Psyllid ID: psy7385

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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-------21
Protein Sequence
MFLLQKLSDLKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTPIQPLKLCSASDFKPIVAKIIHNMWQTSWNDQINGNKLKRIKPDKKKKPVVENWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQPACRQDIRRGPAGKTCCNTSVKAPNRKKEQHCKPHVEKRTHMRKSENIKLMNTLKKVQVVLRLPLA
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHccccccccccccccccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccEEcccccccHHHHHHcccccHHHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHccccccccccccccccccccccHHHEEEEEEEccccHHHHHHHcccccccccHHHHccccccccccccEEEEEEEEEEEccccccHHHHHccccccccHHHcHEEEEEEEEcccc
Coil and Loop (DISEMBL)
mfllqklsdlknlFCLERSLkscgkegtlmwcpsqcgisgneavdmaaknpttpiqplklcsasdfkPIVAKIIHNMWQTswndqingnklkrikpdkkkkpvvenwasrnrdtRYEEVALARMRIghtrlthshlftrspqpacrqdirrgpagktccntsvkapnrkkeqhckphvekrthmrkSENIKLMNTLKKVQVVLRLPLA
Flexible Loop (DISEMBL)
mfllqklsdlknlFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTPIQPLKLCSASDFKPIVAKIIHNMWqtswndqingnklkrikpdkkkkpvvenwasrnrdtryeEVALARMRIGhtrlthshlftrspqpacrqdirrgpagktccntsvkapnrkkeqhckphvekrthmrkseniklmntlkkvqvvlrlpla
Low Complexity Region (SEG)
MFLLQKLSDLKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTPIQPLKLCSASDFKPIVAKIIHNMWQTSWNDQINGNklkrikpdkkkkPVVENWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQPACRQDIRRGPAGKTCCNTSVKAPNRKKEQHCKPHVEKRTHMRKSENIKLMNTLKKVQVVLRLPLA
Disordered region (IsUnstruct)
***LQKLSDLKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTPIQPLKLCSASDFKPIVAKIIHNMWQTSWNDQINGNK***********************TRYEEVALARMRIGHTRLTHSHLF*********************************************************TLKKVQVVL*****
Disordered Region (DISOPRED)
******LSDLKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTPIQPLKLCSASDFKPIVAKIIHNMWQTSWNDQINGNKLKRIKPDKKKKPVVENWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQPACRQDIRRGPAGKTCCNTSVKAPNRKKEQHCKPHVEKRTHMRKSENIKLMNTLKKVQVVLRLPL*
Disordered Region (DISEMBL)
MFLLQKLSDLKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTPIQPLKLCSASDFKPIVAKIIHNMWQTSWNDQINGNKLKRI***********NWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQPACRQDIRRGPAGKTCCNTS********************HMRKSENIKLMNTLKKVQVVLRLPLA
Disordered Region (DISPRO)
MFLLQKLSDLKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTPIQPLKLCSASDFKPIVAKIIHNMWQTSWNDQINGNKLKRIKPDKKKKPVVENWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQPACRQDIRRGPAGKTCCNTSVKAPNRKKEQHCKPHVEKRTHMRKSENIKLMNTLKKVQVVLRLPLA
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFLLQKLSDLKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTPIQPLKLCSASDFKPIVAKIIHNMWQTSWNDQINGNKLKRIKPDKKKKPVVENWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQPACRQDIRRGPAGKTCCNTSVKAPNRKKEQHCKPHVEKRTHMRKSENIKLMNTLKKVQVVLRLPLA
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	208
443694523	364	hypothetical protein CAPTEDRAFT_227708 [	0.514	0.293	0.396	2e-16
443733872	400	hypothetical protein CAPTEDRAFT_197082 [	0.552	0.287	0.385	2e-15
443694031	574	hypothetical protein CAPTEDRAFT_227918 [	0.528	0.191	0.393	3e-15
443682433	619	hypothetical protein CAPTEDRAFT_222606 [	0.5	0.168	0.382	4e-15
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.548	0.227	0.365	7e-14
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.548	0.436	0.365	9e-14
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.581	0.256	0.352	2e-13
443730613	233	hypothetical protein CAPTEDRAFT_206814 [	0.552	0.493	0.336	6e-13
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.548	0.287	0.357	2e-12
427778603	1397	Putative tick transposon [Rhipicephalus	0.524	0.078	0.358	2e-11

