Psyllid ID: psy5357

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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-
Protein Sequence
MIDSMNFVSNIPVARYFDVPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRNKCYLWIDNQCVIHWLTGNKVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWEGLGFLTLETWPDFPFQ
Secondary Structure (PSIPRED)
ccccccccccEEEccEEcccccccccccEEEEEEEEcccccccEEEEEEEEEcccccEEEEEEEEEEEccccccccccHHHHHHHHHHHHccccEEEccccEEEEEEcccccEEEEEcHHHHHHHHHcccccEEEEEcccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHcccccEEEEEccccccccEEEEEEEEcccHHHEEEEEEEEEEcccccEEEEEEEEEccccccccccccHHHHHHHHHHHcccEEEEcccHHEHHHHccccccHHHHHHHHHHHHHHccccccccEEEcccccccccHccccccHHHHHcccccccccHHcccccccccccc
Coil and Loop (DISEMBL)
midsmnfvsnipvaryfdvpnnhddqsvryephafsdacsYSYASVVYLRSVshsgdirtNIVFaksrvaptnkptlprLELLGALIAYRNKCYLWIDNQCVIHWLTGNKVFTTFVNNRVKALKEIKASVFPIvykyiptdsnpadlackgssavyLQGNrlwweglgfltletwpdfpfq
Flexible Loop (DISEMBL)
MIDSMNFVSNIPVARYFDVPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIvfaksrvaptnkptlprLELLGALIAYRNKCYLWIDNQCVIHWLTGNKVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWEGLGFLTLETWPDFPFQ
Low Complexity Region (SEG)
MIDSMNFVSNIPVARYFDVPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRNKCYLWIDNQCVIHWLTGNKVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWEGLGFLTLETWPDFPFQ
Disordered region (IsUnstruct)
******FVSNIPVARYFDVPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRNKCYLWIDNQCVIHWLTGNKVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWEGLGFLTLETWPDF***
Disordered Region (DISOPRED)
MIDSMNFVSNIPVARYFDVPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRNKCYLWIDNQCVIHWLTGNKVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWEGLGFLTLETWP*****
Disordered Region (DISEMBL)
MIDSMNFVSNIPVARYFDVPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRNKCYLWIDNQCVIHWLTGNKVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWEGLGFLTLETWPDFPFQ
Disordered Region (DISPRO)
MIDSMNFVSNIPVARYFDVPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRNKCYLWIDNQCVIHWLTGNKVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWEGLGFLTLETWPDF***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIDSMNFVSNIPVARYFDVPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRNKCYLWIDNQCVIHWLTGNKVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWEGLGFLTLETWPDFPFQ
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	181
291230224	1605	PREDICTED: Pao retrotransposon peptidase	0.900	0.101	0.390	4e-27
291222018	1559	PREDICTED: Pao retrotransposon peptidase	0.922	0.107	0.370	2e-24
291229887	1347	PREDICTED: Pao retrotransposon peptidase	0.933	0.125	0.341	2e-24
339261110	1116	zinc knuckle protein [Trichinella spiral	0.823	0.133	0.392	2e-24
339259576	1520	putative integrase core domain protein [	0.823	0.098	0.392	3e-24
291229885	906	PREDICTED: Pao retrotransposon peptidase	0.928	0.185	0.343	7e-24
339261552	1176	putative integrase core domain protein [	0.823	0.126	0.392	8e-24
339257436	931	putative integrase core domain protein [	0.823	0.160	0.392	1e-23
291231886	1091	PREDICTED: Pao retrotransposon peptidase	0.895	0.148	0.382	7e-23
291222173	1102	PREDICTED: Pao retrotransposon peptidase	0.718	0.117	0.419	7e-23

>gi|291230224|ref|XP_002735068.1| PREDICTED: Pao retrotransposon peptidase family protein-like [Saccoglossus kowalevskii]

 Score =  126 bits (316), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 75/192 (39%), Positives = 100/192 (52%), Gaps = 29/192 (15%)

Query: 1    MIDSMNFVSNIPVARYFDVPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRT 60
            + ++M    NI V R +   N   D   + + HAF+DA S  Y ++VY+     +    T
Sbjct: 884  IAENMRETRNITVKRQYFTEN---DPQSKVDVHAFADASSVGYGAIVYI-----TNQRET 935

Query: 61   NIVFAKSRVAPTNKPTLPRLELLGALIAYR---------------NKCYLWIDNQCVIHW 105
              V AK+RVAP  + TLPRLEL+ AL+A R               N CYLW D+Q V+HW
Sbjct: 936  AFVTAKTRVAPMTETTLPRLELMAALMASRLTKFVITALSGKFNINNCYLWSDSQIVLHW 995

Query: 106  LTGNKVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWE 165
            L  +K    FV NRVK +KE     F  +YKY+PT  NPADL  +G +   L  + +WW 
Sbjct: 996  LNSDKKLPIFVRNRVKEIKE-----FSHIYKYVPTLDNPADLLTRGITCAELINSNIWWN 1050

Query: 166  G-LGFLTLETWP 176
            G L   T   WP
Sbjct: 1051 GPLWLNTPNEWP 1062

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|291222018|ref|XP_002731015.1| PREDICTED: Pao retrotransposon peptidase family protein-like [Saccoglossus kowalevskii]

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 73/197 (37%), Positives = 104/197 (52%), Gaps = 30/197 (15%)

Query: 1   MIDSMNFVSNIPVAR-YFD---VPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSG 56
           +++ +N + N  + R YF+     N+H   +   E   F+DA S +Y +V YLR      
Sbjct: 788 IVEDLNEIRNTKIKRQYFNDDGTINSHIHDNKNVELPVFADANSKAYGAVAYLRR----H 843

Query: 57  DIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYR---------------NKCYLWIDNQC 101
           D +T++V +K+RVAP  + T+PRLEL+ ALIA R                 C LW D+Q 
Sbjct: 844 DNQTSLVMSKTRVAPIKELTIPRLELMAALIASRLMKFVFNALKDKLNITSCTLWSDSQI 903

Query: 102 VIHWLTGNKVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNPADLACKG--SSAVYLQG 159
           V+HW+  NK   TFV NRVK + +     FP  + Y PT  NPAD+  +G   SA  L+ 
Sbjct: 904 VLHWIGSNKKLPTFVANRVKEINQ-----FPCNFNYCPTTDNPADMISRGIHVSARKLEN 958

Query: 160 NRLWWEGLGFLTLETWP 176
             LWW G  +L+   WP
Sbjct: 959 CDLWWNGPPWLSQGDWP 975

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|291229887|ref|XP_002734902.1| PREDICTED: Pao retrotransposon peptidase family protein-like [Saccoglossus kowalevskii]

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 66/193 (34%), Positives = 102/193 (52%), Gaps = 24/193 (12%)

Query: 4    SMNFVSNIPVARYFDVPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIV 63
             ++ +++I + R +   N+ D     Y+ H+F+DA + +Y +V+Y+R +  +G+  T IV
Sbjct: 1069 ELHHLTDITINRSYFGGNSMDVNKQTYQLHSFADASTSAYGAVIYIRCME-TGE--TGIV 1125

Query: 64   FAKSRVAPTNKPTLPRLELLGALIAYR---------------NKCYLWIDNQCVIHWLTG 108
             +K+RV+PT + TLPRLELL  LI  R               + C LW D+Q  + W+  
Sbjct: 1126 ASKNRVSPTTEITLPRLELLACLIGTRLCKFVYNHLKPKLNIDSCTLWSDSQIALSWIAS 1185

Query: 109  NKVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWEGLG 168
            +K    F+ NR K + E   S     Y+Y+PT  NPADL  +G S   L+ +R WW G  
Sbjct: 1186 DKPQPVFIRNRTKEINEFNQS-----YRYVPTKQNPADLLTRGISTKELKSSRKWWNGPD 1240

Query: 169  FLT-LETWPDFPF 180
            FL     WP   +
Sbjct: 1241 FLANTADWPQITY 1253

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|339261110|ref|XP_003368070.1| zinc knuckle protein [Trichinella spiralis] gi|316963673|gb|EFV49170.1| zinc knuckle protein [Trichinella spiralis]

 Score =  117 bits (292), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 66/168 (39%), Positives = 92/168 (54%), Gaps = 19/168 (11%)

Query: 25  DQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLG 84
           D   R E HAF DA   +Y +VVYLR    SG     +  AK+RVAP  + +LPRLEL+G
Sbjct: 826 DHVKRIELHAFCDASERAYGAVVYLRVEPLSGPAWVRLAAAKTRVAPVKRLSLPRLELMG 885

Query: 85  ALIAYRNKCYL-------------WIDNQCVIHWL-TGNKVFTTFVNNRVKALKEIKASV 130
           AL+A R  CY+             W D++  + W+ +    +  FV NRV   +EI+  V
Sbjct: 886 ALMAARLICYVQEALRLDIRSISCWSDSEVTLAWIQSAASQWKPFVRNRV---EEIQQLV 942

Query: 131 FPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWEGLGFLT--LETWP 176
            P  +++ P  SNPAD+  +G+S   L  NR WW+G  +L   +ETWP
Sbjct: 943 EPTCWRHCPGKSNPADVLSRGASLKGLSKNRCWWQGPKWLAEPMETWP 990

Source: Trichinella spiralis

Species: Trichinella spiralis

Genus: Trichinella

Family: Trichinellidae

Order: Trichocephalida

Class: Enoplea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|339259576|ref|XP_003368837.1| putative integrase core domain protein [Trichinella spiralis] gi|316964514|gb|EFV49584.1| putative integrase core domain protein [Trichinella spiralis]

 Score =  116 bits (291), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 66/168 (39%), Positives = 92/168 (54%), Gaps = 19/168 (11%)

Query: 25  DQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLG 84
           D   R E HAF DA   +Y +VVYLR    SG     +  AK+RVAP  + +LPRLEL+G
Sbjct: 826 DHVKRIELHAFCDASERAYGAVVYLRVEPLSGPAWVRLAAAKTRVAPVKRLSLPRLELMG 885

Query: 85  ALIAYRNKCYL-------------WIDNQCVIHWL-TGNKVFTTFVNNRVKALKEIKASV 130
           AL+A R  CY+             W D++  + W+ +    +  FV NRV   +EI+  V
Sbjct: 886 ALMAARLICYVQEALRLDIRSISCWSDSEVTLAWIQSAASQWKPFVRNRV---EEIQQLV 942

Query: 131 FPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWEGLGFLT--LETWP 176
            P  +++ P  SNPAD+  +G+S   L  NR WW+G  +L   +ETWP
Sbjct: 943 EPTCWRHCPGKSNPADVLSRGASLKGLSKNRCWWQGPKWLAEPMETWP 990

Source: Trichinella spiralis

Species: Trichinella spiralis

Genus: Trichinella

Family: Trichinellidae

Order: Trichocephalida

Class: Enoplea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|291229885|ref|XP_002734901.1| PREDICTED: Pao retrotransposon peptidase family protein-like, partial [Saccoglossus kowalevskii]

 Score =  115 bits (288), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 66/192 (34%), Positives = 102/192 (53%), Gaps = 24/192 (12%)

Query: 5   MNFVSNIPVARYFDVPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVF 64
           ++ +++I + R +   N+ D     Y+ H+F+DA + +Y +V+Y+R +  +G+  T IV 
Sbjct: 647 LHHLTDITINRSYFGGNSMDVNKQTYQLHSFADASTSAYGAVIYIRCME-TGE--TGIVA 703

Query: 65  AKSRVAPTNKPTLPRLELLGALIAYR---------------NKCYLWIDNQCVIHWLTGN 109
           +K+RV+PT + TLPRLELL  LI  R               + C LW D+Q  + W+  +
Sbjct: 704 SKNRVSPTTEITLPRLELLACLIGTRLCKFVYNHLKPKLNIDSCTLWSDSQIALSWIASD 763

Query: 110 KVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWEGLGF 169
           K    F+ NR K + E   S     Y+Y+PT  NPADL  +G S   L+ +R WW G  F
Sbjct: 764 KPQPVFIRNRTKEINEFNQS-----YRYVPTKQNPADLLTRGISTKELKYSRKWWNGPEF 818

Query: 170 LT-LETWPDFPF 180
           L     WP   +
Sbjct: 819 LANTADWPQITY 830

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|339261552|ref|XP_003367849.1| putative integrase core domain protein [Trichinella spiralis] gi|316963889|gb|EFV49269.1| putative integrase core domain protein [Trichinella spiralis]

