Psyllid ID: psy17038

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------40
Protein Sequence
MATMLQNSSKDSLSALQSIQNEFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALSSNSPSVNTIPINYFKRFLKSKILSTWNTEWVNLADNKLRQIKEEKRPWNPSLHESRESNSARLPQVSLAELKVIQETLGDLERQGDLDLDLCDSWRNLAESQEANDDGDLSSHHVTLDLANRIVQSYTGIQADLKYGVSGILSEIMDLVQDVVTSSEAGEDGLELPVARKREYQEARQKCQREVRRIREEWWNKKINELQEFANKNDTYNLYRGMKSAVGPIRKPLNIIEDKNGNKISNKEERLERWREHFQHVFNQQTTVNLEGIEIDPITDNLPNDERPTENEIMLETLIFPKSPIKMNFPFLVLCLLAEEHGKMNNRVGHNSGPG
Secondary Structure (PSIPRED)
ccccccHHHHcHHHHHHHHHccccccHHHHHHHHHHHHHcccccEEEEEEcccccccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHccccccccccccHHHHHHHHHHHccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccHHHHHHHHHccccccHHHHHHHHHHHHcccccEEEEEEEcccccccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccHHHHccccccccccccccccccccccccHHHHHHHHHHHHccccHHHcccccccHHHHHHHHcccccccccccccccEEEEccHcEEEEEcccccccccccccHHHHHHHHHHHHHHccHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHccccccccEcEcccccEEccHHHHHHHHHHHHHHHHcccccccHHHcccccccccccccccccHHHHHHHHHHcccccccccccHHHHHHHHHHHccEccccccccccc
Coil and Loop (DISEMBL)
matmlqnssKDSLSALQSIQNEFSSNPIAQEIRNILVKNKHILSLHftwvpshvgivgneeSDRLAKEAlssnspsvntipiNYFKRFLKSKILSTWNTEWVNLADNKLRQIkeekrpwnpslhesresnsarlpqvSLAELKVIQETLgdlerqgdldldLCDSWRNLAesqeanddgdlsshHVTLDLANRIVQSYTGIQADLKYGVSGILSEIMDLVQDVvtsseagedglelPVARKREYQEARQKCQREVRRIREEWWNKKINELQEFankndtynlyrgmksavgpirkplniiedkngnkisnKEERLERWREHFQHVFNqqttvnlegieidpitdnlpnderptenEIMLETlifpkspikmnfPFLVLCLLAEEhgkmnnrvghnsgpg
Flexible Loop (DISEMBL)
matmlqnsskDSLSALQSIQNEFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEalssnspsvntipINYFKRFLKSKILSTWNTEWVNLADNKlrqikeekrpwnpslhesresnsarlpqvSLAELKVIQETlgdlerqgdLDLDLCDSWRNLAESqeanddgdlsSHHVTLDLANRIVQSYTGIQADLKYGVSGILSEIMDLVQDVVTSseagedglelpvaRKREYQEARQKCQREVRRIREEWWNKKINELqefankndtyNLYRGMKsavgpirkplniiedkngnkiSNKEERLERWREHFQHVFnqqttvnlegieidPITDNLPNDERPTENEIMLETLIFPKSPIKMNFPFLVLCLLAEEHgkmnnrvghnsgpg
Low Complexity Region (SEG)
MATMLQNSSKDSLSALQSIQNEFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALSSNSPSVNTIPINYFKRFLKSKILSTWNTEWVNLADNKLRQIKEEKRPWNPSLHESRESNSARLPQVSLAELKVIQETLGDLERQGDLDLDLCDSWRNLAESQEANDDGDLSSHHVTLDLANRIVQSYTGIQADLKYGVSGILSEIMDLVQDVVTSSEAGEDGLELPVARKREYQEARQKCQREVRRIREEWWNKKINELQEFANKNDTYNLYRGMKSAVGPIRKPLNIIEDKNGNKISNKEERLERWREHFQHVFNQQTTVNLEGIEIDPITDNLPNDERPTENEIMLETLIFPKSPIKMNFPFLVLCLLAEEHGKMNNRVGHNSGPG
Disordered region (IsUnstruct)
***************************IAQEIRNILVKNKHILSLHFTWVPSHVGIVG******************VNTIPINYFKRFLKSKILSTWNTEWVNLADNKL******************************AELKVIQETLGDLERQGDLDLDLCDSWRNL**************HHVTLDLANRIVQSYTGIQADLKYGVSGILSEIMDLVQDVVT***************************REVRRIREEWWNKKINELQEFANKNDTYNLYRGMKSAVGPIRKPLNIIE*************LERWREHFQHVFNQQTTVNLEGIEIDPIT************EIMLETLIFPKSPIKMNFPFLVLCLLAE****************
Disordered Region (DISOPRED)
*ATMLQNSSKDSLSALQSIQNEFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALSSNSPSVNTIPINYFKRFLKSKILSTWNTEWVNLADNKLRQIKEEKRPWNPSLHESRESNSARLPQVSLAELKVIQETLGDLERQGDLDLDLCDSWRNLAESQEANDDGDLSSHHVTLDLANRIVQSYTGIQADLKYGVSGILSEIMDLVQDVVTSSEAG**************QE*RQKCQREVRRIREEWWNKKINELQEFANKNDTYNLYRGMKSAVGPIRKPLNIIEDKNGNKISNKEERLERWREHFQHVFNQQTTVNLEGIEIDPITDNLPNDERPTENEIMLETLIFPKSPIKMNFPFLVLCLLAEEHGKMN**********
Disordered Region (DISEMBL)
***************LQSIQNEFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALSSNSPSVNTIPINYFKRFLKSKILSTWNTEWVNLADNKLRQIKEEKRP**************RLPQVSLAELKVIQETLGDLERQGDLDLDLCDSWRNLAESQEANDDGDLSSHHVTLDLANRIVQSYTGIQADLKYGVSGILSEIMDLVQDVVTSSEAGEDGLELPVARKR***********EVRRIREEWWNKKINELQEFANKNDTYNLYRGMKSAVGPIRKPLNIIEDKNGNKISNKEERLERWREHFQHVFNQQTTVNLEGIEIDPITDNLPNDERPTENEIMLETLIFPKSPIKMNFPFLVLCLLAEEHGKMNNRVGHNSGPG
Disordered Region (DISPRO)
******NSSKDSLSALQSIQNEFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALSSNSPSVNTIPINYFKRFLKSKILSTWNTEWVNLADNKLRQIKEEKRPWNPSLHESRESNSARLPQVSLAELKVIQETLGDLERQGDLDLDLCDSWRNLAES**ANDDGDLSSHHVTLDLANRIVQSYTGIQADLKYGVSGILSEIMDLVQDVVTSSEAGEDGLELPVARKREYQEARQKCQREVRRIREEWWNKKINELQEFANKNDTYNLYRGMKSAVGPIRKPLNIIEDKNGNKISNKEERLERWREHFQHVFNQQTTVNLEGIEIDPITDNLPNDERPTENEIMLETLIFPKSPIKMNFPFLVLCLLAEEHGKMNNR********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATMLQNSSKDSLSALQSIQNEFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALSSNSPSVNTIPINYFKRFLKSKILSTWNTEWVNLADNKLRQIKEEKRPWNPSLHESRESNSARLPQVSLAELKVIQETLGDLERQGDLDLDLCDSWRNLAESQEANDDGDLSSHHVTLDLANRIVQSYTGIQADLKYGVSGILSEIMDLVQDVVTSSEAGEDGLELPVARxxxxxxxxxxxxxxxxxxxxxWWNKKINELQEFANKNDTYNLYRGMKSAVGPIRKPLNIIEDKNGNKISNKEERLERWREHFQHVFNQQTTVNLEGIEIDPITDNLPNDERPTENEIMLETLIFPKSPIKMNFPFLVLCLLAEEHGKMNNRVGHNSGPG
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	399
427791807	1212	Putative tick transposon, partial [Rhipi	0.290	0.095	0.333	5e-12
427791321	1210	Putative tick transposon, partial [Rhipi	0.290	0.095	0.333	6e-12
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.285	0.242	0.380	1e-10
358335181	1327	zinc finger protein 341 [Clonorchis sine	0.263	0.079	0.359	9e-10
358340771	888	beta-arrestin [Clonorchis sinensis]	0.263	0.118	0.359	1e-09
432921434	763	PREDICTED: uncharacterized protein LOC10	0.278	0.145	0.296	1e-09
358332951	1917	roundabout homolog 2 [Clonorchis sinensi	0.263	0.054	0.359	1e-09
358342258	1809	E3 ubiquitin-protein ligase RBBP6 [Clono	0.278	0.061	0.354	3e-09
358341719	671	ATP-binding cassette transporter [Clonor	0.263	0.156	0.359	5e-09
1549144	1162	ORF2 [Bombyx mori]	0.220	0.075	0.381	6e-09

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

 Score = 78.6 bits (192), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 39/117 (33%), Positives = 65/117 (55%), Gaps = 1/117 (0%)

