Psyllid ID: psy1455

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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-
Protein Sequence
MWWMWNEVLLRLYKCYVRPIIEYGAPIYGSASEKQLSRLEPIQNMALRIATGAFKSSRIENLQVDAGNNVKIIWIPSHCGIAGNEEVDKAAQSFTNAQIYSLITPVDLKAFLKNEFKKKWQIWWDNIQPPNKIKEIKDTVKEWQTSNRNLRKEEIILSRLRIGHTRLTHGFLMERTDPPQCEIRLKYNLNNLQIKDILGDNPRTIDLLFKFLKDSNLLPKL
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHccccccEEccccccccccHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHHHHHHHccccEEccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHccccccccccccccccHHHHHHHHHHHcccccHHHHHccccccccccEEHHHHHHHHcHHHHcccccccHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
MWWMWNEVLLRLYKCYVrpiieygapiygsasekqlsrlEPIQNMALRIATGAFKSSRIEnlqvdagnnvkIIWIpshcgiagneEVDKAAQSFTNAQIYSLITPVDLKAFLKNEFKKKWQIWwdniqppnkikEIKDTVKEWQTSNRNLRKEEIILSRLRIGhtrlthgflmertdppqceirlKYNLnnlqikdilgdnprTIDLLFKFlkdsnllpkl
Flexible Loop (DISEMBL)
MWWMWNEVLLRLYKCYVRPIIEYGAPIYGSASEKQLSRLEPIQNMALRIATGAFKSSRIENLQVDAGNNVKIIWIPSHCGIAGNEEVDKAAQSFTNAQIYSLITPVDLKAFLKNEFKKKWqiwwdniqppnkikeIKDTVKEwqtsnrnlrkeeiilsrlrightrlthgflmertdppQCEIRLKYNLNNLQIKDILGDNPRTIDLLFkflkdsnllpkl
Low Complexity Region (SEG)
MWWMWNEVLLRLYKCYVRPIIEYGAPIYGSASEKQLSRLEPIQNMALRIATGAFKSSRIENLQVDAGNNVKIIWIPSHCGIAGNEEVDKAAQSFTNAQIYSLITPVDLKAFLKNEFKKKWQIWWDNIQPPNKIKEIKDTVKEWQTSNRNLRKEEIILSRLRIGHTRLTHGFLMERTDPPQCEIRLKYNLNNLQIKDILGDNPRTIDLLFKFLKDSNLLPKL
Disordered region (IsUnstruct)
*WWMWNEVLLRLYKCYVRPIIEYGAPIYGSASEKQLSRLEPIQNMALRIATGAFKSSRIENLQVDAGNNVKIIWIPSHCGIAGNEEVDKAAQSFTNAQIYSLITPVDLKAFLKNEFKKKWQIWWDNIQPPNKIKEIKDTVKEWQTSNRNLRKEEIILSRLRIGHTRLTHGFLMERTDPPQCEIRLKYNLNNLQIKDILGDNPRTIDLLFKFLK********
Disordered Region (DISOPRED)
MWWMWNEVLLRLYKCYVRPIIEYGAPIYGSASEKQLSRLEPIQNMALRIATGAFKSSRIENLQVDAGNNVKIIWIPSHCGIAGNEEVDKAAQSFTNAQIYSLITPVDLKAFLKNEFKKKWQIWWDNIQPPNKIKEIKDTVKEWQTSNRNLRKEEIILSRLRIGHTRLTHGFLMERTDPPQCEIRLKYNLNNLQIKDILGDNPRTIDLLFKFLKDSNLLPK*
Disordered Region (DISEMBL)
MWWMWNEVLLRLYKCYVRPIIEYGAPIYGSASEKQLSRLEPIQNMALRIATGAFKSSRIENLQVDAGNNVKIIWIPSHCGIAGNEEVDKAAQSFTNAQIYSLITPVDLKAFLKNEFKKKWQIWWDNIQPPNKIKEIKDTVKEWQTSNRNLRKEEIILSRLRIGHTRLTHGFLMERTDPPQCEIRLKYNLNNLQIKDILGDNPRTIDLLFKFLKDSNLLPKL
Disordered Region (DISPRO)
*WWMWNEVLLRLYKCYVRPIIEYGAPIYGSASEKQLSRLEPIQNMALRIATGAFKSSRIENLQVDAGNNVKIIWIPSHCGIAGNEEVDKAAQSFTNAQIYSLITPVDLKAFLKNEFKKKWQIWWDNIQPPNKIKEIKDTVKEWQTSNRNLRKEEIILSRLRIGHTRLTHGFLMERTDPPQCEIRLKYNLNNLQIKDILGDNPRTIDLLFKFLKDSNLLPK*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MWWMWNEVLLRLYKCYVRPIIEYGAPIYGSASEKQLSRLEPIQNMALRIATGAFKSSRIENLQVDAGNNVKIIWIPSHCGIAGNEEVDKAAQSFTNAQIYSLITPVDLKAFLKNEFKKKWQIWWDNIQPPNKxxxxxxxxxxxxxxxxxxxxxEIILSRLRIGHTRLTHGFLMERTDPPQCEIRLKYNLNNLQIKDILGDNPRTIDLLFKFLKDSNLLPKL
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	221
443694031	574	hypothetical protein CAPTEDRAFT_227918 [	0.484	0.186	0.451	3e-18
443733872	400	hypothetical protein CAPTEDRAFT_197082 [	0.506	0.28	0.432	5e-18
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.710	0.128	0.339	3e-17
443730613	233	hypothetical protein CAPTEDRAFT_206814 [	0.619	0.587	0.353	4e-17
328720146	164	PREDICTED: hypothetical protein LOC10056	0.610	0.823	0.364	2e-16
427791807	1212	Putative tick transposon, partial [Rhipi	0.511	0.093	0.382	2e-15
427791321	1210	Putative tick transposon, partial [Rhipi	0.511	0.093	0.382	2e-15
427791063	1035	Putative tick transposon, partial [Rhipi	0.506	0.108	0.413	3e-15
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.502	0.235	0.377	1e-14
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.547	0.463	0.382	2e-14