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

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 50/126 (39%), Positives = 67/126 (53%), Gaps = 19/126 (15%)

Query: 29  LMWCPSQCGISGNEAVDMAAKNPTTPIQPLKL------CSASDFKPIVAKIIHNMWQTSW 82
            +WCPS  GI GNE  D  AK      Q L +         +DFKPI    +   WQ+ W
Sbjct: 68  FIWCPSHVGIPGNETADTLAK------QALGMNILNCPIPHTDFKPITRSFVKTQWQSEW 121

Query: 83  NDQINGNKLKRIKPDKKKKPVVENWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQ 142
            DQ  GNKL  I+PD      + +W    R+ R EE+ +AR+RIGHT LTHSHL + +  
Sbjct: 122 -DQETGNKLHDIQPD------IGSWPPCQREKRREEIVIARVRIGHTFLTHSHLLSGNDA 174

Query: 143 PACRQD 148
           P  +++
Sbjct: 175 PMGKEE 180

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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 47/122 (38%), Positives = 62/122 (50%), Gaps = 7/122 (5%)

Query: 24  GKEGTLMWCPSQCGISGNEAVDMAAKNPTTPIQPLKLCSASDFKPIVAKIIHNMWQTSWN 83
           G +  + WCPS  G+ GNE  D+ AK   +         +SDFKPI  +     WQ  W+
Sbjct: 98  GIDLVMTWCPSHVGVMGNERADLLAKEALSFTTCTIRIPSSDFKPITHEFYKEKWQEQWS 157

Query: 84  DQINGNKLKRIKPDKKKKPVVENWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQP 143
            +   NKL  I+P   K      WA  +R+ R EE+ LAR RIGH+ LTH +L  R   P
Sbjct: 158 SE-QENKLYCIQPTLGK------WAKSSREIRREEIVLARARIGHSHLTHGYLLRREMPP 210

Query: 144 AC 145
            C
Sbjct: 211 VC 212

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 46/117 (39%), Positives = 60/117 (51%), Gaps = 7/117 (5%)

Query: 29  LMWCPSQCGISGNEAVDMAAKNPTTPIQPLKLCSASDFKPIVAKIIHNMWQTSWNDQING 88
           + WCPS  G+ GNE  D+ AK   +         +SDFKPI  +     WQ  W+ +   
Sbjct: 1   MAWCPSHVGVMGNERADLLAKEALSFTTCTIRIPSSDFKPITHEFFKEKWQEQWSSE-QE 59

Query: 89  NKLKRIKPDKKKKPVVENWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQPAC 145
           NKL  I+P   K      WA  +R+ R EE+ LAR RIGH+ LTH +L  R   P C
Sbjct: 60  NKLYSIQPTLGK------WAKSSREIRREEIVLARARIGHSHLTHGYLVRREMPPVC 110

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 47/123 (38%), Positives = 65/123 (52%), Gaps = 19/123 (15%)

Query: 29  LMWCPSQCGISGNEAVDMAAKNPTT------PIQPLKLCSASDFKPIVAKIIHNMWQTSW 82
            +WCPS  GI GNE  D  A+  +       PI        +DFKPI    +   WQ+  
Sbjct: 96  FIWCPSHVGIPGNETADTLAQQASGMNILNCPI------PHTDFKPITRSFVETQWQSE- 148

Query: 83  NDQINGNKLKRIKPDKKKKPVVENWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQ 142
           +DQ  GNKL  I+PD      + +W    R+ R +E+ +AR+RIGHT LT+SHL + +  
Sbjct: 149 SDQETGNKLHDIEPD------IGSWPPCQREKRRDEIVIARLRIGHTFLTYSHLLSGNDA 202

Query: 143 PAC 145
           P C
Sbjct: 203 PMC 205

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 45/123 (36%), Positives = 63/123 (51%), Gaps = 9/123 (7%)