Query: 11   DSLSALQSIQNEFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEAL 70
            DSLSAL+++  +    P+  +I N+++ N  ++S+ F WVPSHVGI GNE++D+ A  A 
Sbjct: 1002 DSLSALKALHIKSECEPLVGDILNMVLINSKVISMRFCWVPSHVGIPGNEKADKCASLAA 1061

Query: 71   SSNSPSVNTIPINYFKRFLKSKILSTWNTEWVNLADNKLRQIKEEKRPWNPSLHESR 127
                  +  IP+   +R ++  +L+ W  +W +   NKL  +K     W    H+ R
Sbjct: 1062 HKTLTKIR-IPLKDSQRTIRLALLAKWQQQWDSCTSNKLHLVKPTLGEWKNCRHQER 1117

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 78.2 bits (191), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 39/117 (33%), Positives = 65/117 (55%), Gaps = 1/117 (0%)

Query: 11   DSLSALQSIQNEFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEAL 70
            DSLSAL+++  +    P+  +I N+++ N  ++S+ F WVPSHVGI GNE++D+ A  A 
Sbjct: 999  DSLSALKALHIKSECEPLVGDILNMVLINSKVISMRFCWVPSHVGIPGNEKADKCASLAA 1058

Query: 71   SSNSPSVNTIPINYFKRFLKSKILSTWNTEWVNLADNKLRQIKEEKRPWNPSLHESR 127
                  +  IP+   +R ++  +L+ W  +W +   NKL  +K     W    H+ R
Sbjct: 1059 HKTLTKIR-IPLKDSQRTIRLALLAKWQQQWDSCTSNKLHLVKPTLGEWKNCRHQER 1114

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 74.3 bits (181), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 46/121 (38%), Positives = 62/121 (51%), Gaps = 7/121 (5%)

Query: 11  DSLSALQSIQNEFSSNP----IAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLA 66
           DSLSA+ +I      +P    +   I++I  + K ++   F W PSHVGI GNE +D LA
Sbjct: 84  DSLSAIMAIHGMDVRHPYVLQVLYAIKSISQQEKIVV---FMWCPSHVGIPGNEMADTLA 140

Query: 67  KEALSSNSPSVNTIPINYFKRFLKSKILSTWNTEWVNLADNKLRQIKEEKRPWNPSLHES 126
           KEALSS + +   +P +  +  +K  I S W  EW     NKL  I     PW P   E 
Sbjct: 141 KEALSSTNLAELPVPASDLRCLIKKYIRSRWQHEWDEQHSNKLHSIHPTIGPWPPCQREK 200

Query: 127 R 127
           R
Sbjct: 201 R 201

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|358335181|dbj|GAA53681.1| zinc finger protein 341 [Clonorchis sinensis]

 Score = 71.2 bits (173), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 41/114 (35%), Positives = 66/114 (57%), Gaps = 9/114 (7%)

Query: 248 RQKCQREVRRIREEWWNKKINELQEFANKNDTYNLYRGMKSAVGPIRKPLN-IIEDKNGN 306
           R++ +  V+  RE WW +K  E++E     +   L++ ++ A GP + P++  I+D+NG 
Sbjct: 195 RRQVKVSVKADREVWWTQKAKEMEEAQKSGNARRLFQLIR-ATGPRKPPVSETIKDRNGV 253

Query: 307 KISNKEERLERWREHFQHVFNQQTTVNLEGIEIDPITDNLP---NDERPTENEI 357
            ISNKEERL+RW E+F+    QQ +    G  ++P  D  P   N E PT +E+
Sbjct: 254 TISNKEERLDRWAEYFE----QQLSWPPAGAHLEPTGDVEPWAVNVEPPTASEV 303

Source: Clonorchis sinensis

Species: Clonorchis sinensis

Genus: Clonorchis

Family: Opisthorchiidae

Order: Opisthorchiida

Class: Trematoda

Phylum: Platyhelminthes

Superkingdom: Eukaryota

>gi|358340771|dbj|GAA48599.1| beta-arrestin [Clonorchis sinensis]

 Score = 70.5 bits (171), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 41/114 (35%), Positives = 67/114 (58%), Gaps = 9/114 (7%)

Query: 248 RQKCQREVRRIREEWWNKKINELQEFANKNDTYNLYRGMKSAVGPIRKPLN-IIEDKNGN 306
           R++ +  V+  RE WW +K  E++E     +   L++ ++ A GP + P++  I+D+NG 
Sbjct: 189 RRQVKVSVQADREVWWTQKAKEMEEAQKSGNARRLFQLIR-ATGPRKPPVSETIKDRNGV 247

Query: 307 KISNKEERLERWREHFQHVFNQQTTVNLEGIEIDPITDNLP---NDERPTENEI 357
            ISNKEERL+RW E+F+    QQ + +  G  ++P  D  P   N E PT +E+
Sbjct: 248 TISNKEERLDRWAEYFE----QQLSWSPAGAHLEPTGDVEPWTVNVEPPTASEV 297

Source: Clonorchis sinensis

Species: Clonorchis sinensis

Genus: Clonorchis

Family: Opisthorchiidae

Order: Opisthorchiida

Class: Trematoda

Phylum: Platyhelminthes

Superkingdom: Eukaryota

>gi|432921434|ref|XP_004080155.1| PREDICTED: uncharacterized protein LOC101161343 [Oryzias latipes]

 Score = 70.5 bits (171), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 37/125 (29%), Positives = 68/125 (54%), Gaps = 14/125 (11%)

Query: 241 KREYQEARQKCQREVRRIREEWWNKKINELQEFANKNDTYNLYRGMKSAVGPIRKPLNII 300
           K +Y+  + + Q ++R+++ EWW KK + +Q  A++ND+   +  +K   GP    L+ +
Sbjct: 234 KSKYKTVKSELQTKLRQMKNEWWTKKADGIQSLADRNDSKAFFASLKEVYGPKGACLDPV 293

Query: 301 EDKNGNKI-SNKEERLERWREHFQHVFNQQTTVNLEGIEIDPITDNLPN-------DERP 352
           +  +G+ + ++K + +ERWREHF  + N +TTV+      D    N+P        D  P
Sbjct: 294 KSIDGSVLHTDKSKIMERWREHFSLLLNPETTVD------DVAVSNIPQLPVRYHMDTPP 347

Query: 353 TENEI 357
           T  E+
Sbjct: 348 TTEEL 352

Source: Oryzias latipes

Species: Oryzias latipes

Genus: Oryzias

Family: Adrianichthyidae

Order: Beloniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|358332951|dbj|GAA51532.1| roundabout homolog 2 [Clonorchis sinensis]

 Score = 70.5 bits (171), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 41/114 (35%), Positives = 65/114 (57%), Gaps = 9/114 (7%)

Query: 248  RQKCQREVRRIREEWWNKKINELQEFANKNDTYNLYRGMKSAVGPIRKPLN-IIEDKNGN 306
            R++ +  V+  RE WW +K  E++E     +   L++ +  A GP + P++  I+D+NG 
Sbjct: 1488 RRQVKASVKADREVWWTQKAKEMEEAQKFGNARRLFQ-LIPATGPRKPPVSETIKDRNGV 1546

Query: 307  KISNKEERLERWREHFQHVFNQQTTVNLEGIEIDPITDNLP---NDERPTENEI 357
             ISNKEERL+RW E+F+    QQ +    G  ++P  D  P   N E PT +E+
Sbjct: 1547 TISNKEERLDRWAEYFE----QQLSWPPAGAHLEPTGDVEPWTVNVEPPTASEV 1596

Source: Clonorchis sinensis

Species: Clonorchis sinensis

Genus: Clonorchis

Family: Opisthorchiidae

Order: Opisthorchiida

Class: Trematoda

Phylum: Platyhelminthes

Superkingdom: Eukaryota

>gi|358342258|dbj|GAA49764.1| E3 ubiquitin-protein ligase RBBP6 [Clonorchis sinensis]

 Score = 69.7 bits (169), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 44/124 (35%), Positives = 69/124 (55%), Gaps = 13/124 (10%)

Query: 242  REYQEARQKCQREVRRI----REEWWNKKINELQEFANKNDTYNLYRGMKSAVGPIRKPL 297
            R+ Q  R   +R+V+      RE WW +K  E++E     +   L++ ++ A GP + P+
Sbjct: 1494 RDTQAPRASIRRQVKASVKADREVWWTQKAKEMEEAQKSGNARRLFQLIR-ATGPRKPPV 1552

Query: 298  N-IIEDKNGNKISNKEERLERWREHFQHVFNQQTTVNLEGIEIDPITDNLP---NDERPT 353
            +  I+D+NG  ISNKEERL+RW E+F+    QQ +    G  ++P  D  P   N E PT
Sbjct: 1553 SETIKDRNGVTISNKEERLDRWAEYFE----QQLSWPPAGAHLEPTGDVEPWTVNVEPPT 1608

