Psyllid ID: psy7660

---

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
Protein Sequence
GSKTLQNTSCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAEIVNLSSPADLIPVGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRYEESISWSGNKCFIDHYSHPYLKVLPFNMFKQSYKYLMCPVIASACDSVLVSLSDFLVVLALSERTRVRVWTLDNLYN
Secondary Structure (PSIPRED)
cccccccEEEEEEEcccEEEEEcccccHHHHHHHHHHHHHHHHHcccccccEEEEEcHHHHHHHHHccccccHHHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccEEEEcccccccccccccccHHHHHHHHHcccccccEEEEccccc
Secondary Structure Prediction (SSPRO)
cccccccEEEEEEEcccEEEEEccccccHHHHHHHHHHHHHHHHHHcccccEEEEEcHHHHHHHHHcccccHHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHcHccHHHHcccccccccccccccccEEEEEEEHHHcccccccHHHHEccccHHcccccEEEEccccccccccEEccHHHHHHHHHHHcccEEEEEEHHHccc
Coil and Loop (DISEMBL)
gsktlqntscavyaggttksYILNNINSIFTAELLAIVFCLdsvknrpdvntlIVCDSMSALTSIANKNTTIPLIAHILNTWYSLkscgknvaflwcpshtgisgneIVDRAtrqldgaeivnlsspadlipvGKKYLLEKWQKSWTELINNKLKrikptigpwnvsdcnsryeesiswsgnkcfidhyshpylkvlpfnmfkqsykylmcpvIASACDSVLVSLSDFLVVLALSERTRVRVWTLDNLYN
Flexible Loop (DISEMBL)
gsktlqntscaVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAeivnlsspadlipVGKKYLLEKWQKSWTELINNKlkrikptigpwnvsDCNSRYEESISWSGNKCFIDHYSHPYLKVLPFNMFKQSYKYLMCPVIASACDSVLVSLSDFLVVlalsertrvrvwtldnlyn
Low Complexity Region (SEG)
GSKTLQNTSCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAEIVNLSSPADLIPVGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRYEESISWSGNKCFIDHYSHPYLKVLPFNMFKQSYKYLMCPVIASACDsvlvslsdflvvlalsERTRVRVWTLDNLYN
Disordered region (IsUnstruct)
********SCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAEIVNLSSPADLIPVGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRYEESISWSGNKCFIDHYSHPYLKVLPFNMFKQSYKYLMCPVIASACDSVLVSLSDFLVVLALSERTRVRVWTLDNL**
Disordered Region (DISOPRED)
*****QNTSCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAEIVNLSSPADLIPVGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRYEESISWSGNKCFIDHYSHPYLKVLPFNMFKQSYKYLMCPVIASACDSVLVSLSDFLVVLALSERTRVRVWTLDNLYN
Disordered Region (DISEMBL)
GSKTLQNTSCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAEIVNLSSPADLIPVGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRYEESISWSGNKCFIDHYSHPYLKVLPFNMFKQSYKYLMCPVIASACDSVLVSLSDFLVVLALSERTRVRVWTLDNLYN
Disordered Region (DISPRO)
*****QNTSCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAEIVNLSSPADLIPVGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRYEESISWSGNKCFIDHYSHPYLKVLPFNMFKQSYKYLMCPVIASACDSVLVSLSDFLVVLALSERTRVRVWTLDNLYN
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
GSKTLQNTSCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAEIVNLSSPADLIPVGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRYEESISWSGNKCFIDHYSHPYLKVLPFNMFKQSYKYLMCPVIASACDSVLVSLSDFLVVLALSERTRVRVWTLDNLYN
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	250
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.888	0.471	0.318	3e-23
443713753	266	hypothetical protein CAPTEDRAFT_215116 [	0.7	0.657	0.342	8e-21
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.816	0.781	0.342	2e-19
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.792	0.394	0.343	2e-19
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.792	0.498	0.338	7e-19
443724607	397	hypothetical protein CAPTEDRAFT_208903 [	0.78	0.491	0.333	3e-17
427778603	1397	Putative tick transposon [Rhipicephalus	0.644	0.115	0.310	4e-17
443682433	619	hypothetical protein CAPTEDRAFT_222606 [	0.7	0.282	0.318	2e-16
443710566	377	hypothetical protein CAPTEDRAFT_186063 [	0.668	0.442	0.341	4e-16
443720278	498	hypothetical protein CAPTEDRAFT_219461 [	0.56	0.281	0.354	1e-15

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

 Score =  114 bits (286), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 74/232 (31%), Positives = 115/232 (49%), Gaps = 10/232 (4%)

Query: 1   GSKTLQNTSCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVC-DSM 59
           GSK+  + +C+ ++        L    S+FT+E++AI+  L  V+   + +  ++C DS+
Sbjct: 27  GSKSEDSVACSFFSSRLKLKMKLPVQMSVFTSEIIAILSALRCVEADNEQHQFVICSDSL 86

Query: 60  SALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDR-ATRQLDG 118
           SA+ +I   +   P +  +L    S+    K V F+WCPSH GI GNE+ D  A   L  
Sbjct: 87  SAIMAIHGMDVRHPYVLQVLYAIKSISQQEKIVVFMWCPSHVGIPGNEMADTLAKEALSS 146

Query: 119 AEIVNLSSPA-DLIPVGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRYEESI 177
             +  L  PA DL  + KKY+  +WQ  W E  +NKL  I PTIGPW       R EE I
Sbjct: 147 TNLAELPVPASDLRCLIKKYIRSRWQHEWDEQHSNKLHSIHPTIGPWPPCQREKRREE-I 205

Query: 178 SWSGNKCFIDHYSHPYLKVLPFNMFKQSYKYLMCPVIASACDSVLVSLSDFL 229
             +  +    HY+H Y   +P    +      +CP+       +++  +DFL
Sbjct: 206 VLARIRIGHTHYTHDY---IPRGDDQTECVACVCPLTVQ---HIIIECADFL 251

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443713753|gb|ELU06453.1| hypothetical protein CAPTEDRAFT_215116 [Capitella teleta]

 Score =  106 bits (265), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 61/178 (34%), Positives = 92/178 (51%), Gaps = 3/178 (1%)

Query: 1   GSKTLQNTSCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVC-DSM 59
           GSK+  + + + ++        L    S+FT+E++AI+  L  ++   + +  ++C DS+
Sbjct: 82  GSKSEDSVARSFFSSRLKLKMKLPVQMSVFTSEIIAILSALKCLEADNEQHQFVICSDSL 141

Query: 60  SALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDR-ATRQLDG 118
           SA+ +I   +   P +  +L    S+    K V F+WCPSH GI GNE+    A + L  
Sbjct: 142 SAIMAIHGMDVHHPYVLQVLYAIKSISQQEKIVVFMWCPSHVGIPGNEMAHTLAEKALSS 201

Query: 119 AEIVNLSSPA-DLIPVGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRYEE 175
             +  L  PA DL  + KKY+  +WQ  W E  NNKL  I PTIGPW       R EE
Sbjct: 202 TNLAELPVPASDLRGLIKKYIRSQWQHEWEEQHNNKLHSIHPTIGPWPPCQREKRREE 259

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 =  102 bits (254), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 72/210 (34%), Positives = 102/210 (48%), Gaps = 6/210 (2%)

Query: 1   GSKTLQNTSCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVC-DSM 59
           GSK+    +CA         + L    SI+TAEL+AI   L  ++   D +   +C DS+
Sbjct: 42  GSKSNDAVACAFTCSTYQIQFGLPAQMSIYTAELIAIEQALIFIETVKDEDQFNICSDSL 101

Query: 60  SALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGA 119
           S+LT+++N + T P +  IL    +L   GK V F+WCPSH GI GNE+ DR  +Q    
Sbjct: 102 SSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQALVM 161

Query: 120 EIVNLSSP-ADLIPVGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRYEESIS 178
            +  L  P  D     + Y+   WQ  W E  +NKL  I+P I  W       R  E I 
Sbjct: 162 PVTKLPLPHTDYKSPIRSYVKSLWQNEWDEETDNKLHSIQPVISEWKQGPQIDRRGE-IV 220

Query: 179 WSGNKCFIDHYSHPYL---KVLPFNMFKQS 205
            +  +    H +H YL   +V PF +  QS
Sbjct: 221 LARARIGHSHLTHGYLLRREVAPFCIPCQS 250

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  102 bits (253), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/204 (34%), Positives = 99/204 (48%), Gaps = 6/204 (2%)

Query: 1   GSKTLQNTSCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVC-DSM 59
           GSK+    +CA         + L    SI+TAEL+AI   L  ++   D +   +C DS+
Sbjct: 88  GSKSNNAVACAFTCSTYQIQFGLPTQMSIYTAELIAIEQALIFIETVKDEDQFNICSDSL 147

Query: 60  SALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGA 119
           S+LT+++N + T P +  IL    +L   GK V F+WCPSH GI GNE+ DR  +Q    
Sbjct: 148 SSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQALVM 207

Query: 120 EIVNLSSP-ADLIPVGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRYEESIS 178
            +  L  P  D     + Y+   WQ  W E  +NKL  I+P I  W       R  E I 
Sbjct: 208 PVTKLPLPHTDYKSPIRSYVKSLWQNEWDEETDNKLHSIQPVISEWKQGPQIDRRGE-IV 266

