Psyllid ID: psy13868

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------13
Protein Sequence
MAVEENFDNPVNVVIETAGNWGVKETQLLKKGAVVWYTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKSKITWESTQAICGK
Secondary Structure (PSIPRED)
cccccccccccEEEEccccccccccccccccccEEEEEcccccccccEEEEEEEcccEEEEEEcccccccHHHHHHHHHHHHHHHHHccccccEEEEEEccHHHHHHHHcccccHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccHHHHccccEEEEEccccccccccccccccccEEEEEcccccccccccEEEEcccccEEEEEcccHHHHHHHHHHHHHHHHHHHHHccccccEEEEEccHHHHHHHHHHcccccHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
maveenfdnpVNVVIETagnwgvketqLLKKGAVVWytdgskteagsgagihcvkprvnislplgtytGVYQAEVLAIRNCAEEninmglskreiYIFSDSQAALRAIGnfqtkskitwESTQAICGK
Flexible Loop (DISEMBL)
maveenfdnpvnvvietagnwgvketqLLKKGAVVWYTDGSkteagsgagihcvKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGnfqtkskitwestqaicgk
Low Complexity Region (SEG)
MAVEENFDNPVNVVIETAGNWGVKETQLLKKGAVVWYTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKSKITWESTQAICGK
Disordered region (IsUnstruct)
********NPVNVVIETAGNWGVKETQLLKKGAVVWYTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKSKITWES*******
Disordered Region (DISOPRED)
*******DNPVNVV******************AVVWYTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKSKITWESTQAICG*
Disordered Region (DISEMBL)
MAVEENFDNPVNVVIETAGNWGVKETQLLKKGAVVWYTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKSKITWESTQAICGK
Disordered Region (DISPRO)
*AVEENFDNPVNVVIETAGNWGVKETQLLKKGAVVWYTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKSKITWESTQAICGK
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAVEENFDNPVNVVIETAGNWGVKETQLLKKGAVVWYTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKSKITWESTQAICGK
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	128
156540059	721	PREDICTED: hypothetical protein LOC10011	0.640	0.113	0.439	1e-10
1335691	521	unnamed protein product [Drosophila mira	0.851	0.209	0.306	1e-07
542601	426	hypothetical protein - fruit fly (Drosop	0.851	0.255	0.306	1e-07
198459368	216	GA23309 [Drosophila pseudoobscura pseudo	0.851	0.504	0.297	3e-07
2290213	1189	Lian-Aa1 retrotransposon protein [Aedes	0.656	0.070	0.357	1e-06
195476672	323	GE19196 [Drosophila yakuba] gi|194185869	0.695	0.275	0.337	6e-06
195064567	214	GH23756 [Drosophila grimshawi] gi|193900	0.601	0.359	0.385	2e-05
198470095	88	GA22858 [Drosophila pseudoobscura pseudo	0.593	0.863	0.368	6e-05
195469311	234	GE14539 [Drosophila yakuba] gi|194185682	0.328	0.179	0.547	6e-05
2708267	675	putative reverse transcriptase [Drosophi	0.835	0.158	0.321	8e-05

>gi|156540059|ref|XP_001599613.1| PREDICTED: hypothetical protein LOC100114674, partial [Nasonia vitripennis]

 Score = 71.2 bits (173), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 36/82 (43%), Positives = 49/82 (59%)

Query: 39  DGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIF 98
           DGS+ E G+G+G +  +        LG Y  V+Q E+ AI  CA+ NI +G   R I I 
Sbjct: 194 DGSRAETGTGSGYYSQRDGWGTFFSLGRYATVFQTEINAILTCAQRNIELGARDRIITIC 253

Query: 99  SDSQAALRAIGNFQTKSKITWE 120
           SDSQAALRA+   +T S++ WE
Sbjct: 254 SDSQAALRALMAHRTTSRLVWE 275

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|1335691|emb|CAA41925.1| unnamed protein product [Drosophila miranda]

 Score = 61.2 bits (147), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 34/111 (30%), Positives = 58/111 (52%), Gaps = 2/111 (1%)

Query: 5   ENFDNPVNVVIETAGNWGVKETQLLKKGAVVWYTDGSKTEAGSGAGIHCVKPRVNISLPL 64
           ++   P  V I +  +W + E       AV +YTDGSK +   G G++C +  ++    L
Sbjct: 214 DHLSTPFQVSIPSREDWEMGEPG--PANAVHFYTDGSKLDGRVGGGVYCSELEISHCFRL 271

Query: 65  GTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKS 115
             +  V+QAE+ AI+        + L    + +FSDSQAA++A+G+  + S
Sbjct: 272 PDHCSVFQAEIEAIKEAISIVSKLRLDTHLVCVFSDSQAAIKALGSISSNS 322

Source: Drosophila miranda

Species: Drosophila miranda

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|542601|pir||S37765 hypothetical protein - fruit fly (Drosophila miranda) transposon TRIM

 Score = 61.2 bits (147), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 34/111 (30%), Positives = 58/111 (52%), Gaps = 2/111 (1%)

Query: 5   ENFDNPVNVVIETAGNWGVKETQLLKKGAVVWYTDGSKTEAGSGAGIHCVKPRVNISLPL 64
           ++   P  V I +  +W + E       AV +YTDGSK +   G G++C +  ++    L
Sbjct: 119 DHLSTPFQVSIPSREDWEMGEPG--PANAVHFYTDGSKLDGRVGGGVYCSELEISHCFRL 176

Query: 65  GTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKS 115
             +  V+QAE+ AI+        + L    + +FSDSQAA++A+G+  + S
Sbjct: 177 PDHCSVFQAEIEAIKEAISIVSKLRLDTHLVCVFSDSQAAIKALGSISSNS 227

Source: Drosophila miranda

Species: Drosophila miranda

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198459368|ref|XP_002136090.1| GA23309 [Drosophila pseudoobscura pseudoobscura] gi|198140278|gb|EDY71053.1| GA23309 [Drosophila pseudoobscura pseudoobscura]

 Score = 60.1 bits (144), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/111 (29%), Positives = 57/111 (51%), Gaps = 2/111 (1%)

Query: 5   ENFDNPVNVVIETAGNWGVKETQLLKKGAVVWYTDGSKTEAGSGAGIHCVKPRVNISLPL 64
           ++   P  V I    +W + E       AV +YTDGSK +   G G++C +  ++    L
Sbjct: 66  DHLSTPFQVSIPPREDWEMGEPG--PANAVHFYTDGSKLDGRVGGGVYCSELNISHCFRL 123

Query: 65  GTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKS 115
             +  V+QA++ AI+        + L    + +FSDSQAA++A+G+  + S
Sbjct: 124 PDHCSVFQADIEAIKEAISIVSKLRLDTHLVCVFSDSQAAIKALGSISSNS 174

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|2290213|gb|AAB65093.1| Lian-Aa1 retrotransposon protein [Aedes aegypti]

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/84 (35%), Positives = 50/84 (59%)

Query: 34  VVWYTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKR 93
           +V YTDGS  E  +GAG++  + R+N    LG    V+QAE+ A+    +  +   +  +
Sbjct: 913 IVCYTDGSLLEGRAGAGVYSRELRLNQFYSLGRNCTVFQAEIFALMCGVQSALQQRVMGK 972

Query: 94  EIYIFSDSQAALRAIGNFQTKSKI 117
            IY  SDSQAA++A+ +  ++SK+
Sbjct: 973 VIYFCSDSQAAIKALASANSRSKL 996

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195476672|ref|XP_002086202.1| GE19196 [Drosophila yakuba] gi|194185869|gb|EDW99480.1| GE19196 [Drosophila yakuba]

 Score = 55.8 bits (133), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 30/89 (33%), Positives = 47/89 (52%)

Query: 37  YTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIY 96
           YT GS+ E   GA I+C  P + +S  L +   ++QAEV AI    E   ++      + 
Sbjct: 223 YTHGSEMEGRVGADIYCTDPEMRLSYKLPSQCSIFQAEVFAIGKAEELAQSIDRPHEAVN 282

Query: 97  IFSDSQAALRAIGNFQTKSKITWESTQAI 125
           +F DSQAA+R++ +    SK    S +A+
Sbjct: 283 LFVDSQAAIRSMQSSAVSSKSVLASREAL 311

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195064567|ref|XP_001996589.1| GH23756 [Drosophila grimshawi] gi|193900627|gb|EDV99493.1| GH23756 [Drosophila grimshawi]

 Score = 53.9 bits (128), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 32/83 (38%), Positives = 43/83 (51%), Gaps = 6/83 (7%)

Query: 1   MAVEENFDNPVNVVIETAGNWG-VKETQLLKKGAVVWYTDGSKTEAGSGAGIHCVKPRVN 59
           MA E  F+    V + +   W  + E   +K   + WYTDGS T  G+G G+  V PRV 
Sbjct: 60  MAAEYIFERNFTVRMSSKREWTTLDEVHPMKPHTIKWYTDGSLTNQGTGLGV--VGPRVF 117