Query: 24  GKEGTLMWCPSQCGISGNEAVDMAAKNP-TTPIQPLKLCSASDFKPIVAKIIHNMWQTSW 82
           GK    +WCPS  GI GNE  D  AK     P+  L L   +D+K  +   + ++WQ  W
Sbjct: 177 GKLVVFIWCPSHVGILGNEVADRLAKQALVMPVTKLPL-PHTDYKSPIRSYVKSLWQNEW 235

Query: 83  NDQINGNKLKRIKPDKKKKPVVENWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQ 142
           +++ + NKL  I+P      V+  W    +  R  E+ LAR RIGH+ LTH +L  R   
Sbjct: 236 DEETD-NKLHSIQP------VISEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREVA 288

Query: 143 PAC 145
           P C
Sbjct: 289 PFC 291

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 = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 45/123 (36%), Positives = 63/123 (51%), Gaps = 9/123 (7%)

Query: 24  GKEGTLMWCPSQCGISGNEAVDMAAKNP-TTPIQPLKLCSASDFKPIVAKIIHNMWQTSW 82
           GK    +WCPS  GI GNE  D  AK     P+  L L   +D+K  +   + ++WQ  W
Sbjct: 131 GKLVVFIWCPSHVGILGNEVADRLAKQALVMPVTKLPL-PHTDYKSPIRSYVKSLWQNEW 189

Query: 83  NDQINGNKLKRIKPDKKKKPVVENWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQ 142
           +++ + NKL  I+P      V+  W    +  R  E+ LAR RIGH+ LTH +L  R   
Sbjct: 190 DEETD-NKLHSIQP------VISEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREVA 242

Query: 143 PAC 145
           P C
Sbjct: 243 PFC 245

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 48/136 (35%), Positives = 70/136 (51%), Gaps = 15/136 (11%)

Query: 2   FLLQKLSDLKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTPIQPLKL- 60
           ++LQ L  +K++   E+ +         MWCPS  GI GNE  D  AK   +     +L 
Sbjct: 101 YVLQVLYAIKSISQQEKIV-------VFMWCPSHVGIPGNEMADTLAKEALSSTNLAELP 153

Query: 61  CSASDFKPIVAKIIHNMWQTSWNDQINGNKLKRIKPDKKKKPVVENWASRNRDTRYEEVA 120
             ASD + ++ K I + WQ  W++Q + NKL  I P       +  W    R+ R EE+ 
Sbjct: 154 VPASDLRCLIKKYIRSRWQHEWDEQ-HSNKLHSIHP------TIGPWPPCQREKRREEIV 206

Query: 121 LARMRIGHTRLTHSHL 136
           LAR+RIGHT  TH ++
Sbjct: 207 LARIRIGHTHYTHDYI 222

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 80.1 bits (196), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 41/122 (33%), Positives = 62/122 (50%), Gaps = 7/122 (5%)

Query: 24  GKEGTLMWCPSQCGISGNEAVDMAAKNPTTPIQPLKLCSASDFKPIVAKIIHNMWQTSWN 83
           G +  ++WCPS  G+ GNE  D+ AK   +         A DF  +      + WQ  W+
Sbjct: 78  GFDLVILWCPSHIGVVGNERADLLAKEALSFTACDVRIPAFDFNSVAYSFYRDKWQALWS 137

Query: 84  DQINGNKLKRIKPDKKKKPVVENWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQP 143
            + N NKL  ++P      +++   + +R+ R +E+ LAR RIGHT LTH +L  R   P
Sbjct: 138 LEQN-NKLHSVQP------IIKKLTNSSREDRRKEIVLARARIGHTHLTHGYLLRRELPP 190

Query: 144 AC 145
            C
Sbjct: 191 FC 192

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 44/123 (35%), Positives = 62/123 (50%), Gaps = 9/123 (7%)

Query: 24  GKEGTLMWCPSQCGISGNEAVDMAAKNP-TTPIQPLKLCSASDFKPIVAKIIHNMWQTSW 82
           GK+   +WCPS  GI GNE  D  AK     P+  L L   +D+K  +   + ++WQ  W
Sbjct: 226 GKKVVFIWCPSHVGILGNEVADRQAKQALVMPVTKLPL-PHTDYKSPIRSYVKSLWQNEW 284

