Psyllid ID: psy2212

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------
Protein Sequence
NNTSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRASLPTPPALTDDVESVDSLLSYLKKLNLRVVAVSFEKDEEVDRGTK
Secondary Structure (PSIPRED)
ccEEEEEEEcccEEEEEEccccccHHHHHHHHHHHHHHHHHccccccEEEEccHHHHHHHHcccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHEEEccccccccccccccccccccccccccHHHHccccccHHHHHcccccccccccHHHHHHHHHHHHHcccccccccccHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccEEEEEEEccEEEEEEcccccHHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHcccccHHHHHcccccccccccccccccEEEEccHHHHHHHHHHHcccccccccccHHHHHHHHHHcccEEEEHEEcccHHHccccc
Coil and Loop (DISEMBL)
nntscayiidktSIYSFVLNNVNSVFTSELIAVLLCLKhlkflpkekfviISDSKSTLlalsnpsninpIVSLIHSCWsdllccgkqlaflwcpshtgiqgneavdraarnpsaslpplklcspedfKPFIRKLIKDLWQQswssipnsnklksikpiigpwpssdrqnrYEEVVICRMRightrathghlfkrappstcgcgeilsVQHILTCALHghiraslptppaltddvESVDSLLSYLKKLNLRVVAVSfekdeevdrgtk
Flexible Loop (DISEMBL)
nntscayiidktsIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSaslpplklcspEDFKPFIRKLIKDLWQQSwssipnsnklksikpiigpwpssdrqnRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRASLPTPPALTDDVESVDSLLSYLkklnlrvvavsfekdeevdrgtk
Low Complexity Region (SEG)
NNTSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRASLPTPPALTDDVESVDSLLSYLKKLNLRVVAVSFEKDEEVDRGTK
Disordered region (IsUnstruct)
****CAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQG******************KLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPS*DRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRASLPTPPALTDDVESVDSLLSYLKKLNLRVVAVSF***********
Disordered Region (DISOPRED)
*NTSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRASLPTPPALTDDVESVDSLLSYLKKLNLRVVAV*************
Disordered Region (DISEMBL)
NNTSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRASLPTPPALTDDVESVDSLLSYLKKLNLRVVAVSF***********
Disordered Region (DISPRO)
*NTSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRASLPTPPALTDDVESVDSLLSYLKKLNLRVVAVSFEKD********
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
NNTSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRASLPTPPALTDDVESVDSLLSYLKKLNLRVVAVSFEKDEEVDRGTK
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	267
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.782	0.416	0.395	2e-30
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.782	0.800	0.395	1e-29
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.737	0.418	0.400	2e-28
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.782	0.526	0.381	3e-28
443682433	619	hypothetical protein CAPTEDRAFT_222606 [	0.662	0.285	0.414	8e-27
443724607	397	hypothetical protein CAPTEDRAFT_208903 [	0.906	0.609	0.351	1e-25
443694523	364	hypothetical protein CAPTEDRAFT_227708 [	0.625	0.458	0.435	4e-25
427798889	1199	Putative tick transposon, partial [Rhipi	0.700	0.155	0.354	2e-23
427778603	1397	Putative tick transposon [Rhipicephalus	0.838	0.160	0.345	7e-23
427791063	1035	Putative tick transposon, partial [Rhipi	0.722	0.186	0.333	1e-22

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

 Score =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 85/215 (39%), Positives = 121/215 (56%), Gaps = 6/215 (2%)

Query: 1   NNTSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKE-KFVIISDSKSTLL 59
           N  +CA+      I  F L    S++T+ELIA+   L  ++ +  E +F I SDS S+L 
Sbjct: 93  NAVACAFTCSTYQI-QFGLPTQMSIYTAELIAIEQALIFIETVKDEDQFNICSDSLSSLT 151

Query: 60  ALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPL 119
           ALSN    +P +  I +  ++L+  GK + F+WCPSH GI GNE  DR A+  +  +P  
Sbjct: 152 ALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQ-ALVMPVT 210

Query: 120 KLCSPE-DFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICR 178
           KL  P  D+K  IR  +K LWQ  W      NKL SI+P+I  W    + +R  E+V+ R
Sbjct: 211 KLPLPHTDYKSPIRSYVKSLWQNEWDE-ETDNKLHSIQPVISEWKQGPQIDRRGEIVLAR 269

Query: 179 MRIGHTRATHGHLFKRAPPSTC-GCGEILSVQHIL 212
            RIGH+  THG+L +R     C  C  +L+V+HIL
Sbjct: 270 ARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHIL 304

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  136 bits (342), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 85/215 (39%), Positives = 121/215 (56%), Gaps = 6/215 (2%)

Query: 1   NNTSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKE-KFVIISDSKSTLL 59
           +  +CA+      I  F L    S++T+ELIA+   L  ++ +  E +F I SDS S+L 
Sbjct: 47  DAVACAFTCSTYQI-QFGLPAQMSIYTAELIAIEQALIFIETVKDEDQFNICSDSLSSLT 105

Query: 60  ALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPL 119
           ALSN    +P +  I +  ++L+  GK + F+WCPSH GI GNE  DR A+  +  +P  
Sbjct: 106 ALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQ-ALVMPVT 164

Query: 120 KLCSPE-DFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICR 178
           KL  P  D+K  IR  +K LWQ  W      NKL SI+P+I  W    + +R  E+V+ R
Sbjct: 165 KLPLPHTDYKSPIRSYVKSLWQNEWDE-ETDNKLHSIQPVISEWKQGPQIDRRGEIVLAR 223

Query: 179 MRIGHTRATHGHLFKR-APPSTCGCGEILSVQHIL 212
            RIGH+  THG+L +R   P    C  +LSV+HIL
Sbjct: 224 ARIGHSHLTHGYLLRREVAPFCIPCQSLLSVKHIL 258

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 =  131 bits (330), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 81/202 (40%), Positives = 114/202 (56%), Gaps = 5/202 (2%)

Query: 24  SVFTSELIAVLLCLKHLKFLPKE-KFVIISDSKSTLLALSNPSNINPIVSLIHSCWSDLL 82
           SVFTSE+IA+L  L+ ++   ++ +FVI SDS S ++A+      +P V  +      + 
Sbjct: 54  SVFTSEIIAILSALRCVEADNEQHQFVICSDSLSAIMAIHGMDVRHPYVLQVLYAIKSIS 113

Query: 83  CCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSP-EDFKPFIRKLIKDLWQQ 141
              K + F+WCPSH GI GNE  D  A+   +S    +L  P  D +  I+K I+  WQ 
Sbjct: 114 QQEKIVVFMWCPSHVGIPGNEMADTLAKEALSSTNLAELPVPASDLRCLIKKYIRSRWQH 173

Query: 142 SWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTC- 200
            W    +SNKL SI P IGPWP   R+ R EE+V+ R+RIGHT  TH ++ +    + C 
Sbjct: 174 EWDE-QHSNKLHSIHPTIGPWPPCQREKRREEIVLARIRIGHTHYTHDYIPRGDDQTECV 232

Query: 201 GCGEILSVQH-ILTCALHGHIR 221
            C   L+VQH I+ CA   HIR
Sbjct: 233 ACVCPLTVQHIIIECADFLHIR 254

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 =  131 bits (329), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 82/215 (38%), Positives = 120/215 (55%), Gaps = 6/215 (2%)

Query: 1   NNTSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKE-KFVIISDSKSTLL 59
           +  +CA+      I  F L    S++T+ELIA+   L  ++ +  E +F I SDS S+L 
Sbjct: 142 DTVACAFTCSTYQI-QFGLPAQMSIYTAELIAIEQALIFIETVKDEDQFNICSDSLSSLT 200

Query: 60  ALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPL 119
           ALSN    +P +  I +  ++L+  GK++ F+WCPSH GI GNE  DR A+  +  +P  
Sbjct: 201 ALSNCDITHPYLLSILTKQNNLVRKGKKVVFIWCPSHVGILGNEVADRQAKQ-ALVMPVT 259

Query: 120 KLCSPE-DFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICR 178
           KL  P  D+K  IR  +K LWQ  W      NKL  I+P+I  W    + +R  E+V+  
Sbjct: 260 KLPLPHTDYKSPIRSYVKSLWQNEWDG-ETDNKLHIIQPVISEWKQGPQIDRRGEIVLAC 318

Query: 179 MRIGHTRATHGHLFKR-APPSTCGCGEILSVQHIL 212
            RIGH+  THG+L +R   P    C  +L+V+HIL
Sbjct: 319 ARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHIL 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 =  126 bits (317), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 75/181 (41%), Positives = 102/181 (56%), Gaps = 4/181 (2%)

Query: 24  SVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCWSDLLC 83
           SV+T+ELIA+   L  +  LP ++FVI +DS S++LA+S+   I+  V  I    ++L  
Sbjct: 30  SVYTAELIAINETLTSIALLPYDEFVICTDSFSSILAISSIDLIHSYVQSILQKCTNLAG 89

Query: 84  CGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPE-DFKPFIRKLIKDLWQQS 142
             K++ F+WCPSH GI GNE  D  A+  S  +  L    P  DFKP  R  ++  W QS
Sbjct: 90  RDKRIIFIWCPSHVGIPGNETADTLAQQASG-MNILNCPIPHTDFKPITRSFVETQW-QS 147

Query: 143 WSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTC-G 201
            S     NKL  I+P IG WP   R+ R +E+VI R+RIGHT  T+ HL        C G
Sbjct: 148 ESDQETGNKLHDIEPDIGSWPPCQREKRRDEIVIARLRIGHTFLTYSHLLSGNDAPMCYG 207

Query: 202 C 202
           C
Sbjct: 208 C 208

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 =  122 bits (306), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 89/253 (35%), Positives = 134/253 (52%), Gaps = 11/253 (4%)