Query: 60  ISLPLGTYTGVYQAEVLAIRNCA 82
               LGT+T ++QAE    R CA
Sbjct: 118 YHESLGTHTSIFQAES---RECA 137

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198470095|ref|XP_002133368.1| GA22858 [Drosophila pseudoobscura pseudoobscura] gi|198145292|gb|EDY71996.1| GA22858 [Drosophila pseudoobscura pseudoobscura]

 Score = 52.4 bits (124), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%)

Query: 33  AVVWYTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSK 92
           AV +YTDGSK +   G G++C +  ++    L  +  V+QAEV+AI+          LS 
Sbjct: 9   AVHFYTDGSKLDGRVGGGVYCSELNMSHCFRLPDHYSVFQAEVVAIKEAIYIVPKQLLST 68

Query: 93  REIYIFSDSQAALRAI 108
             + +FSD QAA++A+
Sbjct: 69  HLVCVFSDCQAAIKAL 84

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195469311|ref|XP_002099581.1| GE14539 [Drosophila yakuba] gi|194185682|gb|EDW99293.1| GE14539 [Drosophila yakuba]

 Score = 52.4 bits (124), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/42 (54%), Positives = 29/42 (69%)

Query: 37  YTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAI 78
           YTDGSK E G GAGI+C  P + +S  L +   ++QAEVLAI
Sbjct: 192 YTDGSKMEGGVGAGIYCTDPEMRLSYKLPSQCSIFQAEVLAI 233

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|2708267|gb|AAB92394.1| putative reverse transcriptase [Drosophila subobscura]

 Score = 52.0 bits (123), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 37/115 (32%), Positives = 57/115 (49%), Gaps = 8/115 (6%)

Query: 4   EENFDNPVNVVIETAGNWGVKETQLLKKGAVVWYTDGSKTEAGSGAGIHCVKPRVNISLP 63
            E  D P   +I    +W   E     K A+  +TDGSK +   G GI+     ++ S  
Sbjct: 367 REYTDTPFETIIPHRNDW--LEGPPGPKEAIQIFTDGSKLDNKVGGGIYSELLNISYSFR 424

Query: 64  LGTYTGVYQAEVLAIR---NCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKS 115
           L  +  V+QAEV+AI+   +C +E   +      I I+SDSQAA++++    T S
Sbjct: 425 LPDHCSVFQAEVIAIKEALSCLQE---LTPEATYINIYSDSQAAIKSLNAITTSS 476

Source: Drosophila subobscura

Species: Drosophila subobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	128
TIGR_CMR|BA_1623	128	BA_1623 "RNase H" [Bacillus an	0.585	0.585	0.397	4.3e-06

TIGR_CMR|BA_1623 BA_1623 "RNase H" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 106 (42.4 bits), Expect = 4.3e-06, P = 4.3e-06
 Identities = 35/88 (39%), Positives = 48/88 (54%)

Query:    37 YTDG-SKTEAG-SGAGIHC--VKPRVNISLPLGT---YTGVYQAEVLAIRNCAEENINMG 89
             Y DG SK   G SGAG+    V+P V +SLPLGT   +   Y A + A++ C E N N+ 
Sbjct:     5 YIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNI- 63

Query:    90 LSKREIYIFSDSQAALRAIGNFQTKSKI 117
             +S R     +DSQ   RA+     K+K+
Sbjct:    64 VSFR-----TDSQLVERAVEKEYAKNKM 86


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.314   0.131   0.387    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      128       128   0.00091  102 3  11 23  0.43    31
                                                     29  0.41    33


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  579 (62 KB)
  Total size of DFA:  137 KB (2085 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:05
  No. of threads or processors used:  24
  Search cpu time:  11.80u 0.08s 11.88t   Elapsed:  00:00:15
  Total cpu time:  11.80u 0.08s 11.88t   Elapsed:  00:00:20
  Start:  Thu Aug 15 13:46:53 2013   End:  Thu Aug 15 13:47:13 2013

GO:0004523 "ribonuclease H activity" evidence=ISS

GO:0006401 "RNA catabolic process" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	128
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	1e-22
PRK13907	128	PRK13907, rnhA, ribonuclease H; Provisional	1e-05
pfam00075	126	pfam00075, RNase_H, RNase H	8e-05
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	0.004

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

 Score = 85.8 bits (213), Expect = 1e-22
 Identities = 38/93 (40%), Positives = 53/93 (56%), Gaps = 1/93 (1%)

Query: 35  VWYTDGSKTEAGSGAGIHCVKPRV-NISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKR 93
           V YTDGSK E  +GAG   V+    + S  LG Y  V+ AE+LAI    +  +  G   R
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 94  EIYIFSDSQAALRAIGNFQTKSKITWESTQAIC 126
           +I IFSDSQAAL+A+ + ++ S +     +AI 
Sbjct: 61  KITIFSDSQAALKALRSPRSSSPLVLRIRKAIR 93

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

>gnl|CDD|139967 PRK13907, rnhA, ribonuclease H; Provisional

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 34/88 (38%), Positives = 46/88 (52%), Gaps = 13/88 (14%)

Query: 37  YTDG-SKTEAG-SGAG--IHCVKPRVNISLPLGT---YTGVYQAEVLAIRNCAEENINMG 89
           Y DG SK   G SGAG  I  V+P V +SLPLGT   +   Y A + A++ C E N N+ 
Sbjct: 5   YIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNI- 63

Query: 90  LSKREIYIFSDSQAALRAIGNFQTKSKI 117
                +   +DSQ   RA+     K+K+
Sbjct: 64  -----VSFRTDSQLVERAVEKEYAKNKM 86

Length = 128

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

 Score = 39.2 bits (92), Expect = 8e-05
 Identities = 24/83 (28%), Positives = 33/83 (39%), Gaps = 15/83 (18%)

Query: 31  KGAVVWYTDGS--KTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINM 88
             AV  YTDGS        GAG          S PL   T   +AE+LA+          
Sbjct: 1   PEAVTVYTDGSCNGNPGPGGAGY-VTDGGKQRSKPLP-GTTNQRAELLALI--------E 50

Query: 89  GLSK---REIYIFSDSQAALRAI 108
            L     +++ I++DSQ  +  I
Sbjct: 51  ALEALSGQKVNIYTDSQYVIGGI 73

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|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 = 34.3 bits (79), Expect = 0.004
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 9/78 (11%)

Query: 37  YTDGSKTEAGSGAGI-----HCVKPRV-NISLPLGTYTGVYQAEVLAIRNCAEENINMGL 90
            TDGS       AG            +   SL +   T   +AE+LA+    E  +++GL
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAAT-NNEAELLALLEALELALDLGL 59

Query: 91  SKREIYIFSDSQAALRAI 108
             +++ I +DS+  +  I
Sbjct: 60  --KKLIIETDSKYVVDLI 75

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	128
PRK13907	128	rnhA ribonuclease H; Provisional	99.52
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.48
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.46
PRK08719	147	ribonuclease H; Reviewed	99.45
PRK06548	161	ribonuclease H; Provisional	99.43
PRK00203	150	rnhA ribonuclease H; Reviewed	99.4
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.32
KOG3752|consensus	371		99.27
PRK07708	219	hypothetical protein; Validated	99.26
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.21
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	98.38
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	94.56
.; GO: 0004523 ribonuclease H activity" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF00336">PF00336	245	DNA_pol_viral_C: DNA polymerase (viral) C-terminal	85.51

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.52  E-value=1.5e-13  Score=97.18  Aligned_cols=80  Identities=25%  Similarity=0.257  Sum_probs=63.9

Q ss_pred             cEEEEeeCCccC--CCcceEEEEecCce--eEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHh
Q psy13868         33 AVVWYTDGSKTE--AGSGAGIHCVKPRV--NISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAI  108 (128)
Q Consensus        33 ~i~IyTDGS~~~--~~~G~gv~~~~~~~--~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai  108 (128)
                      +++||||||+..  +..|+|+++.+...  ..+..+ ...+++.||+.|++.||+++.+.+..+  +.|+|||+.+++.+
T Consensus         1 ~~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~-~~~tn~~AE~~All~aL~~a~~~g~~~--v~i~sDS~~vi~~~   77 (128)
T PRK13907          1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPL-GTMSNHEAEYHALLAALKYCTEHNYNI--VSFRTDSQLVERAV   77 (128)
T ss_pred             CEEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecc-cccCCcHHHHHHHHHHHHHHHhCCCCE--EEEEechHHHHHHH
Confidence            478999999974  34999999866532  233333 357999999999999999999887654  99999999999999


Q ss_pred             hCCCCCc
Q psy13868        109 GNFQTKS  115 (128)
Q Consensus       109 ~~~~~~s  115 (128)
                      ++...++
T Consensus        78 ~~~~~~~   84 (128)
T PRK13907         78 EKEYAKN   84 (128)
T ss_pred             hHHHhcC
Confidence            9866544

>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=99.48  E-value=4.2e-13  Score=93.94  Aligned_cols=72  Identities=33%  Similarity=0.436  Sum_probs=56.2