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

 Score = 97.8 bits (242), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 51/113 (45%), Positives = 67/113 (59%), Gaps = 6/113 (5%)

Query: 72  IIWIPSHCGIAGNEEVD---KAAQSFTNAQIYSLITPVDLKAFLKNEFKKKWQIWWDNIQ 128
           + W PSH G+ GNE  D   K A SFT   I   I   D K      FK+KWQ  W + Q
Sbjct: 1   MAWCPSHVGVMGNERADLLAKEALSFTTCTIR--IPSSDFKPITHEFFKEKWQEQWSSEQ 58

Query: 129 PPNKIKEIKDTVKEWQTSNRNLRKEEIILSRLRIGHTRLTHGFLMERTDPPQC 181
             NK+  I+ T+ +W  S+R +R+EEI+L+R RIGH+ LTHG+L+ R  PP C
Sbjct: 59  E-NKLYSIQPTLGKWAKSSREIRREEIVLARARIGHSHLTHGYLVRREMPPVC 110

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 97.1 bits (240), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 51/118 (43%), Positives = 70/118 (59%), Gaps = 6/118 (5%)

Query: 67  GNNVKIIWIPSHCGIAGNEEVD---KAAQSFTNAQIYSLITPVDLKAFLKNEFKKKWQIW 123
           G ++ + W PSH G+ GNE  D   K A SFT   I   I   D K      +K+KWQ  
Sbjct: 98  GIDLVMTWCPSHVGVMGNERADLLAKEALSFTTCTIR--IPSSDFKPITHEFYKEKWQEQ 155

Query: 124 WDNIQPPNKIKEIKDTVKEWQTSNRNLRKEEIILSRLRIGHTRLTHGFLMERTDPPQC 181
           W + Q  NK+  I+ T+ +W  S+R +R+EEI+L+R RIGH+ LTHG+L+ R  PP C
Sbjct: 156 WSSEQE-NKLYCIQPTLGKWAKSSREIRREEIVLARARIGHSHLTHGYLLRREMPPVC 212

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|125901787|gb|ABN58714.1| pol-like protein [Biomphalaria glabrata]

 Score = 94.7 bits (234), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 56/165 (33%), Positives = 93/165 (56%), Gaps = 8/165 (4%)

Query: 55   KSSRIENLQVDAGNNVKIIWIPSHCGIAGNEEVDKAAQSFTNAQIYSLITPV-DLKAFLK 113
            KS ++ +L      +V  IW+PSH GI GNE  D+ A+   N  +     P  DL+  + 
Sbjct: 1039 KSLKLLDLITADRRDVTFIWVPSHVGIEGNEAADREAKRALNHAVSGTQIPYSDLRQSIA 1098

Query: 114  NEFKKKWQIWWDNIQPPNKIKEIKDTVKEWQTSNRNL-RKEEIILSRLRIGHTRLTHGFL 172
            +   ++WQ  W+  +  +K+++I   V+ W+ +++ L R+    +SRLRIGHT +TH F+
Sbjct: 1099 SATYREWQNRWE-AETHSKLRQIVADVR-WRPTSKGLTRRGSTTMSRLRIGHTYITHSFV 1156

Query: 173  MERTDPPQCEIRLKYNLNNLQIKDILGDNPRTIDLLFKFLKDSNL 217
            ++R +PP CE    Y  + L ++ IL D PR  D+  K  + +NL
Sbjct: 1157 LKREEPPLCE----YCDSRLTVEHILVDCPRYQDVRAKHFRATNL 1197

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

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

 Score = 94.0 bits (232), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 53/150 (35%), Positives = 83/150 (55%), Gaps = 13/150 (8%)