Query: 83  NDQINGNKLKRIKPDKKKKPVVENWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQ 142
           + + + NKL  I+P      V+  W    +  R  E+ LA  RIGH+ LTH +L  R   
Sbjct: 285 DGETD-NKLHIIQP------VISEWKQGPQIDRRGEIVLACARIGHSHLTHGYLLRREVA 337

Query: 143 PAC 145
           P C
Sbjct: 338 PFC 340

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 43/120 (35%), Positives = 60/120 (50%), Gaps = 11/120 (9%)

Query: 28   TLMWCPSQCGISGNEAVDMAAKNPTTPIQPLKLCS--ASDFKPIVAKIIHNMWQTSWNDQ 85
             L W P   GI+GNE VD  A+   +    + + S    D  P+V + + + WQ  W+ Q
Sbjct: 1208 VLCWVPGHAGITGNEMVDKNAREAASR-HTIDISSVPGVDLNPVVRRGLRSHWQVEWDKQ 1266

Query: 86   INGNKLKRIKPDKKKKPVVENWASRNRDTRYEEVALARMRIGHTRLTHSHLFTRSPQPAC 145
            ++ NKL  +KP   K           +  R+ EV LAR+RIGHT  TH HL T +  P C
Sbjct: 1267 VD-NKLHLVKPHLSK-------VLPQKLNRFTEVTLARLRIGHTYATHKHLLTGTDPPTC 1318

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

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

No EC number assignment, probably not an enzyme!

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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	208
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	9e-06

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

 Score = 43.4 bits (103), Expect = 9e-06
 Identities = 14/32 (43%), Positives = 16/32 (50%)

Query: 18  RSLKSCGKEGTLMWCPSQCGISGNEAVDMAAK 49
           R L + G +  L W P   GI GNE  D  AK
Sbjct: 93  RELANHGVKVRLHWVPGHSGIEGNERADRLAK 124

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 128

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	208
PRK08719	147	ribonuclease H; Reviewed	98.87
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	98.72
PRK06548	161	ribonuclease H; Provisional	98.71
PRK00203	150	rnhA ribonuclease H; Reviewed	98.7
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	98.53
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	98.34
KOG3752|consensus	371		97.75
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	95.36
PRK13907	128	rnhA ribonuclease H; Provisional	95.16
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	93.52
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	90.78
PRK07708	219	hypothetical protein; Validated	87.5

>PRK08719 ribonuclease H; Reviewed

Probab=98.87  E-value=1.3e-09  Score=87.25  Aligned_cols=42  Identities=29%  Similarity=0.378  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCC
Q psy7385          11 KNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTT   53 (208)
Q Consensus        11 ~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~   53 (208)
                      +++++.+..|.+. ..|+|.|||||+|++|||.||++|++|+.
T Consensus       105 ~dl~~~i~~l~~~-~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719        105 RDLWQQVDELRAR-KYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             HHHHHHHHHHhCC-CcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            5678888888774 56999999999999999999999999874

>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=98.72  E-value=2.3e-09  Score=82.19  Aligned_cols=34  Identities=35%  Similarity=0.596  Sum_probs=29.6

Q ss_pred             HHHhCCCceEEEEeccCCCC-CcchHHhHhhCCCC
Q psy7385          19 SLKSCGKEGTLMWCPSQCGI-SGNEAVDMAAKNPT   52 (208)
Q Consensus        19 ~L~~~g~~I~l~WVPgH~gi-~GNE~AD~~Ak~A~   52 (208)
                      ++...+..|.|.|||||+|+ .|||.||++||+|+
T Consensus        97 ~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   97 ELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             eccccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence            33366889999999999999 69999999999874

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

>PRK06548 ribonuclease H; Provisional

Probab=98.71  E-value=6.3e-09  Score=84.63  Aligned_cols=43  Identities=21%  Similarity=0.247  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385          11 KNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP   54 (208)
Q Consensus        11 ~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~   54 (208)
                      +++++.+..|.+.. .|+|.|||||+|++|||.||++|++|+..
T Consensus       100 ~dL~~~l~~l~~~~-~v~~~wVkgHsg~~gNe~aD~LA~~aa~~  142 (161)
T PRK06548        100 QEIIQEIDSLMENR-NIRMSWVNAHTGHPLNEAADSLARQAANN  142 (161)
T ss_pred             HHHHHHHHHHHhcC-ceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence            46667777777664 69999999999999999999999998865

