Psyllid ID: psy10817

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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-------20
Protein Sequence
MSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRMRIGHTRLTHSYLFSRSPQPTCRCGDILTVKHILTCPLDIQLRSSLPNPPSLTDETTGVDALMSLLKSLNIFEKI
Secondary Structure (PSIPRED)
ccHHHHHHcccccHHHHHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHHcccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccHHHEEHHHHHcccccccccccccccccccEEccccccccEEEcccccHHHHHcccccccccccHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHccccHHHHHHcccccccccccccccccHEEEccHHHHHHHHHcccccccccccHHHHHHHHHHHHcccHccc
Coil and Loop (DISEMBL)
MSSLQAITSKSCNNALLSKIYSTWLDLVAcgkeisfmwcpshcgisgneavdvaaknpspsfpplklcsasdykpLIKKIVQRNWqsswnsvpngnklksikpniekwpssnrktrLEEVVLTRMRightrlthsylfsrspqptcrcgdiltvkhiltcpldiqlrsslpnppsltdettGVDALMSLLKSLNIFEKI
Flexible Loop (DISEMBL)
MSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRnwqsswnsvpngnklksikpniekwpssnrktrleeVVLTRMrightrlthsylfsrspqptcRCGDILTVKHILTCPLDIQLRSSLPNPPSLTDETTGVDALMSLLKSLNIFEKI
Low Complexity Region (SEG)
MSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRMRIGHTRLTHSYLFSRSPQPTCRCGDILTVKHILTCPLDIQLRSSLPNPPSLTDETTGVDALMSLLKSLNIFEKI
Disordered region (IsUnstruct)
***********CNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVA**********LKLCSASDYKPLIKKIVQRNWQSSWNS*************************LEEVVLTRMRIGHTRLTHSYLFSRSPQPTCRCGDILTVKHILTCPLDIQLR******************LMSLL*********
Disordered Region (DISOPRED)
MSSLQA*TSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRMRIGHTRLTHSYLFSRSPQPTCRCGDILTVKHILTCPLDIQLRSSLPNPPSLTDETTGVDALMSLLKSLNIFEKI
Disordered Region (DISEMBL)
********SKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRMRIGHTRLTHSYLFSRSPQPTCRCGDILTVKHILTCPLDIQLRSSLPNPPSLTDETTGVDALMSLLKSLNIFEKI
Disordered Region (DISPRO)
MSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRMRIGHTRLTHSYLFSRSPQPTCRCGDILTVKHILTCPLDIQLRSSLPNPPSLTDETTGVDALMSLLKSLNIFEKI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRMRIGHTRLTHSYLFSRSPQPTCRCGDILTVKHILTCPLDIQLRSSLPNPPSLTDETTGVDALMSLLKSLNIFEKI
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	199
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.824	0.326	0.410	9e-24
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.989	0.496	0.367	5e-23
443733872	400	hypothetical protein CAPTEDRAFT_197082 [	0.809	0.402	0.389	6e-23
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.783	0.597	0.418	1e-22
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.788	0.333	0.393	1e-21
443682433	619	hypothetical protein CAPTEDRAFT_222606 [	0.723	0.232	0.386	2e-21
328720146	164	PREDICTED: hypothetical protein LOC10056	0.623	0.756	0.432	5e-21
443694523	364	hypothetical protein CAPTEDRAFT_227708 [	0.542	0.296	0.425	1e-20
443730613	233	hypothetical protein CAPTEDRAFT_206814 [	0.673	0.575	0.420	6e-20
443724607	397	hypothetical protein CAPTEDRAFT_208903 [	0.989	0.496	0.357	1e-19

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

 Score =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 69/168 (41%), Positives = 93/168 (55%), Gaps = 4/168 (2%)

Query: 1   MSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSP 60
           +SSL A+++    +  L  I +   +LV  GK + F+WCPSH GI GNE  D  AK  + 
Sbjct: 147 LSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQ-AL 205

Query: 61  SFPPLKL-CSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEE 119
             P  KL    +DYK  I+  V+  WQ+ W+     NKL SI+P I +W    +  R  E
Sbjct: 206 VMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDE-ETDNKLHSIQPVISEWKQGPQIDRRGE 264

Query: 120 VVLTRMRIGHTRLTHSYLFSRSPQPTCR-CGDILTVKHILTCPLDIQL 166
           +VL R RIGH+ LTH YL  R   P C  C  +LTVKHIL   +D ++
Sbjct: 265 IVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILIDCIDFKM 312

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 =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 75/204 (36%), Positives = 106/204 (51%), Gaps = 7/204 (3%)

Query: 1   MSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSP 60
           +SSL A+++    +  L  I +   +LV  GK++ F+WCPSH GI GNE  D  AK  + 
Sbjct: 196 LSSLTALSNCDITHPYLLSILTKQNNLVRKGKKVVFIWCPSHVGILGNEVADRQAKQ-AL 254

Query: 61  SFPPLKL-CSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEE 119
             P  KL    +DYK  I+  V+  WQ+ W+     NKL  I+P I +W    +  R  E
Sbjct: 255 VMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDG-ETDNKLHIIQPVISEWKQGPQIDRRGE 313

Query: 120 VVLTRMRIGHTRLTHSYLFSRSPQPTCR-CGDILTVKHILTCPLDIQL-RSSLPNPPSLT 177
           +VL   RIGH+ LTH YL  R   P C  C  +LTVKHIL   +D ++ R    N  S+ 
Sbjct: 314 IVLACARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILIDCIDFEISRRKYFNVFSMR 373

Query: 178 D--ETTGVDALMSLLKSLNIFEKI 199
              E T    ++  LK + +F + 
Sbjct: 374 QLFEDTHPSKILLYLKEIGLFYRF 397

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 =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 65/167 (38%), Positives = 90/167 (53%), Gaps = 6/167 (3%)