Query: 67  GNNVKIIWIPSHCGIAGNEEVD---KAAQSFTNAQIYSLITPVDLKAFLKNEFKKKWQIW 123
           G ++ I+W PSH G+ GNE  D   K A SFT   +   I   D  +   + ++ KWQ  
Sbjct: 78  GFDLVILWCPSHIGVVGNERADLLAKEALSFTACDVR--IPAFDFNSVAYSFYRDKWQAL 135

Query: 124 WDNIQPPNKIKEIKDTVKEWQTSNRNLRKEEIILSRLRIGHTRLTHGFLMERTDPP---- 179
           W +++  NK+  ++  +K+   S+R  R++EI+L+R RIGHT LTHG+L+ R  PP    
Sbjct: 136 W-SLEQNNKLHSVQPIIKKLTNSSREDRRKEIVLARARIGHTHLTHGYLLRRELPPFCVH 194

Query: 180 -QCEIRLKYNLNNLQIKDILGDNPRTIDLL 208
            QC + +K+ L  ++  D      R  D+L
Sbjct: 195 CQCPLTVKHIL--IECVDFYLHRQRYFDVL 222

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 59/162 (36%), Positives = 85/162 (52%), Gaps = 27/162 (16%)

Query: 67  GNNVKIIWIPSHCGIAGNEEVD---KAAQSFTNAQIYSLITPVDLKAFLKNEFKKKWQIW 123
           G ++  +W P HCGI GNE+ D     A S  +  + ++ T  D K  +K    +KW I 
Sbjct: 2   GMDICYMWAPGHCGIQGNEKADLEASKAASSPDTPLLNIYTYEDKKKQIKQVLDQKWLIQ 61

Query: 124 WDNIQPPNKIKEIKDTVKEWQTSNRNLRKEEIILSRLRIGHTRLTHGFLMERTDPPQCE- 182
           W  I    K+ +IK+ ++ W+    N RKEE IL+RLRIGHT +TH  LME+ DPP CE 
Sbjct: 62  W--INQHTKLNQIKNNIQTWKNPGLN-RKEETILNRLRIGHTFITHRHLMEKNDPPICEM 118

Query: 183 -------------------IRLKYNLNNLQIKDILGDNPRTI 205
                              +R KYN++  QI + LG + ++I
Sbjct: 119 CGVDLTVKHIITECRKYDDMRKKYNISQ-QIGEALGPDTQSI 159

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 44/115 (38%), Positives = 65/115 (56%), Gaps = 2/115 (1%)

Query: 69   NVKIIWIPSHCGIAGNEEVDKAAQSFTNAQIYSLITPV-DLKAFLKNEFKKKWQIWWDNI 127
            +++  W+PSH GI GNE+ DK A    +  +  +  P+ D +  ++     KWQ  WD+ 
Sbjct: 1035 SMRFCWVPSHVGIPGNEKADKCASLAAHKTLTKIRIPLKDSQRTIRLALLAKWQQQWDSC 1094

Query: 128  QPPNKIKEIKDTVKEWQTSNRNLRKEEIILSRLRIGHTRLTHGFLMERTDPPQCE 182
               NK+  +K T+ EW+      R  E+IL RLRIGHT LTH FL+ + + P CE
Sbjct: 1095 TS-NKLHLVKPTLGEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCE 1148

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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 44/115 (38%), Positives = 65/115 (56%), Gaps = 2/115 (1%)

Query: 69   NVKIIWIPSHCGIAGNEEVDKAAQSFTNAQIYSLITPV-DLKAFLKNEFKKKWQIWWDNI 127
            +++  W+PSH GI GNE+ DK A    +  +  +  P+ D +  ++     KWQ  WD+ 
Sbjct: 1032 SMRFCWVPSHVGIPGNEKADKCASLAAHKTLTKIRIPLKDSQRTIRLALLAKWQQQWDSC 1091

Query: 128  QPPNKIKEIKDTVKEWQTSNRNLRKEEIILSRLRIGHTRLTHGFLMERTDPPQCE 182
               NK+  +K T+ EW+      R  E+IL RLRIGHT LTH FL+ + + P CE
Sbjct: 1092 TS-NKLHLVKPTLGEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCE 1145

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 87.8 bits (216), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 48/116 (41%), Positives = 67/116 (57%), Gaps = 4/116 (3%)

Query: 69   NVKIIWIPSHCGIAGNEEVDK-AAQSFTNAQIYSLITP-VDLKAFLKNEFKKKWQIWWDN 126
            +V + W+P H  I GN   D+ AA +  NA    L  P +DLK  LK + +  WQ  WD 
Sbjct: 893  HVVVCWVPGHREIQGNVLADQLAASAHENAAHTFLAIPALDLKPLLKRKLRAYWQSIWDT 952

Query: 127  IQPPNKIKEIKDTVKEWQTSNRNLRKEEIILSRLRIGHTRLTHGFLMERTDPPQCE 182
             Q  NK+  IK  + EW  ++++ R+ EI L+RLR GHT  TH +L+   DPP+CE
Sbjct: 953  -QTQNKLHAIKPQLGEWPPASKS-RRTEITLTRLRTGHTHTTHAYLLSGNDPPRCE 1006