Query: 354  ENEI 357
             +E+
Sbjct: 1609 ASEV 1612

Source: Clonorchis sinensis

Species: Clonorchis sinensis

Genus: Clonorchis

Family: Opisthorchiidae

Order: Opisthorchiida

Class: Trematoda

Phylum: Platyhelminthes

Superkingdom: Eukaryota

>gi|358341719|dbj|GAA49321.1| ATP-binding cassette transporter [Clonorchis sinensis]

 Score = 68.6 bits (166), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 41/114 (35%), Positives = 66/114 (57%), Gaps = 9/114 (7%)

Query: 248 RQKCQREVRRIREEWWNKKINELQEFANKNDTYNLYRGMKSAVGPIRKPLN-IIEDKNGN 306
           R++ +  V+  RE WW +K  E++E     +   L++ ++ A GP + P++  I+D+NG 
Sbjct: 143 RRQVKVSVQADREVWWTQKAKEMEEAHKSGNARRLFQLIR-ATGPRKPPVSETIKDRNGV 201

Query: 307 KISNKEERLERWREHFQHVFNQQTTVNLEGIEIDPITDNLP---NDERPTENEI 357
            ISNKEERL+RW E+F+    QQ +    G  ++P  D  P   N E PT +E+
Sbjct: 202 TISNKEERLDRWAEYFE----QQLSRQPAGAHLEPTGDVEPWTVNVEPPTASEV 251

Source: Clonorchis sinensis

Species: Clonorchis sinensis

Genus: Clonorchis

Family: Opisthorchiidae

Order: Opisthorchiida

Class: Trematoda

Phylum: Platyhelminthes

Superkingdom: Eukaryota

>gi|1549144|dbj|BAA07467.1| ORF2 [Bombyx mori]

 Score = 68.2 bits (165), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 37/97 (38%), Positives = 60/97 (61%), Gaps = 9/97 (9%)

Query: 11   DSLSALQSIQNEFSSNPIAQEIRNIL----VKNKHILSLHFTWVPSHVGIVGNEESDRLA 66
            DS +AL ++ N  S +P+A +IR +L    ++NK   ++   W+ +H G+ GNE +D+LA
Sbjct: 953  DSKAALLTVINHGSLHPLAVDIRKMLKQCALQNK---TVALYWIKAHAGLEGNERADQLA 1009

Query: 67   KEA--LSSNSPSVNTIPINYFKRFLKSKILSTWNTEW 101
            KEA  LS  SP+ +  P++Y KR ++S  L  WN  +
Sbjct: 1010 KEAALLSKKSPNYDLCPVSYVKRIIRSGSLDEWNRRY 1046

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

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

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	399
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	2e-14
pfam00075	126	pfam00075, RNase_H, RNase H	7e-11
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	5e-06
cd09277	133	cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI	7e-06
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	0.004

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

 Score = 69.6 bits (171), Expect = 2e-14
 Identities = 27/62 (43%), Positives = 38/62 (61%), Gaps = 1/62 (1%)

Query: 11  DSLSALQSIQNEFSSNPIAQEIR-NILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEA 69
           DS +AL+++++  SS+P+   IR  I     H + +   WVP H GI GNE +DRLAKEA
Sbjct: 67  DSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLAKEA 126

Query: 70  LS 71
             
Sbjct: 127 AK 128

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 = 59.2 bits (144), Expect = 7e-11
 Identities = 24/65 (36%), Positives = 32/65 (49%), Gaps = 7/65 (10%)

Query: 11  DSLSALQSI----QNEFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLA 66
           DS   +  I      +  S PI  EI  +L K   +   +  WVP H GI GNE +D+LA
Sbjct: 65  DSQYVIGGITNGWPTKSESKPIKNEIWELLQKKHKV---YIQWVPGHSGIPGNELADKLA 121

Query: 67  KEALS 71
           K+  S
Sbjct: 122 KQGAS 126

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|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and more complex than their prokaryotic counterparts and unlike prokaryote, RNase H are essential in higher eukaryote

 Score = 45.7 bits (109), Expect = 5e-06
 Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 1/43 (2%)

Query: 30  QEIRNILVK-NKHILSLHFTWVPSHVGIVGNEESDRLAKEALS 71
           +E+  +L +  +  + + F  VP H GI GNEE+DRLAK+   
Sbjct: 108 KELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGAD 150

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). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at the N-terminal called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. Length = 150

>gnl|CDD|187701 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus

 Score = 44.8 bits (107), Expect = 7e-06
 Identities = 15/45 (33%), Positives = 24/45 (53%)

Query: 26  NPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEAL 70
               +E +  + K K  + + F  V +H G   NE +D+LAK+AL
Sbjct: 89  KEGTKEYKEFMDKIKKKIKISFVKVKAHSGDKYNELADKLAKKAL 133

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 involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability. Some bacteria distinguished from other bacterial RNase HI in the presence of a hybrid binding domain (HBD) at the N-terminus which is commonly present at the N-termini of eukaryotic RNase HI. It has been reported that this domain is required for dimerization and processivity of RNase HI upon binding to RNA-DNA hybrids. Length = 133

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

 Score = 37.1 bits (87), Expect = 0.004
 Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 10/43 (23%)

Query: 37  VKNK-------HILSLH---FTWVPSHVGIVGNEESDRLAKEA 69
           VKN         +L+ H   + WV  H G  GNE +D LA  A
Sbjct: 95  VKNVDLWQELDALLAKHQVTWHWVKGHAGHPGNERADELANAA 137

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	399
PRK06548	161	ribonuclease H; Provisional	99.2
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.18
PRK00203	150	rnhA ribonuclease H; Reviewed	99.16
PRK08719	147	ribonuclease H; Reviewed	99.13
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.07
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	98.67
KOG3752|consensus	371		98.15
PRK13907	128	rnhA ribonuclease H; Provisional	97.72
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	97.43
PRK07708	219	hypothetical protein; Validated	96.98
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	96.69
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	90.1

>PRK06548 ribonuclease H; Provisional

Probab=99.20  E-value=2.1e-11  Score=109.93  Aligned_cols=66  Identities=26%  Similarity=0.319  Sum_probs=50.7

Q ss_pred             ccEEEEcCcHHHHHHHhc---------cC--CCC-----hHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHH
Q psy17038          4 MLQNSSKDSLSALQSIQN---------EF--SSN-----PIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAK   67 (399)
Q Consensus         4 ~~i~I~tDs~sal~al~~---------~~--~~~-----~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak   67 (399)
                      ..|.|+|||++|+++|..         |.  +.+     ++++.|.+++..    ..|+|.|||||+|++|||.||+||+
T Consensus        62 ~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~----~~v~~~wVkgHsg~~gNe~aD~LA~  137 (161)
T PRK06548         62 RPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN----RNIRMSWVNAHTGHPLNEAADSLAR  137 (161)
T ss_pred             ceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc----CceEEEEEecCCCCHHHHHHHHHHH
Confidence            469999999999999994         22  112     333344444332    5799999999999999999999999


Q ss_pred             HHhhcC
Q psy17038         68 EALSSN   73 (399)
Q Consensus        68 ~a~~~~   73 (399)
                      +|+...
T Consensus       138 ~aa~~~  143 (161)
T PRK06548        138 QAANNF  143 (161)
T ss_pred             HHHHHh
Confidence            998665

>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=99.18  E-value=3.8e-11  Score=103.01  Aligned_cols=65  Identities=38%  Similarity=0.657  Sum_probs=51.8

Q ss_pred             ccEEEEcCcHHHHHHHhc-----cC---CCC-hHHHHHHHHHHhcCCCccEEEEEeccCCCC-CCChhhhHHHHHHhh
Q psy17038          4 MLQNSSKDSLSALQSIQN-----EF---SSN-PIAQEIRNILVKNKHILSLHFTWVPSHVGI-VGNEESDRLAKEALS   71 (399)
Q Consensus         4 ~~i~I~tDs~sal~al~~-----~~---~~~-~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi-~gNe~AD~~Ak~a~~   71 (399)
                      ..|+|+|||++++.+|..     .+   ... ++...|.+++.. .  ..|.|.|||||+|+ .||+.||+|||.|+.
T Consensus        58 ~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~~~-~--~~v~~~~V~~H~~~~~~N~~aD~lAk~a~~  132 (132)
T PF00075_consen   58 RKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELLSR-G--IKVRFRWVPGHSGVPQGNERADRLAKEAAQ  132 (132)
T ss_dssp             SEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHHHH-S--SEEEEEESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred             ccccccccHHHHHHHHHHhccccccccccccccchhheeecccc-c--eEEeeeeccCcCCCchhHHHHHHHHHHhcC
Confidence            578999999999998887     22   112 466677777744 2  78999999999999 699999999999973

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

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.16  E-value=4e-11  Score=106.74  Aligned_cols=66  Identities=23%  Similarity=0.303  Sum_probs=51.2

