLTHNHLFTKSDPPICQ-CGAPLSVRH-LLSCP 173
             LTHN L TK + P+C+ C  PL++ H L+ CP
Sbjct: 1129 HLTHNFLLTKEEQPMCEKCQEPLTLIHILILCP 1161

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 34/84 (40%), Positives = 53/84 (63%), Gaps = 3/84 (3%)

Query: 109 KLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHTRLTHNHLFTKSDPPICQ-CGAPLSVR 167
           KL  I+ NI+ W     +R+ +E IL R+RIGHT +TH HL  K+DPPIC+ CG  L+V+
Sbjct: 68  KLNQIKNNIQTWKNPGLNRK-EETILNRLRIGHTFITHRHLMEKNDPPICEMCGVDLTVK 126

Query: 168 HLLS-CPRHGHIRASLRPPPSLGD 190
           H+++ C ++  +R        +G+
Sbjct: 127 HIITECRKYDDMRKKYNISQQIGE 150

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 39/92 (42%), Positives = 52/92 (56%), Gaps = 5/92 (5%)

Query: 101 WNNVPNTNKLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHTRLTHNHLFTKSDPPI-CQ 159
           WN   +T KL+   P+IK W  S   +R +EV + R+R+GHTRLT  +   K DPP  C 
Sbjct: 459 WNQ--STAKLREAYPDIKKWPPSNL-KRGEEVTINRLRLGHTRLTQEYHLKKVDPPTCCY 515

Query: 160 CGAPLSVRH-LLSCPRHGHIRASLRPPPSLGD 190
           C   L+VRH LL CP++  IR     P  + D
Sbjct: 516 CEGRLTVRHILLECPKYHDIRNEANFPNRMED 547

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/76 (43%), Positives = 50/76 (65%), Gaps = 5/76 (6%)

Query: 99   ANWNNVPNT---NKLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHTRLTHNHLFTKSDP 155
            A W ++ +T   NKL +I+P +  W  +++ RR  E+ LTR+R GHT  TH +L + +DP
Sbjct: 944  AYWQSIWDTQTQNKLHAIKPQLGEWPPASKSRRT-EITLTRLRTGHTHTTHAYLLSGNDP 1002

Query: 156  PICQ-CGAPLSVRHLL 170
            P C+ CG PL+V H+L
Sbjct: 1003 PRCERCGEPLTVLHIL 1018

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 46/127 (36%), Positives = 65/127 (51%), Gaps = 11/127 (8%)

Query: 74   LEAILESPSDQFLIVSD-SRSAIAALANWNN-------VPNTNKLKSIRPNIKHWNTSTQ 125
            L A+L S S  ++  +D S+S     A   N       +   +KL+   P+IK W  S  
Sbjct: 1351 LAALLTSISSNYIFYTDASKSDTVGAAYVTNDTQQAFRLSPESKLREAYPDIKKWPPSNL 1410

Query: 126  DRRIKEVILTRMRIGHTRLTHNHLFTKSDPPI-CQCGAPLSVRH-LLSCPRHGHIRASLR 183
             +R +EV + R+R+GHTRLT  +   K DPP  C C   L+VRH LL CP++  IR    
Sbjct: 1411 -KRGEEVTINRLRLGHTRLTQEYHLKKVDPPTCCYCEGRLTVRHILLECPKYHDIRNEAN 1469

Query: 184  PPPSLGD 190
             P  + D
Sbjct: 1470 FPNRMED 1476

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270002674|gb|EEZ99121.1| hypothetical protein TcasGA2_TC005227 [Tribolium castaneum]

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 39/92 (42%), Positives = 52/92 (56%), Gaps = 5/92 (5%)

Query: 101 WNNVPNTNKLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHTRLTHNHLFTKSDPPI-CQ 159
           WN   +T KL+   PNIK W  S+  +R +EV + R+R+ HTRLT  +   K DPP  C 
Sbjct: 210 WNQ--STAKLREAYPNIKKW-ASSNLKRGEEVTINRLRLRHTRLTQEYHLKKVDPPTCCY 266

Query: 160 CGAPLSVRH-LLSCPRHGHIRASLRPPPSLGD 190
           C   L+VRH LL CP++  IR     P  + D
Sbjct: 267 CEERLTVRHILLECPKYHDIRNEANFPNRMED 298

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328696858|ref|XP_003240151.1| PREDICTED: hypothetical protein LOC100568880 [Acyrthosiphon pisum]

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 38/110 (34%), Positives = 58/110 (52%), Gaps = 7/110 (6%)

Query: 109 KLKSIRPNIKHWNTSTQDRRIKEVILTRMRIGHTRLT-HNHLFTKSDPPIC-QCGAPLSV 166
           KL  I+     W   +   R +EVILTR+RIGHTR T H +L ++ D P C  CG  L++
Sbjct: 97  KLSEIKRTTDRWKNKSNLNRKEEVILTRLRIGHTRYTLHGYLMSREDQPTCATCGVHLTI 156

Query: 167 RHLL-SCPRHGHIRASLRPPP----SLGDDEEGVNSLFSYLQKLNIYHLI 211
           +H+L  C +    R     P     SLG +E  +    + +++L I +L+
Sbjct: 157 KHILVECRQTEAARTKYSIPEFLYQSLGPNESAIKQTLNLIKELEIENLL 206

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)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	211
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.355	0.154	0.369	4.6e-05
ASPGD|ASPL0000062864	520	AN0621 [Emericella nidulans (t	0.331	0.134	0.298	0.00091

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

 Score = 98 (39.6 bits), Expect = 4.6e-05, Sum P(2) = 4.6e-05
 Identities = 31/84 (36%), Positives = 43/84 (51%)

Query:   125 QD-RRIKEVILTRMRIGHTRLTHNHLFTKSDPPI----CQCG-APLSVRH-LLSCPRHGH 177
             QD  R    I+ +MR G   L H +L+ +  P +    CQCG A  SVRH LL+CP    
Sbjct:   370 QDLHRALSTIIVQMRTGKIGLRH-YLYQRGVPDVPNSDCQCGRATQSVRHILLACPTFSG 428

Query:   178 IRASLRPPPSLGDDEEG-VNSLFS 200
             +R  +    S G + EG V  +F+
Sbjct:   429 LREEIFGGRSGGPEGEGSVKKIFN 452

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

ASPGD|ASPL0000062864 AN0621 [Emericella nidulans (taxid:162425)]

 Score = 78 (32.5 bits), Expect = 0.00091, Sum P(2) = 0.00091
 Identities = 23/77 (29%), Positives = 35/77 (45%)

Query:   102 NNVPNTNKLKSIRPNIKHWNTSTQDRRIKEVILTRM---RIGHTRLTHNH-LFTKSDP-P 156
             N  P T K  +IRP+ K   + +++ ++   +L R+   R GH   T  H  F  +D   
Sbjct:   390 NKAPETYKALNIRPHTKE--SRSREHKLPRWVLGRLVAARTGHGDFTAYHQCFDHTDYLE 447

Query:   157 ICQCGAPLSVRHLLSCP 173
              C CG   +  H   CP
Sbjct:   448 SCTCGKAKTPVHFFFCP 464

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

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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	211
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	4e-20
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	3e-06
pfam00075	126	pfam00075, RNase_H, RNase H	8e-06
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	5e-04

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

 Score = 81.9 bits (203), Expect = 4e-20
 Identities = 34/106 (32%), Positives = 50/106 (47%), Gaps = 14/106 (13%)

