Psyllid ID: psy10246

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------
Protein Sequence
MATRKPKKVGILKATTNITPAYDSLVCLEGRASAFSWPRLAGHSRSACQFQNNEILEKDSPVSAHRILFLLLNPDCNDPSFFLPDPGSFEKDNDNISSVYLVSRSESIARLARYGKSAWFDLQKAGLELPTNAFGVENNVQCSWILSTQASSGCLLINSATGYAMSGYQDTRLYSGAILVMKVLQSVQIFKIGKWLEISVLGSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWLEN
Secondary Structure (PSIPRED)
cccccccEEEEEEEEccccccccEEEEEccccccccccccccccccccccccccccccccccccEEEEEEEEcccccccccccccccccccccccEEEEEEEEcHHHHHHHHHHcccccEEHHHcccccccccccccccEEEEEEEEEEccccEEEEEcccccccccccccccccHHHHHHHHHHHEEEEEEccEEEEEEEccccccEEEEcccccccHHHccccccccEEEEEEcccccccccHHHHHHHHHHHHHHHHHccccccEEEccHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccccccEEEEEEccccccccccEEEEccccccccccHcccccccHHHHcccHHHccccccHHHHHHHHHHcccccccccccccccccccccccccEEEEEEcHHHHHHHHHHcccHHHHHHHccccccccccccccccEEEEEEEccccccEEEEEcccccHcccccccHHHHHHHHHHHHHHHEEEEEEccEEEEEEcccccccEEEEccccHHHHHHHHHHHHccEEEEEEcccccccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHccHHHHcHHHHHcc
Coil and Loop (DISEMBL)
matrkpkkvGILKattnitpaydsLVCLegrasafswprlaghsrsacqfqnneilekdspvsAHRILFLLlnpdcndpsfflpdpgsfekdndniSSVYLVSRSESIARLARYGKSAWFDLQKAglelptnafgvennVQCSWILStqassgcllinsatgyamsgyqdtrlYSGAILVMKVLQSVQIFKIGKWLEisvlgspdvkkvifspwsvRNVRAMKFARdinikflwipshcgivenervDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWLEN
Flexible Loop (DISEMBL)
matrkpkkvgilkattnitpaydSLVCLEGRASAFSWPRLAGHSRSACQFQNNEILEKDSPVSAHRILFLLLNPDCNDPSFFLPDPGSFEKDNDNISSVYLVSRSESIARLARYGKSAWFDLQKAGLELPTNAFGVENNVQCSWILSTQASSGCLLINSATGYAMSGYQDTRLYSGAILVMKVLQSVQIFKIGKWLeisvlgspdvkkvifspwsvrnVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQSKktilnewktdwlen
Low Complexity Region (SEG)
MATRKPKKVGILKATTNITPAYDSLVCLEGRASAFSWPRLAGHSRSACQFQNNEILEKDSPVSAHRILFLLLNPDCNDPSFFLPDPGSFEKDNDNISSVYLVSRSESIARLARYGKSAWFDLQKAGLELPTNAFGVENNVQCSWILSTQASSGCLLINSATGYAMSGYQDTRLYSGAILVMKVLQSVQIFKIGKWLEISVLGSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWLEN
Disordered region (IsUnstruct)
********VGILKATTNITPAYDSLVCLEGRASAFSWPRLAGHSRSACQFQNNEILEKDSPVSAHRILFLLLNPDCNDPSFFLPD********DNISSVYLVSRSESIARLARYGKSAWFDLQKAGLELPTNAFGVENNVQCSWILSTQASSGCLLINSATGYAMSGYQDTRLYSGAILVMKVLQSVQIFKIGKWLEISVLGSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWL**
Disordered Region (DISOPRED)
**********ILKATTNITPAYDSLVCLEGRASAFSWPRLAGHSRSACQFQNNEILEKDSPVSAHRILFLLLNPDCNDPSFFLPDPGSFEKDNDNISSVYLVSRSESIARLARYGKSAWFDLQKAGLELPTNAFGVENNVQCSWILSTQASSGCLLINSATGYAMSGYQDTRLYSGAILVMKVLQSVQIFKIGKWLEISVLGSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERV*****NSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWL**
Disordered Region (DISEMBL)
MATRKPKKVGILKATTNITPAYDSLVCLEGRASAFSWPRLAGHSRSACQFQNNEILEKDSPVSAHRILFLLLNPDCNDPSFFLPDPGSFEKDNDNISSVYLVSRSESIARLARYGKSAWFDLQKAGLELPTNAFGVENNVQCSWILSTQASSGCLLINSATGYAMSGYQDTRLYSGAILVMKVLQSVQIFKIGKWLEISVLGSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWLEN
Disordered Region (DISPRO)
****KPKKVGILKATTNITPAYDSLVCLEGRASAFSWPRLAGHSRSACQFQNNEILEKDSPVSAHRILFLLLNPDCNDPSFFLPDPGSFEKDNDNISSVYLVSRSESIARLARYGKSAWFDLQKAGLELPTNAFGVENNVQCSWILSTQASSGCLLINSATGYAMSGYQDTRLYSGAILVMKVLQSVQIFKIGKWLEISVLGSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWLEN
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATRKPKKVGILKATTNITPAYDSLVCLEGRASAFSWPRLAGHSRSACQFQNNEILEKDSPVSAHRILFLLLNPDCNDPSFFLPDPGSFEKDNDNISSVYLVSRSESIARLARYGKSAWFDLQKAGLELPTNAFGVENNVQCSWILSTQASSGCLLINSATGYAMSGYQDTRLYSGAILVMKVLQSVQIFKIGKWLEISVLGSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWLEN
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

No hits with e-value below 0.001 by BLAST

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

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

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	287
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	8e-07
pfam00075	126	pfam00075, RNase_H, RNase H	2e-04
cd09277	133	cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI	0.001

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

 Score = 46.9 bits (112), Expect = 8e-07
 Identities = 11/25 (44%), Positives = 16/25 (64%)

Query: 228 INIKFLWIPSHCGIVENERVDQAAK 252
           + ++  W+P H GI  NER D+ AK
Sbjct: 100 VKVRLHWVPGHSGIEGNERADRLAK 124

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

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

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 11/50 (22%), Positives = 17/50 (34%)

Query: 207 KKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSIY 256
                    ++N       +   +   W+P H GI  NE  D+ AK    
Sbjct: 77  WPTKSESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNELADKLAKQGAS 126

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|187701 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus

 Score = 37.9 bits (89), Expect = 0.001
 Identities = 11/33 (33%), Positives = 18/33 (54%)

Query: 223 KFARDINIKFLWIPSHCGIVENERVDQAAKNSI 255
           K  + I I F+ + +H G   NE  D+ AK ++
Sbjct: 101 KIKKKIKISFVKVKAHSGDKYNELADKLAKKAL 133

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 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. Some bacteria distinguished from other bacterial RNase HI in the presence of a hybrid binding domain (HBD) at the N-terminus which is commonly present at the N-termini of eukaryotic RNase HI. It has been reported that this domain is required for dimerization and processivity of RNase HI upon binding to RNA-DNA hybrids. Length = 133

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	287
PRK06548	161	ribonuclease H; Provisional	99.87
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.85
PRK08719	147	ribonuclease H; Reviewed	99.84
PRK00203	150	rnhA ribonuclease H; Reviewed	99.84
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.75
KOG3752|consensus	371		99.56
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.5
PRK13907	128	rnhA ribonuclease H; Provisional	99.32
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.03
PRK07708	219	hypothetical protein; Validated	99.02
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	98.05

>PRK06548 ribonuclease H; Provisional

Probab=99.87  E-value=1e-22  Score=177.02  Aligned_cols=119  Identities=16%  Similarity=0.116  Sum_probs=87.6

Q ss_pred             CeEEEEEcCCCCCCCCCCCceEEEEEecCC----cch---h---HHHHHHHHHHHHchhc-------CCCeEEE------
Q psy10246        141 QCSWILSTQASSGCLLINSATGYAMSGYQD----TRL---Y---SGAILVMKVLQSVQIF-------KIGKWLE------  197 (287)
Q Consensus       141 ~~i~IYTD~GS~~C~k~~G~vG~Avv~~~~----~~L---~---AEL~AIl~ALe~a~~~-------~~sk~vI------  197 (287)
                      ..+.|||| ||  |.+++|++|||++....    +..   +   |||+|+++||+.+...       .||+|++      
T Consensus         4 ~~~~IytD-Ga--~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~~~~~v~I~TDS~yvi~~i~~W   80 (161)
T PRK06548          4 NEIIAATD-GS--SLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRHTDRPILILSDSKYVINSLTKW   80 (161)
T ss_pred             CEEEEEEe-ec--cCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhcCCceEEEEeChHHHHHHHHHH
Confidence            34889999 88  99999999999654332    111   1   9999999999876532       2333333      


Q ss_pred             EecccCCCcccCCCChHHHHHHHHHHhh--CCCceEEEEeccCCCCccchHHHHHHHHHHhhccccc
Q psy10246        198 ISVLGSPDVKKVIFSPWSVRNVRAMKFA--RDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKS  262 (287)
Q Consensus       198 I~aL~n~~~K~~~~~p~~I~~ii~eL~~--~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~p~~~~  262 (287)
                      +..|++..|++..+.|+.++++++++.+  +...|+|.|||||+|++|||.||+||++|+......+
T Consensus        81 ~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~~~~~  147 (161)
T PRK06548         81 VYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSWVNAHTGHPLNEAADSLARQAANNFSTRS  147 (161)
T ss_pred             HHHHHHCCCcccCCCccccHHHHHHHHHHHhcCceEEEEEecCCCCHHHHHHHHHHHHHHHHhcccC
Confidence            1233333477777788888888877642  3368999999999999999999999999997655443

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

Probab=99.85  E-value=4.4e-21  Score=166.20  Aligned_cols=115  Identities=20%  Similarity=0.265  Sum_probs=87.3

