Psyllid ID: psy7630

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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
Protein Sequence
MDSFEITHSLFLEETFRKQDVAPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMNSVHLNSCPALEASNDIVGTLCSVLNKIKTNCCPYSRAASQS
Secondary Structure (PSIPRED)
cccccccHHHHHHHHcccccccHHHHHHHHHHHHHHcccccccEEEEccccccccccccEEEEEEccEEEEEEcccccccHHHHHHHHHHHHHHHHccccccccEEEEEccHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHcccc
Secondary Structure Prediction (SSPRO)
cccEEEHHHHHHHHHHHHccHHHHHHHHHHHHHHccccccccEEEEEEccccccccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHEEEEEcccHHcccccccccccccHHHHcccHHHHHHHHHHHHHccccccccHccccc
Coil and Loop (DISEMBL)
MDSFEITHSLFLEETFRKQDVAPLIAKTMALETintrypsddwlhiytdgslinpedgagaGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSdskaaihpmnsvhlnscpaleasNDIVGTLCSVLNKiktnccpysraasqs
Flexible Loop (DISEMBL)
MDSFEITHSlfleetfrkqdvaPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMNSVHLNSCPALEASNDIVGTLCSVLNKIKtnccpysraasqs
Low Complexity Region (SEG)
MDSFEITHSLFLEETFRKQDVAPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEiaaikiallqilNRTNQFERAVILSDSKAAIHPMNSVHLNSCPALEASNDIVGTLCSVLNKIKTNCCPYSRAASQS
Disordered region (IsUnstruct)
*****ITHSLFLEETFRKQDVAPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMNSVHLNSCPALEASNDIVGTLCSVLNKIKTNCCPY*******
Disordered Region (DISOPRED)
***FEITHSLFLEETFRKQDVAPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMNSVHLNSCPALEASNDIVGTLCSVLNKIKTNCCPYS******
Disordered Region (DISEMBL)
MDSFEITHSLFLEETFRKQDVAPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMNSVHLNSCPALEASNDIVGTLCSVLNKIKTNCCPYSRAASQS
Disordered Region (DISPRO)
*DSFEITHSLFLEETFRKQDVAPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMNSVHLNSCPALEASNDIVGTLCSVLNKIKTNCCPYS******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDSFEITHSLFLEETFRKQDVAPLIAKTMALETINTRYPSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMNSVHLNSCPALEASNDIVGTLCSVLNKIKTNCCPYSRAASQS
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	3.1.26.4	LOW CONFIDENCE 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	160
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	1e-11
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	2e-07
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	1e-05
pfam00075	126	pfam00075, RNase_H, RNase H	8e-05
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	0.003

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

 Score = 58.0 bits (141), Expect = 1e-11
 Identities = 27/72 (37%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 45  HIYTDGSLINPEDGAGAGIFCE-LFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFE 103
            IYTDGS +    GAG  I  +   S   +LG + + FD E+ AI  AL   L    +  
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 104 RAVILSDSKAAI 115
           +  I SDS+AA+
Sbjct: 61  KITIFSDSQAAL 72

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 46  IYTDGSLI-NPEDGAGAGI---FCE--LFSFYKRL-GTFTTNFDGEIAAIKIALLQILNR 98
           +YTDG+   N   GA AG    F      +  +RL G   TN   E+ A+  AL  I   
Sbjct: 2   VYTDGACRGNGRSGARAGYGVYFGPGHPRNVSERLPGPPQTNQRAELRAVIHALRLIKEV 61

Query: 99  TNQFERAVILSDSKAAI 115
                + VI +DS+  +
Sbjct: 62  GEGLTKLVIATDSEYVV 78

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

>gnl|CDD|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 = 42.0 bits (99), Expect = 1e-05
 Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 9/80 (11%)

Query: 47  YTDGS-LINPEDGAGAGIFCE-----LFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTN 100
            TDGS   NP      G+  +     LF+    +    TN + E+ A+  AL   L+   
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPA-ATNNEAELLALLEALELALD--L 57

Query: 101 QFERAVILSDSKAAIHPMNS 120
             ++ +I +DSK  +  +NS
Sbjct: 58  GLKKLIIETDSKYVVDLINS 77

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

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

 Score = 39.9 bits (94), Expect = 8e-05
 Identities = 21/76 (27%), Positives = 30/76 (39%), Gaps = 9/76 (11%)

Query: 46  IYTDGSLI--NPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFE 103
           +YTDGS        GAG           K L   TTN   E+ A+  AL  +       +
Sbjct: 6   VYTDGSCNGNPGPGGAGYVTD-GGKQRSKPLP-GTTNQRAELLALIEALEALSG-----Q 58

Query: 104 RAVILSDSKAAIHPMN 119
           +  I +DS+  I  + 
Sbjct: 59  KVNIYTDSQYVIGGIT 74

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

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

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 15/84 (17%)

Query: 44  LHIYTDG-SLINPEDGAGAGIFCELFSFYKRLG-------TFTTNFDGEIAAIKIALLQI 95
           + I+TDG  L NP  G    +       Y             TTN   E+ A+  AL + 
Sbjct: 4   VEIFTDGACLGNPGPGGWGAVL-----RYGDGEKELSGGEGRTTNNRAELRALIEAL-EA 57

Query: 96  LNRTNQFERAVILSDSKAAIHPMN 119
           L +        + +DSK  +  + 
Sbjct: 58  L-KELGACEVTLYTDSKYVVEGIT 80

Length = 154

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	160
PRK06548	161	ribonuclease H; Provisional	99.77
PRK00203	150	rnhA ribonuclease H; Reviewed	99.74
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.73
PRK13907	128	rnhA ribonuclease H; Provisional	99.71
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.71
PRK08719	147	ribonuclease H; Reviewed	99.69
KOG3752|consensus	371		99.68
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.52
PRK07708	219	hypothetical protein; Validated	99.49
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.41
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	98.61
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	92.07
.; 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	87.08

>PRK06548 ribonuclease H; Provisional

Probab=99.77  E-value=5e-18  Score=134.84  Aligned_cols=107  Identities=20%  Similarity=0.179  Sum_probs=75.9

Q ss_pred             eEEEEeeCCCCCCCCC-eEEEEEEecccceeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhhcc-
Q psy7630          43 WLHIYTDGSLINPEDG-AGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMNS-  120 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~G-aG~gi~~~~~~~~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI~~-  120 (160)
                      .++||||||+. |++| .|+|+++........-...+|||+|||+||+.||+.+.+   ....+.|+|||+|++++|++ 
T Consensus         5 ~~~IytDGa~~-gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~---~~~~v~I~TDS~yvi~~i~~W   80 (161)
T PRK06548          5 EIIAATDGSSL-ANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH---TDRPILILSDSKYVINSLTKW   80 (161)
T ss_pred             EEEEEEeeccC-CCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc---CCceEEEEeChHHHHHHHHHH
Confidence            59999999994 5567 688888764322222223589999999999999986621   23469999999999999993 


Q ss_pred             --------CCCCCchh---hhhhhHHHHHHhhhccceeeccccCcc
Q psy7630         121 --------VHLNSCPA---LEASNDIVGTLCSVLNKIKTNCCPYSR  155 (160)
Q Consensus       121 --------~~~~~~~~---~~~~~~I~~~~~~~~~~~~~~~~p~~~  155 (160)
                              |...+..+   .+.-++|..++..  .+|+|.||||..
T Consensus        81 ~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~--~~v~~~wVkgHs  124 (161)
T PRK06548         81 VYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN--RNIRMSWVNAHT  124 (161)
T ss_pred             HHHHHHCCCcccCCCccccHHHHHHHHHHHhc--CceEEEEEecCC
Confidence                    43333321   3344566666644  479999999864

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.74  E-value=1.4e-17  Score=128.74  Aligned_cols=106  Identities=19%  Similarity=0.149  Sum_probs=74.1

