Psyllid ID: psy2213

---

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----
Protein Sequence
MNSLPKEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRASLPTPPALTDD
Secondary Structure (PSIPRED)
ccccccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccEEEEEEEEEccccccccccccccccccccccccccHHHHccccccHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccEEEEEccHHHHHHHcccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHcccccccccccHcHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHccccHHHHHHcccccccccccccccccHEEEccHHHHHHHHHHccccccccc
Coil and Loop (DISEMBL)
mnslpkekFVIISDSKSTLlalsnpsntnpiVSLIHSCWsdllccgkqlaflwcpshtgiqgneavdraarnpsaslpplklcspedfKPFIRKLIKDLWQQswssipnsnklksikpiigpwpssdrqnrYEEVVICRMRightrathghlfkrappstcgcgeilsVQHILTCALHghiraslptppaltdd
Flexible Loop (DISEMBL)
MNSLPKEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSaslpplklcspEDFKPFIRKLIKDLWQQSwssipnsnklksikpiigpwpssdrqnRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGhiraslptppaltdd
Low Complexity Region (SEG)
MNSLPKEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRASLPTPPALTDD
Disordered region (IsUnstruct)
*********VII******LLAL****NTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQG******************KLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPS*DRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRA***********
Disordered Region (DISOPRED)
*****KEKFVIISDSKSTLLALSNP****PIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRA***********
Disordered Region (DISEMBL)
MNSLPKEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRASLPTPPALTDD
Disordered Region (DISPRO)
****PKEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRASLPT*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MNSLPKEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRASLPTPPALTDD
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

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	194
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.855	0.636	0.429	2e-27
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.855	0.330	0.423	3e-27
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.855	0.418	0.411	9e-26
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.907	0.373	0.394	4e-25
443724607	397	hypothetical protein CAPTEDRAFT_208903 [	0.855	0.418	0.4	4e-23
443682433	619	hypothetical protein CAPTEDRAFT_222606 [	0.814	0.255	0.407	4e-22
443733872	400	hypothetical protein CAPTEDRAFT_197082 [	0.654	0.317	0.418	4e-22
443694523	364	hypothetical protein CAPTEDRAFT_227708 [	0.762	0.406	0.430	2e-20
443694031	574	hypothetical protein CAPTEDRAFT_227918 [	0.556	0.188	0.431	3e-19
427798889	1199	Putative tick transposon, partial [Rhipi	0.881	0.142	0.340	1e-18

>gi|443695973|gb|ELT96755.1| hypothetical protein CAPTEDRAFT_23017, partial [Capitella teleta]

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 73/170 (42%), Positives = 101/170 (59%), Gaps = 4/170 (2%)

Query: 6   KEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEA 65
           +++F I SDS S+L ALSN   T+P +  I +  ++L+  GK + F+WCPSH GI GNE 
Sbjct: 91  EDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEV 150

Query: 66  VDRAARNPSASLPPLKLCSPE-DFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWP 124
            DR A+  +  +P  KL  P  D+K  IR  +K LWQ  W      NKL SI+P+I  W 
Sbjct: 151 ADRLAKQ-ALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDE-ETDNKLHSIQPVISEWK 208

Query: 125 SSDRQNRYEEVVICRMRIGHTRATHGHLFKR-APPSTCGCGEILSVQHIL 173
              + +R  E+V+ R RIGH+  THG+L +R   P    C  +LSV+HIL
Sbjct: 209 QGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLSVKHIL 258

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443693558|gb|ELT94903.1| hypothetical protein CAPTEDRAFT_189741, partial [Capitella teleta]

 Score =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 72/170 (42%), Positives = 101/170 (59%), Gaps = 4/170 (2%)

Query: 6   KEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEA 65
           +++F I SDS S+L ALSN   T+P +  I +  ++L+  GK + F+WCPSH GI GNE 
Sbjct: 137 EDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEV 196

Query: 66  VDRAARNPSASLPPLKLCSPE-DFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWP 124
            DR A+  +  +P  KL  P  D+K  IR  +K LWQ  W      NKL SI+P+I  W 
Sbjct: 197 ADRLAKQ-ALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDE-ETDNKLHSIQPVISEWK 254

Query: 125 SSDRQNRYEEVVICRMRIGHTRATHGHLFKR-APPSTCGCGEILSVQHIL 173
              + +R  E+V+ R RIGH+  THG+L +R   P    C  +L+V+HIL
Sbjct: 255 QGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHIL 304

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  122 bits (305), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 70/170 (41%), Positives = 100/170 (58%), Gaps = 4/170 (2%)

Query: 6   KEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEA 65
           +++F I SDS S+L ALSN   T+P +  I +  ++L+  GK++ F+WCPSH GI GNE 
Sbjct: 186 EDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKKVVFIWCPSHVGILGNEV 245

Query: 66  VDRAARNPSASLPPLKLCSPE-DFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWP 124
            DR A+  +  +P  KL  P  D+K  IR  +K LWQ  W      NKL  I+P+I  W 
Sbjct: 246 ADRQAKQ-ALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDG-ETDNKLHIIQPVISEWK 303

Query: 125 SSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCG-CGEILSVQHIL 173
              + +R  E+V+   RIGH+  THG+L +R     C  C  +L+V+HIL
Sbjct: 304 QGPQIDRRGEIVLACARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHIL 353

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443721618|gb|ELU10867.1| hypothetical protein CAPTEDRAFT_200496, partial [Capitella teleta]

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 71/180 (39%), Positives = 98/180 (54%), Gaps = 4/180 (2%)

Query: 6   KEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEA 65
           + +FVI SDS S ++A+      +P V  +      +    K + F+WCPSH GI GNE 
Sbjct: 76  QHQFVICSDSLSAIMAIHGMDVRHPYVLQVLYAIKSISQQEKIVVFMWCPSHVGIPGNEM 135

Query: 66  VDRAARNPSASLPPLKLCSP-EDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWP 124
            D  A+   +S    +L  P  D +  I+K I+  WQ  W    +SNKL SI P IGPWP
Sbjct: 136 ADTLAKEALSSTNLAELPVPASDLRCLIKKYIRSRWQHEWDE-QHSNKLHSIHPTIGPWP 194

Query: 125 SSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTC-GCGEILSVQH-ILTCALHGHIR 182
              R+ R EE+V+ R+RIGHT  TH ++ +    + C  C   L+VQH I+ CA   HIR
Sbjct: 195 PCQREKRREEIVLARIRIGHTHYTHDYIPRGDDQTECVACVCPLTVQHIIIECADFLHIR 254

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443724607|gb|ELU12531.1| hypothetical protein CAPTEDRAFT_208903 [Capitella teleta]

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 68/170 (40%), Positives = 98/170 (57%), Gaps = 4/170 (2%)

Query: 6   KEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEA 65
           +++F I SDS S+L ALSN   T+P +  I +  ++L+  GK + F+WCPSH GI GNE 
Sbjct: 186 EDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEV 245