 Score =  115 bits (288), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 66/168 (39%), Positives = 92/168 (54%), Gaps = 19/168 (11%)

Query: 25  DQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLG 84
           D   R E HAF DA   +Y +VVYLR    SG     +  AK+RVAP  + +LPRLEL+G
Sbjct: 482 DHVKRIELHAFCDASERAYGAVVYLRVEPLSGPAWVRLAAAKTRVAPVKRLSLPRLELMG 541

Query: 85  ALIAYRNKCYL-------------WIDNQCVIHWL-TGNKVFTTFVNNRVKALKEIKASV 130
           AL+A R  CY+             W D++  + W+ +    +  FV NRV   +EI+  V
Sbjct: 542 ALMAARLICYVQEALRLDIRSISCWSDSEVTLAWIQSAASQWKPFVRNRV---EEIQQLV 598

Query: 131 FPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWEGLGFLT--LETWP 176
            P  +++ P  SNPAD+  +G+S   L  NR WW+G  +L   +ETWP
Sbjct: 599 EPTCWRHCPGKSNPADVLSRGASLKGLSKNRCWWQGPKWLAEPMETWP 646

Source: Trichinella spiralis

Species: Trichinella spiralis

Genus: Trichinella

Family: Trichinellidae

Order: Trichocephalida

Class: Enoplea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|339257436|ref|XP_003369907.1| putative integrase core domain protein [Trichinella spiralis] gi|316961789|gb|EFV48405.1| putative integrase core domain protein [Trichinella spiralis]

 Score =  114 bits (286), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 66/168 (39%), Positives = 92/168 (54%), Gaps = 19/168 (11%)

Query: 25  DQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLG 84
           D   R E HAF DA   +Y +VVYLR    SG     +  AK+RVAP  + +LPRLEL+G
Sbjct: 237 DHVKRIELHAFCDASERAYGAVVYLRVEPLSGPAWVRLAAAKTRVAPVKRLSLPRLELMG 296

Query: 85  ALIAYRNKCYL-------------WIDNQCVIHWL-TGNKVFTTFVNNRVKALKEIKASV 130
           AL+A R  CY+             W D++  + W+ +    +  FV NRV   +EI+  V
Sbjct: 297 ALMAARLICYVQEALRLDIRSISCWSDSEVTLAWIQSAASQWKPFVRNRV---EEIQQLV 353

Query: 131 FPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWEGLGFLT--LETWP 176
            P  +++ P  SNPAD+  +G+S   L  NR WW+G  +L   +ETWP
Sbjct: 354 EPTCWRHCPGKSNPADVLSRGASLKGLSKNRCWWQGPKWLAEPMETWP 401

Source: Trichinella spiralis

Species: Trichinella spiralis

Genus: Trichinella

Family: Trichinellidae

Order: Trichocephalida

Class: Enoplea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|291231886|ref|XP_002735894.1| PREDICTED: Pao retrotransposon peptidase family protein-like [Saccoglossus kowalevskii]

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 72/188 (38%), Positives = 101/188 (53%), Gaps = 26/188 (13%)

Query: 4   SMNFVSNIPVARYFDVPNNHDDQSVRYEPHAFSDAC-SYSYASVVYLRSVSHSGDIRTNI 62
           +++ V    V R F   +N   ++  YE H F+DA  + ++ +VVYL++ +H     T+I
Sbjct: 323 NLDSVKGTTVNRIFFTDSN--TETDEYELHVFADASKTTAHGAVVYLKNGNH-----TSI 375

Query: 63  VFAKSRVAPTNKPTLPRLELLGALIAYR--------------NKCYLWIDNQCVIHWLTG 108
           V AKSR+ P    TLP LEL+ A IA R              NKC LW D+Q  IHW+  
Sbjct: 376 VIAKSRLNPVRPMTLPHLELVAATIATRLADFVLKALTNVKINKCVLWSDSQITIHWIRS 435

Query: 109 NKVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNPADLACKGSSAVYLQGNRLWWEGLG 168
           +K    FV NRV   +EI+A  F  + KY PT  NPA+L  +G +   L  ++LWWEG  
Sbjct: 436 HKTLPVFVENRV---REIRAGPFDDI-KYCPTAENPANLLTRGITTNDLNRSKLWWEGPH 491

Query: 169 FLTLETWP 176
           +L    WP
Sbjct: 492 WLKGGKWP 499

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|291222173|ref|XP_002731094.1| PREDICTED: Pao retrotransposon peptidase family protein-like [Saccoglossus kowalevskii]

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 68/162 (41%), Positives = 86/162 (53%), Gaps = 32/162 (19%)

Query: 31   EPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYR 90
            E HAF+D+   +Y +V+YL+ +      R ++V +KSRVAP    TLPRLEL+ ALIA R
Sbjct: 859  ELHAFADSSLCAYGAVIYLKHMD-----RVSLVTSKSRVAPLRDITLPRLELMAALIATR 913

Query: 91   ---------------NKCYLWIDNQCVIHWLTGNKVFTTFVNNRVKALKEIKASVFPIVY 135
                            +CYLW DNQ VIHW+ GNK    FV NRV  +       F  V 
Sbjct: 914  LSQYVLKALNTKYNITQCYLWGDNQIVIHWINGNKPLPVFVKNRVDEINR-----FDCVK 968

Query: 136  KYIPTDSNPADLACKGSSAVYLQGNRLWWEGLGFLT-LETWP 176
            K + TD NPADL  +G S        LWW GL +L   + WP
Sbjct: 969  KCVSTDDNPADLLTRGISF------NLWWSGLSWLPYTDKWP 1004

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

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	181
pfam05380	159	pfam05380, Peptidase_A17, Pao retrotransposon pept	4e-13

>gnl|CDD|147520 pfam05380, Peptidase_A17, Pao retrotransposon peptidase

 Score = 63.2 bits (154), Expect = 4e-13
 Identities = 30/89 (33%), Positives = 47/89 (52%), Gaps = 6/89 (6%)

Query: 2   IDSMNFVSNIPVARYFDVPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTN 61
              ++ +  I V RY         +++  + H F DA   +YA+ VY R V    +I+ +
Sbjct: 57  RKQLSTLQQIRVPRYV---PYSPARNI--QLHGFCDASEKAYAAAVYWR-VEEGEEIQVS 110

Query: 62  IVFAKSRVAPTNKPTLPRLELLGALIAYR 90
           +V AK+RVAP    ++PRLEL  AL+  R
Sbjct: 111 LVAAKTRVAPLKTVSIPRLELCAALLLTR 139

Corresponds to Merops family A17. These proteins are homologous to aspartic proteinases encoded by retroposons and retroviruses. Length = 159

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	181
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	99.96
.; GO: 0004523 ribonuclease H activity" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF00336">PF00336	245	DNA_pol_viral_C: DNA polymerase (viral) C-terminal	98.95
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	98.42
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	98.29
PRK13907	128	rnhA ribonuclease H; Provisional	97.82
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	97.79
PRK00203	150	rnhA ribonuclease H; Reviewed	97.78
PRK08719	147	ribonuclease H; Reviewed	97.73
PRK06548	161	ribonuclease H; Provisional	97.51
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	97.39
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	97.16
PRK07708	219	hypothetical protein; Validated	97.14
KOG3752|consensus	371		93.39

>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family

Probab=99.96  E-value=1.5e-29  Score=200.70  Aligned_cols=84  Identities=40%  Similarity=0.649  Sum_probs=77.3

Q ss_pred             cccccCCCCeeeeeeecCCCCCCCCCCceeeEEEeccCcccceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhh
Q psy5357           2 IDSMNFVSNIPVARYFDVPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLE   81 (181)
Q Consensus         2 ~~~l~~l~~i~ipR~~~~~~~~~~~~~~~~L~~F~DAS~~aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlE   81 (181)
                      .++|.++++++|||++..     ....+++||+|||||+.|||||+|+|. ..+|..+++|++||+||+|+|..||||||
T Consensus        57 ~~~l~~~~~i~iPR~i~~-----~~~~~~~L~~F~DAS~~aygavvYlr~-~~~~~~~~~ll~aKsrv~P~k~~tIPRlE  130 (159)
T PF05380_consen   57 LKELESLSPIRIPRCIPI-----SDYRSVELHVFCDASESAYGAVVYLRS-YSDGSVQVRLLFAKSRVAPLKTVTIPRLE  130 (159)
T ss_pred             HHHHhhcccccCCccccc-----ccccceeeeEeecccccceeeEeEeee-ccCCceeeeeeeecccccCCCCCcHHHHH
Confidence            568889999999997653     356789999999999999999999999 78888999999999999999999999999


Q ss_pred             HhHHHHHhhc
Q psy5357          82 LLGALIAYRN   91 (181)
Q Consensus        82 L~a~~l~~~l   91 (181)
                      |+|+++|+++
T Consensus       131 L~a~~l~~~l  140 (159)
T PF05380_consen  131 LLAALLGVRL  140 (159)
T ss_pred             HHHHHHHHHH
Confidence            9999999998

>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein

Probab=98.95  E-value=5.1e-10  Score=92.62  Aligned_cols=99  Identities=22%  Similarity=0.248  Sum_probs=70.2

Q ss_pred             eeEEEeccCcccceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc--cceeeeccHHHHHHHhc
Q psy5357          31 EPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN--KCYLWIDNQCVIHWLTG  108 (181)
Q Consensus        31 ~L~~F~DAS~~aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l--~~~~~tDS~i~l~~i~~  108 (181)
                      .--||+||+..++|.++--+      ..  +.-+    .+|+.   |.-.||+|+.+|..+  .-.+-|||++|++.-..
T Consensus        94 lc~VfaDATpTgwgi~i~~~------~~--~~Tf----s~~l~---IhtaELlaaClAr~~~~~r~l~tDnt~Vlsrkyt  158 (245)
T PF00336_consen   94 LCQVFADATPTGWGISITGQ------RM--RGTF----SKPLP---IHTAELLAACLARLMSGARCLGTDNTVVLSRKYT  158 (245)
T ss_pred             CCceeccCCCCcceeeecCc------ee--eeee----ccccc---chHHHHHHHHHHHhccCCcEEeecCcEEEecccc
Confidence            33589999999999884322      11  2222    33444   889999999998876  34489999999875332


Q ss_pred             C-ccccceecchhchHHHHHhccCCcceEEeCCCCCCCcccCCCCC
Q psy5357         109 N-KVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNPADLACKGSS  153 (181)
Q Consensus       109 ~-~~~~~fV~nRv~~i~~I~~~~~~~~~~hV~t~~NPAD~~SRG~~  153 (181)
                      . --.-..++|.+-         ...++-||||+.||||..|||..
T Consensus       159 s~PW~lac~A~wiL---------rgts~~yVPS~~NPAD~PsR~~~  195 (245)
T PF00336_consen  159 SFPWLLACAANWIL---------RGTSFYYVPSKYNPADDPSRGKL  195 (245)
T ss_pred             cCcHHHHHHHHHhh---------cCceEEEeccccCcCCCCCCCcc
Confidence            2 111233456555         67899999999999999999974

The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity

>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=98.42  E-value=5.8e-07  Score=64.34  Aligned_cols=109  Identities=22%  Similarity=0.227  Sum_probs=69.9

Q ss_pred             EEeccCcc----cceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-------cceeeeccHHH
Q psy5357          34 AFSDACSY----SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-------KCYLWIDNQCV  102 (181)
Q Consensus        34 ~F~DAS~~----aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-------~~~~~tDS~i~  102 (181)
                      +|+|||-.    .+|+.++++.  .++.  .. ..+....   ...+.-..|+.|++.|.+.       .+.++|||..+
T Consensus         2 ~~~Dgs~~~~~~~~g~g~v~~~--~~~~--~~-~~~~~~~---~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~   73 (130)
T cd06222           2 IYTDGSCRGNPGPAGAGVVLRD--PGGE--VL-LSGGLLG---GNTTNNRAELLALIEALELALELGGKKVNIYTDSQYV   73 (130)
T ss_pred             EEecccCCCCCCceEEEEEEEe--CCCe--EE-EeccccC---CCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHH
Confidence            68999987    3455555553  2221  11 1111111   4567889999999999886       79999999999


Q ss_pred             HHHHhcCcc-ccceecchhchHHHHHhccCCcceEEeCC-----CCCCCcccCC
Q psy5357         103 IHWLTGNKV-FTTFVNNRVKALKEIKASVFPIVYKYIPT-----DSNPADLACK  150 (181)
Q Consensus       103 l~~i~~~~~-~~~fV~nRv~~i~~I~~~~~~~~~~hV~t-----~~NPAD~~SR  150 (181)
                      +..+.+... ...-....+..++++.+......++|||+     ..+.||.++|
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~  127 (130)
T cd06222          74 INALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAK  127 (130)
T ss_pred             HHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHH
Confidence            999998732 22222333332223333446788899999     5558887655

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.