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=98.70  E-value=5.6e-09  Score=83.37  Aligned_cols=41  Identities=17%  Similarity=0.187  Sum_probs=33.4

Q ss_pred             HHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385          13 LFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP   54 (208)
Q Consensus        13 I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~   54 (208)
                      +++.+.++... ..|.|.|||||+|++|||.||++||+|+..
T Consensus       102 l~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~  142 (150)
T PRK00203        102 LWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAEE  142 (150)
T ss_pred             HHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence            44555555444 679999999999999999999999988765

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

Probab=98.53  E-value=4.5e-08  Score=79.00  Aligned_cols=44  Identities=20%  Similarity=0.222  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385          11 KNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP   54 (208)
Q Consensus        11 ~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~   54 (208)
                      +++++.+.++.++--.|.+.|||||.|.++||+||++|+.|+..
T Consensus       102 ~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~  145 (154)
T COG0328         102 KDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARA  145 (154)
T ss_pred             HHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHh
Confidence            36788888888888789999999999999999999999988754

>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=98.34  E-value=6.7e-07  Score=65.71  Aligned_cols=45  Identities=27%  Similarity=0.350  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCC
Q psy7385           8 SDLKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPT   52 (208)
Q Consensus         8 ~~i~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~   52 (208)
                      +.+..++..+..+...+..+.|.|||+|+|+++|+.||.+||+|.
T Consensus        86 ~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          86 VKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             hhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            355666667777777888999999999999999999999999873

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=97.75  E-value=2.3e-05  Score=70.89  Aligned_cols=30  Identities=27%  Similarity=0.365  Sum_probs=28.1

Q ss_pred             CCCceEEEEeccCCCCCcchHHhHhhCCCC
Q psy7385          23 CGKEGTLMWCPSQCGISGNEAVDMAAKNPT   52 (208)
Q Consensus        23 ~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~   52 (208)
                      ++..|++.|||||.||.|||+||.+|++.+
T Consensus       334 ~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs  363 (371)
T KOG3752|consen  334 SNKKVQQEYVGGHSGILGNEMADALARKGS  363 (371)
T ss_pred             ccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence            578999999999999999999999999875

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

Probab=95.36  E-value=0.011  Score=42.56  Aligned_cols=43  Identities=26%  Similarity=0.232  Sum_probs=28.8

Q ss_pred             cccCcccc-ccccc--cCCCCCCCCcccccCCCCCccccCCCcccCCCeeeecCCCCh
Q psy7385         124 MRIGHTRL-THSHL--FTRSPQPACRQDIRRGPAGKTCCNTSVKAPNRKKEQHCKPHV  178 (208)
Q Consensus       124 LRTGH~~L-t~~yl--~~~~d~p~C~~C~~~~p~~~~~Cg~~~t~~~~HiL~~Cp~~~  178 (208)
                      -|.-|.+| +..-|  .+...++.|..|          ++..||+  .|++++||.-.
T Consensus        38 W~~~~~rL~t~~~l~~r~~~~~~~C~~C----------~~~~Et~--~Hlf~~C~~a~   83 (86)
T PF13966_consen   38 WRALHNRLPTKDNLQRRGIQVDPICPLC----------GNEEETI--EHLFFHCPFAR   83 (86)
T ss_pred             eeeccccchhhhhhhccCCccCCccccC----------CCccccc--cceeccCcCcc
Confidence            34556666 23333  344567889876          5568877  99999999654

>PRK13907 rnhA ribonuclease H; Provisional

Probab=95.16  E-value=0.018  Score=44.14  Aligned_cols=40  Identities=20%  Similarity=0.157  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCC
Q psy7385          10 LKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTT   53 (208)
Q Consensus        10 i~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~   53 (208)
                      ++.+++.+..|..+-..+.|.|||.    ++|+.||.+|+.|..
T Consensus        87 ~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~  126 (128)
T PRK13907         87 FAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAIL  126 (128)
T ss_pred             HHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence            5566777777777777788899998    599999999998753