Query: 4   SCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKE-KFVIISDSKSTLLALS 62
           +CA+      I  F L    S++T+ELIA+   L  ++ +  E +F I SDS S+L ALS
Sbjct: 145 ACAFTCSTYQI-QFGLPAQMSIYTAELIAIEQALIFIETMKDEDQFNICSDSLSSLTALS 203

Query: 63  NPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLC 122
           N    +P +  I +  ++L+  GK + F+WCPSH GI GNE  DR A+  +  +P  KL 
Sbjct: 204 NCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQ-ALVMPVTKLP 262

Query: 123 SPE-DFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRI 181
            P  D+K  IR  +K L Q  W      NKL +I+P+I  W    + +R  E+V+    I
Sbjct: 263 LPHTDYKSPIRSYVKSLRQNEWDE-ETDNKLHTIQPVISEWKQGPQIDRRGEIVLACACI 321

Query: 182 GHTRATHGHLFKR-APPSTCGCGEILSVQHILTCALHGHIRA----SLPTPPALTDDVES 236
           GH+  THG+L +R   P    C  +L+V+HIL   +   I      ++ +   L +D   
Sbjct: 322 GHSHLTHGYLLRREVAPFCIPCQSLLTVKHILIDCIDFEISRRKYFNVSSMRQLFEDTHP 381

Query: 237 VDSLLSYLKKLNL 249
             +LL YLK++ L
Sbjct: 382 SKNLL-YLKEIGL 393

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 =  121 bits (303), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 74/170 (43%), Positives = 98/170 (57%), Gaps = 3/170 (1%)

Query: 24  SVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCWSDLLC 83
           SV+T+ELIA+   L  +  LP ++FVI +DS S++LA+S+   I+P V  I    + L  
Sbjct: 2   SVYTAELIAINETLTSIALLPYDEFVICTDSLSSILAISSIDLIHPYVQSILQKCTCLAG 61

Query: 84  CGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPE-DFKPFIRKLIKDLWQQS 142
             K++ F+WCPSH GI GNE  D  A+  +  +  L    P  DFKP  R  +K  WQ  
Sbjct: 62  RDKRIIFIWCPSHVGIPGNETADTLAKQ-ALGMNILNCPIPHTDFKPITRSFVKTQWQSE 120

Query: 143 WSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLF 192
           W      NKL  I+P IG WP   R+ R EE+VI R+RIGHT  TH HL 
Sbjct: 121 WDQ-ETGNKLHDIQPDIGSWPPCQREKRREEIVIARVRIGHTFLTHSHLL 169

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 =  115 bits (288), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 68/192 (35%), Positives = 102/192 (53%), Gaps = 5/192 (2%)

Query: 24   SVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSN-PSNINPIVSLIHSCWSDLL 82
            S+FT+E  A+L  +KH++ L  +K VI +DS S + AL     + NP++  ++S    + 
Sbjct: 995  SIFTAEAYAILAAVKHIRELKLQKAVIYTDSLSVVKALKTLKKHRNPVLVSLYSLLCTIY 1054

Query: 83   CCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPE-DFKPFIRKLIKDLWQQ 141
               + +   W P H  IQGN   D+ A +   S     +  P  D KP++++ I+  WQ 
Sbjct: 1055 TSKQHVVVCWVPGHREIQGNVMADQLAVSAHDSSANTSIAIPALDLKPYLKRKIRAYWQS 1114

Query: 142  SWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRAPPSTCG 201
            +W      NKL  IKP +G WP   + +RY EV + R+R GHT +TH +L        C 
Sbjct: 1115 TWDR-QTHNKLHVIKPQLGHWPPISK-SRYTEVTLTRLRTGHTHSTHAYLLSGGDAPFCD 1172

Query: 202  -CGEILSVQHIL 212
             CGE L+V HIL
Sbjct: 1173 KCGEPLTVIHIL 1184

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427778603|gb|JAA54753.1| Putative tick transposon [Rhipicephalus pulchellus]

 Score =  113 bits (283), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 88/255 (34%), Positives = 128/255 (50%), Gaps = 31/255 (12%)

Query: 24   SVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALS------NPSNINPIVSLIHSC 77
            S+FT+E   +LL ++H+K     + +I +DS S + ALS      NP   N +++ +H  
Sbjct: 1142 SIFTAEAYGILLIVEHIKQHMIRRSIIYTDSLSVVTALSCGKCSKNPV-FNKLLNNMHEA 1200

Query: 78   WSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCS--PEDFKPFIRKLI 135
            ++  L     +   W P H GI GNE VD+ AR  +AS   + + S    D  P +R+ +
Sbjct: 1201 YNQNL----SIVLCWVPGHAGITGNEMVDKNARE-AASRHTIDISSVPGVDLNPVVRRGL 1255

Query: 136  KDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRA 195
            +  WQ  W    + NKL  +KP +       + NR+ EV + R+RIGHT ATH HL    
Sbjct: 1256 RSHWQVEWDKQVD-NKLHLVKPHLSK-VLPQKLNRFTEVTLARLRIGHTYATHKHLLTGT 1313

Query: 196  PPSTC-GCGEILSVQHIL-TC-ALHGH--------IRASLPTPPAL---TDDVESVDSLL 241
             P TC  CGE L++ H+L  C  LH           R  +P  PAL    D +  +  LL
Sbjct: 1314 DPPTCIHCGETLTILHVLIECPGLHQERLTHFRELYRYHIPPHPALFLSLDPMFKLKRLL 1373

Query: 242  SYLKKLNLRVVAVSF 256
             YL K+N  +  VSF
Sbjct: 1374 HYLAKVNF-LAMVSF 1387

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  113 bits (282), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 66/198 (33%), Positives = 103/198 (52%), Gaps = 5/198 (2%)

Query: 18   VLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSN-PSNINPIVSLIHS 76
            VL+   S+FT+E  A+ + +KH++ L     VI +DS S + AL     + NP+++ ++S
Sbjct: 823  VLHQNTSIFTAEAYAIFVAVKHIEQLKLPSAVIYTDSLSVVKALKTLKKHKNPVLASLYS 882

Query: 77   CWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPE-DFKPFIRKLI 135
                +    + +   W P H  IQGN   D+ A +   +     L  P  D KP +++ +
Sbjct: 883  LLCTVYALKQHVVVCWVPGHREIQGNVLADQLAASAHENAAHTFLAIPALDLKPLLKRKL 942

Query: 136  KDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHGHLFKRA 195
            +  WQ  W +    NKL +IKP +G WP + +  R  E+ + R+R GHT  TH +L    
Sbjct: 943  RAYWQSIWDT-QTQNKLHAIKPQLGEWPPASKSRR-TEITLTRLRTGHTHTTHAYLLSGN 1000

Query: 196  PPSTCG-CGEILSVQHIL 212
             P  C  CGE L+V HIL
Sbjct: 1001 DPPRCERCGEPLTVLHIL 1018

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	267
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.805	0.442	0.25	8.2e-10

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

 Score = 165 (63.1 bits), Expect = 8.2e-10, P = 8.2e-10
 Identities = 58/232 (25%), Positives = 103/232 (44%)

Query:     7 YIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSN 66
             Y+I ++S       + ++V+ +EL  +LL L  +     +  VI +D+++TL AL NP +
Sbjct:   205 YLISRSSYMG--QQSESTVYVAELQGILLALVIILQRQMQHAVIFTDNQATLQALRNPGS 262

Query:    67 INP--IVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPL----K 120
              +   I+  I    +     G  + F W P+H G++GNE  DR A+  +          +
Sbjct:   263 QSGQYILEAIIMALNKGRKAGLNVHFRWIPAHRGVEGNEQADRRAKEATGWRRIRGHRGR 322

Query:   121 LCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEV--VICR 178
             +      K    +++   W+  W S  +  +L  + P          Q+ +  +  +I +
Sbjct:   323 MTIRSAVKRRAHEVVNARWENDWKSCHHGRELYELTPTPTRKVLRVHQDLHRALSTIIVQ 382

Query:   179 MRIGHTRATHGHLFKRAPP----STCGCGEIL-SVQHIL-TCALHGHIRASL 224
             MR G     H +L++R  P    S C CG    SV+HIL  C     +R  +
Sbjct:   383 MRTGKIGLRH-YLYQRGVPDVPNSDCQCGRATQSVRHILLACPTFSGLREEI 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   0.135   0.420    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      267       267   0.00095  114 3  11 22  0.46    33
                                                     32  0.39    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  608 (65 KB)
  Total size of DFA:  211 KB (2117 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  24.84u 0.09s 24.93t   Elapsed:  00:00:01
  Total cpu time:  24.85u 0.09s 24.94t   Elapsed:  00:00:01
  Start:  Thu Aug 15 14:22:07 2013   End:  Thu Aug 15 14:22:08 2013

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	267
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	4e-25
pfam00075	126	pfam00075, RNase_H, RNase H	2e-15
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	1e-07
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	2e-07
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	6e-06
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	0.003

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

 Score = 96.2 bits (240), Expect = 4e-25
 Identities = 38/108 (35%), Positives = 58/108 (53%), Gaps = 3/108 (2%)

Query: 6   AYIIDKTSI-YSFVLNNVNSVFTSELIAVLLCLKHLKFLPKE--KFVIISDSKSTLLALS 62
             I+ K +I  S+ L    SVF +EL+A+L  L+      +   K  I SDS++ L AL 
Sbjct: 17  FAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRARKITIFSDSQAALKALR 76

Query: 63  NPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAAR 110
           +P + +P+V  I     +L   G ++   W P H+GI+GNE  DR A+
Sbjct: 77  SPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLAK 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 = 70.8 bits (174), Expect = 2e-15
 Identities = 29/109 (26%), Positives = 46/109 (42%), Gaps = 12/109 (11%)