Query: 179 WSGNKCFIDHYSHPYL---KVLPF 199
            +  +    H +H YL   +V PF
Sbjct: 267 LARARIGHSHLTHGYLLRREVAPF 290

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 =  100 bits (248), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 69/204 (33%), Positives = 98/204 (48%), Gaps = 6/204 (2%)

Query: 1   GSKTLQNTSCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVC-DSM 59
           GSK+    +CA         + L    SI+TAEL+AI   L  ++   D +   +C DS+
Sbjct: 137 GSKSNDTVACAFTCSTYQIQFGLPAQMSIYTAELIAIEQALIFIETVKDEDQFNICSDSL 196

Query: 60  SALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGA 119
           S+LT+++N + T P +  IL    +L   GK V F+WCPSH GI GNE+ DR  +Q    
Sbjct: 197 SSLTALSNCDITHPYLLSILTKQNNLVRKGKKVVFIWCPSHVGILGNEVADRQAKQALVM 256

Query: 120 EIVNLSSP-ADLIPVGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRYEESIS 178
            +  L  P  D     + Y+   WQ  W    +NKL  I+P I  W       R  E I 
Sbjct: 257 PVTKLPLPHTDYKSPIRSYVKSLWQNEWDGETDNKLHIIQPVISEWKQGPQIDRRGE-IV 315

Query: 179 WSGNKCFIDHYSHPYL---KVLPF 199
            +  +    H +H YL   +V PF
Sbjct: 316 LACARIGHSHLTHGYLLRREVAPF 339

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 = 95.1 bits (235), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 99/207 (47%), Gaps = 12/207 (5%)

Query: 1   GSKTLQNTSCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVC-DSM 59
           GSK+    +CA         + L    SI+TAEL+AI   L  ++   D +   +C DS+
Sbjct: 137 GSKSNDAVACAFTCSTYQIQFGLPAQMSIYTAELIAIEQALIFIETMKDEDQFNICSDSL 196

Query: 60  SALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGA 119
           S+LT+++N + T P +  IL    +L   GK V F+WCPSH GI GNE+ DR  +Q    
Sbjct: 197 SSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQALVM 256

Query: 120 EIVNLSSP-ADLIPVGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRYEESI- 177
            +  L  P  D     + Y+    Q  W E  +NKL  I+P I  W       R  E + 
Sbjct: 257 PVTKLPLPHTDYKSPIRSYVKSLRQNEWDEETDNKLHTIQPVISEWKQGPQIDRRGEIVL 316

Query: 178 --SWSGNKCFIDHYSHPYL---KVLPF 199
             +  G+     H +H YL   +V PF
Sbjct: 317 ACACIGH----SHLTHGYLLRREVAPF 339

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 94.4 bits (233), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 51/164 (31%), Positives = 88/164 (53%), Gaps = 3/164 (1%)

Query: 1    GSKTLQNTSCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMS 60
            GSK+  + SCA Y    + +  L+   SIFTAE   I+  ++ +K      ++I  DS+S
Sbjct: 1115 GSKSQTSVSCAAYGESFSDAKTLHAHTSIFTAEAYGILLIVEHIKQHMIRRSIIYTDSLS 1174

Query: 61   ALTSIA-NKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGA 119
             +T+++  K +  P+   +LN  +   +   ++   W P H GI+GNE+VD+  R+    
Sbjct: 1175 VVTALSCGKCSKNPVFNKLLNNMHEAYNQNLSIVLCWVPGHAGITGNEMVDKNAREAASR 1234

Query: 120  EIVNLSS--PADLIPVGKKYLLEKWQKSWTELINNKLKRIKPTI 161
              +++SS    DL PV ++ L   WQ  W + ++NKL  +KP +
Sbjct: 1235 HTIDISSVPGVDLNPVVRRGLRSHWQVEWDKQVDNKLHLVKPHL 1278

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 92.4 bits (228), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 56/176 (31%), Positives = 85/176 (48%), Gaps = 1/176 (0%)

Query: 1   GSKTLQNTSCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMS 60
           GSK+     CA ++     +  L    S++TAEL+AI   L S+   P    +I  DS S
Sbjct: 3   GSKSEDAVGCAFHSRDFNLALGLPCQMSVYTAELIAINETLTSIALLPYDEFVICTDSFS 62

Query: 61  ALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAE 120
           ++ +I++ +     +  IL    +L    K + F+WCPSH GI GNE  D   +Q  G  
Sbjct: 63  SILAISSIDLIHSYVQSILQKCTNLAGRDKRIIFIWCPSHVGIPGNETADTLAQQASGMN 122

Query: 121 IVNLSSP-ADLIPVGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRYEE 175
           I+N   P  D  P+ + ++  +WQ    +   NKL  I+P IG W       R +E
Sbjct: 123 ILNCPIPHTDFKPITRSFVETQWQSESDQETGNKLHDIEPDIGSWPPCQREKRRDE 178

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443710566|gb|ELU04776.1| hypothetical protein CAPTEDRAFT_186063 [Capitella teleta]

 Score = 91.3 bits (225), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 58/170 (34%), Positives = 80/170 (47%), Gaps = 3/170 (1%)

Query: 1   GSKTLQNTSCAVYAGGTTKSYILNNINSIFTAELLAI--VFCLDSVKNRPDVNTLIVCDS 58
           GSK+    +C   A   +    L +  SIF+AELLAI  V  L           LI  DS
Sbjct: 193 GSKSDSAVACFATADNLSIQIRLPDSASIFSAELLAIYQVLTLLECSANDQQQFLIATDS 252

Query: 59  MSALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDG 118
           +S+L +I N N   P +  IL     L   G  +   WCPSH G+ GNE  D   ++   
Sbjct: 253 LSSLQAIGNFNIKHPYVFKILEKCTLLHKKGIYLVMAWCPSHVGVMGNERADLLAKEALS 312

Query: 119 AEIVNLSSP-ADLIPVGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVS 167
                +  P +D  P+  ++  EKWQ+ W+    NKL  I+PT+G W  S
Sbjct: 313 FTTCTIRIPSSDFKPITHEFFKEKWQEQWSSEQENKLYCIQPTLGKWAKS 362

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443720278|gb|ELU10076.1| hypothetical protein CAPTEDRAFT_219461 [Capitella teleta]

 Score = 89.4 bits (220), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 50/141 (35%), Positives = 73/141 (51%), Gaps = 1/141 (0%)

Query: 28  SIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTTIPLIAHILNTWYSLKS 87
           S++TAEL+AI   L S+   P    +I  D +S++ +I++ +   P +  IL     L  
Sbjct: 114 SVYTAELIAINETLTSIALLPYDEFVICTDFLSSILAISSIDLIHPYVQSILQKCTCLAG 173

Query: 88  CGKNVAFLWCPSHTGISGNEIVDRATRQLDGAEIVNLSSP-ADLIPVGKKYLLEKWQKSW 146
             K + F+WCPSH GI GNE  D   +Q  G  I+N   P  D  P+   ++  +WQ  W
Sbjct: 174 RDKRIIFIWCPSHVGIPGNETADTVAKQALGMNILNCHIPHTDFKPITCSFVKTQWQSEW 233

Query: 147 TELINNKLKRIKPTIGPWNVS 167
            +   NKL  I+P IG W  S
Sbjct: 234 DQETGNKLHDIQPDIGSWPPS 254

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

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)

No hits with e-value below 0.001 by BLAST

---

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	250
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	2e-25
pfam00075	126	pfam00075, RNase_H, RNase H	3e-12
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	2e-04

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

 Score = 96.9 bits (242), Expect = 2e-25
 Identities = 37/120 (30%), Positives = 54/120 (45%), Gaps = 5/120 (4%)

Query: 1   GSKTLQNTSCAVYA---GGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPD-VNTLIVC 56
           GSK    T         G  ++SY L    S+F AELLAI+  L            + + 
Sbjct: 6   GSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRARKITIF 65

Query: 57  -DSMSALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQ 115
            DS +AL ++ +  ++ PL+  I      L + G  V   W P H+GI GNE  DR  ++
Sbjct: 66  SDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLAKE 125

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 = 61.9 bits (151), Expect = 3e-12
 Identities = 33/105 (31%), Positives = 47/105 (44%), Gaps = 4/105 (3%)

Query: 11  AVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT 70
            V  GG  +S  L    +   AELLA++  L+++  +  VN  I  DS   +  I N   
Sbjct: 23  YVTDGGKQRSKPLPG-TTNQRAELLALIEALEALSGQK-VN--IYTDSQYVIGGITNGWP 78

Query: 71  TIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQ 115
           T      I N  + L      V   W P H+GI GNE+ D+  +Q
Sbjct: 79  TKSESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNELADKLAKQ 123

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|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 = 39.6 bits (93), Expect = 2e-04
 Identities = 20/92 (21%), Positives = 35/92 (38%), Gaps = 4/92 (4%)

Query: 24  NNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTTIPLIAHILNTWY 83
               +   AELLA++  L+   +      +I  DS   +  I + +        +L    
Sbjct: 34  IPAATNNEAELLALLEALELALDLGLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDIL 93

Query: 84  SLKSCGKNVAFLWCPSHTGISGNEIVDRATRQ 115
            L S   ++ F   P      GNE+ DR  ++
Sbjct: 94  LLLSKFIDIRFEHVPR----EGNEVADRLAKE 121

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	250
PRK06548	161	ribonuclease H; Provisional	99.85
PRK08719	147	ribonuclease H; Reviewed	99.83
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.83
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.82
PRK00203	150	rnhA ribonuclease H; Reviewed	99.8
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.74
KOG3752|consensus	371		99.67
PRK13907	128	rnhA ribonuclease H; Provisional	99.62
PRK07708	219	hypothetical protein; Validated	99.39
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.38
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.37
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	81.89