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

Probab=93.52  E-value=0.045  Score=38.15  Aligned_cols=40  Identities=25%  Similarity=0.121  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCC
Q psy7385           9 DLKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPT   52 (208)
Q Consensus         9 ~i~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~   52 (208)
                      .+..+++.+..+.+.-..+.|.|||    =++|..||.+||.|.
T Consensus        46 ~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~~A~~LA~~a~   85 (87)
T PF13456_consen   46 ELRPLIQDIRSLLDRFWNVSVSHIP----REQNKVADALAKFAL   85 (87)
T ss_dssp             CCHHHHHHHHHHHCCCSCEEEEE------GGGSHHHHHHHHHHH
T ss_pred             cccccchhhhhhhccccceEEEEEC----hHHhHHHHHHHHHHh
Confidence            4567788888888888889999999    799999999998763

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=90.78  E-value=0.22  Score=45.07  Aligned_cols=41  Identities=27%  Similarity=0.297  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385          10 LKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP   54 (208)
Q Consensus        10 i~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~   54 (208)
                      +...++.+..|.+.-..+++.|||.    ++|+.||.+|+.|...
T Consensus        92 l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~  132 (372)
T PRK07238         92 MKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA  132 (372)
T ss_pred             HHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence            4455566667777667799999997    7899999999988655

>PRK07708 hypothetical protein; Validated

Probab=87.50  E-value=0.45  Score=40.51  Aligned_cols=40  Identities=8%  Similarity=-0.144  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHh-CCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385          11 KNLFCLERSLKS-CGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP   54 (208)
Q Consensus        11 ~~I~~~~~~L~~-~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~   54 (208)
                      +..++.+..+.+ -...+.+.|||    -+.|+.||++|+.|...
T Consensus       168 ~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~  208 (219)
T PRK07708        168 NHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEG  208 (219)
T ss_pred             HHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhc
Confidence            344444444433 34457889998    46799999999999976

---

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	208
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	98.94
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	98.77
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	98.75
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	98.69
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	98.69
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	98.68
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	98.62
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	98.6
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	98.43
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	97.73
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	97.53
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	97.24

>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=98.94  E-value=4.4e-10  Score=88.81  Aligned_cols=42  Identities=26%  Similarity=0.283  Sum_probs=34.0

Q ss_pred             HHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385          13 LFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP   54 (208)
Q Consensus        13 I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~   54 (208)
                      +++.+.++...+..|.|.|||||+|++|||.||++|++|+..
T Consensus       106 l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A          106 LVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            344443334467889999999999999999999999999864

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

Probab=98.77  E-value=1.6e-09  Score=85.26  Aligned_cols=42  Identities=26%  Similarity=0.370  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385          12 NLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP   54 (208)
Q Consensus        12 ~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~   54 (208)
                      .+++.+..|.+ +..|.|.|||||+|++|||.||++||+|+..
T Consensus       110 ~l~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~  151 (154)
T 2qkb_A          110 EDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREGAKQ  151 (154)
T ss_dssp             HHHHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHHHHHHh
Confidence            34555555544 5679999999999999999999999988754

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

Probab=98.75  E-value=1.5e-09  Score=84.58  Aligned_cols=40  Identities=15%  Similarity=0.009  Sum_probs=30.1

Q ss_pred             HHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCC
Q psy7385          13 LFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTT   53 (208)
Q Consensus        13 I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~   53 (208)
                      +++.+..+.+. ..|.|.|||||+|++|||.||++||+|+.
T Consensus       104 l~~~~~~~~~~-~~v~~~~V~gH~g~~~N~~AD~LA~~a~~  143 (146)
T 3h08_A          104 LWQEILKLTTL-HRVTFHKVKGHSDNPYNSRADELARLAIK  143 (146)
T ss_dssp             HHHHHHHHHHH-SEEEEEECCC-CCSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhh-CceEEEEcCCcCCcHhHHHHHHHHHHHHH
Confidence            33444444433 46999999999999999999999998864