>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=98.29  E-value=6.7e-07  Score=66.93  Aligned_cols=68  Identities=21%  Similarity=0.311  Sum_probs=47.8

Q ss_pred             CCCcchhhHhHHHHHhhc----cceeeeccHHHHHHHhcC---cccc-c----eecchhchHHHHHhccCCcceEEeCCC
Q psy5357          74 KPTLPRLELLGALIAYRN----KCYLWIDNQCVIHWLTGN---KVFT-T----FVNNRVKALKEIKASVFPIVYKYIPTD  141 (181)
Q Consensus        74 ~~tIPrlEL~a~~l~~~l----~~~~~tDS~i~l~~i~~~---~~~~-~----fV~nRv~~i~~I~~~~~~~~~~hV~t~  141 (181)
                      ..|.-+.||.|+..|.+.    .+.+||||+.++.++...   +.++ .    -+.+++.   +.......+.++|||+.
T Consensus        37 ~~s~~~aEl~Ai~~AL~~~~~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~---~~~~~~~~v~~~~V~~H  113 (132)
T PF00075_consen   37 GQSNNRAELQAIIEALKALEHRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIW---ELLSRGIKVRFRWVPGH  113 (132)
T ss_dssp             SECHHHHHHHHHHHHHHTHSTSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHH---HHHHHSSEEEEEESSSS
T ss_pred             ccchhhhheehHHHHHHHhhcccccccccHHHHHHHHHHhccccccccccccccchhhee---eccccceEEeeeeccCc
Confidence            678889999999999885    589999999999988872   1121 1    1223333   33333456899999998


Q ss_pred             CCC
Q psy5357         142 SNP  144 (181)
Q Consensus       142 ~NP  144 (181)
                      .|-
T Consensus       114 ~~~  116 (132)
T PF00075_consen  114 SGV  116 (132)
T ss_dssp             SSS
T ss_pred             CCC
Confidence            765

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 ....

>PRK13907 rnhA ribonuclease H; Provisional

Probab=97.82  E-value=9.5e-05  Score=55.82  Aligned_cols=106  Identities=17%  Similarity=0.164  Sum_probs=64.1

Q ss_pred             eEEEeccCccc----ceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-------cceeeeccH
Q psy5357          32 PHAFSDACSYS----YASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-------KCYLWIDNQ  100 (181)
Q Consensus        32 L~~F~DAS~~a----ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-------~~~~~tDS~  100 (181)
                      +++|+|||..+    .|+.+.++.  .+|..  . . +.    +....|=-..|+.|++.|.++       .+.++|||+
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~--~~~~~--~-~-~~----~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~   71 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKG--VQPAV--Q-L-SL----PLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQ   71 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEE--CCeeE--E-E-Ee----cccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechH
Confidence            57899988652    233333442  33322  1 1 11    222346679999999998875       788999999


Q ss_pred             HHHHHHhcCccccceecchhchHHHHHhc---cCCcceEEeCCCCCC-CcccCC
Q psy5357         101 CVIHWLTGNKVFTTFVNNRVKALKEIKAS---VFPIVYKYIPTDSNP-ADLACK  150 (181)
Q Consensus       101 i~l~~i~~~~~~~~fV~nRv~~i~~I~~~---~~~~~~~hV~t~~NP-AD~~SR  150 (181)
                      .+..++++......-...-   +++++++   .....+.|||...|- ||.+.|
T Consensus        72 ~vi~~~~~~~~~~~~~~~l---~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~  122 (128)
T PRK13907         72 LVERAVEKEYAKNKMFAPL---LEEALQYIKSFDLFFIKWIPSSQNKVADELAR  122 (128)
T ss_pred             HHHHHHhHHHhcChhHHHH---HHHHHHHHhcCCceEEEEcCchhchhHHHHHH
Confidence            9999999762111101111   2244443   445666899998875 776544

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

Probab=97.79  E-value=0.0001  Score=58.79  Aligned_cols=101  Identities=17%  Similarity=0.255  Sum_probs=64.4

Q ss_pred             eeEEEeccCc------ccceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-------cceeee
Q psy5357          31 EPHAFSDACS------YSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-------KCYLWI   97 (181)
Q Consensus        31 ~L~~F~DAS~------~aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-------~~~~~t   97 (181)
                      .+++|+|+|.      .|||+|++    +.++..  .+      .-+....|=-|+||+|++.|.+.       .+.+||
T Consensus         3 ~v~if~DGa~~gNpG~gG~g~vl~----~~~~~~--~~------s~~~~~tTNNraEl~A~i~AL~~l~~~~~~~v~l~t   70 (154)
T COG0328           3 KVEIFTDGACLGNPGPGGWGAVLR----YGDGEK--EL------SGGEGRTTNNRAELRALIEALEALKELGACEVTLYT   70 (154)
T ss_pred             ceEEEecCccCCCCCCceEEEEEE----cCCceE--EE------eeeeecccChHHHHHHHHHHHHHHHhcCCceEEEEe
Confidence            5789999984      57888776    223322  11      11233567889999999998875       699999


Q ss_pred             ccHHHHHHHh----cC--cccc----ceecch--hchHHHHHhccCCcceEEeCCCCC
Q psy5357          98 DNQCVIHWLT----GN--KVFT----TFVNNR--VKALKEIKASVFPIVYKYIPTDSN  143 (181)
Q Consensus        98 DS~i~l~~i~----~~--~~~~----~fV~nR--v~~i~~I~~~~~~~~~~hV~t~~N  143 (181)
                      ||+.+..-|.    +.  ..|+    .+|.|+  .+.+.+..+....+.|++|++..+
T Consensus        71 DS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g  128 (154)
T COG0328          71 DSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAG  128 (154)
T ss_pred             cHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCC
Confidence            9998886554    33  3333    345544  332223333334579999997654

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=97.78  E-value=0.00011  Score=57.45  Aligned_cols=96  Identities=17%  Similarity=0.269  Sum_probs=59.5

Q ss_pred             eEEEeccCcc------cceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-----cceeeeccH
Q psy5357          32 PHAFSDACSY------SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-----KCYLWIDNQ  100 (181)
Q Consensus        32 L~~F~DAS~~------aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-----~~~~~tDS~  100 (181)
                      +.+|+|+|..      +||+|++  .  .++  ... + +.    +....|-.|.||.|++.|.+.     .+.++|||+
T Consensus         4 v~iytDGs~~~n~~~~g~g~v~~--~--~~~--~~~-~-~~----~~~~~TN~~aEL~Ai~~AL~~~~~~~~v~I~tDS~   71 (150)
T PRK00203          4 VEIYTDGACLGNPGPGGWGAILR--Y--KGH--EKE-L-SG----GEALTTNNRMELMAAIEALEALKEPCEVTLYTDSQ   71 (150)
T ss_pred             EEEEEEecccCCCCceEEEEEEE--E--CCe--eEE-E-ec----CCCCCcHHHHHHHHHHHHHHHcCCCCeEEEEECHH
Confidence            7899999973      4554443  1  222  111 1 11    123578899999999998875     688999998


Q ss_pred             HHHHHHhcC------ccc----cceecch--hchHHHHHhcc--CCcceEEeCCCC
Q psy5357         101 CVIHWLTGN------KVF----TTFVNNR--VKALKEIKASV--FPIVYKYIPTDS  142 (181)
Q Consensus       101 i~l~~i~~~------~~~----~~fV~nR--v~~i~~I~~~~--~~~~~~hV~t~~  142 (181)
                      .++.-|..-      +.|    ..-|.|+  ++   +|.++.  ..+.|.|||+-.
T Consensus        72 yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~---~i~~l~~~~~v~~~wV~~H~  124 (150)
T PRK00203         72 YVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQ---RLDAALKRHQIKWHWVKGHA  124 (150)
T ss_pred             HHHHHHHHHHHHHHHcCCcccCCCccccHHHHH---HHHHHhccCceEEEEecCCC
Confidence            887644431      222    2345565  34   444433  457899998654

>PRK08719 ribonuclease H; Reviewed

Probab=97.73  E-value=0.00033  Score=55.16  Aligned_cols=102  Identities=17%  Similarity=0.153  Sum_probs=62.5

Q ss_pred             eeeEEEeccCcc---------cceeEEEEEEeecCCceeEEEEeccccccCCC-CCCcchhhHhHHHHHhhc---cceee
Q psy5357          30 YEPHAFSDACSY---------SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTN-KPTLPRLELLGALIAYRN---KCYLW   96 (181)
Q Consensus        30 ~~L~~F~DAS~~---------aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk-~~tIPrlEL~a~~l~~~l---~~~~~   96 (181)
                      .++++|+|+|..         |+|+++|.    ++|......  +    .|+. ..|--|+||.|+..|.+.   ...++
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~----~~~~~~~~~--~----~~~~~~~Tnn~aEl~A~~~aL~~~~~~~~i~   72 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYD----EAGEIVDEQ--S----ITVNRYTDNAELELLALIEALEYARDGDVIY   72 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEe----CCCCeeEEE--E----ecCCCCccHHHHHHHHHHHHHHHcCCCCEEE
Confidence            478899999882         55655543    333221111  1    1222 258899999999999886   57899


Q ss_pred             eccHHHHHHHh--------cC-c-cccceecchhchHHHHHhcc--CCcceEEeCCCC
Q psy5357          97 IDNQCVIHWLT--------GN-K-VFTTFVNNRVKALKEIKASV--FPIVYKYIPTDS  142 (181)
Q Consensus        97 tDS~i~l~~i~--------~~-~-~~~~fV~nRv~~i~~I~~~~--~~~~~~hV~t~~  142 (181)
                      |||+.++.-|+        +. + +-...|.|+=- +++|.++.  ..+.|.||++-.
T Consensus        73 tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl-~~~i~~l~~~~~i~~~~VkgH~  129 (147)
T PRK08719         73 SDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDL-WQQVDELRARKYVEVEKVTAHS  129 (147)
T ss_pred             echHHHHHHHHHHHHHHHhCCcccCCCcccccHHH-HHHHHHHhCCCcEEEEEecCCC
Confidence            99998886663        33 2 22344666422 22333332  357899999843

>PRK06548 ribonuclease H; Provisional

Probab=97.51  E-value=0.00089  Score=53.72  Aligned_cols=97  Identities=20%  Similarity=0.091  Sum_probs=59.9

Q ss_pred             eeEEEeccCccc----ceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc------cceeeeccH
Q psy5357          31 EPHAFSDACSYS----YASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN------KCYLWIDNQ  100 (181)
Q Consensus        31 ~L~~F~DAS~~a----ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l------~~~~~tDS~  100 (181)
                      ++++|+|||..+    -|..+|+.   .++    .      ...+....|=-|+||.|+..|...      .+.+||||+
T Consensus         5 ~~~IytDGa~~gnpg~~G~g~~~~---~~~----~------~~g~~~~~TNnraEl~Aii~aL~~~~~~~~~v~I~TDS~   71 (161)
T PRK06548          5 EIIAATDGSSLANPGPSGWAWYVD---ENT----W------DSGGWDIATNNIAELTAVRELLIATRHTDRPILILSDSK   71 (161)
T ss_pred             EEEEEEeeccCCCCCceEEEEEEe---CCc----E------EccCCCCCCHHHHHHHHHHHHHHhhhcCCceEEEEeChH
Confidence            589999988762    22223332   111    1      112233467789999999888754      588999999


