Psyllid ID: psy874

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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-
Protein Sequence
MDPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYISHDVISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYKLLVSGYFGEHL
Secondary Structure (PSIPRED)
ccccccEEEEEcccccccccccccEEEEEEEcccccccEEcccccccHHHHHHHHHHHHHHHHHHHcccccEEEEEEEEEHHHHHHccEEccHHHHHHcccccccccccccccccccccccccHHHHHHHHHHcccccccccccHHHHHHHHHcccHHHHHHHccHHHHHHHHHHHHcEEEEEcccccccc
Secondary Structure Prediction (SSPRO)
ccccccEEEEEcccccccccccccEEEEEEEccccccccccccccccccHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHcccHHHHHHcccEEEEEEEccccccccccccHHHHHHHHHHHHcHHHHHcccccccHHHHHHHHHHcccHEEHHHHHHccc
Coil and Loop (DISEMBL)
mdpdnhvvvftdgacprngkvgasagygvyfgennplnvagkVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYishdvisvgipfpsiqdenvKLKRsyndthaqkkgipfpsiqdeKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYKLLVSGYFGEHL
Flexible Loop (DISEMBL)
MDPDNHVVVFtdgacprngkVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKrsyndthaqkkvrnvssVAMRIAQKVDYISHDVISVgipfpsiqdenVKLKRSYNDthaqkkgipfpsiqdekVKLKRsyndthaqkkvrnvssvamRIAQKVDYKLLVSGYFGEHL
Low Complexity Region (SEG)
MDPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYISHDVISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYKLLVSGYFGEHL
Disordered region (IsUnstruct)
******VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHA***************************NVSSVAMRIAQKVDYISHDVISVGIPFPSIQD**********************************************VSSVAMRIAQKVDYKLLVSGYF****
Disordered Region (DISOPRED)
***DNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYISHDVISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDE****************************QKVDYKLLVSGYFGEH*
Disordered Region (DISEMBL)
MDPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYISHDVISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYKLLVSGYFGEHL
Disordered Region (DISPRO)
***DNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYISHDVISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYKLLVSGYFGEHL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYISHDVISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYKLLVSGYFGEHL
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

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	191	2.2.26 [Sep-21-2011]
Q5BK46	285	Ribonuclease H1 OS=Rattus	yes	N/A	0.324	0.217	0.532	2e-11
O70338	285	Ribonuclease H1 OS=Mus mu	yes	N/A	0.539	0.361	0.364	2e-11
O60930	286	Ribonuclease H1 OS=Homo s	yes	N/A	0.335	0.223	0.5	4e-11
Q9UST8	264	Ribonuclease H OS=Schizos	yes	N/A	0.287	0.208	0.5	3e-07
Q5SXJ3	1174	Fanconi anemia group J pr	no	N/A	0.251	0.040	0.448	2e-05
Q3YK19	1252	Fanconi anemia group J pr	no	N/A	0.314	0.047	0.343	5e-05
Q9BX63	1249	Fanconi anemia group J pr	no	N/A	0.251	0.038	0.428	6e-05
Q07762	494	Ribonuclease H OS=Crithid	N/A	N/A	0.293	0.113	0.372	0.0007

>sp|Q5BK46|RNH1_RAT Ribonuclease H1 OS=Rattus norvegicus GN=Rnaseh1 PE=2 SV=1

 Score = 68.9 bits (167), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 33/62 (53%), Positives = 41/62 (66%)

Query: 7   VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
           VVV+TDG C  NG+  A AG GVY+G  +PLNV  ++ GR TN  AEI  A  A+ QAK+
Sbjct: 139 VVVYTDGCCSSNGRKRARAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAITQAKA 198

Query: 67  AN 68
            N
Sbjct: 199 QN 200

Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
Rattus norvegicus (taxid: 10116)
EC: 3EC: .EC: 1EC: .EC: 2EC: 6EC: .EC: 4

>sp|O70338|RNH1_MOUSE Ribonuclease H1 OS=Mus musculus GN=Rnaseh1 PE=2 SV=1

 Score = 68.9 bits (167), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 43/118 (36%), Positives = 61/118 (51%), Gaps = 15/118 (12%)

Query: 7   VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
           V+V+TDG C  NG+  A AG GVY+G  +PLNV  ++ GR TN  AEI  A  A+ QAK+
Sbjct: 139 VIVYTDGCCSSNGRKRARAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIMQAKA 198

Query: 67  AN-EKVKLKRSYNDT-----------HAQKKVRNVSSVAMRIAQKVDYISHDVISVGI 112
            N  K+ L   Y D+              KK    +S    +  K D++  D ++ G+
Sbjct: 199 QNISKLVL---YTDSMFTINGITNWVQGWKKNGWRTSTGKDVINKEDFMELDELTQGM 253

Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: 4

>sp|O60930|RNH1_HUMAN Ribonuclease H1 OS=Homo sapiens GN=RNASEH1 PE=1 SV=2

 Score = 67.8 bits (164), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 32/64 (50%), Positives = 42/64 (65%)

Query: 5   NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQA 64
           + VVV+TDG C  NG+    AG GVY+G  +PLNV  ++ GR TN  AEI  A  A++QA
Sbjct: 138 DFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQA 197

Query: 65  KSAN 68
           K+ N
Sbjct: 198 KTQN 201

Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: 4

>sp|Q9UST8|RNH1_SCHPO Ribonuclease H OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rnh1 PE=1 SV=1

 Score = 55.1 bits (131), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 28/56 (50%), Positives = 38/56 (67%), Gaps = 1/56 (1%)

Query: 8   VVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRV-TNNNAEIQGAIHALK 62
           VV+ DG+  RNGK GA AG GV+FG ++P N++  + G   TNN AE+Q  I AL+
Sbjct: 125 VVYADGSSLRNGKKGAVAGCGVFFGNDDPRNISVPLAGEEQTNNRAELQAIILALE 180

Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: 4

>sp|Q5SXJ3|FANCJ_MOUSE Fanconi anemia group J protein homolog OS=Mus musculus GN=Brip1 PE=2 SV=1

 Score = 48.5 bits (114), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/49 (44%), Positives = 35/49 (71%), Gaps = 1/49 (2%)

Query: 107 VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYN 155
           VI+VGIPFP+++D  V+LKR YND H++ +G+  P  Q  +++  R+ N
Sbjct: 782 VITVGIPFPNVKDLQVELKRQYNDHHSKSRGL-LPGRQWYEIQAYRALN 829

DNA-dependent ATPase and 5' to 3' DNA helicase required for the maintenance of chromosomal stability. Acts late in the 'Fanconi anemia' pathway, after FANCD2 ubiquitination. Involved in the repair of DNA double-strand breaks by homologous recombination in a manner that depends on its association with BRCA1.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q3YK19|FANCJ_CHICK Fanconi anemia group J protein homolog OS=Gallus gallus GN=BRIP1 PE=2 SV=1

 Score = 47.8 bits (112), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 22/64 (34%), Positives = 41/64 (64%), Gaps = 4/64 (6%)

Query: 95  RIAQKVDYISHD---VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLK 151
           ++++ +D+   +   VI++GIPFP+++D  V+LKR YND H   +G+  P  Q  +++  
Sbjct: 774 KVSEGLDFCDENARAVITIGIPFPNVKDLQVELKRKYNDQHKTTRGL-LPGSQWYEIQAY 832

Query: 152 RSYN 155
           R+ N
Sbjct: 833 RALN 836

DNA-dependent ATPase and 5' to 3' DNA helicase required for the maintenance of chromosomal stability. Acts late in the 'Fanconi anemia' pathway of DNA repair, after FANCD2 ubiquitination. Probably not involved in the repair of DNA double-strand breaks by homologous recombination.

Gallus gallus (taxid: 9031)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9BX63|FANCJ_HUMAN Fanconi anemia group J protein OS=Homo sapiens GN=BRIP1 PE=1 SV=1

 Score = 47.4 bits (111), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 21/49 (42%), Positives = 35/49 (71%), Gaps = 1/49 (2%)

Query: 107 VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYN 155
           VI++GIPFP+++D  V+LKR YND H++ +G+  P  Q  +++  R+ N
Sbjct: 779 VITIGIPFPNVKDLQVELKRQYNDHHSKLRGL-LPGRQWYEIQAYRALN 826

DNA-dependent ATPase and 5' to 3' DNA helicase required for the maintenance of chromosomal stability. Acts late in the Fanconi anemia pathway, after FANCD2 ubiquitination. Involved in the repair of DNA double-strand breaks by homologous recombination in a manner that depends on its association with BRCA1.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q07762|RNH1_CRIFA Ribonuclease H OS=Crithidia fasciculata GN=RNH1 PE=3 SV=1

 Score = 43.9 bits (102), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 3/59 (5%)

Query: 8   VVFTDGACPRNGKVGASAGYGVYFGENNP---LNVAGKVTGRVTNNNAEIQGAIHALKQ 63
           VV+ DGAC  NG   A AGYG ++G  +     ++   +T   TNN  E++  IH + Q
Sbjct: 277 VVYVDGACSHNGTPKARAGYGGFYGSTSDSRNFSLPVPITEAQTNNRGEMRAVIHCIVQ 335

Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.

Crithidia fasciculata (taxid: 5656)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: 4

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	191
289724715	299	ribonuclease H [Glossina morsitans morsi	0.654	0.418	0.36	3e-15
390179738	305	GA21286, isoform B [Drosophila pseudoobs	0.340	0.213	0.6	4e-15
390179740	308	GA21286, isoform A [Drosophila pseudoobs	0.340	0.211	0.6	6e-15
45552509	314	ribonuclease H1, isoform B [Drosophila m	0.335	0.203	0.609	6e-15
2677845	333	ribonuclease H1 [Drosophila melanogaster	0.335	0.192	0.609	7e-15
17137476	333	ribonuclease H1, isoform A [Drosophila m	0.335	0.192	0.609	8e-15
348518291	278	PREDICTED: ribonuclease H1-like isoform	0.335	0.230	0.625	2e-13
348518293	295	PREDICTED: ribonuclease H1-like isoform	0.335	0.216	0.625	2e-13
357604992	323	hypothetical protein KGM_00953 [Danaus p	0.335	0.198	0.562	3e-13
432947322	297	PREDICTED: ribonuclease H1-like isoform	0.308	0.198	0.644	4e-13

>gi|289724715|gb|ADD18320.1| ribonuclease H [Glossina morsitans morsitans]

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 54/150 (36%), Positives = 81/150 (54%), Gaps = 25/150 (16%)

Query: 1   MDPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHA 60
           ++ D +++ +TDG+C  NG   A AGYGVYFG+N+PLNVA  VTGRVTNN  EIQ AI+A
Sbjct: 139 INEDGYILAYTDGSCFNNGGKNACAGYGVYFGDNHPLNVAEPVTGRVTNNVGEIQAAIYA 198

Query: 61  LKQAKSANEKVKLKRSYNDTHAQKKVRNVS-------------SVAMRIAQKVDYISHDV 107
           +K A    +K+ + +    T +Q  +  V+                 R+  +VD+   D 
Sbjct: 199 VKTA----QKMGINKLCISTDSQFLINAVTLWIKGWKAKNWHLKTGDRVKNEVDFKELDS 254

Query: 108 ISVGIPFPSIQDENVKLKRSYNDTHAQKKG 137
           +        +QDE++ +K +Y   H   KG
Sbjct: 255 L--------LQDESLDVKWNYVKAHKGIKG 276

Source: Glossina morsitans morsitans

Species: Glossina morsitans

Genus: Glossina

Family: Glossinidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|390179738|ref|XP_003736961.1| GA21286, isoform B [Drosophila pseudoobscura pseudoobscura] gi|388859951|gb|EIM53034.1| GA21286, isoform B [Drosophila pseudoobscura pseudoobscura]

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 39/65 (60%), Positives = 51/65 (78%)

Query: 1   MDPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHA 60
           +D + +V+V+TDG+C  NG+ GA AGYGVYFG+N+ LN A  V+GRVTNN  EIQ AIHA
Sbjct: 147 IDTEGYVIVYTDGSCIGNGRKGACAGYGVYFGDNHKLNAAKPVSGRVTNNVGEIQAAIHA 206

Query: 61  LKQAK 65
           +K A+
Sbjct: 207 IKTAR 211

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|390179740|ref|XP_001361472.2| GA21286, isoform A [Drosophila pseudoobscura pseudoobscura] gi|388859952|gb|EAL26050.2| GA21286, isoform A [Drosophila pseudoobscura pseudoobscura]

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 39/65 (60%), Positives = 51/65 (78%)

Query: 1   MDPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHA 60
           +D + +V+V+TDG+C  NG+ GA AGYGVYFG+N+ LN A  V+GRVTNN  EIQ AIHA
Sbjct: 153 IDTEGYVIVYTDGSCIGNGRKGACAGYGVYFGDNHKLNAAKPVSGRVTNNVGEIQAAIHA 212

Query: 61  LKQAK 65
           +K A+
Sbjct: 213 IKTAR 217

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|45552509|ref|NP_995777.1| ribonuclease H1, isoform B [Drosophila melanogaster] gi|45445652|gb|AAS64899.1| ribonuclease H1, isoform B [Drosophila melanogaster]

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 39/64 (60%), Positives = 49/64 (76%)

Query: 1   MDPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHA 60
           +D + +V+V+TDG+C  NG+ GA AGYGVYFG+N+ LN A  V GRVTNN  EIQ AIHA
Sbjct: 157 IDAEGYVIVYTDGSCIGNGRAGACAGYGVYFGKNHQLNAAKPVEGRVTNNVGEIQAAIHA 216

Query: 61  LKQA 64
           +K A
Sbjct: 217 IKTA 220

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|2677845|gb|AAC47810.1| ribonuclease H1 [Drosophila melanogaster]

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 39/64 (60%), Positives = 49/64 (76%)

Query: 1   MDPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHA 60
           +D + +V+V+TDG+C  NG+ GA AGYGVYFG+N+ LN A  V GRVTNN  EIQ AIHA
Sbjct: 176 IDAEGYVIVYTDGSCIGNGRTGACAGYGVYFGKNHQLNAAKPVEGRVTNNVGEIQAAIHA 235

Query: 61  LKQA 64
           +K A
Sbjct: 236 IKTA 239

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|17137476|ref|NP_477315.1| ribonuclease H1, isoform A [Drosophila melanogaster] gi|7304133|gb|AAF59170.1| ribonuclease H1, isoform A [Drosophila melanogaster] gi|19527995|gb|AAL90112.1| AT19436p [Drosophila melanogaster] gi|220949756|gb|ACL87421.1| rnh1-PA [synthetic construct] gi|220958970|gb|ACL92028.1| rnh1-PA [synthetic construct]

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 39/64 (60%), Positives = 49/64 (76%)

Query: 1   MDPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHA 60
           +D + +V+V+TDG+C  NG+ GA AGYGVYFG+N+ LN A  V GRVTNN  EIQ AIHA
Sbjct: 176 IDAEGYVIVYTDGSCIGNGRAGACAGYGVYFGKNHQLNAAKPVEGRVTNNVGEIQAAIHA 235

Query: 61  LKQA 64
           +K A
Sbjct: 236 IKTA 239

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|348518291|ref|XP_003446665.1| PREDICTED: ribonuclease H1-like isoform 1 [Oreochromis niloticus]

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/64 (62%), Positives = 46/64 (71%)

Query: 7   VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
           VVV+TDG C  NG+ GA AG GVY+G NNPLNVA ++ GR TN  AEIQ A  AL+QAK 
Sbjct: 132 VVVYTDGCCSGNGQSGARAGIGVYWGCNNPLNVAERLQGRQTNQRAEIQAACRALEQAKQ 191

Query: 67  ANEK 70
            N K
Sbjct: 192 NNIK 195

Source: Oreochromis niloticus

Species: Oreochromis niloticus

Genus: Oreochromis

Family: Cichlidae

Order: Perciformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|348518293|ref|XP_003446666.1| PREDICTED: ribonuclease H1-like isoform 2 [Oreochromis niloticus]

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/64 (62%), Positives = 46/64 (71%)

Query: 7   VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
           VVV+TDG C  NG+ GA AG GVY+G NNPLNVA ++ GR TN  AEIQ A  AL+QAK 
Sbjct: 149 VVVYTDGCCSGNGQSGARAGIGVYWGCNNPLNVAERLQGRQTNQRAEIQAACRALEQAKQ 208

Query: 67  ANEK 70
            N K
Sbjct: 209 NNIK 212

Source: Oreochromis niloticus

Species: Oreochromis niloticus

Genus: Oreochromis

Family: Cichlidae

Order: Perciformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|357604992|gb|EHJ64411.1| hypothetical protein KGM_00953 [Danaus plexippus]

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 36/64 (56%), Positives = 46/64 (71%)

Query: 1   MDPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHA 60
           +D D +V VFTDGAC  NGK GA AG GV++GE +PLN++  V+GR TNN  EIQ A  A
Sbjct: 171 LDEDGYVQVFTDGACSSNGKNGARAGLGVFWGEGHPLNISKPVSGRATNNCGEIQAATEA 230