Q ss_pred             CcEEEEeeCCccC--CCcceEEEEecCceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHhh
Q psy13868         32 GAVVWYTDGSKTE--AGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIG  109 (128)
Q Consensus        32 ~~i~IyTDGS~~~--~~~G~gv~~~~~~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai~  109 (128)
                      +.+.||||||+..  +..|+|+++... ...+..++ ..+++.|||.||..||+ +.. .   +.+.|+|||+++++.|.
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~-~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~~-~---~~v~I~tDS~~v~~~l~   74 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGG-RNFSFRLG-GQSNNRAELQAIIEALK-ALE-H---RKVTIYTDSQYVLNALN   74 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETT-EEEEEEEE-SECHHHHHHHHHHHHHH-THS-T---SEEEEEES-HHHHHHHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECC-eEEEeccc-ccchhhhheehHHHHHH-Hhh-c---ccccccccHHHHHHHHH
Confidence            5789999999863  336777766544 46666677 88999999999999999 442 2   56999999999999888


Q ss_pred             C
Q psy13868        110 N  110 (128)
Q Consensus       110 ~  110 (128)
                      +
T Consensus        75 ~   75 (132)
T PF00075_consen   75 K   75 (132)
T ss_dssp             T
T ss_pred             H
Confidence            7

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 ....

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

Probab=99.46  E-value=4.9e-13  Score=99.05  Aligned_cols=75  Identities=24%  Similarity=0.244  Sum_probs=61.1

Q ss_pred             CcEEEEeeCCccC--CCcceEEEEecC--ceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHH
Q psy13868         32 GAVVWYTDGSKTE--AGSGAGIHCVKP--RVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRA  107 (128)
Q Consensus        32 ~~i~IyTDGS~~~--~~~G~gv~~~~~--~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~a  107 (128)
                      ..+.||||||+..  |..|+|+|....  ....+..+. .+|++.||+.|++.||+++.+.+..  .|.|+|||+++++.
T Consensus         2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~--~v~l~tDS~yv~~~   78 (154)
T COG0328           2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGAC--EVTLYTDSKYVVEG   78 (154)
T ss_pred             CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCc--eEEEEecHHHHHHH
Confidence            4689999999974  338888887532  233555566 8999999999999999999886554  49999999999999


Q ss_pred             hh
Q psy13868        108 IG  109 (128)
Q Consensus       108 i~  109 (128)
                      |.
T Consensus        79 i~   80 (154)
T COG0328          79 IT   80 (154)
T ss_pred             HH
Confidence            98

>PRK08719 ribonuclease H; Reviewed

Probab=99.45  E-value=4.8e-13  Score=98.06  Aligned_cols=71  Identities=24%  Similarity=0.353  Sum_probs=56.1

Q ss_pred             CcEEEEeeCCccCCC-----cceEEEEecC--ce--eEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcH
Q psy13868         32 GAVVWYTDGSKTEAG-----SGAGIHCVKP--RV--NISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQ  102 (128)
Q Consensus        32 ~~i~IyTDGS~~~~~-----~G~gv~~~~~--~~--~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~  102 (128)
                      ..++||||||+..++     .|+|+++..+  ..  ..+..+....|+++|||.|+..||+.+.+.      ..|+|||+
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~------~~i~tDS~   76 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG------DVIYSDSD   76 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC------CEEEechH
Confidence            468999999997533     5889887443  22  355556667899999999999999988542      37999999


Q ss_pred             HHHHHh
Q psy13868        103 AALRAI  108 (128)
Q Consensus       103 sai~ai  108 (128)
                      ++++.|
T Consensus        77 yvi~~i   82 (147)
T PRK08719         77 YCVRGF   82 (147)
T ss_pred             HHHHHH
Confidence            999999

>PRK06548 ribonuclease H; Provisional

Probab=99.43  E-value=1.7e-12  Score=96.77  Aligned_cols=74  Identities=23%  Similarity=0.139  Sum_probs=56.0

Q ss_pred             CCcEEEEeeCCccCC--CcceEEEEecCceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHh
Q psy13868         31 KGAVVWYTDGSKTEA--GSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAI  108 (128)
Q Consensus        31 ~~~i~IyTDGS~~~~--~~G~gv~~~~~~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai  108 (128)
                      +..+.||||||+..+  ..|.|+|+.+. ...+... ...|++.|||.|++.||+.+... .  ..+.|+|||++++++|
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~-~~~~g~~-~~~TNnraEl~Aii~aL~~~~~~-~--~~v~I~TDS~yvi~~i   77 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDEN-TWDSGGW-DIATNNIAELTAVRELLIATRHT-D--RPILILSDSKYVINSL   77 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCC-cEEccCC-CCCCHHHHHHHHHHHHHHhhhcC-C--ceEEEEeChHHHHHHH
Confidence            456999999999753  38899888643 2222222 35799999999999999866432 2  3499999999999999


Q ss_pred             h
Q psy13868        109 G  109 (128)
Q Consensus       109 ~  109 (128)
                      .
T Consensus        78 ~   78 (161)
T PRK06548         78 T   78 (161)
T ss_pred             H
Confidence            9

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.40  E-value=1.7e-12  Score=94.71  Aligned_cols=73  Identities=23%  Similarity=0.172  Sum_probs=56.0

Q ss_pred             cEEEEeeCCccCC--CcceEEEEecCce--eEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHh
Q psy13868         33 AVVWYTDGSKTEA--GSGAGIHCVKPRV--NISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAI  108 (128)
Q Consensus        33 ~i~IyTDGS~~~~--~~G~gv~~~~~~~--~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai  108 (128)
                      ++.||||||+..+  ..|+|+++.....  ..+... ...|+++|||.|+..||+.+.+.    ..+.|+|||+++++.|
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~-~~~TN~~aEL~Ai~~AL~~~~~~----~~v~I~tDS~yvi~~i   77 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGE-ALTTNNRMELMAAIEALEALKEP----CEVTLYTDSQYVRQGI   77 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCC-CCCcHHHHHHHHHHHHHHHcCCC----CeEEEEECHHHHHHHH
Confidence            5899999999743  3888888753322  233333 46789999999999999988542    3599999999999999


Q ss_pred             hC
Q psy13868        109 GN  110 (128)
Q Consensus       109 ~~  110 (128)
                      ..
T Consensus        78 ~~   79 (150)
T PRK00203         78 TE   79 (150)
T ss_pred             HH
Confidence            85

>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=99.32  E-value=2.9e-11  Score=81.12  Aligned_cols=77  Identities=31%  Similarity=0.423  Sum_probs=60.0

Q ss_pred             EEEeeCCccCC--CcceEEEEecCceeEE---eecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHhh
Q psy13868         35 VWYTDGSKTEA--GSGAGIHCVKPRVNIS---LPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIG  109 (128)
Q Consensus        35 ~IyTDGS~~~~--~~G~gv~~~~~~~~~~---~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai~  109 (128)
                      ++|||||...+  ++|+|++..+......   .......+++.+|+.|++.||+++...+.  +++.|++||+.+++.+.
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~--~~i~i~~Ds~~~~~~~~   78 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGG--KKVNIYTDSQYVINALT   78 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCC--ceEEEEECHHHHHHHhh
Confidence            48999999754  5999999866432221   22225789999999999999999986554  45999999999999999


Q ss_pred             CCCC
Q psy13868        110 NFQT  113 (128)
Q Consensus       110 ~~~~  113 (128)
                      +...
T Consensus        79 ~~~~   82 (130)
T cd06222          79 GWYE   82 (130)
T ss_pred             cccc
Confidence            8754

One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.