Q ss_pred             HHHHHHhc--------C--ccccceecchhchHHHHHhcc--CCcceEEeCCC
Q psy5357         101 CVIHWLTG--------N--KVFTTFVNNRVKALKEIKASV--FPIVYKYIPTD  141 (181)
Q Consensus       101 i~l~~i~~--------~--~~~~~fV~nRv~~i~~I~~~~--~~~~~~hV~t~  141 (181)
                      .++.-+..        .  ++-...|.|+=- +++|.++.  ..+.|.||++-
T Consensus        72 yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL-~~~l~~l~~~~~v~~~wVkgH  123 (161)
T PRK06548         72 YVINSLTKWVYSWKMRKWRKADGKPVLNQEI-IQEIDSLMENRNIRMSWVNAH  123 (161)
T ss_pred             HHHHHHHHHHHHHHHCCCcccCCCccccHHH-HHHHHHHHhcCceEEEEEecC
Confidence            99976662        3  223456787733 22333322  35889999864

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

Probab=97.39  E-value=0.00032  Score=48.38  Aligned_cols=69  Identities=20%  Similarity=0.248  Sum_probs=48.5

Q ss_pred             hhHhHHHHHhhc-------cceeeeccHHHHHHHhcCccccceecchhchHHHHHhccCCcceEEeCCCCCC-Cccc
Q psy5357          80 LELLGALIAYRN-------KCYLWIDNQCVIHWLTGNKVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNP-ADLA  148 (181)
Q Consensus        80 lEL~a~~l~~~l-------~~~~~tDS~i~l~~i~~~~~~~~fV~nRv~~i~~I~~~~~~~~~~hV~t~~NP-AD~~  148 (181)
                      .|+.|+..|.++       ++.+.|||..++..|++...........+..|+.+.+......++|||-+.|- ||.+
T Consensus         4 aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~A~~L   80 (87)
T PF13456_consen    4 AEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPREQNKVADAL   80 (87)
T ss_dssp             HHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GGGSHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChHHhHHHHHH
Confidence            689999888876       89999999999999998843333667777733344445567899999999885 5543

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=97.16  E-value=0.0023  Score=56.79  Aligned_cols=116  Identities=13%  Similarity=0.120  Sum_probs=69.2

Q ss_pred             eeeEEEeccCccc----ceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-------cceeeec
Q psy5357          30 YEPHAFSDACSYS----YASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-------KCYLWID   98 (181)
Q Consensus        30 ~~L~~F~DAS~~a----ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-------~~~~~tD   98 (181)
                      +++++|+|||..+    -|+.+.++.  .+|..  .+...+.   ++...|-...|+.|++.|.++       .+.+++|
T Consensus         1 ~~~~i~~DGa~~~n~g~aG~G~vi~~--~~~~~--~~~~~~~---~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~D   73 (372)
T PRK07238          1 MKVVVEADGGSRGNPGPAGYGAVVWD--ADRGE--VLAERAE---AIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMD   73 (372)
T ss_pred             CeEEEEecCCCCCCCCceEEEEEEEe--CCCCc--EEEEeec---ccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeC
Confidence            3689999999873    344444543  33311  1111111   222456678999999999886       7899999


Q ss_pred             cHHHHHHHhcCcccc-ceecchhchHHHHHhccCCcceEEeCCCCCC-CcccCCCC
Q psy5357          99 NQCVIHWLTGNKVFT-TFVNNRVKALKEIKASVFPIVYKYIPTDSNP-ADLACKGS  152 (181)
Q Consensus        99 S~i~l~~i~~~~~~~-~fV~nRv~~i~~I~~~~~~~~~~hV~t~~NP-AD~~SRG~  152 (181)
                      |..++..+.++.+.+ .-...-+..++++........+.||+.+.|- ||.+.+..
T Consensus        74 S~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~a  129 (372)
T PRK07238         74 SKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEA  129 (372)
T ss_pred             cHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHHH
Confidence            999999998751111 0000001111144444567889999987664 77765543

>PRK07708 hypothetical protein; Validated

Probab=97.14  E-value=0.005  Score=51.61  Aligned_cols=114  Identities=18%  Similarity=0.168  Sum_probs=66.4

Q ss_pred             eeeEEEeccCcc----cceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc---------cceee
Q psy5357          30 YEPHAFSDACSY----SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN---------KCYLW   96 (181)
Q Consensus        30 ~~L~~F~DAS~~----aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l---------~~~~~   96 (181)
                      -.+++|+|||..    .+|+.+.++.  .+|.....+- ....+.+  ..|=...|+.|++.|.+.         .+.++
T Consensus        72 ~~~~vY~DGs~~~n~g~aG~GvVI~~--~~g~~~~~~~-~~~~l~~--~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~  146 (219)
T PRK07708         72 HEILVYFDGGFDKETKLAGLGIVIYY--KQGNKRYRIR-RNAYIEG--IYDNNEAEYAALYYAMQELEELGVKHEPVTFR  146 (219)
T ss_pred             CcEEEEEeeccCCCCCCcEEEEEEEE--CCCCEEEEEE-eeccccc--cccCcHHHHHHHHHHHHHHHHcCCCcceEEEE
Confidence            368999999872    3444444443  2332222221 1122322  246678899999998875         27899


Q ss_pred             eccHHHHHHHhcC-ccccceecchhchHHH-HHhccCCcceEEeCCCCCC-Cccc
Q psy5357          97 IDNQCVIHWLTGN-KVFTTFVNNRVKALKE-IKASVFPIVYKYIPTDSNP-ADLA  148 (181)
Q Consensus        97 tDS~i~l~~i~~~-~~~~~fV~nRv~~i~~-I~~~~~~~~~~hV~t~~NP-AD~~  148 (181)
                      +||+.++.|+.+. +...+....-...+.+ +........+.|||-+.|= ||.+
T Consensus       147 ~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~L  201 (219)
T PRK07708        147 GDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQL  201 (219)
T ss_pred             eccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHH
Confidence            9999999999987 3332222212221112 2223233677899998885 6654

>KOG3752|consensus

Probab=93.39  E-value=0.41  Score=43.25  Aligned_cols=65  Identities=25%  Similarity=0.279  Sum_probs=46.6

Q ss_pred             eEEEeccCccc-------ceeEEEEEEeecCCceeEEEEeccccccCCC--CCCcchhhHhHHHHHhhc-------ccee
Q psy5357          32 PHAFSDACSYS-------YASVVYLRSVSHSGDIRTNIVFAKSRVAPTN--KPTLPRLELLGALIAYRN-------KCYL   95 (181)
Q Consensus        32 L~~F~DAS~~a-------ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk--~~tIPrlEL~a~~l~~~l-------~~~~   95 (181)
                      +.+++|+|-.+       =|.+||..--++.+           +-.|+.  ..|--|.||.|+..|..-       ++++
T Consensus       213 ~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N-----------~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I  281 (371)
T KOG3752|consen  213 QVVYTDGSSSGNGRKSSRAGYGVYWGPGHELN-----------VSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVI  281 (371)
T ss_pred             eEEEecCccccCCCCCCcceeEEeeCCCCccc-----------ccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEE
Confidence            67899998665       23456766322221           223443  378889999999998864       8999


Q ss_pred             eeccHHHHHHHh
Q psy5357          96 WIDNQCVIHWLT  107 (181)
Q Consensus        96 ~tDS~i~l~~i~  107 (181)
                      .|||.-++.||+
T Consensus       282 ~TDS~~~i~~l~  293 (371)
T KOG3752|consen  282 RTDSEYFINSLT  293 (371)
T ss_pred             EechHHHHHHHH
Confidence            999999998776

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	181
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	6e-06

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 43.4 bits (101), Expect = 6e-06
 Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 8/33 (24%)

Query: 121 KALKEIKASVFPIVYK-YIPTDSNPADLACKGS 152
           +ALK+++AS+     K Y   DS PA LA K +
Sbjct: 20  QALKKLQASL-----KLYAD-DSAPA-LAIKAT 45

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	181
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	98.44
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	98.42
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	98.26
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	98.17
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	97.98
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	97.86
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	97.8
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	97.8
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	97.79
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	97.75
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	97.7
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	97.63
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	97.51
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	97.51
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	97.27
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	97.15
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	96.63
2zd1_B	428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	83.51

>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain, fusion protein, maltose binding protein, HYDR; HET: MLR TAR; 2.25A {Mycobacterium tuberculosis}

Probab=98.44  E-value=6.1e-07  Score=66.91  Aligned_cols=112  Identities=14%  Similarity=0.137  Sum_probs=67.6

Q ss_pred             eeeEEEeccCccc----ceeEEEEEEeecC-CceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-------cceeee
Q psy5357          30 YEPHAFSDACSYS----YASVVYLRSVSHS-GDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-------KCYLWI   97 (181)
Q Consensus        30 ~~L~~F~DAS~~a----ygavvYlr~~~~~-g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-------~~~~~t   97 (181)
                      .++.+|+|||..+    .|+.++++.  .+ |.. ..-. +. .   +...|--+.||.|++.|.++       .+.++|
T Consensus         2 ~~~~iy~DGs~~~~~g~~g~G~v~~~--~~~~~~-~~~~-~~-~---~~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~t   73 (141)
T 3hst_B            2 VKVVIEADGGSRGNPGPAGYGAVVWT--ADHSTV-LAES-KQ-A---IGRATNNVAEYRGLIAGLDDAVKLGATEAAVLM   73 (141)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEE--TTSCSE-EEEE-EE-E---EEEECHHHHHHHHHHHHHHHHHHHTCSEEEEEE
T ss_pred             cEEEEEEecCCCCCCCCcEEEEEEEe--CCCCcE-EEee-ec-c---CCCCchHHHHHHHHHHHHHHHHHCCCceEEEEe
Confidence            4789999999652    244444442  22 321 1111 11 1   12457789999999999875       799999


Q ss_pred             ccHHHHHHHhcC-ccccceecchhchHHHHHhccCCcceEEeCCCCC-CCcccC
Q psy5357          98 DNQCVIHWLTGN-KVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSN-PADLAC  149 (181)
Q Consensus        98 DS~i~l~~i~~~-~~~~~fV~nRv~~i~~I~~~~~~~~~~hV~t~~N-PAD~~S  149 (181)
                      ||+.++.++++. +.-..-....+..|+++.+....+.|.|||.+.| .||.+.
T Consensus        74 DS~~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~~~N~~AD~LA  127 (141)
T 3hst_B           74 DSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLA  127 (141)
T ss_dssp             SCHHHHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCGGGCHHHHHHH
T ss_pred             ChHHHHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCCcccHHHHHHH
Confidence            999999999974 2111111122221113333345689999998888 466543

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

Probab=98.42  E-value=2.3e-07  Score=70.60  Aligned_cols=110  Identities=19%  Similarity=0.202  Sum_probs=68.1

Q ss_pred             eEEEeccCcc-------c-ceeEEEEEEeecCCceeEEEEeccccccCC-CCCCcchhhHhHHHHHhhc-------ccee
Q psy5357          32 PHAFSDACSY-------S-YASVVYLRSVSHSGDIRTNIVFAKSRVAPT-NKPTLPRLELLGALIAYRN-------KCYL   95 (181)
Q Consensus        32 L~~F~DAS~~-------a-ygavvYlr~~~~~g~~~~~ll~aKsrvaPl-k~~tIPrlEL~a~~l~~~l-------~~~~   95 (181)
                      +.+|+|||-.       | ||++++-     +|... . .+++ .+.|. ...|--+.|+.|++.|.++       .+.+
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~-----~g~~~-~-~~~~-~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i   73 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYL-----DNRKI-E-GYGL-AEKPFSINSTNNVAEYSGLICLMETMLRLGISSPII   73 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEEC-----SSCEE-E-EEEE-CSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEE
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEE-----CCEEE-E-Eecc-ccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEE
Confidence            5689999876       2 5655442     44321 1 1111 12333 2468889999999999875       7999


Q ss_pred             eeccHHHHHHHhcC-ccccceecchhchHHHHHhccCCcceEEeCCCCC-CCcccCC
Q psy5357          96 WIDNQCVIHWLTGN-KVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSN-PADLACK  150 (181)
Q Consensus        96 ~tDS~i~l~~i~~~-~~~~~fV~nRv~~i~~I~~~~~~~~~~hV~t~~N-PAD~~SR  150 (181)
                      +|||+.++.++++. +.-..-...-++.+.++.+.. .+.|.|||.+.| .||.+.|
T Consensus        74 ~tDS~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~~~N~~AD~LA~  129 (149)
T 2ehg_A           74 KGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPREENKEADRLSR  129 (149)
T ss_dssp             EESCHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCGGGCHHHHHHHH
T ss_pred             EeChHHHHHHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCCcccHHHHHHHH
Confidence            99999999999976 211111111122111222222 489999999988 5787654