Query: 5   QAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPP 64
           Q I + +  +  + KI      L   G ++   WCPSH G+ GNE  D+ AK  + SF  
Sbjct: 72  QGIGNFNIKHPYVVKILEKCTLLHKKGIDLVMTWCPSHVGVMGNERADLLAKE-ALSFTT 130

Query: 65  LKL-CSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLT 123
             +   +SD+KP+  +  +  WQ  W+S    NKL  I+P + KW  S+R+ R EE+VL 
Sbjct: 131 CTIRIPSSDFKPITHEFYKEKWQEQWSS-EQENKLYCIQPTLGKWAKSSREIRREEIVLA 189

Query: 124 RMRIGHTRLTHSYLFSRSPQPTCR-CGDILTVKHILT--CPLDIQLR 167
           R RIGH+ LTH YL  R   P C  C +IL++KHI       DI LR
Sbjct: 190 RARIGHSHLTHGYLLRREMPPVCIPCQNILSIKHIFIECVDFDILLR 236

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 =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 67/160 (41%), Positives = 89/160 (55%), Gaps = 4/160 (2%)

Query: 1   MSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSP 60
           +SSL A+++    +  L  I +   +LV  GK + F+WCPSH GI GNE  D  AK  + 
Sbjct: 101 LSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQ-AL 159

Query: 61  SFPPLKL-CSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEE 119
             P  KL    +DYK  I+  V+  WQ+ W+     NKL SI+P I +W    +  R  E
Sbjct: 160 VMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDE-ETDNKLHSIQPVISEWKQGPQIDRRGE 218

Query: 120 VVLTRMRIGHTRLTHSYLFSRSPQPTCR-CGDILTVKHIL 158
           +VL R RIGH+ LTH YL  R   P C  C  +L+VKHIL
Sbjct: 219 IVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLSVKHIL 258

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 63/160 (39%), Positives = 84/160 (52%), Gaps = 3/160 (1%)

Query: 1   MSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSP 60
           +S++ AI      +  + ++      +    K + FMWCPSH GI GNE  D  AK    
Sbjct: 86  LSAIMAIHGMDVRHPYVLQVLYAIKSISQQEKIVVFMWCPSHVGIPGNEMADTLAKEALS 145

Query: 61  SFPPLKL-CSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEE 119
           S    +L   ASD + LIKK ++  WQ  W+   + NKL SI P I  WP   R+ R EE
Sbjct: 146 STNLAELPVPASDLRCLIKKYIRSRWQHEWDE-QHSNKLHSIHPTIGPWPPCQREKRREE 204

Query: 120 VVLTRMRIGHTRLTHSYLFSRSPQPTC-RCGDILTVKHIL 158
           +VL R+RIGHT  TH Y+     Q  C  C   LTV+HI+
Sbjct: 205 IVLARIRIGHTHYTHDYIPRGDDQTECVACVCPLTVQHII 244

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 =  108 bits (269), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 56/145 (38%), Positives = 80/145 (55%), Gaps = 1/145 (0%)

Query: 2   SSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPS 61
           SS+ AI+S    ++ +  I     +L    K I F+WCPSH GI GNE  D  A+  S  
Sbjct: 62  SSILAISSIDLIHSYVQSILQKCTNLAGRDKRIIFIWCPSHVGIPGNETADTLAQQASGM 121

Query: 62  FPPLKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVV 121
                    +D+KP+ +  V+  WQS  +    GNKL  I+P+I  WP   R+ R +E+V
Sbjct: 122 NILNCPIPHTDFKPITRSFVETQWQSESDQ-ETGNKLHDIEPDIGSWPPCQREKRRDEIV 180

Query: 122 LTRMRIGHTRLTHSYLFSRSPQPTC 146
           + R+RIGHT LT+S+L S +  P C
Sbjct: 181 IARLRIGHTFLTYSHLLSGNDAPMC 205

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 =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 58/134 (43%), Positives = 76/134 (56%), Gaps = 10/134 (7%)

Query: 31  GKEISFMWCPSHCGISGNEAVDVAAKNP--SPSFPPLKLCSASDYKPLIKKIVQRNWQSS 88
           G +I +MW P HCGI GNE  D+ A     SP  P L + +  D K  IK+++ + W   
Sbjct: 2   GMDICYMWAPGHCGIQGNEKADLEASKAASSPDTPLLNIYTYEDKKKQIKQVLDQKWLIQ 61

Query: 89  WNSVPNGNKLKSIKPNIEKW--PSSNRKTRLEEVVLTRMRIGHTRLTHSYLFSRSPQPTC 146
           W  +    KL  IK NI+ W  P  NRK   EE +L R+RIGHT +TH +L  ++  P C
Sbjct: 62  W--INQHTKLNQIKNNIQTWKNPGLNRK---EETILNRLRIGHTFITHRHLMEKNDPPIC 116

Query: 147 R-CGDILTVKHILT 159
             CG  LTVKHI+T
Sbjct: 117 EMCGVDLTVKHIIT 130

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 54/127 (42%), Positives = 69/127 (54%), Gaps = 19/127 (14%)

Query: 27  LVACGKEISFMWCPSHCGISGNEAVDVAAKN---------PSPSFPPLKLCSASDYKPLI 77
           L    K I F+WCPSH GI GNE  D  AK          P P          +D+KP+ 
Sbjct: 59  LAGRDKRIIFIWCPSHVGIPGNETADTLAKQALGMNILNCPIPH---------TDFKPIT 109

Query: 78  KKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRMRIGHTRLTHSYL 137
           +  V+  WQS W+    GNKL  I+P+I  WP   R+ R EE+V+ R+RIGHT LTHS+L
Sbjct: 110 RSFVKTQWQSEWDQ-ETGNKLHDIQPDIGSWPPCQREKRREEIVIARVRIGHTFLTHSHL 168

Query: 138 FSRSPQP 144
            S +  P
Sbjct: 169 LSGNDAP 175

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 =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 58/138 (42%), Positives = 79/138 (57%), Gaps = 4/138 (2%)