>KOG3752|consensus

Probab=99.27  E-value=1.9e-11  Score=100.88  Aligned_cols=79  Identities=25%  Similarity=0.320  Sum_probs=67.5

Q ss_pred             ccCCcEEEEeeCCccCCC-----cceEEEEec-CceeEEeecC-CCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCc
Q psy13868         29 LKKGAVVWYTDGSKTEAG-----SGAGIHCVK-PRVNISLPLG-TYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDS  101 (128)
Q Consensus        29 ~~~~~i~IyTDGS~~~~~-----~G~gv~~~~-~~~~~~~~L~-~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS  101 (128)
                      ...+...+|||||+..+|     +|+|||.++ +....+.++. ...|+|.|||.||..||+-+.+....+  ++|.|||
T Consensus       208 e~~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~k--v~I~TDS  285 (371)
T KOG3752|consen  208 EEIEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINK--VVIRTDS  285 (371)
T ss_pred             ccccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCc--EEEEech
Confidence            345669999999998633     999999954 4577788886 789999999999999999998876655  9999999


Q ss_pred             HHHHHHhh
Q psy13868        102 QAALRAIG  109 (128)
Q Consensus       102 ~sai~ai~  109 (128)
                      +.++++|+
T Consensus       286 ~~~i~~l~  293 (371)
T KOG3752|consen  286 EYFINSLT  293 (371)
T ss_pred             HHHHHHHH
Confidence            99999997

>PRK07708 hypothetical protein; Validated

Probab=99.26  E-value=9.3e-11  Score=91.18  Aligned_cols=85  Identities=18%  Similarity=0.148  Sum_probs=67.2

Q ss_pred             cCCcEEEEeeCCcc--CCCcceEEEEecCc--ee----EEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCc
Q psy13868         30 KKGAVVWYTDGSKT--EAGSGAGIHCVKPR--VN----ISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDS  101 (128)
Q Consensus        30 ~~~~i~IyTDGS~~--~~~~G~gv~~~~~~--~~----~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS  101 (128)
                      .++.+.+|+|||..  ++++|+|+++..+.  ..    ....++...|++.||+.|++.||+.+.+.+.....|.|++||
T Consensus        70 ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DS  149 (219)
T PRK07708         70 EPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDS  149 (219)
T ss_pred             CCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEecc
Confidence            35679999999985  34589999885432  22    223566678999999999999999999987655568999999


Q ss_pred             HHHHHHhhCCCCC
Q psy13868        102 QAALRAIGNFQTK  114 (128)
Q Consensus       102 ~sai~ai~~~~~~  114 (128)
                      +.+++.+......
T Consensus       150 qlVi~qi~g~wk~  162 (219)
T PRK07708        150 QVVLNQLAGEWPC  162 (219)
T ss_pred             HHHHHHhCCCcee
Confidence            9999999987644

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.21  E-value=1.6e-10  Score=94.84  Aligned_cols=87  Identities=17%  Similarity=0.125  Sum_probs=66.9

Q ss_pred             cEEEEeeCCccCC--CcceEEEEecCc-----eeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHH
Q psy13868         33 AVVWYTDGSKTEA--GSGAGIHCVKPR-----VNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAAL  105 (128)
Q Consensus        33 ~i~IyTDGS~~~~--~~G~gv~~~~~~-----~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai  105 (128)
                      .+.||||||+..+  ..|+|+++.++.     ...+..++ ..|++.||+.|++.||+++.+.+..  .+.|++||+.++
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~--~v~i~~DS~lvi   78 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGAT--EVEVRMDSKLVV   78 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCC--eEEEEeCcHHHH
Confidence            4789999999853  489999987642     12344455 6788999999999999999887765  499999999999


Q ss_pred             HHhhCCCC-CchhhHHHH
Q psy13868        106 RAIGNFQT-KSKITWEST  122 (128)
Q Consensus       106 ~ai~~~~~-~s~~~~~~~  122 (128)
                      +.+.+... +++--+.+.
T Consensus        79 ~~i~~~~~~~~~~l~~~~   96 (372)
T PRK07238         79 EQMSGRWKVKHPDMKPLA   96 (372)
T ss_pred             HHhCCCCccCChHHHHHH
Confidence            99998764 444334433

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

Probab=98.38  E-value=1.1e-06  Score=56.71  Aligned_cols=52  Identities=27%  Similarity=0.261  Sum_probs=38.7

Q ss_pred             chHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHhhCCCCCchhhHHHHH
Q psy13868         70 VYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKSKITWESTQ  123 (128)
Q Consensus        70 v~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai~~~~~~s~~~~~~~~  123 (128)
                      +..||+.|++.||+++.+.+..+  +.|+|||+.+++.|++..........+.+
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~--i~v~sDs~~vv~~i~~~~~~~~~~~~~~~   52 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRK--IIVESDSQLVVDAINGRSSSRSELRPLIQ   52 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SC--EEEEES-HHHHHHHTTSS---SCCHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCE--EEEEecCccccccccccccccccccccch
Confidence            36899999999999999888765  99999999999999998544333333333

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

Probab=94.56  E-value=0.25  Score=36.15  Aligned_cols=67  Identities=12%  Similarity=0.117  Sum_probs=42.7

Q ss_pred             CCcEEEEeeCCccCCCcceEEEEecC---ceeE-----EeecC--CCCcchHHHHHHHHHHHHHHHh----cCCCCceEE
Q psy13868         31 KGAVVWYTDGSKTEAGSGAGIHCVKP---RVNI-----SLPLG--TYTGVYQAEVLAIRNCAEENIN----MGLSKREIY   96 (128)
Q Consensus        31 ~~~i~IyTDGS~~~~~~G~gv~~~~~---~~~~-----~~~L~--~~~sv~~AEl~AI~~AL~~~~~----~~~~~~~i~   96 (128)
                      ...+++|+|+|.  .+.|+.+|....   ....     +.++.  ...||=+-||+|+..|.+++..    .......++
T Consensus        79 ~~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~~~~l~~~~~~~~  156 (159)
T PF05380_consen   79 SVELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTVKKELDIEISQVV  156 (159)
T ss_pred             ceeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHHHHHcCCCcceeE
Confidence            457999999994  567777776431   1111     11222  2459999999999999999742    233334455


Q ss_pred             EEe
Q psy13868         97 IFS   99 (128)
Q Consensus        97 I~S   99 (128)
                      ++|
T Consensus       157 ~wt  159 (159)
T PF05380_consen  157 FWT  159 (159)
T ss_pred             EeC
Confidence            543

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

Probab=85.51  E-value=1  Score=35.40  Aligned_cols=64  Identities=20%  Similarity=0.191  Sum_probs=39.9

Q ss_pred             ccCCcEEEEeeCCccCCCcceEEEEecCceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHH
Q psy13868         29 LKKGAVVWYTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAAL  105 (128)
Q Consensus        29 ~~~~~i~IyTDGS~~~~~~G~gv~~~~~~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai  105 (128)
                      ....--+||+|+.-.    |.|+.+........+..  .-.|++|||+|...|.-+...    +   .|.|||..++
T Consensus        90 qr~~lc~VfaDATpT----gwgi~i~~~~~~~Tfs~--~l~IhtaELlaaClAr~~~~~----r---~l~tDnt~Vl  153 (245)
T PF00336_consen   90 QRPGLCQVFADATPT----GWGISITGQRMRGTFSK--PLPIHTAELLAACLARLMSGA----R---CLGTDNTVVL  153 (245)
T ss_pred             CCCCCCceeccCCCC----cceeeecCceeeeeecc--cccchHHHHHHHHHHHhccCC----c---EEeecCcEEE
Confidence            345667899998654    44444544333333322  346899999999777665521    2   4888987664

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	128
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.62
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.62
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.61
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.53
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.52
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.52
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.49
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.48
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.48
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.43
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.43
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.42
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.37
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.36
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.24
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.17
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	94.47
2zd1_B	428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	90.13

>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=99.62  E-value=3.2e-15  Score=104.91  Aligned_cols=88  Identities=16%  Similarity=0.155  Sum_probs=68.6

Q ss_pred             cEEEEeeCCccCC--CcceEEEEecCc-----eeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHH
Q psy13868         33 AVVWYTDGSKTEA--GSGAGIHCVKPR-----VNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAAL  105 (128)
Q Consensus        33 ~i~IyTDGS~~~~--~~G~gv~~~~~~-----~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai  105 (128)
                      .++||||||+..+  ..|+|+++.+..     ...+..++ .+|++.||+.|++.||+++.+.+..  ++.|+|||+.++
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~~~--~v~i~tDS~~vv   79 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIG-RATNNVAEYRGLIAGLDDAVKLGAT--EAAVLMDSKLVV   79 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEE-EECHHHHHHHHHHHHHHHHHHHTCS--EEEEEESCHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCC-CCchHHHHHHHHHHHHHHHHHCCCc--eEEEEeChHHHH
Confidence            5899999999854  489999886542     23334444 7899999999999999999887654  499999999999


Q ss_pred             HHhhCCC-CCchhhHHHHH
Q psy13868        106 RAIGNFQ-TKSKITWESTQ  123 (128)
Q Consensus       106 ~ai~~~~-~~s~~~~~~~~  123 (128)
                      +.|.+.. .+++..+++.+
T Consensus        80 ~~i~~~~~~~~~~l~~~~~   98 (141)
T 3hst_B           80 EQMSGRWKVKHPDLLKLYV   98 (141)
T ss_dssp             HHHTTSSCCCSHHHHHHHH
T ss_pred             HHHhCCcccCCHHHHHHHH
Confidence            9999864 55665565554

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

Probab=99.62  E-value=1.4e-15  Score=109.74  Aligned_cols=79  Identities=23%  Similarity=0.329  Sum_probs=64.7

Q ss_pred             cCCcEEEEeeCCccCCC-----cceEEEEecC-ceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHH
Q psy13868         30 KKGAVVWYTDGSKTEAG-----SGAGIHCVKP-RVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQA  103 (128)
Q Consensus        30 ~~~~i~IyTDGS~~~~~-----~G~gv~~~~~-~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~s  103 (128)
                      +.+.+.||||||+..++     .|+|+++.+. ....+.+++..+|++.||+.|++.||+++.+.+.  +.+.|+|||++
T Consensus         4 ~~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~--~~v~i~tDS~~   81 (154)
T 2qkb_A            4 MGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNI--NKLVLYTNSMF   81 (154)
T ss_dssp             ETTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTC--CEEEEEESCHH
T ss_pred             CCCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCC--ceEEEEECcHH
Confidence            46789999999997532     7999998653 2345666766789999999999999999987654  35999999999