Query: 6   AYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKST----LLAL 61
            Y+ D     S  L    +   +EL+A++  L+ L     +K  I +DS+          
Sbjct: 22  GYVTDGGKQRSKPLPG-TTNQRAELLALIEALEAL---SGQKVNIYTDSQYVIGGITNGW 77

Query: 62  SNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAAR 110
              S   PI + I     +LL    ++   W P H+GI GNE  D+ A+
Sbjct: 78  PTKSESKPIKNEIW----ELLQKKHKVYIQWVPGHSGIPGNELADKLAK 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|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term repeat retroelements

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 26/124 (20%), Positives = 44/124 (35%), Gaps = 26/124 (20%)

Query: 6   AYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSK---STLLAL- 61
           A +     +    L    S   +ELIA++  L+  K    +   I +DS      L AL 
Sbjct: 16  AVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKG---KPVNIYTDSAYAFGILHALE 72

Query: 62  ----------SNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTG-----IQGNEAVD 106
                       P  +  ++  +       +   K +A +   +H+G       GN   D
Sbjct: 73  TIWKERGFLTGKPIALASLILQL----QKAIQRPKPVAVIHIRAHSGLPGPLALGNARAD 128

Query: 107 RAAR 110
           +AAR
Sbjct: 129 QAAR 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

>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 = 48.9 bits (117), Expect = 2e-07
 Identities = 24/116 (20%), Positives = 47/116 (40%), Gaps = 8/116 (6%)

Query: 1   NNTSCAYII---DKTSIYSFVLNNVN-SVFTSELIAVLLCLKHLKFLPKEKFVIISDSKS 56
                  ++   +   +++  L+    +   +EL+A+L  L+    L  +K +I +DSK 
Sbjct: 11  GPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLKKLIIETDSKY 70

Query: 57  TLLALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNP 112
            +  +++ S      +L+      LL     + F   P      GNE  DR A+  
Sbjct: 71  VVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEVADRLAKEA 122

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

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

 Score = 44.4 bits (106), Expect = 6e-06
 Identities = 27/103 (26%), Positives = 35/103 (33%), Gaps = 33/103 (32%)

Query: 29  ELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCW---------- 78
           EL AV+  L+ LK       ++ +DS+           IN I   IH  W          
Sbjct: 45  ELTAVIEALEALK--EPCPVLLYTDSQYV---------INGITKWIHG-WKKNGWKTADG 92

Query: 79  -----SDL------LCCGKQLAFLWCPSHTGIQGNEAVDRAAR 110
                 DL      L    Q+ + W   H G  GNE  D  A 
Sbjct: 93  KPVKNVDLWQELDALLAKHQVTWHWVKGHAGHPGNERADELAN 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|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and repair]

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 23/94 (24%), Positives = 33/94 (35%), Gaps = 12/94 (12%)

Query: 29  ELIAVLLCLKHLKFLPKEKFVIISDSKS-----TLLALSNPSNINPIVSLIHSCWSDLLC 83
           EL A++  L+ LK L   +  + +DSK      T   +    N             DL  
Sbjct: 47  ELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWE 106

Query: 84  CGKQLA-------FLWCPSHTGIQGNEAVDRAAR 110
              +L        + W   H G   NE  D+ AR
Sbjct: 107 ELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140

Length = 154

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	267
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.84
PRK06548	161	ribonuclease H; Provisional	99.83
PRK08719	147	ribonuclease H; Reviewed	99.82
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.81
PRK00203	150	rnhA ribonuclease H; Reviewed	99.78
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.69
PRK13907	128	rnhA ribonuclease H; Provisional	99.63
KOG3752|consensus	371		99.6
PRK07708	219	hypothetical protein; Validated	99.45
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.38
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.3
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	96.07
cd01285	109	nucleoside_deaminase Nucleoside deaminases include	82.12
PRK10860	172	tRNA-specific adenosine deaminase; Provisional	80.42

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

Probab=99.84  E-value=4e-21  Score=153.54  Aligned_cols=114  Identities=19%  Similarity=0.171  Sum_probs=92.0

Q ss_pred             CceEEEEEeCCceEEEecC-CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC-----------Ch
Q psy2212           2 NTSCAYIIDKTSIYSFVLN-NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNI-----------NP   69 (267)
Q Consensus         2 ~~~g~ai~~~~~~~~~~l~-~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~-----------~~   69 (267)
                      +..|+++..++..+.++.+ ..+||++||+.|++.||+++...+...|.|+|||++|+++|+.|...           .|
T Consensus        19 gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~p   98 (154)
T COG0328          19 GGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKP   98 (154)
T ss_pred             ceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHHHHhhccccCccccccCc
Confidence            3567777756554433332 38999999999999999999988889999999999999999944222           12


Q ss_pred             H-HHHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212          70 I-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS  115 (267)
Q Consensus        70 ~-~~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  115 (267)
                      + -.+++..+.++......|.+.|||||+|.++||.||+||+.|+..
T Consensus        99 vkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~  145 (154)
T COG0328          99 VKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARA  145 (154)
T ss_pred             cccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHh
Confidence            2 256777788787787899999999999999999999999999875

>PRK06548 ribonuclease H; Provisional

Probab=99.83  E-value=4.2e-20  Score=149.88  Aligned_cols=112  Identities=22%  Similarity=0.226  Sum_probs=83.5

Q ss_pred             CceEEEEEeCCceEEEecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcC---------CCCC--ChH
Q psy2212           2 NTSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSN---------PSNI--NPI   70 (267)
Q Consensus         2 ~~~g~ai~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~---------~~~~--~~~   70 (267)
                      +.+|.+++..+..........+||+.|||.||+.||+.+.. +...+.|+|||++|+++|+.         |...  .|+
T Consensus        19 g~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV   97 (161)
T PRK06548         19 GPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPV   97 (161)
T ss_pred             CceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCcc
Confidence            35566655443222222224689999999999999986643 44579999999999999993         3222  355


Q ss_pred             H-HHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212          71 V-SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS  115 (267)
Q Consensus        71 ~-~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  115 (267)
                      . +++++.+..+... ..|.|.|||||+|++|||.||+||++|+..
T Consensus        98 ~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~  142 (161)
T PRK06548         98 LNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANN  142 (161)
T ss_pred             ccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence            4 6677777777554 479999999999999999999999998865

>PRK08719 ribonuclease H; Reviewed

Probab=99.82  E-value=8.6e-20  Score=146.59  Aligned_cols=106  Identities=23%  Similarity=0.211  Sum_probs=79.6

Q ss_pred             eEEEEEeCCc----eEEEecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhc--------CCCCC---C
Q psy2212           4 SCAYIIDKTS----IYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALS--------NPSNI---N   68 (267)
Q Consensus         4 ~g~ai~~~~~----~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~--------~~~~~---~   68 (267)
                      .|++|.+++.    .....+....||++|||.||+.||+.+...    ..|+|||++|+++|+        +.+..   .
T Consensus        25 ~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~  100 (147)
T PRK08719         25 IGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKK  100 (147)
T ss_pred             EEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHHHHHHHHHHHHHHhCCcccCCCc
Confidence            3555555432    234445566899999999999999998753    379999999999984        33322   1


Q ss_pred             hH-HHHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCC
Q psy2212          69 PI-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSA  114 (267)
Q Consensus        69 ~~-~~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~  114 (267)
                      ++ -.++++.+..+.. ...|+|.|||||+|++|||.||+||++|+.
T Consensus       101 ~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719        101 PVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             ccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            33 2567777776654 567999999999999999999999999864

>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=99.81  E-value=4.9e-20  Score=144.90  Aligned_cols=102  Identities=31%  Similarity=0.408  Sum_probs=78.3

Q ss_pred             ceEEEEEeCCceEEEecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcC-----CCCC---C-hHHHH
Q psy2212           3 TSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSN-----PSNI---N-PIVSL   73 (267)
Q Consensus         3 ~~g~ai~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~-----~~~~---~-~~~~~   73 (267)
                      .+|+ |+..+......++ ..|++.|||.||..||+ +..  ...+.|+|||+++++.+..     ....   . ++...
T Consensus        20 ~~g~-v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~~--~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~   94 (132)
T PF00075_consen   20 GAGY-VVWGGRNFSFRLG-GQSNNRAELQAIIEALK-ALE--HRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNE   94 (132)
T ss_dssp             EEEE-EEETTEEEEEEEE-SECHHHHHHHHHHHHHH-THS--TSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHH
T ss_pred             EEEE-EEECCeEEEeccc-ccchhhhheehHHHHHH-Hhh--cccccccccHHHHHHHHHHhccccccccccccccchhh
Confidence            4555 3454555556666 89999999999999999 443  3899999999999998877     2222   2 45565


Q ss_pred             HHHhHHHHHhcCCeEEEEEecCCCCC-chhhHHhHHhcCCC
Q psy2212          74 IHSCWSDLLCCGKQLAFLWCPSHTGI-QGNEAVDRAARNPS  113 (267)
Q Consensus        74 i~~~~~~l~~~~~~v~~~WvpgH~g~-~gNe~AD~lAk~a~  113 (267)
                      |++.+    ..+..|.|.|||||+|+ .||+.||+|||+|+
T Consensus        95 i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   95 IWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             eeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence            65544    55889999999999999 69999999999874

This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.78  E-value=1.1e-18  Score=140.92  Aligned_cols=109  Identities=19%  Similarity=0.193  Sum_probs=80.3

Q ss_pred             eEEEEEeCCceEEEe-cCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCC---------CCC--ChHH
Q psy2212           4 SCAYIIDKTSIYSFV-LNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNP---------SNI--NPIV   71 (267)
Q Consensus         4 ~g~ai~~~~~~~~~~-l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~---------~~~--~~~~   71 (267)
                      .|+++..++....+. .....||+.|||.|++.||+.+..  ...+.|+|||++++++|..|         ...  .|+.
T Consensus        21 ~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~   98 (150)
T PRK00203         21 WGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVK   98 (150)
T ss_pred             EEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccc
Confidence            345555555443333 235789999999999999998864  46799999999999999962         111  2332