Query: 31  GKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKL-CSASDYKPLIKKIVQRNWQSSW 89
           G ++  +WCPSH G+ GNE  D+ AK  + SF    +   A D+  +     +  WQ+ W
Sbjct: 78  GFDLVILWCPSHIGVVGNERADLLAKE-ALSFTACDVRIPAFDFNSVAYSFYRDKWQALW 136

Query: 90  NSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRMRIGHTRLTHSYLFSRSPQPTC-RC 148
            S+   NKL S++P I+K  +S+R+ R +E+VL R RIGHT LTH YL  R   P C  C
Sbjct: 137 -SLEQNNKLHSVQPIIKKLTNSSREDRRKEIVLARARIGHTHLTHGYLLRRELPPFCVHC 195

Query: 149 GDILTVKHILTCPLDIQL 166
              LTVKHIL   +D  L
Sbjct: 196 QCPLTVKHILIECVDFYL 213

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443724607|gb|ELU12531.1| hypothetical protein CAPTEDRAFT_208903 [Capitella teleta]

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 73/204 (35%), Positives = 103/204 (50%), Gaps = 7/204 (3%)

Query: 1   MSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPSP 60
           +SSL A+++    +  L  I +   +LV  GK + F+WCPSH GI GNE  D  AK  + 
Sbjct: 196 LSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQ-AL 254

Query: 61  SFPPLKL-CSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEE 119
             P  KL    +DYK  I+  V+   Q+ W+     NKL +I+P I +W    +  R  E
Sbjct: 255 VMPVTKLPLPHTDYKSPIRSYVKSLRQNEWDE-ETDNKLHTIQPVISEWKQGPQIDRRGE 313

Query: 120 VVLTRMRIGHTRLTHSYLFSRSPQPTCR-CGDILTVKHILTCPLDIQL-RSSLPNPPSLT 177
           +VL    IGH+ LTH YL  R   P C  C  +LTVKHIL   +D ++ R    N  S+ 
Sbjct: 314 IVLACACIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILIDCIDFEISRRKYFNVSSMR 373

Query: 178 D--ETTGVDALMSLLKSLNIFEKI 199
              E T     +  LK + +F + 
Sbjct: 374 QLFEDTHPSKNLLYLKEIGLFYRF 397

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)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	199
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.693	0.283	0.281	5.5e-09
ASPGD|ASPL0000055652	1054	AN0368 [Emericella nidulans (t	0.713	0.134	0.272	1.8e-05
ASPGD|ASPL0000037597	666	AN2711 [Emericella nidulans (t	0.708	0.211	0.281	2.4e-05
ASPGD|ASPL0000033911	686	AN2796 [Emericella nidulans (t	0.643	0.186	0.294	3.4e-05
ASPGD|ASPL0000077547	1581	AN8648 [Emericella nidulans (t	0.713	0.089	0.272	3.9e-05
ASPGD|ASPL0000010587	342	AN3980 [Emericella nidulans (t	0.643	0.374	0.286	4.9e-05
ASPGD|ASPL0000040226	1538	AN2661 [Emericella nidulans (t	0.708	0.091	0.281	6.6e-05
ASPGD|ASPL0000069810	334	AN7094 [Emericella nidulans (t	0.628	0.374	0.280	8.1e-05

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

 Score = 145 (56.1 bits), Expect = 5.5e-09, P = 5.5e-09
 Identities = 43/153 (28%), Positives = 68/153 (44%)

Query:    31 GKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLK-----LCSASDYKPLIKKIVQRNW 85
             G  + F W P+H G+ GNE  D  AK  +  +  ++     +   S  K    ++V   W
Sbjct:   283 GLNVHFRWIPAHRGVEGNEQADRRAKEAT-GWRRIRGHRGRMTIRSAVKRRAHEVVNARW 341

Query:    86 QSSWNSVPNGNKLKSIKPN-IEKWPSSNRKT-RLEEVVLTRMRIGHTRLTHSYLFSRS-- 141
             ++ W S  +G +L  + P    K    ++   R    ++ +MR G   L H YL+ R   
Sbjct:   342 ENDWKSCHHGRELYELTPTPTRKVLRVHQDLHRALSTIIVQMRTGKIGLRH-YLYQRGVP 400

Query:   142 --PQPTCRCGDIL-TVKHIL-TCPLDIQLRSSL 170
               P   C+CG    +V+HIL  CP    LR  +
Sbjct:   401 DVPNSDCQCGRATQSVRHILLACPTFSGLREEI 433

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

ASPGD|ASPL0000055652 AN0368 [Emericella nidulans (taxid:162425)]

 Score = 127 (49.8 bits), Expect = 1.8e-05, P = 1.8e-05
 Identities = 42/154 (27%), Positives = 70/154 (45%)

Query:    18 SKIYSTWLD----LVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDY 73
             S++ + W++    L    K +   W P H GI+GNE  D  AK  S  + P    S +  
Sbjct:   847 SQLAAQWMESPSILTMQWKPLQVRWIPGHSGIAGNELADKLAKLGSSIYSPDIPPSPAYL 906

Query:    74 KPLIKKIVQRNWQSSW-NSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRM---RIGH 129
             +   K+ ++    +++ N  P   K  +I+P+ ++  S +R+ +L   VL R+   R GH
Sbjct:   907 RQEAKQWLRTETYTAYANKAPETYKALNIRPHTKE--SRSREHKLPRWVLGRLVAARTGH 964

Query:   130 TRLT-HSYLFSRSPQ-PTCRCGDILTVKHILTCP 161
                T +   F  +    +C CG   T  H   CP
Sbjct:   965 GDFTAYHQRFDHTDYLESCTCGKAKTPVHFFFCP 998

GO:0005575 "cellular_component" evidence=ND

GO:0006278 "RNA-dependent DNA replication" evidence=IEA

GO:0003964 "RNA-directed DNA polymerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

ASPGD|ASPL0000037597 AN2711 [Emericella nidulans (taxid:162425)]

 Score = 124 (48.7 bits), Expect = 2.4e-05, P = 2.4e-05
 Identities = 43/153 (28%), Positives = 68/153 (44%)