Q ss_pred             eEEEEeeCCCCCCCCC-eEEEEEEecccc---eeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhh
Q psy7630          43 WLHIYTDGSLINPEDG-AGAGIFCELFSF---YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPM  118 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~G-aG~gi~~~~~~~---~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI  118 (160)
                      .+.||||||+. +++| +|+|+++...+.   .....+..||++|||.||+.||+.+.+    ...+.|+|||++++++|
T Consensus         3 ~v~iytDGs~~-~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~----~~~v~I~tDS~yvi~~i   77 (150)
T PRK00203          3 QVEIYTDGACL-GNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE----PCEVTLYTDSQYVRQGI   77 (150)
T ss_pred             eEEEEEEeccc-CCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC----CCeEEEEECHHHHHHHH
Confidence            58999999995 4445 678887754332   112234689999999999999998832    35799999999999999


Q ss_pred             ccC---------CCCCchh---hhhhhHHHHHHhhhccceeeccccCcc
Q psy7630         119 NSV---------HLNSCPA---LEASNDIVGTLCSVLNKIKTNCCPYSR  155 (160)
Q Consensus       119 ~~~---------~~~~~~~---~~~~~~I~~~~~~~~~~~~~~~~p~~~  155 (160)
                      +.|         .......   .+.-+.|..++..  .+|.|.||||..
T Consensus        78 ~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~--~~v~~~wV~~H~  124 (150)
T PRK00203         78 TEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR--HQIKWHWVKGHA  124 (150)
T ss_pred             HHHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc--CceEEEEecCCC
Confidence            963         2222111   1233556655543  689999999864

>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=99.73  E-value=2e-17  Score=121.92  Aligned_cols=106  Identities=28%  Similarity=0.313  Sum_probs=74.5

Q ss_pred             CeEEEEeeCCCCCCCCC-eEEEEEEecc-cceeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhhc
Q psy7630          42 DWLHIYTDGSLINPEDG-AGAGIFCELF-SFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMN  119 (160)
Q Consensus        42 ~~i~IYTDGSk~ng~~G-aG~gi~~~~~-~~~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI~  119 (160)
                      +.+.||||||+. +.+| .|+|+++... +.+.+++ .+|+++||+.||.+||+.+ .    ..+++|+|||+++++.|+
T Consensus         2 ~~~~iytDgS~~-~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~----~~~v~I~tDS~~v~~~l~   74 (132)
T PF00075_consen    2 KAIIIYTDGSCR-PNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL-E----HRKVTIYTDSQYVLNALN   74 (132)
T ss_dssp             TSEEEEEEEEEC-TTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH-S----TSEEEEEES-HHHHHHHH
T ss_pred             CcEEEEEeCCcc-CCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh-h----cccccccccHHHHHHHHH
Confidence            469999999984 3344 5667755322 2345566 7999999999999999944 2    268999999999999888


Q ss_pred             cC-----CCCCchhhhhhhHHHHHHhhhccceeeccccCcc
Q psy7630         120 SV-----HLNSCPALEASNDIVGTLCSVLNKIKTNCCPYSR  155 (160)
Q Consensus       120 ~~-----~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~p~~~  155 (160)
                      ++     .........+.++|..++.. ..+|+|.||||..
T Consensus        75 ~~~~~~~~~~~~~~~~i~~~i~~~~~~-~~~v~~~~V~~H~  114 (132)
T PF00075_consen   75 KWLHGNGWKKTSNGRPIKNEIWELLSR-GIKVRFRWVPGHS  114 (132)
T ss_dssp             THHHHTTSBSCTSSSBHTHHHHHHHHH-SSEEEEEESSSSS
T ss_pred             Hhccccccccccccccchhheeecccc-ceEEeeeeccCcC
Confidence            72     11111111355677777733 5689999999974

This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.71  E-value=8.7e-17  Score=120.15  Aligned_cols=109  Identities=17%  Similarity=0.178  Sum_probs=79.9

Q ss_pred             eEEEEeeCCCCCCCCC-eEEEEEEecccc--eeec-CCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhh
Q psy7630          43 WLHIYTDGSLINPEDG-AGAGIFCELFSF--YKRL-GTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPM  118 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~G-aG~gi~~~~~~~--~~~L-~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI  118 (160)
                      +++||||||+ ++++| +|+|+++.....  .+.. ...+||++||+.|++.||+.+.+.  ...++.|+|||+++++.+
T Consensus         1 ~~~iy~DGa~-~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~--g~~~v~i~sDS~~vi~~~   77 (128)
T PRK13907          1 MIEVYIDGAS-KGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEH--NYNIVSFRTDSQLVERAV   77 (128)
T ss_pred             CEEEEEeeCC-CCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhC--CCCEEEEEechHHHHHHH
Confidence            4789999999 56666 788998855432  1221 245899999999999999999643  345799999999999999


Q ss_pred             ccCCCCCchhhhhhhHHHHHHhhhccceeeccccCcc
Q psy7630         119 NSVHLNSCPALEASNDIVGTLCSVLNKIKTNCCPYSR  155 (160)
Q Consensus       119 ~~~~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~p~~~  155 (160)
                      +++......-...-+++..++. ....+.+.|||.+.
T Consensus        78 ~~~~~~~~~~~~l~~~~~~l~~-~f~~~~~~~v~r~~  113 (128)
T PRK13907         78 EKEYAKNKMFAPLLEEALQYIK-SFDLFFIKWIPSSQ  113 (128)
T ss_pred             hHHHhcChhHHHHHHHHHHHHh-cCCceEEEEcCchh
Confidence            8865433333445666666664 45677789999863

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

Probab=99.71  E-value=1e-16  Score=126.96  Aligned_cols=109  Identities=18%  Similarity=0.136  Sum_probs=75.4

Q ss_pred             CeEEEEeeCCCCCCCCC-eEEEEEEeccc----ceeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHH
Q psy7630          42 DWLHIYTDGSLINPEDG-AGAGIFCELFS----FYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIH  116 (160)
Q Consensus        42 ~~i~IYTDGSk~ng~~G-aG~gi~~~~~~----~~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~  116 (160)
                      ..++|||||||. |+|| .|+|+++....    .+..+. .+|||+||+.|+++||+++.+  .....+.|+|||+++++
T Consensus         2 ~~v~if~DGa~~-gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~--~~~~~v~l~tDS~yv~~   77 (154)
T COG0328           2 KKVEIFTDGACL-GNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKE--LGACEVTLYTDSKYVVE   77 (154)
T ss_pred             CceEEEecCccC-CCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHh--cCCceEEEEecHHHHHH
Confidence            368999999994 6677 67888775322    122333 799999999999999999953  34568999999999999


Q ss_pred             hhccCCC----CCch--------hhhhhhHHHHHHhhhccceeeccccCcc
Q psy7630         117 PMNSVHL----NSCP--------ALEASNDIVGTLCSVLNKIKTNCCPYSR  155 (160)
Q Consensus       117 aI~~~~~----~~~~--------~~~~~~~I~~~~~~~~~~~~~~~~p~~~  155 (160)
                      +|+.|..    ....        ..+.-+++..++ +...+|...||||-.
T Consensus        78 ~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~-~~~~~v~~~WVkgH~  127 (154)
T COG0328          78 GITRWIVKWKKNGWKTADKKPVKNKDLWEELDELL-KRHELVFWEWVKGHA  127 (154)
T ss_pred             HHHHHHhhccccCccccccCccccHHHHHHHHHHH-hhCCeEEEEEeeCCC
Confidence            9986511    1111        112233333333 233388999999864

>PRK08719 ribonuclease H; Reviewed

Probab=99.69  E-value=2.1e-16  Score=123.20  Aligned_cols=105  Identities=18%  Similarity=0.126  Sum_probs=70.7