>PRK06548 ribonuclease H; Provisional

Probab=99.85  E-value=6.7e-21  Score=157.26  Aligned_cols=115  Identities=26%  Similarity=0.262  Sum_probs=87.1

Q ss_pred             CCCCCc-eEEEEEECCeeEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcC---------CC-
Q psy7660           2 SKTLQN-TSCAVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANK---------NT-   70 (250)
Q Consensus         2 S~~~~~-~G~g~v~~~~~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~---------~~-   70 (250)
                      +..+++ .|+|+++.+.....+....+|++.|||.||+.||+.+.. ...+|.|+|||++|+++|+.+         .. 
T Consensus        14 ~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s   92 (161)
T PRK06548         14 SLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWVYSWKMRKWRKA   92 (161)
T ss_pred             cCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHHHHHHHCCCccc
Confidence            444544 788888754322223335689999999999999986643 345799999999999999942         21 


Q ss_pred             -chHHH-HHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhc
Q psy7660          71 -TIPLI-AHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDG  118 (250)
Q Consensus        71 -~~~~~-~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~  118 (250)
                       ++++. +++++.+..+..+ ..|+|.|||||+|++|||.||+||++|+.
T Consensus        93 ~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~  141 (161)
T PRK06548         93 DGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAAN  141 (161)
T ss_pred             CCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHH
Confidence             44544 5666666666554 47999999999999999999999999985

>PRK08719 ribonuclease H; Reviewed

Probab=99.83  E-value=3.3e-20  Score=151.29  Aligned_cols=106  Identities=20%  Similarity=0.233  Sum_probs=80.9

Q ss_pred             eEEEEEE--CCe----eEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhh--------cCCC---
Q psy7660           8 TSCAVYA--GGT----TKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIA--------NKNT---   70 (250)
Q Consensus         8 ~G~g~v~--~~~----~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~--------~~~~---   70 (250)
                      .|+|+++  ++.    ..+..+....|+++|||.||..||+.+.+.    ..|+|||++++++|+        +.+.   
T Consensus        23 ~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~   98 (147)
T PRK08719         23 GGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYCVRGFNEWLDTWKQKGWRKSD   98 (147)
T ss_pred             cEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHHHHHHHHHHHHHHhCCcccCC
Confidence            4777765  322    234445566899999999999999998753    379999999999994        3332   


Q ss_pred             chHH-HHHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhc
Q psy7660          71 TIPL-IAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDG  118 (250)
Q Consensus        71 ~~~~-~~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~  118 (250)
                      +.++ -.++++.+..|.+ ...|.|.|||||+|++|||.||+||++|++
T Consensus        99 g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         99 KKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             CcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            2233 2456667776755 567999999999999999999999999874

>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=99.83  E-value=1.6e-20  Score=148.52  Aligned_cols=102  Identities=29%  Similarity=0.390  Sum_probs=79.2

Q ss_pred             eEEEEEE-CCeeEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhc-----CCC---ch-HHHHH
Q psy7660           8 TSCAVYA-GGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIAN-----KNT---TI-PLIAH   77 (250)
Q Consensus         8 ~G~g~v~-~~~~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~-----~~~---~~-~~~~~   77 (250)
                      .|+|+++ .+...++.++ .++++.|||.||..||+ +..  ..++.|+|||+++++.|..     .+.   .. ++..+
T Consensus        19 ~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~~--~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~   94 (132)
T PF00075_consen   19 GGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALK-ALE--HRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNE   94 (132)
T ss_dssp             EEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHH-THS--TSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHH
T ss_pred             eEEEEEEECCeEEEeccc-ccchhhhheehHHHHHH-Hhh--cccccccccHHHHHHHHHHhccccccccccccccchhh
Confidence            4666654 3444555566 89999999999999999 443  3999999999999998888     332   12 46566


Q ss_pred             HHHHHHHHHhCCCceEEEeccCCCCC-ccchHHhHHHHhhh
Q psy7660          78 ILNTWYSLKSCGKNVAFLWCPSHTGI-SGNEIVDRATRQLD  117 (250)
Q Consensus        78 i~~~~~~l~~~g~~V~~~WVPgH~gi-~gNe~AD~lAk~a~  117 (250)
                      |++.+    .++..|.|+|||||+|+ .|||.||+|||+|+
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            66554    45889999999999999 69999999999986

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

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

Probab=99.82  E-value=5.6e-20  Score=149.94  Aligned_cols=118  Identities=18%  Similarity=0.124  Sum_probs=93.7

Q ss_pred             CCCCCc-eEEEEEEC--Cee--EEEecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC------
Q psy7660           2 SKTLQN-TSCAVYAG--GTT--KSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT------   70 (250)
Q Consensus         2 S~~~~~-~G~g~v~~--~~~--~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~------   70 (250)
                      |..|+| .|+|+|..  +..  .+.+.. .+|+++||+.|++.||+.+.+.+...|.|+|||++++++|..+..      
T Consensus        12 ~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~   90 (154)
T COG0328          12 CLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNG   90 (154)
T ss_pred             cCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHHHHhhccccC
Confidence            445555 67777763  332  333334 899999999999999999998889999999999999999995411      


Q ss_pred             -----chHH-HHHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhccc
Q psy7660          71 -----TIPL-IAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAE  120 (250)
Q Consensus        71 -----~~~~-~~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~~~  120 (250)
                           ++++ ..++++.+.++..+...|.+.|||||+|.++||.||+||+.|+...
T Consensus        91 w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          91 WKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             ccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence                 1222 3467777777877777999999999999999999999999998754

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.80  E-value=4.1e-19  Score=145.11  Aligned_cols=110  Identities=17%  Similarity=0.197  Sum_probs=81.1

Q ss_pred             eEEEEEE--CCeeEEE-ecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcC--------C-C--chH
Q psy7660           8 TSCAVYA--GGTTKSY-ILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANK--------N-T--TIP   73 (250)
Q Consensus         8 ~G~g~v~--~~~~~~~-~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~--------~-~--~~~   73 (250)
                      .|+|+|+  ++....+ +.....|++.|||.||..||+.+.+  ...+.|+|||++++++|..+        + .  +++
T Consensus        19 ~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~   96 (150)
T PRK00203         19 GGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKP   96 (150)
T ss_pred             eEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCc
Confidence            6777775  3333222 2235788999999999999998865  46799999999999999962        1 1  233


Q ss_pred             HH-HHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhccc
Q psy7660          74 LI-AHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAE  120 (250)
Q Consensus        74 ~~-~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~~~  120 (250)
                      +. .++++.+.++.. ...|.|.|||||+|++||+.||+||++|+...
T Consensus        97 v~n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~  143 (150)
T PRK00203         97 VKNVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAGAEEA  143 (150)
T ss_pred             cccHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHHHHHh
Confidence            32 234444444433 37899999999999999999999999998643

>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=99.74  E-value=9.9e-17  Score=122.82  Aligned_cols=112  Identities=21%  Similarity=0.216  Sum_probs=87.2

Q ss_pred             CceEEEEEECC--eeEEEe---cCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC-chHHHHHHH
Q psy7660           6 QNTSCAVYAGG--TTKSYI---LNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT-TIPLIAHIL   79 (250)
Q Consensus         6 ~~~G~g~v~~~--~~~~~~---l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~-~~~~~~~i~   79 (250)
                      ++.|+|++..+  ....+.   .....+++.||+.|+..||+.+......++.|+|||+.+++.+.+... .......++
T Consensus        13 ~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~   92 (130)
T cd06222          13 GPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWYEGKPVKNVDLW   92 (130)
T ss_pred             CceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhccccCCChhhHHHH
Confidence            36888888643  222221   225789999999999999999998888999999999999999998764 222233333


Q ss_pred             HHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhh
Q psy7660          80 NTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLD  117 (250)
Q Consensus        80 ~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~  117 (250)
                      ..+..+...+..+.|.|||+|+++++|+.||.|||+|.
T Consensus        93 ~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          93 QRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             HHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            44444446788999999999999999999999999874

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

>KOG3752|consensus

Probab=99.67  E-value=2.5e-16  Score=143.02  Aligned_cols=113  Identities=23%  Similarity=0.224  Sum_probs=90.3

Q ss_pred             CceEEEEEECCe---eEEEecC-CCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC-----------
Q psy7660           6 QNTSCAVYAGGT---TKSYILN-NINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT-----------   70 (250)
Q Consensus         6 ~~~G~g~v~~~~---~~~~~l~-~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~-----------   70 (250)
                      ..+|+|||+++.   ..+..+. ..+++|.|||.||..||+.+.+.+..+++|.|||++++++|+.|-+           
T Consensus       229 ~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~  308 (371)
T KOG3752|consen  229 SRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSN  308 (371)
T ss_pred             CcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHHHHHHHhhhccCcccccc
Confidence            459999998653   6777775 8999999999999999999999888899999999999999987632           


Q ss_pred             chH-----H-HHHHHHHHHHHHh--CCCceEEEeccCCCCCccchHHhHHHHhhhc
Q psy7660          71 TIP-----L-IAHILNTWYSLKS--CGKNVAFLWCPSHTGISGNEIVDRATRQLDG  118 (250)
Q Consensus        71 ~~~-----~-~~~i~~~~~~l~~--~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~  118 (250)
                      +++     + .......+++|.+  ++..|.+.|||||.||.|||+||.+|+++..
T Consensus       309 ~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~  364 (371)
T KOG3752|consen  309 GSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGST  364 (371)
T ss_pred             CCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence            122     1 1122233333433  4689999999999999999999999998853