Query: 66  VDRAARNPSASLPPLKLCSPE-DFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWP 124
            DR A+  +  +P  KL  P  D+K  IR  +K L Q  W      NKL +I+P+I  W 
Sbjct: 246 ADRLAKQ-ALVMPVTKLPLPHTDYKSPIRSYVKSLRQNEWDE-ETDNKLHTIQPVISEWK 303

Query: 125 SSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCG-CGEILSVQHIL 173
              + +R  E+V+    IGH+  THG+L +R     C  C  +L+V+HIL
Sbjct: 304 QGPQIDRRGEIVLACACIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHIL 353

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443682433|gb|ELT87030.1| hypothetical protein CAPTEDRAFT_222606 [Capitella teleta]

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 66/162 (40%), Positives = 89/162 (54%), Gaps = 4/162 (2%)

Query: 4   LPKEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGN 63
           LP ++FVI +DS S++LA+S+    +  V  I    ++L    K++ F+WCPSH GI GN
Sbjct: 49  LPYDEFVICTDSFSSILAISSIDLIHSYVQSILQKCTNLAGRDKRIIFIWCPSHVGIPGN 108

Query: 64  EAVDRAARNPSASLPPLKLCSPE-DFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGP 122
           E  D  A+  S  +  L    P  DFKP  R  ++  W QS S     NKL  I+P IG 
Sbjct: 109 ETADTLAQQASG-MNILNCPIPHTDFKPITRSFVETQW-QSESDQETGNKLHDIEPDIGS 166

Query: 123 WPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTC-GC 163
           WP   R+ R +E+VI R+RIGHT  T+ HL        C GC
Sbjct: 167 WPPCQREKRRDEIVIARLRIGHTFLTYSHLLSGNDAPMCYGC 208

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443733872|gb|ELU18078.1| hypothetical protein CAPTEDRAFT_197082 [Capitella teleta]

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 54/129 (41%), Positives = 70/129 (54%), Gaps = 2/129 (1%)

Query: 46  GKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDLWQQSWS 105
           G  L   WCPSH G+ GNE  D  A+   +           DFKP   +  K+ WQ+ WS
Sbjct: 98  GIDLVMTWCPSHVGVMGNERADLLAKEALSFTTCTIRIPSSDFKPITHEFYKEKWQEQWS 157

Query: 106 SIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCG-CG 164
           S    NKL  I+P +G W  S R+ R EE+V+ R RIGH+  THG+L +R  P  C  C 
Sbjct: 158 S-EQENKLYCIQPTLGKWAKSSREIRREEIVLARARIGHSHLTHGYLLRREMPPVCIPCQ 216

Query: 165 EILSVQHIL 173
            ILS++HI 
Sbjct: 217 NILSIKHIF 225

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443694523|gb|ELT95634.1| hypothetical protein CAPTEDRAFT_227708 [Capitella teleta]

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 65/151 (43%), Positives = 85/151 (56%), Gaps = 3/151 (1%)

Query: 4   LPKEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGN 63
           LP ++FVI +DS S++LA+S+    +P V  I    + L    K++ F+WCPSH GI GN
Sbjct: 21  LPYDEFVICTDSLSSILAISSIDLIHPYVQSILQKCTCLAGRDKRIIFIWCPSHVGIPGN 80

Query: 64  EAVDRAARNPSASLPPLKLCSPE-DFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGP 122
           E  D  A+  +  +  L    P  DFKP  R  +K  WQ  W      NKL  I+P IG 
Sbjct: 81  ETADTLAKQ-ALGMNILNCPIPHTDFKPITRSFVKTQWQSEWDQ-ETGNKLHDIQPDIGS 138

Query: 123 WPSSDRQNRYEEVVICRMRIGHTRATHGHLF 153
           WP   R+ R EE+VI R+RIGHT  TH HL 
Sbjct: 139 WPPCQREKRREEIVIARVRIGHTFLTHSHLL 169

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443694031|gb|ELT95266.1| hypothetical protein CAPTEDRAFT_227918 [Capitella teleta]

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/109 (43%), Positives = 61/109 (55%), Gaps = 1/109 (0%)

Query: 53  WCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNK 112
           WCPSH G+ GNE  D  A+   +           DFKP   +  K+ WQ+ WSS    NK
Sbjct: 3   WCPSHVGVMGNERADLLAKEALSFTTCTIRIPSSDFKPITHEFFKEKWQEQWSS-EQENK 61

Query: 113 LKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTC 161
           L SI+P +G W  S R+ R EE+V+ R RIGH+  THG+L +R  P  C
Sbjct: 62  LYSIQPTLGKWAKSSREIRREEIVLARARIGHSHLTHGYLVRREMPPVC 110

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|427798889|gb|JAA64896.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 60/176 (34%), Positives = 89/176 (50%), Gaps = 5/176 (2%)

Query: 1    MNSLPKEKFVIISDSKSTLLALSN-PSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTG 59
            +  L  +K VI +DS S + AL     + NP++  ++S    +    + +   W P H  
Sbjct: 1011 IRELKLQKAVIYTDSLSVVKALKTLKKHRNPVLVSLYSLLCTIYTSKQHVVVCWVPGHRE 1070

Query: 60   IQGNEAVDRAARNPSASLPPLKLCSPE-DFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKP 118
            IQGN   D+ A +   S     +  P  D KP++++ I+  WQ +W      NKL  IKP
Sbjct: 1071 IQGNVMADQLAVSAHDSSANTSIAIPALDLKPYLKRKIRAYWQSTWDR-QTHNKLHVIKP 1129

Query: 119  IIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCG-CGEILSVQHIL 173
             +G WP   + +RY EV + R+R GHT +TH +L        C  CGE L+V HIL
Sbjct: 1130 QLGHWPPISK-SRYTEVTLTRLRTGHTHSTHAYLLSGGDAPFCDKCGEPLTVIHIL 1184

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	194
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.902	0.360	0.257	2.8e-09

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

 Score = 145 (56.1 bits), Expect = 2.8e-09, P = 2.8e-09
 Identities = 49/190 (25%), Positives = 83/190 (43%)

Query:    10 VIISDSKSTLLALSNPSNTNP--IVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVD 67
             VI +D+++TL AL NP + +   I+  I    +     G  + F W P+H G++GNE  D
Sbjct:   245 VIFTDNQATLQALRNPGSQSGQYILEAIIMALNKGRKAGLNVHFRWIPAHRGVEGNEQAD 304

Query:    68 RAARNPSASLPPL----KLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPW 123
             R A+  +          ++      K    +++   W+  W S  +  +L  + P     
Sbjct:   305 RRAKEATGWRRIRGHRGRMTIRSAVKRRAHEVVNARWENDWKSCHHGRELYELTPTPTRK 364

Query:   124 PSSDRQNRYEEV--VICRMRIGHTRATHGHLFKRAPP----STCGCGEIL-SVQHIL-TC 175
                  Q+ +  +  +I +MR G     H +L++R  P    S C CG    SV+HIL  C
Sbjct:   365 VLRVHQDLHRALSTIIVQMRTGKIGLRH-YLYQRGVPDVPNSDCQCGRATQSVRHILLAC 423