Query: 61  LKQA 64
           ++ A
Sbjct: 231 IRTA 234

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|432947322|ref|XP_004083988.1| PREDICTED: ribonuclease H1-like isoform 1 [Oryzias latipes]

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 38/59 (64%), Positives = 44/59 (74%)

Query: 7   VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
           VVV+TDG C  NGK GA AG GVY+G N+PLNVA ++ GR TN  AEIQ A  AL+QAK
Sbjct: 144 VVVYTDGCCSCNGKAGARAGIGVYWGHNHPLNVAERLEGRQTNQRAEIQAACKALQQAK 202

Source: Oryzias latipes

Species: Oryzias latipes

Genus: Oryzias

Family: Adrianichthyidae

Order: Beloniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

---

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	191
FB|FBgn0023171	333	rnh1 "ribonuclease H1" [Drosop	0.774	0.444	0.378	3.7e-18
ZFIN|ZDB-GENE-040718-407	276	rnaseh1 "ribonuclease H1" [Dan	0.371	0.257	0.546	1.8e-14
UNIPROTKB|F1NN23	293	RNASEH1 "Uncharacterized prote	0.329	0.215	0.523	2.9e-12
UNIPROTKB|F1N2X2	280	RNASEH1 "Uncharacterized prote	0.376	0.257	0.5	5.3e-12
RGD|1309012	285	Rnaseh1 "ribonuclease H1" [Rat	0.324	0.217	0.532	5.7e-12
MGI|MGI:1335073	285	Rnaseh1 "ribonuclease H1" [Mus	0.324	0.217	0.516	7.6e-12
UNIPROTKB|J9NUL8	285	RNASEH1 "Uncharacterized prote	0.376	0.252	0.5	9.8e-12
UNIPROTKB|E2R8B0	288	RNASEH1 "Uncharacterized prote	0.376	0.25	0.5	1e-11
UNIPROTKB|O60930	286	RNASEH1 "Ribonuclease H1" [Hom	0.324	0.216	0.516	1.7e-11
UNIPROTKB|I3LTQ9	287	RNASEH1 "Uncharacterized prote	0.324	0.216	0.532	1.7e-11

FB|FBgn0023171 rnh1 "ribonuclease H1" [Drosophila melanogaster (taxid:7227)]

 Score = 220 (82.5 bits), Expect = 3.7e-18, P = 3.7e-18
 Identities = 64/169 (37%), Positives = 95/169 (56%)

Query:     1 MDPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHA 60
             +D + +V+V+TDG+C  NG+ GA AGYGVYFG+N+ LN A  V GRVTNN  EIQ AIHA
Sbjct:   176 IDAEGYVIVYTDGSCIGNGRTGACAGYGVYFGKNHQLNAAKPVEGRVTNNVGEIQAAIHA 235

Query:    61 LKQAKSANEKVKLKRSYNDTHAQKKVRNVSSVAMRIA--QKVDYI--SHDVISVGIPFPS 116
             +K A     + KL  S   T +Q  +   +S+ + +A  +K D+   ++  +   + F  
Sbjct:   236 IKTALDLGIQ-KLCIS---TDSQFLI---NSITLWVAGWKKRDWKLKNNQPVKNVVDFKE 288

Query:   117 I----QDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTHAQK 161
             +    QD N+ +K +Y + H   KGI    + D   KL R  +  + QK
Sbjct:   289 LDKLLQDNNITVKWNYVEAH---KGIEGNEMAD---KLARQGSALYKQK 331

GO:0004523 "ribonuclease H activity" evidence=ISS;IDA

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

ZFIN|ZDB-GENE-040718-407 rnaseh1 "ribonuclease H1" [Danio rerio (taxid:7955)]

 Score = 185 (70.2 bits), Expect = 1.8e-14, P = 1.8e-14
 Identities = 41/75 (54%), Positives = 51/75 (68%)

Query:     7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
             VVV+TDG C  NGK GA AG GVY+G ++P NVA ++ GR TN  AE+Q A  AL+QAK 
Sbjct:   130 VVVYTDGCCSGNGKHGARAGIGVYWGRDHPRNVAERLPGRQTNQRAELQAACKALEQAKE 189

Query:    67 AN-EKVKLKRSYNDT 80
              N +KV L   Y D+
Sbjct:   190 MNFKKVVL---YTDS 201

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|F1NN23 RNASEH1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 167 (63.8 bits), Expect = 2.9e-12, P = 2.9e-12
 Identities = 33/63 (52%), Positives = 43/63 (68%)

Query:     8 VVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSA 67
             VV+TDG C  NG+  A AG GVY+G  +PLN++ ++ GR TN  AEI  A  A++QAKS 
Sbjct:   148 VVYTDGCCSGNGRNRARAGIGVYWGPGHPLNISERLPGRQTNQRAEIHAACKAIEQAKSQ 207

Query:    68 NEK 70
             N K
Sbjct:   208 NIK 210

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0006264 "mitochondrial DNA replication" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

UNIPROTKB|F1N2X2 RNASEH1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 164 (62.8 bits), Expect = 5.3e-12, P = 5.3e-12
 Identities = 37/74 (50%), Positives = 47/74 (63%)

Query:     7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
             VVV+TDG C  NG+  A AG GVY+G  +PLNV  ++ GR TN  AEI  A  A++QAK 
Sbjct:   134 VVVYTDGCCSSNGRKRARAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAK- 192

Query:    67 ANEKVKLKRSYNDT 80
             A +  KL   Y D+
Sbjct:   193 AQDITKLVL-YTDS 205

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0006264 "mitochondrial DNA replication" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

RGD|1309012 Rnaseh1 "ribonuclease H1" [Rattus norvegicus (taxid:10116)]

 Score = 164 (62.8 bits), Expect = 5.7e-12, P = 5.7e-12
 Identities = 33/62 (53%), Positives = 41/62 (66%)

Query:     7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
             VVV+TDG C  NG+  A AG GVY+G  +PLNV  ++ GR TN  AEI  A  A+ QAK+
Sbjct:   139 VVVYTDGCCSSNGRKRARAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAITQAKA 198

Query:    67 AN 68
              N
Sbjct:   199 QN 200

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0006264 "mitochondrial DNA replication" evidence=IEA;ISO

GO:0042803 "protein homodimerization activity" evidence=IEA;ISO

MGI|MGI:1335073 Rnaseh1 "ribonuclease H1" [Mus musculus (taxid:10090)]

 Score = 163 (62.4 bits), Expect = 7.6e-12, P = 7.6e-12
 Identities = 32/62 (51%), Positives = 41/62 (66%)

Query:     7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
             V+V+TDG C  NG+  A AG GVY+G  +PLNV  ++ GR TN  AEI  A  A+ QAK+
Sbjct:   139 VIVYTDGCCSSNGRKRARAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIMQAKA 198

Query:    67 AN 68
              N
Sbjct:   199 QN 200

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=ISS;IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0006264 "mitochondrial DNA replication" evidence=IMP

GO:0016787 "hydrolase activity" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IDA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|J9NUL8 RNASEH1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 162 (62.1 bits), Expect = 9.8e-12, P = 9.8e-12
 Identities = 37/74 (50%), Positives = 47/74 (63%)

Query:     7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
             VVV+TDG C  NG+  A AG GVY+G  +P NV  ++ GR TN  AEI  A  A++QAK+
Sbjct:   139 VVVYTDGCCSSNGRRRARAGIGVYWGPGHPWNVGIRLPGRQTNQRAEIHAACKAIEQAKA 198

Query:    67 ANEKVKLKRSYNDT 80
              N K KL   Y D+
Sbjct:   199 QNIK-KLVL-YTDS 210

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

UNIPROTKB|E2R8B0 RNASEH1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 162 (62.1 bits), Expect = 1.0e-11, P = 1.0e-11
 Identities = 37/74 (50%), Positives = 47/74 (63%)

Query:     7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
             VVV+TDG C  NG+  A AG GVY+G  +P NV  ++ GR TN  AEI  A  A++QAK+
Sbjct:   139 VVVYTDGCCSSNGRRRARAGIGVYWGPGHPWNVGIRLPGRQTNQRAEIHAACKAIEQAKA 198

Query:    67 ANEKVKLKRSYNDT 80
              N K KL   Y D+
Sbjct:   199 QNIK-KLVL-YTDS 210

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

UNIPROTKB|O60930 RNASEH1 "Ribonuclease H1" [Homo sapiens (taxid:9606)]

 Score = 160 (61.4 bits), Expect = 1.7e-11, P = 1.7e-11
 Identities = 32/62 (51%), Positives = 41/62 (66%)

Query:     7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
             VVV+TDG C  NG+    AG GVY+G  +PLNV  ++ GR TN  AEI  A  A++QAK+
Sbjct:   140 VVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKT 199

Query:    67 AN 68
              N
Sbjct:   200 QN 201

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0006264 "mitochondrial DNA replication" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=TAS

GO:0003723 "RNA binding" evidence=TAS

GO:0004540 "ribonuclease activity" evidence=TAS

GO:0006401 "RNA catabolic process" evidence=TAS

UNIPROTKB|I3LTQ9 RNASEH1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 160 (61.4 bits), Expect = 1.7e-11, P = 1.7e-11
 Identities = 33/62 (53%), Positives = 41/62 (66%)

Query:     7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
             VVV+TDG C  NG+  A AG GVY+G  +PLNV  ++ GR TN  AEI  A  AL+ AK+
Sbjct:   141 VVVYTDGCCSSNGRRRARAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKALELAKA 200

Query:    67 AN 68
              N
Sbjct:   201 QN 202

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0006264 "mitochondrial DNA replication" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.26	LOW CONFIDENCE prediction!
3rd Layer	3.1.26.4	LOW CONFIDENCE prediction!

---

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	191
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	4e-25
pfam00075	126	pfam00075, RNase_H, RNase H	2e-09
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	1e-08
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	1e-06
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	6e-04
cd09279	128	cd09279, RNase_HI_archaeal_like, RNAse HI family t	0.001
pfam13307	165	pfam13307, Helicase_C_2, Helicase C-terminal domai	0.003
smart00491	142	smart00491, HELICc2, helicase superfamily c-termin	0.004

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

 Score = 94.6 bits (236), Expect = 4e-25
 Identities = 33/63 (52%), Positives = 42/63 (66%), Gaps = 1/63 (1%)

Query: 8  VVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRV-TNNNAEIQGAIHALKQAKS 66
          VV+TDGAC  NG+ GA AGYGVYFG  +P NV+ ++ G   TN  AE++  IHAL+  K 
Sbjct: 1  VVYTDGACRGNGRSGARAGYGVYFGPGHPRNVSERLPGPPQTNQRAELRAVIHALRLIKE 60

Query: 67 ANE 69
            E
Sbjct: 61 VGE 63

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at the N-terminal called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. Length = 150

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

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 27/114 (23%), Positives = 40/114 (35%), Gaps = 22/114 (19%)

Query: 4   DNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQ 63
              V V+TDG+C  N   G  AGY    G+        K     TN  AE+   I AL+ 
Sbjct: 1   PEAVTVYTDGSCNGNPGPGG-AGYVTDGGKQ-----RSKPLPGTTNQRAELLALIEALEA 54

Query: 64  AKSANEKVKLK-----------RSYNDTHAQKKVRNVSSVAMRIAQKVD-YISH 105
                +KV +              +      K ++N   +   + +K   YI  
Sbjct: 55  LSG--QKVNIYTDSQYVIGGITNGWPTKSESKPIKNE--IWELLQKKHKVYIQW 104

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

>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and repair]

 Score = 51.6 bits (124), Expect = 1e-08
 Identities = 22/60 (36%), Positives = 28/60 (46%), Gaps = 3/60 (5%)

Query: 6  HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
           V +FTDGAC  N   G   G+G      +         GR TNN AE++  I AL+  K
Sbjct: 3  KVEIFTDGACLGNPGPG---GWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALK 59

Length = 154

>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 5/63 (7%)

Query: 10 FTDGACPRNGKVGASAGYGVYFGENN-PLNVAGKVTGRV-TNNNAEIQGAIHALKQAKSA 67
           TDG+C  N      AG G    ++      AG ++    TNN AE+   + AL+ A   
Sbjct: 1  NTDGSCKGNPG---PAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDL 57

Query: 68 NEK 70
            K
Sbjct: 58 GLK 60

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 123

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

 Score = 37.9 bits (89), Expect = 6e-04
 Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 6/68 (8%)

Query: 7  VVVFTDGACPRNGKVGASAGYGVY-FGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
          + ++TDGAC  N   G   G+       ++   ++G   G  TNN  E+   I AL+  K
Sbjct: 2  ITIYTDGACLGNPGPG---GWAAILRYGDHEKELSGGEAGT-TNNRMELTAVIEALEALK 57

Query: 66 SANEKVKL 73
               V L
Sbjct: 58 -EPCPVLL 64

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

>gnl|CDD|187703 cd09279, RNase_HI_archaeal_like, RNAse HI family that includes Archaeal RNase HI

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 17/64 (26%), Positives = 25/64 (39%), Gaps = 1/64 (1%)

Query: 7  VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
            ++ DGA   N    A AG  +   +   L  +  +    TNN AE +  I  L+ A  
Sbjct: 1  WTLYFDGASRGNPG-PAGAGIVIKSPDGEVLEQSIPLGFPATNNEAEYEALIAGLELALE 59

Query: 67 ANEK 70
             K
Sbjct: 60 LGIK 63

Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties. Length = 128

>gnl|CDD|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 3/34 (8%)

Query: 107 VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPF 140
           VI VG+PFPS  D  V+ +R Y D   ++    F
Sbjct: 83  VIIVGLPFPSPDDPLVEARREYLD---KQGKDGF 113

This domain is the second of two tandem AAA domains found in a wide variety of helicase enzymes. Length = 165

>gnl|CDD|214694 smart00491, HELICc2, helicase superfamily c-terminal domain

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 5/92 (5%)

Query: 58  IHALKQAKSANEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYISHD----VISVGIP 113
                + K + E  +L   Y+     +    ++    ++++ +D+   D    VI VGIP
Sbjct: 21  KPVFIEGKDSGETEELLEKYSAACEARGALLLAVARGKVSEGIDF-PDDLGRAVIIVGIP 79

Query: 114 FPSIQDENVKLKRSYNDTHAQKKGIPFPSIQD 145
           FP+     ++ +  Y D     +      + D
Sbjct: 80  FPNPDSPILRARLEYLDEKGGIRPFDEVYLFD 111

Length = 142

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	191
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.97
PRK06548	161	ribonuclease H; Provisional	99.96
PRK08719	147	ribonuclease H; Reviewed	99.94
KOG3752|consensus	371		99.92
PRK00203	150	rnhA ribonuclease H; Reviewed	99.92
PRK13907	128	rnhA ribonuclease H; Provisional	99.81
PRK07708	219	hypothetical protein; Validated	99.68
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.68
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.62
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.17
KOG1132|consensus	945		98.64
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	97.99
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	94.54
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	94.38
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	91.03
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	89.58
KOG1133|consensus	821		85.55

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

Probab=99.97  E-value=3e-30  Score=206.52  Aligned_cols=137  Identities=24%  Similarity=0.301  Sum_probs=109.2

Q ss_pred             CcEEEEEeeccCCCCCCCCceEEEEEEcC-CceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHH
Q psy874            5 NHVVVFTDGACPRNGKVGASAGYGVYFGE-NNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQ   83 (191)
Q Consensus         5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~~~-~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yv   83 (191)
                      ..++|||||||++||||+   |||+++.. ....+++++. +.+|||+|||+|+|+||+.+++.+. +.++ |+|||+||
T Consensus         2 ~~v~if~DGa~~gNpG~g---G~g~vl~~~~~~~~~s~~~-~~tTNNraEl~A~i~AL~~l~~~~~-~~v~-l~tDS~yv   75 (154)
T COG0328           2 KKVEIFTDGACLGNPGPG---GWGAVLRYGDGEKELSGGE-GRTTNNRAELRALIEALEALKELGA-CEVT-LYTDSKYV   75 (154)
T ss_pred             CceEEEecCccCCCCCCc---eEEEEEEcCCceEEEeeee-ecccChHHHHHHHHHHHHHHHhcCC-ceEE-EEecHHHH
Confidence            478999999999999885   99998643 3556688774 4899999999999999999998655 5999 99999999


Q ss_pred             Hccccccccccccccccccccccee-ecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccccccchH--
Q psy874           84 KKVRNVSSVAMRIAQKVDYISHDVI-SVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTH--  158 (191)
Q Consensus        84 v~~~~~~~~~~~w~~~edW~~ng~~-s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~~n~~~--  158 (191)
                      +++++ .     |..+  |++++|. +.+.||  +|||+++.++...+.          ....+|...+++++.||++  
T Consensus        76 ~~~i~-~-----w~~~--w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~----------~v~~~WVkgH~g~~~NeraD~  137 (154)
T COG0328          76 VEGIT-R-----WIVK--WKKNGWKTADKKPVKNKDLWEELDELLKRHE----------LVFWEWVKGHAGHPENERADQ  137 (154)
T ss_pred             HHHHH-H-----HHhh--ccccCccccccCccccHHHHHHHHHHHhhCC----------eEEEEEeeCCCCChHHHHHHH
Confidence            99887 3     7666  9999984 789999  999999888765431          1245666666789999966  