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.62  E-value=3.9e-15  Score=118.02  Aligned_cols=113  Identities=17%  Similarity=0.111  Sum_probs=86.1

Q ss_pred             CCCCC-ceEEEEEECCe--eEEEe-cCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCCchHHHHH
Q psy7660           2 SKTLQ-NTSCAVYAGGT--TKSYI-LNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTTIPLIAH   77 (250)
Q Consensus         2 S~~~~-~~G~g~v~~~~--~~~~~-l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~~~~~~~~   77 (250)
                      ++.++ ..|+|+|+.+.  ..... .....+++.||+.|++.||+.+.+.+..++.|+|||+.+++.+++.+....-...
T Consensus        10 ~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~~~~~~~~~   89 (128)
T PRK13907         10 SKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEYAKNKMFAP   89 (128)
T ss_pred             CCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHHhcChhHHH
Confidence            34443 48888887442  22222 2356789999999999999999998888999999999999999986643223344


Q ss_pred             HHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhc
Q psy7660          78 ILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDG  118 (250)
Q Consensus        78 i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~  118 (250)
                      +++.+..+..+...+.|.|||++    +|+.||.||++|..
T Consensus        90 l~~~~~~l~~~f~~~~~~~v~r~----~N~~Ad~LA~~a~~  126 (128)
T PRK13907         90 LLEEALQYIKSFDLFFIKWIPSS----QNKVADELARKAIL  126 (128)
T ss_pred             HHHHHHHHHhcCCceEEEEcCch----hchhHHHHHHHHHh
Confidence            55555556667778889999994    89999999999875

>PRK07708 hypothetical protein; Validated

Probab=99.39  E-value=6.4e-12  Score=108.83  Aligned_cols=112  Identities=13%  Similarity=0.038  Sum_probs=81.3

Q ss_pred             CceEEEEEEC--CeeEE------EecCCCCchHHHHHHHHHHHHHHhhcCCCCe--EEEEeccHHHHHhhhcCCC-chHH
Q psy7660           6 QNTSCAVYAG--GTTKS------YILNNINSIFTAELLAIVFCLDSVKNRPDVN--TLIVCDSMSALTSIANKNT-TIPL   74 (250)
Q Consensus         6 ~~~G~g~v~~--~~~~~------~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~--i~I~tDS~~al~ai~~~~~-~~~~   74 (250)
                      ++.|+|+++.  +....      ..+....+++.||+.|+..||+.+.+.+.+.  |.|++||+.+++.+.+.+. .++.
T Consensus        87 g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~  166 (219)
T PRK07708         87 KLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWPCYDEH  166 (219)
T ss_pred             CCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCceeCChh
Confidence            4577777752  22211      2345568999999999999999999876654  8999999999999999775 3333


Q ss_pred             HHHHHHHHHHHHhC-CCceEEEeccCCCCCccchHHhHHHHhhhcccc
Q psy7660          75 IAHILNTWYSLKSC-GKNVAFLWCPSHTGISGNEIVDRATRQLDGAEI  121 (250)
Q Consensus        75 ~~~i~~~~~~l~~~-g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~~~~  121 (250)
                      ...+.+.+..+.++ ...+.|.|||.    +.|+.||+||++|.+...
T Consensus       167 l~~y~~~i~~l~~~~~l~~~~~~VpR----~~N~~AD~LAk~Al~~~~  210 (219)
T PRK07708        167 LNHWLDRIEQKLKQLKLTPVYEPISR----KQNKEADQLATQALEGTV  210 (219)
T ss_pred             HHHHHHHHHHHHhhCCceEEEEECCc----hhhhHHHHHHHHHHhcCC
Confidence            34444444433333 34588899988    479999999999997443

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

Probab=99.38  E-value=2.6e-12  Score=93.93  Aligned_cols=85  Identities=18%  Similarity=0.137  Sum_probs=66.4

Q ss_pred             hHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCCchHHHHHHHHHHHHHHhCCCceEEEeccCCCCCccchH
Q psy7660          29 IFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEI  108 (250)
Q Consensus        29 ~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~~~~~~~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~  108 (250)
                      +..||+.|+..||+.+.+.+.++|.|.|||+.+++.|++..........+...+..+......+.|.|||.    ++|..
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r----~~N~~   76 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPR----EQNKV   76 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--G----GGSHH
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEECh----HHhHH
Confidence            46899999999999999999999999999999999999985421133344455555667788999999998    79999


Q ss_pred             HhHHHHhhh
Q psy7660         109 VDRATRQLD  117 (250)
Q Consensus       109 AD~lAk~a~  117 (250)
                      ||.|||.|.
T Consensus        77 A~~LA~~a~   85 (87)
T PF13456_consen   77 ADALAKFAL   85 (87)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999999886

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.37  E-value=7e-12  Score=116.39  Aligned_cols=114  Identities=14%  Similarity=0.109  Sum_probs=86.9

Q ss_pred             CCCCCCc-eEEEEEECCe--e-E--EE-ecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC-ch
Q psy7660           1 GSKTLQN-TSCAVYAGGT--T-K--SY-ILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT-TI   72 (250)
Q Consensus         1 gS~~~~~-~G~g~v~~~~--~-~--~~-~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~-~~   72 (250)
                      ||+.+++ .|+|+++.+.  . .  .+ ..-...+++.||+.|++.||+.+.+.+.+.|.|++||+.+++.+.+.+. .+
T Consensus        10 a~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i~~~~~~~~   89 (372)
T PRK07238         10 GSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKVKH   89 (372)
T ss_pred             CCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHhCCCCccCC
Confidence            3444544 7888886432  1 1  22 1223678899999999999999999888999999999999999998764 33


Q ss_pred             HHHHHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhc
Q psy7660          73 PLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDG  118 (250)
Q Consensus        73 ~~~~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~  118 (250)
                      +-...+...+..|.++...+.|.|||+    ++|+.||.||++|..
T Consensus        90 ~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~  131 (372)
T PRK07238         90 PDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMD  131 (372)
T ss_pred             hHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHH
Confidence            333444555566667778999999998    689999999999974

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

Probab=81.89  E-value=0.69  Score=33.71  Aligned_cols=15  Identities=13%  Similarity=0.297  Sum_probs=13.0

Q ss_pred             CCcccceeeecCccc
Q psy7660         200 NMFKQSYKYLMCPVI  214 (250)
Q Consensus       200 ~~etv~H~l~~Cp~~  214 (250)
                      .+||++|+|+.||.-
T Consensus        68 ~~Et~~Hlf~~C~~a   82 (86)
T PF13966_consen   68 EEETIEHLFFHCPFA   82 (86)
T ss_pred             ccccccceeccCcCc
Confidence            379999999999964

---

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	250
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	2e-05
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	4e-05
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	1e-04
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	4e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-04

>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 = 42.3 bits (100), Expect = 2e-05
 Identities = 13/93 (13%), Positives = 23/93 (24%), Gaps = 13/93 (13%)

Query: 24  NNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSI-----ANKNTTIPLIAHI 78
                    E+ A ++ +        V   I+ D             A    T      +
Sbjct: 45  AATMRNVAGEIAAALYAVKKASQLG-VKIRILHDYAGIAFWATGEWKAKNEFTQAYAKLM 103

Query: 79  LNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDR 111
                         +F    +H+G   N+ VD 
Sbjct: 104 -------NQYRGIYSFEKVKAHSGNEFNDYVDM 129

>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* ... Length = 557

 Score = 43.2 bits (102), Expect = 4e-05
 Identities = 30/84 (35%), Positives = 39/84 (46%), Gaps = 14/84 (16%)

Query: 32  AELLAIVFCL-DSVKNRPDVNTLIVCDSMSALTSIANK--NTTIPLIAHILNTWYSLKSC 88
            EL AI   L DS     +VN  IV DS  AL  I  +   +   L+  I+      +  
Sbjct: 479 TELQAIYLALQDS---GLEVN--IVTDSQYALGIIQAQPDKSESELVNQIIE-----QLI 528

Query: 89  GKNVAFL-WCPSHTGISGNEIVDR 111
            K   +L W P+H GI GNE VD+
Sbjct: 529 KKEKVYLAWVPAHKGIGGNEQVDK 552

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

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 20/94 (21%), Positives = 34/94 (36%), Gaps = 17/94 (18%)

Query: 32  AELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTTIP-----LIAHILNTWYSLK 86
           AEL+A+   L   +    +N  +  DS  A  +    +          I  +L       
Sbjct: 66  AELIALTQALKMAE-GKKLN--VYTDSRYAFATAHVHSEGREIKNKNEILALLK----AL 118

Query: 87  SCGKNVAFLWCPSHTG-----ISGNEIVDRATRQ 115
              K ++ + CP H         GN + D+A R+
Sbjct: 119 FLPKRLSIIHCPGHQKGNSAEARGNRMADQAARE 152

>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 Length = 555

 Score = 40.5 bits (95), Expect = 4e-04
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 14/84 (16%)

Query: 32  AELLAIVFCL-DSVKNRPDVNTLIVCDSMSALTSIANK--NTTIPLIAHILNTWYSLKSC 88
           AEL A    L DS    P VN  I+ DS   +  +A++   +   ++  I+      +  
Sbjct: 476 AELEAFAMALTDS---GPKVN--IIVDSQYVMGIVASQPTESESKIVNQIIE-----EMI 525