Query:   176 ALHGHIRASL 185
                  +R  +
Sbjct:   424 PTFSGLREEI 433


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.320   0.134   0.438    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      194       194   0.00076  111 3  11 22  0.46    32
                                                     31  0.43    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  605 (64 KB)
  Total size of DFA:  186 KB (2106 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  19.55u 0.08s 19.63t   Elapsed:  00:00:08
  Total cpu time:  19.55u 0.08s 19.63t   Elapsed:  00:00:09
  Start:  Thu Aug 15 14:22:11 2013   End:  Thu Aug 15 14:22:20 2013

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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	194
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	1e-18
pfam00075	126	pfam00075, RNase_H, RNase H	6e-11
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	7e-04
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	0.001

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

 Score = 77.3 bits (191), Expect = 1e-18
 Identities = 25/64 (39%), Positives = 38/64 (59%)

Query: 8   KFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVD 67
           K  I SDS++ L AL +P +++P+V  I     +L   G ++   W P H+GI+GNE  D
Sbjct: 61  KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120

Query: 68  RAAR 71
           R A+
Sbjct: 121 RLAK 124

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 = 57.3 bits (139), Expect = 6e-11
 Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 8/72 (11%)

Query: 4   LPKEKFVIISDSKST----LLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTG 59
           L  +K  I +DS+             S + PI + I     +LL    ++   W P H+G
Sbjct: 55  LSGQKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIW----ELLQKKHKVYIQWVPGHSG 110

Query: 60  IQGNEAVDRAAR 71
           I GNE  D+ A+
Sbjct: 111 IPGNELADKLAK 122

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

 Score = 37.9 bits (89), Expect = 7e-04
 Identities = 11/31 (35%), Positives = 13/31 (41%)

Query: 41  DLLCCGKQLAFLWCPSHTGIQGNEAVDRAAR 71
           D L    Q+ + W   H G  GNE  D  A 
Sbjct: 105 DALLAKHQVTWHWVKGHAGHPGNERADELAN 135

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

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 17/84 (20%), Positives = 28/84 (33%), Gaps = 23/84 (27%)

Query: 7   EKFVIISDSK---STLLAL-----------SNPSNTNPIVSLIHSCWSDLLCCGKQLAFL 52
           +   I +DS      L AL             P     ++  +       +   K +A +
Sbjct: 53  KPVNIYTDSAYAFGILHALETIWKERGFLTGKPIALASLILQL----QKAIQRPKPVAVI 108

Query: 53  WCPSHTG-----IQGNEAVDRAAR 71
              +H+G       GN   D+AAR
Sbjct: 109 HIRAHSGLPGPLALGNARADQAAR 132

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	194
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.52
PRK06548	161	ribonuclease H; Provisional	99.52
PRK08719	147	ribonuclease H; Reviewed	99.5
PRK00203	150	rnhA ribonuclease H; Reviewed	99.4
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.31
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.21
KOG3752|consensus	371		98.68
PRK13907	128	rnhA ribonuclease H; Provisional	98.47
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	98.18
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	97.86
PRK07708	219	hypothetical protein; Validated	97.74
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	96.67

>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=99.52  E-value=6.3e-15  Score=108.53  Aligned_cols=65  Identities=37%  Similarity=0.596  Sum_probs=50.9

Q ss_pred             CCeEEEEeCcHHHHHHHhC-----CCCCC----hHHHHHHHHHHHHHhcCCcEEEEeecCCCCC-hhhHHHhHHhcCCC
Q psy2213           6 KEKFVIISDSKSTLLALSN-----PSNTN----PIVSLIHSCWSDLLCCGKQLAFLWCPSHTGI-QGNEAVDRAARNPS   74 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~~-----~~~~~----~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi-~gNe~AD~~Ak~a~   74 (194)
                      ...++|+|||++++..|..     .+...    ++..+|++.   + ..+..|.|.|||||+|+ .|||.||+|||.|+
T Consensus        57 ~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~---~-~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   57 HRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWEL---L-SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             TSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHH---H-HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             cccccccccHHHHHHHHHHhccccccccccccccchhheeec---c-ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence            3789999999999998887     44322    355555533   3 55889999999999999 69999999999875

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=99.52  E-value=2.2e-14  Score=109.74  Aligned_cols=70  Identities=27%  Similarity=0.425  Sum_probs=56.7

Q ss_pred             CCeEEEEeCcHHHHHHHh---------CCCCCC--hHH-HHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCC
Q psy2213           6 KEKFVIISDSKSTLLALS---------NPSNTN--PIV-SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNP   73 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~---------~~~~~~--~~~-~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a   73 (194)
                      ...+.|+|||++++++|.         ++...+  ++. +++++.+..+.. ...|+|.|||||+|++|||.||+||++|
T Consensus        61 ~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~-~~~v~~~wVkgHsg~~gNe~aD~LA~~a  139 (161)
T PRK06548         61 DRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLME-NRNIRMSWVNAHTGHPLNEAADSLARQA  139 (161)
T ss_pred             CceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHh-cCceEEEEEecCCCCHHHHHHHHHHHHH
Confidence            357999999999999999         333332  444 677777777754 4589999999999999999999999998


Q ss_pred             CCC
Q psy2213          74 SAS   76 (194)
Q Consensus        74 ~~~   76 (194)
                      +..
T Consensus       140 a~~  142 (161)
T PRK06548        140 ANN  142 (161)
T ss_pred             HHH
Confidence            865

>PRK08719 ribonuclease H; Reviewed

Probab=99.50  E-value=4.2e-14  Score=106.92  Aligned_cols=66  Identities=26%  Similarity=0.286  Sum_probs=53.7

Q ss_pred             EEEEeCcHHHHHHH--------hCCCCCC---hH-HHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCCC
Q psy2213           9 FVIISDSKSTLLAL--------SNPSNTN---PI-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSA   75 (194)
Q Consensus         9 ~~i~sDs~~al~~l--------~~~~~~~---~~-~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~~   75 (194)
                      ..|+|||++++++|        ++++..+   ++ -.++++.+..+.. ...|+|.|||||+|++|||.||+||+.|++
T Consensus        69 ~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         69 DVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             CEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            47999999999999        4555443   22 1567777777755 678999999999999999999999999875

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.40  E-value=4.3e-13  Score=101.72  Aligned_cols=71  Identities=20%  Similarity=0.278  Sum_probs=54.1

Q ss_pred             CCeEEEEeCcHHHHHHHhC--------CCCC---ChHH-HHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCC
Q psy2213           6 KEKFVIISDSKSTLLALSN--------PSNT---NPIV-SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNP   73 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~~--------~~~~---~~~~-~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a   73 (194)
                      ...+.|+|||++++++|.+        ++..   .++. .++++.+..+. ....|.|.|||||+|++|||.||+||++|
T Consensus        61 ~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~-~~~~v~~~wV~~H~~~~~N~~AD~lA~~a  139 (150)
T PRK00203         61 PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAAL-KRHQIKWHWVKGHAGHPENERCDELARAG  139 (150)
T ss_pred             CCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHh-ccCceEEEEecCCCCCHHHHHHHHHHHHH
Confidence            3579999999999999985        2222   2332 34555555653 34789999999999999999999999998