Q ss_pred             -HHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212          72 -SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS  115 (267)
Q Consensus        72 -~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  115 (267)
                       .++++.+..+.. ...|.|.|||||+|++||+.||+||++|...
T Consensus        99 n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~  142 (150)
T PRK00203         99 NVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAGAEE  142 (150)
T ss_pred             cHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence             345555555533 3689999999999999999999999998875

>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=99.69  E-value=8e-16  Score=117.99  Aligned_cols=111  Identities=23%  Similarity=0.237  Sum_probs=85.3

Q ss_pred             ceEEEEEeCCceEEEe---cCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCC-CChHHHHHHHhH
Q psy2212           3 TSCAYIIDKTSIYSFV---LNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSN-INPIVSLIHSCW   78 (267)
Q Consensus         3 ~~g~ai~~~~~~~~~~---l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~-~~~~~~~i~~~~   78 (267)
                      ++|+++.+.+....+.   .....+++.+|+.|+..||+.+...+..++.|++||+.++..+++... ..+....+...+
T Consensus        16 g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i   95 (130)
T cd06222          16 GAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRL   95 (130)
T ss_pred             EEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhccccCCChhhHHHHHHH
Confidence            3444555554433332   214789999999999999999988889999999999999999998764 223333444444


Q ss_pred             HHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCC
Q psy2212          79 SDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPS  113 (267)
Q Consensus        79 ~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~  113 (267)
                      ..+...+..+.|.|||+|+|+.+|+.||.||+.+.
T Consensus        96 ~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          96 LALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             HHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            44546788999999999999999999999999873

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.

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.63  E-value=2e-15  Score=118.54  Aligned_cols=108  Identities=18%  Similarity=0.105  Sum_probs=85.7

Q ss_pred             ceEEEEEeCCceEEEec-CCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCChHHHHHHHhHHHH
Q psy2212           3 TSCAYIIDKTSIYSFVL-NNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCWSDL   81 (267)
Q Consensus         3 ~~g~ai~~~~~~~~~~l-~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~~~~~~~i~~~~~~l   81 (267)
                      .+|++|.+.+....... ....||+.||+.|++.||+.+...+..++.|+|||+++++.+++.+...+....++..+..+
T Consensus        18 G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l   97 (128)
T PRK13907         18 GAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQY   97 (128)
T ss_pred             EEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHHhcChhHHHHHHHHHHH
Confidence            34566656555444332 35689999999999999999999888899999999999999998765544456666666667


Q ss_pred             HhcCCeEEEEEecCCCCCchhhHHhHHhcCCCC
Q psy2212          82 LCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSA  114 (267)
Q Consensus        82 ~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~  114 (267)
                      ...+..+.|.|||.    +.|+.||.||++|..
T Consensus        98 ~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~  126 (128)
T PRK13907         98 IKSFDLFFIKWIPS----SQNKVADELARKAIL  126 (128)
T ss_pred             HhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence            67788889999997    599999999998864

>KOG3752|consensus

Probab=99.60  E-value=3.3e-15  Score=133.22  Aligned_cols=113  Identities=24%  Similarity=0.136  Sum_probs=88.6

Q ss_pred             ceEEEEEeC---CceEEEecC-CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC-----------
Q psy2212           3 TSCAYIIDK---TSIYSFVLN-NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNI-----------   67 (267)
Q Consensus         3 ~~g~ai~~~---~~~~~~~l~-~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~-----------   67 (267)
                      ++|.+|+=+   +...+.++. +..|||.|||.||..||+.+.+....+++|.|||++++++|+.|...           
T Consensus       230 ~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~  309 (371)
T KOG3752|consen  230 RAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNG  309 (371)
T ss_pred             cceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHHHHHHHhhhccCccccccC
Confidence            578888844   346667766 78999999999999999999988888999999999999999964322           


Q ss_pred             Ch----HH--HHHHHhHHHHHh--cCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212          68 NP----IV--SLIHSCWSDLLC--CGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS  115 (267)
Q Consensus        68 ~~----~~--~~i~~~~~~l~~--~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  115 (267)
                      ++    ++  ......+..|.+  .+.+|.+.|||||.|+.||+.||.+|+++...
T Consensus       310 ~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~  365 (371)
T KOG3752|consen  310 SDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL  365 (371)
T ss_pred             CCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence            12    11  223333444433  36899999999999999999999999998543

>PRK07708 hypothetical protein; Validated

Probab=99.45  E-value=1e-12  Score=112.15  Aligned_cols=111  Identities=13%  Similarity=0.008  Sum_probs=82.1

Q ss_pred             ceEEEEEeCCceEE------EecCCCCChhHHHHHHHHHHHHHhhhCCCCe--EEEEeccHHHHHHhcCCC-CCChHHHH
Q psy2212           3 TSCAYIIDKTSIYS------FVLNNVNSVFTSELIAVLLCLKHLKFLPKEK--FVIISDSKSTLLALSNPS-NINPIVSL   73 (267)
Q Consensus         3 ~~g~ai~~~~~~~~------~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~--i~I~sDS~~ai~~l~~~~-~~~~~~~~   73 (267)
                      .+|++|++.+....      ..++...||+.||+.|++.||+.+...+.+.  |.|++||+.+++.+++.+ ..++....
T Consensus        90 G~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~  169 (219)
T PRK07708         90 GLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNH  169 (219)
T ss_pred             EEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCceeCChhHHH
Confidence            45677776433222      2455568999999999999999999877654  899999999999999865 33455555


Q ss_pred             HHHhHHHHHhc-CCeEEEEEecCCCCCchhhHHhHHhcCCCCCCC
Q psy2212          74 IHSCWSDLLCC-GKQLAFLWCPSHTGIQGNEAVDRAARNPSASLP  117 (267)
Q Consensus        74 i~~~~~~l~~~-~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~~  117 (267)
                      +.+.+..+... ...+.|.|||    ...|+.||+||++|....+
T Consensus       170 y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~  210 (219)
T PRK07708        170 WLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTV  210 (219)
T ss_pred             HHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCC
Confidence            55555444333 3457889998    5689999999999998643

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

Probab=99.38  E-value=1.3e-12  Score=94.78  Aligned_cols=85  Identities=20%  Similarity=0.120  Sum_probs=65.8

Q ss_pred             hhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCChHHHHHHHhHHHHHhcCCeEEEEEecCCCCCchhhH
Q psy2212          25 VFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEA  104 (267)
Q Consensus        25 ~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~  104 (267)
                      +..||+.|+..||+++.+.+..++.|.|||+.+++.|++..........+...+..+...+..+.|.|||    .++|..
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~~   76 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----REQNKV   76 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------GGGSHH
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----hHHhHH
Confidence            4689999999999999999999999999999999999987544223344444455566778999999999    789999


Q ss_pred             HhHHhcCCC
Q psy2212         105 VDRAARNPS  113 (267)
Q Consensus       105 AD~lAk~a~  113 (267)
                      ||.||+.|.
T Consensus        77 A~~LA~~a~   85 (87)
T PF13456_consen   77 ADALAKFAL   85 (87)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999999764

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.30  E-value=2e-11  Score=112.50  Aligned_cols=108  Identities=16%  Similarity=0.147  Sum_probs=84.7

Q ss_pred             ceEEEEEeCC-c-e-EE--EecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCC-CChHHHHHHH
Q psy2212           3 TSCAYIIDKT-S-I-YS--FVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSN-INPIVSLIHS   76 (267)
Q Consensus         3 ~~g~ai~~~~-~-~-~~--~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~-~~~~~~~i~~   76 (267)
                      .+|++|.+.+ . . ..  ..+ ...||+.||+.|++.||+.+.+.+..++.|++||+++++.+++.+. +++-...+++
T Consensus        19 G~G~vi~~~~~~~~~~~~~~~~-~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~   97 (372)
T PRK07238         19 GYGAVVWDADRGEVLAERAEAI-GRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAA   97 (372)
T ss_pred             EEEEEEEeCCCCcEEEEeeccc-CCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHhCCCCccCChHHHHHHH
Confidence            3455555653 2 1 22  233 3789999999999999999999888999999999999999998653 4454555555


Q ss_pred             hHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212          77 CWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS  115 (267)
Q Consensus        77 ~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  115 (267)
                      .+..+...+..+.|.|||.    .+|+.||.||+.|...
T Consensus        98 ~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~  132 (372)
T PRK07238         98 QARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA  132 (372)
T ss_pred             HHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence            6666777888999999996    6999999999998765

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

Probab=96.07  E-value=0.0031  Score=45.70  Aligned_cols=42  Identities=19%  Similarity=0.313  Sum_probs=30.8

Q ss_pred             eeeeeccccc--c-cccccCCCCCCCc-ccCC-CCCcchhhc-CcccH
Q psy2212         177 CRMRIGHTRA--T-HGHLFKRAPPSTC-GCGE-ILSVQHILT-CALHG  218 (267)
Q Consensus       177 ~qlrTGH~~~--~-~~~r~~~~~~p~C-~Cg~-~et~~H~l~-Cp~~~  218 (267)
                      .--+.-|.++  . -+.+.+...++.| .|+. .||++|+|+ ||...
T Consensus        36 f~W~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~   83 (86)
T PF13966_consen   36 FLWRALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR   83 (86)
T ss_pred             EeeeeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCcc
Confidence            3344555555  2 3456677888999 9997 999999999 99753

>cd01285 nucleoside_deaminase Nucleoside deaminases include adenosine, guanine and cytosine deaminases

Probab=82.12  E-value=7  Score=29.29  Aligned_cols=54  Identities=13%  Similarity=0.075  Sum_probs=37.3