Query: 29  ICYTDGSKSPDATGCAFSI---GDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSD-- 83
           + YTDGSK    TG  F+I   G + RS  L P  S+F AEL+AI   L+  L       
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 84  QFLIVSDSRSAIAALANWNNVPNTN-----KLKSIR-PNIK---HW 120
           +  I SDS++A+ AL +  +           ++ +    +K   HW
Sbjct: 61  KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHW 106

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

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 7/85 (8%)

Query: 31  YTDGSKS--PDATGCAFSI----GDMVRSTSLNPIN-SIFSAELIAIFLCLEAILESPSD 83
            TDGS    P   G    +    G  + + SL+    +   AEL+A+   LE  L+    
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60

Query: 84  QFLIVSDSRSAIAALANWNNVPNTN 108
           + +I +DS+  +  + +W+     N
Sbjct: 61  KLIIETDSKYVVDLINSWSKGWKKN 85

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 123

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

 Score = 43.4 bits (103), Expect = 8e-06
 Identities = 24/91 (26%), Positives = 37/91 (40%), Gaps = 8/91 (8%)

Query: 26  NHTICYTDGS--KSPDATGCAFSI-GDMVRSTSLNPINSIFSAELIAIFLCLEAILESPS 82
                YTDGS   +P   G  +   G   RS  L P  +   AEL+A+   +EA+     
Sbjct: 2   EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPL-PGTTNQRAELLAL---IEALEALSG 57

Query: 83  DQFLIVSDSRSAI-AALANWNNVPNTNKLKS 112
            +  I +DS+  I      W     +  +K+
Sbjct: 58  QKVNIYTDSQYVIGGITNGWPTKSESKPIKN 88

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

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

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 4/73 (5%)

Query: 30  CYTDGSKSPDATGCA-FSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIV 88
            +TDGS      G A  +  D++   +L    S   AELIA+   + A+  +      I 
Sbjct: 2   VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIAL---IRALELAKGKPVNIY 58

Query: 89  SDSRSAIAALANW 101
           +DS  A   L   
Sbjct: 59  TDSAYAFGILHAL 71

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	211
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.42
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.37
PRK00203	150	rnhA ribonuclease H; Reviewed	99.35
PRK13907	128	rnhA ribonuclease H; Provisional	99.34
PRK06548	161	ribonuclease H; Provisional	99.32
PRK08719	147	ribonuclease H; Reviewed	99.24
KOG3752|consensus	371		99.07
PRK07708	219	hypothetical protein; Validated	98.94
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	98.93
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	98.77
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	97.97
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	96.66
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	92.43
.; 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	80.77

>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=99.42  E-value=5.3e-13  Score=101.91  Aligned_cols=97  Identities=28%  Similarity=0.280  Sum_probs=69.8

Q ss_pred             CceEEEecCCCCCC--ceeEEEE-eCCeeeeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhc--
Q psy3161          26 NHTICYTDGSKSPD--ATGCAFS-IGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALAN--  100 (211)
Q Consensus        26 ~~~~IyTDgS~~~~--~~G~ai~-~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~--  100 (211)
                      +.+.||||||+..+  ..|+|++ ..+......++ ..|++.||+.||.+||+.+ .  ..+++|+|||+++++.|..  
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v~~~l~~~~   77 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYVLNALNKWL   77 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHHHHHHHTHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHHHHHHHHhc
Confidence            57899999997633  3566654 44444445556 9999999999999999954 3  4999999999999998877  


Q ss_pred             ---CCC----C-chhhhhhhcCC-----CCcccCCCccc
Q psy3161         101 ---WNN----V-PNTNKLKSIRP-----NIKHWNTSTQD  126 (211)
Q Consensus       101 ---~~~----~-~~~~~I~~i~p-----~~~W~~~~~~l  126 (211)
                         ...    . ++...|.+++.     .|+|+|.|.+.
T Consensus        78 ~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~  116 (132)
T PF00075_consen   78 HGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGV  116 (132)
T ss_dssp             HHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSS
T ss_pred             cccccccccccccchhheeeccccceEEeeeeccCcCCC
Confidence               222    1 45556655531     26999999776

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 ....

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

Probab=99.37  E-value=3.1e-12  Score=101.36  Aligned_cols=75  Identities=24%  Similarity=0.301  Sum_probs=60.8

Q ss_pred             CceEEEecCCCCCC--ceeEEEEe--CCee--eeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHh
Q psy3161          26 NHTICYTDGSKSPD--ATGCAFSI--GDMV--RSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALA   99 (211)
Q Consensus        26 ~~~~IyTDgS~~~~--~~G~ai~~--~~~~--~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~   99 (211)
                      ..+.||||||+.++  ..|+|+|.  ++..  .+..+. .+|++.||+.|++.||+++.+.+...+.|+|||+.++++|.
T Consensus         2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~   80 (154)
T COG0328           2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGIT   80 (154)
T ss_pred             CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHH
Confidence            46899999999966  36777553  3322  333334 89999999999999999999888899999999999999998


Q ss_pred             cC
Q psy3161         100 NW  101 (211)
Q Consensus       100 ~~  101 (211)
                      .|
T Consensus        81 ~w   82 (154)
T COG0328          81 RW   82 (154)
T ss_pred             HH
Confidence            55

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.35  E-value=5.7e-12  Score=99.60  Aligned_cols=99  Identities=17%  Similarity=0.222  Sum_probs=68.4

Q ss_pred             ceEEEecCCCCCC--ceeEEEEe--CCeeee-eecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhcC
Q psy3161          27 HTICYTDGSKSPD--ATGCAFSI--GDMVRS-TSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANW  101 (211)
Q Consensus        27 ~~~IyTDgS~~~~--~~G~ai~~--~~~~~~-~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~~  101 (211)
                      ++.||||||+..+  ..|+|++.  ++.... ....+..|+..||+.||+.||+.+..  ...+.|+|||++++++|..|
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w   80 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEW   80 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHH
Confidence            5899999999854  46777553  333222 22235788999999999999998865  46799999999999999862


Q ss_pred             ---------CC---Cch-----hhhhhhcCC----CCcccCCCcccc
Q psy3161         102 ---------NN---VPN-----TNKLKSIRP----NIKHWNTSTQDR  127 (211)
Q Consensus       102 ---------~~---~~~-----~~~I~~i~p----~~~W~~~~~~l~  127 (211)
                               ..   .++     .+.|.++..    .|.|+|.|.+..
T Consensus        81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~wV~~H~~~~  127 (150)
T PRK00203         81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHP  127 (150)
T ss_pred             HHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEEEEecCCCCCH
Confidence                     11   133     233444322    369999986543

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.34  E-value=8.3e-12  Score=95.72  Aligned_cols=97  Identities=20%  Similarity=0.105  Sum_probs=71.7

Q ss_pred             ceEEEecCCCCCC--ceeEEEEeC--Ceeeeee-cCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhcC
Q psy3161          27 HTICYTDGSKSPD--ATGCAFSIG--DMVRSTS-LNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANW  101 (211)
Q Consensus        27 ~~~IyTDgS~~~~--~~G~ai~~~--~~~~~~~-l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~~  101 (211)
                      |++||||||...+  ..|+|++..  +.....+ .....++..||+.|++.||+.+.......+.|+|||+.++..+++.
T Consensus         1 ~~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~   80 (128)
T PRK13907          1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE   80 (128)
T ss_pred             CEEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHH
Confidence            6899999999865  578886642  2221222 2356899999999999999999998888999999999999999885