Q ss_pred             CCCC
Q psy2213          74 SASL   77 (194)
Q Consensus        74 ~~~~   77 (194)
                      +...
T Consensus       140 ~~~~  143 (150)
T PRK00203        140 AEEA  143 (150)
T ss_pred             HHHh
Confidence            7753

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

Probab=99.31  E-value=3.8e-12  Score=96.25  Aligned_cols=73  Identities=21%  Similarity=0.290  Sum_probs=58.0

Q ss_pred             CCCCeEEEEeCcHHHHHHHhCC---CCC--------ChH-HHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhc
Q psy2213           4 LPKEKFVIISDSKSTLLALSNP---SNT--------NPI-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAAR   71 (194)
Q Consensus         4 ~~~~~~~i~sDs~~al~~l~~~---~~~--------~~~-~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak   71 (194)
                      .....+.|+|||+++++.|..+   +..        .|+ ..++++.+.++......|.+.|||||+|.++||.||+||+
T Consensus        61 ~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~  140 (154)
T COG0328          61 LGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAR  140 (154)
T ss_pred             cCCceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHH
Confidence            3567899999999999999822   111        122 3467777788866566999999999999999999999999


Q ss_pred             CCCCC
Q psy2213          72 NPSAS   76 (194)
Q Consensus        72 ~a~~~   76 (194)
                      .++..
T Consensus       141 ~~~~~  145 (154)
T COG0328         141 EAARA  145 (154)
T ss_pred             HHHHh
Confidence            98775

>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=99.21  E-value=7.6e-11  Score=84.29  Aligned_cols=71  Identities=28%  Similarity=0.339  Sum_probs=55.5

Q ss_pred             CCCCeEEEEeCcHHHHHHHhCCCCC-ChHHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCC
Q psy2213           4 LPKEKFVIISDSKSTLLALSNPSNT-NPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPS   74 (194)
Q Consensus         4 ~~~~~~~i~sDs~~al~~l~~~~~~-~~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~   74 (194)
                      .+..++.|++||+.++..+.+.... ......+...+..+...+..+.|.|||+|+|+.+|+.||.+|+.+.
T Consensus        59 ~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          59 LGGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             CCCceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            5678999999999999999987642 2223333334444445688999999999999999999999999863

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=98.68  E-value=2.1e-08  Score=84.80  Aligned_cols=71  Identities=27%  Similarity=0.259  Sum_probs=52.2

Q ss_pred             CCeEEEEeCcHHHHHHHhCCC--------CC---Ch-----H-HHHHHHHHHHHHh--cCCcEEEEeecCCCCChhhHHH
Q psy2213           6 KEKFVIISDSKSTLLALSNPS--------NT---NP-----I-VSLIHSCWSDLLC--CGKQLAFLWCPSHTGIQGNEAV   66 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~~~~--------~~---~~-----~-~~~i~~~~~~l~~--~~~~i~~~Wvp~H~gi~gNe~A   66 (194)
                      ..+++|.|||...++.|+.+.        ..   ++     + .......+.+|..  ++.+|++.|||||.||.|||+|
T Consensus       276 ~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~A  355 (371)
T KOG3752|consen  276 INKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMA  355 (371)
T ss_pred             CCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHH
Confidence            448999999999999998322        11   22     1 1233334445532  3689999999999999999999


Q ss_pred             hHHhcCCCCC
Q psy2213          67 DRAARNPSAS   76 (194)
Q Consensus        67 D~~Ak~a~~~   76 (194)
                      |.+|++++..
T Consensus       356 d~lARkgs~~  365 (371)
T KOG3752|consen  356 DALARKGSTL  365 (371)
T ss_pred             HHHHhhhhhh
Confidence            9999998654

>PRK13907 rnhA ribonuclease H; Provisional

Probab=98.47  E-value=3.6e-07  Score=67.10  Aligned_cols=66  Identities=17%  Similarity=0.134  Sum_probs=50.4

Q ss_pred             CCeEEEEeCcHHHHHHHhCCCCCChHHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCCC
Q psy2213           6 KEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSA   75 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~~~~~~~~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~~   75 (194)
                      ..++.|++||+.+++.+++.+....-...+++.+..+...-..+.|.|||.+    +|+.||.+|+.|..
T Consensus        61 ~~~v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~----~N~~Ad~LA~~a~~  126 (128)
T PRK13907         61 YNIVSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSS----QNKVADELARKAIL  126 (128)
T ss_pred             CCEEEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCch----hchhHHHHHHHHHh
Confidence            4579999999999999998664433344555555556555667788999995    99999999998753

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

Probab=98.18  E-value=2.9e-06  Score=57.32  Aligned_cols=67  Identities=19%  Similarity=0.136  Sum_probs=46.6

Q ss_pred             CCCCeEEEEeCcHHHHHHHhCCCCCChHHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCC
Q psy2213           4 LPKEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPS   74 (194)
Q Consensus         4 ~~~~~~~i~sDs~~al~~l~~~~~~~~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~   74 (194)
                      +..+++.|.|||+.++..|++..........+...+..+......+.|.|||.-    +|..||.+||.|.
T Consensus        19 ~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~----~N~~A~~LA~~a~   85 (87)
T PF13456_consen   19 LGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPRE----QNKVADALAKFAL   85 (87)
T ss_dssp             CT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GG----GSHHHHHHHHHHH
T ss_pred             CCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChH----HhHHHHHHHHHHh
Confidence            456799999999999999998754422333444445566566788999999975    8999999998764

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=97.86  E-value=4.5e-05  Score=65.85  Aligned_cols=68  Identities=18%  Similarity=0.223  Sum_probs=51.9

Q ss_pred             CCCeEEEEeCcHHHHHHHhCCCCC-ChHHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCCCC
Q psy2213           5 PKEKFVIISDSKSTLLALSNPSNT-NPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS   76 (194)
Q Consensus         5 ~~~~~~i~sDs~~al~~l~~~~~~-~~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~~~   76 (194)
                      ..+++.|++||+.+++.+.+.+.. ++-...+.+.+..+...-..+.|.|||.    .+|+.||.+|+.|...
T Consensus        64 g~~~v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~  132 (372)
T PRK07238         64 GATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA  132 (372)
T ss_pred             CCCeEEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence            456899999999999999976643 3333344445556656667899999998    5899999999987654

>PRK07708 hypothetical protein; Validated

Probab=97.74  E-value=9e-05  Score=59.61  Aligned_cols=67  Identities=13%  Similarity=0.019  Sum_probs=48.9

Q ss_pred             CeEEEEeCcHHHHHHHhCCCCC-ChHHHHHHHHHHHHHh-cCCcEEEEeecCCCCChhhHHHhHHhcCCCCCC
Q psy2213           7 EKFVIISDSKSTLLALSNPSNT-NPIVSLIHSCWSDLLC-CGKQLAFLWCPSHTGIQGNEAVDRAARNPSASL   77 (194)
Q Consensus         7 ~~~~i~sDs~~al~~l~~~~~~-~~~~~~i~~~~~~l~~-~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~~~~   77 (194)
                      ..+.|++||+.+++.+.+.+.. ++....+.+.+..+.. -...+.|.|||..    .|+.||+||+.|....
T Consensus       141 ~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~----~N~~AD~LAk~Al~~~  209 (219)
T PRK07708        141 EPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRK----QNKEADQLATQALEGT  209 (219)
T ss_pred             ceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCch----hhhHHHHHHHHHHhcC
Confidence            4589999999999999987644 4444444444444422 2445788999875    6999999999998863