Q ss_pred             CceEEEEEeC-CceEEEecCC----CCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccH
Q psy2212           2 NTSCAYIIDK-TSIYSFVLNN----VNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSK   55 (267)
Q Consensus         2 ~~~g~ai~~~-~~~~~~~l~~----~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~   55 (267)
                      ..+|++|++. ++........    ......||..||..+.+...........+|+.-+
T Consensus        17 ~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~t~E   75 (109)
T cd01285          17 VPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLE   75 (109)
T ss_pred             CcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEEeCC
Confidence            4689999987 5555555442    2356789999999998875443456677777443

These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protei

>PRK10860 tRNA-specific adenosine deaminase; Provisional

Probab=80.42  E-value=6.5  Score=32.32  Aligned_cols=50  Identities=10%  Similarity=-0.005  Sum_probs=33.6

Q ss_pred             ceEEEEEeCCceEEEecCCC----CChhHHHHHHHHHHHHHhhhCCCCeEEEEe
Q psy2212           3 TSCAYIIDKTSIYSFVLNNV----NSVFTSELIAVLLCLKHLKFLPKEKFVIIS   52 (267)
Q Consensus         3 ~~g~ai~~~~~~~~~~l~~~----~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~s   52 (267)
                      .+|++|++.++.+.......    .....||+.||..|.+.+........++|+
T Consensus        34 pvGAVIV~~g~IIa~g~N~~~~~~d~~~HAEi~Ai~~a~~~~~~~~l~g~tlY~   87 (172)
T PRK10860         34 PVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDATLYV   87 (172)
T ss_pred             CEEEEEEeCCEEEEEeeCCCCCCCCCccCHHHHHHHHHHHhcCCCCcCCcEEEe
Confidence            68999998777666554321    123579999999998766443344566665

---

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	267
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	2e-07
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	2e-04
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	4e-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 = 48.7 bits (116), Expect = 2e-07
 Identities = 25/93 (26%), Positives = 39/93 (41%), Gaps = 19/93 (20%)

Query: 29  ELIAVLLCLKHLKFLPKEKFVIISDSKSTLLAL------SNPSNINPIVSLIHSCWSDLL 82
           ELIA+   LK  +    +K  + +DS+                N N I++L+       L
Sbjct: 67  ELIALTQALKMAE---GKKLNVYTDSRYAFATAHVHSEGREIKNKNEILALL-----KAL 118

Query: 83  CCGKQLAFLWCPSHTG-----IQGNEAVDRAAR 110
              K+L+ + CP H        +GN   D+AAR
Sbjct: 119 FLPKRLSIIHCPGHQKGNSAEARGNRMADQAAR 151

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A Length = 147

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 17/102 (16%), Positives = 28/102 (27%), Gaps = 25/102 (24%)

Query: 20  NNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCW- 78
                    E+ A L  +K        K  I+ D                I       W 
Sbjct: 45  AATMRNVAGEIAAALYAVKKAS-QLGVKIRILHDYAG-------------IAFWATGEWK 90

Query: 79  ---------SDLL-CCGKQLAFLWCPSHTGIQGNEAVDRAAR 110
                    + L+       +F    +H+G + N+ VD  A+
Sbjct: 91  AKNEFTQAYAKLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAK 132

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

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 23/104 (22%), Positives = 36/104 (34%), Gaps = 31/104 (29%)

Query: 29  ELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCWS--------- 79
           E+ A    ++  K     K V+ ++S  T         IN I + +   W          
Sbjct: 54  EIHAACKAIEQAKTQNINKLVLYTNSMFT---------INGITNWVQG-WKKNGWKTSAG 103

Query: 80  ------------DLLCCGKQLAFLWCPSHTGIQGNEAVDRAARN 111
                       + L  G  + ++  P H+G  GNE  DR AR 
Sbjct: 104 KEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLARE 147

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	267
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.85
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.84
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.84
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.82
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.81
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.8
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.8
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.77
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.73
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.72
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.69
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.68
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.67
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.67
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	98.99
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	98.78

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

Probab=99.85  E-value=4.7e-21  Score=154.21  Aligned_cols=112  Identities=19%  Similarity=0.190  Sum_probs=87.0

Q ss_pred             ceEEEEEeCC---ceEEEecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCC---------CC--C
Q psy2212           3 TSCAYIIDKT---SIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPS---------NI--N   68 (267)
Q Consensus         3 ~~g~ai~~~~---~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~---------~~--~   68 (267)
                      ++|++|+-.+   ..++..+++.+||+.|||.|++.||+.+...+..+|.|+|||++|++.|.++.         ..  .
T Consensus        25 ~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~~i~~~~~~w~~~~w~~~~~~  104 (154)
T 2qkb_A           25 RAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGK  104 (154)
T ss_dssp             EEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHHHHHTHHHHHHTTTSBCTTSS
T ss_pred             cEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHhhhhhhHHHHHhccccccCCC
Confidence            3787777432   24566777779999999999999999998877899999999999999998742         11  1


Q ss_pred             hH-HHHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212          69 PI-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS  115 (267)
Q Consensus        69 ~~-~~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  115 (267)
                      ++ ...++..+..+.. +..|.|.|||||+|++||+.||+||++|+..
T Consensus       105 ~~~n~~l~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~  151 (154)
T 2qkb_A          105 EVINKEDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREGAKQ  151 (154)
T ss_dssp             BCTTHHHHHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHHHTC
T ss_pred             ccccHHHHHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHHHHHHh
Confidence            21 1344444444433 4579999999999999999999999998765

>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=99.84  E-value=1.5e-20  Score=150.62  Aligned_cols=106  Identities=21%  Similarity=0.238  Sum_probs=77.7

Q ss_pred             eEEEEEeCCceEEEecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCC-----------CCChHH-
Q psy2212           4 SCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPS-----------NINPIV-   71 (267)
Q Consensus         4 ~g~ai~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~-----------~~~~~~-   71 (267)
                      +|+++.++ ......+ ..+||+.||+.|++.||+.+    ..++.|+|||++|+++|++|.           ...++. 
T Consensus        30 ~G~v~~~~-~~~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i~~w~~~W~~~gw~~~~g~~v~n  103 (150)
T 3qio_A           30 AGYVTNRG-RQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKN  103 (150)
T ss_dssp             EEEEETTS-CEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHHHHHHHHHCC------------C
T ss_pred             EEEEEEcC-CEEEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHHHHHHHHHhhcCcCcCcCccccc
Confidence            34433333 3333444 47899999999999999985    379999999999999998752           111221 


Q ss_pred             HHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212          72 SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS  115 (267)
Q Consensus        72 ~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  115 (267)
                      .++++.+..+...+..|.|.|||||+|++|||.||+||++|+..
T Consensus       104 ~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A          104 VDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            33444443333567899999999999999999999999999875

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

Probab=99.84  E-value=4.1e-21  Score=153.13  Aligned_cols=108  Identities=19%  Similarity=0.089  Sum_probs=77.1

Q ss_pred             eEEEEEeCCceEEE--ecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcC-CC-----------CCCh
Q psy2212           4 SCAYIIDKTSIYSF--VLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSN-PS-----------NINP   69 (267)
Q Consensus         4 ~g~ai~~~~~~~~~--~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~-~~-----------~~~~   69 (267)
                      +|+++.+++....+  .+ ..+||+.|||.|++.||+.+.+  ..++.|+|||++|++.|++ |.           ...+
T Consensus        22 ~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~~~~   98 (146)
T 3h08_A           22 WGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKP   98 (146)
T ss_dssp             EEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHHSSHHHHHHHTTCC----CC
T ss_pred             EEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHHHHHHHHHHHCCCccCCCCC
Confidence            45555565533332  33 4689999999999999999975  5799999999999999987 21           1111


Q ss_pred             H-HHHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212          70 I-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS  115 (267)
Q Consensus        70 ~-~~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  115 (267)
                      + ...++..+..+... ..|.|.|||||+|+++||.||+||++|+..
T Consensus        99 v~n~~l~~~~~~~~~~-~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A           99 VENIDLWQEILKLTTL-HRVTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             CTTHHHHHHHHHHHHH-SEEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHhh-CceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence            1 12333333334333 469999999999999999999999998754

>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=99.82  E-value=3e-20  Score=151.01  Aligned_cols=109  Identities=25%  Similarity=0.273  Sum_probs=81.0

Q ss_pred             ceEEEEEeCCceEEE-ecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCChHH-HHHHHhH-H
Q psy2212           3 TSCAYIIDKTSIYSF-VLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIV-SLIHSCW-S   79 (267)
Q Consensus         3 ~~g~ai~~~~~~~~~-~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~~~~~-~~i~~~~-~   79 (267)
                      .+|++|+.++....+ .++..+||+.||+.|++.||+.+   ...++.|+|||++|+++|-......++. .+++..+ .
T Consensus        40 g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~iw~~~~g~~v~n~dl~~~l~~  116 (165)
T 3p1g_A           40 RAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLK  116 (165)
T ss_dssp             EEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHHHSCCCSCCCSSHHHHHHHHH
T ss_pred             EEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhhhcccCCCcccCHHHHHHHHH
Confidence            356666666554433 45678899999999999999998   3689999999999999993212222221 2322222 3


Q ss_pred             HHHhcCCeEEEEEecCCCC-----CchhhHHhHHhcCCCCC
Q psy2212          80 DLLCCGKQLAFLWCPSHTG-----IQGNEAVDRAARNPSAS  115 (267)
Q Consensus        80 ~l~~~~~~v~~~WvpgH~g-----~~gNe~AD~lAk~a~~~  115 (267)
                      .+ ..+..|.|.|||||+|     ++|||.||+||++|+..
T Consensus       117 ~l-~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~  156 (165)
T 3p1g_A          117 AL-FLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMK  156 (165)
T ss_dssp             HT-TSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHH
T ss_pred             HH-hcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhc
Confidence            23 3678999999999999     99999999999999876