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

Probab=98.69  E-value=3.4e-09  Score=83.99  Aligned_cols=41  Identities=17%  Similarity=0.204  Sum_probs=32.9

Q ss_pred             HHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385          13 LFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP   54 (208)
Q Consensus        13 I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~   54 (208)
                      +++.+..|.+ +..|.|.|||||+|++|||.||++||+|+..
T Consensus       105 l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A          105 LWKRLDKAAQ-LHQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             HHHHHHHHHT-TSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHc-cCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            3344444544 3589999999999999999999999998854

>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=98.69  E-value=3.3e-09  Score=83.77  Aligned_cols=41  Identities=17%  Similarity=0.202  Sum_probs=33.3

Q ss_pred             HHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385          13 LFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP   54 (208)
Q Consensus        13 I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~   54 (208)
                      +++.+..+.+ +..|.|.|||||+|++|||.||++||+|+..
T Consensus       103 l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  143 (155)
T 1jl1_A          103 LWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAAAMN  143 (155)
T ss_dssp             HHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHc-cCceEEEEcCCCCCCHHHHHHHHHHHHHHhc
Confidence            3444445544 3689999999999999999999999999865

>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=98.68  E-value=6.9e-10  Score=87.14  Aligned_cols=39  Identities=21%  Similarity=0.092  Sum_probs=32.5

Q ss_pred             HHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385          13 LFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP   54 (208)
Q Consensus        13 I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~   54 (208)
                      ..+.+++|..   .|.|.|||||+|++|||.||++||+|+..
T Consensus        99 ~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  137 (147)
T 2kq2_A           99 YAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALGI  137 (147)
T ss_dssp             HHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHhc
Confidence            3444445544   79999999999999999999999999876

>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=98.62  E-value=4.6e-09  Score=84.33  Aligned_cols=32  Identities=25%  Similarity=0.421  Sum_probs=29.6

Q ss_pred             CCCceEEEEeccCCC-----CCcchHHhHhhCCCCCC
Q psy7385          23 CGKEGTLMWCPSQCG-----ISGNEAVDMAAKNPTTP   54 (208)
Q Consensus        23 ~g~~I~l~WVPgH~g-----i~GNE~AD~~Ak~A~~~   54 (208)
                      .+..|.|.|||||+|     ++|||+||++||+|+..
T Consensus       120 ~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~  156 (165)
T 3p1g_A          120 LPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMK  156 (165)
T ss_dssp             SBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhc
Confidence            578899999999999     99999999999998865

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

Probab=98.60  E-value=5.2e-09  Score=83.70  Aligned_cols=41  Identities=17%  Similarity=0.144  Sum_probs=33.8

Q ss_pred             HHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385          13 LFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP   54 (208)
Q Consensus        13 I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~   54 (208)
                      +++.+..|.+. ..|.|.|||||+|++|||.||++||+|+..
T Consensus       108 l~~~i~~l~~~-~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  148 (166)
T 1ril_A          108 LWEALLLAMAP-HRVRFHFVKGHTGHPENERVDREARRQAQS  148 (166)
T ss_dssp             HHHHHHHHHTT-SEEECCCCCGGGSCTHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHhc-CeEEEEEeeCCCCchhHHHHHHHHHHHHHH
Confidence            44445555443 589999999999999999999999999876

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

Probab=98.43  E-value=3e-08  Score=79.60  Aligned_cols=40  Identities=15%  Similarity=-0.003  Sum_probs=31.0

Q ss_pred             HHHHHHHHHhCCCceEEEEeccCCCC------CcchHHhHhhCCCC
Q psy7385          13 LFCLERSLKSCGKEGTLMWCPSQCGI------SGNEAVDMAAKNPT   52 (208)
Q Consensus        13 I~~~~~~L~~~g~~I~l~WVPgH~gi------~GNE~AD~~Ak~A~   52 (208)
                      +++.+.++.+....|.|.|||||+|+      +|||+||++|++++
T Consensus       116 L~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA  161 (165)
T 2lsn_A          116 KWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGS  161 (165)
T ss_dssp             HHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhh
Confidence            34444444455567999999999996      58999999999875