Q ss_pred             CeEEEEEcCCCCCCCCCCCceEEEEE-ecCC-cc-h-------h---HHHHHHHHHHHHchhc--------CCCeEEE--
Q psy10246        141 QCSWILSTQASSGCLLINSATGYAMS-GYQD-TR-L-------Y---SGAILVMKVLQSVQIF--------KIGKWLE--  197 (287)
Q Consensus       141 ~~i~IYTD~GS~~C~k~~G~vG~Avv-~~~~-~~-L-------~---AEL~AIl~ALe~a~~~--------~~sk~vI--  197 (287)
                      ..+.|||| ||  |++|||++|||++ .+.. .+ +       +   ||++|++.||+.+.+.        +||+|++  
T Consensus         2 ~~v~if~D-Ga--~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~   78 (154)
T COG0328           2 KKVEIFTD-GA--CLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEG   78 (154)
T ss_pred             CceEEEec-Cc--cCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHH
Confidence            35889999 88  9999999999955 3333 11 1       1   9999999999999864        3455554  


Q ss_pred             Ee-cccCC---CcccCCCChHHHHHHHHHHh--hCCC-ceEEEEeccCCCCccchHHHHHHHHHHhhc
Q psy10246        198 IS-VLGSP---DVKKVIFSPWSVRNVRAMKF--ARDI-NIKFLWIPSHCGIVENERVDQAAKNSIYAQ  258 (287)
Q Consensus       198 I~-aL~n~---~~K~~~~~p~~I~~ii~eL~--~~g~-~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~p  258 (287)
                      ++ ++.+|   .|+.....|+.++++++++.  ...+ .|.+.|||||+|+++||+||+||++|+..+
T Consensus        79 i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          79 ITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             HHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            33 22333   36666667888888887664  2334 899999999999999999999999999876

>PRK08719 ribonuclease H; Reviewed

Probab=99.84  E-value=1.8e-21  Score=166.05  Aligned_cols=115  Identities=12%  Similarity=0.052  Sum_probs=83.9

Q ss_pred             CCCeEEEEEcCCCCCCCCCCC---ceEEEEEecC-C------cc--h----h---HHHHHHHHHHHHchhc----CCCeE
Q psy10246        139 NVQCSWILSTQASSGCLLINS---ATGYAMSGYQ-D------TR--L----Y---SGAILVMKVLQSVQIF----KIGKW  195 (287)
Q Consensus       139 ~~~~i~IYTD~GS~~C~k~~G---~vG~Avv~~~-~------~~--L----~---AEL~AIl~ALe~a~~~----~~sk~  195 (287)
                      |...+.|||| ||  |..+++   ++|||++.+. +      ..  +    +   ||++|++.||+.+...    ++|+|
T Consensus         1 ~~~~~~iYtD-Gs--~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~~~i~tDS~y   77 (147)
T PRK08719          1 MRASYSIYID-GA--APNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDGDVIYSDSDY   77 (147)
T ss_pred             CCceEEEEEe-cc--cCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCCCEEEechHH
Confidence            4567899999 88  877776   5788865321 1      01  1    1   9999999999998763    34455


Q ss_pred             EE------EecccCCCcccCCCChHHHHHHHHHHh--hCCCceEEEEeccCCCCccchHHHHHHHHHHh
Q psy10246        196 LE------ISVLGSPDVKKVIFSPWSVRNVRAMKF--ARDINIKFLWIPSHCGIVENERVDQAAKNSIY  256 (287)
Q Consensus       196 vI------I~aL~n~~~K~~~~~p~~I~~ii~eL~--~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~  256 (287)
                      ++      +..|+...|+++.+.+..++++++.+.  .+...|+|.|||||+|++|||.||+||++|++
T Consensus        78 vi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         78 CVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             HHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            44      223444446666667877878776653  23578999999999999999999999999975

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.84  E-value=2.6e-21  Score=163.80  Aligned_cols=116  Identities=17%  Similarity=0.150  Sum_probs=82.7

Q ss_pred             eEEEEEcCCCCCCCCCCCceEEEEEec-CCc------chh------HHHHHHHHHHHHchhcCCCeEEE-------Eecc
Q psy10246        142 CSWILSTQASSGCLLINSATGYAMSGY-QDT------RLY------SGAILVMKVLQSVQIFKIGKWLE-------ISVL  201 (287)
Q Consensus       142 ~i~IYTD~GS~~C~k~~G~vG~Avv~~-~~~------~L~------AEL~AIl~ALe~a~~~~~sk~vI-------I~aL  201 (287)
                      ++.|||| ||  |..+++.+|||++.. .+.      ..+      |||+|++.||+.+...  ..+.|       ++.+
T Consensus         3 ~v~iytD-Gs--~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~~--~~v~I~tDS~yvi~~i   77 (150)
T PRK00203          3 QVEIYTD-GA--CLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKEP--CEVTLYTDSQYVRQGI   77 (150)
T ss_pred             eEEEEEE-ec--ccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCCC--CeEEEEECHHHHHHHH
Confidence            5889999 98  888889999996532 221      111      9999999999988642  33444       1222


Q ss_pred             c-------CCCcccCCCChHHHHHHHHHHhh--CCCceEEEEeccCCCCccchHHHHHHHHHHhhccccc
Q psy10246        202 G-------SPDVKKVIFSPWSVRNVRAMKFA--RDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKS  262 (287)
Q Consensus       202 ~-------n~~~K~~~~~p~~I~~ii~eL~~--~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~p~~~~  262 (287)
                      .       ...|++..+.+..++++++++..  ...+|.|.|||||+|++|||.||+|||+|+..+..++
T Consensus        78 ~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~~~~  147 (150)
T PRK00203         78 TEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELARAGAEEATLED  147 (150)
T ss_pred             HHHHHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEEEEecCCCCCHHHHHHHHHHHHHHHHhhhcc
Confidence            2       22355555566666666655432  3478999999999999999999999999998765544

>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=99.75  E-value=2.7e-18  Score=138.31  Aligned_cols=108  Identities=23%  Similarity=0.337  Sum_probs=72.7

Q ss_pred             CeEEEEEcCCCCCCCCCCCceEEEEEecCC----cchh------HHHHHHHHHHHHchhcCCCeEEE-------EecccC
Q psy10246        141 QCSWILSTQASSGCLLINSATGYAMSGYQD----TRLY------SGAILVMKVLQSVQIFKIGKWLE-------ISVLGS  203 (287)
Q Consensus       141 ~~i~IYTD~GS~~C~k~~G~vG~Avv~~~~----~~L~------AEL~AIl~ALe~a~~~~~sk~vI-------I~aL~n  203 (287)
                      +.+.|||| ||  |..+++.+|+|++.+.+    ..++      |||+||++||+.+ .  ...+.|       +..+..
T Consensus         2 ~~~~iytD-gS--~~~~~~~~~~g~v~~~~~~~~~~~~~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v~~~l~~   75 (132)
T PF00075_consen    2 KAIIIYTD-GS--CRPNPGKGGAGYVVWGGRNFSFRLGGQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYVLNALNK   75 (132)
T ss_dssp             TSEEEEEE-EE--ECTTTTEEEEEEEEETTEEEEEEEESECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHHHHHHHT
T ss_pred             CcEEEEEe-CC--ccCCCCceEEEEEEECCeEEEecccccchhhhheehHHHHHHHh-h--cccccccccHHHHHHHHHH
Confidence            56899999 99  77778877888654433    1221      9999999999944 2  256666       222333


Q ss_pred             C----CcccCC-CChHHHHHHHHHHhhCCCceEEEEeccCCCC-ccchHHHHHHHHHHh
Q psy10246        204 P----DVKKVI-FSPWSVRNVRAMKFARDINIKFLWIPSHCGI-VENERVDQAAKNSIY  256 (287)
Q Consensus       204 ~----~~K~~~-~~p~~I~~ii~eL~~~g~~V~f~WVPGHsGI-~GNE~AD~LAK~Aa~  256 (287)
                      +    .|+... ..+.. .++++.+ .++..|.|.|||||+|+ .|||+||+|||+|+.
T Consensus        76 ~~~~~~~~~~~~~~~i~-~~i~~~~-~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~~  132 (132)
T PF00075_consen   76 WLHGNGWKKTSNGRPIK-NEIWELL-SRGIKVRFRWVPGHSGVPQGNERADRLAKEAAQ  132 (132)
T ss_dssp             HHHHTTSBSCTSSSBHT-HHHHHHH-HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred             hccccccccccccccch-hheeecc-ccceEEeeeeccCcCCCchhHHHHHHHHHHhcC
Confidence            1    222221 11221 2444444 45789999999999999 699999999999973

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 ....