Query: 89  GKNVAFL-WCPSHTGISGNEIVDR 111
            K   ++ W P+H GI GN+ VD 
Sbjct: 526 KKEAIYVAWVPAHKGIGGNQEVDH 549

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 39.5 bits (91), Expect = 8e-04
 Identities = 46/292 (15%), Positives = 82/292 (28%), Gaps = 93/292 (31%)

Query: 1   GSKTL---QNTSCA-VYAGGTTKSYILNNINSIFT-AELLAIVF--CLD-SVKNRP---- 48
             K L   +        +  TT    L++ +   T  E+ ++     LD   ++ P    
Sbjct: 265 SCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL-LLKYLDCRPQDLPREVL 323

Query: 49  DVNTLIVCDSMSALTSIANKNTTIPLIAHILNTW-YSLKSCGKNVAFLWCPSHTGISGNE 107
             N          L+ IA        I   L TW          +               
Sbjct: 324 TTNPR-------RLSIIAE------SIRDGLATWDNWKHVNCDKL-------------TT 357

Query: 108 IVDRATRQLDGAEI----VNLSS-PADL-IPVG----------------------KKYLL 139
           I++ +   L+ AE       LS  P    IP                        K  L+
Sbjct: 358 IIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLV 417

Query: 140 EKWQKSWTELINNKLKRIKPTIGPWNVSDCNSR----YEESISWSGNKCF---IDHYSHP 192
           EK  K  T  I +    +K  +   N    +      Y    ++  +      +D Y + 
Sbjct: 418 EKQPKESTISIPSIYLELKVKLE--NEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYS 475

Query: 193 YL-----------KVLPFNMFKQSYKYLMCPVIAS-----ACDSVLVSLSDF 228
           ++           ++  F M    +++L   +        A  S+L +L   
Sbjct: 476 HIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQL 527

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	250
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.87
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.85
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.85
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.83
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.83
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.83
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.82
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.79
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.75
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.75
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.74
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.72
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.71
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.69
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.1
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	98.79

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

Probab=99.87  E-value=6.7e-22  Score=160.65  Aligned_cols=107  Identities=22%  Similarity=0.280  Sum_probs=86.7

Q ss_pred             eEEEEEECCe---eEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCC---------C-----
Q psy7660           8 TSCAVYAGGT---TKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN---------T-----   70 (250)
Q Consensus         8 ~G~g~v~~~~---~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~---------~-----   70 (250)
                      .|+|+|+.+.   .++..+...++++.|||.|+..||+.+.+.+..+|.|+|||+++++.|..+.         .     
T Consensus        26 aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~~i~~~~~~w~~~~w~~~~~~~  105 (154)
T 2qkb_A           26 AGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKE  105 (154)
T ss_dssp             EEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHHHHHTHHHHHHTTTSBCTTSSB
T ss_pred             EEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHhhhhhhHHHHHhccccccCCCc
Confidence            7999987542   3556676679999999999999999998877899999999999999998731         1     


Q ss_pred             --chHHHHHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhcc
Q psy7660          71 --TIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGA  119 (250)
Q Consensus        71 --~~~~~~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~~  119 (250)
                        ..+++++|.    .+.. +..|.|.|||||+|++|||.||+|||+|+..
T Consensus       106 ~~n~~l~~~i~----~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~  151 (154)
T 2qkb_A          106 VINKEDFVALE----RLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREGAKQ  151 (154)
T ss_dssp             CTTHHHHHHHH----HHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHHHTC
T ss_pred             cccHHHHHHHH----HHHc-CCceEEEEccCCCCCHhHHHHHHHHHHHHHh
Confidence              134444444    3333 5679999999999999999999999999864

>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=99.85  E-value=4e-21  Score=155.94  Aligned_cols=107  Identities=25%  Similarity=0.266  Sum_probs=80.1

Q ss_pred             eEEEEEECCe-eEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCC-----------CchHHH
Q psy7660           8 TSCAVYAGGT-TKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN-----------TTIPLI   75 (250)
Q Consensus         8 ~G~g~v~~~~-~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~-----------~~~~~~   75 (250)
                      .|+|++..+. ...+.+ ..+|++.|||.|+..||+.+    ..+|.|+|||+++++.|+++.           .+.++.
T Consensus        28 ~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i~~w~~~W~~~gw~~~~g~~v~  102 (150)
T 3qio_A           28 GKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVK  102 (150)
T ss_dssp             EEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHHHHHHHHHCC------------
T ss_pred             eEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHHHHHHHHHhhcCcCcCcCcccc
Confidence            6778777543 333333 57899999999999999985    489999999999999998861           122221


Q ss_pred             -HHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhcc
Q psy7660          76 -AHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGA  119 (250)
Q Consensus        76 -~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~~  119 (250)
                       .++++.+..+..++..|.|.|||||+|++|||.||+||++|+..
T Consensus       103 n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A          103 NVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             cHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence             23333333333567899999999999999999999999999864

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

Probab=99.85  E-value=4.5e-21  Score=154.25  Aligned_cols=105  Identities=17%  Similarity=0.081  Sum_probs=80.6

Q ss_pred             ceEEEEEEC--Cee--EEEecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhc-CC------------
Q psy7660           7 NTSCAVYAG--GTT--KSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIAN-KN------------   69 (250)
Q Consensus         7 ~~G~g~v~~--~~~--~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~-~~------------   69 (250)
                      ..|+|+|+.  +..  .+..+ ..+|++.|||.|++.||+.+.+  ..+|.|+|||+++++.|.. +.            
T Consensus        19 ~~g~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~   95 (146)
T 3h08_A           19 KGGWGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAA   95 (146)
T ss_dssp             EEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHHSSHHHHHHHTTCC---
T ss_pred             ceEEEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHHHHHHHHHHHCCCccCC
Confidence            378888763  322  22233 3688999999999999999976  5899999999999999988 20            


Q ss_pred             ----CchHHHHHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhcc
Q psy7660          70 ----TTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGA  119 (250)
Q Consensus        70 ----~~~~~~~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~~  119 (250)
                          ..++++++|..++..     ..|.|.|||||+|++|||.||+|||+|+..
T Consensus        96 ~~~v~n~~l~~~~~~~~~~-----~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A           96 KKPVENIDLWQEILKLTTL-----HRVTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             -CCCTTHHHHHHHHHHHHH-----SEEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             CCCcCCHHHHHHHHHHHhh-----CceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence                125566666554432     469999999999999999999999999853

>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=99.83  E-value=1.7e-21  Score=157.43  Aligned_cols=118  Identities=13%  Similarity=0.055  Sum_probs=89.5

Q ss_pred             CCCCCCceEEEEEE--CCee--EEE-ec--CC--CCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC-
Q psy7660           1 GSKTLQNTSCAVYA--GGTT--KSY-IL--NN--INSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT-   70 (250)
Q Consensus         1 gS~~~~~~G~g~v~--~~~~--~~~-~l--~~--~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~-   70 (250)
                      ||..++..|+|+|+  .+..  .+. +.  +.  .++++.|||.|+..||+.+.+.+. +|.|+|||+.+.+.+.+.+. 
T Consensus        13 Gs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i~~w~~~~w~~   91 (147)
T 2kq2_A           13 GSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGIAFWATGEWKA   91 (147)
T ss_dssp             CCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTHHHHTTSSSSC
T ss_pred             CCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHHHHHHhCCCcc
Confidence            56666678999886  3332  333 33  22  368999999999999999877666 99999999999888877664 


Q ss_pred             chHHHHHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhccccc
Q psy7660          71 TIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAEIV  122 (250)
Q Consensus        71 ~~~~~~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~~~~~  122 (250)
                      ..+....+.+.+.+|..   .|.|.|||||+|++|||.||+|||+|+....+
T Consensus        92 ~~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  140 (147)
T 2kq2_A           92 KNEFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALGIRDL  140 (147)
T ss_dssp             CHHHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHTCCCT
T ss_pred             CCcchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHhcccc
Confidence            34444455555555533   89999999999999999999999999975543

>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=99.83  E-value=2.1e-20  Score=152.15  Aligned_cols=107  Identities=18%  Similarity=0.213  Sum_probs=82.2

Q ss_pred             eEEEEEEC--Cee--EEEecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcC--------C-C----
Q psy7660           8 TSCAVYAG--GTT--KSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANK--------N-T----   70 (250)
Q Consensus         8 ~G~g~v~~--~~~--~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~--------~-~----   70 (250)
                      .|+|+|+.  +..  .+..+ ..+|++.|||.|+..||+.+.+  ..+|.|+|||+++++.|..+        + .    
T Consensus        20 ~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~--~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~   96 (155)
T 1jl1_A           20 GGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKK   96 (155)
T ss_dssp             EEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSC
T ss_pred             eEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc--CCcEEEEeCHHHHHHHHHHHHHHHhhcccccccCC
Confidence            78888863  322  22233 4678999999999999999976  37999999999999999973        1 1    


Q ss_pred             ---chHHHHHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhccccc
Q psy7660          71 ---TIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAEIV  122 (250)
Q Consensus        71 ---~~~~~~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~~~~~  122 (250)
                         ..++.+.|    ..+.. ...|.|.|||||+|++|||.||+||++|+..+.+
T Consensus        97 ~v~n~~l~~~i----~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  146 (155)
T 1jl1_A           97 PVKNVDLWQRL----DAALG-QHQIKWEWVKGHAGHPENERADELARAAAMNPTL  146 (155)
T ss_dssp             BCTTHHHHHHH----HHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             ccCCHHHHHHH----HHHHc-cCceEEEEcCCCCCCHHHHHHHHHHHHHHhccch
Confidence               13444444    44433 4689999999999999999999999999976554