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

Probab=96.67  E-value=0.0011  Score=45.36  Aligned_cols=30  Identities=17%  Similarity=0.362  Sum_probs=25.3

Q ss_pred             ccccCCCCCCCc-ccCC-CCccceeee-cccch
Q psy2213         150 GHLFKRAPPSTC-GCGE-ILSVQHILT-CALHG  179 (194)
Q Consensus       150 ~~~~~~~~~p~C-~Cg~-~et~~H~l~-Cp~~~  179 (194)
                      +.+.+...++.| .|+. .||++|+|+ ||...
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            445667888999 9998 899999999 99764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	194
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	1e-04

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

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 8/75 (10%)

Query: 4   LPKEKFVIISDSKSTLLALSNPSNTNPI--VSLIHSCWSDLLCCGKQLAFLWCPSHTG-- 59
              +K  + +DS+         S    I   + I +     L   K+L+ + CP H    
Sbjct: 78  AEGKKLNVYTDSRYAFATAHVHSEGREIKNKNEILAL-LKALFLPKRLSIIHCPGHQKGN 136

Query: 60  ---IQGNEAVDRAAR 71
               +GN   D+AAR
Sbjct: 137 SAEARGNRMADQAAR 151

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	194
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.58
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.51
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.49
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.47
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.46
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.43
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.4
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.37
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.36
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.27
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.2
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.06
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.06
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	98.93
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	94.86

>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=99.58  E-value=3.1e-15  Score=112.44  Aligned_cols=71  Identities=24%  Similarity=0.335  Sum_probs=52.4

Q ss_pred             CCeEEEEeCcHHHHHHHhCC--------CCC---ChHH-HHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCC
Q psy2213           6 KEKFVIISDSKSTLLALSNP--------SNT---NPIV-SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNP   73 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~~~--------~~~---~~~~-~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a   73 (194)
                      +.++.|+|||+++++.|.++        +..   .++. .++++.+..+..+...|.|.|||||+|++|||.||+||++|
T Consensus        65 ~~~v~i~tDS~~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a  144 (150)
T 3qio_A           65 GLEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAG  144 (150)
T ss_dssp             CSEEEEEESCHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTT
T ss_pred             CCcEEEEeCcHHHHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHH
Confidence            37899999999999999863        111   1221 23444433333567899999999999999999999999999


Q ss_pred             CCC
Q psy2213          74 SAS   76 (194)
Q Consensus        74 ~~~   76 (194)
                      +..
T Consensus       145 ~~~  147 (150)
T 3qio_A          145 IRK  147 (150)
T ss_dssp             TSC
T ss_pred             HHH
Confidence            875

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

Probab=99.51  E-value=9.7e-15  Score=108.90  Aligned_cols=70  Identities=19%  Similarity=0.125  Sum_probs=50.3

Q ss_pred             CCeEEEEeCcHHHHHHHhCC---------CCC---ChH-HHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcC
Q psy2213           6 KEKFVIISDSKSTLLALSNP---------SNT---NPI-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARN   72 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~~~---------~~~---~~~-~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~   72 (194)
                      ..++.|+|||+++++.|.+.         +..   .++ -..+++.+..+.. ...|.|.|||||+|++|||.||+|||+
T Consensus        62 ~~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~-~~~v~~~~V~gH~g~~~N~~AD~LA~~  140 (146)
T 3h08_A           62 PARVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTT-LHRVTFHKVKGHSDNPYNSRADELARL  140 (146)
T ss_dssp             CCEEEEEESCHHHHHHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHH-HSEEEEEECCC-CCSHHHHHHHHHHHH
T ss_pred             cCcEEEEeChHHHHHHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHh-hCceEEEEcCCcCCcHhHHHHHHHHHH
Confidence            47899999999999999872         111   111 1234444444433 357999999999999999999999998


Q ss_pred             CCCC
Q psy2213          73 PSAS   76 (194)
Q Consensus        73 a~~~   76 (194)
                      |+..
T Consensus       141 a~~~  144 (146)
T 3h08_A          141 AIKE  144 (146)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            8754

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

Probab=99.49  E-value=3.7e-14  Score=106.71  Aligned_cols=72  Identities=25%  Similarity=0.333  Sum_probs=54.3

Q ss_pred             CCCeEEEEeCcHHHHHHHhCC--------CCC-C--hH-HHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcC
Q psy2213           5 PKEKFVIISDSKSTLLALSNP--------SNT-N--PI-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARN   72 (194)
Q Consensus         5 ~~~~~~i~sDs~~al~~l~~~--------~~~-~--~~-~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~   72 (194)
                      +..++.|+|||+++++.|.++        +.. +  ++ -..+++.+..+. .+..|.|.|||||+|++|||.||+|||+
T Consensus        69 ~~~~v~i~tDS~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~-~~~~v~~~~V~~H~g~~~N~~AD~LA~~  147 (154)
T 2qkb_A           69 NINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLT-QGMDIQWMHVPGHSGFIGNEEADRLARE  147 (154)
T ss_dssp             TCCEEEEEESCHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHH-TTCEEEEEECCTTSSCHHHHHHHHHHHH
T ss_pred             CCceEEEEECcHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHH-cCCceEEEEccCCCCCHhHHHHHHHHHH
Confidence            357899999999999999862        221 1  11 134444444553 3678999999999999999999999999


Q ss_pred             CCCCC
Q psy2213          73 PSASL   77 (194)
Q Consensus        73 a~~~~   77 (194)
                      |+..+
T Consensus       148 a~~~~  152 (154)
T 2qkb_A          148 GAKQS  152 (154)
T ss_dssp             HHTCC
T ss_pred             HHHhc
Confidence            88753

>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=99.47  E-value=4.7e-14  Score=106.38  Aligned_cols=71  Identities=20%  Similarity=0.310  Sum_probs=54.6

Q ss_pred             CCeEEEEeCcHHHHHHHhC--------CCCC---ChHH-HHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCC
Q psy2213           6 KEKFVIISDSKSTLLALSN--------PSNT---NPIV-SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNP   73 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~~--------~~~~---~~~~-~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a   73 (194)
                      ..++.|+|||+++++.|.+        .+..   .++. ..+++.+..+. .+..|.|.|||||+|++|||.||+||+.|
T Consensus        62 ~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~-~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a  140 (155)
T 1jl1_A           62 HAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAAL-GQHQIKWEWVKGHAGHPENERADELARAA  140 (155)
T ss_dssp             CCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHT-TTCEEEEEECCSSTTCHHHHHHHHHHHHH
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHH-ccCceEEEEcCCCCCCHHHHHHHHHHHHH
Confidence            3789999999999999996        2222   1221 34454555553 35789999999999999999999999999