>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=97.73  E-value=1.6e-05  Score=60.44  Aligned_cols=42  Identities=24%  Similarity=0.345  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385           9 DLKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP   54 (208)
Q Consensus         9 ~i~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~   54 (208)
                      .+..+++.+..|.++...|.|.|||+    +|||.||++||+|...
T Consensus        92 ~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B           92 DLLKLYVQAQALASQFRRINYEWVPR----ARNTYADRLANDAMDA  133 (141)
T ss_dssp             HHHHHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHHHHH
Confidence            45677778888888888999999995    9999999999987643

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

Probab=97.53  E-value=2.8e-05  Score=58.65  Aligned_cols=39  Identities=15%  Similarity=0.125  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHH-HhCCCceEEEEeccCCCCCcchHHhHhhCCCC
Q psy7385          10 LKNLFCLERSL-KSCGKEGTLMWCPSQCGISGNEAVDMAAKNPT   52 (208)
Q Consensus        10 i~~I~~~~~~L-~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~   52 (208)
                      +..+++.+..+ .+....|+|.|||+    +|||.||++||+|+
T Consensus        96 l~~~~~~i~~l~~~~~~~v~~~~V~~----~~N~~AD~LA~~a~  135 (140)
T 3u3g_D           96 LKEKFAKIAHIKMERVPNLVFVHIPR----EKNARADELVNEAI  135 (140)
T ss_dssp             GHHHHHHHHHHHHHHCTTCEEEECCG----GGGHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCCCcEEEEEcCc----hhhHHHHHHHHHHH
Confidence            34455666666 55556899999994    99999999999875

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

Probab=97.24  E-value=8.4e-05  Score=57.33  Aligned_cols=36  Identities=22%  Similarity=0.314  Sum_probs=26.1

Q ss_pred             HHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385          14 FCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP   54 (208)
Q Consensus        14 ~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~   54 (208)
                      ++.+..+.+.- .|.|.|||+    ++||.||++|++|+..
T Consensus        99 ~~~i~~l~~~~-~v~~~~V~~----~~N~~AD~LA~~a~~~  134 (149)
T 2ehg_A           99 YEKAIELKKKL-NATLIWVPR----EENKEADRLSRVAYEL  134 (149)
T ss_dssp             HHHHHHHHHHH-TCEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC-CEEEEEcCC----cccHHHHHHHHHHHHh
Confidence            33333333332 499999999    6999999999988754

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	208
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	98.98
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	98.96
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	98.95

>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=98.98  E-value=3.9e-11  Score=91.47  Aligned_cols=31  Identities=19%  Similarity=0.287  Sum_probs=28.9

Q ss_pred             CCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385          24 GKEGTLMWCPSQCGISGNEAVDMAAKNPTTP   54 (208)
Q Consensus        24 g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~   54 (208)
                      ...|+|.|||||+|++|||+||++||+|+..
T Consensus       111 ~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~  141 (152)
T d1jl1a_         111 QHQIKWEWVKGHAGHPENERADELARAAAMN  141 (152)
T ss_dssp             TCEEEEEECCSSTTCHHHHHHHHHHHHHHHS
T ss_pred             cceeEEEEecccCCCccHHHHHHHHHHHHhC
Confidence            4679999999999999999999999999876

>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=98.96  E-value=3.7e-11  Score=91.84  Aligned_cols=32  Identities=19%  Similarity=0.258  Sum_probs=29.0

Q ss_pred             CCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385          23 CGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP   54 (208)
Q Consensus        23 ~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~   54 (208)
                      .+..|+|.|||||+|++|||.||++||+|+.+
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            35679999999999999999999999999865

>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=98.95  E-value=1.9e-10  Score=85.91  Aligned_cols=29  Identities=28%  Similarity=0.501  Sum_probs=26.9

Q ss_pred             CCceEEEEeccCCCCCcchHHhHhhCCCC
Q psy7385          24 GKEGTLMWCPSQCGISGNEAVDMAAKNPT   52 (208)
Q Consensus        24 g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~   52 (208)
                      ...|.|.|||||+|++|||+||++|++|.
T Consensus        98 ~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          98 KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             cceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            45899999999999999999999999884