Q ss_pred             eEEEEeeCCCC-CCCC-C-eEEEEEEeccc------ceeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHH
Q psy7630          43 WLHIYTDGSLI-NPED-G-AGAGIFCELFS------FYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKA  113 (160)
Q Consensus        43 ~i~IYTDGSk~-ng~~-G-aG~gi~~~~~~------~~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqs  113 (160)
                      .+.||||||+. |+.+ + +|+|+++...+      ....+...+||++||+.||+.||+.+.+      ...|+|||++
T Consensus         4 ~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~------~~~i~tDS~y   77 (147)
T PRK08719          4 SYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARD------GDVIYSDSDY   77 (147)
T ss_pred             eEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCC------CCEEEechHH
Confidence            58999999996 3321 1 57888764322      2333555689999999999999999842      2379999999


Q ss_pred             HHHhhcc---------CCCCCchh---hhhhhHHHHHHhhhccceeeccccCcc
Q psy7630         114 AIHPMNS---------VHLNSCPA---LEASNDIVGTLCSVLNKIKTNCCPYSR  155 (160)
Q Consensus       114 aI~aI~~---------~~~~~~~~---~~~~~~I~~~~~~~~~~~~~~~~p~~~  155 (160)
                      ++++|++         |..+...+   .+.-+.|..+.+  .++|+|.||||..
T Consensus        78 vi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~--~~~i~~~~VkgH~  129 (147)
T PRK08719         78 CVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA--RKYVEVEKVTAHS  129 (147)
T ss_pred             HHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC--CCcEEEEEecCCC
Confidence            9999853         32222211   122334444443  4689999999953

>KOG3752|consensus

Probab=99.68  E-value=1.1e-16  Score=140.93  Aligned_cols=110  Identities=21%  Similarity=0.188  Sum_probs=89.9

Q ss_pred             eEEEEeeCCCC-CCCCC--eEEEEEEec---ccceeecC-CCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHH
Q psy7630          43 WLHIYTDGSLI-NPEDG--AGAGIFCEL---FSFYKRLG-TFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAI  115 (160)
Q Consensus        43 ~i~IYTDGSk~-ng~~G--aG~gi~~~~---~~~~~~L~-~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI  115 (160)
                      ...+|||||++ ||..|  +|+|||++.   .|.+.++. +.+|||+|||.||.+||+-++++  ...+++|.|||++++
T Consensus       212 ~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~--~~~kv~I~TDS~~~i  289 (371)
T KOG3752|consen  212 IQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSK--NINKVVIRTDSEYFI  289 (371)
T ss_pred             ceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhc--CCCcEEEEechHHHH
Confidence            48999999997 88887  999999964   55788987 88999999999999999999653  345899999999999


Q ss_pred             HhhccCCC------------CC-----chhhhhhhHHHHHHhh-hccceeeccccCc
Q psy7630         116 HPMNSVHL------------NS-----CPALEASNDIVGTLCS-VLNKIKTNCCPYS  154 (160)
Q Consensus       116 ~aI~~~~~------------~~-----~~~~~~~~~I~~~~~~-~~~~~~~~~~p~~  154 (160)
                      ++|+.|-.            ..     .....--+.+-.+++. +-.+++++||||-
T Consensus       290 ~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh  346 (371)
T KOG3752|consen  290 NSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGH  346 (371)
T ss_pred             HHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCc
Confidence            99987621            11     2245566777788866 4579999999995

>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=99.52  E-value=2.9e-13  Score=94.75  Aligned_cols=106  Identities=25%  Similarity=0.221  Sum_probs=75.1

Q ss_pred             EEEeeCCCCCCCCCeEEEEEEecccc-----eeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhhc
Q psy7630          45 HIYTDGSLINPEDGAGAGIFCELFSF-----YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMN  119 (160)
Q Consensus        45 ~IYTDGSk~ng~~GaG~gi~~~~~~~-----~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI~  119 (160)
                      .+|||||......++|+|+++...+.     ........|++.||+.|++.||+++..  ....++.|+|||+.+++.++
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~--~~~~~i~i~~Ds~~~~~~~~   78 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALE--LGGKKVNIYTDSQYVINALT   78 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHh--CCCceEEEEECHHHHHHHhh
Confidence            38999999433234888888855431     112225689999999999999999853  34568999999999999999


Q ss_pred             cCCC-CCchhhhhhhHHHHHHhhhccceeeccccC
Q psy7630         120 SVHL-NSCPALEASNDIVGTLCSVLNKIKTNCCPY  153 (160)
Q Consensus       120 ~~~~-~~~~~~~~~~~I~~~~~~~~~~~~~~~~p~  153 (160)
                      ++.. .........+.|..++ ....+++++|||+
T Consensus        79 ~~~~~~~~~~~~~~~~i~~~~-~~~~~~~i~~v~~  112 (130)
T cd06222          79 GWYEGKPVKNVDLWQRLLALL-KRFHKVRFEWVPG  112 (130)
T ss_pred             ccccCCChhhHHHHHHHHHHH-hCCCeEEEEEcCC
Confidence            8754 2222333444555544 3456899999998

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.

>PRK07708 hypothetical protein; Validated

Probab=99.49  E-value=4.7e-13  Score=110.81  Aligned_cols=114  Identities=16%  Similarity=0.089  Sum_probs=78.7

Q ss_pred             CCCeEEEEeeCCCCCCCCC-eEEEEEEecc--cce------eecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcC
Q psy7630          40 SDDWLHIYTDGSLINPEDG-AGAGIFCELF--SFY------KRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSD  110 (160)
Q Consensus        40 ~~~~i~IYTDGSk~ng~~G-aG~gi~~~~~--~~~------~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SD  110 (160)
                      +.+.+++|+|||. ++++| +|+|+++...  +..      ..++..+|||+||+.|++.||+.+.+.......+.|++|
T Consensus        70 ep~~~~vY~DGs~-~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~D  148 (219)
T PRK07708         70 EPHEILVYFDGGF-DKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGD  148 (219)
T ss_pred             CCCcEEEEEeecc-CCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEec
Confidence            3457999999998 55555 7888877432  222      245556899999999999999999754222234899999


Q ss_pred             cHHHHHhhcc-CCCCCchhhhhhhHHHHHHhhhccceeeccccCc
Q psy7630         111 SKAAIHPMNS-VHLNSCPALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       111 SqsaI~aI~~-~~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      |+.+++.++. |..+.+....-...+..+++...-++.+.|||-.
T Consensus       149 SqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~  193 (219)
T PRK07708        149 SQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRK  193 (219)
T ss_pred             cHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCch
Confidence            9999999976 4444444334445555555544335777899863

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.41  E-value=3.1e-12  Score=111.20  Aligned_cols=107  Identities=16%  Similarity=0.070  Sum_probs=75.4

Q ss_pred             eEEEEeeCCCCCCCCC-eEEEEEEeccc-c------eeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHH
Q psy7630          43 WLHIYTDGSLINPEDG-AGAGIFCELFS-F------YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAA  114 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~G-aG~gi~~~~~~-~------~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsa  114 (160)
                      .++||||||+. +++| +|+|+++...+ .      ...+ +.+||++||+.|++.||+++.+.  ...++.|++||+++
T Consensus         2 ~~~i~~DGa~~-~n~g~aG~G~vi~~~~~~~~~~~~~~~~-~~~tnn~AE~~All~gL~~a~~~--g~~~v~i~~DS~lv   77 (372)
T PRK07238          2 KVVVEADGGSR-GNPGPAGYGAVVWDADRGEVLAERAEAI-GRATNNVAEYRGLIAGLEAAAEL--GATEVEVRMDSKLV   77 (372)
T ss_pred             eEEEEecCCCC-CCCCceEEEEEEEeCCCCcEEEEeeccc-CCCCchHHHHHHHHHHHHHHHhC--CCCeEEEEeCcHHH
Confidence            47899999994 5556 78888775432 1      1223 36899999999999999999643  34579999999999