Q ss_pred             CC-C----chhhhhhhcCCC-----CcccCCC
Q psy3161         102 NN-V----PNTNKLKSIRPN-----IKHWNTS  123 (211)
Q Consensus       102 ~~-~----~~~~~I~~i~p~-----~~W~~~~  123 (211)
                      .. +    ++.+.++.+...     ++|+|..
T Consensus        81 ~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~  112 (128)
T PRK13907         81 YAKNKMFAPLLEEALQYIKSFDLFFIKWIPSS  112 (128)
T ss_pred             HhcChhHHHHHHHHHHHHhcCCceEEEEcCch
Confidence            54 2    345555555433     3788764

>PRK06548 ribonuclease H; Provisional

Probab=99.32  E-value=7.4e-12  Score=100.30  Aligned_cols=75  Identities=29%  Similarity=0.298  Sum_probs=57.1

Q ss_pred             CCceEEEecCCCCCC--ceeEEEEeCCeeeeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhc
Q psy3161          25 ANHTICYTDGSKSPD--ATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALAN  100 (211)
Q Consensus        25 ~~~~~IyTDgS~~~~--~~G~ai~~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~  100 (211)
                      +..+.||||||+.++  ..|+|++..+...........|++.||+.||+.||+.+.. ...++.|+|||++++++|..
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~   79 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTK   79 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHH
Confidence            345899999999865  4788877543322222235689999999999999986653 34579999999999999993

>PRK08719 ribonuclease H; Reviewed

Probab=99.24  E-value=3e-11  Score=95.45  Aligned_cols=71  Identities=23%  Similarity=0.303  Sum_probs=54.3

Q ss_pred             CCceEEEecCCCCCCc-----eeEEEEe--CC--ee--eeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHH
Q psy3161          25 ANHTICYTDGSKSPDA-----TGCAFSI--GD--MV--RSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRS   93 (211)
Q Consensus        25 ~~~~~IyTDgS~~~~~-----~G~ai~~--~~--~~--~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~s   93 (211)
                      .+.+.||||||+..++     .|+|++.  ++  ..  ....+....|+++||+.||+.||+.+...    ..|+|||+.
T Consensus         2 ~~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~y   77 (147)
T PRK08719          2 RASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDY   77 (147)
T ss_pred             CceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHH
Confidence            4578999999997553     4777653  32  22  33335556899999999999999998753    379999999


Q ss_pred             HHHHHh
Q psy3161          94 AIAALA   99 (211)
Q Consensus        94 al~al~   99 (211)
                      ++++|+
T Consensus        78 vi~~i~   83 (147)
T PRK08719         78 CVRGFN   83 (147)
T ss_pred             HHHHHH
Confidence            999984

>KOG3752|consensus

Probab=99.07  E-value=4.3e-10  Score=99.50  Aligned_cols=78  Identities=28%  Similarity=0.336  Sum_probs=66.9

Q ss_pred             CceEEEecCCCCCC-----ceeEEEEeCC---eeeeeecC-CCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHH
Q psy3161          26 NHTICYTDGSKSPD-----ATGCAFSIGD---MVRSTSLN-PINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIA   96 (211)
Q Consensus        26 ~~~~IyTDgS~~~~-----~~G~ai~~~~---~~~~~~l~-~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~   96 (211)
                      +...||||||+..+     .+|+||+.++   ...+..+. ...++|.||+.||..||+.+.+.+..+++|.|||+..++
T Consensus       211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~  290 (371)
T KOG3752|consen  211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFIN  290 (371)
T ss_pred             cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHH
Confidence            34889999999975     4899999753   45666664 889999999999999999999888889999999999999


Q ss_pred             HHhcCCC
Q psy3161          97 ALANWNN  103 (211)
Q Consensus        97 al~~~~~  103 (211)
                      +|+.|..
T Consensus       291 ~l~~wv~  297 (371)
T KOG3752|consen  291 SLTLWVQ  297 (371)
T ss_pred             HHHHHHh
Confidence            9987654

>PRK07708 hypothetical protein; Validated

Probab=98.94  E-value=8.2e-09  Score=86.65  Aligned_cols=91  Identities=18%  Similarity=0.182  Sum_probs=66.7

Q ss_pred             HHHHHHHHHHHhhcCCceEEEecCCCCC--CceeEEEEe--CC--eeee----eecCCCCchhHHHHHHHHHHHHHHHcC
Q psy3161          11 VFQQKFSEVINTKYANHTICYTDGSKSP--DATGCAFSI--GD--MVRS----TSLNPINSIFSAELIAIFLCLEAILES   80 (211)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~~IyTDgS~~~--~~~G~ai~~--~~--~~~~----~~l~~~~si~~AEl~AI~~AL~~~~~~   80 (211)
                      +++++..++-..  ++.+.||+|||...  +++|+|++.  +.  ....    ..+....+++.||+.|++.||+.+...
T Consensus        59 ~~~~~~~~~~~e--p~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~  136 (219)
T PRK07708         59 ELKKLSKEVEEE--PHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEEL  136 (219)
T ss_pred             HHhhhhhhhccC--CCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHc
Confidence            345555555454  67899999999863  457777553  22  2221    234556899999999999999999987


Q ss_pred             CCC--cEEEEeCcHHHHHHHhcCCC
Q psy3161          81 PSD--QFLIVSDSRSAIAALANWNN  103 (211)
Q Consensus        81 ~~~--~i~I~SDS~sal~al~~~~~  103 (211)
                      +.+  .+.|++||+.+++.+.+.+.
T Consensus       137 g~~~~~V~I~~DSqlVi~qi~g~wk  161 (219)
T PRK07708        137 GVKHEPVTFRGDSQVVLNQLAGEWP  161 (219)
T ss_pred             CCCcceEEEEeccHHHHHHhCCCce
Confidence            654  38999999999999988654

>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=98.93  E-value=8.3e-09  Score=75.92  Aligned_cols=96  Identities=25%  Similarity=0.270  Sum_probs=70.4

Q ss_pred             EEEecCCCCCC--ceeEEEEe--CCeeeee---ecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhcC
Q psy3161          29 ICYTDGSKSPD--ATGCAFSI--GDMVRST---SLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANW  101 (211)
Q Consensus        29 ~IyTDgS~~~~--~~G~ai~~--~~~~~~~---~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~~  101 (211)
                      .+|||||...+  ++|+|++.  .+....+   ......+++.||+.|++.||+++......++.|++||+.++..+.++
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            48999999866  57777664  2222121   12258899999999999999999887889999999999999999987


Q ss_pred             CC------CchhhhhhhcC---C--CCcccCCCc
Q psy3161         102 NN------VPNTNKLKSIR---P--NIKHWNTST  124 (211)
Q Consensus       102 ~~------~~~~~~I~~i~---p--~~~W~~~~~  124 (211)
                      ..      .++...|++++   .  .|.|+|.|.
T Consensus        81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~  114 (130)
T cd06222          81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHS  114 (130)
T ss_pred             ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCC
Confidence            53      12344454443   1  258888865

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.