>KOG3752|consensus

Probab=99.56  E-value=9e-15  Score=141.24  Aligned_cols=112  Identities=17%  Similarity=0.100  Sum_probs=78.2

Q ss_pred             EEEEEcCCCCCCCCCC---CceEEEEEecCC------cchh--------HHHHHHHHHHHHchhcCCCeEEE-------E
Q psy10246        143 SWILSTQASSGCLLIN---SATGYAMSGYQD------TRLY--------SGAILVMKVLQSVQIFKIGKWLE-------I  198 (287)
Q Consensus       143 i~IYTD~GS~~C~k~~---G~vG~Avv~~~~------~~L~--------AEL~AIl~ALe~a~~~~~sk~vI-------I  198 (287)
                      .++||| ||  |+++.   ..+||||....+      +++.        |||.||++||+.+.+....+++|       +
T Consensus       213 ~vvytD-GS--~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i  289 (371)
T KOG3752|consen  213 QVVYTD-GS--SSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFI  289 (371)
T ss_pred             eEEEec-Cc--cccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHH
Confidence            789999 99  88753   468999763222      2332        99999999999999877778888       2


Q ss_pred             ec----ccCCC---cccCCCCh-----HHHHHHHHH---Hhh--CCCceEEEEeccCCCCccchHHHHHHHHHHhh
Q psy10246        199 SV----LGSPD---VKKVIFSP-----WSVRNVRAM---KFA--RDINIKFLWIPSHCGIVENERVDQAAKNSIYA  257 (287)
Q Consensus       199 ~a----L~n~~---~K~~~~~p-----~~I~~ii~e---L~~--~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~  257 (287)
                      ++    +++|.   |+.....+     +.+.+...+   |.+  ++.+|+|.||+||.||.|||+||.||++++.+
T Consensus       290 ~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~  365 (371)
T KOG3752|consen  290 NSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL  365 (371)
T ss_pred             HHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence            22    23332   44433333     233333322   221  35899999999999999999999999998654

>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=99.50  E-value=2.8e-13  Score=103.46  Aligned_cols=108  Identities=20%  Similarity=0.179  Sum_probs=70.2

Q ss_pred             EEEEcCCCCCCCCCCCceEEEEEecCC--------cch-------hHHHHHHHHHHHHchhcCCCeEEE-------Eecc
Q psy10246        144 WILSTQASSGCLLINSATGYAMSGYQD--------TRL-------YSGAILVMKVLQSVQIFKIGKWLE-------ISVL  201 (287)
Q Consensus       144 ~IYTD~GS~~C~k~~G~vG~Avv~~~~--------~~L-------~AEL~AIl~ALe~a~~~~~sk~vI-------I~aL  201 (287)
                      .+||| ||  +....+.+|+|++....        ...       .+|+.|++.||+.+......++.|       +..+
T Consensus         1 ~~~~D-gs--~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~   77 (130)
T cd06222           1 VIYTD-GS--CRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINAL   77 (130)
T ss_pred             CEEec-cc--CCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHh
Confidence            38999 98  33444688888553221        111       199999999999998766666666       2334


Q ss_pred             cCCCcccCCCChHHHHHHHHHHhhCCCceEEEEeccCCCCccchHHHHHHHHHH
Q psy10246        202 GSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSI  255 (287)
Q Consensus       202 ~n~~~K~~~~~p~~I~~ii~eL~~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa  255 (287)
                      .++.. ........+...+.++..+...+.|.|||+|+|+++|+.||.|||+|.
T Consensus        78 ~~~~~-~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          78 TGWYE-GKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             hcccc-CCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            44321 011111122222333334668899999999999999999999999873

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.

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.32  E-value=1e-11  Score=101.59  Aligned_cols=102  Identities=12%  Similarity=-0.007  Sum_probs=68.6

Q ss_pred             EEEEEcCCCCCCCCCCCceEEEEEec-CCc------ch------hHHHHHHHHHHHHchhcCCCeEEE-------Eeccc
Q psy10246        143 SWILSTQASSGCLLINSATGYAMSGY-QDT------RL------YSGAILVMKVLQSVQIFKIGKWLE-------ISVLG  202 (287)
Q Consensus       143 i~IYTD~GS~~C~k~~G~vG~Avv~~-~~~------~L------~AEL~AIl~ALe~a~~~~~sk~vI-------I~aL~  202 (287)
                      +.|||| ||  |.+++|.+|||++.. ..+      ..      .||++|++.||+.+...+..++.+       +..+.
T Consensus         2 ~~iy~D-Ga--~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~   78 (128)
T PRK13907          2 IEVYID-GA--SKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVE   78 (128)
T ss_pred             EEEEEe-eC--CCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHh
Confidence            579999 88  888999999996532 211      11      199999999999999877666555       23344


Q ss_pred             CCCcccCCCChHHHHHHHHH---HhhCCCceEEEEeccCCCCccchHHHHHHHHHHh
Q psy10246        203 SPDVKKVIFSPWSVRNVRAM---KFARDINIKFLWIPSHCGIVENERVDQAAKNSIY  256 (287)
Q Consensus       203 n~~~K~~~~~p~~I~~ii~e---L~~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~  256 (287)
                      +. |+...    .+++++++   +..+-..+.|.|||.    ++|+.||.||+.|..
T Consensus        79 ~~-~~~~~----~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~  126 (128)
T PRK13907         79 KE-YAKNK----MFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAIL  126 (128)
T ss_pred             HH-HhcCh----hHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence            32 11111    22333322   233445677899998    599999999999875

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.03  E-value=1.7e-09  Score=103.38  Aligned_cols=108  Identities=11%  Similarity=0.047  Sum_probs=71.9

Q ss_pred             eEEEEEcCCCCCCCCCCCceEEEEEe-cCC-c--------ch------hHHHHHHHHHHHHchhcCCCeEEE-------E
Q psy10246        142 CSWILSTQASSGCLLINSATGYAMSG-YQD-T--------RL------YSGAILVMKVLQSVQIFKIGKWLE-------I  198 (287)
Q Consensus       142 ~i~IYTD~GS~~C~k~~G~vG~Avv~-~~~-~--------~L------~AEL~AIl~ALe~a~~~~~sk~vI-------I  198 (287)
                      .+.|||| ||  |.+++|.+|+|++. +.+ .        .+      .||+.|++.||+.+.+.+..++.+       +
T Consensus         2 ~~~i~~D-Ga--~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi   78 (372)
T PRK07238          2 KVVVEAD-GG--SRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVV   78 (372)
T ss_pred             eEEEEec-CC--CCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHH
Confidence            3689999 88  88999999999553 221 1        11      199999999999998876655555       2


Q ss_pred             ecccCCCcccCCCChHHHHHHHHHHhhCCCceEEEEeccCCCCccchHHHHHHHHHHhh
Q psy10246        199 SVLGSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSIYA  257 (287)
Q Consensus       199 ~aL~n~~~K~~~~~p~~I~~ii~eL~~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~  257 (287)
                      +.+.+ .|+.....-..+.+.+.++..+-..|.|.|||.    ++|+.||.||+.|...
T Consensus        79 ~~i~~-~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~  132 (372)
T PRK07238         79 EQMSG-RWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA  132 (372)
T ss_pred             HHhCC-CCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence            23332 222222122333333344444446899999997    7899999999999753

>PRK07708 hypothetical protein; Validated

Probab=99.02  E-value=2.4e-09  Score=97.47  Aligned_cols=116  Identities=10%  Similarity=0.018  Sum_probs=76.1

Q ss_pred             ccCCCeEEEEEcCCCCCCCCCCCceEEEEEec--CCc---------ch----h---HHHHHHHHHHHHchhcCCCe--EE
Q psy10246        137 ENNVQCSWILSTQASSGCLLINSATGYAMSGY--QDT---------RL----Y---SGAILVMKVLQSVQIFKIGK--WL  196 (287)
Q Consensus       137 e~~~~~i~IYTD~GS~~C~k~~G~vG~Avv~~--~~~---------~L----~---AEL~AIl~ALe~a~~~~~sk--~v  196 (287)
                      +.-++.+.+|+| ||  |.+++|++|+|++..  .+.         .+    .   ||..|++.||+.+.+.+.+.  +.
T Consensus        68 ~~ep~~~~vY~D-Gs--~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~  144 (219)
T PRK07708         68 EEEPHEILVYFD-GG--FDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVT  144 (219)
T ss_pred             ccCCCcEEEEEe-ec--cCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEE
Confidence            334467999999 88  667888899996543  121         11    1   99999999999998876544  33


Q ss_pred             E-------EecccCCCcccCCCChHHHHHHHHHHhh-CCCceEEEEeccCCCCccchHHHHHHHHHHhhccc
Q psy10246        197 E-------ISVLGSPDVKKVIFSPWSVRNVRAMKFA-RDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLL  260 (287)
Q Consensus       197 I-------I~aL~n~~~K~~~~~p~~I~~ii~eL~~-~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~p~~  260 (287)
                      |       +..+.+ .|+.+.+....+.+.+.++.. -...+.|.|||    -+.|+.||+||+.|+.....
T Consensus       145 I~~DSqlVi~qi~g-~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~~  211 (219)
T PRK07708        145 FRGDSQVVLNQLAG-EWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTVI  211 (219)
T ss_pred             EEeccHHHHHHhCC-CceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCCC
Confidence            3       223332 344444444444444443332 23457889997    46799999999999986544

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

Probab=98.05  E-value=2.3e-05  Score=58.37  Aligned_cols=76  Identities=17%  Similarity=0.122  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHHchhcCCCeEEE-------EecccCCCcccCCCChHHHHHHHHHHhhCCCceEEEEeccCCCCccchHH
Q psy10246        175 SGAILVMKVLQSVQIFKIGKWLE-------ISVLGSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERV  247 (287)
Q Consensus       175 AEL~AIl~ALe~a~~~~~sk~vI-------I~aL~n~~~K~~~~~p~~I~~ii~eL~~~g~~V~f~WVPGHsGI~GNE~A  247 (287)
                      ||+.|++.||+.+.+.+..++.+       ++.+++.. ....... .+..-+..+...-..+.|.|||    =++|..|
T Consensus         4 aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~-~~~~~~~-~~~~~i~~~~~~~~~~~~~~i~----r~~N~~A   77 (87)
T PF13456_consen    4 AEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRS-SSRSELR-PLIQDIRSLLDRFWNVSVSHIP----REQNKVA   77 (87)
T ss_dssp             HHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS----SCCH-HHHHHHHHHHCCCSCEEEEE------GGGSHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccc-ccccccc-ccchhhhhhhccccceEEEEEC----hHHhHHH
Confidence            89999999999999988888777       34455432 1112222 2333334444456789999999    7899999


Q ss_pred             HHHHHHHHh
Q psy10246        248 DQAAKNSIY  256 (287)
Q Consensus       248 D~LAK~Aa~  256 (287)
                      |.|||.|.+
T Consensus        78 ~~LA~~a~~   86 (87)
T PF13456_consen   78 DALAKFALS   86 (87)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhh
Confidence            999999864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	287
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	2e-05