Q ss_pred             ccEEEEcCcHHHHHHHhccC---------C--CC-----hHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHH
Q psy17038          4 MLQNSSKDSLSALQSIQNEF---------S--SN-----PIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAK   67 (399)
Q Consensus         4 ~~i~I~tDs~sal~al~~~~---------~--~~-----~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak   67 (399)
                      ..|.|+|||++++++|..|.         .  .+     ++++.|.+++..    ..|.|.|||||+|++||+.||+||+
T Consensus        62 ~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~----~~v~~~wV~~H~~~~~N~~AD~lA~  137 (150)
T PRK00203         62 CEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR----HQIKWHWVKGHAGHPENERCDELAR  137 (150)
T ss_pred             CeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc----CceEEEEecCCCCCHHHHHHHHHHH
Confidence            46899999999999998631         1  11     233444444322    6899999999999999999999999


Q ss_pred             HHhhcC
Q psy17038         68 EALSSN   73 (399)
Q Consensus        68 ~a~~~~   73 (399)
                      +|+...
T Consensus       138 ~a~~~~  143 (150)
T PRK00203        138 AGAEEA  143 (150)
T ss_pred             HHHHHh
Confidence            998876

>PRK08719 ribonuclease H; Reviewed

Probab=99.13  E-value=7.1e-11  Score=105.09  Aligned_cols=62  Identities=24%  Similarity=0.292  Sum_probs=46.5

Q ss_pred             EEEEcCcHHHHHHHh--------ccC-CC--C-----hHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHHHH
Q psy17038          6 QNSSKDSLSALQSIQ--------NEF-SS--N-----PIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEA   69 (399)
Q Consensus         6 i~I~tDs~sal~al~--------~~~-~~--~-----~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~a   69 (399)
                      ..|+|||++|+++|.        +.+ .+  .     ++.+.|..+.+    ...|+|.|||||+|++|||.||+||++|
T Consensus        69 ~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~----~~~i~~~~VkgH~g~~~Ne~aD~lA~~a  144 (147)
T PRK08719         69 DVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA----RKYVEVEKVTAHSGIEGNEAADMLAQAA  144 (147)
T ss_pred             CEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC----CCcEEEEEecCCCCChhHHHHHHHHHHH
Confidence            579999999999994        333 11  1     22333333333    2679999999999999999999999999


Q ss_pred             hh
Q psy17038         70 LS   71 (399)
Q Consensus        70 ~~   71 (399)
                      +.
T Consensus       145 ~~  146 (147)
T PRK08719        145 AE  146 (147)
T ss_pred             hh
Confidence            75

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

Probab=99.07  E-value=1.8e-10  Score=102.73  Aligned_cols=68  Identities=24%  Similarity=0.358  Sum_probs=53.1

Q ss_pred             cccEEEEcCcHHHHHHHhccC----CCC------------hHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHH
Q psy17038          3 TMLQNSSKDSLSALQSIQNEF----SSN------------PIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLA   66 (399)
Q Consensus         3 ~~~i~I~tDs~sal~al~~~~----~~~------------~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~A   66 (399)
                      .+.|.|+|||++++++|..|.    ...            ++++.+.++....   ..|.+.|||||+|.++||+||+||
T Consensus        63 ~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~---~~v~~~WVkgH~g~~~NeraD~LA  139 (154)
T COG0328          63 ACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRH---ELVFWEWVKGHAGHPENERADQLA  139 (154)
T ss_pred             CceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhC---CeEEEEEeeCCCCChHHHHHHHHH
Confidence            467999999999999999552    111            2344444454443   389999999999999999999999


Q ss_pred             HHHhhcC
Q psy17038         67 KEALSSN   73 (399)
Q Consensus        67 k~a~~~~   73 (399)
                      +.|+...
T Consensus       140 ~~~~~~~  146 (154)
T COG0328         140 REAARAA  146 (154)
T ss_pred             HHHHHhh
Confidence            9998765

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

Probab=98.67  E-value=6.4e-08  Score=79.93  Aligned_cols=68  Identities=31%  Similarity=0.427  Sum_probs=50.0

Q ss_pred             cccEEEEcCcHHHHHHHhccCC--CChHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHHHHh
Q psy17038          3 TMLQNSSKDSLSALQSIQNEFS--SNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEAL   70 (399)
Q Consensus         3 ~~~i~I~tDs~sal~al~~~~~--~~~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~a~   70 (399)
                      ...+.|++||++++..+.++..  .......++.+.....+...+.|.|||+|+|+.+|+.||.+|+.|.
T Consensus        61 ~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          61 GKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             CceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            3568999999999999998752  1222222333322222237899999999999999999999999873

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

>KOG3752|consensus

Probab=98.15  E-value=3.3e-06  Score=84.41  Aligned_cols=69  Identities=20%  Similarity=0.191  Sum_probs=50.8

Q ss_pred             cccEEEEcCcHHHHHHHhccCC-----------CCh----------HHHHHHHHHHhcCCCccEEEEEeccCCCCCCChh
Q psy17038          3 TMLQNSSKDSLSALQSIQNEFS-----------SNP----------IAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEE   61 (399)
Q Consensus         3 ~~~i~I~tDs~sal~al~~~~~-----------~~~----------~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~   61 (399)
                      +.+++|.|||.+++++|+.|-.           .++          .+..+-++.+.. ....|++.|||||.||.||++
T Consensus       276 ~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~-~~~~vq~~~V~Gh~gi~gne~  354 (371)
T KOG3752|consen  276 INKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEI-SNKKVQQEYVGGHSGILGNEM  354 (371)
T ss_pred             CCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhh-ccCceEEEEecCcCCcchHHH
Confidence            4589999999999999997741           112          112233333331 127999999999999999999


Q ss_pred             hhHHHHHHhhc
Q psy17038         62 SDRLAKEALSS   72 (399)
Q Consensus        62 AD~~Ak~a~~~   72 (399)
                      ||.+|++++..
T Consensus       355 Ad~lARkgs~~  365 (371)
T KOG3752|consen  355 ADALARKGSTL  365 (371)
T ss_pred             HHHHHhhhhhh
Confidence            99999998543

>PRK13907 rnhA ribonuclease H; Provisional

Probab=97.72  E-value=7.6e-05  Score=64.20  Aligned_cols=62  Identities=23%  Similarity=0.403  Sum_probs=46.7

Q ss_pred             ccEEEEcCcHHHHHHHhccCCCC----hHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHHHHhhc
Q psy17038          4 MLQNSSKDSLSALQSIQNEFSSN----PIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALSS   72 (399)
Q Consensus         4 ~~i~I~tDs~sal~al~~~~~~~----~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~a~~~   72 (399)
                      ..|.|+|||+++++.+.+.+...    .+.+.+..++...   ..+.|.|||.+    .|+.||.+|+.|...
T Consensus        62 ~~v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~f---~~~~~~~v~r~----~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         62 NIVSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIKSF---DLFFIKWIPSS----QNKVADELARKAILQ  127 (128)
T ss_pred             CEEEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHhcC---CceEEEEcCch----hchhHHHHHHHHHhc
Confidence            36899999999999998865322    3344455555443   57788999984    999999999999754

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

Probab=97.43  E-value=0.00044  Score=54.38  Aligned_cols=61  Identities=30%  Similarity=0.341  Sum_probs=44.2

Q ss_pred             ccEEEEcCcHHHHHHHhccC-CCC---hHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHHHHhh
Q psy17038          4 MLQNSSKDSLSALQSIQNEF-SSN---PIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALS   71 (399)
Q Consensus         4 ~~i~I~tDs~sal~al~~~~-~~~---~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~a~~   71 (399)
                      .+|.|.|||+.+++.|.+.. ...   .+.+.|+.+++..   ..+.|.|||    =++|..||.+||.|.+
T Consensus        22 ~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~---~~~~~~~i~----r~~N~~A~~LA~~a~~   86 (87)
T PF13456_consen   22 RKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRF---WNVSVSHIP----REQNKVADALAKFALS   86 (87)
T ss_dssp             SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCC---SCEEEEE------GGGSHHHHHHHHHHHH
T ss_pred             CEEEEEecCccccccccccccccccccccchhhhhhhccc---cceEEEEEC----hHHhHHHHHHHHHHhh
Confidence            57999999999999998875 222   3444555665553   689999999    5689999999999864

>PRK07708 hypothetical protein; Validated

Probab=96.98  E-value=0.0017  Score=61.66  Aligned_cols=63  Identities=24%  Similarity=0.268  Sum_probs=47.2

Q ss_pred             cEEEEcCcHHHHHHHhccC-CCChH----HHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHHHHhhcC
Q psy17038          5 LQNSSKDSLSALQSIQNEF-SSNPI----AQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALSSN   73 (399)
Q Consensus         5 ~i~I~tDs~sal~al~~~~-~~~~~----~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~a~~~~   73 (399)
                      .|.|++||+.+++.+..-+ ..++.    ...+.++++...  ..+.|.|||-    ..|+.||+||+.|++..
T Consensus       142 ~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~--l~~~~~~VpR----~~N~~AD~LAk~Al~~~  209 (219)
T PRK07708        142 PVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLK--LTPVYEPISR----KQNKEADQLATQALEGT  209 (219)
T ss_pred             eEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCC--ceEEEEECCc----hhhhHHHHHHHHHHhcC
Confidence            3899999999999998865 33333    334555555543  5688899985    56999999999999865