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 = 85.9 bits (211), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 43/114 (37%), Positives = 62/114 (54%), Gaps = 3/114 (2%)

Query: 70  VKIIWIPSHCGIAGNEEVDK-AAQSFTNAQIYSLITPV-DLKAFLKNEFKKKWQIWWDNI 127
           V  +W PSH GI GNE  D  A ++ ++  +  L  P  DL+  +K   + +WQ  WD  
Sbjct: 119 VVFMWCPSHVGIPGNEMADTLAKEALSSTNLAELPVPASDLRCLIKKYIRSRWQHEWDE- 177

Query: 128 QPPNKIKEIKDTVKEWQTSNRNLRKEEIILSRLRIGHTRLTHGFLMERTDPPQC 181
           Q  NK+  I  T+  W    R  R+EEI+L+R+RIGHT  TH ++    D  +C
Sbjct: 178 QHSNKLHSIHPTIGPWPPCQREKRREEIVLARIRIGHTHYTHDYIPRGDDQTEC 231

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 = 85.5 bits (210), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 47/123 (38%), Positives = 67/123 (54%), Gaps = 2/123 (1%)

Query: 60  ENLQVDAGNNVKIIWIPSHCGIAGNEEVDKAAQSFTNAQIYSLITP-VDLKAFLKNEFKK 118
           +N  V  G  V  IW PSH GI GNE  D+ A+      +  L  P  D K+ +++  K 
Sbjct: 124 QNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKS 183

Query: 119 KWQIWWDNIQPPNKIKEIKDTVKEWQTSNRNLRKEEIILSRLRIGHTRLTHGFLMERTDP 178
            WQ  WD  +  NK+  I+  + EW+   +  R+ EI+L+R RIGH+ LTHG+L+ R   
Sbjct: 184 LWQNEWDE-ETDNKLHSIQPVISEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREVA 242

Query: 179 PQC 181
           P C
Sbjct: 243 PFC 245

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

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!
3rd Layer	3.1.26.4	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	221
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	8e-09
pfam00075	126	pfam00075, RNase_H, RNase H	2e-05

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

 Score = 51.9 bits (125), Expect = 8e-09
 Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 42  IQNMALRIATGAFKSSRIENLQVDAGNNVKIIWIPSHCGIAGNEEVDKAA 91
           +++              I  L  + G  V++ W+P H GI GNE  D+ A
Sbjct: 75  LRSPRSSSPLVLRIRKAIRELA-NHGVKVRLHWVPGHSGIEGNERADRLA 123

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 = 42.6 bits (101), Expect = 2e-05
 Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 3/44 (6%)

Query: 53  AFKSSRIENL---QVDAGNNVKIIWIPSHCGIAGNEEVDKAAQS 93
             +S  I+N     +   + V I W+P H GI GNE  DK A+ 
Sbjct: 80  KSESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNELADKLAKQ 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	221
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	98.3
PRK08719	147	ribonuclease H; Reviewed	98.18
PRK00203	150	rnhA ribonuclease H; Reviewed	98.15
PRK06548	161	ribonuclease H; Provisional	97.93
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	97.63
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	97.17
KOG3752|consensus	371		97.01

>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=98.30  E-value=3.4e-07  Score=69.79  Aligned_cols=31  Identities=35%  Similarity=0.787  Sum_probs=27.9

Q ss_pred             hcCCcceeeeccCCCCC-ccchhHhHHHhhcc
Q psy1455          65 DAGNNVKIIWIPSHCGI-AGNEEVDKAAQSFT   95 (221)
Q Consensus        65 ~~g~~v~~~wvPgH~gI-~GNE~AD~~Ak~~~   95 (221)
                      ..+.+|.|.|||||+|+ .|||.||++||.++
T Consensus       100 ~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen  100 SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence            45789999999999999 69999999999764

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 ....

>PRK08719 ribonuclease H; Reviewed

Probab=98.18  E-value=7.9e-07  Score=70.20  Aligned_cols=29  Identities=34%  Similarity=0.479  Sum_probs=26.4

Q ss_pred             CCcceeeeccCCCCCccchhHhHHHhhcc
Q psy1455          67 GNNVKIIWIPSHCGIAGNEEVDKAAQSFT   95 (221)
Q Consensus        67 g~~v~~~wvPgH~gI~GNE~AD~~Ak~~~   95 (221)
                      ...|.|.|||||+|++|||.||.+|+.++
T Consensus       117 ~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~  145 (147)
T PRK08719        117 RKYVEVEKVTAHSGIEGNEAADMLAQAAA  145 (147)
T ss_pred             CCcEEEEEecCCCCChhHHHHHHHHHHHh
Confidence            45799999999999999999999999765

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=98.15  E-value=8.7e-07  Score=69.97  Aligned_cols=32  Identities=25%  Similarity=0.463  Sum_probs=28.3