Q ss_pred             CCCC
Q psy2213          74 SASL   77 (194)
Q Consensus        74 ~~~~   77 (194)
                      +..+
T Consensus       141 ~~~~  144 (155)
T 1jl1_A          141 AMNP  144 (155)
T ss_dssp             HHSC
T ss_pred             Hhcc
Confidence            8764

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

Probab=99.46  E-value=6.2e-14  Score=106.08  Aligned_cols=69  Identities=22%  Similarity=0.274  Sum_probs=53.5

Q ss_pred             CeEEEEeCcHHHHHHHhC--------CCCCC---hH-HHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCC
Q psy2213           7 EKFVIISDSKSTLLALSN--------PSNTN---PI-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPS   74 (194)
Q Consensus         7 ~~~~i~sDs~~al~~l~~--------~~~~~---~~-~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~   74 (194)
                      .++.|+|||+++++.|.+        .+..+   ++ -..+++.+..+.. +..|.|.|||||+|++|||.||+||+.|+
T Consensus        65 ~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~  143 (158)
T 2e4l_A           65 CKIILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQ-LHQIDWRWVKGHAGHAENERCDQLARAAA  143 (158)
T ss_dssp             CEEEEEECCHHHHHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHT-TSEEEEEECCTTCCCHHHHHHHHHHHHHH
T ss_pred             CeEEEEeCHHHHHHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHc-cCcEEEEEccCCCCchhHHHHHHHHHHHH
Confidence            789999999999999987        33221   21 1244444445533 56999999999999999999999999998


Q ss_pred             CC
Q psy2213          75 AS   76 (194)
Q Consensus        75 ~~   76 (194)
                      ..
T Consensus       144 ~~  145 (158)
T 2e4l_A          144 EA  145 (158)
T ss_dssp             HS
T ss_pred             Hh
Confidence            76

>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=99.43  E-value=9.1e-14  Score=105.98  Aligned_cols=71  Identities=24%  Similarity=0.338  Sum_probs=52.0

Q ss_pred             CCeEEEEeCcHHHHHHHhCCCCCChHH-HHH-HHHHHHHHhcCCcEEEEeecCCCC-----ChhhHHHhHHhcCCCCCC
Q psy2213           6 KEKFVIISDSKSTLLALSNPSNTNPIV-SLI-HSCWSDLLCCGKQLAFLWCPSHTG-----IQGNEAVDRAARNPSASL   77 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~~~~~~~~~~-~~i-~~~~~~l~~~~~~i~~~Wvp~H~g-----i~gNe~AD~~Ak~a~~~~   77 (194)
                      ..++.|+|||++++++|-......++. .++ ++.+..+ ..+..|.|.|||||+|     ++|||+||++|++|+...
T Consensus        80 ~~~v~I~tDS~~vi~~iw~~~~g~~v~n~dl~~~l~~~l-~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~  157 (165)
T 3p1g_A           80 GKKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKAL-FLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKA  157 (165)
T ss_dssp             TSEEEEEECCHHHHHHHHSCCCSCCCSSHHHHHHHHHHT-TSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEchHHHHhhhhcccCCCcccCHHHHHHHHHHH-hcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcC
Confidence            578999999999999993211112221 232 2222344 3678999999999999     999999999999998763

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

Probab=99.40  E-value=1.1e-13  Score=105.54  Aligned_cols=70  Identities=23%  Similarity=0.266  Sum_probs=53.8

Q ss_pred             CeEEEEeCcHHHHHHHhC---------CCC-CC--hH-HHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCC
Q psy2213           7 EKFVIISDSKSTLLALSN---------PSN-TN--PI-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNP   73 (194)
Q Consensus         7 ~~~~i~sDs~~al~~l~~---------~~~-~~--~~-~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a   73 (194)
                      .++.|+|||+++++.|.+         ++. .+  ++ -..+++.+..+.. ...|.|.|||||+|++|||.||+|||.|
T Consensus        67 ~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a  145 (166)
T 1ril_A           67 CEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA-PHRVRFHFVKGHTGHPENERVDREARRQ  145 (166)
T ss_dssp             CEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT-TSEEECCCCCGGGSCTHHHHHHHHHHHH
T ss_pred             CeEEEEeChHHHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHh-cCeEEEEEeeCCCCchhHHHHHHHHHHH
Confidence            589999999999999998         222 21  11 1244444555533 4689999999999999999999999999


Q ss_pred             CCCC
Q psy2213          74 SASL   77 (194)
Q Consensus        74 ~~~~   77 (194)
                      +...
T Consensus       146 ~~~~  149 (166)
T 1ril_A          146 AQSQ  149 (166)
T ss_dssp             HTSS
T ss_pred             HHHh
Confidence            8874

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

Probab=99.37  E-value=3.1e-13  Score=102.98  Aligned_cols=70  Identities=16%  Similarity=0.137  Sum_probs=51.5

Q ss_pred             CCeEEEEeCcHHHHHHHhC--------CCCC---ChH-HHHHHHHHHHHHhcCCcEEEEeecCCCCC------hhhHHHh
Q psy2213           6 KEKFVIISDSKSTLLALSN--------PSNT---NPI-VSLIHSCWSDLLCCGKQLAFLWCPSHTGI------QGNEAVD   67 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~~--------~~~~---~~~-~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi------~gNe~AD   67 (194)
                      +.+|.|+|||+++++.|..        ++..   .++ -.++++.+.++......|.|.|||||+|+      +|||+||
T Consensus        75 ~~~v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD  154 (165)
T 2lsn_A           75 PGPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALAD  154 (165)
T ss_dssp             SSCEEEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHH
T ss_pred             CCeEEEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHH
Confidence            3579999999999999974        2222   122 13444445454455678999999999995      5899999


Q ss_pred             HHhcCCCC
Q psy2213          68 RAARNPSA   75 (194)
Q Consensus        68 ~~Ak~a~~   75 (194)
                      +||++|+.
T Consensus       155 ~LA~~gA~  162 (165)
T 2lsn_A          155 KLATQGSY  162 (165)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHhhh
Confidence            99998864

>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=99.36  E-value=2.6e-14  Score=106.95  Aligned_cols=68  Identities=15%  Similarity=0.095  Sum_probs=53.9

Q ss_pred             eEEEEeCcHHHHHHHhCCCCCC-hHHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCCCCCC
Q psy2213           8 KFVIISDSKSTLLALSNPSNTN-PIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLP   78 (194)
Q Consensus         8 ~~~i~sDs~~al~~l~~~~~~~-~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~~~~~   78 (194)
                      ++.|++||+.+.+-+.+.+..+ +....+.+.+.+|..   .|.|.|||||+|++|||.||+|||+|+....
T Consensus        71 ~v~I~tDS~~i~~w~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~  139 (147)
T 2kq2_A           71 KIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALGIRD  139 (147)
T ss_dssp             CCCBSSCCSTHHHHTTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHTCCC
T ss_pred             eEEEEECcHHHHHHHhCCCccCCcchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHhccc
Confidence            7899999998888887766554 344455544455532   8999999999999999999999999988753

>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=99.27  E-value=5.1e-12  Score=112.87  Aligned_cols=65  Identities=26%  Similarity=0.413  Sum_probs=52.3