>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=99.81  E-value=5e-20  Score=148.42  Aligned_cols=109  Identities=19%  Similarity=0.231  Sum_probs=80.4

Q ss_pred             eEEEEEeCCceEEE--ecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCC--------C-CC--ChH
Q psy2212           4 SCAYIIDKTSIYSF--VLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNP--------S-NI--NPI   70 (267)
Q Consensus         4 ~g~ai~~~~~~~~~--~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~--------~-~~--~~~   70 (267)
                      +|+++.+.+....+  .+ +.+||+.|||.|++.||+.+..  ..++.|+|||++|++.|++|        + ..  .++
T Consensus        22 ~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~--~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v   98 (155)
T 1jl1_A           22 YGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPV   98 (155)
T ss_dssp             EEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBC
T ss_pred             EEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc--CCcEEEEeCHHHHHHHHHHHHHHHhhcccccccCCcc
Confidence            34555555433322  33 4679999999999999999976  37999999999999999973        1 11  122


Q ss_pred             H-HHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCCC
Q psy2212          71 V-SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASL  116 (267)
Q Consensus        71 ~-~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~  116 (267)
                      . ..++..+..+.. ...|.|.|||||+|++||+.||+||++|+...
T Consensus        99 ~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~  144 (155)
T 1jl1_A           99 KNVDLWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAAAMNP  144 (155)
T ss_dssp             TTHHHHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHHHHSC
T ss_pred             CCHHHHHHHHHHHc-cCceEEEEcCCCCCCHHHHHHHHHHHHHHhcc
Confidence            1 334444444433 46899999999999999999999999998763

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

Probab=99.80  E-value=6.5e-20  Score=148.20  Aligned_cols=108  Identities=19%  Similarity=0.203  Sum_probs=79.2

Q ss_pred             eEEEEEeCCceEEE--ecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcC--------CCCC---ChH
Q psy2212           4 SCAYIIDKTSIYSF--VLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSN--------PSNI---NPI   70 (267)
Q Consensus         4 ~g~ai~~~~~~~~~--~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~--------~~~~---~~~   70 (267)
                      +|+++.+++....+  .+ +.+||+.|||.|++.||+.+..  ..+|.|+|||++|++.|.+        .+..   .++
T Consensus        24 ~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v  100 (158)
T 2e4l_A           24 YGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKE--PCKIILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPV  100 (158)
T ss_dssp             EEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEECCHHHHHHHHTHHHHHHHTTTBCTTSSBC
T ss_pred             EEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhcc--CCeEEEEeCHHHHHHHHHHHHHHHHHccccccCCCcc
Confidence            34444455433322  33 3579999999999999999865  3899999999999999998        2211   122


Q ss_pred             H-HHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212          71 V-SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS  115 (267)
Q Consensus        71 ~-~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  115 (267)
                      . ..++..+..+.. ...|.|.|||||+|++||+.||+||++|+..
T Consensus       101 ~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A          101 KNVDLWKRLDKAAQ-LHQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             TTHHHHHHHHHHHT-TSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             cCHHHHHHHHHHHc-cCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            1 234444444433 3689999999999999999999999999875

>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=99.80  E-value=1.7e-20  Score=149.94  Aligned_cols=109  Identities=16%  Similarity=0.072  Sum_probs=83.2

Q ss_pred             eEEEEEeCCceEEE---ec--CC--CCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC-ChHHHHHH
Q psy2212           4 SCAYIIDKTSIYSF---VL--NN--VNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNI-NPIVSLIH   75 (267)
Q Consensus         4 ~g~ai~~~~~~~~~---~l--~~--~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~-~~~~~~i~   75 (267)
                      +|+++.+.+....+   .+  +.  .+||+.||+.|++.||+.+...+. +|.|+|||+.+.+.+.+.+.. .+....+.
T Consensus        22 ~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i~~w~~~~w~~~~~~~~~~~  100 (147)
T 2kq2_A           22 WAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGIAFWATGEWKAKNEFTQAYA  100 (147)
T ss_dssp             EEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTHHHHTTSSSSCCHHHHHHHH
T ss_pred             EEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHHHHHHhCCCccCCcchHHHH
Confidence            45555555543332   22  22  369999999999999999877666 999999999998877765433 34455666


Q ss_pred             HhHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCCC
Q psy2212          76 SCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASL  116 (267)
Q Consensus        76 ~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~  116 (267)
                      +++..|..   .|.|.|||||+|++|||.||+||++|+...
T Consensus       101 ~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~  138 (147)
T 2kq2_A          101 KLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALGIR  138 (147)
T ss_dssp             CGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHhcc
Confidence            66666633   799999999999999999999999998764

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

Probab=99.77  E-value=1.2e-19  Score=147.77  Aligned_cols=93  Identities=25%  Similarity=0.226  Sum_probs=73.0

Q ss_pred             CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcC----------CCCC--ChHH-HHHHHhHHHHHhcCCe
Q psy2212          21 NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSN----------PSNI--NPIV-SLIHSCWSDLLCCGKQ   87 (267)
Q Consensus        21 ~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~----------~~~~--~~~~-~~i~~~~~~l~~~~~~   87 (267)
                      ..+||+.|||.|++.||+.+...  .+|.|+|||++|++.|.+          |...  .++. ..++..+..+.. ...
T Consensus        44 ~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~-~~~  120 (166)
T 1ril_A           44 ACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA-PHR  120 (166)
T ss_dssp             EEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT-TSE
T ss_pred             CCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHh-cCe
Confidence            46799999999999999998753  589999999999999998          2211  1221 234444444433 358


Q ss_pred             EEEEEecCCCCCchhhHHhHHhcCCCCCC
Q psy2212          88 LAFLWCPSHTGIQGNEAVDRAARNPSASL  116 (267)
Q Consensus        88 v~~~WvpgH~g~~gNe~AD~lAk~a~~~~  116 (267)
                      |.|.|||||+|+++|+.||+||++|+...
T Consensus       121 v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~  149 (166)
T 1ril_A          121 VRFHFVKGHTGHPENERVDREARRQAQSQ  149 (166)
T ss_dssp             EECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             EEEEEeeCCCCchhHHHHHHHHHHHHHHh
Confidence            99999999999999999999999998763

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

Probab=99.73  E-value=4.9e-18  Score=137.86  Aligned_cols=93  Identities=18%  Similarity=0.183  Sum_probs=70.8

Q ss_pred             CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCC---------C--CChHH-HHHHHhHHHHHhcCCeE
Q psy2212          21 NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPS---------N--INPIV-SLIHSCWSDLLCCGKQL   88 (267)
Q Consensus        21 ~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~---------~--~~~~~-~~i~~~~~~l~~~~~~v   88 (267)
                      +..+++.||+.|+..||+.+...+ .+|.|+|||+||+++|+.|.         .  ..|+. .+++..+..+......|
T Consensus        52 nn~te~~Aei~Al~~al~~al~~~-~~v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v  130 (165)
T 2lsn_A           52 GNHTAQMAEIAAVEFACKKALKIP-GPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDI  130 (165)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHHHSS-SCEEEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTC
T ss_pred             hHHHHHHHHHHHHHHHHHHHhcCC-CeEEEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCE
Confidence            567889999999999998887643 57999999999999997531         1  12321 34444454444556789


Q ss_pred             EEEEecCCCCC------chhhHHhHHhcCCCC
Q psy2212          89 AFLWCPSHTGI------QGNEAVDRAARNPSA  114 (267)
Q Consensus        89 ~~~WvpgH~g~------~gNe~AD~lAk~a~~  114 (267)
                      .|.|||||+|+      +|||.||+||++|+.
T Consensus       131 ~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~  162 (165)
T 2lsn_A          131 TIQHEKGHQPTNTSIHTEGNALADKLATQGSY  162 (165)
T ss_dssp             EEEECCSSSCSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCccCCCCChHHHHHHHHHHHhhh
Confidence            99999999994      689999999998763

>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=99.72  E-value=3.4e-17  Score=129.02  Aligned_cols=108  Identities=15%  Similarity=0.113  Sum_probs=85.3

Q ss_pred             ceEEEEEeCC--c---eEEEecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCC-CCChHHHHHHH
Q psy2212           3 TSCAYIIDKT--S---IYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPS-NINPIVSLIHS   76 (267)
Q Consensus         3 ~~g~ai~~~~--~---~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~-~~~~~~~~i~~   76 (267)
                      .+|+++.+.+  .   .....+ +.+||+.||+.|++.||+.+...+..++.|+|||+++++.+++.+ ..++.+..+++
T Consensus        20 g~G~v~~~~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~i~~~~~~~~~~l~~~~~   98 (141)
T 3hst_B           20 GYGAVVWTADHSTVLAESKQAI-GRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYV   98 (141)
T ss_dssp             EEEEEEEETTSCSEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHHHTTSSCCCSHHHHHHHH
T ss_pred             EEEEEEEeCCCCcEEEeeeccC-CCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHHHhCCcccCCHHHHHHHH
Confidence            3455566653  2   222233 478999999999999999999888899999999999999999854 44555556666


Q ss_pred             hHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212          77 CWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS  115 (267)
Q Consensus        77 ~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  115 (267)
                      .+..+...+..|.|.|||+    ++|+.||+||++|+..
T Consensus        99 ~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B           99 QAQALASQFRRINYEWVPR----ARNTYADRLANDAMDA  133 (141)
T ss_dssp             HHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHHHHH
Confidence            6666767788999999995    7999999999998764

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

Probab=99.69  E-value=3.8e-17  Score=128.35  Aligned_cols=90  Identities=13%  Similarity=0.168  Sum_probs=73.5