Q ss_pred             CCcceeeeccCCCCCccchhHhHHHhhccccc
Q psy1455          67 GNNVKIIWIPSHCGIAGNEEVDKAAQSFTNAQ   98 (221)
Q Consensus        67 g~~v~~~wvPgH~gI~GNE~AD~~Ak~~~~~~   98 (221)
                      ...|.|.|||||+|++|||.||++|+.+...+
T Consensus       112 ~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~  143 (150)
T PRK00203        112 RHQIKWHWVKGHAGHPENERCDELARAGAEEA  143 (150)
T ss_pred             cCceEEEEecCCCCCHHHHHHHHHHHHHHHHh
Confidence            36799999999999999999999999876544

>PRK06548 ribonuclease H; Provisional

Probab=97.93  E-value=4.1e-06  Score=67.11  Aligned_cols=29  Identities=31%  Similarity=0.589  Sum_probs=26.3

Q ss_pred             CcceeeeccCCCCCccchhHhHHHhhccc
Q psy1455          68 NNVKIIWIPSHCGIAGNEEVDKAAQSFTN   96 (221)
Q Consensus        68 ~~v~~~wvPgH~gI~GNE~AD~~Ak~~~~   96 (221)
                      ..|+|.|||||+|.+|||.||.+|++++.
T Consensus       113 ~~v~~~wVkgHsg~~gNe~aD~LA~~aa~  141 (161)
T PRK06548        113 RNIRMSWVNAHTGHPLNEAADSLARQAAN  141 (161)
T ss_pred             CceEEEEEecCCCCHHHHHHHHHHHHHHH
Confidence            47999999999999999999999987653

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

Probab=97.63  E-value=2.2e-05  Score=62.24  Aligned_cols=28  Identities=29%  Similarity=0.426  Sum_probs=25.8

Q ss_pred             cceeeeccCCCCCccchhHhHHHhhccc
Q psy1455          69 NVKIIWIPSHCGIAGNEEVDKAAQSFTN   96 (221)
Q Consensus        69 ~v~~~wvPgH~gI~GNE~AD~~Ak~~~~   96 (221)
                      .|.+.|||||.|-++||+||++|+.+..
T Consensus       117 ~v~~~WVkgH~g~~~NeraD~LA~~~~~  144 (154)
T COG0328         117 LVFWEWVKGHAGHPENERADQLAREAAR  144 (154)
T ss_pred             eEEEEEeeCCCCChHHHHHHHHHHHHHH
Confidence            7899999999999999999999987754

>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=97.17  E-value=0.00028  Score=51.63  Aligned_cols=29  Identities=38%  Similarity=0.713  Sum_probs=26.3

Q ss_pred             cCCcceeeeccCCCCCccchhHhHHHhhc
Q psy1455          66 AGNNVKIIWIPSHCGIAGNEEVDKAAQSF   94 (221)
Q Consensus        66 ~g~~v~~~wvPgH~gI~GNE~AD~~Ak~~   94 (221)
                      .+..+.|.|||+|+++.+|+.||.+|+.+
T Consensus       101 ~~~~~~i~~v~~h~~~~~n~~ad~la~~~  129 (130)
T cd06222         101 RFHKVRFEWVPGHSGIEGNERADALAKEA  129 (130)
T ss_pred             CCCeEEEEEcCCCCCCcchHHHHHHHHhh
Confidence            46689999999999999999999999864

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=97.01  E-value=0.00048  Score=61.42  Aligned_cols=30  Identities=30%  Similarity=0.450  Sum_probs=27.3

Q ss_pred             cCCcceeeeccCCCCCccchhHhHHHhhcc
Q psy1455          66 AGNNVKIIWIPSHCGIAGNEEVDKAAQSFT   95 (221)
Q Consensus        66 ~g~~v~~~wvPgH~gI~GNE~AD~~Ak~~~   95 (221)
                      .+..|.+.|||||.||.|||+||.+|+++.
T Consensus       334 ~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs  363 (371)
T KOG3752|consen  334 SNKKVQQEYVGGHSGILGNEMADALARKGS  363 (371)
T ss_pred             ccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence            468899999999999999999999998764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	221
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	98.36
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	98.35
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	98.27
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	98.27
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	98.25
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	98.23
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	98.17
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	98.03
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	97.74
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	97.72
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	97.5
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	95.47
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	95.26
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	95.22

>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=98.36  E-value=1.3e-07  Score=73.57  Aligned_cols=31  Identities=39%  Similarity=0.705  Sum_probs=28.1

Q ss_pred             cCCcceeeeccCCCCCccchhHhHHHhhccc
Q psy1455          66 AGNNVKIIWIPSHCGIAGNEEVDKAAQSFTN   96 (221)
Q Consensus        66 ~g~~v~~~wvPgH~gI~GNE~AD~~Ak~~~~   96 (221)
                      ....|.|.|||||+|++|||.||++|+++..
T Consensus       116 ~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~  146 (150)
T 3qio_A          116 KKEKVYLAWVPAHKGIGGNEQVDKLVSAGIR  146 (150)
T ss_dssp             TCSEEEEEECCTTSCCHHHHHHHHHHHTTTS
T ss_pred             hcCceEEEEccCcCCChhHHHHHHHHHHHHH
Confidence            4578999999999999999999999998764