>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 = 42.7 bits (101), Expect = 2e-05
 Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 1/43 (2%)

Query: 213 PWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSI 255
            ++    + M   R     F  + +H G   N+ VD  AK+++
Sbjct: 94  EFTQAYAKLMNQYRG-IYSFEKVKAHSGNEFNDYVDMKAKSAL 135

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	287
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.87
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.86
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.85
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.84
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.83
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.83
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.83
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.82
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.79
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.67
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.67
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.65
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.64
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.59
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.0
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	98.88

>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=99.87  E-value=5.5e-23  Score=173.46  Aligned_cols=116  Identities=15%  Similarity=0.119  Sum_probs=76.7

Q ss_pred             CCCeEEEEEcCCCCCCCCCCCceEEEEEecCCc--c--hh------HHHHHHHHHHHHchh----cCCCeEEE--Ee---
Q psy10246        139 NVQCSWILSTQASSGCLLINSATGYAMSGYQDT--R--LY------SGAILVMKVLQSVQI----FKIGKWLE--IS---  199 (287)
Q Consensus       139 ~~~~i~IYTD~GS~~C~k~~G~vG~Avv~~~~~--~--L~------AEL~AIl~ALe~a~~----~~~sk~vI--I~---  199 (287)
                      ..+.+.|||| ||  |.+++|.+|+|++...+.  .  ++      ||++|++.||+.+..    ..||+|++  ++   
T Consensus         9 ~~~~~~iytD-Gs--~~~n~g~~g~G~v~~~~~~~~~~~~~~Tnn~aEl~A~i~AL~~~~~~v~i~tDS~~v~~~i~~w~   85 (150)
T 3qio_A            9 IVGAETFYVD-GA--ANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIITQWI   85 (150)
T ss_dssp             CTTCEEEEEE-EE--ECTTTCCEEEEEEETTSCEEEEEESSCCHHHHHHHHHHHHHHHSCSEEEEEESCHHHHHHHHHHH
T ss_pred             CCCCEEEEEc-cC--CCCCCCCeEEEEEEEcCCEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEeCcHHHHHHHHHHH
Confidence            3456999999 88  999999999997654431  1  11      999999999998631    12333333  11   


Q ss_pred             -cccCCCcccCCCChHHHHHHHHHHh---hCCCceEEEEeccCCCCccchHHHHHHHHHHhh
Q psy10246        200 -VLGSPDVKKVIFSPWSVRNVRAMKF---ARDINIKFLWIPSHCGIVENERVDQAAKNSIYA  257 (287)
Q Consensus       200 -aL~n~~~K~~~~~p~~I~~ii~eL~---~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~  257 (287)
                       .|+...|++..+.+..++++++++.   .+..+|.|.|||||+|++|||+||+||++|+..
T Consensus        86 ~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           86 HNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence             2333346665556667777776543   366899999999999999999999999999864

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

Probab=99.86  E-value=1.6e-22  Score=167.21  Aligned_cols=115  Identities=11%  Similarity=0.025  Sum_probs=77.7

Q ss_pred             CCCeEEEEEcCCCCCCCCCCCceEEEEEec-CC------cchh------HHHHHHHHHHHHchhcCCCeEEE-------E
Q psy10246        139 NVQCSWILSTQASSGCLLINSATGYAMSGY-QD------TRLY------SGAILVMKVLQSVQIFKIGKWLE-------I  198 (287)
Q Consensus       139 ~~~~i~IYTD~GS~~C~k~~G~vG~Avv~~-~~------~~L~------AEL~AIl~ALe~a~~~~~sk~vI-------I  198 (287)
                      |.+.+.|||| ||  |.+++|.+|||++.. .+      +.++      ||++|++.||+.+.+  ..++.|       +
T Consensus         1 m~~~i~iytD-Gs--~~~n~g~~g~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi   75 (146)
T 3h08_A            1 MEKTITIYTD-GA--ASGNPGKGGWGALLMYGSSRKEISGYDPATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLV   75 (146)
T ss_dssp             -CCEEEEEEE-EE--ESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHH
T ss_pred             CCceEEEEEe-cC--CCCCCCceEEEEEEEECCeeEEeecCCCCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHH
Confidence            3567999999 99  889999999996533 22      1111      999999999999875  344555       2


Q ss_pred             ecccC--------CCcccCCCChHHHHHHHHHHh--hCCCceEEEEeccCCCCccchHHHHHHHHHHhhc
Q psy10246        199 SVLGS--------PDVKKVIFSPWSVRNVRAMKF--ARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQ  258 (287)
Q Consensus       199 ~aL~n--------~~~K~~~~~p~~I~~ii~eL~--~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~p  258 (287)
                      ..+..        ..|+++.+.+..++++++++.  .+...|.|.|||||+|++|||+||+|||+|+...
T Consensus        76 ~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~~  145 (146)
T 3h08_A           76 NAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLHRVTFHKVKGHSDNPYNSRADELARLAIKEN  145 (146)
T ss_dssp             HHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHHSEEEEEECCC-CCSHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhhCceEEEEcCCcCCcHhHHHHHHHHHHHHHhC
Confidence            23333        224555555555555544432  1236799999999999999999999999998753

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

Probab=99.85  E-value=7.8e-22  Score=164.97  Aligned_cols=117  Identities=15%  Similarity=0.147  Sum_probs=84.4

Q ss_pred             CCCeEEEEEcCCCCCCCCCCCc---eEEEEEecCC------cchh-------HHHHHHHHHHHHchhcCCCeEEE-----
Q psy10246        139 NVQCSWILSTQASSGCLLINSA---TGYAMSGYQD------TRLY-------SGAILVMKVLQSVQIFKIGKWLE-----  197 (287)
Q Consensus       139 ~~~~i~IYTD~GS~~C~k~~G~---vG~Avv~~~~------~~L~-------AEL~AIl~ALe~a~~~~~sk~vI-----  197 (287)
                      +.+.+.|||| ||  |.++++.   +|||++...+      ..++       ||++|++.||+.+......++.|     
T Consensus         4 ~~~~~~iytD-Gs--~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~   80 (154)
T 2qkb_A            4 MGDFVVVYTD-GC--CSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSM   80 (154)
T ss_dssp             ETTEEEEEEE-EE--EETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCH
T ss_pred             CCCeEEEEEc-cC--cCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcH
Confidence            4567899999 98  8777653   8999764322      1221       99999999999998766666666     


Q ss_pred             --EecccCC-------CcccCCCChHHHHHHHHHHh--hCCCceEEEEeccCCCCccchHHHHHHHHHHhhc
Q psy10246        198 --ISVLGSP-------DVKKVIFSPWSVRNVRAMKF--ARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQ  258 (287)
Q Consensus       198 --I~aL~n~-------~~K~~~~~p~~I~~ii~eL~--~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~p  258 (287)
                        ++.+.+|       .|+.+.+.+..++++++++.  .++..|.|.|||||+|++|||+||+|||+|+..+
T Consensus        81 ~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           81 FTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             HHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTTCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             HHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcCCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence              2233332       35555555555555555443  2357899999999999999999999999998764

>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=99.84  E-value=1.6e-21  Score=163.93  Aligned_cols=117  Identities=17%  Similarity=0.152  Sum_probs=82.5

Q ss_pred             CeEEEEEcCCCCCCCCCCCceEEEEEec-CC------cchh------HHHHHHHHHHHHchhcCCCeEEE-------Eec
Q psy10246        141 QCSWILSTQASSGCLLINSATGYAMSGY-QD------TRLY------SGAILVMKVLQSVQIFKIGKWLE-------ISV  200 (287)
Q Consensus       141 ~~i~IYTD~GS~~C~k~~G~vG~Avv~~-~~------~~L~------AEL~AIl~ALe~a~~~~~sk~vI-------I~a  200 (287)
                      ..+.|||| ||  |.+++|.+|||++.. .+      +.++      ||++|++.||+.+...  .++.|       +..
T Consensus         3 ~~~~iytD-Gs--~~~n~~~~G~G~v~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL~~~~~~--~~v~I~tDS~~vi~~   77 (155)
T 1jl1_A            3 KQVEIFTA-GS--ALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEH--AEVILSTDSQYVRQG   77 (155)
T ss_dssp             CCEEEEEE-EE--ESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCSC--CEEEEEECCHHHHHH
T ss_pred             ceEEEEEc-cc--cCCCCCceEEEEEEEECCeEEEEecCCCCCcHHHHHHHHHHHHHHHhCcC--CcEEEEeCHHHHHHH
Confidence            35889999 98  888899999996533 22      1111      9999999999998753  44544       223


Q ss_pred             ccCC-------CcccCCCChHHHHHHHHHHh--hCCCceEEEEeccCCCCccchHHHHHHHHHHhhccccc
Q psy10246        201 LGSP-------DVKKVIFSPWSVRNVRAMKF--ARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKS  262 (287)
Q Consensus       201 L~n~-------~~K~~~~~p~~I~~ii~eL~--~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~p~~~~  262 (287)
                      +..|       .|++..+.+..++++++++.  .+...|.|.|||||+|++|||+||+|||+|+..+.+.+
T Consensus        78 i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~~~  148 (155)
T 1jl1_A           78 ITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLED  148 (155)
T ss_dssp             HHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCC
T ss_pred             HHHHHHHHhhcccccccCCccCCHHHHHHHHHHHccCceEEEEcCCCCCCHHHHHHHHHHHHHHhccchhh
Confidence            4432       24444444544444444332  13468999999999999999999999999999876643

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

Probab=99.83  E-value=3.5e-21  Score=162.61  Aligned_cols=115  Identities=20%  Similarity=0.199  Sum_probs=80.6