Q ss_pred             CCeEEEEeCcHHHHHHHhCCCCC--ChHHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCC
Q psy2213           6 KEKFVIISDSKSTLLALSNPSNT--NPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPS   74 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~~~~~~--~~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~   74 (194)
                      ..++.|++||+++++.|+++...  .++..++.   ..+ ..+..|.|.|||||+|++|||.||+||++|+
T Consensus       489 ~~~v~I~tDS~~v~~~i~~~~~~~~~~l~~~~~---~~~-~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          489 GPKVNIIVDSQYVMGIVASQPTESESKIVNQII---EEM-IKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             CSEEEEEESCHHHHHHHHTCCSEESCHHHHHHH---HHH-HHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             CCeEEEEEehHHHHHHHhcccccccHHHHHHHH---HHh-ccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            46899999999999999986533  34554443   233 3478899999999999999999999999985

>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=99.20  E-value=1e-11  Score=110.94  Aligned_cols=64  Identities=27%  Similarity=0.468  Sum_probs=49.1

Q ss_pred             CCeEEEEeCcHHHHHHHhCCCCC--ChHHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCC
Q psy2213           6 KEKFVIISDSKSTLLALSNPSNT--NPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNP   73 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~~~~~~--~~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a   73 (194)
                      ..++.|++||+++++.|.++...  .++..++.   ..+. ....|.|.|||||+|++|||.||+||++|
T Consensus       492 ~~~v~I~tDS~~vi~~i~~~~~~~~~~l~~~~~---~~l~-~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          492 GLEVNIVTDSQYALGIIQAQPDKSESELVNQII---EQLI-KKEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             CSEEEEEECCHHHHHHHTTCCSEESSHHHHHHH---HHHH-HCSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             CCcEEEEeChHHHHHHHhcCCccCCHHHHHHHH---HHHh-cCCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            46899999999999999986544  34554443   3443 35689999999999999999999999986

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

Probab=99.06  E-value=2.3e-10  Score=83.61  Aligned_cols=66  Identities=12%  Similarity=0.145  Sum_probs=50.5

Q ss_pred             CCeEEEEeCcHHHHHHHhCCCCC-ChHHHHHHHHHHHH-HhcCCcEEEEeecCCCCChhhHHHhHHhcCCCC
Q psy2213           6 KEKFVIISDSKSTLLALSNPSNT-NPIVSLIHSCWSDL-LCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSA   75 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~~~~~~-~~~~~~i~~~~~~l-~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~~   75 (194)
                      ..++.|++||+++++.+.+.+.. ++-...+.+.+..+ ......|.|.|||+    +|||.||+|||.|..
T Consensus        69 ~~~v~i~tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~  136 (140)
T 3u3g_D           69 DMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPR----EKNARADELVNEAID  136 (140)
T ss_dssp             TCEEEEEESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCG----GGGHHHHHHHHHHHH
T ss_pred             CceEEEEeChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCc----hhhHHHHHHHHHHHH
Confidence            34899999999999999987753 33333444445555 45556899999995    799999999998764

>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=99.06  E-value=3.3e-10  Score=83.16  Aligned_cols=68  Identities=18%  Similarity=0.224  Sum_probs=54.2

Q ss_pred             CCCeEEEEeCcHHHHHHHhCCCCC-ChHHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCCCC
Q psy2213           5 PKEKFVIISDSKSTLLALSNPSNT-NPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS   76 (194)
Q Consensus         5 ~~~~~~i~sDs~~al~~l~~~~~~-~~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~~~   76 (194)
                      ..+++.|++||+++++.+.+.+.. ++....+.+.+..+......|.|.|||+    +|||.||+||+.|...
T Consensus        65 ~~~~v~i~tDS~~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B           65 GATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----ARNTYADRLANDAMDA  133 (141)
T ss_dssp             TCSEEEEEESCHHHHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             CCceEEEEeChHHHHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHHHHH
Confidence            357899999999999999986543 4444555556667766678999999996    7999999999988654

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

Probab=98.93  E-value=6.5e-10  Score=82.68  Aligned_cols=66  Identities=15%  Similarity=0.167  Sum_probs=49.9

Q ss_pred             CCeEEEEeCcHHHHHHHhCCCCC-ChHHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCCCC
Q psy2213           6 KEKFVIISDSKSTLLALSNPSNT-NPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS   76 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~~~~~~-~~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~~~   76 (194)
                      .+++.|++||+++++.+++++.. ++....+++.+..+.... .|.|.|||+    ++|+.||+||+.|+..
T Consensus        68 ~~~v~i~tDS~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~----~~N~~AD~LA~~a~~~  134 (149)
T 2ehg_A           68 ISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPR----EENKEADRLSRVAYEL  134 (149)
T ss_dssp             CCSCEEEESCHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             CCEEEEEeChHHHHHHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCC----cccHHHHHHHHHHHHh
Confidence            46899999999999999987654 233344444444443322 599999999    5999999999998775

>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=94.86  E-value=0.0039  Score=45.75  Aligned_cols=59  Identities=15%  Similarity=0.041  Sum_probs=40.8

Q ss_pred             eEEEEeCcHHHHHHHhCCCC-CC--------hHHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhH
Q psy2213           8 KFVIISDSKSTLLALSNPSN-TN--------PIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDR   68 (194)
Q Consensus         8 ~~~i~sDs~~al~~l~~~~~-~~--------~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~   68 (194)
                      ++.|+|||+++++.+++.+. .+        .+.+.|..+..-++  +..++...|..|++.-||.-||-
T Consensus        72 ~v~i~tDS~~vi~w~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~--~~~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A           72 RKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLN--THTYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             CCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHH--HCCCCCCEEECCHHHHCSCTTCC
T ss_pred             eEEEEEehHHHHHHHHcCCccCCCCCCcccHHHHHHHHHHHHHHh--hCCCceeEEEeccCccCcCcccc
Confidence            78999999999999987652 21        13333333333332  45667777899999999998883

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	194
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	0.002
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	0.003
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	0.004

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

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

 Score = 34.6 bits (78), Expect = 0.002
 Identities = 11/47 (23%), Positives = 18/47 (38%)

Query: 25  PSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAAR 71
            ++  P+ ++      D      Q+ + W   H G   NE  D  AR
Sbjct: 90  TADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELAR 136

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

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

 Score = 34.1 bits (77), Expect = 0.003
 Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 2/67 (2%)

Query: 5   PKEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNE 64
              K  II DS+  +  +++    +    +            + +   W P+H GI GN+
Sbjct: 59  SGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEM--IKKEAIYVAWVPAHKGIGGNQ 116

Query: 65  AVDRAAR 71
            VD    
Sbjct: 117 EVDHLVS 123

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

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

 Score = 34.2 bits (77), Expect = 0.004
 Identities = 12/37 (32%), Positives = 15/37 (40%)

Query: 36  HSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARN 72
                 L     ++ F +   HTG   NE VDR AR 
Sbjct: 103 LWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARR 139

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	194
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.61
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.44
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.43
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	98.56
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	97.11