>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=98.35  E-value=1e-07  Score=73.88  Aligned_cols=30  Identities=23%  Similarity=0.147  Sum_probs=27.6

Q ss_pred             cceeeeccCCCCCccchhHhHHHhhccccc
Q psy1455          69 NVKIIWIPSHCGIAGNEEVDKAAQSFTNAQ   98 (221)
Q Consensus        69 ~v~~~wvPgH~gI~GNE~AD~~Ak~~~~~~   98 (221)
                      .|.|.|||||+|++|||.||++|+++...+
T Consensus       109 ~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~  138 (147)
T 2kq2_A          109 IYSFEKVKAHSGNEFNDYVDMKAKSALGIR  138 (147)
T ss_dssp             TCCBCCCCCCCCCHHHHHHHHHHHHHHTCC
T ss_pred             CeeEEEecCcCCCcchHHHHHHHHHHHhcc
Confidence            899999999999999999999999887554

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

Probab=98.27  E-value=1.7e-07  Score=72.22  Aligned_cols=30  Identities=17%  Similarity=0.085  Sum_probs=26.0

Q ss_pred             CCcceeeeccCCCCCccchhHhHHHhhccc
Q psy1455          67 GNNVKIIWIPSHCGIAGNEEVDKAAQSFTN   96 (221)
Q Consensus        67 g~~v~~~wvPgH~gI~GNE~AD~~Ak~~~~   96 (221)
                      ..+|.|.|||||+|++|||.||++|+.+..
T Consensus       114 ~~~v~~~~V~gH~g~~~N~~AD~LA~~a~~  143 (146)
T 3h08_A          114 LHRVTFHKVKGHSDNPYNSRADELARLAIK  143 (146)
T ss_dssp             HSEEEEEECCC-CCSHHHHHHHHHHHHHHH
T ss_pred             hCceEEEEcCCcCCcHhHHHHHHHHHHHHH
Confidence            457999999999999999999999997764

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

Probab=98.27  E-value=2.2e-07  Score=72.26  Aligned_cols=32  Identities=31%  Similarity=0.614  Sum_probs=28.5

Q ss_pred             cCCcceeeeccCCCCCccchhHhHHHhhcccc
Q psy1455          66 AGNNVKIIWIPSHCGIAGNEEVDKAAQSFTNA   97 (221)
Q Consensus        66 ~g~~v~~~wvPgH~gI~GNE~AD~~Ak~~~~~   97 (221)
                      .+..|.|.|||||+|++|||.||++|+.+...
T Consensus       120 ~~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~  151 (154)
T 2qkb_A          120 QGMDIQWMHVPGHSGFIGNEEADRLAREGAKQ  151 (154)
T ss_dssp             TTCEEEEEECCTTSSCHHHHHHHHHHHHHHTC
T ss_pred             cCCceEEEEccCCCCCHhHHHHHHHHHHHHHh
Confidence            35689999999999999999999999987654

>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=98.25  E-value=1.7e-07  Score=74.20  Aligned_cols=33  Identities=27%  Similarity=0.330  Sum_probs=29.5

Q ss_pred             cCCcceeeeccCCCC-----CccchhHhHHHhhccccc
Q psy1455          66 AGNNVKIIWIPSHCG-----IAGNEEVDKAAQSFTNAQ   98 (221)
Q Consensus        66 ~g~~v~~~wvPgH~g-----I~GNE~AD~~Ak~~~~~~   98 (221)
                      .+..|.|.|||||+|     ++|||+||++|+++...+
T Consensus       120 ~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~  157 (165)
T 3p1g_A          120 LPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKA  157 (165)
T ss_dssp             SBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcC
Confidence            467899999999999     999999999999887654

>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=98.23  E-value=2.7e-07  Score=72.02  Aligned_cols=33  Identities=24%  Similarity=0.434  Sum_probs=29.2

Q ss_pred             CCcceeeeccCCCCCccchhHhHHHhhcccccc
Q psy1455          67 GNNVKIIWIPSHCGIAGNEEVDKAAQSFTNAQI   99 (221)
Q Consensus        67 g~~v~~~wvPgH~gI~GNE~AD~~Ak~~~~~~~   99 (221)
                      +..|.|.|||||+|++|||.||++|+.+...+.
T Consensus       113 ~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~  145 (155)
T 1jl1_A          113 QHQIKWEWVKGHAGHPENERADELARAAAMNPT  145 (155)
T ss_dssp             TCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCC
T ss_pred             cCceEEEEcCCCCCCHHHHHHHHHHHHHHhccc
Confidence            458999999999999999999999998876543