Query:    19 KIYSTWLD----LVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYK 74
             ++ + WL+    L    K +   W P H GI+GNE  D  AK  S  + P    S +  +
Sbjct:   460 QLATQWLEAPSILTRPRKPLQVRWIPGHSGIAGNELADKLAKLGSSIYSPNIPPSPAYLR 519

Query:    75 PLIKKIVQRNWQSSWNS-VPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRM---RIGHT 130
                K+ ++    +++ S  P   K   I+P+ ++  S  R+ +L   VL R+   R GH 
Sbjct:   520 REAKQWLRTEAYTAYASKAPQAYKTLDIRPHTKE--SRTREHKLPRWVLGRLVAARTGHG 577

Query:   131 RLT-HSYLFSRSPQ-PTCRCGDILTVKHILTCP 161
               T +   F+ S    +C CG   T  H   CP
Sbjct:   578 DFTAYHQRFNHSDYLESCSCGKTKTPVHFFFCP 610

GO:0006278 "RNA-dependent DNA replication" evidence=IEA

GO:0003964 "RNA-directed DNA polymerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

ASPGD|ASPL0000033911 AN2796 [Emericella nidulans (taxid:162425)]

 Score = 123 (48.4 bits), Expect = 3.4e-05, P = 3.4e-05
 Identities = 40/136 (29%), Positives = 61/136 (44%)

Query:    32 KEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNS 91
             K +   W P H GI+GNE  D  AK  S  + P    S +  +   K+ ++    +++ S
Sbjct:   497 KPLQVRWIPGHSGIAGNELADKLAKLGSSIYSPNIPPSPAYLRREAKQWLRTEAYTAYAS 556

Query:    92 -VPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRM---RIGHTRLT-HSYLFSRSPQ-PT 145
               P   K   I+P+ ++  S  R+ +L   VL R+   R GH   T +   F+ S    +
Sbjct:   557 KAPQAYKTLDIRPHTKE--SRTREHKLPRWVLGRLVAARTGHGDFTAYHQRFNHSDYLES 614

Query:   146 CRCGDILTVKHILTCP 161
             C CG   T  H   CP
Sbjct:   615 CSCGKTKTPVHFFFCP 630

GO:0005575 "cellular_component" evidence=ND

GO:0006278 "RNA-dependent DNA replication" evidence=IEA

GO:0003964 "RNA-directed DNA polymerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

ASPGD|ASPL0000077547 AN8648 [Emericella nidulans (taxid:162425)]

 Score = 126 (49.4 bits), Expect = 3.9e-05, P = 3.9e-05
 Identities = 42/154 (27%), Positives = 70/154 (45%)

Query:    18 SKIYSTWLD----LVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDY 73
             S++ + W++    L    K +   W P H GI+GNE  D  AK  S  + P    S +  
Sbjct:  1374 SQLAAQWMESPSILTMQRKPLQVRWIPGHSGIAGNELADKLAKLGSSIYSPDIPPSPAYL 1433

Query:    74 KPLIKKIVQRNWQSSW-NSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRM---RIGH 129
             +   K+ ++    +++ N  P   K  +I+P+ ++  S +R+ +L   VL R+   R GH
Sbjct:  1434 RREAKQWLRTETYTAYANKAPETYKALNIRPHTKE--SRSREHKLPRWVLGRLVAARTGH 1491

Query:   130 TRLT-HSYLFSRSPQ-PTCRCGDILTVKHILTCP 161
                T +   F  +    +C CG   T  H   CP
Sbjct:  1492 GDFTAYHQRFDHTDYLESCTCGKAKTPVHFFFCP 1525

GO:0006278 "RNA-dependent DNA replication" evidence=IEA

GO:0003964 "RNA-directed DNA polymerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

ASPGD|ASPL0000010587 AN3980 [Emericella nidulans (taxid:162425)]

 Score = 118 (46.6 bits), Expect = 4.9e-05, P = 4.9e-05
 Identities = 39/136 (28%), Positives = 61/136 (44%)

Query:    32 KEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNS 91
             K +   W P H GI+GN+  D  AK  S  + P    S +  +   K+ ++    +++ S
Sbjct:   153 KPLQVCWIPGHSGIAGNKLADKLAKLGSSIYSPNIPPSPAYLQRETKQQLRTETYTAYAS 212

Query:    92 -VPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRM---RIGHTRLT-HSYLFSRSPQ-PT 145
               P   K   I+P+ ++  S  R+ +L   VL R+   R GH   T +   F+ S    +
Sbjct:   213 KAPQAYKTLDIRPHTKE--SRTREHKLPRWVLGRLVAARTGHGDFTAYHQRFNHSDYLES 270

Query:   146 CRCGDILTVKHILTCP 161
             C CG   T  H   CP
Sbjct:   271 CSCGRTKTPVHFFFCP 286

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

ASPGD|ASPL0000040226 AN2661 [Emericella nidulans (taxid:162425)]

 Score = 124 (48.7 bits), Expect = 6.6e-05, P = 6.6e-05
 Identities = 43/153 (28%), Positives = 68/153 (44%)

Query:    19 KIYSTWLD----LVACGKEISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYK 74
             ++ + WL+    L    K +   W P H GI+GNE  D  AK  S  + P    S +  +
Sbjct:  1332 QLATQWLEAPSILTRPRKPLQVRWIPGHSGIAGNELADKLAKLGSSIYSPNIPPSPAYLR 1391

Query:    75 PLIKKIVQRNWQSSWNS-VPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRM---RIGHT 130
                K+ ++    +++ S  P   K   I+P+ ++  S  R+ +L   VL R+   R GH 
Sbjct:  1392 REAKQWLRTEAYTAYASKAPQAYKTLDIRPHTKE--SRTREHKLPRWVLGRLVAARTGHG 1449

Query:   131 RLT-HSYLFSRSPQ-PTCRCGDILTVKHILTCP 161
               T +   F+ S    +C CG   T  H   CP
Sbjct:  1450 DFTAYHQRFNHSDYLESCSCGKTKTPVHFFFCP 1482