Q ss_pred             HHhhccCCCCCch-hhhhhhHHHHHHhhhccceeeccccCc
Q psy7630         115 IHPMNSVHLNSCP-ALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       115 I~aI~~~~~~~~~-~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      ++.|++......+ -...-++|..++ ...+.+.+.|||..
T Consensus        78 i~~i~~~~~~~~~~l~~~~~~i~~l~-~~f~~~~i~~v~r~  117 (372)
T PRK07238         78 VEQMSGRWKVKHPDMKPLAAQARELA-SQFGRVTYTWIPRA  117 (372)
T ss_pred             HHHhCCCCccCChHHHHHHHHHHHHH-hcCCceEEEECCch
Confidence            9999864321222 222233455544 44578999999974

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

Probab=98.61  E-value=2.1e-07  Score=63.38  Aligned_cols=72  Identities=17%  Similarity=0.163  Sum_probs=54.2

Q ss_pred             hHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhhccCCCCCchhhhhhhHHHHHHhhhccceeeccccCc
Q psy7630          80 NFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMNSVHLNSCPALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus        80 n~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI~~~~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      +..||+.|++.||+++.+  ....++.|.|||+.+++.|++.......-....++|..++.. .+.+++.|+|-.
T Consensus         1 ~~~aE~~al~~al~~a~~--~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~-~~~~~~~~i~r~   72 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWE--LGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDR-FWNVSVSHIPRE   72 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHC--CT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCC-CSCEEEEE--GG
T ss_pred             CcHHHHHHHHHHHHHHHH--CCCCEEEEEecCccccccccccccccccccccchhhhhhhcc-ccceEEEEEChH
Confidence            468999999999999953  345789999999999999988743333555778888888877 788999999965

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

Probab=92.07  E-value=0.47  Score=37.00  Aligned_cols=50  Identities=22%  Similarity=0.215  Sum_probs=33.9

Q ss_pred             eEEEEeeCCCCCCCCCeEEEEEEeccc---ce-------eecC--CCcchHHHHHHHHHHHHHHHH
Q psy7630          43 WLHIYTDGSLINPEDGAGAGIFCELFS---FY-------KRLG--TFTTNFDGEIAAIKIALLQIL   96 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~GaG~gi~~~~~~---~~-------~~L~--~~~Sn~~AEl~AI~~AL~~i~   96 (160)
                      .+++|+|+|. .   +-|+.+|.....   ..       -|+.  ...|+=+-||+|+..|.+++.
T Consensus        81 ~L~~F~DAS~-~---aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~  142 (159)
T PF05380_consen   81 ELHVFCDASE-S---AYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLAN  142 (159)
T ss_pred             eeeEeecccc-c---ceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHH
Confidence            5899999998 2   245556664311   11       1222  245999999999999999873

>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=87.08  E-value=1.2  Score=37.67  Aligned_cols=89  Identities=17%  Similarity=0.085  Sum_probs=53.0

Q ss_pred             eEEEEeeCCCCCCCCCeEEEEEEecccceeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhhccCC
Q psy7630          43 WLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMNSVH  122 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~GaG~gi~~~~~~~~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI~~~~  122 (160)
                      --.||+|+.-      .|.|+.+......+....--.++.||+.|...|--++      ..++ |.|||-.++..=   .
T Consensus        94 lc~VfaDATp------Tgwgi~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~------~~r~-l~tDnt~Vlsrk---y  157 (245)
T PF00336_consen   94 LCQVFADATP------TGWGISITGQRMRGTFSKPLPIHTAELLAACLARLMS------GARC-LGTDNTVVLSRK---Y  157 (245)
T ss_pred             CCceeccCCC------CcceeeecCceeeeeecccccchHHHHHHHHHHHhcc------CCcE-EeecCcEEEecc---c
Confidence            4689999987      2333333222222333334569999999998887766      2344 999999887432   2


Q ss_pred             CCCchhhh-hhhHHHHHHhhhccceeeccccCc
Q psy7630         123 LNSCPALE-ASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       123 ~~~~~~~~-~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      .+=+|-+. +++.       .+..+.|-+||-.
T Consensus       158 ts~PW~lac~A~w-------iLrgts~~yVPS~  183 (245)
T PF00336_consen  158 TSFPWLLACAANW-------ILRGTSFYYVPSK  183 (245)
T ss_pred             ccCcHHHHHHHHH-------hhcCceEEEeccc
Confidence            22244222 2233       3456778888753

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

ID	Length	Definition	E-value
Query	160
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	7e-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 = 39.6 bits (93), Expect = 7e-05
 Identities = 17/76 (22%), Positives = 25/76 (32%), Gaps = 10/76 (13%)

Query: 44  LHIYTDGSLINPEDGAGAGIFC-----ELFSFYKRLGTFTT--NFDGEIAAIKIALLQIL 96
             +YTDGS +N +                 +   +     T  N  GEIAA   A+ +  
Sbjct: 7   YDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKAS 66

Query: 97  NRTNQFERAVILSDSK 112
                  +  IL D  
Sbjct: 67  QLG---VKIRILHDYA 79

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	160
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.8
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.77
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.77
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.76
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.76
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.76
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.74
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.74
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.73
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.73
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.7
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.7
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.62
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.62
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.55
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.53
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	93.75

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

Probab=99.80  E-value=2.2e-19  Score=137.10  Aligned_cols=109  Identities=22%  Similarity=0.179  Sum_probs=80.9

Q ss_pred             CeEEEEeeCCCC-CCCCC--eEEEEEEeccc---ceeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHH
Q psy7630          42 DWLHIYTDGSLI-NPEDG--AGAGIFCELFS---FYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAI  115 (160)
Q Consensus        42 ~~i~IYTDGSk~-ng~~G--aG~gi~~~~~~---~~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI  115 (160)
                      +.+.||||||+. |+++|  +|+|+++....   .+.++++.+||++||+.|++.||+.+.+  ....++.|+|||++++
T Consensus         6 ~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~--~~~~~v~i~tDS~~vi   83 (154)
T 2qkb_A            6 DFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKT--QNINKLVLYTNSMFTI   83 (154)
T ss_dssp             TEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHH--TTCCEEEEEESCHHHH
T ss_pred             CeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHh--CCCceEEEEECcHHHH
Confidence            579999999995 44443  78898875422   3556776799999999999999999964  2346899999999999


Q ss_pred             HhhccC---------CCCCc---hhhhhhhHHHHHHhhhccceeeccccCc
Q psy7630         116 HPMNSV---------HLNSC---PALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       116 ~aI~~~---------~~~~~---~~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      ++|++|         ..+..   .-.+.-++|..++..  .+|+|.||||.
T Consensus        84 ~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~--~~v~~~~V~~H  132 (154)
T 2qkb_A           84 NGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQG--MDIQWMHVPGH  132 (154)
T ss_dssp             HHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTT--CEEEEEECCTT
T ss_pred             hhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcC--CceEEEEccCC
Confidence            999874         22221   112345566666654  36999999984

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

Probab=99.77  E-value=1.3e-18  Score=127.84  Aligned_cols=108  Identities=21%  Similarity=0.107  Sum_probs=77.2

Q ss_pred             eEEEEeeCCCCCCCCC-eEEEEEEeccc-c-----eeecCCCcchHHHHHHHHHHHHHHHHhhcCCCC----cEEEEcCc
Q psy7630          43 WLHIYTDGSLINPEDG-AGAGIFCELFS-F-----YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFE----RAVILSDS  111 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~G-aG~gi~~~~~~-~-----~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~----~i~I~SDS  111 (160)
                      .+.||||||+. +++| +|+|+++...+ .     +..+ +.+||++||+.|++.||+++.+.  ...    ++.|+|||
T Consensus         3 ~~~iy~DGs~~-~n~g~~G~G~v~~~~~g~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~--~~~~~~~~v~i~tDS   78 (140)
T 3u3g_D            3 KIIIYTDGGAR-GNPGPAGIGVVITDEKGNTLHESSAYI-GETTNNVAEYEALIRALEDLQMF--GDKLVDMEVEVRMDS   78 (140)
T ss_dssp             EEEEEEEEEES-STTEEEEEEEEEECTTSCEEEEEEEEE-EEECHHHHHHHHHHHHHHHHGGG--GGGGTTCEEEEEESC
T ss_pred             eEEEEEecCCC-CCCCCcEEEEEEEeCCCCEEEEEEeeC-CCCchHHHHHHHHHHHHHHHHHc--CCCCCCceEEEEeCh
Confidence            58999999994 5566 78898885422 1     2223 34899999999999999999542  234    89999999