Q ss_pred             HHHHhhC
Q psy13868        104 ALRAIGN  110 (128)
Q Consensus       104 ai~ai~~  110 (128)
                      +++.|.+
T Consensus        82 vi~~i~~   88 (154)
T 2qkb_A           82 TINGITN   88 (154)
T ss_dssp             HHHHHHT
T ss_pred             HHhhhhh
Confidence            9999987

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

Probab=99.61  E-value=2.9e-15  Score=104.51  Aligned_cols=92  Identities=22%  Similarity=0.220  Sum_probs=68.7

Q ss_pred             CcEEEEeeCCccCC--CcceEEEEecCc--e--eEEeecCCCCcchHHHHHHHHHHHHHHHhcCCC--CceEEEEeCcHH
Q psy13868         32 GAVVWYTDGSKTEA--GSGAGIHCVKPR--V--NISLPLGTYTGVYQAEVLAIRNCAEENINMGLS--KREIYIFSDSQA  103 (128)
Q Consensus        32 ~~i~IyTDGS~~~~--~~G~gv~~~~~~--~--~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~--~~~i~I~SDS~s  103 (128)
                      +.++||||||+..+  ..|+|+++.++.  .  ..+..++ .+|++.||+.|++.||+++.+.+..  ..++.|+|||+.
T Consensus         2 ~~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~   80 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIG-ETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSEL   80 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEE-EECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHH
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCC-CCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHH
Confidence            35899999999753  489999986532  2  3344444 5799999999999999999876543  126999999999


Q ss_pred             HHHHhhCCCC-CchhhHHHHHh
Q psy13868        104 ALRAIGNFQT-KSKITWESTQA  124 (128)
Q Consensus       104 ai~ai~~~~~-~s~~~~~~~~~  124 (128)
                      +++.+.+... +++..+++.+.
T Consensus        81 vi~~i~~~~~~~~~~l~~~~~~  102 (140)
T 3u3g_D           81 IVRQMQGVYKVKEPTLKEKFAK  102 (140)
T ss_dssp             HHHHHTTSSCCCCGGGHHHHHH
T ss_pred             HHHHhCCCcccCCHHHHHHHHH
Confidence            9999998663 55555554443

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

Probab=99.53  E-value=6.7e-14  Score=99.85  Aligned_cols=89  Identities=19%  Similarity=0.159  Sum_probs=64.8

Q ss_pred             cEEEEeeCCcc-C--CCcce-EEEEecCc-e--eEEeecC---CCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcH
Q psy13868         33 AVVWYTDGSKT-E--AGSGA-GIHCVKPR-V--NISLPLG---TYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQ  102 (128)
Q Consensus        33 ~i~IyTDGS~~-~--~~~G~-gv~~~~~~-~--~~~~~L~---~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~  102 (128)
                      +++||||||+. .  ++.|+ |+++.+.. .  ..+..++   ...|++.||+.|++.||+++.+.+..+  +.|+|||+
T Consensus         1 m~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~--v~i~tDS~   78 (149)
T 2ehg_A            1 MIIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISS--PIIKGDSQ   78 (149)
T ss_dssp             CCEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCS--CEEEESCH
T ss_pred             CEEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCE--EEEEeChH
Confidence            46899999997 2  44786 88875432 2  1223333   378999999999999999998876554  99999999


Q ss_pred             HHHHHhhCCCC-CchhhHHHHH
Q psy13868        103 AALRAIGNFQT-KSKITWESTQ  123 (128)
Q Consensus       103 sai~ai~~~~~-~s~~~~~~~~  123 (128)
                      .+++.+.+... +++...++.|
T Consensus        79 ~vi~~i~~~w~~~~~~~~~l~~  100 (149)
T 2ehg_A           79 LVIKQMNGEYKVKAKRIIPLYE  100 (149)
T ss_dssp             HHHHHHTTSSCCCCTTHHHHHH
T ss_pred             HHHHHHhCccccCCHHHHHHHH
Confidence            99999998743 3333334433

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

Probab=99.52  E-value=1.9e-14  Score=102.65  Aligned_cols=74  Identities=22%  Similarity=0.186  Sum_probs=59.4

Q ss_pred             CcEEEEeeCCccCCC--cceEEEEecCc--eeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHH
Q psy13868         32 GAVVWYTDGSKTEAG--SGAGIHCVKPR--VNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRA  107 (128)
Q Consensus        32 ~~i~IyTDGS~~~~~--~G~gv~~~~~~--~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~a  107 (128)
                      +.+.||||||+..++  .|+|+++....  ...+..++ .+|++.||+.|++.||+++.+    .+.+.|+|||+++++.
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~~-~~Tnn~aEl~A~~~AL~~~~~----~~~v~I~tDS~~vi~~   77 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDP-ATTNNRMELMAAIKGLEALKE----PARVQLYSDSAYLVNA   77 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEE-EECHHHHHHHHHHHHHHTCSS----CCEEEEEESCHHHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCCC-CCcHHHHHHHHHHHHHHhcCc----cCcEEEEeChHHHHHH
Confidence            568999999998643  89999886543  23333443 678999999999999999865    2469999999999999


Q ss_pred             hhC
Q psy13868        108 IGN  110 (128)
Q Consensus       108 i~~  110 (128)
                      |.+
T Consensus        78 i~~   80 (146)
T 3h08_A           78 MNE   80 (146)
T ss_dssp             HHS
T ss_pred             HHH
Confidence            988

>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=99.52  E-value=1.5e-14  Score=104.06  Aligned_cols=84  Identities=15%  Similarity=0.033  Sum_probs=64.9

Q ss_pred             cCCcEEEEeeCCccCCCcceEEEEecCce--eEEe-ec--CC--CCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcH
Q psy13868         30 KKGAVVWYTDGSKTEAGSGAGIHCVKPRV--NISL-PL--GT--YTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQ  102 (128)
Q Consensus        30 ~~~~i~IyTDGS~~~~~~G~gv~~~~~~~--~~~~-~L--~~--~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~  102 (128)
                      +++.+.||||||+..+..|+|+++.....  ..+. .+  +.  .+|++.||+.|++.||+++.+.+.   ++.|+|||+
T Consensus         3 ~~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~---~v~I~tDS~   79 (147)
T 2kq2_A            3 DRTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV---KIRILHDYA   79 (147)
T ss_dssp             TTSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC---CCCBSSCCS
T ss_pred             CCCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC---eEEEEECcH
Confidence            57789999999999866999999854322  2333 23  22  368999999999999999887765   499999999


Q ss_pred             HHHHHhhCCCCCch
Q psy13868        103 AALRAIGNFQTKSK  116 (128)
Q Consensus       103 sai~ai~~~~~~s~  116 (128)
                      .+.+.+.+....+.
T Consensus        80 ~i~~w~~~~w~~~~   93 (147)
T 2kq2_A           80 GIAFWATGEWKAKN   93 (147)
T ss_dssp             THHHHTTSSSSCCH
T ss_pred             HHHHHHhCCCccCC
Confidence            98888877655443

>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=99.49  E-value=8.3e-14  Score=100.79  Aligned_cols=73  Identities=23%  Similarity=0.144  Sum_probs=58.1

Q ss_pred             cEEEEeeCCccCCC--cceEEEEecCc--eeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHh
Q psy13868         33 AVVWYTDGSKTEAG--SGAGIHCVKPR--VNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAI  108 (128)
Q Consensus        33 ~i~IyTDGS~~~~~--~G~gv~~~~~~--~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai  108 (128)
                      .+.||||||+..++  .|+|+++....  ...+..+ ..+|++.||+.|++.||+++.+.    +.+.|+|||+++++.|
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~~----~~v~I~tDS~~vi~~i   78 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKEH----AEVILSTDSQYVRQGI   78 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCSC----CEEEEEECCHHHHHHH
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCcC----CcEEEEeCHHHHHHHH
Confidence            58999999998533  89999986433  2233334 36789999999999999998642    4699999999999999


Q ss_pred             hC
Q psy13868        109 GN  110 (128)
Q Consensus       109 ~~  110 (128)
                      .+
T Consensus        79 ~~   80 (155)
T 1jl1_A           79 TQ   80 (155)
T ss_dssp             HT
T ss_pred             HH
Confidence            97

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

Probab=99.48  E-value=9.9e-14  Score=100.78  Aligned_cols=74  Identities=26%  Similarity=0.140  Sum_probs=58.1