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

Probab=98.26  E-value=2.2e-06  Score=63.45  Aligned_cols=110  Identities=15%  Similarity=0.183  Sum_probs=65.9

Q ss_pred             eeEEEeccCccc----ceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-----------ccee
Q psy5357          31 EPHAFSDACSYS----YASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-----------KCYL   95 (181)
Q Consensus        31 ~L~~F~DAS~~a----ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-----------~~~~   95 (181)
                      ++.+|+|||-.+    .|+.++++  +.+|.....  .++ .+   ...|--+.||.|++.|.++           .+.+
T Consensus         3 ~~~iy~DGs~~~n~g~~G~G~v~~--~~~g~~~~~--~~~-~~---~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i   74 (140)
T 3u3g_D            3 KIIIYTDGGARGNPGPAGIGVVIT--DEKGNTLHE--SSA-YI---GETTNNVAEYEALIRALEDLQMFGDKLVDMEVEV   74 (140)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEE--CTTSCEEEE--EEE-EE---EEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEE
T ss_pred             eEEEEEecCCCCCCCCcEEEEEEE--eCCCCEEEE--EEe-eC---CCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEE
Confidence            578999999742    34444444  234532111  111 11   1357889999999998864           4789


Q ss_pred             eeccHHHHHHHhcCcc-ccceecchhchHHHH-HhccCCcceEEeCCCCCC-Cccc
Q psy5357          96 WIDNQCVIHWLTGNKV-FTTFVNNRVKALKEI-KASVFPIVYKYIPTDSNP-ADLA  148 (181)
Q Consensus        96 ~tDS~i~l~~i~~~~~-~~~fV~nRv~~i~~I-~~~~~~~~~~hV~t~~NP-AD~~  148 (181)
                      +|||+.++.++++... -..-....+..|.++ .+....+.|.|||...|- ||.+
T Consensus        75 ~tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~~~N~~AD~L  130 (140)
T 3u3g_D           75 RMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADEL  130 (140)
T ss_dssp             EESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCGGGGHHHHHH
T ss_pred             EeChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCchhhHHHHHH
Confidence            9999999999997511 111111122212233 333457999999987773 5543

>1rw3_A POL polyprotein; RNA and DNA dependent DNA polymerase, reverse transcriptase, transferase, replication; 3.00A {Moloney murine leukemia virus} SCOP: e.8.1.2

Probab=98.17  E-value=2.2e-07  Score=82.72  Aligned_cols=87  Identities=9%  Similarity=-0.070  Sum_probs=64.8

Q ss_pred             ceeeEEEeccCcccceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc--------cceeeeccH
Q psy5357          29 RYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN--------KCYLWIDNQ  100 (181)
Q Consensus        29 ~~~L~~F~DAS~~aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l--------~~~~~tDS~  100 (181)
                      ...+++|||||..++|||.+-.   .+|..+....+||+...+.++++++.+||+|++.|++.        .+.++||+.
T Consensus       344 ~~~~~l~~DAS~~~~gavL~q~---~~~~~~~i~y~Sk~l~~~e~~ys~~ekEllAi~~a~~~~~~yl~g~~~~v~tDh~  420 (455)
T 1rw3_A          344 TKPFELFVDEKQGYAKGVLTQK---LGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVIKAPHA  420 (455)
T ss_dssp             CCTTSCEEEEEECSSSBEECCB---CTTTTCCCCCCCBCSCSSCSSSCCSSHHHHHHHHHHHHHHGGGCSSCEEEECSSC
T ss_pred             CCcEEEEEeccCCcceeEEEEe---cCCcEEEEEEEcccCCccccccchHHHHHHHHHHHHHHHHHHcCCCcEEEEecCh
Confidence            3467889999999999987643   24444444455776666667899999999999999874        799999998


Q ss_pred             HHHHHHhcC-ccccceecchhc
Q psy5357         101 CVIHWLTGN-KVFTTFVNNRVK  121 (181)
Q Consensus       101 i~l~~i~~~-~~~~~fV~nRv~  121 (181)
                       +++|+++. .+|  +..+|+.
T Consensus       421 -~~~~l~~~~~~~--~~~~Rl~  439 (455)
T 1rw3_A          421 -VEALVKQPPDRW--LSNARMT  439 (455)
T ss_dssp             -TTTTSSSTTTTT--CCCCCCS
T ss_pred             -HHHHhCCCcccc--ccchHHH
Confidence             88998876 333  3344544

>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=97.98  E-value=9.4e-06  Score=62.14  Aligned_cols=99  Identities=17%  Similarity=0.191  Sum_probs=61.0

Q ss_pred             eeEEEeccCc----ccceeEEEEEEeecCCceeEEEEecc-ccccCC-CCCCcchhhHhHHHHHhhc------cceeeec
Q psy5357          31 EPHAFSDACS----YSYASVVYLRSVSHSGDIRTNIVFAK-SRVAPT-NKPTLPRLELLGALIAYRN------KCYLWID   98 (181)
Q Consensus        31 ~L~~F~DAS~----~aygavvYlr~~~~~g~~~~~ll~aK-srvaPl-k~~tIPrlEL~a~~l~~~l------~~~~~tD   98 (181)
                      .+.+|+|||.    .|||++++  .   +|..  .-+ +. ....|. ...|--+.||.|+..|.++      .+.++||
T Consensus         6 ~i~iytDGs~~~g~~G~G~vi~--~---~g~~--~~~-~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~~v~I~tD   77 (147)
T 2kq2_A            6 EYDVYTDGSYVNGQYAWAYAFV--K---DGKV--HYE-DADVGKNPAAATMRNVAGEIAAALYAVKKASQLGVKIRILHD   77 (147)
T ss_dssp             CCEEECCCCCBTTBCEEEEEEE--E---TTEE--EEE-EEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTCCCCBSSC
T ss_pred             eEEEEECCCCCCCCcEEEEEEE--E---CCEE--EEE-EeccccccccccccHHHHHHHHHHHHHHHHHHCCCeEEEEEC
Confidence            5789999997    45555443  2   3421  111 11 111111 1357889999999999874      7999999


Q ss_pred             cHHHHHHHhcC-ccc-cceecchhchHHHHHhccCCcceEEeCCC
Q psy5357          99 NQCVIHWLTGN-KVF-TTFVNNRVKALKEIKASVFPIVYKYIPTD  141 (181)
Q Consensus        99 S~i~l~~i~~~-~~~-~~fV~nRv~~i~~I~~~~~~~~~~hV~t~  141 (181)
                      |+.+..|+.+. +.- +..+.|+ .   .++++...+.|.|||+-
T Consensus        78 S~~i~~w~~~~w~~~~~~~~~~~-~---l~~~l~~~v~~~wV~gH  118 (147)
T 2kq2_A           78 YAGIAFWATGEWKAKNEFTQAYA-K---LMNQYRGIYSFEKVKAH  118 (147)
T ss_dssp             CSTHHHHTTSSSSCCHHHHHHHH-C---GGGGGSTTCCBCCCCCC
T ss_pred             cHHHHHHHhCCCccCCcchHHHH-H---HHHHhcCCeeEEEecCc
Confidence            99999999875 221 1223222 1   23333337899999974

>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=97.86  E-value=8e-05  Score=58.41  Aligned_cols=103  Identities=13%  Similarity=0.094  Sum_probs=64.5

Q ss_pred             CCceeeEEEeccCcc------cceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc----cceee
Q psy5357          27 SVRYEPHAFSDACSY------SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN----KCYLW   96 (181)
Q Consensus        27 ~~~~~L~~F~DAS~~------aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l----~~~~~   96 (181)
                      ....++.+|+|||..      +||+++|-     +|.. ..  .+  ..  ....|.-|.||.|+..|.++    .+.+|
T Consensus        19 ~~~~~i~iytDGs~~~npG~~g~G~vi~~-----~~~~-~~--~~--~~--~~~~Tnn~aEl~Ai~~AL~~~~~~~v~I~   86 (165)
T 3p1g_A           19 IPDADYTWYTDGSSFLQEGQRRAGAAVTT-----ETEV-IW--AR--AL--PAGTSAQRAELIALTQALKMAEGKKLNVY   86 (165)
T ss_dssp             CTTCSEEEEEEEEEEEETTEEEEEEEEEC-----SSCE-EE--EE--EE--CTTCCHHHHHHHHHHHHHHHTBTSEEEEE
T ss_pred             CCCCCEEEEEEcccCCCCCceEEEEEEEE-----CCEE-EE--Ee--cC--CCCCcHHHHHHHHHHHHHHHccCceEEEE
Confidence            344579999999985      35554432     3321 11  11  11  12468899999999999986    79999


Q ss_pred             eccHHHHHHHhcCccccceecchhchHHHH-Hh--ccCCcceEEeCCCCC
Q psy5357          97 IDNQCVIHWLTGNKVFTTFVNNRVKALKEI-KA--SVFPIVYKYIPTDSN  143 (181)
Q Consensus        97 tDS~i~l~~i~~~~~~~~fV~nRv~~i~~I-~~--~~~~~~~~hV~t~~N  143 (181)
                      |||+.++.-|... .-+..|.|+-- +++| .+  ....+.|.||++-.+
T Consensus        87 tDS~~vi~~iw~~-~~g~~v~n~dl-~~~l~~~l~~~~~v~~~wVkgH~g  134 (165)
T 3p1g_A           87 TDSRYAFATAHVH-SEGREIKNKNE-ILALLKALFLPKRLSIIHCPGHQK  134 (165)
T ss_dssp             ECCHHHHHHHHSC-CCSCCCSSHHH-HHHHHHHTTSBSEEEEEECCSSCC
T ss_pred             EchHHHHhhhhcc-cCCCcccCHHH-HHHHHHHHhcCCceEEEEecCCCC
Confidence            9999888755322 22344666421 2244 22  235689999998763

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

Probab=97.80  E-value=0.00014  Score=57.16  Aligned_cols=108  Identities=12%  Similarity=0.036  Sum_probs=56.0

Q ss_pred             CceeeEEEeccCccc---------ceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc------c
Q psy5357          28 VRYEPHAFSDACSYS---------YASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN------K   92 (181)
Q Consensus        28 ~~~~L~~F~DAS~~a---------ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l------~   92 (181)
                      .+.|+.+|+|+|-.+         .|..+|++......  +..--..    .|....|=-+.|+.|+..+.+.      .
T Consensus         4 ~~~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~--~~~~~~~----~~tnn~te~~Aei~Al~~al~~al~~~~~   77 (165)
T 2lsn_A            4 GQYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEY--QVLNQWS----IPLGNHTAQMAEIAAVEFACKKALKIPGP   77 (165)
T ss_dssp             CCCSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSC--CEEEEEE----EEESSCCHHHHHHHHHHHHHHHHHHSSSC
T ss_pred             CCceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCcc--EEecccc----CCchHHHHHHHHHHHHHHHHHHHhcCCCe
Confidence            467899999999432         33444555322211  1111111    1122233334444444443332      6


Q ss_pred             ceeeeccHHHHHHHh--------cC--ccccceecchhchHHHHHh---ccCCcceEEeCCCC
Q psy5357          93 CYLWIDNQCVIHWLT--------GN--KVFTTFVNNRVKALKEIKA---SVFPIVYKYIPTDS  142 (181)
Q Consensus        93 ~~~~tDS~i~l~~i~--------~~--~~~~~fV~nRv~~i~~I~~---~~~~~~~~hV~t~~  142 (181)
                      +.++|||+-++.-|.        +.  +.-+..|.|+=- +++|.+   ....+.|.||++-.
T Consensus        78 v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL-~~~l~~~~~~~~~v~~~~VkgH~  139 (165)
T 2lsn_A           78 VLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISK-WKSIAECLSMKPDITIQHEKGHQ  139 (165)
T ss_dssp             EEEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHH-HHHHHHHHHHCTTCEEEECCSSS
T ss_pred             EEEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHH-HHHHHHHHhCCCCEEEEEEeCCC
Confidence            999999999885443        32  222345666521 123333   23468999999753

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

Probab=97.80  E-value=4.4e-05  Score=58.38  Aligned_cols=102  Identities=20%  Similarity=0.190  Sum_probs=62.1