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=98.77  E-value=4.8e-08  Score=87.71  Aligned_cols=95  Identities=15%  Similarity=0.135  Sum_probs=68.5

Q ss_pred             eEEEecCCCCCC--ceeEEEEe--CC-e-e-eeee-cCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHh
Q psy3161          28 TICYTDGSKSPD--ATGCAFSI--GD-M-V-RSTS-LNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALA   99 (211)
Q Consensus        28 ~~IyTDgS~~~~--~~G~ai~~--~~-~-~-~~~~-l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~   99 (211)
                      +.||||||..++  ..|+|++.  .+ . . ..++ .....++..||+.|++.||+++.+.....+.|++||+.+++.+.
T Consensus         3 ~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i~   82 (372)
T PRK07238          3 VVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMS   82 (372)
T ss_pred             EEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHhC
Confidence            789999999976  47777653  32 1 1 1222 23477888999999999999999988889999999999999998


Q ss_pred             cCCC--Cc----hhhhhhhcC---CC--CcccCC
Q psy3161         100 NWNN--VP----NTNKLKSIR---PN--IKHWNT  122 (211)
Q Consensus       100 ~~~~--~~----~~~~I~~i~---p~--~~W~~~  122 (211)
                      +...  ++    +...++++.   +.  ++|++.
T Consensus        83 ~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r  116 (372)
T PRK07238         83 GRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR  116 (372)
T ss_pred             CCCccCChHHHHHHHHHHHHHhcCCceEEEECCc
Confidence            7554  32    344555553   32  366654

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

Probab=97.97  E-value=2.5e-05  Score=54.68  Aligned_cols=52  Identities=19%  Similarity=0.277  Sum_probs=41.5

Q ss_pred             hhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhcCCC--Cc---hhhhhhhc
Q psy3161          62 IFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANWNN--VP---NTNKLKSI  113 (211)
Q Consensus        62 i~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~~~~--~~---~~~~I~~i  113 (211)
                      +..||+.|+..||+++.+.+..+++|.|||+.+++.|++...  +.   +.+.|+.+
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~   57 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSL   57 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhh
Confidence            468999999999999999999999999999999999988754  33   44555555

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

Probab=96.66  E-value=0.001  Score=47.49  Aligned_cols=30  Identities=30%  Similarity=0.609  Sum_probs=24.8

Q ss_pred             ccccCCCCCCCcc-CC-Cccccceec-cccCch
Q psy3161         147 NHLFTKSDPPICQ-CG-APLSVRHLL-SCPRHG  176 (211)
Q Consensus       147 ~~~~~~~~~p~C~-Cg-~~~t~~Hil-~C~~~~  176 (211)
                      +++.+...++.|. |+ ..||++|+| +||...
T Consensus        51 l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~   83 (86)
T PF13966_consen   51 LQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR   83 (86)
T ss_pred             hhccCCccCCccccCCCccccccceeccCcCcc
Confidence            4556667789999 99 599999999 999753

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

Probab=92.43  E-value=0.66  Score=36.73  Aligned_cols=52  Identities=19%  Similarity=0.150  Sum_probs=34.1

Q ss_pred             CceEEEecCCCCCCceeEEEEeC---Ceeeee-------ec--CCCCchhHHHHHHHHHHHHHHHc
Q psy3161          26 NHTICYTDGSKSPDATGCAFSIG---DMVRST-------SL--NPINSIFSAELIAIFLCLEAILE   79 (211)
Q Consensus        26 ~~~~IyTDgS~~~~~~G~ai~~~---~~~~~~-------~l--~~~~si~~AEl~AI~~AL~~~~~   79 (211)
                      ..+++|+|||.  .+.|+.+|..   +.....       ++  ....||-.-|++|+..|.+++..
T Consensus        80 ~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~  143 (159)
T PF05380_consen   80 VELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT  143 (159)
T ss_pred             eeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence            36889999994  4455555532   211111       12  23559999999999999999763

>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=80.77  E-value=3.8  Score=34.27  Aligned_cols=60  Identities=17%  Similarity=0.121  Sum_probs=39.3

Q ss_pred             ceEEEecCCCCCCceeEEEEeCCeeeeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHH
Q psy3161          27 HTICYTDGSKSPDATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAI   95 (211)
Q Consensus        27 ~~~IyTDgS~~~~~~G~ai~~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal   95 (211)
                      --.||+|+.-...+    +..+.....+.+..--.|++||++|...|.-+...    + .|.|||-.++
T Consensus        94 lc~VfaDATpTgwg----i~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~~~----r-~l~tDnt~Vl  153 (245)
T PF00336_consen   94 LCQVFADATPTGWG----ISITGQRMRGTFSKPLPIHTAELLAACLARLMSGA----R-CLGTDNTVVL  153 (245)
T ss_pred             CCceeccCCCCcce----eeecCceeeeeecccccchHHHHHHHHHHHhccCC----c-EEeecCcEEE
Confidence            45899998665443    22333333333344667999999999888766543    2 5999998766

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

---

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	211
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.53
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.4
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.39
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.38
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.38
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.35
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.34
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.33
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.32
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.24
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.21
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.18
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.15
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.15
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.13
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.1
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	93.95

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

Probab=99.53  E-value=2.1e-14  Score=112.55  Aligned_cols=103  Identities=17%  Similarity=0.226  Sum_probs=76.2

Q ss_pred             CCceEEEecCCCCCCc-----eeEEEEeCC---eeeeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHH
Q psy3161          25 ANHTICYTDGSKSPDA-----TGCAFSIGD---MVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIA   96 (211)
Q Consensus        25 ~~~~~IyTDgS~~~~~-----~G~ai~~~~---~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~   96 (211)
                      .+.+.||||||+..++     +|+|++..+   ......+...++++.||+.|++.||+.+.+.+..++.|+|||+.+++
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            4579999999998653     788888642   12344555678999999999999999998877789999999999999


Q ss_pred             HHhcCC---------C---Cc-----hhhhhhhcCC----CCcccCCCcccc
Q psy3161          97 ALANWN---------N---VP-----NTNKLKSIRP----NIKHWNTSTQDR  127 (211)
Q Consensus        97 al~~~~---------~---~~-----~~~~I~~i~p----~~~W~~~~~~l~  127 (211)
                      .|.++.         .   .+     +.+.|.++..    .|.|+|.|.+..
T Consensus        85 ~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~~~v~~~~V~~H~g~~  136 (154)
T 2qkb_A           85 GITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFI  136 (154)
T ss_dssp             HHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTTCEEEEEECCTTSSCH
T ss_pred             hhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcCCceEEEEccCCCCCH
Confidence            998742         1   11     2344444433    259999986443

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

Probab=99.40  E-value=2.4e-13  Score=105.38  Aligned_cols=73  Identities=27%  Similarity=0.355  Sum_probs=57.3

Q ss_pred             CceEEEecCCCCCC--ceeEEEEe--CCeeeeee-cCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhc
Q psy3161          26 NHTICYTDGSKSPD--ATGCAFSI--GDMVRSTS-LNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALAN  100 (211)
Q Consensus        26 ~~~~IyTDgS~~~~--~~G~ai~~--~~~~~~~~-l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~  100 (211)
                      +.+.||||||+..+  ..|+|++.  ++....+. ..+.++++.||+.|++.||+.+.+  ..++.|+|||+++++.|.+
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~~   80 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDPATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMNE   80 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHHS
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCCCCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHHH
Confidence            56899999998865  37777663  33222221 124689999999999999999876  5899999999999999987

>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=99.39  E-value=6.3e-13  Score=103.59  Aligned_cols=105  Identities=11%  Similarity=0.055  Sum_probs=73.1

Q ss_pred             CCceEEEecCCCCCCceeEEEEe--CCee--eee-ec--CC--CCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHH
Q psy3161          25 ANHTICYTDGSKSPDATGCAFSI--GDMV--RST-SL--NP--INSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAI   95 (211)
Q Consensus        25 ~~~~~IyTDgS~~~~~~G~ai~~--~~~~--~~~-~l--~~--~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal   95 (211)
                      ++.+.||||||+.++.+|+|++.  .+..  ... ..  +.  .++++.||+.|++.||+++.+.+. ++.|+|||+.+.
T Consensus         4 ~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i~   82 (147)
T 2kq2_A            4 RTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGIA   82 (147)
T ss_dssp             TSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTHH
T ss_pred             CCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHHH
Confidence            46789999999999778888664  3332  222 22  22  368999999999999998876555 899999999877