Q ss_pred             HHHHHhhccCCC-CCchhhhhhhHHHHHHhhhccceeeccccCc
Q psy7630         112 KAAIHPMNSVHL-NSCPALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       112 qsaI~aI~~~~~-~~~~~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      +++++.|+++.. .........+.|..++.+...+|+|.|||+.
T Consensus        79 ~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~~  122 (140)
T 3u3g_D           79 ELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPRE  122 (140)
T ss_dssp             HHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCGG
T ss_pred             HHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCch
Confidence            999999988532 2222233445566551334469999999953

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

Probab=99.77  E-value=5.3e-19  Score=133.50  Aligned_cols=105  Identities=21%  Similarity=0.133  Sum_probs=75.4

Q ss_pred             CeEEEEeeCCCCCCCCC-eEEEEEEecccc----eeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHH
Q psy7630          42 DWLHIYTDGSLINPEDG-AGAGIFCELFSF----YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIH  116 (160)
Q Consensus        42 ~~i~IYTDGSk~ng~~G-aG~gi~~~~~~~----~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~  116 (160)
                      +.+.||||||+. +++| +|+|+++...+.    +..+ +.+||++||+.|++.||+.+.+    ..++.|+|||+++++
T Consensus         3 ~~i~iytDGs~~-~n~g~~g~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~----~~~v~I~tDS~~vi~   76 (146)
T 3h08_A            3 KTITIYTDGAAS-GNPGKGGWGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALKE----PARVQLYSDSAYLVN   76 (146)
T ss_dssp             CEEEEEEEEEES-STTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS----CCEEEEEESCHHHHH
T ss_pred             ceEEEEEecCCC-CCCCceEEEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcCc----cCcEEEEeChHHHHH
Confidence            369999999994 5556 788988755432    2233 3589999999999999999842    468999999999999


Q ss_pred             hhcc-C---------CCCCc---hhhhhhhHHHHHHhhhccceeeccccCc
Q psy7630         117 PMNS-V---------HLNSC---PALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       117 aI~~-~---------~~~~~---~~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      +|++ |         ..+..   .-.+.-+.|..++...  +|+|.||||-
T Consensus        77 ~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~--~v~~~~V~gH  125 (146)
T 3h08_A           77 AMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLH--RVTFHKVKGH  125 (146)
T ss_dssp             HHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHHS--EEEEEECCC-
T ss_pred             HHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhhC--ceEEEEcCCc
Confidence            9988 3         11111   1134555666666543  7999999975

>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=99.76  E-value=1.2e-18  Score=136.62  Aligned_cols=105  Identities=21%  Similarity=0.221  Sum_probs=72.8

Q ss_pred             eEEEEeeCCCCCCCCC-eEEEEEEecccc---eeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhh
Q psy7630          43 WLHIYTDGSLINPEDG-AGAGIFCELFSF---YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPM  118 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~G-aG~gi~~~~~~~---~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI  118 (160)
                      .+.||||||+. +++| +|+|+++...+.   ...++..+|||+||+.|++.||+++ +    ..++.|+|||++++++|
T Consensus        23 ~i~iytDGs~~-~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~-~----~~~v~I~tDS~~vi~~i   96 (165)
T 3p1g_A           23 DYTWYTDGSSF-LQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA-E----GKKLNVYTDSRYAFATA   96 (165)
T ss_dssp             SEEEEEEEEEE-EETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT-B----TSEEEEEECCHHHHHHH
T ss_pred             CEEEEEEcccC-CCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc-c----CceEEEEEchHHHHhhh
Confidence            48999999994 5567 677776644332   2245677999999999999999988 2    46899999999999999


Q ss_pred             ccCCCCCchhhhhhhHHHHHHhh--hccceeeccccCcc
Q psy7630         119 NSVHLNSCPALEASNDIVGTLCS--VLNKIKTNCCPYSR  155 (160)
Q Consensus       119 ~~~~~~~~~~~~~~~~I~~~~~~--~~~~~~~~~~p~~~  155 (160)
                        |.............+..++..  ...+|+|.||||-.
T Consensus        97 --w~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~  133 (165)
T 3p1g_A           97 --HVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQ  133 (165)
T ss_dssp             --HSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSC
T ss_pred             --hcccCCCcccCHHHHHHHHHHHhcCCceEEEEecCCC
Confidence              422222111111113333222  45789999999854

>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=99.76  E-value=4.7e-18  Score=125.71  Aligned_cols=107  Identities=19%  Similarity=0.147  Sum_probs=76.8

Q ss_pred             eEEEEeeCCCCCCCCC-eEEEEEEeccc-------ceeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHH
Q psy7630          43 WLHIYTDGSLINPEDG-AGAGIFCELFS-------FYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAA  114 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~G-aG~gi~~~~~~-------~~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsa  114 (160)
                      .+.||||||+ .+++| +|+|+++...+       ....+ +.+||++||+.|++.||+++.+.  ...++.|+|||+++
T Consensus         3 ~~~iy~DGs~-~~~~g~~g~G~v~~~~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~--~~~~v~i~tDS~~v   78 (141)
T 3hst_B            3 KVVIEADGGS-RGNPGPAGYGAVVWTADHSTVLAESKQAI-GRATNNVAEYRGLIAGLDDAVKL--GATEAAVLMDSKLV   78 (141)
T ss_dssp             EEEEEEEEEE-SSSSEEEEEEEEEEETTSCSEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHH--TCSEEEEEESCHHH
T ss_pred             EEEEEEecCC-CCCCCCcEEEEEEEeCCCCcEEEeeeccC-CCCchHHHHHHHHHHHHHHHHHC--CCceEEEEeChHHH
Confidence            5899999999 46667 78888775432       12223 36899999999999999999653  24689999999999


Q ss_pred             HHhhcc-CCCCCchhhhhhhHHHHHHhhhccceeeccccCc
Q psy7630         115 IHPMNS-VHLNSCPALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       115 I~aI~~-~~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      ++.|++ |..........-+.|..++. ...+|+|.|||+.
T Consensus        79 v~~i~~~~~~~~~~l~~~~~~i~~l~~-~~~~v~~~~V~~~  118 (141)
T 3hst_B           79 VEQMSGRWKVKHPDLLKLYVQAQALAS-QFRRINYEWVPRA  118 (141)
T ss_dssp             HHHHTTSSCCCSHHHHHHHHHHHHHHT-TSSEEEEEECCGG
T ss_pred             HHHHhCCcccCCHHHHHHHHHHHHHHh-cCCeEEEEEcCCc
Confidence            999987 33333222233345555543 3468999999963

>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=99.76  E-value=2.6e-18  Score=132.24  Aligned_cols=108  Identities=24%  Similarity=0.174  Sum_probs=74.5

Q ss_pred             CCCCeEEEEeeCCCCCCCCC-eEEEEEEeccc-ceeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHH
Q psy7630          39 PSDDWLHIYTDGSLINPEDG-AGAGIFCELFS-FYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIH  116 (160)
Q Consensus        39 ~~~~~i~IYTDGSk~ng~~G-aG~gi~~~~~~-~~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~  116 (160)
                      +..+.+.||||||+. +++| .|+|+++.... ....+ +.+||++||+.|++.||+.+      ..++.|+|||+++++
T Consensus         8 P~~~~~~iytDGs~~-~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~------~~~v~i~tDS~~v~~   79 (150)
T 3qio_A            8 PIVGAETFYVDGAAN-RETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS------GLEVNIVTDSQYALG   79 (150)
T ss_dssp             CCTTCEEEEEEEEEC-TTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS------CSEEEEEESCHHHHH
T ss_pred             CCCCCEEEEEccCCC-CCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC------CCcEEEEeCcHHHHH
Confidence            334579999999994 5555 57787764432 23344 45999999999999999975      368999999999999