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=96.69  E-value=0.0037  Score=63.53  Aligned_cols=63  Identities=21%  Similarity=0.394  Sum_probs=47.6

Q ss_pred             ccEEEEcCcHHHHHHHhccC-CCC-hHH---HHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHHHHhhcC
Q psy17038          4 MLQNSSKDSLSALQSIQNEF-SSN-PIA---QEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALSSN   73 (399)
Q Consensus         4 ~~i~I~tDs~sal~al~~~~-~~~-~~~---~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~a~~~~   73 (399)
                      ..|.|++||+.+++.+.+.+ ..+ ...   ..++++++..   ..|.|.|||.    .+|+.||.||+.|....
T Consensus        66 ~~v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f---~~~~i~~v~r----~~N~~AD~LA~~a~~~~  133 (372)
T PRK07238         66 TEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQF---GRVTYTWIPR----ARNAHADRLANEAMDAA  133 (372)
T ss_pred             CeEEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcC---CceEEEECCc----hhhhHHHHHHHHHHHhh
Confidence            46899999999999998754 222 222   3344554443   5899999997    68999999999998665

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

Probab=90.10  E-value=0.19  Score=40.27  Aligned_cols=31  Identities=16%  Similarity=0.218  Sum_probs=22.8

Q ss_pred             ccccCCCCCCcccccccchhhccccCCCCCCcceeeecccc
Q psy17038        152 LERQGDLDLDLCDSWRNLAESQEANDDGDLSSHHVTLDLAN  192 (399)
Q Consensus       152 l~r~~~~~s~~C~cg~~~~ea~~~~~~~~eTv~H~L~~Cp~  192 (399)
                      |.+.+...++.|..|.          ...||+.|+|+.||.
T Consensus        51 l~~r~~~~~~~C~~C~----------~~~Et~~Hlf~~C~~   81 (86)
T PF13966_consen   51 LQRRGIQVDPICPLCG----------NEEETIEHLFFHCPF   81 (86)
T ss_pred             hhccCCccCCccccCC----------CccccccceeccCcC
Confidence            5555666678888552          127999999999996

---

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	399
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	4e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	1e-04
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	6e-04
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	7e-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 = 45.4 bits (108), Expect = 4e-06
 Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 2/45 (4%)

Query: 26  NPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEAL 70
           N   Q    ++ + + I    F  V +H G   N+  D  AK AL
Sbjct: 93  NEFTQAYAKLMNQYRGIY--SFEKVKAHSGNEFNDYVDMKAKSAL 135

>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 = 47.2 bits (111), Expect = 8e-06
 Identities = 62/419 (14%), Positives = 119/419 (28%), Gaps = 129/419 (30%)

Query: 4   MLQN-----SSKDSLSALQSIQNEFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVG 58
           MLQ          +  +  S   +   + I  E+R +L    +   L    V  +V    
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL---LVLLNV---- 253

Query: 59  NEESDRLAKEALSSNSPSVNTIPINYFKRFLKSKILSTWNTEWVNLAD----NKLRQIKE 114
                          +        N F   L  KIL T  T +  + D         I  
Sbjct: 254 --------------QNAKA----WNAFN--LSCKILLT--TRFKQVTDFLSAATTTHISL 291

Query: 115 EKRPWNPSLHESRE-------SNSARLP----QVSLAELKVIQETLGDLERQGDLDLDLC 163
           +      +  E +             LP      +   L +I E++ D        L   
Sbjct: 292 DHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRD-------GLATW 344

Query: 164 DSWRN---------LAESQEANDDGDLSSHHVTLDLANRIVQSYTGIQADLKYGVSGIL- 213
           D+W++         +  S    +  +         L+  +      I       +  ++ 
Sbjct: 345 DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD--RLS--VFPPSAHIPTI----LLSLIW 396

Query: 214 -----SEIMDLVQDVVTSSEAGEDGLELPVARKREYQEARQKCQREV---RRIREEWWNK 265
                S++M +V  +   S   +   E  ++    Y E + K + E    R I + +   
Sbjct: 397 FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIP 456

Query: 266 KINELQEFA-NKNDTYNL-YRG--MKSA-----VGPIRKP---LNIIEDK---------N 304
           K  +  +      D Y   + G  +K+      +   R        +E K          
Sbjct: 457 KTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNA 516

Query: 305 GNKISNKEERLERWREHFQHVFNQQTTVNLEGIEIDPITDNLPNDERPTENEIMLETLI 363
              I N  ++L+ ++ +                    I DN P  ER      ++  ++
Sbjct: 517 SGSILNTLQQLKFYKPY--------------------ICDNDPKYER------LVNAIL 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 = 41.4 bits (96), Expect = 5e-04
 Identities = 41/342 (11%), Positives = 88/342 (25%), Gaps = 111/342 (32%)

Query: 143 KVIQETLGDLERQGDLDL-DLCDSWRNLAESQEANDDGDLSSHHVTLDLANRIVQSYTGI 201
            ++           + D  D+ D  +++   +E +           +   + +  +    
Sbjct: 20  DILSVFEDAFVD--NFDCKDVQDMPKSILSKEEIDH---------IIMSKDAVSGTLRLF 68

Query: 202 QADLKYGVSGI---LSEIMDLVQDVVTSSEAGEDGLELPVARKREYQEARQKCQREVRRI 258
              L      +   + E++ +    + S    E     P    R Y E R +   + +  
Sbjct: 69  WTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQ--RQPSMMTRMYIEQRDRLYNDNQVF 126

Query: 259 ------REEWWNKKINELQEFANKNDTYNLYRGM----KSA------------------- 289
                 R + + K    L E   +     L  G+    K+                    
Sbjct: 127 AKYNVSRLQPYLKLRQALLEL--RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKI 184

Query: 290 ----VGPIRKPLNIIE---------DKNGNK----ISNKEERLERWREHFQHVFNQQTTV 332
               +     P  ++E         D N        SN + R+   +   + +   +   
Sbjct: 185 FWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYE 244

Query: 333 N----LEGIEIDP--------------------ITDNLPNDER-------------PTEN 355
           N    L  ++ +                     +TD L                  P E 
Sbjct: 245 NCLLVLLNVQ-NAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV 303

Query: 356 EIMLETLI------FPKSPIKMNFPFLVLCLLAEEHGKMNNR 391
           + +L   +       P+  +  N P   L ++AE        
Sbjct: 304 KSLLLKYLDCRPQDLPREVLTTN-P-RRLSIIAESIRDGLAT 343

>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 = 1e-04
 Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 5/61 (8%)

Query: 7   NSSKDSLSALQSIQN--EFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDR 64
           N   DS  AL  IQ   + S + +  +I   L+K + +   +  WVP+H GI GNE+ D+
Sbjct: 496 NIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKV---YLAWVPAHKGIGGNEQVDK 552

Query: 65  L 65
           L
Sbjct: 553 L 553

>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A Length = 150

 Score = 39.1 bits (92), Expect = 6e-04
 Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 2/31 (6%)

Query: 39  NKHILSLHFTWVPSHVGIVGNEESDRLAKEA 69
            K  + L   WVP+H GI GNE+ D+L    
Sbjct: 116 KKEKVYLA--WVPAHKGIGGNEQVDKLVSAG 144

>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 = 40.9 bits (96), Expect = 7e-04
 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 5/57 (8%)

Query: 11  DSLSALQSIQN--EFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRL 65
           DS   +  + +    S + I  +I   ++K + I   +  WVP+H GI GN+E D L
Sbjct: 497 DSQYVMGIVASQPTESESKIVNQIIEEMIKKEAI---YVAWVPAHKGIGGNQEVDHL 550

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	399
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.31
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.3
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.26
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.25
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.23
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.17
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.16
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.14
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	98.96
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	98.92
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	98.85
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	98.64
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	98.56
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	98.5
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	92.73

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

Probab=99.31  E-value=1.9e-12  Score=112.89  Aligned_cols=66  Identities=21%  Similarity=0.174  Sum_probs=52.7

Q ss_pred             ccEEEEcCcHHHHHHHhc-cC----------------CCChHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHH
Q psy17038          4 MLQNSSKDSLSALQSIQN-EF----------------SSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLA   66 (399)
Q Consensus         4 ~~i~I~tDs~sal~al~~-~~----------------~~~~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~A   66 (399)
                      ..|.|+|||++++++|.. |.                ...++.+.|.++++.    ..|.|.|||||+|++|||.||+||
T Consensus        63 ~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~----~~v~~~~V~gH~g~~~N~~AD~LA  138 (146)
T 3h08_A           63 ARVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTL----HRVTFHKVKGHSDNPYNSRADELA  138 (146)
T ss_dssp             CEEEEEESCHHHHHHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHH----SEEEEEECCC-CCSHHHHHHHHHH
T ss_pred             CcEEEEeChHHHHHHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhh----CceEEEEcCCcCCcHhHHHHHHHH
Confidence            579999999999999988 31                113456666666654    469999999999999999999999