Q ss_pred             -hhhhhhc
Q psy874          159 -AQKKVRN  165 (191)
Q Consensus       159 -~~~~~~~  165 (191)
                       |.+++++
T Consensus       138 LA~~~~~~  145 (154)
T COG0328         138 LAREAARA  145 (154)
T ss_pred             HHHHHHHh
Confidence             4444443

>PRK06548 ribonuclease H; Provisional

Probab=99.96  E-value=2e-29  Score=203.36  Aligned_cols=138  Identities=19%  Similarity=0.177  Sum_probs=102.6

Q ss_pred             CcEEEEEeeccCCCCCCCCceEEEEEEcCCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHH
Q psy874            5 NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQK   84 (191)
Q Consensus         5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~~~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv   84 (191)
                      ..++|||||||++||+++   |||+++....  ..+++ .+.+|||+|||+|+++||+.+....  .+++ |+|||+||+
T Consensus         4 ~~~~IytDGa~~gnpg~~---G~g~~~~~~~--~~~g~-~~~~TNnraEl~Aii~aL~~~~~~~--~~v~-I~TDS~yvi   74 (161)
T PRK06548          4 NEIIAATDGSSLANPGPS---GWAWYVDENT--WDSGG-WDIATNNIAELTAVRELLIATRHTD--RPIL-ILSDSKYVI   74 (161)
T ss_pred             CEEEEEEeeccCCCCCce---EEEEEEeCCc--EEccC-CCCCCHHHHHHHHHHHHHHhhhcCC--ceEE-EEeChHHHH
Confidence            349999999999999884   9999876433  23444 3468999999999999998776432  3799 999999999


Q ss_pred             ccccccccccccccccccccccee-ecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccccccchHhhh
Q psy874           85 KVRNVSSVAMRIAQKVDYISHDVI-SVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTHAQK  161 (191)
Q Consensus        85 ~~~~~~~~~~~w~~~edW~~ng~~-s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~~n~~~~~~  161 (191)
                      +.++   +   |..+  |++|+|+ +.|+||  +|||+++..+.+..        .   ..+.|+..+.+...|+.    
T Consensus        75 ~~i~---~---W~~~--Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~--------~---v~~~wVkgHsg~~gNe~----  131 (161)
T PRK06548         75 NSLT---K---WVYS--WKMRKWRKADGKPVLNQEIIQEIDSLMENR--------N---IRMSWVNAHTGHPLNEA----  131 (161)
T ss_pred             HHHH---H---HHHH--HHHCCCcccCCCccccHHHHHHHHHHHhcC--------c---eEEEEEecCCCCHHHHH----
Confidence            9664   2   8888  9999985 889999  89999887775431        1   14555555667789984    


Q ss_pred             hhhccchhhHHHHhhcc
Q psy874          162 KVRNVSSVAMRIAQKVD  178 (191)
Q Consensus       162 ~~~~~~~~~~~~~~~~~  178 (191)
                          +|.+|+.-|.+..
T Consensus       132 ----aD~LA~~aa~~~~  144 (161)
T PRK06548        132 ----ADSLARQAANNFS  144 (161)
T ss_pred             ----HHHHHHHHHHHhc
Confidence                4445555444443

>PRK08719 ribonuclease H; Reviewed

Probab=99.94  E-value=8.9e-27  Score=185.17  Aligned_cols=127  Identities=19%  Similarity=0.175  Sum_probs=96.7

Q ss_pred             CcEEEEEeeccCCCCCCCCceEEEEEEc--CCcee-EEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChH
Q psy874            5 NHVVVFTDGACPRNGKVGASAGYGVYFG--ENNPL-NVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTH   81 (191)
Q Consensus         5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~~--~~~~~-~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~   81 (191)
                      ..++|||||||.+||++.++||||+++.  .+... ..+.++.+.+|||+|||+|++.||+.+.+     ..+ |+|||+
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~-----~~~-i~tDS~   76 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARD-----GDV-IYSDSD   76 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCC-----CCE-EEechH
Confidence            5689999999999998767889999753  23322 34555555689999999999999999876     247 999999


Q ss_pred             HHHccccccccccccccccccccccee-ecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEec--cccccc
Q psy874           82 AQKKVRNVSSVAMRIAQKVDYISHDVI-SVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKL--KRSYND  156 (191)
Q Consensus        82 Yvv~~~~~~~~~~~w~~~edW~~ng~~-s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a--~r~~n~  156 (191)
                      ||+++++.      |..+  |++++|. +.|.||  .|||+.+.+|.++             ..+.|.+|+.  +.+.|+
T Consensus        77 yvi~~i~~------~~~~--W~~~~w~~s~g~~v~n~dl~~~i~~l~~~-------------~~i~~~~VkgH~g~~~Ne  135 (147)
T PRK08719         77 YCVRGFNE------WLDT--WKQKGWRKSDKKPVANRDLWQQVDELRAR-------------KYVEVEKVTAHSGIEGNE  135 (147)
T ss_pred             HHHHHHHH------HHHH--HHhCCcccCCCcccccHHHHHHHHHHhCC-------------CcEEEEEecCCCCChhHH
Confidence            99997652      7777  9999996 778999  8899976665431             1355566555  457888


Q ss_pred             hH
Q psy874          157 TH  158 (191)
Q Consensus       157 ~~  158 (191)
                      .+
T Consensus       136 ~a  137 (147)
T PRK08719        136 AA  137 (147)
T ss_pred             HH
Confidence            55

>KOG3752|consensus

Probab=99.92  E-value=2.9e-25  Score=197.23  Aligned_cols=141  Identities=32%  Similarity=0.417  Sum_probs=113.9

Q ss_pred             CcEEEEEeeccCCCCCCCCceEEEEEEcCCceeEEEeccC-CCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHH
Q psy874            5 NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVT-GRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQ   83 (191)
Q Consensus         5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~~~~~~~~~s~~l~-g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yv   83 (191)
                      +.++|||||+|.+|+.++++|||||||+++++.|.++|+. |.+|||||||.|+++||+.+.+.... +|+ |+|||+|+
T Consensus       211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~-kv~-I~TDS~~~  288 (371)
T KOG3752|consen  211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNIN-KVV-IRTDSEYF  288 (371)
T ss_pred             cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCC-cEE-EEechHHH
Confidence            4589999999999999999999999999999999999998 69999999999999999999987665 899 99999999


Q ss_pred             Hccccccccccccccccccccccee-ecCCC-----c--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEecccc-c
Q psy874           84 KKVRNVSSVAMRIAQKVDYISHDVI-SVGIP-----F--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRS-Y  154 (191)
Q Consensus        84 v~~~~~~~~~~~w~~~edW~~ng~~-s~G~P-----V--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~-~  154 (191)
                      ++.++      .|..+  |++++|. +.+.+     |  +|...++-+|.+..       ++   ..++|++|+.+.- +
T Consensus       289 i~~l~------~wv~~--~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~-------~~---~~vq~~~V~Gh~gi~  350 (371)
T KOG3752|consen  289 INSLT------LWVQG--WKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEI-------SN---KKVQQEYVGGHSGIL  350 (371)
T ss_pred             HHHHH------HHHhh--hccCccccccCCCccceeeecchHHHHHHHHHhhh-------cc---CceEEEEecCcCCcc
Confidence            99776      28888  9999985 66777     6  66666666655544       12   3689999988643 3


Q ss_pred             cchHhhhhhhc
Q psy874          155 NDTHAQKKVRN  165 (191)
Q Consensus       155 n~~~~~~~~~~  165 (191)
                      +-.-|...+|+
T Consensus       351 gne~Ad~lARk  361 (371)
T KOG3752|consen  351 GNEMADALARK  361 (371)
T ss_pred             hHHHHHHHHhh
Confidence            33334444444

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.92  E-value=1.8e-25  Score=177.09  Aligned_cols=124  Identities=21%  Similarity=0.262  Sum_probs=95.7

Q ss_pred             cEEEEEeeccCCCCCCCCceEEEEEEc-CCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHH
Q psy874            6 HVVVFTDGACPRNGKVGASAGYGVYFG-ENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQK   84 (191)
Q Consensus         6 ~i~IYtDGac~~N~~~~~~AG~Gv~~~-~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv   84 (191)
                      +++|||||||.+||++   +|||+++. .++...+++.. +.+|||+|||+|++.||+.+.+.   +.++ |+|||+||+
T Consensus         3 ~v~iytDGs~~~n~~~---~g~g~v~~~~~~~~~~~~~~-~~~TN~~aEL~Ai~~AL~~~~~~---~~v~-I~tDS~yvi   74 (150)
T PRK00203          3 QVEIYTDGACLGNPGP---GGWGAILRYKGHEKELSGGE-ALTTNNRMELMAAIEALEALKEP---CEVT-LYTDSQYVR   74 (150)
T ss_pred             eEEEEEEecccCCCCc---eEEEEEEEECCeeEEEecCC-CCCcHHHHHHHHHHHHHHHcCCC---CeEE-EEECHHHHH
Confidence            5899999999999976   59998764 34445566553 47899999999999999988752   4799 999999999


Q ss_pred             ccccccccccccccccccccccee-ecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEe--ccccccchH
Q psy874           85 KVRNVSSVAMRIAQKVDYISHDVI-SVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVK--LKRSYNDTH  158 (191)
Q Consensus        85 ~~~~~~~~~~~w~~~edW~~ng~~-s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~--a~r~~n~~~  158 (191)
                      +.++.      |..+  |++++|. +.|.||  +|||+++.++.+.             ..+.|.+|+  .++..|+.+
T Consensus        75 ~~i~~------w~~~--Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-------------~~v~~~wV~~H~~~~~N~~A  132 (150)
T PRK00203         75 QGITE------WIHG--WKKNGWKTADKKPVKNVDLWQRLDAALKR-------------HQIKWHWVKGHAGHPENERC  132 (150)
T ss_pred             HHHHH------HHHH--HHHcCCcccCCCccccHHHHHHHHHHhcc-------------CceEEEEecCCCCCHHHHHH
Confidence            97652      7777  9999996 689999  8899987766432             124445544  566788866

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.81  E-value=4.5e-19  Score=136.07  Aligned_cols=79  Identities=22%  Similarity=0.297  Sum_probs=64.9

Q ss_pred             cEEEEEeeccCCCCCCCCceEEEEEEcCC-ceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHH
Q psy874            6 HVVVFTDGACPRNGKVGASAGYGVYFGEN-NPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQK   84 (191)
Q Consensus         6 ~i~IYtDGac~~N~~~~~~AG~Gv~~~~~-~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv   84 (191)
                      |++|||||||.+||++   +|||+++.+. .....+++ .+..|||+||++|++.||+.+.+.+.. ++. |+|||+||+
T Consensus         1 ~~~iy~DGa~~~~~g~---~G~G~vi~~~~~~~~~~~~-~~~~tn~~AE~~All~aL~~a~~~g~~-~v~-i~sDS~~vi   74 (128)
T PRK13907          1 MIEVYIDGASKGNPGP---SGAGVFIKGVQPAVQLSLP-LGTMSNHEAEYHALLAALKYCTEHNYN-IVS-FRTDSQLVE   74 (128)
T ss_pred             CEEEEEeeCCCCCCCc---cEEEEEEEECCeeEEEEec-ccccCCcHHHHHHHHHHHHHHHhCCCC-EEE-EEechHHHH
Confidence            6899999999999987   5999987543 22334444 356899999999999999999998875 899 999999999


Q ss_pred             cccccc
Q psy874           85 KVRNVS   90 (191)
Q Consensus        85 ~~~~~~   90 (191)
                      +.++..
T Consensus        75 ~~~~~~   80 (128)
T PRK13907         75 RAVEKE   80 (128)
T ss_pred             HHHhHH
Confidence            977653

>PRK07708 hypothetical protein; Validated

Probab=99.68  E-value=9.8e-16  Score=129.21  Aligned_cols=85  Identities=19%  Similarity=0.272  Sum_probs=65.4

Q ss_pred             CCCCcEEEEEeeccCCCCCCCCceEEEEEE--cCCc-ee--EEEeccCCCCChHHHHHHHHHHHHHHhHhcCCc-ceeEE
Q psy874            2 DPDNHVVVFTDGACPRNGKVGASAGYGVYF--GENN-PL--NVAGKVTGRVTNNNAEIQGAIHALKQAKSANEK-VKLKR   75 (191)
Q Consensus         2 ~~~~~i~IYtDGac~~N~~~~~~AG~Gv~~--~~~~-~~--~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~-~~v~~   75 (191)
                      .+++.+++||||||.+|+++   +|+|+++  ..+. ..  ..+..+.+..|||.||+.|++.||+.+.+.|.. .+|. 
T Consensus        69 ~ep~~~~vY~DGs~~~n~g~---aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~-  144 (219)
T PRK07708         69 EEPHEILVYFDGGFDKETKL---AGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVT-  144 (219)
T ss_pred             cCCCcEEEEEeeccCCCCCC---cEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEE-
Confidence            35678999999999999876   5888865  3332 22  222344446899999999999999999998764 2489 


Q ss_pred             EEcChHHHHcccccc
Q psy874           76 SYNDTHAQKKVRNVS   90 (191)
Q Consensus        76 I~TDS~Yvv~~~~~~   90 (191)
                      |++||++|+++++..
T Consensus       145 I~~DSqlVi~qi~g~  159 (219)
T PRK07708        145 FRGDSQVVLNQLAGE  159 (219)
T ss_pred             EEeccHHHHHHhCCC
Confidence            999999999976643

>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site

Probab=99.68  E-value=4.6e-17  Score=123.73  Aligned_cols=74  Identities=28%  Similarity=0.391  Sum_probs=57.7

Q ss_pred             CcEEEEEeeccCCCCCCCCceEEEEEEcCCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHH
Q psy874            5 NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQK   84 (191)
Q Consensus         5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~~~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv   84 (191)
                      +.++|||||||..+++.   +|+|+++..+  .+.+.++. .+||++|||+|+++||+.+ ..   .+++ |+|||+|++
T Consensus         2 ~~~~iytDgS~~~~~~~---~~~g~v~~~~--~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~~---~~v~-I~tDS~~v~   70 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGK---GGAGYVVWGG--RNFSFRLG-GQSNNRAELQAIIEALKAL-EH---RKVT-IYTDSQYVL   70 (132)
T ss_dssp             TSEEEEEEEEECTTTTE---EEEEEEEETT--EEEEEEEE-SECHHHHHHHHHHHHHHTH-ST---SEEE-EEES-HHHH
T ss_pred             CcEEEEEeCCccCCCCc---eEEEEEEECC--eEEEeccc-ccchhhhheehHHHHHHHh-hc---cccc-ccccHHHHH
Confidence            56899999999988765   3667665434  36676665 7999999999999999955 32   4899 999999999


Q ss_pred             ccccc
Q psy874           85 KVRNV   89 (191)
Q Consensus        85 ~~~~~   89 (191)
                      +.++.
T Consensus        71 ~~l~~   75 (132)
T PF00075_consen   71 NALNK   75 (132)
T ss_dssp             HHHHT
T ss_pred             HHHHH
Confidence            96543

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 ....