GO:0006278 "RNA-dependent DNA replication" evidence=IEA

GO:0003964 "RNA-directed DNA polymerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

ASPGD|ASPL0000069810 AN7094 [Emericella nidulans (taxid:162425)]

 Score = 116 (45.9 bits), Expect = 8.1e-05, P = 8.1e-05
 Identities = 39/139 (28%), Positives = 57/139 (41%)

Query:    32 KEISFMWCPSHCGISGNEAVDVAAKNPS----PSFPPLKLCSASDYKPLIKKIVQRNWQS 87
             K +   W P H GI+GN+  D  AK  S    P  PP       + K   + +    + +
Sbjct:   145 KPLQVCWIPGHSGIAGNKLADKLAKLGSSIYSPDIPPSPAYLQQEAK---QWLCTETYTA 201

Query:    88 SWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRMRI---GHTRLT--HSYLFSRSP 142
               N  P   K  +I+P+ ++  S +R+ +L   VL R+     GH   T  H Y      
Sbjct:   202 YANKAPETYKALNIRPHTKE--SRSREHKLPWWVLGRLVAACTGHRDFTAYHQYFDYTDY 259

Query:   143 QPTCRCGDILTVKHILTCP 161
               +C CG   T  H   CP
Sbjct:   260 LESCTCGKAKTPVHFFFCP 278


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.317   0.131   0.407    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      199       199   0.00085  111 3  11 22  0.49    32
                                                     31  0.45    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  8
  No. of states in DFA:  619 (66 KB)
  Total size of DFA:  188 KB (2106 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  20.55u 0.09s 20.64t   Elapsed:  00:00:05
  Total cpu time:  20.55u 0.09s 20.64t   Elapsed:  00:00:05
  Start:  Thu Aug 15 17:07:23 2013   End:  Thu Aug 15 17:07:28 2013

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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	199
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	2e-13
pfam00075	126	pfam00075, RNase_H, RNase H	4e-06

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

 Score = 63.8 bits (156), Expect = 2e-13
 Identities = 18/56 (32%), Positives = 29/56 (51%)

Query: 1   MSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAK 56
            ++L+A+ S   ++ L+ +I     +L   G ++   W P H GI GNE  D  AK
Sbjct: 69  QAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLAK 124

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

>gnl|CDD|215695 pfam00075, RNase_H, RNase H

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 2/54 (3%)

Query: 4   LQAITSKSCNNALLSK-IYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAK 56
           +  IT         SK I +   +L+    ++   W P H GI GNE  D  AK
Sbjct: 70  IGGIT-NGWPTKSESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNELADKLAK 122

RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. Length = 126

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	199
PRK08719	147	ribonuclease H; Reviewed	99.0
PRK06548	161	ribonuclease H; Provisional	98.95
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	98.93
PRK00203	150	rnhA ribonuclease H; Reviewed	98.79
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	98.57
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	98.5
KOG3752|consensus	371		97.94
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	96.45
PRK13907	128	rnhA ribonuclease H; Provisional	95.88
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	94.99
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	92.08
PRK07708	219	hypothetical protein; Validated	89.59

>PRK08719 ribonuclease H; Reviewed

Probab=99.00  E-value=3.1e-10  Score=85.58  Aligned_cols=41  Identities=29%  Similarity=0.408  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCCC
Q psy10817         18 SKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS   59 (199)
Q Consensus        18 ~~i~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a~   59 (199)
                      .+++..+..|.. ...|+|.|||||+|++|||.||++|++|+
T Consensus       105 ~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~  145 (147)
T PRK08719        105 RDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAA  145 (147)
T ss_pred             HHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHh
Confidence            577777777766 56799999999999999999999999874

>PRK06548 ribonuclease H; Provisional

Probab=98.95  E-value=5e-10  Score=85.48  Aligned_cols=47  Identities=26%  Similarity=0.391  Sum_probs=41.4

Q ss_pred             CCCHHHH-HHHHHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817         11 SCNNALL-SKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus        11 ~~~~~~i-~~i~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      ++|+++. ++++..+.++... ..|+|.|||||+|.+|||.||+||++|
T Consensus        92 s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~a  139 (161)
T PRK06548         92 ADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQA  139 (161)
T ss_pred             cCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHH
Confidence            4777877 7888888888765 489999999999999999999999998

>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=98.93  E-value=1.3e-10  Score=85.33  Aligned_cols=40  Identities=33%  Similarity=0.685  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHHHcCCeeEEEEecCCCCC-ccchhhhhhhCCC
Q psy10817         15 ALLSKIYSTWLDLVACGKEISFMWCPSHCGI-SGNEAVDVAAKNP   58 (199)
Q Consensus        15 ~~i~~i~~~~~~l~~~~~~i~l~WvPgH~gi-~gNE~AD~~Ak~a   58 (199)
                      ++..+|++.+    ..+..|.|.|||||+|+ .|||.||++||+|
T Consensus        90 ~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a  130 (132)
T PF00075_consen   90 PIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEA  130 (132)
T ss_dssp             BHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHH
T ss_pred             cchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHh
Confidence            4666666665    45899999999999999 6999999999975

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=98.79  E-value=3.1e-09  Score=80.38  Aligned_cols=46  Identities=17%  Similarity=0.319  Sum_probs=35.3

Q ss_pred             CCHHHH-HHHHHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817         12 CNNALL-SKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus        12 ~~~~~i-~~i~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      .|+++. .+++..+.++.. ...|.|.|||||+|++|||.||++||+|
T Consensus        93 ~g~~v~n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a  139 (150)
T PRK00203         93 DKKPVKNVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAG  139 (150)
T ss_pred             CCCccccHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHH
Confidence            344442 245555556544 4789999999999999999999999998