Q ss_pred             HHHhhcC
Q psy17038         67 KEALSSN   73 (399)
Q Consensus        67 k~a~~~~   73 (399)
                      ++|+...
T Consensus       139 ~~a~~~~  145 (146)
T 3h08_A          139 RLAIKEN  145 (146)
T ss_dssp             HHHHHHC
T ss_pred             HHHHHhC
Confidence            9998753

>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=99.30  E-value=1.2e-12  Score=115.44  Aligned_cols=70  Identities=27%  Similarity=0.418  Sum_probs=50.6

Q ss_pred             cccEEEEcCcHHHHHHHhccC-----------CCChHH--HHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHHHH
Q psy17038          3 TMLQNSSKDSLSALQSIQNEF-----------SSNPIA--QEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEA   69 (399)
Q Consensus         3 ~~~i~I~tDs~sal~al~~~~-----------~~~~~~--~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~a   69 (399)
                      +..|.|+|||++++++|..|.           ...++.  ..++++++...+...|.|.|||||+|++|||.||+||++|
T Consensus        65 ~~~v~i~tDS~~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a  144 (150)
T 3qio_A           65 GLEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAG  144 (150)
T ss_dssp             CSEEEEEESCHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTT
T ss_pred             CCcEEEEeCcHHHHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHH
Confidence            467999999999999998862           111111  1233333322223789999999999999999999999999


Q ss_pred             hhc
Q psy17038         70 LSS   72 (399)
Q Consensus        70 ~~~   72 (399)
                      +..
T Consensus       145 ~~~  147 (150)
T 3qio_A          145 IRK  147 (150)
T ss_dssp             TSC
T ss_pred             HHH
Confidence            865

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

Probab=99.26  E-value=4.4e-12  Score=111.69  Aligned_cols=66  Identities=24%  Similarity=0.385  Sum_probs=52.6

Q ss_pred             ccEEEEcCcHHHHHHHhccC---------C-------CChHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHH
Q psy17038          4 MLQNSSKDSLSALQSIQNEF---------S-------SNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAK   67 (399)
Q Consensus         4 ~~i~I~tDs~sal~al~~~~---------~-------~~~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak   67 (399)
                      ..|.|+|||++++++|..|.         .       ..++++.|.+++..    ..|.|.|||||+|++|||.||+||+
T Consensus        71 ~~v~i~tDS~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~----~~v~~~~V~~H~g~~~N~~AD~LA~  146 (154)
T 2qkb_A           71 NKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQG----MDIQWMHVPGHSGFIGNEEADRLAR  146 (154)
T ss_dssp             CEEEEEESCHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTT----CEEEEEECCTTSSCHHHHHHHHHHH
T ss_pred             ceEEEEECcHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcC----CceEEEEccCCCCCHhHHHHHHHHH
Confidence            57999999999999998741         1       12345555555442    5799999999999999999999999


Q ss_pred             HHhhcC
Q psy17038         68 EALSSN   73 (399)
Q Consensus        68 ~a~~~~   73 (399)
                      +|+..+
T Consensus       147 ~a~~~~  152 (154)
T 2qkb_A          147 EGAKQS  152 (154)
T ss_dssp             HHHTCC
T ss_pred             HHHHhc
Confidence            998764

>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=99.25  E-value=5.1e-12  Score=111.60  Aligned_cols=66  Identities=26%  Similarity=0.272  Sum_probs=52.2

Q ss_pred             ccEEEEcCcHHHHHHHhccC---------C-------CChHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHH
Q psy17038          4 MLQNSSKDSLSALQSIQNEF---------S-------SNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAK   67 (399)
Q Consensus         4 ~~i~I~tDs~sal~al~~~~---------~-------~~~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak   67 (399)
                      ..|.|+|||++++++|..|.         .       ..++.+.|.++++    ...|.|.|||||+|++||+.||+||+
T Consensus        63 ~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~----~~~v~~~wV~gH~g~~~Ne~AD~LA~  138 (155)
T 1jl1_A           63 AEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG----QHQIKWEWVKGHAGHPENERADELAR  138 (155)
T ss_dssp             CEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT----TCEEEEEECCSSTTCHHHHHHHHHHH
T ss_pred             CcEEEEeCHHHHHHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHHc----cCceEEEEcCCCCCCHHHHHHHHHHH
Confidence            57999999999999999731         1       1234444444433    26899999999999999999999999


Q ss_pred             HHhhcC
Q psy17038         68 EALSSN   73 (399)
Q Consensus        68 ~a~~~~   73 (399)
                      .|+..+
T Consensus       139 ~a~~~~  144 (155)
T 1jl1_A          139 AAAMNP  144 (155)
T ss_dssp             HHHHSC
T ss_pred             HHHhcc
Confidence            999876

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

Probab=99.23  E-value=7.3e-12  Score=111.01  Aligned_cols=65  Identities=22%  Similarity=0.280  Sum_probs=52.5

Q ss_pred             ccEEEEcCcHHHHHHHhcc--------C-C-------CChHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHH
Q psy17038          4 MLQNSSKDSLSALQSIQNE--------F-S-------SNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAK   67 (399)
Q Consensus         4 ~~i~I~tDs~sal~al~~~--------~-~-------~~~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak   67 (399)
                      ..|.|+|||++++++|..|        + .       ..++.+.|.++++.    ..|.|.|||||+|++||+.||+||+
T Consensus        65 ~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~----~~v~~~wV~gH~g~~~Ne~AD~LAk  140 (158)
T 2e4l_A           65 CKIILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQL----HQIDWRWVKGHAGHAENERCDQLAR  140 (158)
T ss_dssp             CEEEEEECCHHHHHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTT----SEEEEEECCTTCCCHHHHHHHHHHH
T ss_pred             CeEEEEeCHHHHHHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHcc----CcEEEEEccCCCCchhHHHHHHHHH
Confidence            5799999999999999882        1 1       11444555555542    5899999999999999999999999


Q ss_pred             HHhhc
Q psy17038         68 EALSS   72 (399)
Q Consensus        68 ~a~~~   72 (399)
                      .|+..
T Consensus       141 ~a~~~  145 (158)
T 2e4l_A          141 AAAEA  145 (158)
T ss_dssp             HHHHS
T ss_pred             HHHHh
Confidence            99987

>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=99.17  E-value=1.2e-11  Score=110.68  Aligned_cols=71  Identities=24%  Similarity=0.170  Sum_probs=52.9

Q ss_pred             cccEEEEcCcHHHHHHHhccCCCChH--HHHHHHHHHhcCCCccEEEEEeccCCC-----CCCChhhhHHHHHHhhcC
Q psy17038          3 TMLQNSSKDSLSALQSIQNEFSSNPI--AQEIRNILVKNKHILSLHFTWVPSHVG-----IVGNEESDRLAKEALSSN   73 (399)
Q Consensus         3 ~~~i~I~tDs~sal~al~~~~~~~~~--~~~i~~l~~~~~~~~~V~~~WvpgH~g-----i~gNe~AD~~Ak~a~~~~   73 (399)
                      ...|.|||||++++++|-.....+++  ...|++++........|.|.|||||+|     ++|||.||+||++|+..+
T Consensus        80 ~~~v~I~tDS~~vi~~iw~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~  157 (165)
T 3p1g_A           80 GKKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKA  157 (165)
T ss_dssp             TSEEEEEECCHHHHHHHHSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEchHHHHhhhhcccCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcC
Confidence            35799999999999999211112222  122555554433347999999999999     999999999999999876

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

Probab=99.16  E-value=1.8e-11  Score=109.45  Aligned_cols=66  Identities=18%  Similarity=0.174  Sum_probs=53.1

Q ss_pred             ccEEEEcCcHHHHHHHhc----------cCC-------CChHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHH
Q psy17038          4 MLQNSSKDSLSALQSIQN----------EFS-------SNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLA   66 (399)
Q Consensus         4 ~~i~I~tDs~sal~al~~----------~~~-------~~~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~A   66 (399)
                      ..|.|+|||++++++|..          |..       ..++.+.|.+++..    ..|.|.|||||+|++||+.||+||
T Consensus        67 ~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~----~~v~~~wV~gH~g~~~Ne~AD~LA  142 (166)
T 1ril_A           67 CEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP----HRVRFHFVKGHTGHPENERVDREA  142 (166)
T ss_dssp             CEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTT----SEEECCCCCGGGSCTHHHHHHHHH
T ss_pred             CeEEEEeChHHHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhc----CeEEEEEeeCCCCchhHHHHHHHH
Confidence            479999999999999998          221       12345555555442    589999999999999999999999


Q ss_pred             HHHhhcC
Q psy17038         67 KEALSSN   73 (399)
Q Consensus        67 k~a~~~~   73 (399)
                      ++|+...
T Consensus       143 k~a~~~~  149 (166)
T 1ril_A          143 RRQAQSQ  149 (166)
T ss_dssp             HHHHTSS
T ss_pred             HHHHHHh
Confidence            9999876