Q ss_pred             hhccCC---------CCCc---hhhhhhhHHHHHHhhhccceeeccccCcc
Q psy7630         117 PMNSVH---------LNSC---PALEASNDIVGTLCSVLNKIKTNCCPYSR  155 (160)
Q Consensus       117 aI~~~~---------~~~~---~~~~~~~~I~~~~~~~~~~~~~~~~p~~~  155 (160)
                      +|++|-         ....   .-.+.-+.|...+. ...+|+|.||||..
T Consensus        80 ~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~-~~~~v~~~wV~gH~  129 (150)
T 3qio_A           80 IITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLI-KKEKVYLAWVPAHK  129 (150)
T ss_dssp             HHHHHHHHHCC------------CHHHHHHHHHHHT-TCSEEEEEECCTTS
T ss_pred             HHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHh-hcCceEEEEccCcC
Confidence            999861         1111   11122333333332 35789999999964

>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=99.74  E-value=2.3e-18  Score=132.19  Aligned_cols=104  Identities=19%  Similarity=0.171  Sum_probs=75.3

Q ss_pred             eEEEEeeCCCCCCCCC-eEEEEEEecccc----eeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHh
Q psy7630          43 WLHIYTDGSLINPEDG-AGAGIFCELFSF----YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHP  117 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~G-aG~gi~~~~~~~----~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~a  117 (160)
                      .+.||||||+. +++| +|+|+++...+.    +..+ +.+||++||+.|++.||+.+.+    ..++.|+|||++++++
T Consensus         4 ~~~iytDGs~~-~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~----~~~v~I~tDS~~vi~~   77 (155)
T 1jl1_A            4 QVEIFTAGSAL-GNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE----HAEVILSTDSQYVRQG   77 (155)
T ss_dssp             CEEEEEEEEES-STTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS----CCEEEEEECCHHHHHH
T ss_pred             eEEEEEccccC-CCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc----CCcEEEEeCHHHHHHH
Confidence            58999999994 5566 788888754332    2223 3589999999999999999842    3689999999999999


Q ss_pred             hccC---------CCCCch---hhhhhhHHHHHHhhhccceeeccccCc
Q psy7630         118 MNSV---------HLNSCP---ALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       118 I~~~---------~~~~~~---~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      |++|         ..+...   -.+.-+.|..++..  .+|+|.||||-
T Consensus        78 i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~--~~v~~~wV~gH  124 (155)
T 1jl1_A           78 ITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQ--HQIKWEWVKGH  124 (155)
T ss_dssp             HHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTT--CEEEEEECCSS
T ss_pred             HHHHHHHHhhcccccccCCccCCHHHHHHHHHHHcc--CceEEEEcCCC
Confidence            9973         222111   12344556666643  48999999975

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

Probab=99.74  E-value=1e-17  Score=126.39  Aligned_cols=108  Identities=16%  Similarity=0.102  Sum_probs=79.3

Q ss_pred             eEEEEeeCCCCCCCCC-eEE-EEEEecccce---e--ecC---CCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcH
Q psy7630          43 WLHIYTDGSLINPEDG-AGA-GIFCELFSFY---K--RLG---TFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSK  112 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~G-aG~-gi~~~~~~~~---~--~L~---~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSq  112 (160)
                      ++.||||||+..+++| +|+ |+++...+..   +  .++   +.+||++||+.|++.||+.+.+.  ...++.|+|||+
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 MIIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRL--GISSPIIKGDSQ   78 (149)
T ss_dssp             CCEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHH--TCCSCEEEESCH
T ss_pred             CEEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHc--CCCEEEEEeChH
Confidence            3689999999424555 775 8877553321   1  222   37899999999999999999653  245899999999


Q ss_pred             HHHHhhccC-CCCCchhhhhhhHHHHHHhhhccceeeccccCc
Q psy7630         113 AAIHPMNSV-HLNSCPALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       113 saI~aI~~~-~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      ++++.|+++ ..+...-...-+.|..++...  +++|.|||+.
T Consensus        79 ~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~--~v~~~~V~~~  119 (149)
T 2ehg_A           79 LVIKQMNGEYKVKAKRIIPLYEKAIELKKKL--NATLIWVPRE  119 (149)
T ss_dssp             HHHHHHTTSSCCCCTTHHHHHHHHHHHHHHH--TCEEEECCGG
T ss_pred             HHHHHHhCccccCCHHHHHHHHHHHHHHhcC--CEEEEEcCCc
Confidence            999999886 334344445566777777655  6999999984

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

Probab=99.73  E-value=5.1e-18  Score=130.79  Aligned_cols=104  Identities=20%  Similarity=0.192  Sum_probs=75.0

Q ss_pred             eEEEEeeCCCCCCCCC-eEEEEEEecccc----eeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHh
Q psy7630          43 WLHIYTDGSLINPEDG-AGAGIFCELFSF----YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHP  117 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~G-aG~gi~~~~~~~----~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~a  117 (160)
                      .+.||||||+. +++| +|+|+++...+.    +..+ +.+||++||+.|++.||+.+.+    ..++.|+|||++++++
T Consensus         6 ~i~iytDGs~~-~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~----~~~v~I~tDS~~vi~~   79 (158)
T 2e4l_A            6 LIHIFTDGSCL-GNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKE----PCKIILTSDSQYMRQG   79 (158)
T ss_dssp             EEEEEEEEEES-SSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS----CCEEEEEECCHHHHHH
T ss_pred             eEEEEEccccc-CCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhcc----CCeEEEEeCHHHHHHH
Confidence            58999999994 5556 788988754332    2233 3489999999999999998832    2689999999999999


Q ss_pred             hcc---------CCCCCc--h-hhhhhhHHHHHHhhhccceeeccccCc
Q psy7630         118 MNS---------VHLNSC--P-ALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       118 I~~---------~~~~~~--~-~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      |++         |.....  . -.+.-+.|..++..  .+|+|.||||-
T Consensus        80 i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~--~~v~~~wV~gH  126 (158)
T 2e4l_A           80 IMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQL--HQIDWRWVKGH  126 (158)
T ss_dssp             HHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTT--SEEEEEECCTT
T ss_pred             HHHHHHHHHHccccccCCCcccCHHHHHHHHHHHcc--CcEEEEEccCC
Confidence            988         322211  1 11334566666654  48999999975

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

Probab=99.73  E-value=3.2e-18  Score=133.21  Aligned_cols=105  Identities=14%  Similarity=0.145  Sum_probs=75.5

Q ss_pred             eEEEEeeCCCCCCCCC-eEEEEEEecccceeecC---CCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhh
Q psy7630          43 WLHIYTDGSLINPEDG-AGAGIFCELFSFYKRLG---TFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPM  118 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~G-aG~gi~~~~~~~~~~L~---~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI  118 (160)
                      .+.||||||+. +++| +|+|+++...+....+.   +.+||++||+.|++.||+.+.+    ..++.|+|||++++++|
T Consensus         8 ~i~iytDGs~~-~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~----~~~v~I~tDS~~vi~~i   82 (166)
T 1ril_A            8 RVALFTDGACL-GNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE----PCEVDLYTDSHYLKKAF   82 (166)
T ss_dssp             CCCEEEEEEES-STTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS----CCEEEEECCCHHHHHHH
T ss_pred             cEEEEECcccc-CCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHhcc----CCeEEEEeChHHHHHHH
Confidence            58899999994 5556 78898885433211111   3589999999999999998732    25899999999999999