Q ss_pred             CeEEEEEcCCCCCCCCCCCceEEEEEe-cCC------cchh------HHHHHHHHHHHHchhcCCCeEEE-------Eec
Q psy10246        141 QCSWILSTQASSGCLLINSATGYAMSG-YQD------TRLY------SGAILVMKVLQSVQIFKIGKWLE-------ISV  200 (287)
Q Consensus       141 ~~i~IYTD~GS~~C~k~~G~vG~Avv~-~~~------~~L~------AEL~AIl~ALe~a~~~~~sk~vI-------I~a  200 (287)
                      ..+.|||| ||  |.+++|.+|||++. +.+      +.++      ||++|++.||+.+...  .++.|       +..
T Consensus         5 ~~i~iytD-Gs--~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~tn~~aEl~A~~~AL~~~~~~--~~v~I~tDS~~vi~~   79 (158)
T 2e4l_A            5 KLIHIFTD-GS--CLGNPGPGGYGIVMNYKGHTKEMSDGFSLTTNNRMELLAPIVALEALKEP--CKIILTSDSQYMRQG   79 (158)
T ss_dssp             CEEEEEEE-EE--ESSSSEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCSSC--CEEEEEECCHHHHHH
T ss_pred             CeEEEEEc-cc--ccCCCCcEEEEEEEEECCEEEEEecCcCCCccHHHHHHHHHHHHHHhccC--CeEEEEeCHHHHHHH
Confidence            46889999 98  88889999999654 332      1111      9999999999998653  45555       223


Q ss_pred             ccCC-------CcccCCCChHHHHHHHHHHh--hCCCceEEEEeccCCCCccchHHHHHHHHHHhh-ccc
Q psy10246        201 LGSP-------DVKKVIFSPWSVRNVRAMKF--ARDINIKFLWIPSHCGIVENERVDQAAKNSIYA-QLL  260 (287)
Q Consensus       201 L~n~-------~~K~~~~~p~~I~~ii~eL~--~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~-p~~  260 (287)
                      +..|       .|++..+.+..+.++++++.  .+...|.|.|||||+|++|||+||+|||+|+.. +.+
T Consensus        80 i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~~~  149 (158)
T 2e4l_A           80 IMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQLHQIDWRWVKGHAGHAENERCDQLARAAAEANPTQ  149 (158)
T ss_dssp             HHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTTSEEEEEECCTTCCCHHHHHHHHHHHHHHHSCCCC
T ss_pred             HHHHHHHHHHccccccCCCcccCHHHHHHHHHHHccCcEEEEEccCCCCchhHHHHHHHHHHHHHhchhh
Confidence            3332       24444434444444443332  134789999999999999999999999999987 544

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

Probab=99.83  E-value=7e-22  Score=170.13  Aligned_cols=114  Identities=9%  Similarity=0.009  Sum_probs=75.1

Q ss_pred             CeEEEEEcCCCCCCCCCCCc-----eEEEEEe-cCC--c------chh----HHHHHHHHHHH----Hchhc-------C
Q psy10246        141 QCSWILSTQASSGCLLINSA-----TGYAMSG-YQD--T------RLY----SGAILVMKVLQ----SVQIF-------K  191 (287)
Q Consensus       141 ~~i~IYTD~GS~~C~k~~G~-----vG~Avv~-~~~--~------~L~----AEL~AIl~ALe----~a~~~-------~  191 (287)
                      ..++|||| ||  |++|||+     +|||++. +.+  .      ..+    ||++|.+.||+    .+...       +
T Consensus         6 ~evviYTD-Gs--c~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~~~~v~I~T   82 (165)
T 2lsn_A            6 YEGVFYTD-GS--AIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIPGPVLVIT   82 (165)
T ss_dssp             CSEEEEEE-EE--EEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHSSSCEEEEE
T ss_pred             ceEEEEEc-CC--CCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcCCCeEEEEe
Confidence            34889999 99  9999987     8999653 222  1      111    55555555554    44332       2


Q ss_pred             CCeEEE--Ee----cccCCCcccCCCChHHHHHHHHHHh---hCCCceEEEEeccCCCC------ccchHHHHHHHHHHh
Q psy10246        192 IGKWLE--IS----VLGSPDVKKVIFSPWSVRNVRAMKF---ARDINIKFLWIPSHCGI------VENERVDQAAKNSIY  256 (287)
Q Consensus       192 ~sk~vI--I~----aL~n~~~K~~~~~p~~I~~ii~eL~---~~g~~V~f~WVPGHsGI------~GNE~AD~LAK~Aa~  256 (287)
                      ||+|++  ++    .|+...|++....|+.+++++++|.   ....+|.|.|||||+|+      +|||+||+||++|+.
T Consensus        83 DS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~  162 (165)
T 2lsn_A           83 DSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSY  162 (165)
T ss_dssp             SCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhhh
Confidence            334433  21    2232336666667777777776553   34578999999999995      689999999999986


Q ss_pred             h
Q psy10246        257 A  257 (287)
Q Consensus       257 ~  257 (287)
                      .
T Consensus       163 ~  163 (165)
T 2lsn_A          163 V  163 (165)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.83  E-value=5.5e-21  Score=164.23  Aligned_cols=111  Identities=14%  Similarity=0.040  Sum_probs=80.5

Q ss_pred             eEEEEEcCCCCCCCCCCCceEEEEEecCC-c-----chh-------HHHHHHHHHHHHchhcCCCeEEE-------Eecc
Q psy10246        142 CSWILSTQASSGCLLINSATGYAMSGYQD-T-----RLY-------SGAILVMKVLQSVQIFKIGKWLE-------ISVL  201 (287)
Q Consensus       142 ~i~IYTD~GS~~C~k~~G~vG~Avv~~~~-~-----~L~-------AEL~AIl~ALe~a~~~~~sk~vI-------I~aL  201 (287)
                      .+.|||| ||  |.+++|.+|||++.+.+ .     .++       ||++|++.||+.+.   ..++.|       ++.+
T Consensus        23 ~i~iytD-Gs--~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~---~~~v~I~tDS~~vi~~i   96 (165)
T 3p1g_A           23 DYTWYTD-GS--SFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAE---GKKLNVYTDSRYAFATA   96 (165)
T ss_dssp             SEEEEEE-EE--EEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHTB---TSEEEEEECCHHHHHHH
T ss_pred             CEEEEEE-cc--cCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHcc---CceEEEEEchHHHHhhh
Confidence            5899999 98  88899999999654332 1     111       99999999999983   344555       2223


Q ss_pred             cCCCcccCCCChHHHHHHHHHHh---hCCCceEEEEeccCCC-----CccchHHHHHHHHHHhhccccc
Q psy10246        202 GSPDVKKVIFSPWSVRNVRAMKF---ARDINIKFLWIPSHCG-----IVENERVDQAAKNSIYAQLLKS  262 (287)
Q Consensus       202 ~n~~~K~~~~~p~~I~~ii~eL~---~~g~~V~f~WVPGHsG-----I~GNE~AD~LAK~Aa~~p~~~~  262 (287)
                          |....+.+..++++++++.   .++.+|.|.|||||+|     ++|||+||+|||+|+..+..+.
T Consensus        97 ----w~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~~~~~  161 (165)
T 3p1g_A           97 ----HVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLET  161 (165)
T ss_dssp             ----HSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             ----hcccCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcCCCcc
Confidence                2223334555566555542   2568999999999999     9999999999999998876543

>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=99.82  E-value=1.2e-21  Score=164.00  Aligned_cols=113  Identities=12%  Similarity=0.002  Sum_probs=81.8

Q ss_pred             CCeEEEEEcCCCCCCCCCCCceEEEEEec-CC------c-ch--------h---HHHHHHHHHHHHchhcCCCeEEE---
Q psy10246        140 VQCSWILSTQASSGCLLINSATGYAMSGY-QD------T-RL--------Y---SGAILVMKVLQSVQIFKIGKWLE---  197 (287)
Q Consensus       140 ~~~i~IYTD~GS~~C~k~~G~vG~Avv~~-~~------~-~L--------~---AEL~AIl~ALe~a~~~~~sk~vI---  197 (287)
                      ++.+.|||| ||  |.+  |++|||++.. .+      . .+        .   ||++|++.||+.+.+.+. ++.|   
T Consensus         4 ~~~i~iytD-Gs--~~~--g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tD   77 (147)
T 2kq2_A            4 RTEYDVYTD-GS--YVN--GQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHD   77 (147)
T ss_dssp             TSCCEEECC-CC--CBT--TBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSC
T ss_pred             CCeEEEEEC-CC--CCC--CCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEEC
Confidence            356889999 99  765  8889995532 21      1 11        1   999999999998776544 4444   


Q ss_pred             ---EecccCCCcccCCCChHHHHHHHHHHhhCCCceEEEEeccCCCCccchHHHHHHHHHHhhcccc
Q psy10246        198 ---ISVLGSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLK  261 (287)
Q Consensus       198 ---I~aL~n~~~K~~~~~p~~I~~ii~eL~~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~p~~~  261 (287)
                         +..+....|+.+.+.+..++++++++..   +|.|.|||||+|++|||+||+|||+|+..+..+
T Consensus        78 S~~i~~w~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~~  141 (147)
T 2kq2_A           78 YAGIAFWATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALGIRDLE  141 (147)
T ss_dssp             CSTHHHHTTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHTCCCTT
T ss_pred             cHHHHHHHhCCCccCCcchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHhccccc
Confidence               1112222355555556777888887753   899999999999999999999999999876554

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

Probab=99.79  E-value=4.6e-20  Score=157.33  Aligned_cols=113  Identities=16%  Similarity=0.125  Sum_probs=79.4