Q ss_pred             HHHhcCCC--Cc----hhhhhhhcCC--CCcccCCCccccchh
Q psy3161          96 AALANWNN--VP----NTNKLKSIRP--NIKHWNTSTQDRRIK  130 (211)
Q Consensus        96 ~al~~~~~--~~----~~~~I~~i~p--~~~W~~~~~~l~R~~  130 (211)
                      .-+.+...  ++    +.+.++++..  .|.|+|.|.+...++
T Consensus        83 ~w~~~~w~~~~~~~~~~~~l~~~l~~~v~~~wV~gH~g~~~Ne  125 (147)
T 2kq2_A           83 FWATGEWKAKNEFTQAYAKLMNQYRGIYSFEKVKAHSGNEFND  125 (147)
T ss_dssp             HHTTSSSSCCHHHHHHHHCGGGGGSTTCCBCCCCCCCCCHHHH
T ss_pred             HHHhCCCccCCcchHHHHHHHHHhcCCeeEEEecCcCCCcchH
Confidence            76665433  22    2344455533  369999986544443

>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=99.38  E-value=1e-12  Score=102.91  Aligned_cols=73  Identities=22%  Similarity=0.359  Sum_probs=58.0

Q ss_pred             cCCceEEEecCCCCCC--ceeEEEEeC-CeeeeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhc
Q psy3161          24 YANHTICYTDGSKSPD--ATGCAFSIG-DMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALAN  100 (211)
Q Consensus        24 ~~~~~~IyTDgS~~~~--~~G~ai~~~-~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~  100 (211)
                      ..+.+.||||||+..+  ..|+|++.. +......+ +.++++.||+.|++.||+.+    ..++.|+|||+++++.|.+
T Consensus         9 ~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i~~   83 (150)
T 3qio_A            9 IVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIITQ   83 (150)
T ss_dssp             CTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHHHH
Confidence            4568999999998765  367776653 22223333 57899999999999999985    4789999999999999988


Q ss_pred             C
Q psy3161         101 W  101 (211)
Q Consensus       101 ~  101 (211)
                      |
T Consensus        84 w   84 (150)
T 3qio_A           84 W   84 (150)
T ss_dssp             H
T ss_pred             H
Confidence            6

>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=99.38  E-value=6.4e-13  Score=104.29  Aligned_cols=100  Identities=17%  Similarity=0.228  Sum_probs=70.4

Q ss_pred             ceEEEecCCCCCC--ceeEEEEe--CCeee--eeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhc
Q psy3161          27 HTICYTDGSKSPD--ATGCAFSI--GDMVR--STSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALAN  100 (211)
Q Consensus        27 ~~~IyTDgS~~~~--~~G~ai~~--~~~~~--~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~  100 (211)
                      .+.||||||+.++  ..|+|++.  .+...  ...+ +.++++.||+.|++.||+.+.+  ..++.|+|||+.+++.|.+
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~--~~~v~I~tDS~~vi~~i~~   80 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQ   80 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHT
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc--CCcEEEEeCHHHHHHHHHH
Confidence            5899999999865  37778664  33222  2222 4678999999999999999876  3789999999999999987


Q ss_pred             C---------CC---Cc-----hhhhhhhcCCC----CcccCCCccccch
Q psy3161         101 W---------NN---VP-----NTNKLKSIRPN----IKHWNTSTQDRRI  129 (211)
Q Consensus       101 ~---------~~---~~-----~~~~I~~i~p~----~~W~~~~~~l~R~  129 (211)
                      |         ..   .+     +.+.|.++...    |.|+|.|.+...+
T Consensus        81 w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~N  130 (155)
T 1jl1_A           81 WIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPEN  130 (155)
T ss_dssp             THHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTCHHH
T ss_pred             HHHHHhhcccccccCCccCCHHHHHHHHHHHccCceEEEEcCCCCCCHHH
Confidence            2         11   12     33444444332    5999998654433

>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=99.35  E-value=1.1e-12  Score=100.24  Aligned_cols=96  Identities=10%  Similarity=0.128  Sum_probs=69.3

Q ss_pred             ceEEEecCCCCCC--ceeEEEEe--CC---eeeee-ecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHH
Q psy3161          27 HTICYTDGSKSPD--ATGCAFSI--GD---MVRST-SLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAAL   98 (211)
Q Consensus        27 ~~~IyTDgS~~~~--~~G~ai~~--~~---~~~~~-~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al   98 (211)
                      .+.||||||+..+  ..|+|++.  .+   ....+ ...+.++++.||+.|++.||+++.+.+..++.|+|||+.+++.+
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~i   82 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQM   82 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCCCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHHH
Confidence            4899999999865  47777653  32   11122 12247899999999999999999987788999999999999999


Q ss_pred             hcCC-C-Cc-h---hhhhhhcCC---C--CcccCC
Q psy3161          99 ANWN-N-VP-N---TNKLKSIRP---N--IKHWNT  122 (211)
Q Consensus        99 ~~~~-~-~~-~---~~~I~~i~p---~--~~W~~~  122 (211)
                      .+.. . ++ +   ...|+++..   .  |.|+|.
T Consensus        83 ~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~  117 (141)
T 3hst_B           83 SGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR  117 (141)
T ss_dssp             TTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG
T ss_pred             hCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC
Confidence            8854 3 43 2   334444432   2  488875

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

Probab=99.34  E-value=1.3e-12  Score=102.97  Aligned_cols=101  Identities=19%  Similarity=0.266  Sum_probs=70.1

Q ss_pred             CceEEEecCCCCCC--ceeEEEEe--CCeee--eeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHh
Q psy3161          26 NHTICYTDGSKSPD--ATGCAFSI--GDMVR--STSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALA   99 (211)
Q Consensus        26 ~~~~IyTDgS~~~~--~~G~ai~~--~~~~~--~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~   99 (211)
                      ..+.||||||+.++  ..|+|++.  ++...  ...+ +..+++.||+.|++.||+.+.+  ..++.|+|||+++++.|.
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~   81 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKE--PCKIILTSDSQYMRQGIM   81 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEECCHHHHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhcc--CCeEEEEeCHHHHHHHHH
Confidence            35899999999855  46788664  33222  2222 4688999999999999999865  389999999999999998


Q ss_pred             cC--------C-C---Cc-----hhhhhhhcCC----CCcccCCCccccch
Q psy3161         100 NW--------N-N---VP-----NTNKLKSIRP----NIKHWNTSTQDRRI  129 (211)
Q Consensus       100 ~~--------~-~---~~-----~~~~I~~i~p----~~~W~~~~~~l~R~  129 (211)
                      +|        . .   .+     +.+.|.++..    .|.|+|.|.+...+
T Consensus        82 ~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~N  132 (158)
T 2e4l_A           82 TWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQLHQIDWRWVKGHAGHAEN  132 (158)
T ss_dssp             THHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTTSEEEEEECCTTCCCHHH
T ss_pred             HHHHHHHHccccccCCCcccCHHHHHHHHHHHccCcEEEEEccCCCCchhH
Confidence            82        1 1   12     2334444432    25899998654433

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

Probab=99.33  E-value=1.7e-12  Score=98.71  Aligned_cols=96  Identities=21%  Similarity=0.225  Sum_probs=68.3