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

Probab=99.14  E-value=3.2e-11  Score=107.97  Aligned_cols=67  Identities=18%  Similarity=0.108  Sum_probs=51.0

Q ss_pred             cccEEEEcCcHHHHHHHhccC-----------C-----CChHHHHHHHHHHhcCCCccEEEEEeccCCCC------CCCh
Q psy17038          3 TMLQNSSKDSLSALQSIQNEF-----------S-----SNPIAQEIRNILVKNKHILSLHFTWVPSHVGI------VGNE   60 (399)
Q Consensus         3 ~~~i~I~tDs~sal~al~~~~-----------~-----~~~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi------~gNe   60 (399)
                      +..|.|+|||+|++++|..|.           .     ..++.+.+.+++...   ..|.|.|||||+|+      +|||
T Consensus        75 ~~~v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~---~~v~~~~VkgH~g~~~~~~~~gNe  151 (165)
T 2lsn_A           75 PGPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMK---PDITIQHEKGHQPTNTSIHTEGNA  151 (165)
T ss_dssp             SSCEEEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHC---TTCEEEECCSSSCSSSCHHHHHHH
T ss_pred             CCeEEEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCC---CCEEEEEEeCCCCccCCCCChHHH
Confidence            346999999999999997642           1     124455555555443   68999999999995      5799


Q ss_pred             hhhHHHHHHhhc
Q psy17038         61 ESDRLAKEALSS   72 (399)
Q Consensus        61 ~AD~~Ak~a~~~   72 (399)
                      +||+||++|+..
T Consensus       152 ~AD~LA~~gA~~  163 (165)
T 2lsn_A          152 LADKLATQGSYV  163 (165)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhh
Confidence            999999999853

>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=98.96  E-value=6.8e-11  Score=103.58  Aligned_cols=67  Identities=21%  Similarity=0.131  Sum_probs=51.6

Q ss_pred             cEEEEcCcHHHHHHHhccC-CCChHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHHHHhhcC
Q psy17038          5 LQNSSKDSLSALQSIQNEF-SSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALSSN   73 (399)
Q Consensus         5 ~i~I~tDs~sal~al~~~~-~~~~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~a~~~~   73 (399)
                      .|.|+|||+.+..-+.+.+ .+......+.++++...  ..|.|.|||||+|++|||.||+||++|+...
T Consensus        71 ~v~I~tDS~~i~~w~~~~w~~~~~~~~~~~~l~~~l~--~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~  138 (147)
T 2kq2_A           71 KIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMNQYR--GIYSFEKVKAHSGNEFNDYVDMKAKSALGIR  138 (147)
T ss_dssp             CCCBSSCCSTHHHHTTSSSSCCHHHHHHHHCGGGGGS--TTCCBCCCCCCCCCHHHHHHHHHHHHHHTCC
T ss_pred             eEEEEECcHHHHHHHhCCCccCCcchHHHHHHHHHhc--CCeeEEEecCcCCCcchHHHHHHHHHHHhcc
Confidence            6899999998877666544 22333344455555443  3899999999999999999999999999876

>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=98.92  E-value=1e-09  Score=115.24  Aligned_cols=65  Identities=28%  Similarity=0.423  Sum_probs=54.4

Q ss_pred             cccEEEEcCcHHHHHHHhccC--CCChHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHHHHh
Q psy17038          3 TMLQNSSKDSLSALQSIQNEF--SSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEAL   70 (399)
Q Consensus         3 ~~~i~I~tDs~sal~al~~~~--~~~~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~a~   70 (399)
                      ...|.|+|||++|+++|..|.  ..+++.+.+.+++...   ..|.|.|||||+|++|||.||+||++|+
T Consensus       489 ~~~v~I~tDS~~v~~~i~~~~~~~~~~l~~~~~~~~~~~---~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          489 GPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIKK---EAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             CSEEEEEESCHHHHHHHHTCCSEESCHHHHHHHHHHHHC---SEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             CCeEEEEEehHHHHHHHhcccccccHHHHHHHHHHhccC---CcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            357999999999999999876  4457777666555443   6899999999999999999999999874

>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=98.85  E-value=1.6e-09  Score=113.89  Aligned_cols=64  Identities=33%  Similarity=0.481  Sum_probs=50.8

Q ss_pred             cccEEEEcCcHHHHHHHhccCC--CChHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHHHH
Q psy17038          3 TMLQNSSKDSLSALQSIQNEFS--SNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEA   69 (399)
Q Consensus         3 ~~~i~I~tDs~sal~al~~~~~--~~~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~a   69 (399)
                      ...|.|+|||++|+++|..|..  .+++.+.+.+.+...   ..|.|.|||||+|++|||.||+||++|
T Consensus       492 ~~~v~I~tDS~~vi~~i~~~~~~~~~~l~~~~~~~l~~~---~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          492 GLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKK---EKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             CSEEEEEECCHHHHHHHTTCCSEESSHHHHHHHHHHHHC---SEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             CCcEEEEeChHHHHHHHhcCCccCCHHHHHHHHHHHhcC---CCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            3579999999999999999863  356776665444443   589999999999999999999999976

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

Probab=98.64  E-value=3.3e-08  Score=84.11  Aligned_cols=62  Identities=23%  Similarity=0.343  Sum_probs=48.1

Q ss_pred             ccEEEEcCcHHHHHHHhccCC-CC-hH---HHHHHHH-HHhcCCCccEEEEEeccCCCCCCChhhhHHHHHHhhc
Q psy17038          4 MLQNSSKDSLSALQSIQNEFS-SN-PI---AQEIRNI-LVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALSS   72 (399)
Q Consensus         4 ~~i~I~tDs~sal~al~~~~~-~~-~~---~~~i~~l-~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~a~~~   72 (399)
                      ..|.|+|||+++++.|..++. .+ .+   .+.|.++ +...   ..|.|.|||+    ++|+.||+||+.|+..
T Consensus        70 ~~v~i~tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~---~~v~~~~V~~----~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D           70 MEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERV---PNLVFVHIPR----EKNARADELVNEAIDK  137 (140)
T ss_dssp             CEEEEEESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHC---TTCEEEECCG----GGGHHHHHHHHHHHHH
T ss_pred             ceEEEEeChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCC---CcEEEEEcCc----hhhHHHHHHHHHHHHh
Confidence            389999999999999998662 22 33   3445555 5443   5899999994    8999999999999864

>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=98.56  E-value=1.1e-07  Score=81.31  Aligned_cols=66  Identities=18%  Similarity=0.343  Sum_probs=48.0

Q ss_pred             ccEEEEcCcHHHHHHHhccC-CCCh-HHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHHHHhhcC
Q psy17038          4 MLQNSSKDSLSALQSIQNEF-SSNP-IAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALSSN   73 (399)
Q Consensus         4 ~~i~I~tDs~sal~al~~~~-~~~~-~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~a~~~~   73 (399)
                      ..|.|+|||+++++.|...+ ..+. +...+.++.........|.|.|||+    ++|+.||+||+.|+...
T Consensus        67 ~~v~i~tDS~~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~~  134 (141)
T 3hst_B           67 TEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----ARNTYADRLANDAMDAA  134 (141)
T ss_dssp             SEEEEEESCHHHHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHHHHHH
T ss_pred             ceEEEEeChHHHHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHHHHHh
Confidence            57999999999999998854 3333 3333333322222226899999996    79999999999998764

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

Probab=98.50  E-value=1.7e-07  Score=81.41  Aligned_cols=62  Identities=23%  Similarity=0.364  Sum_probs=49.2

Q ss_pred             ccEEEEcCcHHHHHHHhccCC-CC----hHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHHHHhhcC
Q psy17038          4 MLQNSSKDSLSALQSIQNEFS-SN----PIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALSSN   73 (399)
Q Consensus         4 ~~i~I~tDs~sal~al~~~~~-~~----~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~a~~~~   73 (399)
                      ..|.|+|||+++++.|..++. .+    .+.+.|.++++..    .|.|.|||+|    +|+.||+||+.|+...
T Consensus        69 ~~v~i~tDS~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~----~v~~~~V~~~----~N~~AD~LA~~a~~~~  135 (149)
T 2ehg_A           69 SSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKL----NATLIWVPRE----ENKEADRLSRVAYELV  135 (149)
T ss_dssp             CSCEEEESCHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHH----TCEEEECCGG----GCHHHHHHHHHHHHHH
T ss_pred             CEEEEEeChHHHHHHHhCccccCCHHHHHHHHHHHHHHhcC----CEEEEEcCCc----ccHHHHHHHHHHHHhh
Confidence            568999999999999999752 22    3444555565543    5999999994    9999999999998765

>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=92.73  E-value=0.018  Score=49.76  Aligned_cols=58  Identities=9%  Similarity=0.006  Sum_probs=41.4