Q ss_pred             eEEEEEcCCCCCCCCCCCceEEEEEec-CC------cchh------HHHHHHHHHHHHchhcCCCeEEE-------Eecc
Q psy10246        142 CSWILSTQASSGCLLINSATGYAMSGY-QD------TRLY------SGAILVMKVLQSVQIFKIGKWLE-------ISVL  201 (287)
Q Consensus       142 ~i~IYTD~GS~~C~k~~G~vG~Avv~~-~~------~~L~------AEL~AIl~ALe~a~~~~~sk~vI-------I~aL  201 (287)
                      .+.|||| ||  |.+++|.+|||++.. .+      +.++      ||++|++.||+.+...  .++.|       +..+
T Consensus         8 ~i~iytD-Gs--~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i   82 (166)
T 1ril_A            8 RVALFTD-GA--CLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAF   82 (166)
T ss_dssp             CCCEEEE-EE--ESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHH
T ss_pred             cEEEEEC-cc--ccCCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHH
Confidence            5789999 98  888889999997643 22      1111      9999999999988653  24444       2233


Q ss_pred             cC-C-------CcccCCCChHHHHHHHHHHh--hCCCceEEEEeccCCCCccchHHHHHHHHHHhhcc
Q psy10246        202 GS-P-------DVKKVIFSPWSVRNVRAMKF--ARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQL  259 (287)
Q Consensus       202 ~n-~-------~~K~~~~~p~~I~~ii~eL~--~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~p~  259 (287)
                      .+ |       .|+++.+.+..++++++++.  .+...|.|.|||||+|++|||+||+|||+|+....
T Consensus        83 ~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~  150 (166)
T 1ril_A           83 TEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQA  150 (166)
T ss_dssp             HSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             hhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhcCeEEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence            33 2       24454444444444444332  13468999999999999999999999999998654

>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=99.67  E-value=1.3e-16  Score=128.87  Aligned_cols=109  Identities=12%  Similarity=0.068  Sum_probs=77.0

Q ss_pred             eEEEEEcCCCCCCCCCCCceEEEEEec-CC-c--------chh------HHHHHHHHHHHHchhcCCCeEEE-------E
Q psy10246        142 CSWILSTQASSGCLLINSATGYAMSGY-QD-T--------RLY------SGAILVMKVLQSVQIFKIGKWLE-------I  198 (287)
Q Consensus       142 ~i~IYTD~GS~~C~k~~G~vG~Avv~~-~~-~--------~L~------AEL~AIl~ALe~a~~~~~sk~vI-------I  198 (287)
                      .+.|||| ||  |.+++|.+|||++.. .+ +        .++      ||++|++.||+.+.+.+..++.|       +
T Consensus         3 ~~~iy~D-Gs--~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv   79 (141)
T 3hst_B            3 KVVIEAD-GG--SRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVV   79 (141)
T ss_dssp             EEEEEEE-EE--ESSSSEEEEEEEEEEETTSCSEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHH
T ss_pred             EEEEEEe-cC--CCCCCCCcEEEEEEEeCCCCcEEEeeeccCCCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHH
Confidence            5789999 88  888899999996532 21 1        111      99999999999998877777766       3


Q ss_pred             ecccCCCcccCCCChHHHHHHHHHHhhCCCceEEEEeccCCCCccchHHHHHHHHHHhhc
Q psy10246        199 SVLGSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQ  258 (287)
Q Consensus       199 ~aL~n~~~K~~~~~p~~I~~ii~eL~~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~p  258 (287)
                      +.+.+ .|+......+.+.+.+.++..+...|.|.|||+    ++||.||+|||+|+...
T Consensus        80 ~~i~~-~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~~  134 (141)
T 3hst_B           80 EQMSG-RWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----ARNTYADRLANDAMDAA  134 (141)
T ss_dssp             HHHTT-SSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHHHHHH
T ss_pred             HHHhC-CcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHHHHHh
Confidence            34443 232222222333334445555568999999995    99999999999998764

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

Probab=99.67  E-value=1.3e-16  Score=128.06  Aligned_cols=109  Identities=15%  Similarity=0.064  Sum_probs=75.3

Q ss_pred             eEEEEEcCCCCCCCCCCCceEEEEEecC-Cc--------chh------HHHHHHHHHHHHchhcCCC----eEEE-----
Q psy10246        142 CSWILSTQASSGCLLINSATGYAMSGYQ-DT--------RLY------SGAILVMKVLQSVQIFKIG----KWLE-----  197 (287)
Q Consensus       142 ~i~IYTD~GS~~C~k~~G~vG~Avv~~~-~~--------~L~------AEL~AIl~ALe~a~~~~~s----k~vI-----  197 (287)
                      .+.|||| ||  |.+++|.+|||++... ++        .++      ||++|++.||+.+.+.+..    ++.|     
T Consensus         3 ~~~iy~D-Gs--~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~   79 (140)
T 3u3g_D            3 KIIIYTD-GG--ARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSE   79 (140)
T ss_dssp             EEEEEEE-EE--ESSTTEEEEEEEEEECTTSCEEEEEEEEEEEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCH
T ss_pred             eEEEEEe-cC--CCCCCCCcEEEEEEEeCCCCEEEEEEeeCCCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChH
Confidence            5889999 98  8888999999966433 21        111      9999999999999876555    6666     


Q ss_pred             --EecccCCCcccCCCChHHHHHHHHHH-hhCCCceEEEEeccCCCCccchHHHHHHHHHHhhc
Q psy10246        198 --ISVLGSPDVKKVIFSPWSVRNVRAMK-FARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQ  258 (287)
Q Consensus       198 --I~aL~n~~~K~~~~~p~~I~~ii~eL-~~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~p  258 (287)
                        ++.+.++ |+......+.+.+.+.++ ..+...|.|.|||+    +|||.||+|||+|+...
T Consensus        80 ~vi~~i~~~-~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~~  138 (140)
T 3u3g_D           80 LIVRQMQGV-YKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPR----EKNARADELVNEAIDKA  138 (140)
T ss_dssp             HHHHHHTTS-SCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCG----GGGHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCC-cccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCc----hhhHHHHHHHHHHHHhc
Confidence              3445542 222222233333334444 33445899999994    99999999999998753

>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=99.65  E-value=1.8e-16  Score=156.57  Aligned_cols=107  Identities=17%  Similarity=0.146  Sum_probs=75.3

Q ss_pred             cCCCeEEEEEcCCCCCCCCCCCceEEEEEecCC-c---ch-----h-HHHHHHHHHHHHchhcCCCeEEE-------Eec
Q psy10246        138 NNVQCSWILSTQASSGCLLINSATGYAMSGYQD-T---RL-----Y-SGAILVMKVLQSVQIFKIGKWLE-------ISV  200 (287)
Q Consensus       138 ~~~~~i~IYTD~GS~~C~k~~G~vG~Avv~~~~-~---~L-----~-AEL~AIl~ALe~a~~~~~sk~vI-------I~a  200 (287)
                      .+.+.+.|||| ||  |.+++|.+|+|++...+ .   .+     . ||++|++.||+.    ...++.|       +..
T Consensus       432 p~~~~~~iytD-Gs--~~~n~g~~g~G~v~~~~~~~~~~~~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~  504 (555)
T 1mu2_A          432 PIPGAETFYTD-GS--CNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGI  504 (555)
T ss_dssp             CCTTCEEEEEE-EE--ECTTTCCEEEEEEETTSCEEEEEESSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHH
T ss_pred             CCCCceEEEEc-cc--ccCCCCCceEEEEEEeCCEeeccCCCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHH
Confidence            45667999999 88  88999989999765433 1   11     1 999999999998    3345555       345


Q ss_pred             ccCCCcccCCCChHHHHHHHHHHhhCCCceEEEEeccCCCCccchHHHHHHHHHH
Q psy10246        201 LGSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSI  255 (287)
Q Consensus       201 L~n~~~K~~~~~p~~I~~ii~eL~~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa  255 (287)
                      +.+|.  .....+ ..+++++.+. ++..|.|.|||||+|++|||+||+|||+|+
T Consensus       505 i~~~~--~~~~~~-l~~~~~~~~~-~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          505 VASQP--TESESK-IVNQIIEEMI-KKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             HHTCC--SEESCH-HHHHHHHHHH-HCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             Hhccc--ccccHH-HHHHHHHHhc-cCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            66554  222112 2233444333 357899999999999999999999999874

>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=99.64  E-value=1.3e-16  Score=157.77  Aligned_cols=108  Identities=15%  Similarity=0.087  Sum_probs=75.2

Q ss_pred             cccCCCeEEEEEcCCCCCCCCCCCceEEEEEecCCc--c--h------hHHHHHHHHHHHHchhcCCCeEEE-------E
Q psy10246        136 VENNVQCSWILSTQASSGCLLINSATGYAMSGYQDT--R--L------YSGAILVMKVLQSVQIFKIGKWLE-------I  198 (287)
Q Consensus       136 ~e~~~~~i~IYTD~GS~~C~k~~G~vG~Avv~~~~~--~--L------~AEL~AIl~ALe~a~~~~~sk~vI-------I  198 (287)
                      .+...+.+.|||| ||  |.+++|.+|+|++...+.  .  +      .||++|++.||+.+    ..++.|       +
T Consensus       433 ~ep~~~~~~iytD-Gs--~~~n~g~~g~g~v~~~~~~~~~~~~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi  505 (557)
T 2zd1_A          433 KEPIVGAETFYVD-GA--ANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYAL  505 (557)
T ss_dssp             SSCCTTSCEEEEE-EE--ECTTTCCEEEEEEETTSCEEEEEECSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHH
T ss_pred             cCCCCCCEEEEEc-cC--CCCCCCceEEEEEEECCcEEEecCCCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHH
Confidence            3445567999999 88  889999999997765431  1  1      19999999999998    234544       3