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.62  E-value=4.9e-15  Score=132.41  Aligned_cols=78  Identities=29%  Similarity=0.334  Sum_probs=64.1

Q ss_pred             cEEEEEeeccCCCCCCCCceEEEEEEcC--Cc-e-eEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChH
Q psy874            6 HVVVFTDGACPRNGKVGASAGYGVYFGE--NN-P-LNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTH   81 (191)
Q Consensus         6 ~i~IYtDGac~~N~~~~~~AG~Gv~~~~--~~-~-~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~   81 (191)
                      .++|||||||++||++   ||||+++..  +. . ..++..+ +..|||+||+.|++.||+.+.+.+.. +++ |+|||+
T Consensus         2 ~~~i~~DGa~~~n~g~---aG~G~vi~~~~~~~~~~~~~~~~-~~~tnn~AE~~All~gL~~a~~~g~~-~v~-i~~DS~   75 (372)
T PRK07238          2 KVVVEADGGSRGNPGP---AGYGAVVWDADRGEVLAERAEAI-GRATNNVAEYRGLIAGLEAAAELGAT-EVE-VRMDSK   75 (372)
T ss_pred             eEEEEecCCCCCCCCc---eEEEEEEEeCCCCcEEEEeeccc-CCCCchHHHHHHHHHHHHHHHhCCCC-eEE-EEeCcH
Confidence            4789999999999976   599998643  22 2 2445553 47899999999999999999998875 899 999999


Q ss_pred             HHHccccc
Q psy874           82 AQKKVRNV   89 (191)
Q Consensus        82 Yvv~~~~~   89 (191)
                      ||++.++.
T Consensus        76 lvi~~i~~   83 (372)
T PRK07238         76 LVVEQMSG   83 (372)
T ss_pred             HHHHHhCC
Confidence            99998764

>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=99.17  E-value=1.7e-10  Score=83.74  Aligned_cols=78  Identities=32%  Similarity=0.447  Sum_probs=58.7

Q ss_pred             EEEEeeccCCCCCCCCceEEEEEEcCC-ceeEEEeccC-CCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHHc
Q psy874            8 VVFTDGACPRNGKVGASAGYGVYFGEN-NPLNVAGKVT-GRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQKK   85 (191)
Q Consensus         8 ~IYtDGac~~N~~~~~~AG~Gv~~~~~-~~~~~s~~l~-g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv~   85 (191)
                      ++|||||+..+.+.   +|+|+++... .......... ...||+.+|+.|++.||+.+...+.. ++. |+|||+++++
T Consensus         1 ~~~~Dgs~~~~~~~---~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~-~i~-i~~Ds~~~~~   75 (130)
T cd06222           1 VIYTDGSCRGNPGP---AGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGK-KVN-IYTDSQYVIN   75 (130)
T ss_pred             CEEecccCCCCCCc---eEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCc-eEE-EEECHHHHHH
Confidence            48999999877643   6999987443 2222222211 46899999999999999999876654 899 9999999999


Q ss_pred             ccccc
Q psy874           86 VRNVS   90 (191)
Q Consensus        86 ~~~~~   90 (191)
                      .++..
T Consensus        76 ~~~~~   80 (130)
T cd06222          76 ALTGW   80 (130)
T ss_pred             Hhhcc
Confidence            77643

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.

>KOG1132|consensus

Probab=98.64  E-value=8.4e-09  Score=100.51  Aligned_cols=78  Identities=26%  Similarity=0.500  Sum_probs=70.3

Q ss_pred             cccccccccccc---eeecCCCcchhHHHHHHHHHHHHHHhhhhcC---CCCCCcceEEEeccccccchHhhhhhhccch
Q psy874           95 RIAQKVDYISHD---VISVGIPFPSIQDENVKLKRSYNDTHAQKKG---IPFPSIQDEKVKLKRSYNDTHAQKKVRNVSS  168 (191)
Q Consensus        95 ~w~~~edW~~ng---~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g---~~~~~~~~~~v~a~r~~n~~~~~~~~~~~~~  168 (191)
                      +.+++-|+.+..   ++..|+|+|.+.++.|+|++.|+|++.+.+|   ..+++.+||..+++||+||           +
T Consensus       634 KVSEGlDFsD~~~RaVI~tGlPyP~~~D~~V~lK~~y~D~~~~~~g~~s~~lsg~eWY~~qA~RAvNQ-----------A  702 (945)
T KOG1132|consen  634 KVSEGLDFSDDNGRAVIITGLPYPPVMDPRVKLKKQYLDENSSLKGAKSQLLSGQEWYSQQAYRAVNQ-----------A  702 (945)
T ss_pred             cccCCCCccccCCceeEEecCCCCCCCCHHHHHHHHhhhhhccccccccccccchHHHHhhHHHHHHH-----------H
Confidence            488999998853   6899999999999999999999999998665   3467899999999999999           9


Q ss_pred             hhHHHHhhcccceee
Q psy874          169 VAMRIAQKVDYKLLV  183 (191)
Q Consensus       169 ~~~~~~~~~~~~~~~  183 (191)
                      ++|+|+||-||++++
T Consensus       703 iGRviRHR~D~Gav~  717 (945)
T KOG1132|consen  703 IGRVIRHRNDYGAVI  717 (945)
T ss_pred             HHHHHhhhcccceee
Confidence            999999999999986

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

Probab=97.99  E-value=3.4e-05  Score=53.87  Aligned_cols=40  Identities=20%  Similarity=0.088  Sum_probs=34.3

Q ss_pred             hHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHHcccccc
Q psy874           49 NNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQKKVRNVS   90 (191)
Q Consensus        49 NnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv~~~~~~   90 (191)
                      |..||+.|++.||+.+.+.|.. ++. |+|||+-+++.++..
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~-~i~-v~sDs~~vv~~i~~~   40 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIR-KII-VESDSQLVVDAINGR   40 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-S-CEE-EEES-HHHHHHHTTS
T ss_pred             CcHHHHHHHHHHHHHHHHCCCC-EEE-EEecCcccccccccc
Confidence            5689999999999999999887 999 999999999987654

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=94.54  E-value=0.0065  Score=47.88  Aligned_cols=73  Identities=27%  Similarity=0.448  Sum_probs=55.3

Q ss_pred             ccccccccccc---eeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccccccchHhhhhhhccchhhHH
Q psy874           96 IAQKVDYISHD---VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSVAMR  172 (191)
Q Consensus        96 w~~~edW~~ng---~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~~n~~~~~~~~~~~~~~~~~  172 (191)
                      .++|.|++.+.   ++-.|.|+|..-+..++++..|.+...   +. .+...|+..++.+.+||           +++|.
T Consensus        59 ~~EGiD~~g~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~---~~-~~~~~~~~~~a~~~~~Q-----------a~GR~  123 (142)
T smart00491       59 VSEGIDFPDDLGRAVIIVGIPFPNPDSPILRARLEYLDEKG---GI-RPFDEVYLFDAMRALAQ-----------AIGRA  123 (142)
T ss_pred             eecceecCCCccEEEEEEecCCCCCCCHHHHHHHHHHHHhc---CC-CcHHHHHHHHHHHHHHH-----------HhCcc
Confidence            67888888863   567799997666666666766655432   11 23467888899999999           99999


Q ss_pred             HHhhcccceee
Q psy874          173 IAQKVDYKLLV  183 (191)
Q Consensus       173 ~~~~~~~~~~~  183 (191)
                      |+++-||+.++
T Consensus       124 iR~~~D~g~i~  134 (142)
T smart00491      124 IRHKNDYGVVV  134 (142)
T ss_pred             ccCccceEEEE
Confidence            99999999886

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=94.38  E-value=0.0097  Score=57.89  Aligned_cols=74  Identities=19%  Similarity=0.280  Sum_probs=52.5

Q ss_pred             ccccccccccccc---eeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCc-ceEEEeccccccchHhhhhhhccchh
Q psy874           94 MRIAQKVDYISHD---VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSI-QDEKVKLKRSYNDTHAQKKVRNVSSV  169 (191)
Q Consensus        94 ~~w~~~edW~~ng---~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~-~~~~v~a~r~~n~~~~~~~~~~~~~~  169 (191)
                      -+.++|.|+..+.   ++-.|.|++..-+..+..+..|-+..   .+  ..+. .||..++.|.+||           ++
T Consensus       592 Gk~sEGIDf~~~~~r~ViivGlPf~~~~~~~~~~~~~~~~~~---~~--~~~~~~~y~~~a~~~v~Q-----------ai  655 (705)
T TIGR00604       592 GKVSEGIDFCDDLGRAVIMVGIPYEYTESRILLARLEFLRDQ---YP--IRENQDFYEFDAMRAVNQ-----------AI  655 (705)
T ss_pred             CcccCccccCCCCCcEEEEEccCCCCCCCHHHHHHHHHHHhh---cC--CCccHHHHHHHHHHHHHH-----------Hh
Confidence            3588999999863   55789999443333444443332221   11  1345 8999999999999           99


Q ss_pred             hHHHHhhcccceee
Q psy874          170 AMRIAQKVDYKLLV  183 (191)
Q Consensus       170 ~~~~~~~~~~~~~~  183 (191)
                      +|.|+++-||++++
T Consensus       656 GR~IR~~~D~G~ii  669 (705)
T TIGR00604       656 GRVIRHKDDYGSIV  669 (705)
T ss_pred             CccccCcCceEEEE
Confidence            99999999999987

All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF13307 Helicase_C_2: Helicase C-terminal domain; PDB: 4A15_A 2VSF_A 3CRV_A 3CRW_1 2VL7_A

Probab=91.03  E-value=0.03  Score=44.76  Aligned_cols=72  Identities=26%  Similarity=0.392  Sum_probs=46.0

Q ss_pred             ccccccccccc---eeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccccccchHhhhhhhccchhhHH
Q psy874           96 IAQKVDYISHD---VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSVAMR  172 (191)
Q Consensus        96 w~~~edW~~ng---~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~~n~~~~~~~~~~~~~~~~~  172 (191)
                      .++|.|++...   ++-.|.|+|.+-+..+..+..|.+...   +  .+...|+..++-+.++|           +++|.
T Consensus        71 ~~EGiD~~~~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~---~--~~~~~~~~~~a~~~l~Q-----------a~GR~  134 (167)
T PF13307_consen   71 FSEGIDFPGDLLRAVIIVGLPFPPPSDPLVQAKREYLDKQG---K--NPFRDWYLPPAIRKLKQ-----------AIGRL  134 (167)
T ss_dssp             CGSSS--ECESEEEEEEES-----TTCHHHHHHHHHHHHCC---T--TCHHHHTHHHHHHHHHH-----------HHHCC
T ss_pred             EEEeecCCCchhheeeecCCCCCCCCCHHHHHHHHHHHHHh---c--cchhhHhhHHHHHHHhh-----------hcCcc
Confidence            67887888653   567899997766666777766655532   1  23578888889999999           99999


Q ss_pred             HHhhcccceee
Q psy874          173 IAQKVDYKLLV  183 (191)
Q Consensus       173 ~~~~~~~~~~~  183 (191)
                      |+++=||+.++
T Consensus       135 iR~~~D~g~i~  145 (167)
T PF13307_consen  135 IRSEDDYGVII  145 (167)
T ss_dssp             --STT-EEEEE
T ss_pred             eeccCCcEEEE
Confidence            99999999987

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=89.58  E-value=0.07  Score=41.98  Aligned_cols=72  Identities=22%  Similarity=0.283  Sum_probs=48.8

Q ss_pred             ccccccccccc---eeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCcce-EEEeccccccchHhhhhhhccchhhH
Q psy874           96 IAQKVDYISHD---VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQD-EKVKLKRSYNDTHAQKKVRNVSSVAM  171 (191)
Q Consensus        96 w~~~edW~~ng---~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~-~~v~a~r~~n~~~~~~~~~~~~~~~~  171 (191)
                      .++|.|++.+.   ++-.|.|++..-+..+.++..|.+...   +.  ++... +..++.|.++|           +++|
T Consensus        58 ~~EGiD~~g~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~---~~--~~~~~~~~~~a~~~l~Q-----------a~GR  121 (141)
T smart00492       58 FSEGVDFPGDYLRAVIIDGLPFPYPDSPILKARLELLRDKG---QI--RPFDFVSLPDAMRTLAQ-----------CVGR  121 (141)
T ss_pred             eecceecCCCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhC---CC--CchhHHHHHHHHHHHHH-----------HhCc
Confidence            34566677653   457799997666667777766655431   11  22222 23567788899           9999


Q ss_pred             HHHhhcccceee
Q psy874          172 RIAQKVDYKLLV  183 (191)
Q Consensus       172 ~~~~~~~~~~~~  183 (191)
                      .|+++=||+.++
T Consensus       122 ~iR~~~D~g~i~  133 (141)
T smart00492      122 LIRGANDYGVVV  133 (141)
T ss_pred             cccCcCceEEEE
Confidence            999999999876

>KOG1133|consensus

Probab=85.55  E-value=0.3  Score=47.96  Aligned_cols=77  Identities=18%  Similarity=0.326  Sum_probs=54.9

Q ss_pred             ccccccccccccc-c--eeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccccccchHhhhhhhccchh
Q psy874           93 AMRIAQKVDYISH-D--VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSV  169 (191)
Q Consensus        93 ~~~w~~~edW~~n-g--~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~~n~~~~~~~~~~~~~~  169 (191)
                      |-+-++|..|.+. |  ++-.|-|+|+...-=+..+.+|.+.-.   +.|+.+.++|+--..+|.||           |+
T Consensus       696 GGKlSEGINF~D~LgRaVvvVGlPyPN~~s~EL~er~k~l~~k~---~~~gagke~yEnlCMkAVNQ-----------sI  761 (821)
T KOG1133|consen  696 GGKLSEGINFSDDLGRAVVVVGLPYPNIQSVELQERMKHLDGKL---PTPGAGKELYENLCMKAVNQ-----------SI  761 (821)
T ss_pred             ccccccccccccccccEEEEeecCCCCCCCHHHHHHHHHhhhcc---CCCCchHHHHHHHHHHHHHH-----------HH
Confidence            3356677667764 3  668899997655533444556655533   33556788887777889999           99


Q ss_pred             hHHHHhhcccceee
Q psy874          170 AMRIAQKVDYKLLV  183 (191)
Q Consensus       170 ~~~~~~~~~~~~~~  183 (191)
                      +|.|+|.-||-.|+
T Consensus       762 GRAIRH~~DYA~i~  775 (821)
T KOG1133|consen  762 GRAIRHRKDYASIY  775 (821)
T ss_pred             HHHHhhhccceeEE
Confidence            99999999998875

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	191
2qk9_A	154	Human Rnase H Catalytic Domain Mutant D210n In Comp		8e-12
2qkb_A	154	Human Rnase H Catalytic Domain Mutant D210n In Comp		1e-11

>pdb|2QK9|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex With 18-Mer RnaDNA HYBRID Length = 154

Iteration: 1
 Score = 66.6 bits (161), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 39/115 (33%), Positives = 58/115 (50%), Gaps = 9/115 (7%)
Query: 7   VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
           VVV+TDG C  NG+    AG GVY+G  +PLNV  ++ GR TN  AEI  A  A++QAK+
Sbjct: 8   VVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKT 67
Query: 67  ---------ANEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYISHDVISVGI 112
                     N    +    N     KK    +S    +  K D+++ + ++ G+
Sbjct: 68  QNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGM 122

>pdb|2QKB|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex With 20-Mer RnaDNA HYBRID Length = 154

Iteration: 1
 Score = 65.9 bits (159), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 32/62 (51%), Positives = 41/62 (66%)
Query: 7  VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
          VVV+TDG C  NG+    AG GVY+G  +PLNV  ++ GR TN  AEI  A  A++QAK+
Sbjct: 8  VVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKT 67
Query: 67 AN 68
           N
Sbjct: 68 QN 69

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	191
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	4e-19
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	9e-10
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	8e-09
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	2e-08
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	6e-08
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	2e-06
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	6e-06
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	2e-05
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	1e-04
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	6e-04
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	6e-04

>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A* Length = 154

 Score = 78.8 bits (195), Expect = 4e-19
 Identities = 34/70 (48%), Positives = 45/70 (64%), Gaps = 1/70 (1%)

Query: 5  NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQA 64
          + VVV+TDG C  NG+    AG GVY+G  +PLNV  ++ GR TN  AEI  A  A++QA
Sbjct: 6  DFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQA 65

Query: 65 KSAN-EKVKL 73
          K+ N  K+ L
Sbjct: 66 KTQNINKLVL 75

>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 Length = 165

 Score = 54.1 bits (130), Expect = 9e-10
 Identities = 16/69 (23%), Positives = 23/69 (33%), Gaps = 3/69 (4%)

Query: 3  PDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALK 62
          PD     +TDG+          AG  V       +  A  +    +   AE+     ALK
Sbjct: 20 PDADYTWYTDGSSFLQEGQR-RAGAAVTTE--TEVIWARALPAGTSAQRAELIALTQALK 76

Query: 63 QAKSANEKV 71
           A+     V
Sbjct: 77 MAEGKKLNV 85

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A Length = 147

 Score = 51.2 bits (123), Expect = 8e-09
 Identities = 19/82 (23%), Positives = 30/82 (36%), Gaps = 7/82 (8%)

Query: 1  MDPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKV----TGRVTNNNAEIQG 56
          MD      V+TDG+   NG+      Y            A          + N   EI  
Sbjct: 1  MDDRTEYDVYTDGSY-VNGQYAW--AYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAA 57

Query: 57 AIHALKQAKSANEKVKLKRSYN 78
          A++A+K+A     K+++   Y 
Sbjct: 58 ALYAVKKASQLGVKIRILHDYA 79

>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism} Length = 140

 Score = 49.8 bits (120), Expect = 2e-08
 Identities = 26/97 (26%), Positives = 40/97 (41%), Gaps = 16/97 (16%)

Query: 5  NHVVVFTDGACPRN-GKVGASAGYGV--YFGENNPLNVAGKVTGRVTNNNAEIQGAIHAL 61
          N ++++TDG    N G     AG GV     + N L+ +    G  TNN AE +  I AL
Sbjct: 2  NKIIIYTDGGARGNPGP----AGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRAL 57

Query: 62 KQAKSANEKVKLKRS--YNDT---HAQK----KVRNV 89
          +  +   +K+         D+     Q     KV+  
Sbjct: 58 EDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKVKEP 94