Q ss_pred             eeeEEEeccCccc-------ceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-------ccee
Q psy5357          30 YEPHAFSDACSYS-------YASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-------KCYL   95 (181)
Q Consensus        30 ~~L~~F~DAS~~a-------ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-------~~~~   95 (181)
                      -.+.+|+|||..+       .|+.+|++.  .++. ..    ++ ++..  ..|--+.||.|+..|.++       .+.+
T Consensus         6 ~~~~iytDGs~~~n~~~~~~aG~Gvv~~~--~~~~-~~----~~-~l~~--~~tn~~aEl~A~~~aL~~~~~~~~~~v~i   75 (154)
T 2qkb_A            6 DFVVVYTDGCCSSNGRRRPRAGIGVYWGP--GHPL-NV----GI-RLPG--RQTNQRAEIHAACKAIEQAKTQNINKLVL   75 (154)
T ss_dssp             TEEEEEEEEEEETTTSSSCEEEEEEECST--TCTT-CE----EE-ECCS--SCCHHHHHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CeEEEEEccCcCCCCCCCCcEEEEEEEEC--CCce-eE----Ee-ecCC--CCchHHHHHHHHHHHHHHHHhCCCceEEE
Confidence            3688999998642       344444441  1221 11    11 1111  468899999999998875       7899


Q ss_pred             eeccHHHHHHHhcC------cccc----ceecchhchHHHHHhcc--CCcceEEeCCCC
Q psy5357          96 WIDNQCVIHWLTGN------KVFT----TFVNNRVKALKEIKASV--FPIVYKYIPTDS  142 (181)
Q Consensus        96 ~tDS~i~l~~i~~~------~~~~----~fV~nRv~~i~~I~~~~--~~~~~~hV~t~~  142 (181)
                      +|||+.++.-|.+-      +.|+    ..|.|+- -+++|.++.  ..+.|.|||+-.
T Consensus        76 ~tDS~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~-l~~~i~~l~~~~~v~~~~V~~H~  133 (154)
T 2qkb_A           76 YTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKE-DFVALERLTQGMDIQWMHVPGHS  133 (154)
T ss_dssp             EESCHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHH-HHHHHHHHHTTCEEEEEECCTTS
T ss_pred             EECcHHHHhhhhhhHHHHHhccccccCCCccccHH-HHHHHHHHHcCCceEEEEccCCC
Confidence            99999998776652      1222    2355431 122554433  348899999753

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

Probab=97.79  E-value=8.6e-05  Score=57.28  Aligned_cols=108  Identities=20%  Similarity=0.229  Sum_probs=63.9

Q ss_pred             eeEEEeccCccc----ceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-----cceeeeccHH
Q psy5357          31 EPHAFSDACSYS----YASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-----KCYLWIDNQC  101 (181)
Q Consensus        31 ~L~~F~DAS~~a----ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-----~~~~~tDS~i  101 (181)
                      .+.+|+|||..+    .|+.++++.   +|.  ...+ +. .+   ...|--+.||.|+..|.++     .+.++|||+.
T Consensus         6 ~i~iytDGs~~~n~g~~G~G~v~~~---~~~--~~~~-~~-~~---~~~tn~~aEl~A~~~AL~~~~~~~~v~I~tDS~~   75 (158)
T 2e4l_A            6 LIHIFTDGSCLGNPGPGGYGIVMNY---KGH--TKEM-SD-GF---SLTTNNRMELLAPIVALEALKEPCKIILTSDSQY   75 (158)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEE---TTE--EEEE-EE-EE---EEECHHHHHHHHHHHHHHTCSSCCEEEEEECCHH
T ss_pred             eEEEEEcccccCCCCcEEEEEEEEE---CCE--EEEE-ec-Cc---CCCccHHHHHHHHHHHHHHhccCCeEEEEeCHHH
Confidence            688999998752    233334442   231  1111 11 11   2357789999999999986     6899999999


Q ss_pred             HHHHHhcC------ccc----cceecchhchHHHHHhcc--CCcceEEeCCC-----CCCCcccC
Q psy5357         102 VIHWLTGN------KVF----TTFVNNRVKALKEIKASV--FPIVYKYIPTD-----SNPADLAC  149 (181)
Q Consensus       102 ~l~~i~~~------~~~----~~fV~nRv~~i~~I~~~~--~~~~~~hV~t~-----~NPAD~~S  149 (181)
                      ++.-|.+-      +.|    ...|.|+-- +++|.++.  ..+.|.|||+-     ..-||.+.
T Consensus        76 vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l-~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA  139 (158)
T 2e4l_A           76 MRQGIMTWIHGWKKKGWMTSNRTPVKNVDL-WKRLDKAAQLHQIDWRWVKGHAGHAENERCDQLA  139 (158)
T ss_dssp             HHHHHHTHHHHHHHTTTBCTTSSBCTTHHH-HHHHHHHHTTSEEEEEECCTTCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccccccCCCcccCHHH-HHHHHHHHccCcEEEEEccCCCCchhHHHHHHHH
Confidence            99866541      122    234555411 12444333  35889999964     23456543

>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=97.75  E-value=8.9e-05  Score=56.95  Aligned_cols=100  Identities=19%  Similarity=0.250  Sum_probs=61.9

Q ss_pred             eeEEEeccCccc----ceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-----cceeeeccHH
Q psy5357          31 EPHAFSDACSYS----YASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-----KCYLWIDNQC  101 (181)
Q Consensus        31 ~L~~F~DAS~~a----ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-----~~~~~tDS~i  101 (181)
                      .+.+|+|||..+    .|+.++++.   ++. . ..+ +. .+   ...|--+.||.|+..|.++     .+.++|||+.
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~---~~~-~-~~~-~~-~~---~~~tn~~aEl~A~~~aL~~~~~~~~v~I~tDS~~   73 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRY---RGR-E-KTF-SA-GY---TRTTNNRMELMAAIVALEALKEHAEVILSTDSQY   73 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEE---TTE-E-EEE-EE-EE---EEECHHHHHHHHHHHHHHTCCSCCEEEEEECCHH
T ss_pred             eEEEEEccccCCCCCceEEEEEEEE---CCe-E-EEE-ec-CC---CCCcHHHHHHHHHHHHHHHhCcCCcEEEEeCHHH
Confidence            478999998752    334444443   221 1 111 11 11   2357789999999999986     6999999999


Q ss_pred             HHHHHhcC------ccc----cceecchhchHHHHHhcc--CCcceEEeCCC
Q psy5357         102 VIHWLTGN------KVF----TTFVNNRVKALKEIKASV--FPIVYKYIPTD  141 (181)
Q Consensus       102 ~l~~i~~~------~~~----~~fV~nRv~~i~~I~~~~--~~~~~~hV~t~  141 (181)
                      ++.-|.+-      +.|    ...|.|+-- +++|.++.  ..+.|.|||+-
T Consensus        74 vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l-~~~i~~l~~~~~v~~~wV~gH  124 (155)
T 1jl1_A           74 VRQGITQWIHNWKKRGWKTADKKPVKNVDL-WQRLDAALGQHQIKWEWVKGH  124 (155)
T ss_dssp             HHHHHHTTHHHHHHTTTBCTTSCBCTTHHH-HHHHHHHTTTCEEEEEECCSS
T ss_pred             HHHHHHHHHHHHhhcccccccCCccCCHHH-HHHHHHHHccCceEEEEcCCC
Confidence            99877752      122    235665311 22555544  35889999964

>4htu_A Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine, W-C base PAIR, wobble base PAIR, D helix; HET: DNA UCL; 1.49A {Bacillus halodurans} PDB: 3d0p_A* 4hue_A* 4huf_A* 4hug_A* 1zbf_A 1zbi_A 2g8u_A 3uld_A* 3ey1_A* 3twh_A* 2g8f_A 2g8v_A 2g8w_A 2g8i_A 2g8h_A 2g8k_A 3i8d_A* 2r7y_A* 1zbl_A

Probab=97.70  E-value=6.1e-06  Score=63.26  Aligned_cols=77  Identities=17%  Similarity=0.170  Sum_probs=51.2

Q ss_pred             eeEEEeccCc------ccceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc------cceeeec
Q psy5357          31 EPHAFSDACS------YSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN------KCYLWID   98 (181)
Q Consensus        31 ~L~~F~DAS~------~aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l------~~~~~tD   98 (181)
                      ...+|+|||.      .|||+|++     .+|.. ..+ ..     ++...|--|+||+|++.|.++      .+.++||
T Consensus         5 ~~~iytDGac~GNPGp~G~ggV~~-----~~g~~-~~~-~g-----~~~~tTNN~aEl~A~i~aL~~l~~~~~~v~i~tD   72 (134)
T 4htu_A            5 WESLSVDVGSQGNPGIVEYKGVDT-----KTGEV-LFE-RE-----PIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSN   72 (134)
T ss_dssp             SSSEEEEEEEETTTEEEEEEEEET-----TTCCE-EEE-EE-----EEEEECHHHHHHHHHHHHHHHHHHTTCCCCEEES
T ss_pred             ceEEEEeeccCCCCCCeEEEEEEE-----ECCEE-EEE-ec-----CCCCCchHHHHHHHHHHHHHHHHhCCCCEEEEcc
Confidence            4568999886      45766542     24422 111 11     123468889999999998875      6899999


Q ss_pred             cHHHHHHHhcC---ccccceecch
Q psy5357          99 NQCVIHWLTGN---KVFTTFVNNR  119 (181)
Q Consensus        99 S~i~l~~i~~~---~~~~~fV~nR  119 (181)
                      |+.++.||++.   ...+.-|.|+
T Consensus        73 SqyVi~wi~~~~~kt~~~~~vkN~   96 (134)
T 4htu_A           73 SQTAIKWVKDKKAKSTLVRNEETA   96 (134)
T ss_dssp             CHHHHHHHHHTCCCCCCCCSSTTH
T ss_pred             hHHHHHHHHcCCcccCCCCCccCH
Confidence            99999999975   2223445554

>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=97.63  E-value=3.7e-05  Score=59.21  Aligned_cols=97  Identities=14%  Similarity=0.154  Sum_probs=59.2

Q ss_pred             eeeEEEeccCc------ccceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc---cceeeeccH
Q psy5357          30 YEPHAFSDACS------YSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN---KCYLWIDNQ  100 (181)
Q Consensus        30 ~~L~~F~DAS~------~aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l---~~~~~tDS~  100 (181)
                      -.+.+|+|||.      .+||++++      ++.. ..+        ++...|--|.||.|+..|.+.   .+.++|||+
T Consensus        11 ~~~~iytDGs~~~n~g~~g~G~v~~------~~~~-~~~--------~~~~~Tnn~aEl~A~i~AL~~~~~~v~i~tDS~   75 (150)
T 3qio_A           11 GAETFYVDGAANRETKLGKAGYVTN------RGRQ-KVV--------TLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQ   75 (150)
T ss_dssp             TCEEEEEEEEECTTTCCEEEEEEET------TSCE-EEE--------EESSCCHHHHHHHHHHHHHHHSCSEEEEEESCH
T ss_pred             CCEEEEEccCCCCCCCCeEEEEEEE------cCCE-EEE--------eCCCCCHHHHHHHHHHHHHHhCCCcEEEEeCcH
Confidence            36899999995      34444322      2221 111        134578999999999999986   799999999


Q ss_pred             HHHHHHhcC------cccc----ceecchhchHHHHHh---ccCCcceEEeCCCC
Q psy5357         101 CVIHWLTGN------KVFT----TFVNNRVKALKEIKA---SVFPIVYKYIPTDS  142 (181)
Q Consensus       101 i~l~~i~~~------~~~~----~fV~nRv~~i~~I~~---~~~~~~~~hV~t~~  142 (181)
                      .++.-|.+-      +.|+    ..|.|+-- +++|.+   ....+.|.||++..
T Consensus        76 ~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l-~~~l~~~l~~~~~v~~~wV~gH~  129 (150)
T 3qio_A           76 YALGIITQWIHNWKKRGWKTADKKPVKNVDL-VNQIIEQLIKKEKVYLAWVPAHK  129 (150)
T ss_dssp             HHHHHHHHHHHHHCC------------CHHH-HHHHHHHHTTCSEEEEEECCTTS
T ss_pred             HHHHHHHHHHHHHhhcCcCcCcCcccccHHH-HHHHHHHHhhcCceEEEEccCcC
Confidence            998766542      2222    24555421 223332   23468999999874

>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...