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

Probab=98.57  E-value=3.9e-08  Score=74.23  Aligned_cols=40  Identities=20%  Similarity=0.395  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817         19 KIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus        19 ~i~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      ++|..+.++...-..|.+.|||||.|-++||.||++|+.+
T Consensus       103 dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~  142 (154)
T COG0328         103 DLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREA  142 (154)
T ss_pred             HHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHH
Confidence            5566777777766699999999999999999999999998

>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=98.50  E-value=2e-07  Score=66.31  Aligned_cols=56  Identities=29%  Similarity=0.467  Sum_probs=40.6

Q ss_pred             hhHHhhcCC-CCHHHHHHHHHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817          3 SLQAITSKS-CNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus         3 al~al~~~~-~~~~~i~~i~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      ++..+.++. .........+..+.++...+..+.|.|||+|+|+.+|+.||.+||.+
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~  129 (130)
T cd06222          73 VINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEA  129 (130)
T ss_pred             HHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhh
Confidence            345555542 12333445555555555678899999999999999999999999976

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=97.94  E-value=8.7e-06  Score=68.95  Aligned_cols=41  Identities=24%  Similarity=0.385  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCCC
Q psy10817         17 LSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS   59 (199)
Q Consensus        17 i~~i~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a~   59 (199)
                      +.++-++..++  .+..|++.|||||.||.|||+||.+|++++
T Consensus       323 ~~e~~~l~q~~--~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs  363 (371)
T KOG3752|consen  323 FNELDELEQEI--SNKKVQQEYVGGHSGILGNEMADALARKGS  363 (371)
T ss_pred             HHHHHHHHhhh--ccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence            44444444443  478999999999999999999999999984

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

Probab=96.45  E-value=0.0018  Score=44.13  Aligned_cols=27  Identities=30%  Similarity=0.768  Sum_probs=22.9

Q ss_pred             cCCCCCCCcc-cCC-CCccccc-ccCcccH
Q psy10817        138 FSRSPQPTCR-CGD-ILTVKHI-LTCPLDI  164 (199)
Q Consensus       138 ~~~~~~~~C~-Cg~-~~t~~Hi-~~Cp~~~  164 (199)
                      .+...++.|. |+. .||++|+ ++||...
T Consensus        54 r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~   83 (86)
T PF13966_consen   54 RGIQVDPICPLCGNEEETIEHLFFHCPFAR   83 (86)
T ss_pred             cCCccCCccccCCCccccccceeccCcCcc
Confidence            3456789999 997 9999999 9999854

>PRK13907 rnhA ribonuclease H; Provisional

Probab=95.88  E-value=0.0073  Score=43.98  Aligned_cols=37  Identities=19%  Similarity=0.294  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817         18 SKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus        18 ~~i~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      +.+++.+..|...-..+.|.|||.+    .|+.||.+|+.|
T Consensus        88 ~~l~~~~~~l~~~f~~~~~~~v~r~----~N~~Ad~LA~~a  124 (128)
T PRK13907         88 APLLEEALQYIKSFDLFFIKWIPSS----QNKVADELARKA  124 (128)
T ss_pred             HHHHHHHHHHHhcCCceEEEEcCch----hchhHHHHHHHH
Confidence            4445555556555667788999995    899999999987

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

Probab=94.99  E-value=0.013  Score=39.02  Aligned_cols=52  Identities=21%  Similarity=0.204  Sum_probs=34.0

Q ss_pred             hhHHhhcCCCCHHHHHHHHHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817          3 SLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus         3 al~al~~~~~~~~~i~~i~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      .+.+|+........+..+...+..+.+.-..+.+.|||--    +|..||.+||.|
T Consensus        33 vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~----~N~~A~~LA~~a   84 (87)
T PF13456_consen   33 VVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPRE----QNKVADALAKFA   84 (87)
T ss_dssp             HHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GG----GSHHHHHHHHHH
T ss_pred             ccccccccccccccccccchhhhhhhccccceEEEEEChH----HhHHHHHHHHHH
Confidence            4566666632211445555566666667789999999986    799999999865

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=92.08  E-value=0.19  Score=43.40  Aligned_cols=38  Identities=16%  Similarity=0.322  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817         17 LSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus        17 i~~i~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      +......+.+|..+-..+.+.|||.    .+|+.||.+|+.|
T Consensus        92 l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a  129 (372)
T PRK07238         92 MKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEA  129 (372)
T ss_pred             HHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHH
Confidence            3444455566666667899999998    5899999999998

>PRK07708 hypothetical protein; Validated

Probab=89.59  E-value=0.27  Score=39.48  Aligned_cols=26  Identities=12%  Similarity=-0.024  Sum_probs=21.2

Q ss_pred             CCeeEEEEecCCCCCccchhhhhhhCCCCC
Q psy10817         31 GKEISFMWCPSHCGISGNEAVDVAAKNPSP   60 (199)
Q Consensus        31 ~~~i~l~WvPgH~gi~gNE~AD~~Ak~a~~   60 (199)
                      ...+.+.|||-.    -|+.||++|+.|..
T Consensus       182 ~l~~~~~~VpR~----~N~~AD~LAk~Al~  207 (219)
T PRK07708        182 KLTPVYEPISRK----QNKEADQLATQALE  207 (219)
T ss_pred             CceEEEEECCch----hhhHHHHHHHHHHh
Confidence            446788999875    59999999999943

---

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	199
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.0
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	98.91
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	98.81
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	98.81
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	98.79
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	98.76
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	98.74
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	98.66
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	98.54
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	97.94
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	97.78
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	97.56

>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=99.00  E-value=2.1e-10  Score=85.76  Aligned_cols=39  Identities=26%  Similarity=0.484  Sum_probs=32.0

Q ss_pred             HHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCCC
Q psy10817         21 YSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS   59 (199)
Q Consensus        21 ~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a~   59 (199)
                      +..+.++......|.|.|||||+|++|||.||+||++|.
T Consensus       107 ~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~  145 (150)
T 3qio_A          107 VNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGI  145 (150)
T ss_dssp             HHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHH
Confidence            333333334688999999999999999999999999994