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

 Score = 48.7 bits (117), Expect = 6e-08
 Identities = 15/62 (24%), Positives = 20/62 (32%), Gaps = 6/62 (9%)

Query: 5  NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQA 64
               + DGA  R  K+G     G          V    T   TN   E+Q    AL+ +
Sbjct: 11 GAETFYVDGAANRETKLG---KAGYVTNRGRQKVVTLTDT---TNQKTELQAIYLALQDS 64

Query: 65 KS 66
            
Sbjct: 65 GL 66

>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* Length = 142

 Score = 44.8 bits (106), Expect = 2e-06
 Identities = 13/80 (16%), Positives = 22/80 (27%), Gaps = 4/80 (5%)

Query: 7  VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
            +  D     N  +     Y     +   +    +     TNN  E    +H L+  K 
Sbjct: 12 ESLSVDVGSQGNPGIV---EYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKE 68

Query: 67 ANEKVKLKR-SYNDTHAQKK 85
           N +  +   S       K 
Sbjct: 69 RNSRKPIYSNSQTAIKWVKD 88

>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A Length = 149

 Score = 43.1 bits (102), Expect = 6e-06
 Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 6/64 (9%)

Query: 7  VVVFTDGACPRNGKVGASAGYG--VYFGENNPLNVA---GKVTGRVTNNNAEIQGAIHAL 61
          ++ + DG C      G  A +G  +Y                +   TNN AE  G I  +
Sbjct: 2  IIGYFDGLC-EPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLM 60

Query: 62 KQAK 65
          +   
Sbjct: 61 ETML 64

>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain, fusion protein, maltose binding protein, HYDR; HET: MLR TAR; 2.25A {Mycobacterium tuberculosis} Length = 141

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 6  HVVVFTDGACPRNGKVGASAGYGVYFGENN-PLNVAGKVTGRVTNNNAEIQGAIHALKQA 64
           VV+  DG    N    A  G  V+  +++  L  + +  GR TNN AE +G I  L  A
Sbjct: 3  KVVIEADGGSRGNPG-PAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDA 61

Query: 65 K 65
           
Sbjct: 62 V 62

>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A Length = 166

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 23/72 (31%), Positives = 29/72 (40%), Gaps = 9/72 (12%)

Query: 1  MDPDNHVVVFTDGACPRNGKVGASAGYGV---YFGENNPLNVAGKVTGRVTNNNAEIQGA 57
            P   V +FTDGAC  N   G   G+     +      L+     T   TNN  E++ A
Sbjct: 3  PSPRKRVALFTDGACLGNPGPG---GWAALLRFHAHEKLLSGGEACT---TNNRMELKAA 56

Query: 58 IHALKQAKSANE 69
          I  LK  K   E
Sbjct: 57 IEGLKALKEPCE 68

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii} Length = 540

 Score = 38.8 bits (90), Expect = 6e-04
 Identities = 6/31 (19%), Positives = 15/31 (48%)

Query: 107 VISVGIPFPSIQDENVKLKRSYNDTHAQKKG 137
           ++  G+P+P++ D+ V+ +         K  
Sbjct: 456 LVLAGLPYPNVSDDMVRKRIERLSKLTGKDE 486

>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A Length = 158

 Score = 37.5 bits (88), Expect = 6e-04
 Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 15/68 (22%)

Query: 1  MDPDNHVVVFTDGAC---PRNGKVGASAGYGV---YFGENNPLNVAGKVTGRVTNNNAEI 54
          M     + +FTDG+C   P  G      GYG+   Y G    ++    +T   TNN  E+
Sbjct: 1  MTELKLIHIFTDGSCLGNPGPG------GYGIVMNYKGHTKEMSDGFSLT---TNNRMEL 51

Query: 55 QGAIHALK 62
             I AL+
Sbjct: 52 LAPIVALE 59

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	191
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.96
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.96
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.95
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.94
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.93
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.93
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.93
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.92
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.88
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.87
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.86
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.85
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.83
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.81
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.68
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.67
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	89.65
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	83.6
2zd1_B	428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	81.16

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

Probab=99.96  E-value=7.9e-30  Score=204.93  Aligned_cols=125  Identities=19%  Similarity=0.162  Sum_probs=94.9

Q ss_pred             CCcEEEEEeeccCCCCCC--CCceEEEEEEcCC-ceeEEEec--c-CCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEE
Q psy874            4 DNHVVVFTDGACPRNGKV--GASAGYGVYFGEN-NPLNVAGK--V-TGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSY   77 (191)
Q Consensus         4 ~~~i~IYtDGac~~N~~~--~~~AG~Gv~~~~~-~~~~~s~~--l-~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~   77 (191)
                      +..++|||||||++||+|  .++|||||++..+ +...+++.  . .+.+||++||+.|++.||+.+...+  ++|+ |+
T Consensus         5 ~~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~~--~~v~-I~   81 (165)
T 2lsn_A            5 QYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIP--GPVL-VI   81 (165)
T ss_dssp             CCSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHSS--SCEE-EE
T ss_pred             CceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcCC--CeEE-EE
Confidence            356889999999999987  3568999987543 22333322  1 3478888899988888888776543  4899 99


Q ss_pred             cChHHHHccccccccccccccccccccccee-ecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEecc
Q psy874           78 NDTHAQKKVRNVSSVAMRIAQKVDYISHDVI-SVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLK  151 (191)
Q Consensus        78 TDS~Yvv~~~~~~~~~~~w~~~edW~~ng~~-s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~  151 (191)
                      |||+||++.++   +   |..+  |++|||. +.|+||  +|||+++.++.+..            +.+.|.+|+.|
T Consensus        82 TDS~Yvi~~it---~---w~~~--Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~------------~~v~~~~VkgH  138 (165)
T 2lsn_A           82 TDSFYVAESAN---K---ELPY--WKSNGFVNNKKKPLKHISKWKSIAECLSMK------------PDITIQHEKGH  138 (165)
T ss_dssp             ESCHHHHHHHH---T---HHHH--HHHTTSCSCSSSCCSSHHHHHHHHHHHHHC------------TTCEEEECCSS
T ss_pred             eChHHHHhhhh---h---hhhh--heeccccccCCCcccCHHHHHHHHHHHhCC------------CCEEEEEEeCC
Confidence            99999999664   2   7777  9999985 789999  89999877764421            25788888876

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

Probab=99.96  E-value=6.8e-30  Score=201.03  Aligned_cols=138  Identities=33%  Similarity=0.419  Sum_probs=112.2

Q ss_pred             CCcEEEEEeeccCCCCCCCCceEEEEEEcCCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHH
Q psy874            4 DNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQ   83 (191)
Q Consensus         4 ~~~i~IYtDGac~~N~~~~~~AG~Gv~~~~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yv   83 (191)
                      ++.++|||||||.+||++++.+|||+++.+++..+++.++.+.+|||+|||+|++.||+.+.+.+.. +++ |+|||+||
T Consensus         5 ~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~-~v~-i~tDS~~v   82 (154)
T 2qkb_A            5 GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNIN-KLV-LYTNSMFT   82 (154)
T ss_dssp             TTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCC-EEE-EEESCHHH
T ss_pred             CCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCc-eEE-EEECcHHH
Confidence            5789999999999999887789999999876666778887778999999999999999999887654 899 99999999


Q ss_pred             Hccccccccccccccccccccccee-ecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEecc--ccccchH
Q psy874           84 KKVRNVSSVAMRIAQKVDYISHDVI-SVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLK--RSYNDTH  158 (191)
Q Consensus        84 v~~~~~~~~~~~w~~~edW~~ng~~-s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~--r~~n~~~  158 (191)
                      ++.++.      |..+  |++++|. +.|.|+  ++||+++..+.+          +.   .+.|.+|+.+  +..|+.+
T Consensus        83 i~~i~~------~~~~--w~~~~w~~~~~~~~~n~~l~~~i~~l~~----------~~---~v~~~~V~~H~g~~~N~~A  141 (154)
T 2qkb_A           83 INGITN------WVQG--WKKNGWKTSAGKEVINKEDFVALERLTQ----------GM---DIQWMHVPGHSGFIGNEEA  141 (154)
T ss_dssp             HHHHHT------HHHH--HHTTTSBCTTSSBCTTHHHHHHHHHHHT----------TC---EEEEEECCTTSSCHHHHHH
T ss_pred             Hhhhhh------hHHH--HHhccccccCCCccccHHHHHHHHHHHc----------CC---ceEEEEccCCCCCHhHHHH
Confidence            997653      6677  9999985 678899  788988776643          11   4778887775  5788755


Q ss_pred             ---hhhhhh
Q psy874          159 ---AQKKVR  164 (191)
Q Consensus       159 ---~~~~~~  164 (191)
                         |.++++
T Consensus       142 D~LA~~a~~  150 (154)
T 2qkb_A          142 DRLAREGAK  150 (154)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHH
Confidence               555544

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

Probab=99.95  E-value=2e-28  Score=190.66  Aligned_cols=132  Identities=22%  Similarity=0.326  Sum_probs=102.0

Q ss_pred             CcEEEEEeeccCCCCCCCCceEEEEEEcCC-ceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHH
Q psy874            5 NHVVVFTDGACPRNGKVGASAGYGVYFGEN-NPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQ   83 (191)
Q Consensus         5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~~~~-~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yv   83 (191)
                      ..++|||||||++||++   +|||+++..+ +...+++++ +.+|||+|||+|++.||+.+.+   .++++ |+|||+||
T Consensus         3 ~~i~iytDGs~~~n~g~---~g~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~---~~~v~-I~tDS~~v   74 (146)
T 3h08_A            3 KTITIYTDGAASGNPGK---GGWGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALKE---PARVQ-LYSDSAYL   74 (146)
T ss_dssp             CEEEEEEEEEESSTTEE---EEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS---CCEEE-EEESCHHH
T ss_pred             ceEEEEEecCCCCCCCc---eEEEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcCc---cCcEE-EEeChHHH
Confidence            47999999999999965   6999987543 456677764 4789999999999999999876   34899 99999999


Q ss_pred             Hccccccccccccccccccccccee-ecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEe--ccccccchH
Q psy874           84 KKVRNVSSVAMRIAQKVDYISHDVI-SVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVK--LKRSYNDTH  158 (191)
Q Consensus        84 v~~~~~~~~~~~w~~~edW~~ng~~-s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~--a~r~~n~~~  158 (191)
                      ++.++..     |..+  |++++|. +.|.||  ++||+++..+.+.+             .+.|.+|+  .++..|+++
T Consensus        75 i~~i~~~-----w~~~--W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~-------------~v~~~~V~gH~g~~~N~~A  134 (146)
T 3h08_A           75 VNAMNEG-----WLKR--WVKNGWKTAAKKPVENIDLWQEILKLTTLH-------------RVTFHKVKGHSDNPYNSRA  134 (146)
T ss_dssp             HHHHHSS-----HHHH--HHHTTCC----CCCTTHHHHHHHHHHHHHS-------------EEEEEECCC-CCSHHHHHH
T ss_pred             HHHHHHH-----HHHH--HHHCCCccCCCCCcCCHHHHHHHHHHHhhC-------------ceEEEEcCCcCCcHhHHHH
Confidence            9987643     6777  9999985 778999  88999888876532             25566555  568999976


Q ss_pred             ---hhhhhh
Q psy874          159 ---AQKKVR  164 (191)
Q Consensus       159 ---~~~~~~  164 (191)
                         |.++++
T Consensus       135 D~LA~~a~~  143 (146)
T 3h08_A          135 DELARLAIK  143 (146)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence               555554

>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=99.94  E-value=1.6e-27  Score=188.15  Aligned_cols=130  Identities=14%  Similarity=0.127  Sum_probs=91.2

Q ss_pred             CCcEEEEEeeccCCCCCCCCceEEEEEEcCCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHH
Q psy874            4 DNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQ   83 (191)
Q Consensus         4 ~~~i~IYtDGac~~N~~~~~~AG~Gv~~~~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yv   83 (191)
                      ++.++|||||||++||++   +|||+++..++...++   .+.+|||+|||+|++.||+.+.     ++++ |+|||+||
T Consensus        10 ~~~~~iytDGs~~~n~g~---~g~G~v~~~~~~~~~~---~~~~Tnn~aEl~A~i~AL~~~~-----~~v~-i~tDS~~v   77 (150)
T 3qio_A           10 VGAETFYVDGAANRETKL---GKAGYVTNRGRQKVVT---LTDTTNQKTELQAIYLALQDSG-----LEVN-IVTDSQYA   77 (150)
T ss_dssp             TTCEEEEEEEEECTTTCC---EEEEEEETTSCEEEEE---ESSCCHHHHHHHHHHHHHHHSC-----SEEE-EEESCHHH
T ss_pred             CCCEEEEEccCCCCCCCC---eEEEEEEEcCCEEEEe---CCCCCHHHHHHHHHHHHHHhCC-----CcEE-EEeCcHHH
Confidence            578999999999999988   4999987655443332   2479999999999999999852     4899 99999999


Q ss_pred             Hccccccccccccccccccccccee-ecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEecc--ccccchH
Q psy874           84 KKVRNVSSVAMRIAQKVDYISHDVI-SVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLK--RSYNDTH  158 (191)
Q Consensus        84 v~~~~~~~~~~~w~~~edW~~ng~~-s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~--r~~n~~~  158 (191)
                      ++.++.      |..+  |++|||. +.|.||  +|||++++++..+         .   ..+.|.+|+.+  ...|+++
T Consensus        78 ~~~i~~------w~~~--W~~~gw~~~~g~~v~n~~l~~~l~~~l~~---------~---~~v~~~wV~gH~g~~~Ne~A  137 (150)
T 3qio_A           78 LGIITQ------WIHN--WKKRGWKTADKKPVKNVDLVNQIIEQLIK---------K---EKVYLAWVPAHKGIGGNEQV  137 (150)
T ss_dssp             HHHHHH------HHHH--HCC------------CHHHHHHHHHHHTT---------C---SEEEEEECCTTSCCHHHHHH
T ss_pred             HHHHHH------HHHH--HhhcCcCcCcCcccccHHHHHHHHHHHhh---------c---CceEEEEccCcCCChhHHHH
Confidence            997652      7777  9999995 778999  8899887654321         1   24777777765  4677765


Q ss_pred             ---hhhhhhc
Q psy874          159 ---AQKKVRN  165 (191)
Q Consensus       159 ---~~~~~~~  165 (191)
                         |.+++++
T Consensus       138 D~LA~~a~~~  147 (150)
T 3qio_A          138 DKLVSAGIRK  147 (150)
T ss_dssp             HHHHHTTTSC
T ss_pred             HHHHHHHHHH
Confidence               6666654

>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ...