>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=99.83  E-value=2.7e-20  Score=153.37  Aligned_cols=110  Identities=20%  Similarity=0.221  Sum_probs=82.3

Q ss_pred             CceEEEEEE--CCeeEEE-ecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC-----chHHHHH
Q psy7660           6 QNTSCAVYA--GGTTKSY-ILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT-----TIPLIAH   77 (250)
Q Consensus         6 ~~~G~g~v~--~~~~~~~-~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~-----~~~~~~~   77 (250)
                      |..|+|+++  .+..+.+ ++...++++.||+.|+..||+.+   ...+|.|+|||+++++.|-....     ..+++++
T Consensus        37 G~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~iw~~~~g~~v~n~dl~~~  113 (165)
T 3p1g_A           37 GQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATAHVHSEGREIKNKNEILA  113 (165)
T ss_dssp             TEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHHHSCCCSCCCSSHHHHHH
T ss_pred             CceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhhhcccCCCcccCHHHHHH
Confidence            336777654  3333322 45678899999999999999998   36899999999999999932122     2444444


Q ss_pred             HHHHHHHHHhCCCceEEEeccCCCC-----CccchHHhHHHHhhhccccc
Q psy7660          78 ILNTWYSLKSCGKNVAFLWCPSHTG-----ISGNEIVDRATRQLDGAEIV  122 (250)
Q Consensus        78 i~~~~~~l~~~g~~V~~~WVPgH~g-----i~gNe~AD~lAk~a~~~~~~  122 (250)
                      +..   .+ ..+..|.|.|||||+|     ++|||.||+|||+|+.....
T Consensus       114 l~~---~l-~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~~~  159 (165)
T 3p1g_A          114 LLK---AL-FLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVL  159 (165)
T ss_dssp             HHH---HT-TSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHH---HH-hcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcCCC
Confidence            432   23 3578999999999999     99999999999999975443

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

Probab=99.82  E-value=4.2e-20  Score=150.89  Aligned_cols=104  Identities=20%  Similarity=0.266  Sum_probs=80.2

Q ss_pred             eEEEEEEC--Cee--EEEecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhc--------CCC-----
Q psy7660           8 TSCAVYAG--GTT--KSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIAN--------KNT-----   70 (250)
Q Consensus         8 ~G~g~v~~--~~~--~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~--------~~~-----   70 (250)
                      .|+|+|+.  +..  .+..+ ..++++.|||.|+..||+.+.+.  .+|.|+|||+++++.|..        .+.     
T Consensus        22 ~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~~--~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~   98 (158)
T 2e4l_A           22 GGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKEP--CKIILTSDSQYMRQGIMTWIHGWKKKGWMTSNRT   98 (158)
T ss_dssp             EEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSSC--CEEEEEECCHHHHHHHHTHHHHHHHTTTBCTTSS
T ss_pred             EEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhccC--CeEEEEeCHHHHHHHHHHHHHHHHHccccccCCC
Confidence            78888863  322  22233 35789999999999999998653  899999999999999988        221     


Q ss_pred             ---chHHHHHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhcc
Q psy7660          71 ---TIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGA  119 (250)
Q Consensus        71 ---~~~~~~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~~  119 (250)
                         ..++.+.|.    .+.. +..|.|.|||||+|++|||.||+||++|+..
T Consensus        99 ~v~n~~l~~~i~----~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A           99 PVKNVDLWKRLD----KAAQ-LHQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             BCTTHHHHHHHH----HHHT-TSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             cccCHHHHHHHH----HHHc-cCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence               234444443    3433 4689999999999999999999999999976

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

Probab=99.79  E-value=1.4e-19  Score=149.02  Aligned_cols=108  Identities=21%  Similarity=0.147  Sum_probs=81.1

Q ss_pred             ceEEEEEECC--eeEEEe-cCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhc----------CCC---
Q psy7660           7 NTSCAVYAGG--TTKSYI-LNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIAN----------KNT---   70 (250)
Q Consensus         7 ~~G~g~v~~~--~~~~~~-l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~----------~~~---   70 (250)
                      ..|+|+|+.+  ....+. ....+|++.|||.|++.||+.+.+.  .+|.|+|||+++++.|.+          +..   
T Consensus        23 ~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~g  100 (166)
T 1ril_A           23 PGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEG  100 (166)
T ss_dssp             EEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTS
T ss_pred             CEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHHhhhHHHHHHhcccccccC
Confidence            3788888742  222111 1246789999999999999988663  589999999999999998          211   


Q ss_pred             ----chHHHHHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhcccc
Q psy7660          71 ----TIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAEI  121 (250)
Q Consensus        71 ----~~~~~~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~~~~  121 (250)
                          .+++++.|.    .+.. ...|.|.|||||+|++|||.||+|||+|+....
T Consensus       101 ~~v~n~~l~~~i~----~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~  150 (166)
T 1ril_A          101 KPVKNRDLWEALL----LAMA-PHRVRFHFVKGHTGHPENERVDREARRQAQSQA  150 (166)
T ss_dssp             SBCTTHHHHHHHH----HHHT-TSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             CccCcHHHHHHHH----HHHh-cCeEEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence                134444444    3433 368999999999999999999999999997543

>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=99.75  E-value=4.3e-18  Score=135.01  Aligned_cols=108  Identities=14%  Similarity=0.166  Sum_probs=86.0

Q ss_pred             ceEEEEEEC--C-e----eEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC-chHHHHHH
Q psy7660           7 NTSCAVYAG--G-T----TKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT-TIPLIAHI   78 (250)
Q Consensus         7 ~~G~g~v~~--~-~----~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~-~~~~~~~i   78 (250)
                      ..|+|+++.  + .    ..+..+ ..++++.||+.|+..||+.+.+.+..+|.|+|||+++++.+.+.+. .++....+
T Consensus        18 ~~g~G~v~~~~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~i~~~~~~~~~~l~~~   96 (141)
T 3hst_B           18 PAGYGAVVWTADHSTVLAESKQAI-GRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKL   96 (141)
T ss_dssp             EEEEEEEEEETTSCSEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHHHTTSSCCCSHHHHHH
T ss_pred             CcEEEEEEEeCCCCcEEEeeeccC-CCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHHHhCCcccCCHHHHHH
Confidence            478888763  2 1    122223 3789999999999999999998778999999999999999999654 44444555


Q ss_pred             HHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhcc
Q psy7660          79 LNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGA  119 (250)
Q Consensus        79 ~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~~  119 (250)
                      .+.+..+..++..|.|.|||+    ++|+.||+|||+|+..
T Consensus        97 ~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B           97 YVQAQALASQFRRINYEWVPR----ARNTYADRLANDAMDA  133 (141)
T ss_dssp             HHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHHHHH
Confidence            666667777788999999996    7999999999999864

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

Probab=99.75  E-value=9.8e-18  Score=138.05  Aligned_cols=106  Identities=16%  Similarity=0.163  Sum_probs=78.2

Q ss_pred             eEEEEEEC--C--ee--EEEec-CCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCC---------C-
Q psy7660           8 TSCAVYAG--G--TT--KSYIL-NNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN---------T-   70 (250)
Q Consensus         8 ~G~g~v~~--~--~~--~~~~l-~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~---------~-   70 (250)
                      .|+|+|+.  +  ..  ..+.. ....+.+.||+.|+..||+.+++.+ .+|.|+|||+++++.|..+.         . 
T Consensus        28 aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~~-~~v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~  106 (165)
T 2lsn_A           28 AGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIP-GPVLVITDSFYVAESANKELPYWKSNGFVNN  106 (165)
T ss_dssp             EEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHSS-SCEEEEESCHHHHHHHHTHHHHHHHTTSCSC
T ss_pred             EEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcCC-CeEEEEeChHHHHhhhhhhhhhheecccccc
Confidence            78998862  2  12  23333 3567888999999999999887643 57999999999999997531         1 


Q ss_pred             ------chHHHHHHHHHHHHHHhCCCceEEEeccCCCCC------ccchHHhHHHHhhhc
Q psy7660          71 ------TIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGI------SGNEIVDRATRQLDG  118 (250)
Q Consensus        71 ------~~~~~~~i~~~~~~l~~~g~~V~~~WVPgH~gi------~gNe~AD~lAk~a~~  118 (250)
                            ..++.+++.+    +......|.|.|||||+|+      +|||.||+||++|+.
T Consensus       107 ~~~pVkN~dL~~~l~~----~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~  162 (165)
T 2lsn_A          107 KKKPLKHISKWKSIAE----CLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSY  162 (165)
T ss_dssp             SSSCCSSHHHHHHHHH----HHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcccCHHHHHHHHH----HHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhhh
Confidence                  2444444443    3344568999999999995      589999999999984

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

Probab=99.74  E-value=6e-18  Score=133.60  Aligned_cols=108  Identities=15%  Similarity=0.105  Sum_probs=80.9