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

Probab=98.91  E-value=7.2e-10  Score=82.15  Aligned_cols=40  Identities=18%  Similarity=0.086  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817         14 NALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus        14 ~~~i~~i~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      ..++++|...+.     ...|.|.|||||+|++|||.||+|||+|
T Consensus       102 ~~l~~~~~~~~~-----~~~v~~~~V~gH~g~~~N~~AD~LA~~a  141 (146)
T 3h08_A          102 IDLWQEILKLTT-----LHRVTFHKVKGHSDNPYNSRADELARLA  141 (146)
T ss_dssp             HHHHHHHHHHHH-----HSEEEEEECCC-CCSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh-----hCceEEEEcCCcCCcHhHHHHHHHHHHH
Confidence            455555555433     2479999999999999999999999987

>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=98.81  E-value=1.9e-09  Score=80.78  Aligned_cols=37  Identities=22%  Similarity=0.409  Sum_probs=30.5

Q ss_pred             HHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817         21 YSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus        21 ~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      +..+.++.. ...|.|.|||||+|++|||.||+|||+|
T Consensus       104 ~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LA~~a  140 (155)
T 1jl1_A          104 WQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAA  140 (155)
T ss_dssp             HHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHc-cCceEEEEcCCCCCCHHHHHHHHHHHHH
Confidence            334444433 4699999999999999999999999999

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

Probab=98.81  E-value=1.3e-09  Score=81.45  Aligned_cols=37  Identities=32%  Similarity=0.575  Sum_probs=30.2

Q ss_pred             HHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817         21 YSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus        21 ~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      +..+.++.. +..|.|.|||||+|++|||.||+|||+|
T Consensus       112 ~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a  148 (154)
T 2qkb_A          112 FVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREG  148 (154)
T ss_dssp             HHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHHHH
Confidence            333444433 5689999999999999999999999988

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

Probab=98.79  E-value=1.6e-09  Score=81.53  Aligned_cols=37  Identities=22%  Similarity=0.379  Sum_probs=30.7

Q ss_pred             HHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817         21 YSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus        21 ~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      +..+.++.. +..|.|.|||||+|++|||.||+|||+|
T Consensus       106 ~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a  142 (158)
T 2e4l_A          106 WKRLDKAAQ-LHQIDWRWVKGHAGHAENERCDQLARAA  142 (158)
T ss_dssp             HHHHHHHHT-TSEEEEEECCTTCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHc-cCcEEEEEccCCCCchhHHHHHHHHHHH
Confidence            334444443 4699999999999999999999999999

>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=98.76  E-value=4.4e-10  Score=83.63  Aligned_cols=43  Identities=23%  Similarity=0.154  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCCC
Q psy10817         14 NALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNPS   59 (199)
Q Consensus        14 ~~~i~~i~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a~   59 (199)
                      +.......+.+.+|..   .|.|.|||||+|++|||.||+|||+|.
T Consensus        93 ~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~  135 (147)
T 2kq2_A           93 NEFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSAL  135 (147)
T ss_dssp             HHHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHH
Confidence            3334455555555532   899999999999999999999999993

>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=98.74  E-value=1.7e-09  Score=82.05  Aligned_cols=29  Identities=34%  Similarity=0.590  Sum_probs=27.8

Q ss_pred             cCCeeEEEEecCCCC-----CccchhhhhhhCCC
Q psy10817         30 CGKEISFMWCPSHCG-----ISGNEAVDVAAKNP   58 (199)
Q Consensus        30 ~~~~i~l~WvPgH~g-----i~gNE~AD~~Ak~a   58 (199)
                      .+..|.|.|||||+|     ++|||.||++||+|
T Consensus       120 ~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~a  153 (165)
T 3p1g_A          120 LPKRLSIIHCPGHQKGNSAEARGNRMADQAAREA  153 (165)
T ss_dssp             SBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHH
T ss_pred             cCCceEEEEecCCCCCCcCcchHHHHHHHHHHHH
Confidence            678999999999999     99999999999998

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

Probab=98.66  E-value=3.4e-09  Score=80.36  Aligned_cols=38  Identities=26%  Similarity=0.429  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817         20 IYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus        20 i~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      ++..+.++.. ...|.|.|||||+|++|||.||+|||+|
T Consensus       108 l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a  145 (166)
T 1ril_A          108 LWEALLLAMA-PHRVRFHFVKGHTGHPENERVDREARRQ  145 (166)
T ss_dssp             HHHHHHHHHT-TSEEECCCCCGGGSCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHh-cCeEEEEEeeCCCCchhHHHHHHHHHHH
Confidence            3334444443 4699999999999999999999999999

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

Probab=98.54  E-value=1.5e-08  Score=76.73  Aligned_cols=38  Identities=16%  Similarity=0.201  Sum_probs=30.4

Q ss_pred             HHHHHHHHHcCCeeEEEEecCCCCC------ccchhhhhhhCCC
Q psy10817         21 YSTWLDLVACGKEISFMWCPSHCGI------SGNEAVDVAAKNP   58 (199)
Q Consensus        21 ~~~~~~l~~~~~~i~l~WvPgH~gi------~gNE~AD~~Ak~a   58 (199)
                      +..+.++......|.|.|||||+|+      +|||.||+||++|
T Consensus       117 ~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~g  160 (165)
T 2lsn_A          117 WKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQG  160 (165)
T ss_dssp             HHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHh
Confidence            3445555455678999999999996      5899999999987

>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=97.94  E-value=6.9e-06  Score=59.66  Aligned_cols=52  Identities=19%  Similarity=0.362  Sum_probs=40.0

Q ss_pred             hhHHhhcC-CCCHHHHHHHHHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817          3 SLQAITSK-SCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus         3 al~al~~~-~~~~~~i~~i~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      .+..|... +..++.+..++..+..|......|.|.|||+    +|||.||+|||+|
T Consensus        78 vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a  130 (141)
T 3hst_B           78 VVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----ARNTYADRLANDA  130 (141)
T ss_dssp             HHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHH
T ss_pred             HHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHH
Confidence            34555553 4555556677777777877778999999996    6999999999988