Q ss_pred             cc----------CCCCCch---hhhhhhHHHHHHhhhccceeeccccCc
Q psy7630         119 NS----------VHLNSCP---ALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       119 ~~----------~~~~~~~---~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      ++          |..+...   -.+.-+.|..++..  .+|+|.||||-
T Consensus        83 ~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~--~~v~~~wV~gH  129 (166)
T 1ril_A           83 TEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP--HRVRFHFVKGH  129 (166)
T ss_dssp             HSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTT--SEEECCCCCGG
T ss_pred             hhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhc--CeEEEEEeeCC
Confidence            98          4332221   12345566666654  48999999975

>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=99.70  E-value=1.3e-17  Score=127.22  Aligned_cols=103  Identities=17%  Similarity=0.023  Sum_probs=71.5

Q ss_pred             CeEEEEeeCCCCCCCCC-eEEEEEEecccc----ee-ec--CC--CcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCc
Q psy7630          42 DWLHIYTDGSLINPEDG-AGAGIFCELFSF----YK-RL--GT--FTTNFDGEIAAIKIALLQILNRTNQFERAVILSDS  111 (160)
Q Consensus        42 ~~i~IYTDGSk~ng~~G-aG~gi~~~~~~~----~~-~L--~~--~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDS  111 (160)
                      +.+.||||||+.+   | +|+|+++...+.    +. .+  +.  .+|||+||+.|++.||+++++. . . ++.|+|||
T Consensus         5 ~~i~iytDGs~~~---g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~-~-~-~v~I~tDS   78 (147)
T 2kq2_A            5 TEYDVYTDGSYVN---GQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQL-G-V-KIRILHDY   78 (147)
T ss_dssp             SCCEEECCCCCBT---TBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHH-T-C-CCCBSSCC
T ss_pred             CeEEEEECCCCCC---CCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHC-C-C-eEEEEECc
Confidence            4689999999954   4 788888754332    22 22  22  3699999999999999988654 2 3 89999999


Q ss_pred             HHHHHhhcc-CCCCCchhhhhhhHHHHHHhhhccceeeccccCc
Q psy7630         112 KAAIHPMNS-VHLNSCPALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       112 qsaI~aI~~-~~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      +.+.+-+.+ |..+..    ..+....++.....+|+|.||||-
T Consensus        79 ~~i~~w~~~~w~~~~~----~~~~~~~l~~~l~~~v~~~wV~gH  118 (147)
T 2kq2_A           79 AGIAFWATGEWKAKNE----FTQAYAKLMNQYRGIYSFEKVKAH  118 (147)
T ss_dssp             STHHHHTTSSSSCCHH----HHHHHHCGGGGGSTTCCBCCCCCC
T ss_pred             HHHHHHHhCCCccCCc----chHHHHHHHHHhcCCeeEEEecCc
Confidence            987776643 333322    233444445554559999999984

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

Probab=99.70  E-value=5.7e-17  Score=127.31  Aligned_cols=108  Identities=23%  Similarity=0.178  Sum_probs=71.4

Q ss_pred             eEEEEeeCCCC-CCCCC----eEEEEEEeccc------ceeecC-CCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcC
Q psy7630          43 WLHIYTDGSLI-NPEDG----AGAGIFCELFS------FYKRLG-TFTTNFDGEIAAIKIALLQILNRTNQFERAVILSD  110 (160)
Q Consensus        43 ~i~IYTDGSk~-ng~~G----aG~gi~~~~~~------~~~~L~-~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SD  110 (160)
                      .+.|||||||. ||.+.    +|+||++...+      ..+..+ +..++++||+.|+..||+.+++.   ..++.|+||
T Consensus         7 evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~---~~~v~I~TD   83 (165)
T 2lsn_A            7 EGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKI---PGPVLVITD   83 (165)
T ss_dssp             SEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHS---SSCEEEEES
T ss_pred             eEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcC---CCeEEEEeC
Confidence            48899999996 54431    78999875332      122322 45778888888888888877542   357999999


Q ss_pred             cHHHHHhhccC---------CCCCchh---hhhhhHHHHHHhhhccceeeccccCc
Q psy7630         111 SKAAIHPMNSV---------HLNSCPA---LEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       111 SqsaI~aI~~~---------~~~~~~~---~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      |+|++++|+.|         ......+   .+.-+.+..+++ ..++|+|.||||-
T Consensus        84 S~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~-~~~~v~~~~VkgH  138 (165)
T 2lsn_A           84 SFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLS-MKPDITIQHEKGH  138 (165)
T ss_dssp             CHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHH-HCTTCEEEECCSS
T ss_pred             hHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHh-CCCCEEEEEEeCC
Confidence            99999999864         2221111   122233444442 3468999999985

>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=99.62  E-value=9.6e-16  Score=137.78  Aligned_cols=102  Identities=25%  Similarity=0.239  Sum_probs=75.9

Q ss_pred             CeEEEEeeCCCCCCCCC-eEEEEEEecccc-eeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhhc
Q psy7630          42 DWLHIYTDGSLINPEDG-AGAGIFCELFSF-YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMN  119 (160)
Q Consensus        42 ~~i~IYTDGSk~ng~~G-aG~gi~~~~~~~-~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI~  119 (160)
                      +.+.||||||+ ++++| +|+|+++...+. ...+ ..+|||+||+.|++.||+.      ...++.|+|||++++++|+
T Consensus       435 ~~~~iytDGs~-~~n~g~~g~G~v~~~~~~~~~~~-~~~TNn~aEl~A~i~aL~~------~~~~v~I~tDS~~v~~~i~  506 (555)
T 1mu2_A          435 GAETFYTDGSC-NRQSKEGKAGYVTDRGKDKVKKL-EQTTNQQAELEAFAMALTD------SGPKVNIIVDSQYVMGIVA  506 (555)
T ss_dssp             TCEEEEEEEEE-CTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHT------SCSEEEEEESCHHHHHHHH
T ss_pred             CceEEEEcccc-cCCCCCceEEEEEEeCCEeeccC-CCCCHHHHHHHHHHHHHHc------CCCeEEEEEehHHHHHHHh
Confidence            46999999999 45555 577877744332 3333 3589999999999999997      2468999999999999999


Q ss_pred             cCCCCCchhhhhhhHHHHHHhhhccceeeccccCc
Q psy7630         120 SVHLNSCPALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       120 ~~~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      +|......  ..-+.+..++.. ..+|.+.||||-
T Consensus       507 ~~~~~~~~--~l~~~~~~~~~~-~~~v~~~wV~~H  538 (555)
T 1mu2_A          507 SQPTESES--KIVNQIIEEMIK-KEAIYVAWVPAH  538 (555)
T ss_dssp             TCCSEESC--HHHHHHHHHHHH-CSEEEEEECCSS
T ss_pred             cccccccH--HHHHHHHHHhcc-CCcEEEEEEECC
Confidence            98654443  344455555444 468999999994

>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=99.62  E-value=8.9e-16  Score=138.05  Aligned_cols=102  Identities=27%  Similarity=0.207  Sum_probs=75.6

Q ss_pred             CeEEEEeeCCCCCCCCC-eEEEEEEeccc-ceeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhhc
Q psy7630          42 DWLHIYTDGSLINPEDG-AGAGIFCELFS-FYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMN  119 (160)
Q Consensus        42 ~~i~IYTDGSk~ng~~G-aG~gi~~~~~~-~~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI~  119 (160)
                      +.+.||||||+ ++++| +|+|+++.... ..+.+ ..+|||+||+.|++.||+.+      ..++.|+|||++++++|+
T Consensus       438 ~~~~iytDGs~-~~n~g~~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~------~~~v~I~tDS~~vi~~i~  509 (557)
T 2zd1_A          438 GAETFYVDGAA-NRETKLGKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS------GLEVNIVTDSQYALGIIQ  509 (557)
T ss_dssp             TSCEEEEEEEE-CTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS------CSEEEEEECCHHHHHHHT
T ss_pred             CCEEEEEccCC-CCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC------CCcEEEEeChHHHHHHHh
Confidence            46899999999 45555 57777764322 22333 45899999999999999987      358999999999999999