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

Probab=98.17  E-value=4.2e-07  Score=71.15  Aligned_cols=31  Identities=29%  Similarity=0.494  Sum_probs=28.2

Q ss_pred             CCcceeeeccCCCCCccchhHhHHHhhcccc
Q psy1455          67 GNNVKIIWIPSHCGIAGNEEVDKAAQSFTNA   97 (221)
Q Consensus        67 g~~v~~~wvPgH~gI~GNE~AD~~Ak~~~~~   97 (221)
                      +..|.|.|||||+|++|||.||++|+.+...
T Consensus       115 ~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A          115 LHQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             TSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             cCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            4689999999999999999999999988765

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

Probab=98.03  E-value=9.8e-07  Score=69.67  Aligned_cols=32  Identities=28%  Similarity=0.475  Sum_probs=28.3

Q ss_pred             CCcceeeeccCCCCCccchhHhHHHhhccccc
Q psy1455          67 GNNVKIIWIPSHCGIAGNEEVDKAAQSFTNAQ   98 (221)
Q Consensus        67 g~~v~~~wvPgH~gI~GNE~AD~~Ak~~~~~~   98 (221)
                      +..|.|.|||||+|++|||.||++|+.+....
T Consensus       118 ~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~  149 (166)
T 1ril_A          118 PHRVRFHFVKGHTGHPENERVDREARRQAQSQ  149 (166)
T ss_dssp             TSEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             cCeEEEEEeeCCCCchhHHHHHHHHHHHHHHh
Confidence            45899999999999999999999999876543

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

Probab=97.74  E-value=7.5e-06  Score=64.69  Aligned_cols=29  Identities=24%  Similarity=0.192  Sum_probs=25.6

Q ss_pred             CCcceeeeccCCCCC------ccchhHhHHHhhcc
Q psy1455          67 GNNVKIIWIPSHCGI------AGNEEVDKAAQSFT   95 (221)
Q Consensus        67 g~~v~~~wvPgH~gI------~GNE~AD~~Ak~~~   95 (221)
                      ...|.|.|||||+|+      +|||+||++|++++
T Consensus       127 ~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA  161 (165)
T 2lsn_A          127 KPDITIQHEKGHQPTNTSIHTEGNALADKLATQGS  161 (165)
T ss_dssp             CTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhh
Confidence            457999999999996      58999999999876

>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=97.72  E-value=1.3e-05  Score=74.48  Aligned_cols=29  Identities=34%  Similarity=0.704  Sum_probs=26.6

Q ss_pred             cCCcceeeeccCCCCCccchhHhHHHhhc
Q psy1455          66 AGNNVKIIWIPSHCGIAGNEEVDKAAQSF   94 (221)
Q Consensus        66 ~g~~v~~~wvPgH~gI~GNE~AD~~Ak~~   94 (221)
                      .+..|.|.|||||+|++|||.||++|+++
T Consensus       526 ~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  554 (555)
T 1mu2_A          526 KKEAIYVAWVPAHKGIGGNQEVDHLVSQG  554 (555)
T ss_dssp             HCSEEEEEECCSSSCCTTHHHHHHHHHTT
T ss_pred             cCCcEEEEEEECCCCChhHHHHHHHHHhh
Confidence            45789999999999999999999999876

>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=97.50  E-value=1.6e-05  Score=73.84  Aligned_cols=28  Identities=43%  Similarity=0.788  Sum_probs=23.5

Q ss_pred             CCcceeeeccCCCCCccchhHhHHHhhc
Q psy1455          67 GNNVKIIWIPSHCGIAGNEEVDKAAQSF   94 (221)
Q Consensus        67 g~~v~~~wvPgH~gI~GNE~AD~~Ak~~   94 (221)
                      ...|.|.|||||+|++|||.||++|+++
T Consensus       530 ~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          530 KEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             CSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             CCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            4579999999999999999999999864

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

Probab=95.47  E-value=0.0045  Score=46.01  Aligned_cols=25  Identities=20%  Similarity=0.347  Sum_probs=21.7

Q ss_pred             CcceeeeccCCCCCccchhHhHHHhhccc
Q psy1455          68 NNVKIIWIPSHCGIAGNEEVDKAAQSFTN   96 (221)
Q Consensus        68 ~~v~~~wvPgH~gI~GNE~AD~~Ak~~~~   96 (221)
                      ..|.|.|||.    +|||.||++|+.+..
T Consensus       112 ~~v~~~~V~~----~~N~~AD~LA~~a~~  136 (140)
T 3u3g_D          112 PNLVFVHIPR----EKNARADELVNEAID  136 (140)
T ss_dssp             TTCEEEECCG----GGGHHHHHHHHHHHH
T ss_pred             CcEEEEEcCc----hhhHHHHHHHHHHHH
Confidence            4899999994    799999999997764

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

Probab=95.26  E-value=0.0059  Score=46.40  Aligned_cols=25  Identities=28%  Similarity=0.628  Sum_probs=21.5