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

Probab=97.78  E-value=8.6e-06  Score=58.90  Aligned_cols=52  Identities=10%  Similarity=0.203  Sum_probs=34.5

Q ss_pred             hhHHhhcC-CCCHHHHHHHHHHHHHH-HHcCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817          3 SLQAITSK-SCNNALLSKIYSTWLDL-VACGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus         3 al~al~~~-~~~~~~i~~i~~~~~~l-~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      ++..+... ...+.-+..++..+..+ ...-..|+|.|||.    +|||.||+|||+|
T Consensus        81 vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~----~~N~~AD~LA~~a  134 (140)
T 3u3g_D           81 IVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPR----EKNARADELVNEA  134 (140)
T ss_dssp             HHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCG----GGGHHHHHHHHHH
T ss_pred             HHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCc----hhhHHHHHHHHHH
Confidence            34555553 22333334445555555 55556999999995    7999999999987

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

Probab=97.56  E-value=2.2e-05  Score=57.80  Aligned_cols=22  Identities=18%  Similarity=0.543  Sum_probs=20.6

Q ss_pred             eeEEEEecCCCCCccchhhhhhhCCC
Q psy10817         33 EISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus        33 ~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      .|.|.|||+|    +||.||+|||+|
T Consensus       110 ~v~~~~V~~~----~N~~AD~LA~~a  131 (149)
T 2ehg_A          110 NATLIWVPRE----ENKEADRLSRVA  131 (149)
T ss_dssp             TCEEEECCGG----GCHHHHHHHHHH
T ss_pred             CEEEEEcCCc----ccHHHHHHHHHH
Confidence            4999999995    899999999998

---

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	199
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.09
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.07
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.0
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	94.22

>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=99.09  E-value=3.2e-11  Score=85.72  Aligned_cols=52  Identities=21%  Similarity=0.454  Sum_probs=36.2

Q ss_pred             hhHHhhcCC--CCHHHHHHHHHHHHHHHHcCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817          3 SLQAITSKS--CNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus         3 al~al~~~~--~~~~~i~~i~~~~~~l~~~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      ++..+.+..  +.+....   ..+..+. ....|.|.|||||+|++|||.||+|||+|
T Consensus        72 v~~~~~~~~~~~~~~~~~---~~~~~~~-~~~~v~~~wV~gH~g~~gNe~AD~LA~~a  125 (126)
T d1mu2a1          72 VMGIVASQPTESESKIVN---QIIEEMI-KKEAIYVAWVPAHKGIGGNQEVDHLVSQG  125 (126)
T ss_dssp             HHHHHHTCCSEESCHHHH---HHHHHHH-HCSEEEEEECCSSSCCTTHHHHHHHHHTT
T ss_pred             HHHHHhcCCccccchHHH---HHHHHhh-hcceeEEEEEeCCCCCcchHHHHHHHHhh
Confidence            455666641  2233322   2233343 35699999999999999999999999987

>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=99.07  E-value=2.5e-11  Score=88.49  Aligned_cols=30  Identities=27%  Similarity=0.492  Sum_probs=27.8

Q ss_pred             cCCeeEEEEecCCCCCccchhhhhhhCCCC
Q psy10817         30 CGKEISFMWCPSHCGISGNEAVDVAAKNPS   59 (199)
Q Consensus        30 ~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a~   59 (199)
                      ....|+|+|||||+|++|||.||+|||+|.
T Consensus       110 ~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa  139 (152)
T d1jl1a_         110 GQHQIKWEWVKGHAGHPENERADELARAAA  139 (152)
T ss_dssp             TTCEEEEEECCSSTTCHHHHHHHHHHHHHH
T ss_pred             hcceeEEEEecccCCCccHHHHHHHHHHHH
Confidence            456899999999999999999999999993

>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=99.00  E-value=2.8e-11  Score=88.08  Aligned_cols=29  Identities=28%  Similarity=0.455  Sum_probs=27.4

Q ss_pred             cCCeeEEEEecCCCCCccchhhhhhhCCC
Q psy10817         30 CGKEISFMWCPSHCGISGNEAVDVAAKNP   58 (199)
Q Consensus        30 ~~~~i~l~WvPgH~gi~gNE~AD~~Ak~a   58 (199)
                      ....|+|.|||||+|++|||.||+|||+|
T Consensus       112 ~~~~v~~~wVkgHsg~~gNe~AD~LAk~a  140 (147)
T d1rila_         112 APHRVRFHFVKGHTGHPENERVDREARRQ  140 (147)
T ss_dssp             TTSEEECCCCCGGGSCTHHHHHHHHHHHH
T ss_pred             hhcccceEEccCCCCCcchHHHHHHHHHH
Confidence            46789999999999999999999999998

>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=94.22  E-value=0.019  Score=38.30  Aligned_cols=36  Identities=22%  Similarity=0.563  Sum_probs=22.6

Q ss_pred             hhHHhhcC--CCCHHHHHHHHHHHHHHHHcCCeeEEEEecCC
Q psy10817          3 SLQAITSK--SCNNALLSKIYSTWLDLVACGKEISFMWCPSH   42 (199)
Q Consensus         3 al~al~~~--~~~~~~i~~i~~~~~~l~~~~~~i~l~WvPgH   42 (199)
                      ++.+|...  +..+.+..+|.+.   |. ....|.|.|||||
T Consensus        73 vi~~i~~~~~~~~~~l~~~il~~---l~-~~~~v~i~WVpgH  110 (110)
T d1s1ta1          73 ALGIIQAQPDQSESELVNQIIEQ---LI-KKEKVYLAWVPAH  110 (110)
T ss_dssp             HHHHHHHCCSEESCHHHHHHHHH---HH-HCSEEEEEECCSS
T ss_pred             HHHHHhcCccccchHHHHHHHHH---Hh-cCCceEEEEeCCC
Confidence            34555553  3555555555433   33 3568999999999