Q ss_pred             CCCChhHHHHHHHHHHHHHhhhCCCC----eEEEEeccHHHHHHhcCCCC-CChHHHHHHHhHHHH-HhcCCeEEEEEec
Q psy2212          21 NVNSVFTSELIAVLLCLKHLKFLPKE----KFVIISDSKSTLLALSNPSN-INPIVSLIHSCWSDL-LCCGKQLAFLWCP   94 (267)
Q Consensus        21 ~~~t~~~AEl~Ai~~AL~~~~~~~~~----~i~I~sDS~~ai~~l~~~~~-~~~~~~~i~~~~~~l-~~~~~~v~~~Wvp   94 (267)
                      +.+||+.||+.|++.||+.+...+..    ++.|+|||+++++.+++++. .++-+..++..+..+ ...+..|.|.|||
T Consensus        41 ~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~  120 (140)
T 3u3g_D           41 GETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIP  120 (140)
T ss_dssp             EEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECC
T ss_pred             CCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcC
Confidence            35799999999999999999887666    99999999999999998663 344344444455555 5666789999999


Q ss_pred             CCCCCchhhHHhHHhcCCCC
Q psy2212          95 SHTGIQGNEAVDRAARNPSA  114 (267)
Q Consensus        95 gH~g~~gNe~AD~lAk~a~~  114 (267)
                      +    ++|+.||+||++|+.
T Consensus       121 ~----~~N~~AD~LA~~a~~  136 (140)
T 3u3g_D          121 R----EKNARADELVNEAID  136 (140)
T ss_dssp             G----GGGHHHHHHHHHHHH
T ss_pred             c----hhhHHHHHHHHHHHH
Confidence            4    799999999998864

>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=99.68  E-value=2.7e-16  Score=150.58  Aligned_cols=85  Identities=25%  Similarity=0.317  Sum_probs=72.0

Q ss_pred             CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC--ChHHHHHHHhHHHHHhcCCeEEEEEecCCCC
Q psy2212          21 NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNI--NPIVSLIHSCWSDLLCCGKQLAFLWCPSHTG   98 (267)
Q Consensus        21 ~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~--~~~~~~i~~~~~~l~~~~~~v~~~WvpgH~g   98 (267)
                      ..+||+.||+.|++.||+.    +..++.|+|||++|++.+++|...  .++.+.+.+.+    ..+..|.|.|||||+|
T Consensus       469 ~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~~~~~~~~~l~~~~~~~~----~~~~~v~~~wV~~H~g  540 (555)
T 1mu2_A          469 EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEM----IKKEAIYVAWVPAHKG  540 (555)
T ss_dssp             SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTCCSEESCHHHHHHHHHH----HHCSEEEEEECCSSSC
T ss_pred             CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhcccccccHHHHHHHHHHh----ccCCcEEEEEEECCCC
Confidence            4689999999999999998    468999999999999999987633  46666554433    3467899999999999


Q ss_pred             CchhhHHhHHhcCCC
Q psy2212          99 IQGNEAVDRAARNPS  113 (267)
Q Consensus        99 ~~gNe~AD~lAk~a~  113 (267)
                      ++|||.||+||++|+
T Consensus       541 ~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          541 IGGNQEVDHLVSQGI  555 (555)
T ss_dssp             CTTHHHHHHHHHTTC
T ss_pred             ChhHHHHHHHHHhhC
Confidence            999999999999985

>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=99.67  E-value=1.7e-16  Score=152.05  Aligned_cols=100  Identities=24%  Similarity=0.301  Sum_probs=75.6

Q ss_pred             eEEEEEe-CCceEEEecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC--ChHHHHHHHhHHH
Q psy2212           4 SCAYIID-KTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNI--NPIVSLIHSCWSD   80 (267)
Q Consensus         4 ~g~ai~~-~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~--~~~~~~i~~~~~~   80 (267)
                      +|++++. .+....+.+ ..+||+.||+.|++.||+.+    ..++.|+|||++|++.|+++...  .++.+.+.+.+  
T Consensus       455 ~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~~~~~~~~~l~~~~~~~l--  527 (557)
T 2zd1_A          455 GKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--  527 (557)
T ss_dssp             EEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTTCCSEESSHHHHHHHHHH--
T ss_pred             eEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhcCCccCCHHHHHHHHHHH--
Confidence            4444443 233333343 47899999999999999998    57999999999999999998755  46666554433  


Q ss_pred             HHhcCCeEEEEEecCCCCCchhhHHhHHhcCC
Q psy2212          81 LLCCGKQLAFLWCPSHTGIQGNEAVDRAARNP  112 (267)
Q Consensus        81 l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a  112 (267)
                        .....|.|.|||||+|++|||.||+||++|
T Consensus       528 --~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          528 --IKKEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             --HHCSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             --hcCCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence              234689999999999999999999999986

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

Probab=99.67  E-value=2e-16  Score=126.19  Aligned_cols=106  Identities=12%  Similarity=0.098  Sum_probs=80.4

Q ss_pred             EEEEEeCCceE-EE--ecC---CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC-ChHHHHHHHh
Q psy2212           5 CAYIIDKTSIY-SF--VLN---NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNI-NPIVSLIHSC   77 (267)
Q Consensus         5 g~ai~~~~~~~-~~--~l~---~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~-~~~~~~i~~~   77 (267)
                      |+++.+++... .+  .++   ..+||+.||+.|++.||+.+...+..++.|+|||+++++.+++++.. ++....+++.
T Consensus        22 G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi~~i~~~w~~~~~~~~~l~~~  101 (149)
T 2ehg_A           22 GFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEK  101 (149)
T ss_dssp             EEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHHHHHTTSSCCCCTTHHHHHHH
T ss_pred             EEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHHHHHhCccccCCHHHHHHHHH
Confidence            55666644432 22  223   37899999999999999999987788999999999999999997543 3334444444


Q ss_pred             HHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212          78 WSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS  115 (267)
Q Consensus        78 ~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~  115 (267)
                      +..+.... .|.|.|||+|    +|+.||+||++|+..
T Consensus       102 i~~l~~~~-~v~~~~V~~~----~N~~AD~LA~~a~~~  134 (149)
T 2ehg_A          102 AIELKKKL-NATLIWVPRE----ENKEADRLSRVAYEL  134 (149)
T ss_dssp             HHHHHHHH-TCEEEECCGG----GCHHHHHHHHHHHHH
T ss_pred             HHHHHhcC-CEEEEEcCCc----ccHHHHHHHHHHHHh
Confidence            44454444 4999999984    999999999998865

>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=98.99  E-value=2.4e-10  Score=90.18  Aligned_cols=100  Identities=15%  Similarity=0.013  Sum_probs=67.3

Q ss_pred             eEEEEEe--CCceEEEecC-CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC---------ChHH
Q psy2212           4 SCAYIID--KTSIYSFVLN-NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNI---------NPIV   71 (267)
Q Consensus         4 ~g~ai~~--~~~~~~~~l~-~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~---------~~~~   71 (267)
                      +|++++.  .+.......+ +.+||+.||+.|++.||+.+.+.+. ++.|+|||++|++.+.+.+..         .++.
T Consensus        27 ~G~G~vl~~~g~~~~~~~~~~~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~~~~~~k~~~~~~v~n~dLw  105 (142)
T 1zbf_A           27 VEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIW  105 (142)
T ss_dssp             EEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHH
T ss_pred             eEEEEEEEeCCEEEEEecccCCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHHHcCCccCCCCCCcccHHHH
Confidence            4555553  3333333222 3579999999999999999998766 999999999999999986522         1233


Q ss_pred             HHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHh
Q psy2212          72 SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVD  106 (267)
Q Consensus        72 ~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD  106 (267)
                      +.|..+...+...  .+....|+-|++.-||.-||
T Consensus       106 ~~l~~~~~w~~~~--~~~~~~~kw~~~~~ge~pad  138 (142)
T 1zbf_A          106 KLVDEAEEWLNTH--TYETPILKWQTDKWGEIKAD  138 (142)
T ss_dssp             HHHHHHHHHHHHC--CCCCCEEECCHHHHCSCTTC
T ss_pred             HHHHHHHHHHhhC--CCceeEEEeccCccCcCccc
Confidence            4443333333333  34444566688888888888

>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=98.78  E-value=9.4e-09  Score=79.83  Aligned_cols=44  Identities=18%  Similarity=0.189  Sum_probs=38.5

Q ss_pred             CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCC
Q psy2212          21 NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPS   65 (267)
Q Consensus        21 ~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~   65 (267)
                      +.+||+.||++|++.||+.+.+.+.. +.|+|||++|++.|.++.
T Consensus        41 ~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi~~~~   84 (134)
T 4htu_A           41 PIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWVKDKK   84 (134)
T ss_dssp             EEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHHHHTC
T ss_pred             CCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHHHcCC
Confidence            37899999999999999999885544 899999999999998753

---

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	267
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	7e-05
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	0.002
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	0.003

>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 = 39.5 bits (91), Expect = 7e-05
 Identities = 23/106 (21%), Positives = 40/106 (37%), Gaps = 7/106 (6%)

Query: 5   CAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNP 64
             Y+ D+       L    +   +EL A  + L         K  II DS+  +  +++ 
Sbjct: 25  AGYVTDRGKDKVKKLEQT-TNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVAS- 78

Query: 65  SNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAAR 110
                  S I +   + +   + +   W P+H GI GN+ VD    
Sbjct: 79  -QPTESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVS 123

>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 = 35.8 bits (81), Expect = 0.002
 Identities = 11/47 (23%), Positives = 18/47 (38%)

Query: 64  PSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAAR 110
            ++  P+ ++      D      Q+ + W   H G   NE  D  AR
Sbjct: 90  TADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELAR 136

>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 = 35.3 bits (80), Expect = 0.003
 Identities = 12/37 (32%), Positives = 15/37 (40%)

Query: 75  HSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARN 111
                 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	267
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.85
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.79
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.76
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.58
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.29
d1wkqa_	158	Guanine deaminase GuaD {Bacillus subtilis [TaxId:	82.36