>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=99.61  E-value=4.7e-16  Score=111.71  Aligned_cols=66  Identities=24%  Similarity=0.396  Sum_probs=51.7

Q ss_pred             CCCeEEEEeCcHHHHHHHhCCCCC--ChHHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCC
Q psy2213           5 PKEKFVIISDSKSTLLALSNPSNT--NPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPS   74 (194)
Q Consensus         5 ~~~~~~i~sDs~~al~~l~~~~~~--~~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~   74 (194)
                      ...++.|++||+++++.+.+....  ....   .+.+..+ .....|.|.|||||+|++|||+||+||++|.
T Consensus        59 ~~~~i~I~tDS~~v~~~~~~~~~~~~~~~~---~~~~~~~-~~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          59 SGPKVNIIVDSQYVMGIVASQPTESESKIV---NQIIEEM-IKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             SCSEEEEEESCHHHHHHHHTCCSEESCHHH---HHHHHHH-HHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             CCcceEEEechHHHHHHHhcCCccccchHH---HHHHHHh-hhcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            357899999999999999986643  2222   2233344 3356899999999999999999999999873

>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=99.44  E-value=7.1e-14  Score=102.59  Aligned_cols=79  Identities=18%  Similarity=0.241  Sum_probs=55.8

Q ss_pred             CCCeEEEEeCcHHHHHHHhCCC--------CC-C--hH-HHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcC
Q psy2213           5 PKEKFVIISDSKSTLLALSNPS--------NT-N--PI-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARN   72 (194)
Q Consensus         5 ~~~~~~i~sDs~~al~~l~~~~--------~~-~--~~-~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~   72 (194)
                      ....+.|++||++++..+....        .. .  ++ -.++...+..+ .....|+|+|||||+|++|||+||+|||+
T Consensus        59 ~~~~i~i~tds~~~i~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~-~~~~~V~~~wV~gH~g~~gNe~AD~LAk~  137 (152)
T d1jl1a_          59 EHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAA-LGQHQIKWEWVKGHAGHPENERADELARA  137 (152)
T ss_dssp             SCCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHH-TTTCEEEEEECCSSTTCHHHHHHHHHHHH
T ss_pred             ccceEEEeecceeeEEcccchhhHhHhccchhcccCeeecHHHHHHHHHH-hhcceeEEEEecccCCCccHHHHHHHHHH
Confidence            3467899999999999887432        11 1  11 12334344444 34678999999999999999999999999


Q ss_pred             CCCCCCCCCCCCc
Q psy2213          73 PSASLPPLKLCSP   85 (194)
Q Consensus        73 a~~~~~~~~~~s~   85 (194)
                      |+..+ ++...+|
T Consensus       138 aa~~~-~~~d~~~  149 (152)
T d1jl1a_         138 AAMNP-TLEDTGY  149 (152)
T ss_dssp             HHHSC-CBCCTTC
T ss_pred             HHhCC-CCCccCC
Confidence            98864 3444444

>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=99.43  E-value=2.5e-14  Score=104.96  Aligned_cols=72  Identities=22%  Similarity=0.239  Sum_probs=53.6

Q ss_pred             CCCeEEEEeCcHHHHHHHhCCC----------CC--ChHH-HHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhc
Q psy2213           5 PKEKFVIISDSKSTLLALSNPS----------NT--NPIV-SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAAR   71 (194)
Q Consensus         5 ~~~~~~i~sDs~~al~~l~~~~----------~~--~~~~-~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak   71 (194)
                      ....+.|++||+++++.|....          ..  .++. .++++.+..+ .....|+|.|||||+|++|||.||+|||
T Consensus        60 ~~~~i~i~tds~~~~~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~-~~~~~v~~~wVkgHsg~~gNe~AD~LAk  138 (147)
T d1rila_          60 EPCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLA-MAPHRVRFHFVKGHTGHPENERVDREAR  138 (147)
T ss_dssp             SCCEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHH-HTTSEEECCCCCGGGSCTHHHHHHHHHH
T ss_pred             CCceEEEecchhhhhccccccchhhhhhccccccccccchhHHHHHHHHHH-hhhcccceEEccCCCCCcchHHHHHHHH
Confidence            3567899999999999886532          11  1221 2344444455 3467899999999999999999999999


Q ss_pred             CCCCCC
Q psy2213          72 NPSASL   77 (194)
Q Consensus        72 ~a~~~~   77 (194)
                      +|+...
T Consensus       139 ~aa~~~  144 (147)
T d1rila_         139 RQAQSQ  144 (147)
T ss_dssp             HHHTSS
T ss_pred             HHHHHh
Confidence            998764

>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=98.56  E-value=4.6e-08  Score=67.67  Aligned_cols=48  Identities=21%  Similarity=0.380  Sum_probs=36.7

Q ss_pred             CCeEEEEeCcHHHHHHHhCCCCC--ChHHHHHHHHHHHHHhcCCcEEEEeecCC
Q psy2213           6 KEKFVIISDSKSTLLALSNPSNT--NPIVSLIHSCWSDLLCCGKQLAFLWCPSH   57 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~~~~~~--~~~~~~i~~~~~~l~~~~~~i~~~Wvp~H   57 (194)
                      ..++.|+|||+++++++......  ..+..+|.   ..+ .....|.|.|||||
T Consensus        61 ~~~v~I~TDS~yvi~~i~~~~~~~~~~l~~~il---~~l-~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          61 GLEVNIVTDSQYALGIIQAQPDQSESELVNQII---EQL-IKKEKVYLAWVPAH  110 (110)
T ss_dssp             CSEEEEEECCHHHHHHHHHCCSEESCHHHHHHH---HHH-HHCSEEEEEECCSS
T ss_pred             CCeEEEEEehHHHHHHHhcCccccchHHHHHHH---HHH-hcCCceEEEEeCCC
Confidence            46799999999999999976644  34555544   344 34678999999999

>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=97.11  E-value=3.2e-05  Score=54.46  Aligned_cols=62  Identities=13%  Similarity=0.045  Sum_probs=42.8

Q ss_pred             CCeEEEEeCcHHHHHHHhCCC-CC---Ch-HHHHHHHHHHHHH--hcCCcEEEEeecCCCCChhhHHHh
Q psy2213           6 KEKFVIISDSKSTLLALSNPS-NT---NP-IVSLIHSCWSDLL--CCGKQLAFLWCPSHTGIQGNEAVD   67 (194)
Q Consensus         6 ~~~~~i~sDs~~al~~l~~~~-~~---~~-~~~~i~~~~~~l~--~~~~~i~~~Wvp~H~gi~gNe~AD   67 (194)
                      +.++.|+|||+++++.+.+.. .+   .+ --.++++.+.++.  ...+.+.+.|+..|+.--||..||
T Consensus        63 ~~~i~I~tDS~yvi~wv~~~~~kt~~~~~vkN~~l~~~i~~a~~~lk~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          63 NSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             TCCCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             CceEEEEeccHHHHHHHHhCceecCcCCCcccHHHHHHHHHHHHHHHhCCcCceeEEecCcccccCCCC
Confidence            357899999999999997533 11   11 1233443343321  236779999999999999999988