Probab=99.93  E-value=7.6e-27  Score=184.30  Aligned_cols=131  Identities=20%  Similarity=0.178  Sum_probs=101.8

Q ss_pred             CcEEEEEeeccCCCCCCCCceEEEEEEc-CCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHH
Q psy874            5 NHVVVFTDGACPRNGKVGASAGYGVYFG-ENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQ   83 (191)
Q Consensus         5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~~-~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yv   83 (191)
                      ..++|||||||.+||++   +|||+++. .++...+++++ +.+|||+|||+|++.||+.+.+.   ++++ |+|||+||
T Consensus         3 ~~~~iytDGs~~~n~~~---~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~~---~~v~-I~tDS~~v   74 (155)
T 1jl1_A            3 KQVEIFTAGSALGNPGP---GGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKEH---AEVI-LSTDSQYV   74 (155)
T ss_dssp             CCEEEEEEEEESSTTEE---EEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCSC---CEEE-EEECCHHH
T ss_pred             ceEEEEEccccCCCCCc---eEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCcC---CcEE-EEeCHHHH
Confidence            35899999999999976   69999874 34556677764 46899999999999999998763   4899 99999999


Q ss_pred             Hccccccccccccccccccccccee-ecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEecc--ccccchH
Q psy874           84 KKVRNVSSVAMRIAQKVDYISHDVI-SVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLK--RSYNDTH  158 (191)
Q Consensus        84 v~~~~~~~~~~~w~~~edW~~ng~~-s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~--r~~n~~~  158 (191)
                      ++.++.      |..+  |++|+|. +.|.||  ++||+++..+.+.             ..+.|.+|++|  +..|+.+
T Consensus        75 i~~i~~------w~~~--W~~n~~~~~~g~~v~n~~l~~~i~~l~~~-------------~~v~~~wV~gH~g~~~Ne~A  133 (155)
T 1jl1_A           75 RQGITQ------WIHN--WKKRGWKTADKKPVKNVDLWQRLDAALGQ-------------HQIKWEWVKGHAGHPENERA  133 (155)
T ss_dssp             HHHHHT------THHH--HHHTTTBCTTSCBCTTHHHHHHHHHHTTT-------------CEEEEEECCSSTTCHHHHHH
T ss_pred             HHHHHH------HHHH--HhhcccccccCCccCCHHHHHHHHHHHcc-------------CceEEEEcCCCCCCHHHHHH
Confidence            997653      7777  9999985 778999  6888876665321             14777777765  8899855


Q ss_pred             ---hhhhhh
Q psy874          159 ---AQKKVR  164 (191)
Q Consensus       159 ---~~~~~~  164 (191)
                         |.++++
T Consensus       134 D~LA~~a~~  142 (155)
T 1jl1_A          134 DELARAAAM  142 (155)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence               444443

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

Probab=99.93  E-value=1.4e-26  Score=183.53  Aligned_cols=131  Identities=21%  Similarity=0.245  Sum_probs=102.6

Q ss_pred             CcEEEEEeeccCCCCCCCCceEEEEEEc-CCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHH
Q psy874            5 NHVVVFTDGACPRNGKVGASAGYGVYFG-ENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQ   83 (191)
Q Consensus         5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~~-~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yv   83 (191)
                      ..++|||||||.+||++   +|||+++. .++...+++++ +.+|||+|||+|++.||+.+.+.   ++++ |+|||+||
T Consensus         5 ~~i~iytDGs~~~n~g~---~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~~---~~v~-I~tDS~~v   76 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGP---GGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKEP---CKII-LTSDSQYM   76 (158)
T ss_dssp             CEEEEEEEEEESSSSEE---EEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSSC---CEEE-EEECCHHH
T ss_pred             CeEEEEEcccccCCCCc---EEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhccC---CeEE-EEeCHHHH
Confidence            56999999999999976   69999874 34556677764 36899999999999999998753   4899 99999999


Q ss_pred             Hccccccccccccccccccccccee-ecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEecc--ccccchH
Q psy874           84 KKVRNVSSVAMRIAQKVDYISHDVI-SVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLK--RSYNDTH  158 (191)
Q Consensus        84 v~~~~~~~~~~~w~~~edW~~ng~~-s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~--r~~n~~~  158 (191)
                      ++.++.      |..+  |++|+|. +.|.||  ++||+++..+.+.             ..+.|.+|++|  +..|+.+
T Consensus        77 i~~i~~------w~~~--W~~n~~~~~~g~~v~n~~l~~~i~~l~~~-------------~~v~~~wV~gH~g~~~Ne~A  135 (158)
T 2e4l_A           77 RQGIMT------WIHG--WKKKGWMTSNRTPVKNVDLWKRLDKAAQL-------------HQIDWRWVKGHAGHAENERC  135 (158)
T ss_dssp             HHHHHT------HHHH--HHHTTTBCTTSSBCTTHHHHHHHHHHHTT-------------SEEEEEECCTTCCCHHHHHH
T ss_pred             HHHHHH------HHHH--HHHccccccCCCcccCHHHHHHHHHHHcc-------------CcEEEEEccCCCCchhHHHH
Confidence            997653      7777  9999985 778999  7899877665431             14778877765  8899855


Q ss_pred             ---hhhhhh
Q psy874          159 ---AQKKVR  164 (191)
Q Consensus       159 ---~~~~~~  164 (191)
                         |.++++
T Consensus       136 D~LAk~a~~  144 (158)
T 2e4l_A          136 DQLARAAAE  144 (158)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence               444443

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

Probab=99.93  E-value=6.4e-27  Score=187.10  Aligned_cols=138  Identities=23%  Similarity=0.318  Sum_probs=103.1

Q ss_pred             CCCC--CcEEEEEeeccCCCCCCCCceEEEEEEc-CCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEE
Q psy874            1 MDPD--NHVVVFTDGACPRNGKVGASAGYGVYFG-ENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSY   77 (191)
Q Consensus         1 ~~~~--~~i~IYtDGac~~N~~~~~~AG~Gv~~~-~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~   77 (191)
                      |+++  +.++|||||||.+||++   +|||+++. .++...+++++ +.+|||+|||+|++.||+.+.+.   ++++ |+
T Consensus         1 ~~p~~m~~i~iytDGs~~~n~g~---~G~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~Ai~~AL~~~~~~---~~v~-I~   72 (166)
T 1ril_A            1 MNPSPRKRVALFTDGACLGNPGP---GGWAALLRFHAHEKLLSGGE-ACTTNNRMELKAAIEGLKALKEP---CEVD-LY   72 (166)
T ss_dssp             -----CCCCCEEEEEEESSTTEE---EEEEEEECBTTBCCEECCEE-EEECHHHHHHHHHHHHHHSCCSC---CEEE-EE
T ss_pred             CCCCCCccEEEEECccccCCCCC---EEEEEEEEECCEEEEEecCC-CCCcHHHHHHHHHHHHHHHhccC---CeEE-EE
Confidence            4554  35899999999999976   69999874 34555666653 46899999999999999988763   4899 99


Q ss_pred             cChHHHHccccccccccccccccccccccee-ecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEec--cc
Q psy874           78 NDTHAQKKVRNVSSVAMRIAQKVDYISHDVI-SVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKL--KR  152 (191)
Q Consensus        78 TDS~Yvv~~~~~~~~~~~w~~~edW~~ng~~-s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a--~r  152 (191)
                      |||+||++.++..     |..+  |++|+|. +.|.||  ++||+++..+.+.          .   .+.|.+|++  ++
T Consensus        73 tDS~~vi~~i~~~-----w~~~--W~~~~w~~~~g~~v~n~~l~~~i~~l~~~----------~---~v~~~wV~gH~g~  132 (166)
T 1ril_A           73 TDSHYLKKAFTEG-----WLEG--WRKRGWRTAEGKPVKNRDLWEALLLAMAP----------H---RVRFHFVKGHTGH  132 (166)
T ss_dssp             CCCHHHHHHHHSS-----HHHH--HHHTTSBCTTSSBCTTHHHHHHHHHHHTT----------S---EEECCCCCGGGSC
T ss_pred             eChHHHHHHHhhh-----HHHH--HHhcccccccCCccCcHHHHHHHHHHHhc----------C---eEEEEEeeCCCCc
Confidence            9999999977642     6677  9999985 778999  6799887766432          1   355555554  59


Q ss_pred             cccchH---hhhhhhcc
Q psy874          153 SYNDTH---AQKKVRNV  166 (191)
Q Consensus       153 ~~n~~~---~~~~~~~~  166 (191)
                      ..|+.+   |.++++..
T Consensus       133 ~~Ne~AD~LAk~a~~~~  149 (166)
T 1ril_A          133 PENERVDREARRQAQSQ  149 (166)
T ss_dssp             THHHHHHHHHHHHHTSS
T ss_pred             hhHHHHHHHHHHHHHHh
Confidence            999866   66666554

>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=99.92  E-value=1e-25  Score=175.83  Aligned_cols=117  Identities=15%  Similarity=0.057  Sum_probs=88.4

Q ss_pred             CCCcEEEEEeeccCCCCCCCCceEEE-EEEcCCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChH
Q psy874            3 PDNHVVVFTDGACPRNGKVGASAGYG-VYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTH   81 (191)
Q Consensus         3 ~~~~i~IYtDGac~~N~~~~~~AG~G-v~~~~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~   81 (191)
                      |++...|||||||++||+|   +||| |++..++....++++ +.+|||+|||+|+++||+.+++.+.  ++. |+|||+
T Consensus         2 ep~~~~iytDGac~GNPGp---~G~ggV~~~~g~~~~~~g~~-~~tTNN~aEl~A~i~aL~~l~~~~~--~v~-i~tDSq   74 (134)
T 4htu_A            2 EIIWESLSVDVGSQGNPGI---VEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERNS--RKP-IYSNSQ   74 (134)
T ss_dssp             CCCSSSEEEEEEEETTTEE---EEEEEEETTTCCEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHTTC--CCC-EEESCH
T ss_pred             CccceEEEEeeccCCCCCC---eEEEEEEEECCEEEEEecCC-CCCchHHHHHHHHHHHHHHHHhCCC--CEE-EEcchH
Confidence            6788899999999999987   5994 555656667777663 4799999999999999999998654  578 999999


Q ss_pred             HHHcccccccccccccccccccccce-eecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceE
Q psy874           82 AQKKVRNVSSVAMRIAQKVDYISHDV-ISVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDE  146 (191)
Q Consensus        82 Yvv~~~~~~~~~~~w~~~edW~~ng~-~s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~  146 (191)
                      ||++          |..+  |   +| ++.++||  +|||+++..+.+-+...     ....+-+.|+
T Consensus        75 yVi~----------wi~~--~---~~kt~~~~~vkN~dLw~~ld~~~~~l~~~-----~~~~~~~kw~  122 (134)
T 4htu_A           75 TAIK----------WVKD--K---KAKSTLVRNEETALIWKLVDEAEEWLNTH-----TYETPILKWQ  122 (134)
T ss_dssp             HHHH----------HHHH--T---CCCCCCCCSSTTHHHHHHHHHHHHHHHHC-----CCCCCEEECC
T ss_pred             HHHH----------HHHc--C---CcccCCCCCccCHHHHHHHHHHHHHHHhC-----CCCCceEEEE
Confidence            9997          3333  2   23 4668999  89999877775555432     2333446665

>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=99.88  E-value=2.9e-23  Score=163.10  Aligned_cols=105  Identities=14%  Similarity=0.004  Sum_probs=80.3

Q ss_pred             CCCcEEEEEeeccCCCCCCCCceEEEEEEc-CCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChH
Q psy874            3 PDNHVVVFTDGACPRNGKVGASAGYGVYFG-ENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTH   81 (191)
Q Consensus         3 ~~~~i~IYtDGac~~N~~~~~~AG~Gv~~~-~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~   81 (191)
                      +++.++|||||||++||++   +|||+++. .++....++++ +.+|||+|||+|+++||+.+.+.+.  ++. |+|||+
T Consensus         8 ~~~~~~iy~DGa~~gNpG~---~G~G~vl~~~g~~~~~~~~~-~~~TNN~aEl~A~i~aL~~~~~~~~--~v~-i~tDS~   80 (142)
T 1zbf_A            8 EIIWESLSVDVGSQGNPGI---VEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERNS--RKP-IYSNSQ   80 (142)
T ss_dssp             CCCSSSEEEEEEECSSSEE---EEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHHTTC--CCC-EEESCH
T ss_pred             CCCeEEEEEeeccCCCCCC---eEEEEEEEeCCEEEEEeccc-CCcCcHHHHHHHHHHHHHHHHhCCC--eEE-EEEehH
Confidence            3467899999999999976   69999885 45555566653 4689999999999999999998764  799 999999


Q ss_pred             HHHcccccccccccccccccccccceeecCCCc--chhHHHHHHHHHHH
Q psy874           82 AQKKVRNVSSVAMRIAQKVDYISHDVISVGIPF--PSIQDENVKLKRSY  128 (191)
Q Consensus        82 Yvv~~~~~~~~~~~w~~~edW~~ng~~s~G~PV--~dL~~~~v~l~~~~  128 (191)
                      ||++.+          .+. |.+   ++.+.||  +|||+++..+.+-.
T Consensus        81 ~vi~w~----------~~~-~~k---~~~~~~v~n~dLw~~l~~~~~w~  115 (142)
T 1zbf_A           81 TAIKWV----------KDK-KAK---STLVRNEETALIWKLVDEAEEWL  115 (142)
T ss_dssp             HHHHHH----------HHT-CCC---CCCCCSTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHH----------HcC-Ccc---CCCCCCcccHHHHHHHHHHHHHH
Confidence            999922          111 211   2346788  88999877765444

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

Probab=99.87  E-value=1.1e-21  Score=149.05  Aligned_cols=127  Identities=22%  Similarity=0.361  Sum_probs=86.6

Q ss_pred             CcEEEEEeeccCCCCCCCCceEEEEEEcC--Ccee-EEEeccCCCCChHHHHHHHHHHHHHHhHhcCCc---ceeEEEEc
Q psy874            5 NHVVVFTDGACPRNGKVGASAGYGVYFGE--NNPL-NVAGKVTGRVTNNNAEIQGAIHALKQAKSANEK---VKLKRSYN   78 (191)
Q Consensus         5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~~~--~~~~-~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~---~~v~~I~T   78 (191)
                      ..++|||||||.+||++   +|||+++..  ++.. ..++++ +.+|||+|||+|++.||+.+.+.+..   .+++ |+|
T Consensus         2 ~~~~iy~DGs~~~n~g~---~G~G~v~~~~~g~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~-i~t   76 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGP---AGIGVVITDEKGNTLHESSAYI-GETTNNVAEYEALIRALEDLQMFGDKLVDMEVE-VRM   76 (140)
T ss_dssp             CEEEEEEEEEESSTTEE---EEEEEEEECTTSCEEEEEEEEE-EEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEE-EEE
T ss_pred             ceEEEEEecCCCCCCCC---cEEEEEEEeCCCCEEEEEEeeC-CCCchHHHHHHHHHHHHHHHHHcCCCCCCceEE-EEe
Confidence            35899999999999876   699998743  3332 556654 46899999999999999999876431   1799 999


Q ss_pred             ChHHHHcccccccccccccccccccccceeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccccccchH
Q psy874           79 DTHAQKKVRNVSSVAMRIAQKVDYISHDVISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTH  158 (191)
Q Consensus        79 DS~Yvv~~~~~~~~~~~w~~~edW~~ng~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~~n~~~  158 (191)
                      ||+||++.++..           |+-..        ++||+.+..+.+..-..+        ..+.|.+|+  |..|+.+
T Consensus        77 DS~~vi~~i~~~-----------~~~~~--------~~l~~~~~~i~~l~~~~~--------~~v~~~~V~--~~~N~~A  127 (140)
T 3u3g_D           77 DSELIVRQMQGV-----------YKVKE--------PTLKEKFAKIAHIKMERV--------PNLVFVHIP--REKNARA  127 (140)
T ss_dssp             SCHHHHHHHTTS-----------SCCCC--------GGGHHHHHHHHHHHHHHC--------TTCEEEECC--GGGGHHH
T ss_pred             ChHHHHHHhCCC-----------cccCC--------HHHHHHHHHHHHHhhcCC--------CcEEEEEcC--chhhHHH
Confidence            999999966532           32111        455553323222101221        257888776  7899865


Q ss_pred             ---hhhhhhc
Q psy874          159 ---AQKKVRN  165 (191)
Q Consensus       159 ---~~~~~~~  165 (191)
                         |+++++.
T Consensus       128 D~LA~~a~~~  137 (140)
T 3u3g_D          128 DELVNEAIDK  137 (140)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence               6665544

>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=99.86  E-value=1.8e-21  Score=148.69  Aligned_cols=124  Identities=24%  Similarity=0.277  Sum_probs=86.6

Q ss_pred             cEEEEEeeccCCCCCCCCceEEEEEEcC---Cce-eEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChH
Q psy874            6 HVVVFTDGACPRNGKVGASAGYGVYFGE---NNP-LNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTH   81 (191)
Q Consensus         6 ~i~IYtDGac~~N~~~~~~AG~Gv~~~~---~~~-~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~   81 (191)
                      .++|||||||.+||++   +|||+++..   +.. ..+++++ +.+|||+|||+|++.||+.+.+.+.. +++ |+|||+
T Consensus         3 ~~~iy~DGs~~~~~g~---~g~G~v~~~~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~-~v~-i~tDS~   76 (141)
T 3hst_B            3 KVVIEADGGSRGNPGP---AGYGAVVWTADHSTVLAESKQAI-GRATNNVAEYRGLIAGLDDAVKLGAT-EAA-VLMDSK   76 (141)
T ss_dssp             EEEEEEEEEESSSSEE---EEEEEEEEETTSCSEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHHTCS-EEE-EEESCH
T ss_pred             EEEEEEecCCCCCCCC---cEEEEEEEeCCCCcEEEeeeccC-CCCchHHHHHHHHHHHHHHHHHCCCc-eEE-EEeChH
Confidence            5899999999999876   699998743   222 3456554 47899999999999999999987765 899 999999


Q ss_pred             HHHcccccccccccccccccccccceeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccccccchH---
Q psy874           82 AQKKVRNVSSVAMRIAQKVDYISHDVISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTH---  158 (191)
Q Consensus        82 Yvv~~~~~~~~~~~w~~~edW~~ng~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~~n~~~---  158 (191)
                      ||++.++..           |+.+.        ++||+.+.++ ...   ..   .  +..+.|.+|+  |..|+.+   
T Consensus        77 ~vv~~i~~~-----------~~~~~--------~~l~~~~~~i-~~l---~~---~--~~~v~~~~V~--~~~N~~AD~L  126 (141)
T 3hst_B           77 LVVEQMSGR-----------WKVKH--------PDLLKLYVQA-QAL---AS---Q--FRRINYEWVP--RARNTYADRL  126 (141)
T ss_dssp             HHHHHHTTS-----------SCCCS--------HHHHHHHHHH-HHH---HT---T--SSEEEEEECC--GGGCHHHHHH
T ss_pred             HHHHHHhCC-----------cccCC--------HHHHHHHHHH-HHH---Hh---c--CCeEEEEEcC--CcccHHHHHH
Confidence            999976532           43111        5555532222 111   11   1  1357888666  7889866   