Q ss_pred             ceEEEEEECC--e-e---EEEecCCCCchHHHHHHHHHHHHHHhhcCCCC----eEEEEeccHHHHHhhhcCCC-chHHH
Q psy7660           7 NTSCAVYAGG--T-T---KSYILNNINSIFTAELLAIVFCLDSVKNRPDV----NTLIVCDSMSALTSIANKNT-TIPLI   75 (250)
Q Consensus         7 ~~G~g~v~~~--~-~---~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~----~i~I~tDS~~al~ai~~~~~-~~~~~   75 (250)
                      ..|+|+++.+  . .   .+..+ ..++++.||+.|+..||+.+.+.+..    +|.|+|||+++++.+.+++. .++-.
T Consensus        18 ~~G~G~v~~~~~g~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~vi~~i~~~~~~~~~~l   96 (140)
T 3u3g_D           18 PAGIGVVITDEKGNTLHESSAYI-GETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKVKEPTL   96 (140)
T ss_dssp             EEEEEEEEECTTSCEEEEEEEEE-EEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHHHHHHTTSSCCCCGGG
T ss_pred             CcEEEEEEEeCCCCEEEEEEeeC-CCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHHHHHhCCCcccCCHHH
Confidence            4888888733  2 1   22222 35799999999999999999886666    99999999999999999764 22222


Q ss_pred             HHHHHHHHHH-HhCCCceEEEeccCCCCCccchHHhHHHHhhhcc
Q psy7660          76 AHILNTWYSL-KSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGA  119 (250)
Q Consensus        76 ~~i~~~~~~l-~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~~  119 (250)
                      ..+.+.+..+ ..+...|.|.|||+    ++||.||+|||+|+..
T Consensus        97 ~~~~~~i~~l~~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D           97 KEKFAKIAHIKMERVPNLVFVHIPR----EKNARADELVNEAIDK  137 (140)
T ss_dssp             HHHHHHHHHHHHHHCTTCEEEECCG----GGGHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcCCCcEEEEEcCc----hhhHHHHHHHHHHHHh
Confidence            2333444444 45556899999995    7999999999999853

>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=99.72  E-value=2.2e-17  Score=159.03  Aligned_cols=101  Identities=23%  Similarity=0.287  Sum_probs=81.3

Q ss_pred             eEEEEEECCe-eEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC--chHHHHHHHHHHHH
Q psy7660           8 TSCAVYAGGT-TKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT--TIPLIAHILNTWYS   84 (250)
Q Consensus         8 ~G~g~v~~~~-~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~--~~~~~~~i~~~~~~   84 (250)
                      .|+|++.... .....+ ..+|++.||+.|+..||+.    ...++.|+|||++|++.|+++..  ++++.+++.+.+. 
T Consensus       452 ~g~G~v~~~~~~~~~~~-~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~~~~~~~~~l~~~~~~~~~-  525 (555)
T 1mu2_A          452 GKAGYVTDRGKDKVKKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMI-  525 (555)
T ss_dssp             EEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTCCSEESCHHHHHHHHHHH-
T ss_pred             ceEEEEEEeCCEeeccC-CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhcccccccHHHHHHHHHHhc-
Confidence            6788776432 233333 4688999999999999997    46899999999999999999764  5677665554433 


Q ss_pred             HHhCCCceEEEeccCCCCCccchHHhHHHHhhh
Q psy7660          85 LKSCGKNVAFLWCPSHTGISGNEIVDRATRQLD  117 (250)
Q Consensus        85 l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~  117 (250)
                         .+..|.|.|||||+|++|||.||+||++|+
T Consensus       526 ---~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          526 ---KKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             ---HCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             ---cCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence               367899999999999999999999999985

>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=99.71  E-value=2.9e-17  Score=158.34  Aligned_cols=100  Identities=27%  Similarity=0.346  Sum_probs=78.6

Q ss_pred             eEEEEEECC-eeEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC--chHHHHHHHHHHHH
Q psy7660           8 TSCAVYAGG-TTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT--TIPLIAHILNTWYS   84 (250)
Q Consensus         8 ~G~g~v~~~-~~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~--~~~~~~~i~~~~~~   84 (250)
                      .|+|++..+ ....++. ..+|++.||+.|+..||+.+    ..++.|+|||++|++.|+++..  ++++.+++.+.+. 
T Consensus       455 ~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~~~~~~~~~l~~~~~~~l~-  528 (557)
T 2zd1_A          455 GKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLI-  528 (557)
T ss_dssp             EEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTTCCSEESSHHHHHHHHHHH-
T ss_pred             eEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhcCCccCCHHHHHHHHHHHh-
Confidence            677777643 3333333 46889999999999999998    5799999999999999999876  4677766554433 


Q ss_pred             HHhCCCceEEEeccCCCCCccchHHhHHHHhh
Q psy7660          85 LKSCGKNVAFLWCPSHTGISGNEIVDRATRQL  116 (250)
Q Consensus        85 l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a  116 (250)
                        . ...|.|.|||||+|++|||.||+||++|
T Consensus       529 --~-~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          529 --K-KEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             --H-CSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             --c-CCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence              2 4589999999999999999999999986

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

Probab=99.69  E-value=8.7e-17  Score=129.30  Aligned_cols=105  Identities=15%  Similarity=0.151  Sum_probs=79.6

Q ss_pred             CceEE-EEEECC--eeE-EEe--cC---CCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC-c----
Q psy7660           6 QNTSC-AVYAGG--TTK-SYI--LN---NINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT-T----   71 (250)
Q Consensus         6 ~~~G~-g~v~~~--~~~-~~~--l~---~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~-~----   71 (250)
                      +..|+ |+++.+  ..+ .+.  +.   ..++++.||+.|+..||+.+.+.+..+|.|+|||+++++.+.+++. .    
T Consensus        16 g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi~~i~~~w~~~~~~~   95 (149)
T 2ehg_A           16 GGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQMNGEYKVKAKRI   95 (149)
T ss_dssp             SSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHHHHHTTSSCCCCTTH
T ss_pred             ChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHHHHHhCccccCCHHH
Confidence            45786 877532  222 222  22   3789999999999999999998778899999999999999999864 2    


Q ss_pred             hHHHHHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhcc
Q psy7660          72 IPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGA  119 (250)
Q Consensus        72 ~~~~~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~~  119 (250)
                      .++..++...+..    . .|.|.|||+|    +|+.||+||++|+..
T Consensus        96 ~~l~~~i~~l~~~----~-~v~~~~V~~~----~N~~AD~LA~~a~~~  134 (149)
T 2ehg_A           96 IPLYEKAIELKKK----L-NATLIWVPRE----ENKEADRLSRVAYEL  134 (149)
T ss_dssp             HHHHHHHHHHHHH----H-TCEEEECCGG----GCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhc----C-CEEEEEcCCc----ccHHHHHHHHHHHHh
Confidence            3444444444433    3 4999999994    999999999999863

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

Probab=99.10  E-value=6.3e-11  Score=94.96  Aligned_cols=106  Identities=17%  Similarity=0.019  Sum_probs=76.0

Q ss_pred             CCCCc-eEEEEEECC--eeEEEec-CCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC--------
Q psy7660           3 KTLQN-TSCAVYAGG--TTKSYIL-NNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT--------   70 (250)
Q Consensus         3 ~~~~~-~G~g~v~~~--~~~~~~l-~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~--------   70 (250)
                      ..|++ .|+|+|+..  ....+.. -..+|++.||+.|++.||+.+.+... +|.|+|||+++++.+.+.+.        
T Consensus        21 ~gNpG~~G~G~vl~~~g~~~~~~~~~~~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~~~~~~k~~~~~~v   99 (142)
T 1zbf_A           21 QGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWVKDKKAKSTLVRNE   99 (142)
T ss_dssp             CSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHHHHTCCCCCCCCST
T ss_pred             CCCCCCeEEEEEEEeCCEEEEEecccCCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHHHcCCccCCCCCCc
Confidence            34444 799999842  2222211 13678999999999999999988666 99999999999999998762        


Q ss_pred             -chHHHHHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhH
Q psy7660          71 -TIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDR  111 (250)
Q Consensus        71 -~~~~~~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~  111 (250)
                       ..++.+.|..+..-+...  .+....|.-|++.-||..||.
T Consensus       100 ~n~dLw~~l~~~~~w~~~~--~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A          100 ETALIWKLVDEAEEWLNTH--TYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             TTHHHHHHHHHHHHHHHHC--CCCCCEEECCHHHHCSCTTCC
T ss_pred             ccHHHHHHHHHHHHHHhhC--CCceeEEEeccCccCcCcccc
Confidence             246666665555555444  344445566888899999984

>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=98.79  E-value=2.3e-08  Score=79.14  Aligned_cols=87  Identities=18%  Similarity=0.050  Sum_probs=58.8

Q ss_pred             CCCCCc-eEEEEEE-CC-eeEEE-ecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC-------
Q psy7660           2 SKTLQN-TSCAVYA-GG-TTKSY-ILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT-------   70 (250)
Q Consensus         2 S~~~~~-~G~g~v~-~~-~~~~~-~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~-------   70 (250)
                      |..|+| .|+|+|+ .+ ..... +-...+|++.||+.|++.||+.+.+.+.. +.|+|||+++++.|.++.-       
T Consensus        14 c~GNPGp~G~ggV~~~~g~~~~~~g~~~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi~~~~~kt~~~~~   92 (134)
T 4htu_A           14 SQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWVKDKKAKSTLVRN   92 (134)
T ss_dssp             EETTTEEEEEEEEETTTCCEEEEEEEEEEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHHHHTCCCCCCCCS
T ss_pred             cCCCCCCeEEEEEEEECCEEEEEecCCCCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHHHcCCcccCCCCC
Confidence            345555 7885665 32 22211 11237899999999999999999875544 8999999999999987531       