Q ss_pred             cEEEEcCcHHHHHHHhccCC---------CChHHHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhh
Q psy17038          5 LQNSSKDSLSALQSIQNEFS---------SNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESD   63 (399)
Q Consensus         5 ~i~I~tDs~sal~al~~~~~---------~~~~~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD   63 (399)
                      .|.|+|||+++++.+.+.+.         ..++.+.+.++..-.. .+.++...|..|++..||..||
T Consensus        72 ~v~i~tDS~~vi~w~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~-~~~~~~~~~kw~~~~~ge~pad  138 (142)
T 1zbf_A           72 RKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLN-THTYETPILKWQTDKWGEIKAD  138 (142)
T ss_dssp             CCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHH-HCCCCCCEEECCHHHHCSCTTC
T ss_pred             eEEEEEehHHHHHHHHcCCccCCCCCCcccHHHHHHHHHHHHHHh-hCCCceeEEEeccCccCcCccc
Confidence            68999999999999988651         1245555544422111 1567788888899999999998

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	399
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	1e-06
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	2e-05
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	5e-04

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

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

 Score = 44.9 bits (105), Expect = 1e-06
 Identities = 14/60 (23%), Positives = 31/60 (51%), Gaps = 1/60 (1%)

Query: 11  DSLSALQSIQNEFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEAL 70
           DS   +  + ++ +    ++ +  I+ +     +++  WVP+H GI GN+E D L  + +
Sbjct: 68  DSQYVMGIVASQPT-ESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI 126

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

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

 Score = 42.2 bits (98), Expect = 2e-05
 Identities = 10/31 (32%), Positives = 14/31 (45%)

Query: 46  HFTWVPSHVGIVGNEESDRLAKEALSSNSPS 76
            F +V  H G   NE  DR A+    S + +
Sbjct: 117 RFHFVKGHTGHPENERVDREARRQAQSQAKT 147

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

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

 Score = 38.1 bits (87), Expect = 5e-04
 Identities = 11/40 (27%), Positives = 17/40 (42%)

Query: 30  QEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEA 69
            ++   L        + + WV  H G   NE +D LA+ A
Sbjct: 99  VDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAA 138

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	399
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.35
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.18
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.11
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	98.24
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	96.57

>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=99.35  E-value=4.5e-13  Score=112.20  Aligned_cols=65  Identities=26%  Similarity=0.414  Sum_probs=50.5

Q ss_pred             CcccEEEEcCcHHHHHHHhccCC--CChHHH-HHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHHHHh
Q psy17038          2 ATMLQNSSKDSLSALQSIQNEFS--SNPIAQ-EIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEAL   70 (399)
Q Consensus         2 ~~~~i~I~tDs~sal~al~~~~~--~~~~~~-~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~a~   70 (399)
                      ....|.|||||+++++.+.+++.  .+.... .+..+...    ..|.|.|||||+|++|||.||+||++|.
T Consensus        59 ~~~~i~I~tDS~~v~~~~~~~~~~~~~~~~~~~~~~~~~~----~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          59 SGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIKK----EAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             SCSEEEEEESCHHHHHHHHTCCSEESCHHHHHHHHHHHHC----SEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             CCcceEEEechHHHHHHHhcCCccccchHHHHHHHHhhhc----ceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            34679999999999999999762  233333 34433332    5899999999999999999999999873

>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=99.18  E-value=5.8e-12  Score=107.68  Aligned_cols=70  Identities=20%  Similarity=0.256  Sum_probs=50.7

Q ss_pred             cccEEEEcCcHHHHHHHhccC------------CCChH--HHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHHH
Q psy17038          3 TMLQNSSKDSLSALQSIQNEF------------SSNPI--AQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKE   68 (399)
Q Consensus         3 ~~~i~I~tDs~sal~al~~~~------------~~~~~--~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~   68 (399)
                      ...+.|+|||++++++|..+.            ..+++  ...|++++.... ...|+|.|||||+|++|||.||+||++
T Consensus        61 ~~~i~i~tds~~~~~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~-~~~v~~~wVkgHsg~~gNe~AD~LAk~  139 (147)
T d1rila_          61 PCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA-PHRVRFHFVKGHTGHPENERVDREARR  139 (147)
T ss_dssp             CCEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT-TSEEECCCCCGGGSCTHHHHHHHHHHH
T ss_pred             CceEEEecchhhhhccccccchhhhhhccccccccccchhHHHHHHHHHHhh-hcccceEEccCCCCCcchHHHHHHHHH
Confidence            356899999999999997643            01111  112333332221 268999999999999999999999999


Q ss_pred             HhhcC
Q psy17038         69 ALSSN   73 (399)
Q Consensus        69 a~~~~   73 (399)
                      |+.+.
T Consensus       140 aa~~~  144 (147)
T d1rila_         140 QAQSQ  144 (147)
T ss_dssp             HHTSS
T ss_pred             HHHHh
Confidence            98764

>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=99.11  E-value=2.3e-11  Score=103.76  Aligned_cols=69  Identities=23%  Similarity=0.261  Sum_probs=50.3

Q ss_pred             ccEEEEcCcHHHHHHHhccCC-----------CChH--HHHHHHHHHhcCCCccEEEEEeccCCCCCCChhhhHHHHHHh
Q psy17038          4 MLQNSSKDSLSALQSIQNEFS-----------SNPI--AQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEAL   70 (399)
Q Consensus         4 ~~i~I~tDs~sal~al~~~~~-----------~~~~--~~~i~~l~~~~~~~~~V~~~WvpgH~gi~gNe~AD~~Ak~a~   70 (399)
                      ..+.|+|||++++..+..+..           .+.+  ...++.+..... ...|+|+|||||+|++|||.||+|||+|+
T Consensus        61 ~~i~i~tds~~~i~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~-~~~V~~~wV~gH~g~~gNe~AD~LAk~aa  139 (152)
T d1jl1a_          61 AEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAAA  139 (152)
T ss_dssp             CEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHHH
T ss_pred             ceEEEeecceeeEEcccchhhHhHhccchhcccCeeecHHHHHHHHHHhh-cceeEEEEecccCCCccHHHHHHHHHHHH
Confidence            458899999999998876530           1111  112333322221 26899999999999999999999999999


Q ss_pred             hcC
Q psy17038         71 SSN   73 (399)
Q Consensus        71 ~~~   73 (399)
                      ..+
T Consensus       140 ~~~  142 (152)
T d1jl1a_         140 MNP  142 (152)
T ss_dssp             HSC
T ss_pred             hCC
Confidence            876

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

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

Probab=98.24  E-value=6.4e-07  Score=72.63  Aligned_cols=48  Identities=31%  Similarity=0.427  Sum_probs=37.9

Q ss_pred             cccEEEEcCcHHHHHHHhccC--CCChHHHHHHHHHHhcCCCccEEEEEeccC
Q psy17038          3 TMLQNSSKDSLSALQSIQNEF--SSNPIAQEIRNILVKNKHILSLHFTWVPSH   53 (399)
Q Consensus         3 ~~~i~I~tDs~sal~al~~~~--~~~~~~~~i~~l~~~~~~~~~V~~~WvpgH   53 (399)
                      ...|.|+|||+|++++|..+.  ..+...++|.+.+...   ..|.|.|||||
T Consensus        61 ~~~v~I~TDS~yvi~~i~~~~~~~~~~l~~~il~~l~~~---~~v~i~WVpgH  110 (110)
T d1s1ta1          61 GLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKK---EKVYLAWVPAH  110 (110)
T ss_dssp             CSEEEEEECCHHHHHHHHHCCSEESCHHHHHHHHHHHHC---SEEEEEECCSS
T ss_pred             CCeEEEEEehHHHHHHHhcCccccchHHHHHHHHHHhcC---CceEEEEeCCC
Confidence            457999999999999999876  3456666665555443   58999999999

>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=96.57  E-value=0.00015  Score=60.12  Aligned_cols=57  Identities=12%  Similarity=0.082  Sum_probs=43.5

Q ss_pred             cccEEEEcCcHHHHHHHhccC--C-------CChHHHHHHHH---HHhcCCCccEEEEEeccCCCCCCChhhh
Q psy17038          3 TMLQNSSKDSLSALQSIQNEF--S-------SNPIAQEIRNI---LVKNKHILSLHFTWVPSHVGIVGNEESD   63 (399)
Q Consensus         3 ~~~i~I~tDs~sal~al~~~~--~-------~~~~~~~i~~l---~~~~~~~~~V~~~WvpgH~gi~gNe~AD   63 (399)
                      +.++.|+|||++|++.+.++.  .       .+++.+.|.++   ++.    +.+.+.||..|++..||-.||
T Consensus        63 ~~~i~I~tDS~yvi~wv~~~~~kt~~~~~vkN~~l~~~i~~a~~~lk~----h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          63 NSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNT----HTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             TCCCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHHH----CCCCCCEEECCHHHHCSCTTC
T ss_pred             CceEEEEeccHHHHHHHHhCceecCcCCCcccHHHHHHHHHHHHHHHh----CCcCceeEEecCcccccCCCC
Confidence            357899999999999998765  1       12455555443   333    679999999999999999998