Probab=97.51  E-value=0.00012  Score=66.93  Aligned_cols=100  Identities=13%  Similarity=0.238  Sum_probs=63.7

Q ss_pred             eeEEEeccCcc------cceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc---cceeeeccHH
Q psy5357          31 EPHAFSDACSY------SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN---KCYLWIDNQC  101 (181)
Q Consensus        31 ~L~~F~DAS~~------aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l---~~~~~tDS~i  101 (181)
                      .+.+|+|||..      |||++++      +|.. ..+        +....|--+.||.|++.|.++   .+.++|||+.
T Consensus       439 ~~~iytDGs~~~n~g~~g~g~v~~------~~~~-~~~--------~~~~~TNn~aEl~Ai~~aL~~~~~~v~I~tDS~~  503 (557)
T 2zd1_A          439 AETFYVDGAANRETKLGKAGYVTN------KGRQ-KVV--------PLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQY  503 (557)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEET------TSCE-EEE--------EECSCCHHHHHHHHHHHHHHHSCSEEEEEECCHH
T ss_pred             CEEEEEccCCCCCCCceEEEEEEE------CCcE-EEe--------cCCCCCHHHHHHHHHHHHHHhCCCcEEEEeChHH
Confidence            48899999852      3444432      2321 111        123568889999999999987   8999999999


Q ss_pred             HHHHHhcC-cc-ccceecchhchHHHHHhccCCcceEEeCCC-----CCCCcccC
Q psy5357         102 VIHWLTGN-KV-FTTFVNNRVKALKEIKASVFPIVYKYIPTD-----SNPADLAC  149 (181)
Q Consensus       102 ~l~~i~~~-~~-~~~fV~nRv~~i~~I~~~~~~~~~~hV~t~-----~NPAD~~S  149 (181)
                      ++..|.+. .. .... .+++  ++++.+. ..+.|.||++-     ..-||.+.
T Consensus       504 vi~~i~~~~~~~~~~l-~~~~--~~~l~~~-~~v~~~wV~~H~g~~~Ne~AD~LA  554 (557)
T 2zd1_A          504 ALGIIQAQPDKSESEL-VNQI--IEQLIKK-EKVYLAWVPAHKGIGGNEQVDKLV  554 (557)
T ss_dssp             HHHHHTTCCSEESSHH-HHHH--HHHHHHC-SEEEEEECCSSSCCTTCCGGGGCC
T ss_pred             HHHHHhcCCccCCHHH-HHHH--HHHHhcC-CCEEEEEcCCCCCChhHHHHHHHH
Confidence            99999875 11 1111 1221  1133333 46899999984     34466543

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

Probab=97.51  E-value=0.0002  Score=53.99  Aligned_cols=100  Identities=13%  Similarity=0.142  Sum_probs=59.5

Q ss_pred             eeEEEeccCccc----ceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-----cceeeeccHH
Q psy5357          31 EPHAFSDACSYS----YASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-----KCYLWIDNQC  101 (181)
Q Consensus        31 ~L~~F~DAS~~a----ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-----~~~~~tDS~i  101 (181)
                      ++.+|+|||-.+    .|+.++++.   ++ . ..-+ +.    +....|--+.||.|+..|.+.     .+.++|||+.
T Consensus         4 ~i~iytDGs~~~n~g~~g~G~v~~~---~~-~-~~~~-~~----~~~~~Tnn~aEl~A~~~AL~~~~~~~~v~I~tDS~~   73 (146)
T 3h08_A            4 TITIYTDGAASGNPGKGGWGALLMY---GS-S-RKEI-SG----YDPATTNNRMELMAAIKGLEALKEPARVQLYSDSAY   73 (146)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEEE---TT-E-EEEE-EE----EEEEECHHHHHHHHHHHHHHTCSSCCEEEEEESCHH
T ss_pred             eEEEEEecCCCCCCCceEEEEEEEE---CC-e-eEEe-ec----CCCCCcHHHHHHHHHHHHHHhcCccCcEEEEeChHH
Confidence            689999999533    344444443   22 1 1111 11    112457889999999999987     6999999999


Q ss_pred             HHHHHhcC-------cccc----ceecchhchHHHHHhcc--CCcceEEeCCC
Q psy5357         102 VIHWLTGN-------KVFT----TFVNNRVKALKEIKASV--FPIVYKYIPTD  141 (181)
Q Consensus       102 ~l~~i~~~-------~~~~----~fV~nRv~~i~~I~~~~--~~~~~~hV~t~  141 (181)
                      ++.-|.+.       +.|+    .-|.|+-- +++|.++.  ..+.|.|||+-
T Consensus        74 vi~~i~~~w~~~W~~~~w~~~~~~~v~n~~l-~~~~~~~~~~~~v~~~~V~gH  125 (146)
T 3h08_A           74 LVNAMNEGWLKRWVKNGWKTAAKKPVENIDL-WQEILKLTTLHRVTFHKVKGH  125 (146)
T ss_dssp             HHHHHHSSHHHHHHHTTCC----CCCTTHHH-HHHHHHHHHHSEEEEEECCC-
T ss_pred             HHHHHHHHHHHHHHHCCCccCCCCCcCCHHH-HHHHHHHHhhCceEEEEcCCc
Confidence            99866652       2222    23444321 11333322  25889999854

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

Probab=97.27  E-value=0.00023  Score=55.45  Aligned_cols=99  Identities=16%  Similarity=0.232  Sum_probs=59.9

Q ss_pred             eeEEEeccCccc----ceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-----cceeeeccHH
Q psy5357          31 EPHAFSDACSYS----YASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-----KCYLWIDNQC  101 (181)
Q Consensus        31 ~L~~F~DAS~~a----ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-----~~~~~tDS~i  101 (181)
                      .+.+|+|||..+    .|+.++++.  .++.  .. + +..    ....|--+.||.|++.|.++     .+.++|||+.
T Consensus         8 ~i~iytDGs~~~n~g~~G~G~v~~~--~~~~--~~-~-~~~----~~~~Tnn~aEl~Ai~~AL~~~~~~~~v~I~tDS~~   77 (166)
T 1ril_A            8 RVALFTDGACLGNPGPGGWAALLRF--HAHE--KL-L-SGG----EACTTNNRMELKAAIEGLKALKEPCEVDLYTDSHY   77 (166)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECB--TTBC--CE-E-CCE----EEEECHHHHHHHHHHHHHHSCCSCCEEEEECCCHH
T ss_pred             cEEEEECccccCCCCCEEEEEEEEE--CCEE--EE-E-ecC----CCCCcHHHHHHHHHHHHHHHhccCCeEEEEeChHH
Confidence            578999998752    233344432  2221  11 1 111    12357889999999999986     7999999999


Q ss_pred             HHHHHhcC-------cccc----ceecchhchHHHHHhcc--CCcceEEeCC
Q psy5357         102 VIHWLTGN-------KVFT----TFVNNRVKALKEIKASV--FPIVYKYIPT  140 (181)
Q Consensus       102 ~l~~i~~~-------~~~~----~fV~nRv~~i~~I~~~~--~~~~~~hV~t  140 (181)
                      ++.-|.+.       +.|+    ..|.|+- -+++|.++.  ..+.|.|||+
T Consensus        78 vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~-l~~~i~~l~~~~~v~~~wV~g  128 (166)
T 1ril_A           78 LKKAFTEGWLEGWRKRGWRTAEGKPVKNRD-LWEALLLAMAPHRVRFHFVKG  128 (166)
T ss_dssp             HHHHHHSSHHHHHHHTTSBCTTSSBCTTHH-HHHHHHHHHTTSEEECCCCCG
T ss_pred             HHHHHhhhHHHHHHhcccccccCCccCcHH-HHHHHHHHHhcCeEEEEEeeC
Confidence            99866651       1232    3566631 122444433  2588899984

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

Probab=97.15  E-value=0.00075  Score=51.72  Aligned_cols=68  Identities=19%  Similarity=0.217  Sum_probs=47.8

Q ss_pred             eeeEEEeccCcc------cceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc------cceeee
Q psy5357          30 YEPHAFSDACSY------SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN------KCYLWI   97 (181)
Q Consensus        30 ~~L~~F~DAS~~------aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l------~~~~~t   97 (181)
                      ..+.+|+|||..      +||++++     .+|..  .. .+ .   ++...|--|+||.|++.|.++      .+.++|
T Consensus        10 ~~~~iy~DGa~~gNpG~~G~G~vl~-----~~g~~--~~-~~-~---~~~~~TNN~aEl~A~i~aL~~~~~~~~~v~i~t   77 (142)
T 1zbf_A           10 IWESLSVDVGSQGNPGIVEYKGVDT-----KTGEV--LF-ER-E---PIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYS   77 (142)
T ss_dssp             CSSSEEEEEEECSSSEEEEEEEEET-----TTCCE--EE-EC-C---CEEEECHHHHHHHHHHHHHHHHHHTTCCCCEEE
T ss_pred             CeEEEEEeeccCCCCCCeEEEEEEE-----eCCEE--EE-Ee-c---ccCCcCcHHHHHHHHHHHHHHHHhCCCeEEEEE
Confidence            356789999864      4555443     24422  11 11 1   222468889999999998875      689999


Q ss_pred             ccHHHHHHHhcC
Q psy5357          98 DNQCVIHWLTGN  109 (181)
Q Consensus        98 DS~i~l~~i~~~  109 (181)
                      ||+.++.|+++.
T Consensus        78 DS~~vi~w~~~~   89 (142)
T 1zbf_A           78 NSQTAIKWVKDK   89 (142)
T ss_dssp             SCHHHHHHHHHT
T ss_pred             ehHHHHHHHHcC
Confidence            999999999987

>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B

Probab=96.63  E-value=0.0026  Score=57.88  Aligned_cols=64  Identities=20%  Similarity=0.279  Sum_probs=45.0

Q ss_pred             CCCcchhhHhHHHHHhhc---cceeeeccHHHHHHHhcCc--cccceecchhchHHHHHhccCCcceEEeCCC
Q psy5357          74 KPTLPRLELLGALIAYRN---KCYLWIDNQCVIHWLTGNK--VFTTFVNNRVKALKEIKASVFPIVYKYIPTD  141 (181)
Q Consensus        74 ~~tIPrlEL~a~~l~~~l---~~~~~tDS~i~l~~i~~~~--~~~~fV~nRv~~i~~I~~~~~~~~~~hV~t~  141 (181)
                      ..|--+.||.|++.|.+.   .+.++|||+.++..|.+-+  ..+... +++.  +.+.+ ...+.|.||++-
T Consensus       470 ~~TNn~aEl~A~i~aL~~~~~~v~I~tDS~~v~~~i~~~~~~~~~~l~-~~~~--~~~~~-~~~v~~~wV~~H  538 (555)
T 1mu2_A          470 QTTNQQAELEAFAMALTDSGPKVNIIVDSQYVMGIVASQPTESESKIV-NQII--EEMIK-KEAIYVAWVPAH  538 (555)
T ss_dssp             SCCHHHHHHHHHHHHHHTSCSEEEEEESCHHHHHHHHTCCSEESCHHH-HHHH--HHHHH-CSEEEEEECCSS
T ss_pred             CCCHHHHHHHHHHHHHHcCCCeEEEEEehHHHHHHHhcccccccHHHH-HHHH--HHhcc-CCcEEEEEEECC
Confidence            567889999999999987   8999999999999998631  111111 1111  13333 346899999984

>2zd1_B P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} SCOP: e.8.1.2 PDB: 2ykm_B* 2ykn_B* 2ze2_B* 3bgr_B* 3ig1_B* 3irx_B* 3is9_B* 3qo9_B* 3v4i_B* 3v6d_B* 3v81_B* 3klf_B* 3kk1_B* 3kjv_B* 3kk2_B* 3kk3_B* 2be2_B* 1n5y_B* 1bqm_B* 1n6q_B* ...