>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=99.85  E-value=2.8e-21  Score=148.61  Aligned_cols=102  Identities=23%  Similarity=0.256  Sum_probs=76.9

Q ss_pred             ceEEEEEeC-CceEEEecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC--ChHHHHHHHhHH
Q psy2212           3 TSCAYIIDK-TSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNI--NPIVSLIHSCWS   79 (267)
Q Consensus         3 ~~g~ai~~~-~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~--~~~~~~i~~~~~   79 (267)
                      .+|++++.. +......++ ..||+.|||.||+.||+..    ...+.|+|||++|++.++++...  ......+   +.
T Consensus        22 ~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~~----~~~i~I~tDS~~v~~~~~~~~~~~~~~~~~~~---~~   93 (126)
T d1mu2a1          22 EGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTDS----GPKVNIIVDSQYVMGIVASQPTESESKIVNQI---IE   93 (126)
T ss_dssp             CEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHTS----CSEEEEEESCHHHHHHHHTCCSEESCHHHHHH---HH
T ss_pred             cEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhccC----CcceEEEechHHHHHHHhcCCccccchHHHHH---HH
Confidence            345555544 334444554 6799999999999999863    56899999999999999997654  2333222   22


Q ss_pred             HHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCC
Q psy2212          80 DLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPS  113 (267)
Q Consensus        80 ~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~  113 (267)
                      .+ .....|.|.|||||+|++|||.||+||++|.
T Consensus        94 ~~-~~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          94 EM-IKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             HH-HHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             Hh-hhcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            23 3456899999999999999999999999984

>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=99.79  E-value=6.7e-20  Score=144.65  Aligned_cols=116  Identities=18%  Similarity=0.209  Sum_probs=82.1

Q ss_pred             eEEEEEeCCceEEEecC-CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC-----------ChHH
Q psy2212           4 SCAYIIDKTSIYSFVLN-NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNI-----------NPIV   71 (267)
Q Consensus         4 ~g~ai~~~~~~~~~~l~-~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~-----------~~~~   71 (267)
                      .|++|++++....+..+ +.+||+.||++||+.||+++..  ...+.|++||++++..+..+...           .++.
T Consensus        20 ~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~~--~~~i~i~tds~~~i~~~~~~~~~~~~~~~~~~~~~~~~   97 (152)
T d1jl1a_          20 YGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVK   97 (152)
T ss_dssp             EEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCT
T ss_pred             EEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhcc--cceEEEeecceeeEEcccchhhHhHhccchhcccCeee
Confidence            35555566655444432 5679999999999999998753  56899999999999988754211           1111


Q ss_pred             -HHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCCCCCCCCCC
Q psy2212          72 -SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCS  123 (267)
Q Consensus        72 -~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~~~~~~~~  123 (267)
                       ..++..+..+ .....|.|.|||||+|++|||.||+||++|+... ...+.+
T Consensus        98 n~~~~~~i~~~-~~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~-~~~d~~  148 (152)
T d1jl1a_          98 NVDLWQRLDAA-LGQHQIKWEWVKGHAGHPENERADELARAAAMNP-TLEDTG  148 (152)
T ss_dssp             THHHHHHHHHH-TTTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSC-CBCCTT
T ss_pred             cHHHHHHHHHH-hhcceeEEEEecccCCCccHHHHHHHHHHHHhCC-CCCccC
Confidence             2233333333 3456899999999999999999999999999873 333433

>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=99.76  E-value=5.9e-20  Score=144.60  Aligned_cols=93  Identities=25%  Similarity=0.201  Sum_probs=71.5

Q ss_pred             CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC------------ChHH-HHHHHhHHHHHhcCCe
Q psy2212          21 NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNI------------NPIV-SLIHSCWSDLLCCGKQ   87 (267)
Q Consensus        21 ~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~------------~~~~-~~i~~~~~~l~~~~~~   87 (267)
                      ..+||+.||+.||+.||+.+..  ...+.|++||+++++.+..+...            .++. .+++..+..+ .....
T Consensus        39 ~~~Tnn~aEl~Ai~~AL~~~~~--~~~i~i~tds~~~~~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~-~~~~~  115 (147)
T d1rila_          39 ACTTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLA-MAPHR  115 (147)
T ss_dssp             EEECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHH-HTTSE
T ss_pred             ccccHHHHHHHHHHHHhhhccC--CceEEEecchhhhhccccccchhhhhhccccccccccchhHHHHHHHHHH-hhhcc
Confidence            4579999999999999998653  56899999999999988753211            1221 2334444444 34578


Q ss_pred             EEEEEecCCCCCchhhHHhHHhcCCCCCC
Q psy2212          88 LAFLWCPSHTGIQGNEAVDRAARNPSASL  116 (267)
Q Consensus        88 v~~~WvpgH~g~~gNe~AD~lAk~a~~~~  116 (267)
                      |.|.|||||+|++|||.||+||++|+.+.
T Consensus       116 v~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_         116 VRFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             EECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             cceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence            99999999999999999999999998763

>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=99.58  E-value=5.1e-15  Score=110.34  Aligned_cols=84  Identities=19%  Similarity=0.234  Sum_probs=62.4

Q ss_pred             eEEEEEeCC-ceEEEecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC--ChHHHHHHHhHHH
Q psy2212           4 SCAYIIDKT-SIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNI--NPIVSLIHSCWSD   80 (267)
Q Consensus         4 ~g~ai~~~~-~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~--~~~~~~i~~~~~~   80 (267)
                      +|++++..+ ......++ .+||+.|||.||+.||+..    ..++.|+|||+||+++++++...  .++.++|.+.+  
T Consensus        24 g~~g~~~~~~~~~~~~~~-~~TNn~aEl~Avi~aL~~~----~~~v~I~TDS~yvi~~i~~~~~~~~~~l~~~il~~l--   96 (110)
T d1s1ta1          24 GKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--   96 (110)
T ss_dssp             EEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHHHCCSEESCHHHHHHHHHH--
T ss_pred             cEEEEEEecCCeEEEecc-cCcHHHHHHHHHHHHHHhC----CCeEEEEEehHHHHHHHhcCccccchHHHHHHHHHH--
Confidence            444444432 34444454 6799999999999999853    46899999999999999987755  45666654433  


Q ss_pred             HHhcCCeEEEEEecCC
Q psy2212          81 LLCCGKQLAFLWCPSH   96 (267)
Q Consensus        81 l~~~~~~v~~~WvpgH   96 (267)
                        .....|.+.|||||
T Consensus        97 --~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          97 --IKKEKVYLAWVPAH  110 (110)
T ss_dssp             --HHCSEEEEEECCSS
T ss_pred             --hcCCceEEEEeCCC
Confidence              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=99.29  E-value=7.1e-13  Score=100.81  Aligned_cols=95  Identities=14%  Similarity=0.030  Sum_probs=66.5

Q ss_pred             CCceEEEecC-CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC----C-hHHHHHHHhHHHHH--
Q psy2212          11 KTSIYSFVLN-NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNI----N-PIVSLIHSCWSDLL--   82 (267)
Q Consensus        11 ~~~~~~~~l~-~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~----~-~~~~~i~~~~~~l~--   82 (267)
                      .+....++.+ +.+||++|||+|++.||+.+...+ .++.|+|||++|++.+.++...    . .--++++++++++.  
T Consensus        29 ~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~~kt~~~~~vkN~~l~~~i~~a~~~  107 (132)
T d1zbfa1          29 TGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEW  107 (132)
T ss_dssp             TCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHH
T ss_pred             CCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCceecCcCCCcccHHHHHHHHHHHHH
Confidence            3444444332 578999999999999999998754 6799999999999999875522    1 11233433333321  


Q ss_pred             hcCCeEEEEEecCCCCCchhhHHh
Q psy2212          83 CCGKQLAFLWCPSHTGIQGNEAVD  106 (267)
Q Consensus        83 ~~~~~v~~~WvpgH~g~~gNe~AD  106 (267)
                      -....+.+.|++.|+..-||..||
T Consensus       108 lk~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1         108 LNTHTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             HHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             HHhCCcCceeEEecCcccccCCCC
Confidence            123457788999999999999888

>d1wkqa_ c.97.1.2 (A:) Guanine deaminase GuaD {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Cytidine deaminase-like
superfamily: Cytidine deaminase-like
family: Deoxycytidylate deaminase-like
domain: Guanine deaminase GuaD
species: Bacillus subtilis [TaxId: 1423]

Probab=82.36  E-value=1.2  Score=33.05  Aligned_cols=51  Identities=18%  Similarity=0.138  Sum_probs=36.6

Q ss_pred             CceEEEEEeCCceEEEecCC----CCChhHHHHHHHHHHHHHhhhCCCCeEEEEe
Q psy2212           2 NTSCAYIIDKTSIYSFVLNN----VNSVFTSELIAVLLCLKHLKFLPKEKFVIIS   52 (267)
Q Consensus         2 ~~~g~ai~~~~~~~~~~l~~----~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~s   52 (267)
                      +.+|++|++++..+......    ......||+.||..|...+........++|+
T Consensus        26 ~PvGaviv~~~~ii~~g~n~~~~~~~~t~HAE~~ai~~a~~~~~~~~l~~~tlyv   80 (158)
T d1wkqa_          26 GPFGAVIVKDGAIIAEGQNNVTTSNDPTAHAEVTAIRKACKVLGAYQLDDCILYT   80 (158)
T ss_dssp             SSCEEEEEETTEEEEEEECCHHHHTCTTCCHHHHHHHHHHHHHTSSSCTTEEEEE
T ss_pred             CCEEEEEEecccceeeccceeeccCCCcccHHHHHHHHHHHhcCccccCCCEEEE
Confidence            34899999988877766542    1122479999999999887665555666666