Q ss_pred             cceeeeccCCCCCccchhHhHHHhhcccc
Q psy1455          69 NVKIIWIPSHCGIAGNEEVDKAAQSFTNA   97 (221)
Q Consensus        69 ~v~~~wvPgH~gI~GNE~AD~~Ak~~~~~   97 (221)
                      +|.|.|||+|    +||.||++|+.+...
T Consensus       110 ~v~~~~V~~~----~N~~AD~LA~~a~~~  134 (149)
T 2ehg_A          110 NATLIWVPRE----ENKEADRLSRVAYEL  134 (149)
T ss_dssp             TCEEEECCGG----GCHHHHHHHHHHHHH
T ss_pred             CEEEEEcCCc----ccHHHHHHHHHHHHh
Confidence            5999999994    899999999977643

>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=95.22  E-value=0.0072  Score=45.12  Aligned_cols=26  Identities=23%  Similarity=0.414  Sum_probs=22.4

Q ss_pred             CCcceeeeccCCCCCccchhHhHHHhhccc
Q psy1455          67 GNNVKIIWIPSHCGIAGNEEVDKAAQSFTN   96 (221)
Q Consensus        67 g~~v~~~wvPgH~gI~GNE~AD~~Ak~~~~   96 (221)
                      ...|.|.|||+    +|||.||++|+.+..
T Consensus       107 ~~~v~~~~V~~----~~N~~AD~LA~~a~~  132 (141)
T 3hst_B          107 FRRINYEWVPR----ARNTYADRLANDAMD  132 (141)
T ss_dssp             SSEEEEEECCG----GGCHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCC----cccHHHHHHHHHHHH
Confidence            46899999996    799999999997764

---

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	221
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	0.003

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

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

 Score = 34.5 bits (78), Expect = 0.003
 Identities = 10/23 (43%), Positives = 15/23 (65%)

Query: 69  NVKIIWIPSHCGIAGNEEVDKAA 91
            + + W+P+H GI GN+EVD   
Sbjct: 100 AIYVAWVPAHKGIGGNQEVDHLV 122

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	221
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	98.85
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	98.6
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	98.58

>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=98.85  E-value=3.2e-10  Score=85.91  Aligned_cols=39  Identities=21%  Similarity=0.325  Sum_probs=33.1

Q ss_pred             cCCcceeeeccCCCCCccchhHhHHHhhccccccccCCC
Q psy1455          66 AGNNVKIIWIPSHCGIAGNEEVDKAAQSFTNAQIYSLIT  104 (221)
Q Consensus        66 ~g~~v~~~wvPgH~gI~GNE~AD~~Ak~~~~~~~~~~~s  104 (221)
                      ...+|.|.|||||+|++|||+||++||+++..|..++.+
T Consensus       110 ~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~d~~  148 (152)
T d1jl1a_         110 GQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTG  148 (152)
T ss_dssp             TTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCCTT
T ss_pred             hcceeEEEEecccCCCccHHHHHHHHHHHHhCCCCCccC
Confidence            345899999999999999999999999998877655433

>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=98.60  E-value=4e-09  Score=79.67  Aligned_cols=32  Identities=28%  Similarity=0.472  Sum_probs=28.5

Q ss_pred             cCCcceeeeccCCCCCccchhHhHHHhhcccc
Q psy1455          66 AGNNVKIIWIPSHCGIAGNEEVDKAAQSFTNA   97 (221)
Q Consensus        66 ~g~~v~~~wvPgH~gI~GNE~AD~~Ak~~~~~   97 (221)
                      .+.+|+|.|||||+|++|||+||++|++++..
T Consensus       112 ~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~  143 (147)
T d1rila_         112 APHRVRFHFVKGHTGHPENERVDREARRQAQS  143 (147)
T ss_dssp             TTSEEECCCCCGGGSCTHHHHHHHHHHHHHTS
T ss_pred             hhcccceEEccCCCCCcchHHHHHHHHHHHHH
Confidence            45689999999999999999999999988653

>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=98.58  E-value=9.7e-09  Score=75.68  Aligned_cols=29  Identities=34%  Similarity=0.704  Sum_probs=26.2

Q ss_pred             cCCcceeeeccCCCCCccchhHhHHHhhc
Q psy1455          66 AGNNVKIIWIPSHCGIAGNEEVDKAAQSF   94 (221)
Q Consensus        66 ~g~~v~~~wvPgH~gI~GNE~AD~~Ak~~   94 (221)
                      ...+|.|.|||||+|++|||+||++|+++
T Consensus        97 ~~~~v~~~wV~gH~g~~gNe~AD~LA~~a  125 (126)
T d1mu2a1          97 KKEAIYVAWVPAHKGIGGNQEVDHLVSQG  125 (126)
T ss_dssp             HCSEEEEEECCSSSCCTTHHHHHHHHHTT
T ss_pred             hcceeEEEEEeCCCCCcchHHHHHHHHhh
Confidence            34689999999999999999999999875