Q ss_pred             CcEEEEeeCCccCC--CcceEEEEecCc--eeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHH
Q psy13868         32 GAVVWYTDGSKTEA--GSGAGIHCVKPR--VNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRA  107 (128)
Q Consensus        32 ~~i~IyTDGS~~~~--~~G~gv~~~~~~--~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~a  107 (128)
                      ..+.||||||+..+  ..|+|+++....  ...+..++ .+|++.||+.|++.||+++.+.    +.+.|+|||+++++.
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~-~~tn~~aEl~A~~~AL~~~~~~----~~v~I~tDS~~vi~~   79 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGFS-LTTNNRMELLAPIVALEALKEP----CKIILTSDSQYMRQG   79 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEEE-EECHHHHHHHHHHHHHHTCSSC----CEEEEEECCHHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCcC-CCccHHHHHHHHHHHHHHhccC----CeEEEEeCHHHHHHH
Confidence            46899999999853  389999885432  22333343 5789999999999999987532    569999999999999


Q ss_pred             hhC
Q psy13868        108 IGN  110 (128)
Q Consensus       108 i~~  110 (128)
                      |.+
T Consensus        80 i~~   82 (158)
T 2e4l_A           80 IMT   82 (158)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            988

>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=99.48  E-value=2.6e-13  Score=99.95  Aligned_cols=77  Identities=22%  Similarity=0.330  Sum_probs=58.6

Q ss_pred             cccCCcEEEEeeCCccC--CCcceEEEEecC-ceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHH
Q psy13868         28 LLKKGAVVWYTDGSKTE--AGSGAGIHCVKP-RVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAA  104 (128)
Q Consensus        28 ~~~~~~i~IyTDGS~~~--~~~G~gv~~~~~-~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sa  104 (128)
                      +++...+.||||||+..  +..|+|+++... .......++..+|++.||+.|+..||+++ .    .+++.|+|||+++
T Consensus        18 P~~~~~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~-~----~~~v~I~tDS~~v   92 (165)
T 3p1g_A           18 PIPDADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA-E----GKKLNVYTDSRYA   92 (165)
T ss_dssp             CCTTCSEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT-B----TSEEEEEECCHHH
T ss_pred             CCCCCCEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc-c----CceEEEEEchHHH
Confidence            34556799999999973  447888866432 22222246678899999999999999998 2    3469999999999


Q ss_pred             HHHhh
Q psy13868        105 LRAIG  109 (128)
Q Consensus       105 i~ai~  109 (128)
                      ++.|-
T Consensus        93 i~~iw   97 (165)
T 3p1g_A           93 FATAH   97 (165)
T ss_dssp             HHHHH
T ss_pred             Hhhhh
Confidence            99984

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

Probab=99.43  E-value=1.8e-13  Score=100.36  Aligned_cols=74  Identities=18%  Similarity=0.055  Sum_probs=57.8

Q ss_pred             CcEEEEeeCCccCCC--cceEEEEecCc--eeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHH
Q psy13868         32 GAVVWYTDGSKTEAG--SGAGIHCVKPR--VNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRA  107 (128)
Q Consensus        32 ~~i~IyTDGS~~~~~--~G~gv~~~~~~--~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~a  107 (128)
                      ..+.||||||+..++  .|+|+++....  ...+..+ ..+|++.||+.|++.||+++.+.    ..+.|+|||+++++.
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~Ai~~AL~~~~~~----~~v~I~tDS~~vi~~   81 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGE-ACTTNNRMELKAAIEGLKALKEP----CEVDLYTDSHYLKKA   81 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEE-EEECHHHHHHHHHHHHHHSCCSC----CEEEEECCCHHHHHH
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCC-CCCcHHHHHHHHHHHHHHHhccC----CeEEEEeChHHHHHH
Confidence            578999999998543  89999985432  2222223 35789999999999999987543    359999999999999


Q ss_pred             hhC
Q psy13868        108 IGN  110 (128)
Q Consensus       108 i~~  110 (128)
                      |.+
T Consensus        82 i~~   84 (166)
T 1ril_A           82 FTE   84 (166)
T ss_dssp             HHS
T ss_pred             Hhh
Confidence            998

>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=99.43  E-value=4.3e-13  Score=97.11  Aligned_cols=74  Identities=30%  Similarity=0.328  Sum_probs=58.7

Q ss_pred             cCCcEEEEeeCCccCCC--cceEEEEecCceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHH
Q psy13868         30 KKGAVVWYTDGSKTEAG--SGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRA  107 (128)
Q Consensus        30 ~~~~i~IyTDGS~~~~~--~G~gv~~~~~~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~a  107 (128)
                      +.+.+.||||||+..++  .|+|+++.+... ....+ ..+|++.||+.|+..||+.+      .+++.|+|||+++++.
T Consensus         9 ~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~-~~~~~-~~~Tnn~aEl~A~i~AL~~~------~~~v~i~tDS~~v~~~   80 (150)
T 3qio_A            9 IVGAETFYVDGAANRETKLGKAGYVTNRGRQ-KVVTL-TDTTNQKTELQAIYLALQDS------GLEVNIVTDSQYALGI   80 (150)
T ss_dssp             CTTCEEEEEEEEECTTTCCEEEEEEETTSCE-EEEEE-SSCCHHHHHHHHHHHHHHHS------CSEEEEEESCHHHHHH
T ss_pred             CCCCEEEEEccCCCCCCCCeEEEEEEEcCCE-EEEeC-CCCCHHHHHHHHHHHHHHhC------CCcEEEEeCcHHHHHH
Confidence            46789999999997433  888888865432 23344 47899999999999999984      2569999999999999


Q ss_pred             hhCC
Q psy13868        108 IGNF  111 (128)
Q Consensus       108 i~~~  111 (128)
                      |.+.
T Consensus        81 i~~w   84 (150)
T 3qio_A           81 ITQW   84 (150)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9874

>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=99.42  E-value=3.4e-13  Score=97.32  Aligned_cols=80  Identities=15%  Similarity=-0.056  Sum_probs=62.5

Q ss_pred             cCCcEEEEeeCCccCC--CcceEEEEecCc--eeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHH
Q psy13868         30 KKGAVVWYTDGSKTEA--GSGAGIHCVKPR--VNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAAL  105 (128)
Q Consensus        30 ~~~~i~IyTDGS~~~~--~~G~gv~~~~~~--~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai  105 (128)
                      +.+.+.||||||+..+  ..|+|+++....  ...+..++ .+|++.||+.|++.||+++.+.+.   .+.|+|||+.++
T Consensus         8 ~~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~-~~TNN~aEl~A~i~aL~~~~~~~~---~v~i~tDS~~vi   83 (142)
T 1zbf_A            8 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKERNS---RKPIYSNSQTAI   83 (142)
T ss_dssp             CCCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEE-EECHHHHHHHHHHHHHHHHHHTTC---CCCEEESCHHHH
T ss_pred             CCCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccC-CcCcHHHHHHHHHHHHHHHHhCCC---eEEEEEehHHHH
Confidence            3567899999999743  389999985321  22222333 578999999999999999988765   499999999999


Q ss_pred             HHhhCCCC
Q psy13868        106 RAIGNFQT  113 (128)
Q Consensus       106 ~ai~~~~~  113 (128)
                      +.+++...
T Consensus        84 ~w~~~~~~   91 (142)
T 1zbf_A           84 KWVKDKKA   91 (142)
T ss_dssp             HHHHHTCC
T ss_pred             HHHHcCCc
Confidence            99998873

>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=99.37  E-value=4e-13  Score=96.47  Aligned_cols=79  Identities=15%  Similarity=-0.057  Sum_probs=58.4

Q ss_pred             CCcEEEEeeCCccCCC--cceEEEEecC--ceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHH
Q psy13868         31 KGAVVWYTDGSKTEAG--SGAGIHCVKP--RVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALR  106 (128)
Q Consensus        31 ~~~i~IyTDGS~~~~~--~G~gv~~~~~--~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~  106 (128)
                      +....||||||+..+.  .|.|.|+...  ....+..++ .+|++.||++|++.||+.+.+.+..   +.|+|||+++++
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~~-~tTNN~aEl~A~i~aL~~l~~~~~~---v~i~tDSqyVi~   78 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKERNSR---KPIYSNSQTAIK   78 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEEE-EECHHHHHHHHHHHHHHHHHHTTCC---CCEEESCHHHHH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCCC-CCchHHHHHHHHHHHHHHHHhCCCC---EEEEcchHHHHH
Confidence            3456799999997433  7885555332  223333444 6899999999999999999876532   799999999999


Q ss_pred             HhhCCCC
Q psy13868        107 AIGNFQT  113 (128)
Q Consensus       107 ai~~~~~  113 (128)
                      .|.+...
T Consensus        79 wi~~~~~   85 (134)
T 4htu_A           79 WVKDKKA   85 (134)
T ss_dssp             HHHHTCC
T ss_pred             HHHcCCc
Confidence            9986543

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

Probab=99.36  E-value=3.3e-12  Score=94.12  Aligned_cols=78  Identities=21%  Similarity=0.291  Sum_probs=57.2