Q ss_pred             ecccCCCcccCCCChHHHHHHHHHHhhCCCceEEEEeccCCCCccchHHHHHHHHH
Q psy10246        199 SVLGSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNS  254 (287)
Q Consensus       199 ~aL~n~~~K~~~~~p~~I~~ii~eL~~~g~~V~f~WVPGHsGI~GNE~AD~LAK~A  254 (287)
                      +.+.+|..+.+.   ...+++++.+.. ...|.|.|||||+|++|||+||+|||+|
T Consensus       506 ~~i~~~~~~~~~---~l~~~~~~~l~~-~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          506 GIIQAQPDKSES---ELVNQIIEQLIK-KEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             HHHTTCCSEESS---HHHHHHHHHHHH-CSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             HHHhcCCccCCH---HHHHHHHHHHhc-CCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            456666533222   122344444433 3689999999999999999999999986

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

Probab=99.59  E-value=2.2e-15  Score=124.24  Aligned_cols=107  Identities=11%  Similarity=0.092  Sum_probs=72.2

Q ss_pred             EEEEEcCCCCCCC-CCCCceEE-EEEecCC-----------cch--h-----HHHHHHHHHHHHchhcCCCeEEE-----
Q psy10246        143 SWILSTQASSGCL-LINSATGY-AMSGYQD-----------TRL--Y-----SGAILVMKVLQSVQIFKIGKWLE-----  197 (287)
Q Consensus       143 i~IYTD~GS~~C~-k~~G~vG~-Avv~~~~-----------~~L--~-----AEL~AIl~ALe~a~~~~~sk~vI-----  197 (287)
                      +.|||| ||  |. +++|++|+ |++...+           +.+  .     ||++|++.||+.+...+..++.|     
T Consensus         2 ~~iy~D-Gs--~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~   78 (149)
T 2ehg_A            2 IIGYFD-GL--CEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQ   78 (149)
T ss_dssp             CEEEEE-EE--EESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCH
T ss_pred             EEEEEe-ec--cCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChH
Confidence            579999 88  88 78899995 8543222           101  1     99999999999998876656655     


Q ss_pred             --EecccCCCcccCCCChHHHHHHHHHHhhCCCceEEEEeccCCCCccchHHHHHHHHHHhhc
Q psy10246        198 --ISVLGSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQ  258 (287)
Q Consensus       198 --I~aL~n~~~K~~~~~p~~I~~ii~eL~~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~p  258 (287)
                        +..+.++ |+.+.+....+.+.+..+..+ ..|.|.|||+    ++||.||+|||+|+..+
T Consensus        79 ~vi~~i~~~-w~~~~~~~~~l~~~i~~l~~~-~~v~~~~V~~----~~N~~AD~LA~~a~~~~  135 (149)
T 2ehg_A           79 LVIKQMNGE-YKVKAKRIIPLYEKAIELKKK-LNATLIWVPR----EENKEADRLSRVAYELV  135 (149)
T ss_dssp             HHHHHHTTS-SCCCCTTHHHHHHHHHHHHHH-HTCEEEECCG----GGCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCc-cccCCHHHHHHHHHHHHHHhc-CCEEEEEcCC----cccHHHHHHHHHHHHhh
Confidence              3455554 343333222222222222222 2599999999    59999999999999764

>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=99.00  E-value=1.7e-11  Score=103.23  Aligned_cols=104  Identities=5%  Similarity=-0.092  Sum_probs=72.9

Q ss_pred             eEEEEEcCCCCCCCCCCCceEEEEEecCC-------cchh------HHHHHHHHHHHHchhcCCCeEEE-------Eecc
Q psy10246        142 CSWILSTQASSGCLLINSATGYAMSGYQD-------TRLY------SGAILVMKVLQSVQIFKIGKWLE-------ISVL  201 (287)
Q Consensus       142 ~i~IYTD~GS~~C~k~~G~vG~Avv~~~~-------~~L~------AEL~AIl~ALe~a~~~~~sk~vI-------I~aL  201 (287)
                      .+.|||| ||  |.+|+|++|||++...+       ..+.      ||++|++.||+.+.+.+. ++.|       ++++
T Consensus        11 ~~~iy~D-Ga--~~gNpG~~G~G~vl~~~g~~~~~~~~~~~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~   86 (142)
T 1zbf_A           11 WESLSVD-VG--SQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWV   86 (142)
T ss_dssp             SSSEEEE-EE--ECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHH
T ss_pred             eEEEEEe-ec--cCCCCCCeEEEEEEEeCCEEEEEecccCCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHH
Confidence            4679999 88  89999999999765422       1121      999999999999987654 3333       3344


Q ss_pred             cCCCcccCCCChHHHHHHHHHHhh-----CCCceEEEEeccCCCCccchHHHH
Q psy10246        202 GSPDVKKVIFSPWSVRNVRAMKFA-----RDINIKFLWIPSHCGIVENERVDQ  249 (287)
Q Consensus       202 ~n~~~K~~~~~p~~I~~ii~eL~~-----~g~~V~f~WVPGHsGI~GNE~AD~  249 (287)
                      ++..++++...++.++++++.+.+     +.+.++...|+-|++.-||+.||.
T Consensus        87 ~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~~~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A           87 KDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             HHTCCCCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTCC
T ss_pred             HcCCccCCCCCCcccHHHHHHHHHHHHHHhhCCCceeEEEeccCccCcCcccc
Confidence            443334444456666666665432     346788888999999999999983

>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=98.88  E-value=3.4e-10  Score=95.10  Aligned_cols=79  Identities=5%  Similarity=-0.059  Sum_probs=56.5

Q ss_pred             eEEEEEcCCCCCCCCCCCceEEE-EEecCCc------chh------HHHHHHHHHHHHchhcC-------CCeEEEEecc
Q psy10246        142 CSWILSTQASSGCLLINSATGYA-MSGYQDT------RLY------SGAILVMKVLQSVQIFK-------IGKWLEISVL  201 (287)
Q Consensus       142 ~i~IYTD~GS~~C~k~~G~vG~A-vv~~~~~------~L~------AEL~AIl~ALe~a~~~~-------~sk~vII~aL  201 (287)
                      ...|||| ||  |++|||++||| |+...+.      .+.      ||++|+++||+.+.+.+       ||+|+ ++++
T Consensus         5 ~~~iytD-Ga--c~GNPGp~G~ggV~~~~g~~~~~~g~~~~tTNN~aEl~A~i~aL~~l~~~~~~v~i~tDSqyV-i~wi   80 (134)
T 4htu_A            5 WESLSVD-VG--SQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYSNSQTA-IKWV   80 (134)
T ss_dssp             SSSEEEE-EE--EETTTEEEEEEEEETTTCCEEEEEEEEEEECHHHHHHHHHHHHHHHHHHTTCCCCEEESCHHH-HHHH
T ss_pred             ceEEEEe-ec--cCCCCCCeEEEEEEEECCEEEEEecCCCCCchHHHHHHHHHHHHHHHHhCCCCEEEEcchHHH-HHHH
Confidence            4569999 88  99999999995 5433221      111      99999999999998753       23333 3567


Q ss_pred             cCCCcccCCCChHHHHHHHHHHh
Q psy10246        202 GSPDVKKVIFSPWSVRNVRAMKF  224 (287)
Q Consensus       202 ~n~~~K~~~~~p~~I~~ii~eL~  224 (287)
                      .++.|++....+++++++++++.
T Consensus        81 ~~~~~kt~~~~~vkN~dLw~~ld  103 (134)
T 4htu_A           81 KDKKAKSTLVRNEETALIWKLVD  103 (134)
T ss_dssp             HHTCCCCCCCCSSTTHHHHHHHH
T ss_pred             HcCCcccCCCCCccCHHHHHHHH
Confidence            77777777777877877776654

---

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	287
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	3e-04
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	7e-04
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	0.004

>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 = 38.4 bits (88), Expect = 3e-04
 Identities = 11/39 (28%), Positives = 19/39 (48%)

Query: 220 RAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQ 258
             +       ++F ++  H G  ENERVD+ A+    +Q
Sbjct: 106 ALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQ 144

>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 = 36.8 bits (84), Expect = 7e-04
 Identities = 12/44 (27%), Positives = 18/44 (40%)

Query: 212 SPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSI 255
           S   + N    +  +   I   W+P+H GI  N+ VD      I
Sbjct: 83  SESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI 126

>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 = 35.0 bits (79), Expect = 0.004
 Identities = 12/40 (30%), Positives = 18/40 (45%)

Query: 222 MKFARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLK 261
                   IK+ W+  H G  ENER D+ A+ +     L+
Sbjct: 106 DAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLE 145

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	287
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.9
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.88
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.83
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.36
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.32

>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=99.90  E-value=4.9e-25  Score=179.10  Aligned_cols=121  Identities=18%  Similarity=0.194  Sum_probs=81.8

Q ss_pred             eEEEEEcCCCCCCCCCCCceEEEEEe-cCCc------chh------HHHHHHHHHHHHchhcC------CCeEEE--Ee-
Q psy10246        142 CSWILSTQASSGCLLINSATGYAMSG-YQDT------RLY------SGAILVMKVLQSVQIFK------IGKWLE--IS-  199 (287)
Q Consensus       142 ~i~IYTD~GS~~C~k~~G~vG~Avv~-~~~~------~L~------AEL~AIl~ALe~a~~~~------~sk~vI--I~-  199 (287)
                      .|.|||| ||  |++|+|++|||++. ..+.      .++      ||++|++.||+.+....      ++++++  ++ 
T Consensus         2 ~I~IYtD-GS--~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~~~~~i~i~tds~~~i~~~~~   78 (152)
T d1jl1a_           2 QVEIFTA-GS--ALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAEVILSTDSQYVRQGITQ   78 (152)
T ss_dssp             CEEEEEE-EE--ESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCSCCEEEEEECCHHHHHHHHT
T ss_pred             EEEEEEe-CC--CCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhcccceEEEeecceeeEEcccc
Confidence            4789999 99  88999999999653 3331      111      99999999999865421      111111  10 