Q ss_pred             hhhhhhc
Q psy874          159 AQKKVRN  165 (191)
Q Consensus       159 ~~~~~~~  165 (191)
                      |+++++.
T Consensus       127 A~~a~~~  133 (141)
T 3hst_B          127 ANDAMDA  133 (141)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            6655543

>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A 4e89_A

Probab=99.85  E-value=5.3e-22  Score=159.13  Aligned_cols=120  Identities=17%  Similarity=0.075  Sum_probs=87.3

Q ss_pred             cEEEEEeeccCCCCCCCCceEEEEEE-cCCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHH
Q psy874            6 HVVVFTDGACPRNGKVGASAGYGVYF-GENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQK   84 (191)
Q Consensus         6 ~i~IYtDGac~~N~~~~~~AG~Gv~~-~~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv   84 (191)
                      .++|||||||++||++   +|||+++ ..++....+ .+.+.+|||+|||+|++.||+.+.    .++++ |+|||+||+
T Consensus        23 ~i~iytDGs~~~npG~---~g~G~vi~~~~~~~~~~-~~~~~~Tnn~aEl~Ai~~AL~~~~----~~~v~-I~tDS~~vi   93 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQ---RRAGAAVTTETEVIWAR-ALPAGTSAQRAELIALTQALKMAE----GKKLN-VYTDSRYAF   93 (165)
T ss_dssp             SEEEEEEEEEEEETTE---EEEEEEEECSSCEEEEE-EECTTCCHHHHHHHHHHHHHHHTB----TSEEE-EEECCHHHH
T ss_pred             CEEEEEEcccCCCCCc---eEEEEEEEECCEEEEEe-cCCCCCcHHHHHHHHHHHHHHHcc----CceEE-EEEchHHHH
Confidence            4899999999999976   5899854 444544444 345678999999999999999983    24899 999999999


Q ss_pred             cccccccccccccccccccccceeecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccc-------ccc
Q psy874           85 KVRNVSSVAMRIAQKVDYISHDVISVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKR-------SYN  155 (191)
Q Consensus        85 ~~~~~~~~~~~w~~~edW~~ng~~s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r-------~~n  155 (191)
                      +.+              |.    ++.|.||  +|||++++....         .+   ..+.|.+|+.+.       ..|
T Consensus        94 ~~i--------------w~----~~~g~~v~n~dl~~~l~~~l~---------~~---~~v~~~wVkgH~g~~~~~~~gN  143 (165)
T 3p1g_A           94 ATA--------------HV----HSEGREIKNKNEILALLKALF---------LP---KRLSIIHCPGHQKGNSAEARGN  143 (165)
T ss_dssp             HHH--------------HS----CCCSCCCSSHHHHHHHHHHTT---------SB---SEEEEEECCSSCCSCSHHHHHH
T ss_pred             hhh--------------hc----ccCCCcccCHHHHHHHHHHHh---------cC---CceEEEEecCCCCCCcCcchHH
Confidence            955              21    2457888  788887654321         01   358888888764       567


Q ss_pred             chH---hhhhhh
Q psy874          156 DTH---AQKKVR  164 (191)
Q Consensus       156 ~~~---~~~~~~  164 (191)
                      +++   |.++++
T Consensus       144 e~AD~LA~~aa~  155 (165)
T 3p1g_A          144 RMADQAAREAAM  155 (165)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            755   555544

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

Probab=99.83  E-value=3.7e-20  Score=143.86  Aligned_cols=123  Identities=18%  Similarity=0.172  Sum_probs=85.9

Q ss_pred             cEEEEEeeccC-CCCCCCCceE-EEEEE-cCCceeE-EEeccC---CCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEc
Q psy874            6 HVVVFTDGACP-RNGKVGASAG-YGVYF-GENNPLN-VAGKVT---GRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYN   78 (191)
Q Consensus         6 ~i~IYtDGac~-~N~~~~~~AG-~Gv~~-~~~~~~~-~s~~l~---g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~T   78 (191)
                      +++|||||||. +||++   +| ||+++ .+|+... .+..+.   +.+|||+|||+|++.||+.+.+.+.. +++ |+|
T Consensus         1 m~~iy~DGs~~~~n~g~---~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~-~v~-i~t   75 (149)
T 2ehg_A            1 MIIGYFDGLCEPKNPGG---IATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGIS-SPI-IKG   75 (149)
T ss_dssp             CCEEEEEEEEESSSSSS---EEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCC-SCE-EEE
T ss_pred             CEEEEEeeccCCCCCCh---heEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCC-EEE-EEe
Confidence            57899999999 89876   58 49865 3455433 233222   37899999999999999999987765 899 999


Q ss_pred             ChHHHHcccccccccccccccccccccceeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccccccchH
Q psy874           79 DTHAQKKVRNVSSVAMRIAQKVDYISHDVISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTH  158 (191)
Q Consensus        79 DS~Yvv~~~~~~~~~~~w~~~edW~~ng~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~~n~~~  158 (191)
                      ||+||++.++..           |+.+     .....+||+++..+.+.+             ++.|.+|+  |..|+.+
T Consensus        76 DS~~vi~~i~~~-----------w~~~-----~~~~~~l~~~i~~l~~~~-------------~v~~~~V~--~~~N~~A  124 (149)
T 2ehg_A           76 DSQLVIKQMNGE-----------YKVK-----AKRIIPLYEKAIELKKKL-------------NATLIWVP--REENKEA  124 (149)
T ss_dssp             SCHHHHHHHTTS-----------SCCC-----CTTHHHHHHHHHHHHHHH-------------TCEEEECC--GGGCHHH
T ss_pred             ChHHHHHHHhCc-----------cccC-----CHHHHHHHHHHHHHHhcC-------------CEEEEEcC--CcccHHH
Confidence            999999966432           3322     123478888777665543             25677555  4778754


Q ss_pred             ---hhhhhh
Q psy874          159 ---AQKKVR  164 (191)
Q Consensus       159 ---~~~~~~  164 (191)
                         |+++++
T Consensus       125 D~LA~~a~~  133 (149)
T 2ehg_A          125 DRLSRVAYE  133 (149)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence               554443

>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=99.81  E-value=1.7e-21  Score=152.62  Aligned_cols=77  Identities=21%  Similarity=0.207  Sum_probs=60.2

Q ss_pred             CCCCCcEEEEEeeccCCCCCCCCceEEEEEEc-CCceeEEEe-cc--CC--CCChHHHHHHHHHHHHHHhHhcCCcceeE
Q psy874            1 MDPDNHVVVFTDGACPRNGKVGASAGYGVYFG-ENNPLNVAG-KV--TG--RVTNNNAEIQGAIHALKQAKSANEKVKLK   74 (191)
Q Consensus         1 ~~~~~~i~IYtDGac~~N~~~~~~AG~Gv~~~-~~~~~~~s~-~l--~g--~~TNnrAEL~Avi~AL~~~~~~~~~~~v~   74 (191)
                      |-+++.++|||||||++  ++   +|||+++. +++...+++ .+  +.  .+|||+|||+|++.||+.+.+.+.  +++
T Consensus         1 ~~~~~~i~iytDGs~~~--g~---~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~--~v~   73 (147)
T 2kq2_A            1 MDDRTEYDVYTDGSYVN--GQ---YAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV--KIR   73 (147)
T ss_dssp             CCTTSCCEEECCCCCBT--TB---CEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC--CCC
T ss_pred             CCCCCeEEEEECCCCCC--CC---cEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC--eEE
Confidence            56788999999999987  33   69999874 455556665 32  21  479999999999999998877654  799


Q ss_pred             EEEcChHHHHc
Q psy874           75 RSYNDTHAQKK   85 (191)
Q Consensus        75 ~I~TDS~Yvv~   85 (191)
                       |+|||+.+.+
T Consensus        74 -I~tDS~~i~~   83 (147)
T 2kq2_A           74 -ILHDYAGIAF   83 (147)
T ss_dssp             -BSSCCSTHHH
T ss_pred             -EEECcHHHHH
Confidence             9999976554

>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=99.68  E-value=7.4e-17  Score=149.38  Aligned_cols=112  Identities=18%  Similarity=0.141  Sum_probs=80.0

Q ss_pred             CCcEEEEEeeccCCCCCCCCceEEEEEEcCCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHH
Q psy874            4 DNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQ   83 (191)
Q Consensus         4 ~~~i~IYtDGac~~N~~~~~~AG~Gv~~~~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yv   83 (191)
                      ++.++|||||||.+||++   +|||+++..++..  ++. .+.+|||+|||+|++.||+.    + .++++ |+|||+||
T Consensus       434 ~~~~~iytDGs~~~n~g~---~g~G~v~~~~~~~--~~~-~~~~TNn~aEl~A~i~aL~~----~-~~~v~-I~tDS~~v  501 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKE---GKAGYVTDRGKDK--VKK-LEQTTNQQAELEAFAMALTD----S-GPKVN-IIVDSQYV  501 (555)
T ss_dssp             TTCEEEEEEEEECTTTCC---EEEEEEETTSCEE--EEE-ESSCCHHHHHHHHHHHHHHT----S-CSEEE-EEESCHHH
T ss_pred             CCceEEEEcccccCCCCC---ceEEEEEEeCCEe--ecc-CCCCCHHHHHHHHHHHHHHc----C-CCeEE-EEEehHHH
Confidence            467999999999999987   4999987555432  333 24789999999999999997    2 24899 99999999


Q ss_pred             HcccccccccccccccccccccceeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEec--cccccchH
Q psy874           84 KKVRNVSSVAMRIAQKVDYISHDVISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKL--KRSYNDTH  158 (191)
Q Consensus        84 v~~~~~~~~~~~w~~~edW~~ng~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a--~r~~n~~~  158 (191)
                      ++.++.            |+..    ++   +++|++++++...         .   ..+.|.+|+.  ++..|+++
T Consensus       502 ~~~i~~------------~~~~----~~---~~l~~~~~~~~~~---------~---~~v~~~wV~~H~g~~~Ne~A  547 (555)
T 1mu2_A          502 MGIVAS------------QPTE----SE---SKIVNQIIEEMIK---------K---EAIYVAWVPAHKGIGGNQEV  547 (555)
T ss_dssp             HHHHHT------------CCSE----ES---CHHHHHHHHHHHH---------C---SEEEEEECCSSSCCTTHHHH
T ss_pred             HHHHhc------------cccc----cc---HHHHHHHHHHhcc---------C---CcEEEEEEECCCCChhHHHH
Confidence            996643            3321    11   6677755554332         1   2466777666  56889865

>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=99.67  E-value=8.4e-17  Score=149.09  Aligned_cols=74  Identities=19%  Similarity=0.230  Sum_probs=60.8

Q ss_pred             CCcEEEEEeeccCCCCCCCCceEEEEEEcCCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHH
Q psy874            4 DNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQ   83 (191)
Q Consensus         4 ~~~i~IYtDGac~~N~~~~~~AG~Gv~~~~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yv   83 (191)
                      ++.++|||||||.+||++   +|||+++..++...+  . .+.+|||+|||+|++.||+.+     .+++. |+|||+||
T Consensus       437 ~~~~~iytDGs~~~n~g~---~g~g~v~~~~~~~~~--~-~~~~TNn~aEl~Ai~~aL~~~-----~~~v~-I~tDS~~v  504 (557)
T 2zd1_A          437 VGAETFYVDGAANRETKL---GKAGYVTNKGRQKVV--P-LTNTTNQKTELQAIYLALQDS-----GLEVN-IVTDSQYA  504 (557)
T ss_dssp             TTSCEEEEEEEECTTTCC---EEEEEEETTSCEEEE--E-ECSCCHHHHHHHHHHHHHHHS-----CSEEE-EEECCHHH
T ss_pred             CCCEEEEEccCCCCCCCc---eEEEEEEECCcEEEe--c-CCCCCHHHHHHHHHHHHHHhC-----CCcEE-EEeChHHH
Confidence            456999999999999987   499998765554433  2 247899999999999999998     24899 99999999


Q ss_pred             Hccccc
Q psy874           84 KKVRNV   89 (191)
Q Consensus        84 v~~~~~   89 (191)
                      ++.++.
T Consensus       505 i~~i~~  510 (557)
T 2zd1_A          505 LGIIQA  510 (557)
T ss_dssp             HHHHTT
T ss_pred             HHHHhc
Confidence            997653

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=89.65  E-value=0.029  Score=51.20  Aligned_cols=72  Identities=18%  Similarity=0.213  Sum_probs=54.0

Q ss_pred             ccccccccc---cc---ceeecCCCcchhHHHHHHHHHHHHHHhhhhcCCCCCCc-ceEEEeccccccchHhhhhhhccc
Q psy874           95 RIAQKVDYI---SH---DVISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSI-QDEKVKLKRSYNDTHAQKKVRNVS  167 (191)
Q Consensus        95 ~w~~~edW~---~n---g~~s~G~PV~dL~~~~v~l~~~~~d~~~~~~g~~~~~~-~~~~v~a~r~~n~~~~~~~~~~~~  167 (191)
                      ++++|.|++   .+   .++-.|.|+|.. +..++.+.+|-+.-   .|.  +++ .+|..++.+.+||           
T Consensus       448 ~~~EGiD~~d~~g~~l~~viI~~lPfp~~-dp~~~ar~~~~~~~---~g~--~~~~~~y~~pa~~~l~Q-----------  510 (551)
T 3crv_A          448 KLAEGIELRNNDRSLISDVVIVGIPYPPP-DDYLKILAQRVSLK---MNR--ENEEFLFKIPALVTIKQ-----------  510 (551)
T ss_dssp             CSCCSSCCEETTEESEEEEEEESCCCCCC-SHHHHHHHHHTTCC---SST--TTHHHHTHHHHHHHHHH-----------
T ss_pred             eecccccccccCCcceeEEEEEcCCCCCC-CHHHHHHHHHHHHh---hCC--chhHHHHHHHHHHHHHH-----------
Confidence            688999998   32   356789999877 87777776664421   132  233 4477888999999           


Q ss_pred             hhhHHHHhhcccceee
Q psy874          168 SVAMRIAQKVDYKLLV  183 (191)
Q Consensus       168 ~~~~~~~~~~~~~~~~  183 (191)
                      +++|.|+++=||+.++
T Consensus       511 a~GRlIR~~~D~G~v~  526 (551)
T 3crv_A          511 AIGRAIRDVNDKCNVW  526 (551)
T ss_dssp             HHHTTCCSTTCEEEEE
T ss_pred             HhccCccCCCccEEEE
Confidence            9999999999999886

>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=83.60  E-value=0.68  Score=41.11  Aligned_cols=75  Identities=12%  Similarity=0.018  Sum_probs=44.8

Q ss_pred             CCCcEEEEEeeccCCCCCCCCceEEEEEEcC----Ccee-EEEeccCC---CCChHHHHHHHHHHHHHHhHhcCCcceeE
Q psy874            3 PDNHVVVFTDGACPRNGKVGASAGYGVYFGE----NNPL-NVAGKVTG---RVTNNNAEIQGAIHALKQAKSANEKVKLK   74 (191)
Q Consensus         3 ~~~~i~IYtDGac~~N~~~~~~AG~Gv~~~~----~~~~-~~s~~l~g---~~TNnrAEL~Avi~AL~~~~~~~~~~~v~   74 (191)
                      ....+.+|||.|...   .    | ||....    .++. -+|..+.+   +-+....|+.|++.|++.....=...+++
T Consensus       343 ~~~~~~l~~DAS~~~---~----g-avL~q~~~~~~~~i~y~Sk~l~~~e~~ys~~ekEllAi~~a~~~~~~yl~g~~~~  414 (455)
T 1rw3_A          343 LTKPFELFVDEKQGY---A----K-GVLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLV  414 (455)
T ss_dssp             SCCTTSCEEEEEECS---S----S-BEECCBCTTTTCCCCCCCBCSCSSCSSSCCSSHHHHHHHHHHHHHHGGGCSSCEE
T ss_pred             CCCcEEEEEeccCCc---c----e-eEEEEecCCcEEEEEEEcccCCccccccchHHHHHHHHHHHHHHHHHHcCCCcEE
Confidence            345678999986432   1    1 344332    1222 22444433   33456789999999999887531123799


Q ss_pred             EEEcChHHHHccc
Q psy874           75 RSYNDTHAQKKVR   87 (191)
Q Consensus        75 ~I~TDS~Yvv~~~   87 (191)
                       |+||+. +...+
T Consensus       415 -v~tDh~-~~~~l  425 (455)
T 1rw3_A          415 -IKAPHA-VEALV  425 (455)
T ss_dssp             -EECSSC-TTTTS
T ss_pred             -EEecCh-HHHHh
Confidence             999997 55533

>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=81.16  E-value=3.8  Score=36.23  Aligned_cols=74  Identities=11%  Similarity=0.021  Sum_probs=44.3