Q ss_pred             ceEEEecCCCCCC--ceeEEEEeC--C--eeeee-ecCCCCchhHHHHHHHHHHHHHHHcCCCC----cEEEEeCcHHHH
Q psy3161          27 HTICYTDGSKSPD--ATGCAFSIG--D--MVRST-SLNPINSIFSAELIAIFLCLEAILESPSD----QFLIVSDSRSAI   95 (211)
Q Consensus        27 ~~~IyTDgS~~~~--~~G~ai~~~--~--~~~~~-~l~~~~si~~AEl~AI~~AL~~~~~~~~~----~i~I~SDS~sal   95 (211)
                      .+.||||||+..+  ..|+|++..  +  ....+ ...+.++++.||+.|++.||+++.+.+..    ++.|+|||+.++
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            5899999999865  477886642  2  21121 11235799999999999999999876666    999999999999


Q ss_pred             HHHhcCCC--Cc-h---hhhhhhc----CCC--CcccCC
Q psy3161          96 AALANWNN--VP-N---TNKLKSI----RPN--IKHWNT  122 (211)
Q Consensus        96 ~al~~~~~--~~-~---~~~I~~i----~p~--~~W~~~  122 (211)
                      +.+.++..  ++ +   ...|.++    ++.  |.|+|.
T Consensus        83 ~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~  121 (140)
T 3u3g_D           83 RQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPR  121 (140)
T ss_dssp             HHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCG
T ss_pred             HHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCc
Confidence            99998654  33 2   3344443    233  478774

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

Probab=99.32  E-value=1.2e-12  Score=104.08  Aligned_cols=73  Identities=21%  Similarity=0.137  Sum_probs=56.4

Q ss_pred             CceEEEecCCCCCC--ceeEEEEeC--Ceeeeee-cCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhc
Q psy3161          26 NHTICYTDGSKSPD--ATGCAFSIG--DMVRSTS-LNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALAN  100 (211)
Q Consensus        26 ~~~~IyTDgS~~~~--~~G~ai~~~--~~~~~~~-l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~  100 (211)
                      ..+.||||||+..+  ..|+|++..  +....+. ....++++.||+.|++.||+.+...  .++.|+|||+++++.|.+
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i~~   84 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAFTE   84 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHHHS
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHHhh
Confidence            46899999999865  377887753  2221111 1246889999999999999988653  589999999999999988

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

Probab=99.24  E-value=1.3e-11  Score=95.75  Aligned_cols=97  Identities=15%  Similarity=0.125  Sum_probs=69.0

Q ss_pred             ceEEEecCCCC-C--CceeE-EEEe--CCe-eeeee--cC---CCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHH
Q psy3161          27 HTICYTDGSKS-P--DATGC-AFSI--GDM-VRSTS--LN---PINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSA   94 (211)
Q Consensus        27 ~~~IyTDgS~~-~--~~~G~-ai~~--~~~-~~~~~--l~---~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sa   94 (211)
                      |+.||||||+. .  ++.|+ |++.  .+. ...+.  +.   +..+++.||+.|++.||+.+...+..++.|+|||+.+
T Consensus         1 m~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~v   80 (149)
T 2ehg_A            1 MIIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLV   80 (149)
T ss_dssp             CCEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHH
T ss_pred             CEEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHH
Confidence            57899999987 3  35675 7543  222 22222  22   3789999999999999999988777899999999999


Q ss_pred             HHHHhcCCC--Cc----hhhhhhhcC----CCCcccCCC
Q psy3161          95 IAALANWNN--VP----NTNKLKSIR----PNIKHWNTS  123 (211)
Q Consensus        95 l~al~~~~~--~~----~~~~I~~i~----p~~~W~~~~  123 (211)
                      ++.+.++..  ++    +.+.|+++.    -.|.|+|.+
T Consensus        81 i~~i~~~w~~~~~~~~~l~~~i~~l~~~~~v~~~~V~~~  119 (149)
T 2ehg_A           81 IKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPRE  119 (149)
T ss_dssp             HHHHTTSSCCCCTTHHHHHHHHHHHHHHHTCEEEECCGG
T ss_pred             HHHHhCccccCCHHHHHHHHHHHHHHhcCCEEEEEcCCc
Confidence            999998754  22    333444332    235888875

>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=99.21  E-value=3.1e-11  Score=95.95  Aligned_cols=96  Identities=23%  Similarity=0.198  Sum_probs=66.7

Q ss_pred             ceEEEecCCCCC--CceeEEEE--eCCeee-eeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhcC
Q psy3161          27 HTICYTDGSKSP--DATGCAFS--IGDMVR-STSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANW  101 (211)
Q Consensus        27 ~~~IyTDgS~~~--~~~G~ai~--~~~~~~-~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~~  101 (211)
                      .+.||||||+..  +..|+|++  .++... ...++..++++.||+.|++.||+++   ...++.|+|||+++++.|...
T Consensus        23 ~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~iw~~   99 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATAHVH   99 (165)
T ss_dssp             SEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHHHSC
T ss_pred             CEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhhhcc
Confidence            489999999984  44666643  333322 2245678899999999999999998   268999999999999999432


Q ss_pred             CC-Cch--hhhhhhc----C--C--CCcccCCCcc
Q psy3161         102 NN-VPN--TNKLKSI----R--P--NIKHWNTSTQ  125 (211)
Q Consensus       102 ~~-~~~--~~~I~~i----~--p--~~~W~~~~~~  125 (211)
                      .. .++  ...++++    .  .  .|.|++.|.+
T Consensus       100 ~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g  134 (165)
T 3p1g_A          100 SEGREIKNKNEILALLKALFLPKRLSIIHCPGHQK  134 (165)
T ss_dssp             CCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCC
T ss_pred             cCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCC
Confidence            22 332  1223322    1  1  2699999865

>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=99.18  E-value=2e-11  Score=93.83  Aligned_cols=77  Identities=18%  Similarity=0.073  Sum_probs=57.4

Q ss_pred             CCceEEEecCCCCCC--ceeEE-EEeC-Ce-eeeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHh
Q psy3161          25 ANHTICYTDGSKSPD--ATGCA-FSIG-DM-VRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALA   99 (211)
Q Consensus        25 ~~~~~IyTDgS~~~~--~~G~a-i~~~-~~-~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~   99 (211)
                      ++...||||||+..+  ..|+| |+.. +. .....-...++++.||+.|++.||+.+.+.+.. +.|+|||+.+++.|.
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi~   81 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWVK   81 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEEEEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHHH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCCCCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHHH
Confidence            567889999999866  37774 4432 21 111111237899999999999999999875444 899999999999998


Q ss_pred             cCC
Q psy3161         100 NWN  102 (211)
Q Consensus       100 ~~~  102 (211)
                      ++.
T Consensus        82 ~~~   84 (134)
T 4htu_A           82 DKK   84 (134)
T ss_dssp             HTC
T ss_pred             cCC
Confidence            754

>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=99.15  E-value=3.6e-11  Score=93.41  Aligned_cols=77  Identities=19%  Similarity=0.033  Sum_probs=60.1

Q ss_pred             CCceEEEecCCCCCC--ceeEEEEeC--Ceeeeeec-CCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHh
Q psy3161          25 ANHTICYTDGSKSPD--ATGCAFSIG--DMVRSTSL-NPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALA   99 (211)
Q Consensus        25 ~~~~~IyTDgS~~~~--~~G~ai~~~--~~~~~~~l-~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~   99 (211)
                      ...+.||||||+..+  ..|+|++..  +....... ...+|++.||+.|++.||+.+.+... ++.|+|||+.+++.+.
T Consensus         9 ~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~~   87 (142)
T 1zbf_A            9 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWVK   87 (142)
T ss_dssp             CCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHHH
T ss_pred             CCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccCCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHHH
Confidence            457899999999865  478887753  22221211 13678999999999999999998666 8999999999999998