Probab=83.51  E-value=1.4  Score=38.74  Aligned_cols=71  Identities=8%  Similarity=-0.055  Sum_probs=47.4

Q ss_pred             ceeeEEEeccCcc-cceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhH-HHHHhhc-----------ccee
Q psy5357          29 RYEPHAFSDACSY-SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLG-ALIAYRN-----------KCYL   95 (181)
Q Consensus        29 ~~~L~~F~DAS~~-aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a-~~l~~~l-----------~~~~   95 (181)
                      .-.+.+.||||.. ++|+|++-    ++|.    .+++++ .++.++.++.-+|++| ++.+.+-           .++.
T Consensus       322 ~~~~~l~~das~~g~~g~vl~q----~~~~----~~~s~~-~~~~~~y~~~~~e~la~vv~al~~~r~yl~G~~~~~~i~  392 (428)
T 2zd1_B          322 SKDLIAEIQKQGQGQWTYQIYQ----EPFK----NLKTGK-YARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLP  392 (428)
T ss_dssp             TSCCEEEEEEEETTEEEEEEES----STTC----EEEEEE-EECCSSCTTCHHHHHHHHHHHHHHHHHHHHSSCCEEEES
T ss_pred             CCCEEEEEecCCCCcEEEEEec----CCCc----eeeecc-cchhhhcccchHHHHHHHHHHhhccceEEECCCCcEECC
Confidence            4578899999995 56777542    2332    223443 4466778888999998 7777652           3578


Q ss_pred             eeccHHHHHHHhc
Q psy5357          96 WIDNQCVIHWLTG  108 (181)
Q Consensus        96 ~tDS~i~l~~i~~  108 (181)
                      +||.+..-+|...
T Consensus       393 ~td~~~~~~~~~~  405 (428)
T 2zd1_B          393 IQKETWETWWTEY  405 (428)
T ss_dssp             SCHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHhc
Confidence            9999976666543

---

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	181
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	98.11
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	98.11
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	97.58
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	97.51
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	97.31

>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=98.11  E-value=5.6e-06  Score=59.71  Aligned_cols=95  Identities=17%  Similarity=0.252  Sum_probs=60.2

Q ss_pred             eEEEeccCcc---cceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc---cceeeeccHHHHHH
Q psy5357          32 PHAFSDACSY---SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN---KCYLWIDNQCVIHW  105 (181)
Q Consensus        32 L~~F~DAS~~---aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l---~~~~~tDS~i~l~~  105 (181)
                      ..+|+|+|..   +-|++.|+.   .+|....         .++...|-.+.||.|++.+.+.   .+.++|||+.++.+
T Consensus         8 ~t~YTDGS~~~n~~~~~~g~~~---~~~~~~~---------~~~~~~tnn~AEl~Ai~~al~~~~~~i~I~tDS~~v~~~   75 (126)
T d1mu2a1           8 ETFYTDGSCNRQSKEGKAGYVT---DRGKDKV---------KKLEQTTNQQAELEAFAMALTDSGPKVNIIVDSQYVMGI   75 (126)
T ss_dssp             EEEEEEEEECTTTCCEEEEEEE---TTSCEEE---------EEESSCCHHHHHHHHHHHHHHTSCSEEEEEESCHHHHHH
T ss_pred             cEEEEcCCCCCCCCcEEEEEEe---cCCCEEE---------EecCCCcchHHHHHHHHHHhccCCcceEEEechHHHHHH
Confidence            4799999943   222332322   3342221         1233468889999999999887   89999999999999


Q ss_pred             HhcC-ccccc-eecchhchHHHHHhccCCcceEEeCCCC
Q psy5357         106 LTGN-KVFTT-FVNNRVKALKEIKASVFPIVYKYIPTDS  142 (181)
Q Consensus       106 i~~~-~~~~~-fV~nRv~~i~~I~~~~~~~~~~hV~t~~  142 (181)
                      +.+. +.+.. ....++.   +..+. ..+.+.|||+-.
T Consensus        76 ~~~~~~~~~~~~~~~~~~---~~~~~-~~v~~~wV~gH~  110 (126)
T d1mu2a1          76 VASQPTESESKIVNQIIE---EMIKK-EAIYVAWVPAHK  110 (126)
T ss_dssp             HHTCCSEESCHHHHHHHH---HHHHC-SEEEEEECCSSS
T ss_pred             HhcCCccccchHHHHHHH---Hhhhc-ceeEEEEEeCCC
Confidence            9986 33322 1112222   33332 368899999754

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

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

Probab=98.11  E-value=1e-06  Score=63.29  Aligned_cols=92  Identities=12%  Similarity=0.226  Sum_probs=58.4

Q ss_pred             EEEeccCccc---ceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc---cceeeeccHHHHHHH
Q psy5357          33 HAFSDACSYS---YASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN---KCYLWIDNQCVIHWL  106 (181)
Q Consensus        33 ~~F~DAS~~a---ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l---~~~~~tDS~i~l~~i  106 (181)
                      .+|+|+|...   -|++.|+.   .++....         .++...|--|+||.|++.|.+.   .+.+||||+.++.-+
T Consensus        10 t~ytDGs~~~n~~~g~~g~~~---~~~~~~~---------~~~~~~TNn~aEl~Avi~aL~~~~~~v~I~TDS~yvi~~i   77 (110)
T d1s1ta1          10 TFYVDGAANRETKLGKAGYVT---NRGRQKV---------VTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGII   77 (110)
T ss_dssp             EEEEEEEEETTTTEEEEEEEE---TTSCEEE---------EEESSCCHHHHHHHHHHHHHHHSCSEEEEEECCHHHHHHH
T ss_pred             EEEEeCCCCCCCCCcEEEEEE---ecCCeEE---------EecccCcHHHHHHHHHHHHHHhCCCeEEEEEehHHHHHHH
Confidence            5899999432   23333332   2332221         1233468889999999999876   899999999999999


Q ss_pred             hcC-ccccceecchhc-hHHHHHhccCCcceEEeCC
Q psy5357         107 TGN-KVFTTFVNNRVK-ALKEIKASVFPIVYKYIPT  140 (181)
Q Consensus       107 ~~~-~~~~~fV~nRv~-~i~~I~~~~~~~~~~hV~t  140 (181)
                      .+. ..+   -.+-++ .++++.+ ...+.+.|||+
T Consensus        78 ~~~~~~~---~~~l~~~il~~l~~-~~~v~i~WVpg  109 (110)
T d1s1ta1          78 QAQPDQS---ESELVNQIIEQLIK-KEKVYLAWVPA  109 (110)
T ss_dssp             HHCCSEE---SCHHHHHHHHHHHH-CSEEEEEECCS
T ss_pred             hcCcccc---chHHHHHHHHHHhc-CCceEEEEeCC
Confidence            865 332   233333 1223333 24578899986

>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=97.58  E-value=0.00012  Score=53.09  Aligned_cols=98  Identities=18%  Similarity=0.246  Sum_probs=58.8

Q ss_pred             eeEEEeccCc------ccceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-----cceeeecc
Q psy5357          31 EPHAFSDACS------YSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-----KCYLWIDN   99 (181)
Q Consensus        31 ~L~~F~DAS~------~aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-----~~~~~tDS   99 (181)
                      ++.+|+|+|.      .|||++++-     +|.. ..+  +..    ....|=-+.|++|++.|.+.     .+.++|||
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~-----~~~~-~~~--~~~----~~~~tnn~aE~~Ai~~Al~~~~~~~~i~i~tds   69 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRY-----RGRE-KTF--SAG----YTRTTNNRMELMAAIVALEALKEHAEVILSTDS   69 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEE-----TTEE-EEE--EEE----EEEECHHHHHHHHHHHHHHTCCSCCEEEEEECC
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEE-----CCeE-EEe--ccc----cCcccHHHHHHhhhhhhhhhhcccceEEEeecc
Confidence            5789999984      356665442     2221 111  111    12235668999999999875     67889999


Q ss_pred             HHHHHHHhcC----------ccccceecchhchHHHHHhccC--CcceEEeCCC
Q psy5357         100 QCVIHWLTGN----------KVFTTFVNNRVKALKEIKASVF--PIVYKYIPTD  141 (181)
Q Consensus       100 ~i~l~~i~~~----------~~~~~fV~nRv~~i~~I~~~~~--~~~~~hV~t~  141 (181)
                      ..++..+...          ......+.|.-. +++|.+...  .+.|.|||+-
T Consensus        70 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~n~~~-~~~i~~~~~~~~V~~~wV~gH  122 (152)
T d1jl1a_          70 QYVRQGITQWIHNWKKRGWKTADKKPVKNVDL-WQRLDAALGQHQIKWEWVKGH  122 (152)
T ss_dssp             HHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHH-HHHHHHHTTTCEEEEEECCSS
T ss_pred             eeeEEcccchhhHhHhccchhcccCeeecHHH-HHHHHHHhhcceeEEEEeccc
Confidence            9988666533          112234444311 225555443  5889999974

>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=97.51  E-value=3.9e-05  Score=56.16  Aligned_cols=95  Identities=15%  Similarity=0.231  Sum_probs=56.4

Q ss_pred             eeEEEeccCcc------cceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-----cceeeecc
Q psy5357          31 EPHAFSDACSY------SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-----KCYLWIDN   99 (181)
Q Consensus        31 ~L~~F~DAS~~------aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-----~~~~~tDS   99 (181)
                      ++++|+|+|..      |||++++     .+|..  ..+...     ....|--|.||.|++.|...     .+.++|||
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~-----~~~~~--~~~~~~-----~~~~Tnn~aEl~Ai~~AL~~~~~~~~i~i~tds   70 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLR-----FHAHE--KLLSGG-----EACTTNNRMELKAAIEGLKALKEPCEVDLYTDS   70 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEEC-----BTTBC--CEECCE-----EEEECHHHHHHHHHHHHHHSCCSCCEEEEECCC
T ss_pred             EEEEEEccCCCCCCCccEEEEEEE-----ECCcc--eEEecc-----cccccHHHHHHHHHHHHhhhccCCceEEEecch
Confidence            47899998843      4665432     12211  111111     11247789999999999876     67899999


Q ss_pred             HHHHHHHhcC-----------ccccceecch--hchHHHHHhcc--CCcceEEeCC
Q psy5357         100 QCVIHWLTGN-----------KVFTTFVNNR--VKALKEIKASV--FPIVYKYIPT  140 (181)
Q Consensus       100 ~i~l~~i~~~-----------~~~~~fV~nR--v~~i~~I~~~~--~~~~~~hV~t  140 (181)
                      ..++.-+...           ..-...|.|+  ++   +|.++.  ..+.|.|||+
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~---~l~~~~~~~~v~~~wVkg  123 (147)
T d1rila_          71 HYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWE---ALLLAMAPHRVRFHFVKG  123 (147)
T ss_dssp             HHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHH---HHHHHHTTSEEECCCCCG
T ss_pred             hhhhccccccchhhhhhccccccccccchhHHHHH---HHHHHhhhcccceEEccC
Confidence            9988655432           1122334453  22   443333  3478899985

>d1zbfa1 c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: BH0863-like Ribonuclease H
species: Bacillus halodurans [TaxId: 86665]

Probab=97.31  E-value=5.9e-05  Score=55.84  Aligned_cols=64  Identities=20%  Similarity=0.269  Sum_probs=46.2

Q ss_pred             EEeccCcc------cceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc------cceeeeccHH
Q psy5357          34 AFSDACSY------SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN------KCYLWIDNQC  101 (181)
Q Consensus        34 ~F~DAS~~------aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l------~~~~~tDS~i  101 (181)
                      +|+|||..      |||+|+.     .+|..  .+. +    .|+...|=-|+||+|++.|.++      ++.+||||+.
T Consensus         7 Iy~DGa~~GNPGp~g~g~v~~-----~~~~~--~~~-s----g~~~~~TNN~aEl~A~i~aL~~~~~~~~~i~I~tDS~y   74 (132)
T d1zbfa1           7 LSVDVGSQGNPGIVEYKGVDT-----KTGEV--LFE-R----EPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQT   74 (132)
T ss_dssp             EEEEEEECSSSEEEEEEEEET-----TTCCE--EEE-C----CCEEEECHHHHHHHHHHHHHHHHHHTTCCCCEEESCHH
T ss_pred             EEEeecCCCCCchheEEEEEE-----cCCEE--EEE-E----cCcCccchHHHHHHHHHHHHHHhhcCCceEEEEeccHH
Confidence            68999876      4876422     23321  222 1    1444567889999999999875      7899999999


Q ss_pred             HHHHHhcC
Q psy5357         102 VIHWLTGN  109 (181)
Q Consensus       102 ~l~~i~~~  109 (181)
                      ++.|+++.
T Consensus        75 vi~wv~~~   82 (132)
T d1zbfa1          75 AIKWVKDK   82 (132)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHhC
Confidence            99999875