Q ss_pred             CCCCcEEEEEeeccCCCCCCCCceEEEEEE-cCCceeEEEeccCC---CCChHHHHHHH-HHHHHHHhHh--cC-Cccee
Q psy874            2 DPDNHVVVFTDGACPRNGKVGASAGYGVYF-GENNPLNVAGKVTG---RVTNNNAEIQG-AIHALKQAKS--AN-EKVKL   73 (191)
Q Consensus         2 ~~~~~i~IYtDGac~~N~~~~~~AG~Gv~~-~~~~~~~~s~~l~g---~~TNnrAEL~A-vi~AL~~~~~--~~-~~~~v   73 (191)
                      |++..+.++||++-.        +.||.+. .++...-.|+.+..   -.|+. -|+.| ++.||+....  .| .+..+
T Consensus       320 d~~~~~~l~~das~~--------g~~g~vl~q~~~~~~~s~~~~~~~~y~~~~-~e~la~vv~al~~~r~yl~G~~~~~~  390 (428)
T 2zd1_B          320 DPSKDLIAEIQKQGQ--------GQWTYQIYQEPFKNLKTGKYARMRGAHTND-VKQLTEAVQKITTESIVIWGKTPKFK  390 (428)
T ss_dssp             CTTSCCEEEEEEEET--------TEEEEEEESSTTCEEEEEEEECCSSCTTCH-HHHHHHHHHHHHHHHHHHHSSCCEEE
T ss_pred             CCCCCEEEEEecCCC--------CcEEEEEecCCCceeeecccchhhhcccch-HHHHHHHHHHhhccceEEECCCCcEE
Confidence            556779999999832        1567654 43322223444332   33444 45555 9999987653  13 23356


Q ss_pred             EEEEcChHHHHc
Q psy874           74 KRSYNDTHAQKK   85 (191)
Q Consensus        74 ~~I~TDS~Yvv~   85 (191)
                      + ++||.+...-
T Consensus       391 i-~~td~~~~~~  401 (428)
T 2zd1_B          391 L-PIQKETWETW  401 (428)
T ss_dssp             E-SSCHHHHHHH
T ss_pred             C-CccHHHHHHH
Confidence            7 8899988654

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	191
d1s1ta1	110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	7e-07
d1zbfa1	132	c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Ba	2e-06
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	2e-06
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	3e-05
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	2e-04

>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]} Length = 110

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]

 Score = 43.8 bits (103), Expect = 7e-07
 Identities = 16/60 (26%), Positives = 21/60 (35%), Gaps = 6/60 (10%)

Query: 7  VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
             + DGA  R  K+G  AGY    G               TN   E+Q    AL+ +  
Sbjct: 9  ETFYVDGAANRETKLGK-AGYVTNRGRQKV-----VTLTDTTNQKTELQAIYLALQDSGL 62

>d1zbfa1 c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Bacillus halodurans [TaxId: 86665]} Length = 132

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]

 Score = 43.0 bits (101), Expect = 2e-06
 Identities = 13/72 (18%), Positives = 23/72 (31%), Gaps = 4/72 (5%)

Query: 9  VFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSAN 68
          +  D     N  +     Y     +   +    +     TNN  E    +H L+  K  N
Sbjct: 7  LSVDVGSQGNPGIV---EYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN 63

Query: 69 EKVKLKRSYNDT 80
           +  +  S + T
Sbjct: 64 SRKPI-YSNSQT 74

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

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

 Score = 43.4 bits (101), Expect = 2e-06
 Identities = 20/61 (32%), Positives = 25/61 (40%), Gaps = 3/61 (4%)

Query: 5  NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQA 64
            V +FTDGAC  N   G  A    +      L+         TNN  E++ AI  LK  
Sbjct: 2  KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGE---ACTTNNRMELKAAIEGLKAL 58

Query: 65 K 65
          K
Sbjct: 59 K 59

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

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

 Score = 39.5 bits (91), Expect = 3e-05
 Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 6/63 (9%)

Query: 7  VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
             +TDG+C R  K G  AGY    G++       K   + TN  AE++    AL  +  
Sbjct: 8  ETFYTDGSCNRQSKEGK-AGYVTDRGKDKV-----KKLEQTTNQQAELEAFAMALTDSGP 61

Query: 67 ANE 69
             
Sbjct: 62 KVN 64

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

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

 Score = 37.7 bits (86), Expect = 2e-04
 Identities = 17/55 (30%), Positives = 20/55 (36%), Gaps = 3/55 (5%)

Query: 6  HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHA 60
           V +FT G+   N   G   GYG                 R TNN  E+  AI A
Sbjct: 2  QVEIFTAGSALGNPGPG---GYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVA 53

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	191
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.92
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.9
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.87
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.86
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.82

>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=99.92  E-value=1.6e-26  Score=177.96  Aligned_cols=134  Identities=22%  Similarity=0.274  Sum_probs=95.9

Q ss_pred             CcEEEEEeeccCCCCCCCCceEEEEEE-cCCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHH
Q psy874            5 NHVVVFTDGACPRNGKVGASAGYGVYF-GENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQ   83 (191)
Q Consensus         5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~-~~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yv   83 (191)
                      ..|+|||||||++||++   +|||+++ ..+....+++. .+.+|||+|||+|+++||+.+..   .+.+. |+|||+|+
T Consensus         2 ~~i~iytDGs~~~N~g~---~G~g~vi~~~~~~~~~~~~-~~~~Tnn~aEl~Ai~~AL~~~~~---~~~i~-i~tds~~~   73 (147)
T d1rila_           2 KRVALFTDGACLGNPGP---GGWAALLRFHAHEKLLSGG-EACTTNNRMELKAAIEGLKALKE---PCEVD-LYTDSHYL   73 (147)
T ss_dssp             CCCCEEEEEEESSTTEE---EEEEEEECBTTBCCEECCE-EEEECHHHHHHHHHHHHHHSCCS---CCEEE-EECCCHHH
T ss_pred             CEEEEEEccCCCCCCCc---cEEEEEEEECCcceEEecc-cccccHHHHHHHHHHHHhhhccC---CceEE-Eecchhhh
Confidence            46899999999999976   6999976 33444444444 23689999999999999987654   24789 99999999


Q ss_pred             Hcccccccccccccccccccccce-eecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEeccccccchH--
Q psy874           84 KKVRNVSSVAMRIAQKVDYISHDV-ISVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYNDTH--  158 (191)
Q Consensus        84 v~~~~~~~~~~~w~~~edW~~ng~-~s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a~r~~n~~~--  158 (191)
                      ++.++..     +...  |+.+++ ++.|.||  .|||+++..+.+.++           -.+.|...|.++..|+.+  
T Consensus        74 ~~~~~~~-----~~~~--~~~~~~~~~~~~~v~n~dL~~~l~~~~~~~~-----------v~~~wVkgHsg~~gNe~AD~  135 (147)
T d1rila_          74 KKAFTEG-----WLEG--WRKRGWRTAEGKPVKNRDLWEALLLAMAPHR-----------VRFHFVKGHTGHPENERVDR  135 (147)
T ss_dssp             HHHHHSS-----HHHH--HHHTTSBCTTSSBCTTHHHHHHHHHHHTTSE-----------EECCCCCGGGSCTHHHHHHH
T ss_pred             hcccccc-----chhh--hhhccccccccccchhHHHHHHHHHHhhhcc-----------cceEEccCCCCCcchHHHHH
Confidence            9976543     3333  777774 6889999  789998776644321           124455455678889855  


Q ss_pred             -hhhhhh
Q psy874          159 -AQKKVR  164 (191)
Q Consensus       159 -~~~~~~  164 (191)
                       |.++++
T Consensus       136 LAk~aa~  142 (147)
T d1rila_         136 EARRQAQ  142 (147)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHH
Confidence             444443

>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=99.90  E-value=2e-24  Score=166.20  Aligned_cols=95  Identities=16%  Similarity=0.051  Sum_probs=74.5

Q ss_pred             EEEEeeccCCCCCCCCceEEEEEE-cCCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHHHcc
Q psy874            8 VVFTDGACPRNGKVGASAGYGVYF-GENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQKKV   86 (191)
Q Consensus         8 ~IYtDGac~~N~~~~~~AG~Gv~~-~~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yvv~~   86 (191)
                      .|||||||++||||   +|||+++ ..++....++++ +.+|||+|||+|+++||+.+.+.+  .++. |||||+||++ 
T Consensus         6 sIy~DGa~~GNPGp---~g~g~v~~~~~~~~~~sg~~-~~~TNN~aEl~A~i~aL~~~~~~~--~~i~-I~tDS~yvi~-   77 (132)
T d1zbfa1           6 SLSVDVGSQGNPGI---VEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERN--SRKP-IYSNSQTAIK-   77 (132)
T ss_dssp             SEEEEEEECSSSEE---EEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHHTT--CCCC-EEESCHHHHH-
T ss_pred             eEEEeecCCCCCch---heEEEEEEcCCEEEEEEcCc-CccchHHHHHHHHHHHHHHhhcCC--ceEE-EEeccHHHHH-
Confidence            48999999999998   5999876 445666677764 578999999999999999998765  3799 9999999998 


Q ss_pred             cccccccccccccccccccce-eecCCCc--chhHHHHHHH
Q psy874           87 RNVSSVAMRIAQKVDYISHDV-ISVGIPF--PSIQDENVKL  124 (191)
Q Consensus        87 ~~~~~~~~~w~~~edW~~ng~-~s~G~PV--~dL~~~~v~l  124 (191)
                               |..+  |+   | ++.+.||  ++||+.+.++
T Consensus        78 ---------wv~~--~~---~kt~~~~~vkN~~l~~~i~~a  104 (132)
T d1zbfa1          78 ---------WVKD--KK---AKSTLVRNEETALIWKLVDEA  104 (132)
T ss_dssp             ---------HHHH--TC---CCCCCCCSTTTHHHHHHHHHH
T ss_pred             ---------HHHh--Cc---eecCcCCCcccHHHHHHHHHH
Confidence                     3333  32   3 3568899  8899865444

>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=99.87  E-value=9.5e-24  Score=161.74  Aligned_cols=132  Identities=20%  Similarity=0.185  Sum_probs=95.1

Q ss_pred             CcEEEEEeeccCCCCCCCCceEEEEEEc-CCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHH
Q psy874            5 NHVVVFTDGACPRNGKVGASAGYGVYFG-ENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQ   83 (191)
Q Consensus         5 ~~i~IYtDGac~~N~~~~~~AG~Gv~~~-~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yv   83 (191)
                      ..|.|||||||++||++   ||||+++. .+....++.++ +.+|||+||++|++.||+.+...   ..+. |+|||+|+
T Consensus         1 k~I~IYtDGS~~~N~g~---aG~G~vi~~~~~~~~~~~~~-~~~tnn~aE~~Ai~~Al~~~~~~---~~i~-i~tds~~~   72 (152)
T d1jl1a_           1 KQVEIFTAGSALGNPGP---GGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKEH---AEVI-LSTDSQYV   72 (152)
T ss_dssp             CCEEEEEEEEESSTTEE---EEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCSC---CEEE-EEECCHHH
T ss_pred             CEEEEEEeCCCCCCCCc---EEEEEEEEECCeEEEecccc-CcccHHHHHHhhhhhhhhhhccc---ceEE-Eeecceee
Confidence            36899999999999976   69999863 44445556553 46899999999999999876552   3788 99999999


Q ss_pred             Hcccccccccccccccccccccce-eecCCCc--chhHHHHHHHHHHHHHHhhhhcCCCCCCcceEEEec--cccccchH
Q psy874           84 KKVRNVSSVAMRIAQKVDYISHDV-ISVGIPF--PSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKL--KRSYNDTH  158 (191)
Q Consensus        84 v~~~~~~~~~~~w~~~edW~~ng~-~s~G~PV--~dL~~~~v~l~~~~~d~~~~~~g~~~~~~~~~~v~a--~r~~n~~~  158 (191)
                      ++.++.      |...  |..++| .+.+.|+  .++++++..+.++             ..+.|++|+.  ++..|+++
T Consensus        73 i~~~~~------~~~~--~~~~~~~~~~~~~~~n~~~~~~i~~~~~~-------------~~V~~~wV~gH~g~~gNe~A  131 (152)
T d1jl1a_          73 RQGITQ------WIHN--WKKRGWKTADKKPVKNVDLWQRLDAALGQ-------------HQIKWEWVKGHAGHPENERA  131 (152)
T ss_dssp             HHHHHT------THHH--HHHTTTBCTTSCBCTTHHHHHHHHHHTTT-------------CEEEEEECCSSTTCHHHHHH
T ss_pred             EEcccc------hhhH--hHhccchhcccCeeecHHHHHHHHHHhhc-------------ceeEEEEecccCCCccHHHH
Confidence            996643      4444  777886 4778888  5667665444221             2466666665  57899876


Q ss_pred             ---hhhhhhc
Q psy874          159 ---AQKKVRN  165 (191)
Q Consensus       159 ---~~~~~~~  165 (191)
                         |.+++.+
T Consensus       132 D~LAk~aa~~  141 (152)
T d1jl1a_         132 DELARAAAMN  141 (152)
T ss_dssp             HHHHHHHHHS
T ss_pred             HHHHHHHHhC
Confidence               6666543

>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=99.86  E-value=5.1e-22  Score=147.83  Aligned_cols=74  Identities=18%  Similarity=0.221  Sum_probs=58.7

Q ss_pred             CCcEEEEEeeccCCCCCCCCceEEEEEEcCCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHH
Q psy874            4 DNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQ   83 (191)
Q Consensus         4 ~~~i~IYtDGac~~N~~~~~~AG~Gv~~~~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yv   83 (191)
                      ++..++||||||++||++   +|+|++...+...  +.++ +.+|||+|||+||++||+...     .++. |+|||+||
T Consensus         6 ~~~~t~ytDGs~~~n~~~---g~~g~~~~~~~~~--~~~~-~~~TNn~aEl~Avi~aL~~~~-----~~v~-I~TDS~yv   73 (110)
T d1s1ta1           6 VGAETFYVDGAANRETKL---GKAGYVTNRGRQK--VVTL-TDTTNQKTELQAIYLALQDSG-----LEVN-IVTDSQYA   73 (110)
T ss_dssp             TTSEEEEEEEEEETTTTE---EEEEEEETTSCEE--EEEE-SSCCHHHHHHHHHHHHHHHSC-----SEEE-EEECCHHH
T ss_pred             CCCcEEEEeCCCCCCCCC---cEEEEEEecCCeE--EEec-ccCcHHHHHHHHHHHHHHhCC-----CeEE-EEEehHHH
Confidence            466789999999999977   5888887655443  2332 468999999999999998532     3899 99999999


Q ss_pred             Hccccc
Q psy874           84 KKVRNV   89 (191)
Q Consensus        84 v~~~~~   89 (191)
                      ++.++.
T Consensus        74 i~~i~~   79 (110)
T d1s1ta1          74 LGIIQA   79 (110)
T ss_dssp             HHHHHH
T ss_pred             HHHHhc
Confidence            997753

>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=99.82  E-value=8.2e-21  Score=142.78  Aligned_cols=74  Identities=22%  Similarity=0.258  Sum_probs=59.3

Q ss_pred             CCcEEEEEeeccCCCCCCCCceEEEEEEcCCceeEEEeccCCCCChHHHHHHHHHHHHHHhHhcCCcceeEEEEcChHHH
Q psy874            4 DNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQ   83 (191)
Q Consensus         4 ~~~i~IYtDGac~~N~~~~~~AG~Gv~~~~~~~~~~s~~l~g~~TNnrAEL~Avi~AL~~~~~~~~~~~v~~I~TDS~Yv   83 (191)
                      ++.++|||||||+.||++   +|+|++...++....  .+ +.+|||+|||+|+++||+...     .++. |+|||+||
T Consensus         5 ~~~~t~YTDGS~~~n~~~---~~~g~~~~~~~~~~~--~~-~~~tnn~AEl~Ai~~al~~~~-----~~i~-I~tDS~~v   72 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKE---GKAGYVTDRGKDKVK--KL-EQTTNQQAELEAFAMALTDSG-----PKVN-IIVDSQYV   72 (126)
T ss_dssp             TTCEEEEEEEEECTTTCC---EEEEEEETTSCEEEE--EE-SSCCHHHHHHHHHHHHHHTSC-----SEEE-EEESCHHH
T ss_pred             CCCcEEEEcCCCCCCCCc---EEEEEEecCCCEEEE--ec-CCCcchHHHHHHHHHHhccCC-----cceE-EEechHHH
Confidence            567899999999999876   689988876655433  32 368999999999999998532     3899 99999999


Q ss_pred             Hccccc
Q psy874           84 KKVRNV   89 (191)
Q Consensus        84 v~~~~~   89 (191)
                      ++.++.
T Consensus        73 ~~~~~~   78 (126)
T d1mu2a1          73 MGIVAS   78 (126)
T ss_dssp             HHHHHT
T ss_pred             HHHHhc
Confidence            996654