Q ss_pred             cCC
Q psy3161         100 NWN  102 (211)
Q Consensus       100 ~~~  102 (211)
                      +..
T Consensus        88 ~~~   90 (142)
T 1zbf_A           88 DKK   90 (142)
T ss_dssp             HTC
T ss_pred             cCC
Confidence            866

>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=99.15  E-value=5.4e-11  Score=110.58  Aligned_cols=98  Identities=16%  Similarity=0.211  Sum_probs=70.7

Q ss_pred             CCceEEEecCCCCCCc--eeEEEEeC-CeeeeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhcC
Q psy3161          25 ANHTICYTDGSKSPDA--TGCAFSIG-DMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANW  101 (211)
Q Consensus        25 ~~~~~IyTDgS~~~~~--~G~ai~~~-~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~~  101 (211)
                      .+.+.||||||+..++  .|+|++.. +....+.+ ..+|++.||+.|++.||+.+    ..++.|+|||+.+++.|.++
T Consensus       437 ~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~~  511 (557)
T 2zd1_A          437 VGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQ  511 (557)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTTC
T ss_pred             CCCEEEEEccCCCCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhcC
Confidence            4568999999987553  67776643 32223333 57899999999999999998    57899999999999999998


Q ss_pred             CC---Cchhhhhh-hc--CC--CCcccCCCcccc
Q psy3161         102 NN---VPNTNKLK-SI--RP--NIKHWNTSTQDR  127 (211)
Q Consensus       102 ~~---~~~~~~I~-~i--~p--~~~W~~~~~~l~  127 (211)
                      ..   .++.+.+. .+  ..  .|.|++.|.+..
T Consensus       512 ~~~~~~~l~~~~~~~l~~~~~v~~~wV~~H~g~~  545 (557)
T 2zd1_A          512 PDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIG  545 (557)
T ss_dssp             CSEESSHHHHHHHHHHHHCSEEEEEECCSSSCCT
T ss_pred             CccCCHHHHHHHHHHHhcCCCEEEEEcCCCCCCh
Confidence            76   23444333 22  11  258999886443

>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=99.13  E-value=1e-10  Score=108.72  Aligned_cols=101  Identities=16%  Similarity=0.139  Sum_probs=72.8

Q ss_pred             CCceEEEecCCCCCCc--eeEEEEeC-CeeeeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhcC
Q psy3161          25 ANHTICYTDGSKSPDA--TGCAFSIG-DMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANW  101 (211)
Q Consensus        25 ~~~~~IyTDgS~~~~~--~G~ai~~~-~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~~  101 (211)
                      .+.+.||||||+..++  .|+|++.. +......+ ..++++.||+.|++.||+.    ...++.|+|||+.+++.|.+|
T Consensus       434 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~~  508 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQ  508 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTC
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCCEeeccC-CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhcc
Confidence            4569999999998653  67776642 22222332 4788999999999999998    467999999999999999998


Q ss_pred             CC---Cchhhhhhhc---CC--CCcccCCCccccchh
Q psy3161         102 NN---VPNTNKLKSI---RP--NIKHWNTSTQDRRIK  130 (211)
Q Consensus       102 ~~---~~~~~~I~~i---~p--~~~W~~~~~~l~R~~  130 (211)
                      ..   .++.+.+.++   ..  .|.|++.|.+..-++
T Consensus       509 ~~~~~~~l~~~~~~~~~~~~~v~~~wV~~H~g~~~Ne  545 (555)
T 1mu2_A          509 PTESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQ  545 (555)
T ss_dssp             CSEESCHHHHHHHHHHHHCSEEEEEECCSSSCCTTHH
T ss_pred             cccccHHHHHHHHHHhccCCcEEEEEEECCCCChhHH
Confidence            75   3454444333   11  259999986554443

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

Probab=99.10  E-value=1.6e-10  Score=91.77  Aligned_cols=74  Identities=19%  Similarity=0.232  Sum_probs=55.1

Q ss_pred             CceEEEecCCCCCC--c-----eeEEEEeC--C----eeeeeec-CCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCc
Q psy3161          26 NHTICYTDGSKSPD--A-----TGCAFSIG--D----MVRSTSL-NPINSIFSAELIAIFLCLEAILESPSDQFLIVSDS   91 (211)
Q Consensus        26 ~~~~IyTDgS~~~~--~-----~G~ai~~~--~----~~~~~~l-~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS   91 (211)
                      ..+.||||||+..+  +     .|+|++..  +    ....+.. ....+...||+.|+..||+.+.+. ..++.|+|||
T Consensus         6 ~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~-~~~v~I~TDS   84 (165)
T 2lsn_A            6 YEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKI-PGPVLVITDS   84 (165)
T ss_dssp             CSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHS-SSCEEEEESC
T ss_pred             ceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcC-CCeEEEEeCh
Confidence            35789999999855  2     68887741  1    1223333 356677889999999999887764 3579999999


Q ss_pred             HHHHHHHhc
Q psy3161          92 RSAIAALAN  100 (211)
Q Consensus        92 ~sal~al~~  100 (211)
                      +++++.|..
T Consensus        85 ~Yvi~~it~   93 (165)
T 2lsn_A           85 FYVAESANK   93 (165)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHhhhhh
Confidence            999999975

>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=93.95  E-value=0.0088  Score=53.68  Aligned_cols=71  Identities=10%  Similarity=-0.093  Sum_probs=46.3

Q ss_pred             ceEEEecCCCCCCceeEEEEeCC-----ee---eeeec---CCCCchhHHHHHHHHHHHHHHHcC-CCCcEEEEeCcHHH
Q psy3161          27 HTICYTDGSKSPDATGCAFSIGD-----MV---RSTSL---NPINSIFSAELIAIFLCLEAILES-PSDQFLIVSDSRSA   94 (211)
Q Consensus        27 ~~~IyTDgS~~~~~~G~ai~~~~-----~~---~~~~l---~~~~si~~AEl~AI~~AL~~~~~~-~~~~i~I~SDS~sa   94 (211)
                      .+.+|||+|..  +.|+ ++...     ..   .+-++   ....++++.|++||..|++..... ...++.|+||+. +
T Consensus       346 ~~~l~~DAS~~--~~ga-vL~q~~~~~~~~i~y~Sk~l~~~e~~ys~~ekEllAi~~a~~~~~~yl~g~~~~v~tDh~-~  421 (455)
T 1rw3_A          346 PFELFVDEKQG--YAKG-VLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVIKAPHA-V  421 (455)
T ss_dssp             TTSCEEEEEEC--SSSB-EECCBCTTTTCCCCCCCBCSCSSCSSSCCSSHHHHHHHHHHHHHHGGGCSSCEEEECSSC-T
T ss_pred             cEEEEEeccCC--ccee-EEEEecCCcEEEEEEEcccCCccccccchHHHHHHHHHHHHHHHHHHcCCCcEEEEecCh-H
Confidence            46899999853  3332 33211     11   11122   246788999999999999987653 467899999996 5


Q ss_pred             HHHHhcC
Q psy3161          95 IAALANW  101 (211)
Q Consensus        95 l~al~~~  101 (211)
                      +.-+.+.
T Consensus       422 ~~~l~~~  428 (455)
T 1rw3_A          422 EALVKQP  428 (455)
T ss_dssp             TTTSSST
T ss_pred             HHHhCCC
Confidence            5555443