Q ss_pred             cCCcEEEEeeCCccCC--C-----cceEEEEec--C--ceeEEeecC-CCCcchHHHHHHHHHHHHHHHhcCCCCceEEE
Q psy13868         30 KKGAVVWYTDGSKTEA--G-----SGAGIHCVK--P--RVNISLPLG-TYTGVYQAEVLAIRNCAEENINMGLSKREIYI   97 (128)
Q Consensus        30 ~~~~i~IyTDGS~~~~--~-----~G~gv~~~~--~--~~~~~~~L~-~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I   97 (128)
                      ....+.|||||||..+  +     .|+|||+..  +  .....+.++ ...+.+.||+.|+..||+.+++.+   .+|.|
T Consensus         4 ~~~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~~---~~v~I   80 (165)
T 2lsn_A            4 GQYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIP---GPVLV   80 (165)
T ss_dssp             CCCSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHSS---SCEEE
T ss_pred             CCceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcCC---CeEEE
Confidence            4566899999999742  2     799998742  2  223333333 456788899999999998887654   24999


Q ss_pred             EeCcHHHHHHhhC
Q psy13868         98 FSDSQAALRAIGN  110 (128)
Q Consensus        98 ~SDS~sai~ai~~  110 (128)
                      +|||+++++.|..
T Consensus        81 ~TDS~Yvi~~it~   93 (165)
T 2lsn_A           81 ITDSFYVAESANK   93 (165)
T ss_dssp             EESCHHHHHHHHT
T ss_pred             EeChHHHHhhhhh
Confidence            9999999999964

>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=99.24  E-value=2.4e-11  Score=103.05  Aligned_cols=86  Identities=30%  Similarity=0.333  Sum_probs=64.4

Q ss_pred             CCcEEEEeeCCccCC-C-cceEEEEecCceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHh
Q psy13868         31 KGAVVWYTDGSKTEA-G-SGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAI  108 (128)
Q Consensus        31 ~~~i~IyTDGS~~~~-~-~G~gv~~~~~~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai  108 (128)
                      .+.+.||||||+..+ + .|+|+++.... .....+ ..+||+.||+.|++.||+.+      .+.+.|+|||+++++.|
T Consensus       437 ~~~~~iytDGs~~~n~g~~g~g~v~~~~~-~~~~~~-~~~TNn~aEl~Ai~~aL~~~------~~~v~I~tDS~~vi~~i  508 (557)
T 2zd1_A          437 VGAETFYVDGAANRETKLGKAGYVTNKGR-QKVVPL-TNTTNQKTELQAIYLALQDS------GLEVNIVTDSQYALGII  508 (557)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEETTSC-EEEEEE-CSCCHHHHHHHHHHHHHHHS------CSEEEEEECCHHHHHHH
T ss_pred             CCCEEEEEccCCCCCCCceEEEEEEECCc-EEEecC-CCCCHHHHHHHHHHHHHHhC------CCcEEEEeChHHHHHHH
Confidence            567999999999743 3 78888875432 222333 36899999999999999988      24599999999999999


Q ss_pred             hCCCCC--chhhHHHHHh
Q psy13868        109 GNFQTK--SKITWESTQA  124 (128)
Q Consensus       109 ~~~~~~--s~~~~~~~~~  124 (128)
                      .+...+  .++..++.+.
T Consensus       509 ~~~~~~~~~~l~~~~~~~  526 (557)
T 2zd1_A          509 QAQPDKSESELVNQIIEQ  526 (557)
T ss_dssp             TTCCSEESSHHHHHHHHH
T ss_pred             hcCCccCCHHHHHHHHHH
Confidence            997766  2344444443

>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=99.17  E-value=1.2e-10  Score=98.71  Aligned_cols=86  Identities=26%  Similarity=0.268  Sum_probs=62.8

Q ss_pred             CCcEEEEeeCCccCCC--cceEEEEecCceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHh
Q psy13868         31 KGAVVWYTDGSKTEAG--SGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAI  108 (128)
Q Consensus        31 ~~~i~IyTDGS~~~~~--~G~gv~~~~~~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai  108 (128)
                      .+.+.||||||+..++  .|+|+++.... ..+..++ .+|++.||+.|++.||+.    +  .+.+.|+|||+++++.|
T Consensus       434 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~-~~~~~~~-~~TNn~aEl~A~i~aL~~----~--~~~v~I~tDS~~v~~~i  505 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKEGKAGYVTDRGK-DKVKKLE-QTTNQQAELEAFAMALTD----S--GPKVNIIVDSQYVMGIV  505 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSC-EEEEEES-SCCHHHHHHHHHHHHHHT----S--CSEEEEEESCHHHHHHH
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCC-EeeccCC-CCCHHHHHHHHHHHHHHc----C--CCeEEEEEehHHHHHHH
Confidence            5679999999997543  78888885433 2233343 678999999999999997    2  34699999999999999


Q ss_pred             hCCC--CCchhhHHHHHh
Q psy13868        109 GNFQ--TKSKITWESTQA  124 (128)
Q Consensus       109 ~~~~--~~s~~~~~~~~~  124 (128)
                      ++..  ...++..++.+.
T Consensus       506 ~~~~~~~~~~l~~~~~~~  523 (555)
T 1mu2_A          506 ASQPTESESKIVNQIIEE  523 (555)
T ss_dssp             HTCCSEESCHHHHHHHHH
T ss_pred             hcccccccHHHHHHHHHH
Confidence            9754  223344444433

>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=94.47  E-value=0.01  Score=48.69  Aligned_cols=78  Identities=13%  Similarity=0.055  Sum_probs=49.6

Q ss_pred             cCCcEEEEeeCCccCCCcceEEEEec------CceeEEeecC---CCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeC
Q psy13868         30 KKGAVVWYTDGSKTEAGSGAGIHCVK------PRVNISLPLG---TYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSD  100 (128)
Q Consensus        30 ~~~~i~IyTDGS~~~~~~G~gv~~~~------~~~~~~~~L~---~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SD  100 (128)
                      +...+.+|||+|.  .++| ||+.-.      +....+-++.   ...+++..|++||..|++.....-. .+.+.|+||
T Consensus       343 ~~~~~~l~~DAS~--~~~g-avL~q~~~~~~~~i~y~Sk~l~~~e~~ys~~ekEllAi~~a~~~~~~yl~-g~~~~v~tD  418 (455)
T 1rw3_A          343 LTKPFELFVDEKQ--GYAK-GVLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTM-GQPLVIKAP  418 (455)
T ss_dssp             SCCTTSCEEEEEE--CSSS-BEECCBCTTTTCCCCCCCBCSCSSCSSSCCSSHHHHHHHHHHHHHHGGGC-SSCEEEECS
T ss_pred             CCCcEEEEEeccC--Ccce-eEEEEecCCcEEEEEEEcccCCccccccchHHHHHHHHHHHHHHHHHHcC-CCcEEEEec
Confidence            3567789999985  3344 344321      1112222332   3467889999999999998865422 245999999


Q ss_pred             cHHHHHHhhCCC
Q psy13868        101 SQAALRAIGNFQ  112 (128)
Q Consensus       101 S~sai~ai~~~~  112 (128)
                      +. ++..+.+..
T Consensus       419 h~-~~~~l~~~~  429 (455)
T 1rw3_A          419 HA-VEALVKQPP  429 (455)
T ss_dssp             SC-TTTTSSSTT
T ss_pred             Ch-HHHHhCCCc
Confidence            97 666666544

>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=90.13  E-value=1  Score=36.62  Aligned_cols=77  Identities=4%  Similarity=-0.144  Sum_probs=47.1

Q ss_pred             cCCcEEEEeeCCccCCCcceEEEEecC--ceeE--EeecCCCCcchHHHHHH-HHHHHHHHHhc--CCCCceEEEEeCcH
Q psy13868         30 KKGAVVWYTDGSKTEAGSGAGIHCVKP--RVNI--SLPLGTYTGVYQAEVLA-IRNCAEENINM--GLSKREIYIFSDSQ  102 (128)
Q Consensus        30 ~~~~i~IyTDGS~~~~~~G~gv~~~~~--~~~~--~~~L~~~~sv~~AEl~A-I~~AL~~~~~~--~~~~~~i~I~SDS~  102 (128)
                      +...+.++||+|..  + .+|.+..++  ....  ++.-......+.-|++| |..||+.....  |.....++++||.+
T Consensus       321 ~~~~~~l~~das~~--g-~~g~vl~q~~~~~~~s~~~~~~~~y~~~~~e~la~vv~al~~~r~yl~G~~~~~~i~~td~~  397 (428)
T 2zd1_B          321 PSKDLIAEIQKQGQ--G-QWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKET  397 (428)
T ss_dssp             TTSCCEEEEEEEET--T-EEEEEEESSTTCEEEEEEEECCSSCTTCHHHHHHHHHHHHHHHHHHHHSSCCEEEESSCHHH
T ss_pred             CCCCEEEEEecCCC--C-cEEEEEecCCCceeeecccchhhhcccchHHHHHHHHHHhhccceEEECCCCcEECCccHHH
Confidence            57889999999952  2 223333322  2222  23322344556777777 99999976432  54445678899998