Q ss_pred             --chHHHHHHHHHHHHHHhCC
Q psy7660          71 --TIPLIAHILNTWYSLKSCG   89 (250)
Q Consensus        71 --~~~~~~~i~~~~~~l~~~g   89 (250)
                        ..++.+.+..+..-|....
T Consensus        93 vkN~dLw~~ld~~~~~l~~~~  113 (134)
T 4htu_A           93 EETALIWKLVDEAEEWLNTHT  113 (134)
T ss_dssp             STTHHHHHHHHHHHHHHHHCC
T ss_pred             ccCHHHHHHHHHHHHHHHhCC
Confidence              2466666655555555544

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	250
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.87
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.82
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.8
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.6
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.39

>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=99.87  E-value=5.6e-22  Score=154.17  Aligned_cols=106  Identities=22%  Similarity=0.257  Sum_probs=78.8

Q ss_pred             CCCCc-eEEEEEECCe-eEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC--chHHHHHH
Q psy7660           3 KTLQN-TSCAVYAGGT-TKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT--TIPLIAHI   78 (250)
Q Consensus         3 ~~~~~-~G~g~v~~~~-~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~--~~~~~~~i   78 (250)
                      ..+++ .|+|++.... .....++ .+|++.|||.||.+||+.    ...++.|+|||+++++.+.++..  .......+
T Consensus        17 ~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v~~~~~~~~~~~~~~~~~~~   91 (126)
T d1mu2a1          17 NRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQPTESESKIVNQI   91 (126)
T ss_dssp             CTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTCCSEESCHHHHHH
T ss_pred             CCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhcc----CCcceEEEechHHHHHHHhcCCccccchHHHHH
Confidence            34445 5566666544 3333343 678999999999999985    35789999999999999999876  23333222


Q ss_pred             HHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhh
Q psy7660          79 LNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLD  117 (250)
Q Consensus        79 ~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~  117 (250)
                         +..+. +...|.|.|||||+|++|||.||+||++|.
T Consensus        92 ---~~~~~-~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          92 ---IEEMI-KKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             ---HHHHH-HCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             ---HHHhh-hcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence               22332 256899999999999999999999999984

>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=99.82  E-value=1.2e-20  Score=149.81  Aligned_cols=117  Identities=15%  Similarity=0.206  Sum_probs=85.2

Q ss_pred             eEEEEEE--CCeeEEEec-CCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC-----------chH
Q psy7660           8 TSCAVYA--GGTTKSYIL-NNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT-----------TIP   73 (250)
Q Consensus         8 ~G~g~v~--~~~~~~~~l-~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~-----------~~~   73 (250)
                      .|+|+|+  .+....+.. ...++++.||+.||..||+.+..  ...+.|+|||++++..+..+..           +.+
T Consensus        18 aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~~--~~~i~i~tds~~~i~~~~~~~~~~~~~~~~~~~~~~   95 (152)
T d1jl1a_          18 GGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKP   95 (152)
T ss_dssp             EEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCB
T ss_pred             EEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhcc--cceEEEeecceeeEEcccchhhHhHhccchhcccCe
Confidence            7888875  444333322 35678999999999999998753  5679999999999998876531           111


Q ss_pred             HH-HHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhcccccCCCCh
Q psy7660          74 LI-AHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAEIVNLSSP  127 (250)
Q Consensus        74 ~~-~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~~~~~~~~~~  127 (250)
                      +. ..+...+..+ .....|.|+|||||+|++|||.||+|||+|+..+.+++.+|
T Consensus        96 ~~n~~~~~~i~~~-~~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~d~~~  149 (152)
T d1jl1a_          96 VKNVDLWQRLDAA-LGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTGY  149 (152)
T ss_dssp             CTTHHHHHHHHHH-TTTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCCTTC
T ss_pred             eecHHHHHHHHHH-hhcceeEEEEecccCCCccHHHHHHHHHHHHhCCCCCccCC
Confidence            10 1223333333 24568999999999999999999999999998887776665

>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=99.80  E-value=2.1e-20  Score=148.48  Aligned_cols=113  Identities=18%  Similarity=0.112  Sum_probs=80.1

Q ss_pred             CCc-eEEEEEEC--Ce-eEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC----------
Q psy7660           5 LQN-TSCAVYAG--GT-TKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT----------   70 (250)
Q Consensus         5 ~~~-~G~g~v~~--~~-~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~----------   70 (250)
                      |++ .|+|+|+.  +. ....+....+|+++|||.||..||+.+..  ...+.|+|||+++++.+.....          
T Consensus        15 N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~--~~~i~i~tds~~~~~~~~~~~~~~~~~~~~~~   92 (147)
T d1rila_          15 NPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRT   92 (147)
T ss_dssp             TTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHHHHHHHSSHHHHHHHTTSBC
T ss_pred             CCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhccC--CceEEEecchhhhhccccccchhhhhhccccc
Confidence            444 67787762  22 22222234578999999999999997643  5689999999999998876421          


Q ss_pred             --chHHH-HHHHHHHHHHHhCCCceEEEeccCCCCCccchHHhHHHHhhhccc
Q psy7660          71 --TIPLI-AHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAE  120 (250)
Q Consensus        71 --~~~~~-~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD~lAk~a~~~~  120 (250)
                        ++++. .++++.+..+ .....|.|.|||||+|++|||.||+|||+|+...
T Consensus        93 ~~~~~v~n~dL~~~l~~~-~~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_          93 AEGKPVKNRDLWEALLLA-MAPHRVRFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             TTSSBCTTHHHHHHHHHH-HTTSEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             cccccchhHHHHHHHHHH-hhhcccceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence              11111 1223333333 3467899999999999999999999999999754

>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=99.60  E-value=3.3e-15  Score=113.14  Aligned_cols=89  Identities=22%  Similarity=0.268  Sum_probs=65.8

Q ss_pred             CCCCc-eEEEEEECCe-eEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC--chHHHHHH
Q psy7660           3 KTLQN-TSCAVYAGGT-TKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT--TIPLIAHI   78 (250)
Q Consensus         3 ~~~~~-~G~g~v~~~~-~~~~~l~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~--~~~~~~~i   78 (250)
                      ..+++ .|+|++..+. .....+ ..+|++.|||.||+.||+..    ..++.|+|||++++++|..+..  .+++..+|
T Consensus        18 ~~n~~~g~~g~~~~~~~~~~~~~-~~~TNn~aEl~Avi~aL~~~----~~~v~I~TDS~yvi~~i~~~~~~~~~~l~~~i   92 (110)
T d1s1ta1          18 NRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQPDQSESELVNQI   92 (110)
T ss_dssp             ETTTTEEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHHHCCSEESCHHHHHH
T ss_pred             CCCCCCcEEEEEEecCCeEEEec-ccCcHHHHHHHHHHHHHHhC----CCeEEEEEehHHHHHHHhcCccccchHHHHHH
Confidence            45555 4455555443 333333 46799999999999999853    4689999999999999999876  46776666


Q ss_pred             HHHHHHHHhCCCceEEEeccCC
Q psy7660          79 LNTWYSLKSCGKNVAFLWCPSH  100 (250)
Q Consensus        79 ~~~~~~l~~~g~~V~~~WVPgH  100 (250)
                      .+.+.    ....|.|.|||||
T Consensus        93 l~~l~----~~~~v~i~WVpgH  110 (110)
T d1s1ta1          93 IEQLI----KKEKVYLAWVPAH  110 (110)
T ss_dssp             HHHHH----HCSEEEEEECCSS
T ss_pred             HHHHh----cCCceEEEEeCCC
Confidence            55443    2568999999999

>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=99.39  E-value=7.8e-14  Score=108.35  Aligned_cols=106  Identities=19%  Similarity=0.033  Sum_probs=78.3

Q ss_pred             CCCCCc-eEEEEEECCe--eEEEec-CCCCchHHHHHHHHHHHHHHhhcCCCCeEEEEeccHHHHHhhhcCCC-------
Q psy7660           2 SKTLQN-TSCAVYAGGT--TKSYIL-NNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT-------   70 (250)
Q Consensus         2 S~~~~~-~G~g~v~~~~--~~~~~l-~~~~s~~~AEl~AI~~AL~~~~~~~~~~i~I~tDS~~al~ai~~~~~-------   70 (250)
                      |..|+| .|+|+|+...  ...+.- -..+|+++|||.|++.||+.+.+.+ .++.|+|||+++++.+.++.-       
T Consensus        13 ~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~~kt~~~~~   91 (132)
T d1zbfa1          13 SQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKKAKSTLVRN   91 (132)
T ss_dssp             ECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTCCCCCCCCS
T ss_pred             CCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCceecCcCCC
Confidence            455665 7888887432  222221 2567899999999999999998754 579999999999999987641       


Q ss_pred             --chHHHHHHHHHHHHHHhCCCceEEEeccCCCCCccchHHh
Q psy7660          71 --TIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVD  110 (250)
Q Consensus        71 --~~~~~~~i~~~~~~l~~~g~~V~~~WVPgH~gi~gNe~AD  110 (250)
                        .+++.+.|.++..-|.  ...+.+.|+..|+..-||..||
T Consensus        92 vkN~~l~~~i~~a~~~lk--~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          92 EETALIWKLVDEAEEWLN--THTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             TTTHHHHHHHHHHHHHHH--HCCCCCCEEECCHHHHCSCTTC
T ss_pred             cccHHHHHHHHHHHHHHH--hCCcCceeEEecCcccccCCCC
Confidence              3566655555444343  3568888999999999999998