---

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	211
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.56
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.52
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.29
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.17
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.08

>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=99.56  E-value=3.5e-15  Score=109.51  Aligned_cols=95  Identities=17%  Similarity=0.254  Sum_probs=66.4

Q ss_pred             cCCceEEEecCCCCCC--ceeEEEEeCC-eeeeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhc
Q psy3161          24 YANHTICYTDGSKSPD--ATGCAFSIGD-MVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALAN  100 (211)
Q Consensus        24 ~~~~~~IyTDgS~~~~--~~G~ai~~~~-~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~  100 (211)
                      .++...+|||||+..+  ..|+|++..+ ......+ ...|+..||+.||++||+.    ...++.|+|||+++++++.+
T Consensus         5 i~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~-~~~TNn~aEl~Avi~aL~~----~~~~v~I~TDS~yvi~~i~~   79 (110)
T d1s1ta1           5 IVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQD----SGLEVNIVTDSQYALGIIQA   79 (110)
T ss_dssp             CTTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHH----SCSEEEEEECCHHHHHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEec-ccCcHHHHHHHHHHHHHHh----CCCeEEEEEehHHHHHHHhc
Confidence            3556789999997755  3556666543 2333333 4679999999999999985    34679999999999999999


Q ss_pred             CCC---Cchhhh-hhhc--CCC--CcccCCC
Q psy3161         101 WNN---VPNTNK-LKSI--RPN--IKHWNTS  123 (211)
Q Consensus       101 ~~~---~~~~~~-I~~i--~p~--~~W~~~~  123 (211)
                      +..   .++..+ ++.+  ...  +.|+|.|
T Consensus        80 ~~~~~~~~l~~~il~~l~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          80 QPDQSESELVNQIIEQLIKKEKVYLAWVPAH  110 (110)
T ss_dssp             CCSEESCHHHHHHHHHHHHCSEEEEEECCSS
T ss_pred             CccccchHHHHHHHHHHhcCCceEEEEeCCC
Confidence            877   334333 3333  222  4888876

>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=99.52  E-value=1.7e-14  Score=107.65  Aligned_cols=101  Identities=14%  Similarity=0.082  Sum_probs=70.8

Q ss_pred             CCceEEEecCCCCCC--ceeEEEEeCCeeeeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhcCC
Q psy3161          25 ANHTICYTDGSKSPD--ATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANWN  102 (211)
Q Consensus        25 ~~~~~IyTDgS~~~~--~~G~ai~~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~~~  102 (211)
                      ++...||||||+..+  ..|+|++.......+...+..|++.||+.||++||+.    ...++.|+|||++++..+.++.
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v~~~~~~~~   80 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQP   80 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEESSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTCC
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecCCCcchHHHHHHHHHHhcc----CCcceEEEechHHHHHHHhcCC
Confidence            456789999997754  3556666543322222234679999999999999985    4578999999999999999977


Q ss_pred             C---Cc-hhhhhhhcCC----CCcccCCCccccch
Q psy3161         103 N---VP-NTNKLKSIRP----NIKHWNTSTQDRRI  129 (211)
Q Consensus       103 ~---~~-~~~~I~~i~p----~~~W~~~~~~l~R~  129 (211)
                      .   +. ..+.++.+..    .|.|+|.|.+..-+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~v~~~wV~gH~g~~gN  115 (126)
T d1mu2a1          81 TESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGN  115 (126)
T ss_dssp             SEESCHHHHHHHHHHHHCSEEEEEECCSSSCCTTH
T ss_pred             ccccchHHHHHHHHhhhcceeEEEEEeCCCCCcch
Confidence            6   22 3344444422    25999999765433

>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=99.29  E-value=1.7e-12  Score=97.60  Aligned_cols=74  Identities=19%  Similarity=0.047  Sum_probs=56.9

Q ss_pred             EEEecCCCCCC--ceeEEEEeC--Ceeeeee-cCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhcCCC
Q psy3161          29 ICYTDGSKSPD--ATGCAFSIG--DMVRSTS-LNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANWNN  103 (211)
Q Consensus        29 ~IyTDgS~~~~--~~G~ai~~~--~~~~~~~-l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~~~~  103 (211)
                      .||||||+.++  .+|.|+|..  +....++ .-+..|+..||+.|++.||+.+.+.+ .++.|+|||+.++..+.++..
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~~   84 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKKA   84 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTCC
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCce
Confidence            48999999976  377776653  2222222 12578899999999999999998754 578999999999999988663

>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=99.17  E-value=8.9e-12  Score=94.59  Aligned_cols=74  Identities=19%  Similarity=0.095  Sum_probs=55.1

Q ss_pred             CceEEEecCCCCCC--ceeEEEEe--CC-eeeeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhc
Q psy3161          26 NHTICYTDGSKSPD--ATGCAFSI--GD-MVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALAN  100 (211)
Q Consensus        26 ~~~~IyTDgS~~~~--~~G~ai~~--~~-~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~  100 (211)
                      ..+.||||||+.++  ..|+|++.  .+ ........+..|+..||+.||++||+++..  ...+.|+|||+.+++.+..
T Consensus         2 ~~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~--~~~i~i~tds~~~~~~~~~   79 (147)
T d1rila_           2 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYLKKAFTE   79 (147)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHHHHHHHS
T ss_pred             CEEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhccC--CceEEEecchhhhhccccc
Confidence            35899999999876  36777654  22 222222234578999999999999997653  5679999999999998866


Q ss_pred             C
Q psy3161         101 W  101 (211)
Q Consensus       101 ~  101 (211)
                      +
T Consensus        80 ~   80 (147)
T d1rila_          80 G   80 (147)
T ss_dssp             S
T ss_pred             c
Confidence            3

>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=99.08  E-value=5.6e-11  Score=90.00  Aligned_cols=101  Identities=17%  Similarity=0.191  Sum_probs=68.9

Q ss_pred             ceEEEecCCCCCC--ceeEEEE--eCCeeeeeec-CCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhcC
Q psy3161          27 HTICYTDGSKSPD--ATGCAFS--IGDMVRSTSL-NPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANW  101 (211)
Q Consensus        27 ~~~IyTDgS~~~~--~~G~ai~--~~~~~~~~~l-~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~~  101 (211)
                      .|.||||||+.++  .+|+|++  ..+....+.. .+..+++.||+.||+.||+++..  ...+.|+|||+.++..+..+
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~~--~~~i~i~tds~~~i~~~~~~   79 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQW   79 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHTT
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhcc--cceEEEeecceeeEEcccch
Confidence            4899999998866  3777765  3443333322 35678999999999999998654  56789999999999888654


Q ss_pred             CC------------Cc-----hhhhhhhcCCC----CcccCCCccccch
Q psy3161         102 NN------------VP-----NTNKLKSIRPN----IKHWNTSTQDRRI  129 (211)
Q Consensus       102 ~~------------~~-----~~~~I~~i~p~----~~W~~~~~~l~R~  129 (211)
                      ..            .+     ....|.++...    |+|+|+|.+...+
T Consensus        80 ~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~~~~V~~~wV~gH~g~~gN  128 (152)
T d1jl1a_          80 IHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPEN  128 (152)
T ss_dssp             HHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTCHHH
T ss_pred             hhHhHhccchhcccCeeecHHHHHHHHHHhhcceeEEEEecccCCCccH
Confidence            31            11     12333343332    6999999655433