Q ss_pred             HHHHHhh
Q psy13868        103 AALRAIG  109 (128)
Q Consensus       103 sai~ai~  109 (128)
                      ..-.-..
T Consensus       398 ~~~~~~~  404 (428)
T 2zd1_B          398 WETWWTE  404 (428)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            7654443

---

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	128
d1s1ta1	110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	2e-06

>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 = 41.1 bits (96), Expect = 2e-06
 Identities = 23/100 (23%), Positives = 38/100 (38%), Gaps = 8/100 (8%)

Query: 31  KGAVVWYTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGL 90
            GA  +Y DG+            V  R    +   T T   + E+ AI    ++      
Sbjct: 6   VGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD------ 59

Query: 91  SKREIYIFSDSQAALRAIGNFQTKS--KITWESTQAICGK 128
           S  E+ I +DSQ AL  I     +S  ++  +  + +  K
Sbjct: 60  SGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKK 99

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	128
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.59
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.49
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.47
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.38
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.36

>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=99.59  E-value=3.3e-15  Score=101.91  Aligned_cols=87  Identities=24%  Similarity=0.260  Sum_probs=63.0

Q ss_pred             CcEEEEeeCCccCC-C-cceEEEEecCceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHhh
Q psy13868         32 GAVVWYTDGSKTEA-G-SGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIG  109 (128)
Q Consensus        32 ~~i~IyTDGS~~~~-~-~G~gv~~~~~~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai~  109 (128)
                      +...+|||||+..+ + .|+|++..+. ......++ ..|+++|||.||+.||+..      .+++.|+|||++++++|.
T Consensus         7 ~~~t~ytDGs~~~n~~~g~~g~~~~~~-~~~~~~~~-~~TNn~aEl~Avi~aL~~~------~~~v~I~TDS~yvi~~i~   78 (110)
T d1s1ta1           7 GAETFYVDGAANRETKLGKAGYVTNRG-RQKVVTLT-DTTNQKTELQAIYLALQDS------GLEVNIVTDSQYALGIIQ   78 (110)
T ss_dssp             TSEEEEEEEEEETTTTEEEEEEEETTS-CEEEEEES-SCCHHHHHHHHHHHHHHHS------CSEEEEEECCHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCCCcEEEEEEecC-CeEEEecc-cCcHHHHHHHHHHHHHHhC------CCeEEEEEehHHHHHHHh
Confidence            45579999998753 3 6666666543 23334454 5799999999999999742      235999999999999999


Q ss_pred             CCCC--CchhhHHHHHhhh
Q psy13868        110 NFQT--KSKITWESTQAIC  126 (128)
Q Consensus       110 ~~~~--~s~~~~~~~~~~~  126 (128)
                      ....  ..++.++..|.+.
T Consensus        79 ~~~~~~~~~l~~~il~~l~   97 (110)
T d1s1ta1          79 AQPDQSESELVNQIIEQLI   97 (110)
T ss_dssp             HCCSEESCHHHHHHHHHHH
T ss_pred             cCccccchHHHHHHHHHHh
Confidence            8544  4457777776654

>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=99.49  E-value=1.3e-13  Score=94.66  Aligned_cols=85  Identities=27%  Similarity=0.254  Sum_probs=60.4

Q ss_pred             CCcEEEEeeCCccCC-C-cceEEEEecCceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHh
Q psy13868         31 KGAVVWYTDGSKTEA-G-SGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAI  108 (128)
Q Consensus        31 ~~~i~IyTDGS~~~~-~-~G~gv~~~~~~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai  108 (128)
                      ++...||||||+..+ + .|+|+++... ......++ ..|+++|||.||++||+..      .+.+.|+|||+++++.+
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~-~~~~~~~~-~~tnn~AEl~Ai~~al~~~------~~~i~I~tDS~~v~~~~   76 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRG-KDKVKKLE-QTTNQQAELEAFAMALTDS------GPKVNIIVDSQYVMGIV   76 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTS-CEEEEEES-SCCHHHHHHHHHHHHHHTS------CSEEEEEESCHHHHHHH
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCC-CEEEEecC-CCcchHHHHHHHHHHhccC------CcceEEEechHHHHHHH
Confidence            355789999998743 3 6667666543 23334454 5799999999999999853      24599999999999999


Q ss_pred             hCCCCCc--hhhHHHHH
Q psy13868        109 GNFQTKS--KITWESTQ  123 (128)
Q Consensus       109 ~~~~~~s--~~~~~~~~  123 (128)
                      .+.....  ...++..+
T Consensus        77 ~~~~~~~~~~~~~~~~~   93 (126)
T d1mu2a1          77 ASQPTESESKIVNQIIE   93 (126)
T ss_dssp             HTCCSEESCHHHHHHHH
T ss_pred             hcCCccccchHHHHHHH
Confidence            9976533  34444433

>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=99.47  E-value=4.1e-14  Score=99.69  Aligned_cols=73  Identities=16%  Similarity=-0.016  Sum_probs=56.4

Q ss_pred             EEeeCCccCC--CcceEEEEecCcee--EEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHhhCC
Q psy13868         36 WYTDGSKTEA--GSGAGIHCVKPRVN--ISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNF  111 (128)
Q Consensus        36 IyTDGS~~~~--~~G~gv~~~~~~~~--~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai~~~  111 (128)
                      ||||||+..+  ..|.|+|+......  .+.++ +..|+++||++|++.||+++.+.+.   ++.|+|||+++++.+++.
T Consensus         7 Iy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~-~~~TNN~aEl~A~i~aL~~~~~~~~---~i~I~tDS~yvi~wv~~~   82 (132)
T d1zbfa1           7 LSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERNS---RKPIYSNSQTAIKWVKDK   82 (132)
T ss_dssp             EEEEEEECSSSEEEEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHHTTC---CCCEEESCHHHHHHHHHT
T ss_pred             EEEeecCCCCCchheEEEEEEcCCEEEEEEcCc-CccchHHHHHHHHHHHHHHhhcCCc---eEEEEeccHHHHHHHHhC
Confidence            8999999843  38888887544322  22233 3679999999999999999987642   389999999999999765


Q ss_pred             C
Q psy13868        112 Q  112 (128)
Q Consensus       112 ~  112 (128)
                      .
T Consensus        83 ~   83 (132)
T d1zbfa1          83 K   83 (132)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.38  E-value=2.1e-13  Score=95.44  Aligned_cols=76  Identities=16%  Similarity=0.035  Sum_probs=55.3

Q ss_pred             CcEEEEeeCCccCCC--cceEEEEecCc-eeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHh
Q psy13868         32 GAVVWYTDGSKTEAG--SGAGIHCVKPR-VNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAI  108 (128)
Q Consensus        32 ~~i~IyTDGS~~~~~--~G~gv~~~~~~-~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai  108 (128)
                      ..+.||||||+.+++  .|+|+|+.... ..........+|+++||+.|++.||+++..    ...+.|+|||+++++.|
T Consensus         2 ~~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~----~~~i~i~tds~~~~~~~   77 (147)
T d1rila_           2 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE----PCEVDLYTDSHYLKKAF   77 (147)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS----CCEEEEECCCHHHHHHH
T ss_pred             CEEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhccC----CceEEEecchhhhhccc
Confidence            458899999998643  78888874322 222222223568999999999999987532    24599999999999988


Q ss_pred             hCC
Q psy13868        109 GNF  111 (128)
Q Consensus       109 ~~~  111 (128)
                      ...
T Consensus        78 ~~~   80 (147)
T d1rila_          78 TEG   80 (147)
T ss_dssp             HSS
T ss_pred             ccc
Confidence            663

>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=99.36  E-value=7.8e-13  Score=92.16  Aligned_cols=74  Identities=23%  Similarity=0.166  Sum_probs=56.0

Q ss_pred             cEEEEeeCCccCCC--cceEEEEecCc--eeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHh
Q psy13868         33 AVVWYTDGSKTEAG--SGAGIHCVKPR--VNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAI  108 (128)
Q Consensus        33 ~i~IyTDGS~~~~~--~G~gv~~~~~~--~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai  108 (128)
                      .|+||||||+.+++  .|+|+|+....  ...+..+ +..|+++||++|+..||+++..    ...+.++|||+.++..+
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~-~~~tnn~aE~~Ai~~Al~~~~~----~~~i~i~tds~~~i~~~   76 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE----HAEVILSTDSQYVRQGI   76 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS----CCEEEEEECCHHHHHHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEecccc-CcccHHHHHHhhhhhhhhhhcc----cceEEEeecceeeEEcc
Confidence            58999999998643  89999875432  3333333 3578999999999999987633    24589999999999888


Q ss_pred             hCC
Q psy13868        109 GNF  111 (128)
Q Consensus       109 ~~~  111 (128)
                      ...
T Consensus        77 ~~~   79 (152)
T d1jl1a_          77 TQW   79 (152)
T ss_dssp             HTT
T ss_pred             cch
Confidence            644