Q ss_pred             ---cccCCCcccCCCChHHHHHHHHHHh--hCCCceEEEEeccCCCCccchHHHHHHHHHHhhcccccchh
Q psy10246        200 ---VLGSPDVKKVIFSPWSVRNVRAMKF--ARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVV  265 (287)
Q Consensus       200 ---aL~n~~~K~~~~~p~~I~~ii~eL~--~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~p~~~~~~~  265 (287)
                         .+....|+.....+..+.++++.+.  .+..+|+|+|||||+|++|||+||+|||+|+..|.+++..+
T Consensus        79 ~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~d~~~  149 (152)
T d1jl1a_          79 WIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTGY  149 (152)
T ss_dssp             THHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCCTTC
T ss_pred             hhhHhHhccchhcccCeeecHHHHHHHHHHhhcceeEEEEecccCCCccHHHHHHHHHHHHhCCCCCccCC
Confidence               1111123333334444444444432  24578999999999999999999999999999998887765

>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=99.88  E-value=1e-24  Score=178.38  Aligned_cols=113  Identities=17%  Similarity=0.152  Sum_probs=77.8

Q ss_pred             CeEEEEEcCCCCCCCCCCCceEEEEEecC-C--cch----h------HHHHHHHHHHHHchhcCCCeEEE-------Eec
Q psy10246        141 QCSWILSTQASSGCLLINSATGYAMSGYQ-D--TRL----Y------SGAILVMKVLQSVQIFKIGKWLE-------ISV  200 (287)
Q Consensus       141 ~~i~IYTD~GS~~C~k~~G~vG~Avv~~~-~--~~L----~------AEL~AIl~ALe~a~~~~~sk~vI-------I~a  200 (287)
                      ..+.|||| ||  |++|+|.+|||++... +  ..+    +      ||++||++||+.+...  ..+.|       +..
T Consensus         2 ~~i~iytD-Gs--~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~~--~~i~i~tds~~~~~~   76 (147)
T d1rila_           2 KRVALFTD-GA--CLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKA   76 (147)
T ss_dssp             CCCCEEEE-EE--ESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHH
T ss_pred             CEEEEEEc-cC--CCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhccCC--ceEEEecchhhhhcc
Confidence            35889999 99  9999999999966432 2  111    1      9999999999986532  22322       112


Q ss_pred             ccCC--------CcccCCCChHHHHHHHHHHh--hCCCceEEEEeccCCCCccchHHHHHHHHHHhhc
Q psy10246        201 LGSP--------DVKKVIFSPWSVRNVRAMKF--ARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQ  258 (287)
Q Consensus       201 L~n~--------~~K~~~~~p~~I~~ii~eL~--~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa~~p  258 (287)
                      +..+        .+......+..+.++++++.  .+..+|+|.|||||+|++|||+||+|||+|+...
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_          77 FTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             HHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             ccccchhhhhhccccccccccchhHHHHHHHHHHhhhcccceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence            2111        12233334555566665543  3567899999999999999999999999998764

>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=99.83  E-value=4.7e-21  Score=153.69  Aligned_cols=106  Identities=16%  Similarity=0.146  Sum_probs=72.8

Q ss_pred             CCCeEEEEEcCCCCCCCCCCCceEEEEEecCCc----chh------HHHHHHHHHHHHchhcCCCeEEE-------Eecc
Q psy10246        139 NVQCSWILSTQASSGCLLINSATGYAMSGYQDT----RLY------SGAILVMKVLQSVQIFKIGKWLE-------ISVL  201 (287)
Q Consensus       139 ~~~~i~IYTD~GS~~C~k~~G~vG~Avv~~~~~----~L~------AEL~AIl~ALe~a~~~~~sk~vI-------I~aL  201 (287)
                      .+...+|||| ||  |.++++.+|+|++.+.+.    .++      ||++||++||+...    .++.|       +..+
T Consensus         4 ~~~~~t~YTD-GS--~~~n~~~~~~g~~~~~~~~~~~~~~~~tnn~AEl~Ai~~al~~~~----~~i~I~tDS~~v~~~~   76 (126)
T d1mu2a1           4 IPGAETFYTD-GS--CNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTDSG----PKVNIIVDSQYVMGIV   76 (126)
T ss_dssp             CTTCEEEEEE-EE--ECTTTCCEEEEEEETTSCEEEEEESSCCHHHHHHHHHHHHHHTSC----SEEEEEESCHHHHHHH
T ss_pred             CCCCcEEEEc-CC--CCCCCCcEEEEEEecCCCEEEEecCCCcchHHHHHHHHHHhccCC----cceEEEechHHHHHHH
Confidence            3455789999 99  888888888887655441    111      99999999998643    34444       2344


Q ss_pred             cCCCcccCCCChHHHHHHHHHHhhCCCceEEEEeccCCCCccchHHHHHHHHHH
Q psy10246        202 GSPDVKKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSI  255 (287)
Q Consensus       202 ~n~~~K~~~~~p~~I~~ii~eL~~~g~~V~f~WVPGHsGI~GNE~AD~LAK~Aa  255 (287)
                      .++. +...  .......+..+.. ...|.|.|||||+|++|||+||+||++|+
T Consensus        77 ~~~~-~~~~--~~~~~~~~~~~~~-~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          77 ASQP-TESE--SKIVNQIIEEMIK-KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             HTCC-SEES--CHHHHHHHHHHHH-CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             hcCC-cccc--chHHHHHHHHhhh-cceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            4432 1111  1223344444443 36899999999999999999999999873

>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=99.36  E-value=1.1e-14  Score=120.23  Aligned_cols=100  Identities=5%  Similarity=-0.073  Sum_probs=73.9

Q ss_pred             EEEcCCCCCCCCCCCceEEEEEecCC-------cchh------HHHHHHHHHHHHchhcCCCeEEE-------EecccCC
Q psy10246        145 ILSTQASSGCLLINSATGYAMSGYQD-------TRLY------SGAILVMKVLQSVQIFKIGKWLE-------ISVLGSP  204 (287)
Q Consensus       145 IYTD~GS~~C~k~~G~vG~Avv~~~~-------~~L~------AEL~AIl~ALe~a~~~~~sk~vI-------I~aL~n~  204 (287)
                      |||| ||  |++|||++|||++....       +.++      ||++|++.||+.+.... .++.|       ++++++|
T Consensus         7 Iy~D-Ga--~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~   82 (132)
T d1zbfa1           7 LSVD-VG--SQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDK   82 (132)
T ss_dssp             EEEE-EE--ECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHT
T ss_pred             EEEe-ec--CCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhC
Confidence            8999 88  99999999999664333       1122      99999999999987643 23333       4567777


Q ss_pred             CcccCCCChHHHHHHHHHHh-----hCCCceEEEEeccCCCCccchHHH
Q psy10246        205 DVKKVIFSPWSVRNVRAMKF-----ARDINIKFLWIPSHCGIVENERVD  248 (287)
Q Consensus       205 ~~K~~~~~p~~I~~ii~eL~-----~~g~~V~f~WVPGHsGI~GNE~AD  248 (287)
                      .|++....+..++++++.+.     -+.+.+.+.||+.|+..-||..||
T Consensus        83 ~~kt~~~~~vkN~~l~~~i~~a~~~lk~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          83 KAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CCCCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             ceecCcCCCcccHHHHHHHHHHHHHHHhCCcCceeEEecCcccccCCCC
Confidence            77776666666666655442     134689999999999999999887

>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=99.32  E-value=5.8e-13  Score=105.54  Aligned_cols=91  Identities=9%  Similarity=0.103  Sum_probs=56.9

Q ss_pred             CCeEEEEEcCCCCCCCCCCCceEEEEEecCC----cchh------HHHHHHHHHHHHchh----cCCCeEEEEecccCCC
Q psy10246        140 VQCSWILSTQASSGCLLINSATGYAMSGYQD----TRLY------SGAILVMKVLQSVQI----FKIGKWLEISVLGSPD  205 (287)
Q Consensus       140 ~~~i~IYTD~GS~~C~k~~G~vG~Avv~~~~----~~L~------AEL~AIl~ALe~a~~----~~~sk~vII~aL~n~~  205 (287)
                      .+..+|||| ||  |.+++|.+|+|++.+.+    ..+.      ||++||++||+....    ++||+|+ +.++.++.
T Consensus         6 ~~~~t~ytD-Gs--~~~n~~~g~~g~~~~~~~~~~~~~~~~TNn~aEl~Avi~aL~~~~~~v~I~TDS~yv-i~~i~~~~   81 (110)
T d1s1ta1           6 VGAETFYVD-GA--ANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYA-LGIIQAQP   81 (110)
T ss_dssp             TTSEEEEEE-EE--EETTTTEEEEEEEETTSCEEEEEESSCCHHHHHHHHHHHHHHHSCSEEEEEECCHHH-HHHHHHCC
T ss_pred             CCCcEEEEe-CC--CCCCCCCcEEEEEEecCCeEEEecccCcHHHHHHHHHHHHHHhCCCeEEEEEehHHH-HHHHhcCc
Confidence            455689999 98  88888888888776554    1111      999999999986432    1233333 23344332


Q ss_pred             cccCCCChHHHHHHHHHHhhCCCceEEEEeccC
Q psy10246        206 VKKVIFSPWSVRNVRAMKFARDINIKFLWIPSH  238 (287)
Q Consensus       206 ~K~~~~~p~~I~~ii~eL~~~g~~V~f~WVPGH  238 (287)
                      .+...   ...+++++.+.. ...|.|.|||||
T Consensus        82 ~~~~~---~l~~~il~~l~~-~~~v~i~WVpgH  110 (110)
T d1s1ta1          82 DQSES---ELVNQIIEQLIK-KEKVYLAWVPAH  110 (110)
T ss_dssp             SEESC---HHHHHHHHHHHH-CSEEEEEECCSS
T ss_pred             cccch---HHHHHHHHHHhc-CCceEEEEeCCC
Confidence            11111   122444555543 478999999999