Q ss_pred             cCCCCCchhhhhhhHHHHHHhhhccceeeccccCc
Q psy7630         120 SVHLNSCPALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       120 ~~~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      +|...+..  +.-+.+...+.. ..+|++.||||.
T Consensus       510 ~~~~~~~~--~l~~~~~~~l~~-~~~v~~~wV~~H  541 (557)
T 2zd1_A          510 AQPDKSES--ELVNQIIEQLIK-KEKVYLAWVPAH  541 (557)
T ss_dssp             TCCSEESS--HHHHHHHHHHHH-CSEEEEEECCSS
T ss_pred             cCCccCCH--HHHHHHHHHHhc-CCCEEEEEcCCC
Confidence            98654333  334455544544 358999999994

>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=99.55  E-value=1.8e-15  Score=116.06  Aligned_cols=75  Identities=23%  Similarity=0.158  Sum_probs=56.6

Q ss_pred             eEEEEeeCCCCCCCCC-eEEEEEEecccc----eeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHh
Q psy7630          43 WLHIYTDGSLINPEDG-AGAGIFCELFSF----YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHP  117 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~G-aG~gi~~~~~~~----~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~a  117 (160)
                      ...||||||| .|+|| +|+|.++...+.    ...+ +.+|||+||+.|++.||+.+.+.   ..++.|+||||++++-
T Consensus         5 ~~~iytDGac-~GNPGp~G~ggV~~~~g~~~~~~g~~-~~tTNN~aEl~A~i~aL~~l~~~---~~~v~i~tDSqyVi~w   79 (134)
T 4htu_A            5 WESLSVDVGS-QGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKER---NSRKPIYSNSQTAIKW   79 (134)
T ss_dssp             SSSEEEEEEE-ETTTEEEEEEEEETTTCCEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHT---TCCCCEEESCHHHHHH
T ss_pred             ceEEEEeecc-CCCCCCeEEEEEEEECCEEEEEecCC-CCCchHHHHHHHHHHHHHHHHhC---CCCEEEEcchHHHHHH
Confidence            5789999999 47888 777454433332    2222 26899999999999999999642   2248999999999999


Q ss_pred             hccCC
Q psy7630         118 MNSVH  122 (160)
Q Consensus       118 I~~~~  122 (160)
                      |.++.
T Consensus        80 i~~~~   84 (134)
T 4htu_A           80 VKDKK   84 (134)
T ss_dssp             HHHTC
T ss_pred             HHcCC
Confidence            98753

>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=99.53  E-value=6.8e-15  Score=113.14  Aligned_cols=77  Identities=22%  Similarity=0.107  Sum_probs=60.1

Q ss_pred             CCeEEEEeeCCCCCCCCC-eEEEEEEeccccee----ecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHH
Q psy7630          41 DDWLHIYTDGSLINPEDG-AGAGIFCELFSFYK----RLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAI  115 (160)
Q Consensus        41 ~~~i~IYTDGSk~ng~~G-aG~gi~~~~~~~~~----~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI  115 (160)
                      .+.+.||||||+ .|++| +|+|+++...+...    .++ .+|||+||+.|++.||+.+.+.  .. ++.|+|||++++
T Consensus         9 ~~~~~iy~DGa~-~gNpG~~G~G~vl~~~g~~~~~~~~~~-~~TNN~aEl~A~i~aL~~~~~~--~~-~v~i~tDS~~vi   83 (142)
T 1zbf_A            9 IIWESLSVDVGS-QGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKER--NS-RKPIYSNSQTAI   83 (142)
T ss_dssp             CCSSSEEEEEEE-CSSSEEEEEEEEETTTCCEEEECCCEE-EECHHHHHHHHHHHHHHHHHHT--TC-CCCEEESCHHHH
T ss_pred             CCeEEEEEeecc-CCCCCCeEEEEEEEeCCEEEEEecccC-CcCcHHHHHHHHHHHHHHHHhC--CC-eEEEEEehHHHH
Confidence            347899999999 46778 78999885333221    222 5899999999999999999642  22 899999999999


Q ss_pred             HhhccCC
Q psy7630         116 HPMNSVH  122 (160)
Q Consensus       116 ~aI~~~~  122 (160)
                      +.+++..
T Consensus        84 ~w~~~~~   90 (142)
T 1zbf_A           84 KWVKDKK   90 (142)
T ss_dssp             HHHHHTC
T ss_pred             HHHHcCC
Confidence            9998764

>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=93.75  E-value=0.023  Score=49.37  Aligned_cols=72  Identities=15%  Similarity=0.057  Sum_probs=47.0

Q ss_pred             eEEEEeeCCCCCCCCCeEEEEEEeccc--------ceeecC---CCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCc
Q psy7630          43 WLHIYTDGSLINPEDGAGAGIFCELFS--------FYKRLG---TFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDS  111 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~GaG~gi~~~~~~--------~~~~L~---~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDS  111 (160)
                      .+.+|||+|.  +.  .| ||......        .+.++.   ...+.+..|+.||..|++...... ...++.|+||+
T Consensus       346 ~~~l~~DAS~--~~--~g-avL~q~~~~~~~~i~y~Sk~l~~~e~~ys~~ekEllAi~~a~~~~~~yl-~g~~~~v~tDh  419 (455)
T 1rw3_A          346 PFELFVDEKQ--GY--AK-GVLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLT-MGQPLVIKAPH  419 (455)
T ss_dssp             TTSCEEEEEE--CS--SS-BEECCBCTTTTCCCCCCCBCSCSSCSSSCCSSHHHHHHHHHHHHHHGGG-CSSCEEEECSS
T ss_pred             cEEEEEeccC--Cc--ce-eEEEEecCCcEEEEEEEcccCCccccccchHHHHHHHHHHHHHHHHHHc-CCCcEEEEecC
Confidence            4789999987  22  22 24332211        122333   245788999999999999884333 34689999999


Q ss_pred             HHHHHhhccC
Q psy7630         112 KAAIHPMNSV  121 (160)
Q Consensus       112 qsaI~aI~~~  121 (160)
                      . ++.-+.+.
T Consensus       420 ~-~~~~l~~~  428 (455)
T 1rw3_A          420 A-VEALVKQP  428 (455)
T ss_dssp             C-TTTTSSST
T ss_pred             h-HHHHhCCC
Confidence            7 66666554

---

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	160
d1s1ta1	110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	4e-06
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	2e-04

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

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

 Score = 41.5 bits (97), Expect = 4e-06
 Identities = 21/91 (23%), Positives = 30/91 (32%), Gaps = 6/91 (6%)

Query: 39  PSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNR 98
           P       Y DG+         AG             T TTN   E+ AI +AL      
Sbjct: 4   PIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSG-- 61

Query: 99  TNQFERAVILSDSKAAIHPMNSVHLNSCPAL 129
                   I++DS+ A+  + +    S   L
Sbjct: 62  ----LEVNIVTDSQYALGIIQAQPDQSESEL 88

>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 = 2e-04
 Identities = 19/89 (21%), Positives = 29/89 (32%), Gaps = 6/89 (6%)

Query: 39  PSDDWLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNR 98
           P       YTDGS         AG   +      +    TTN   E+ A        +  
Sbjct: 3   PIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAF------AMAL 56

Query: 99  TNQFERAVILSDSKAAIHPMNSVHLNSCP 127
           T+   +  I+ DS+  +  + S    S  
Sbjct: 57  TDSGPKVNIIVDSQYVMGIVASQPTESES 85

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	160
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.84
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.78
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.72
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.71
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.64

>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=99.84  E-value=3.3e-21  Score=140.69  Aligned_cols=101  Identities=27%  Similarity=0.179  Sum_probs=73.0

Q ss_pred             CeEEEEeeCCCCCCCCC-eEEEEEEeccc-ceeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhhc
Q psy7630          42 DWLHIYTDGSLINPEDG-AGAGIFCELFS-FYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMN  119 (160)
Q Consensus        42 ~~i~IYTDGSk~ng~~G-aG~gi~~~~~~-~~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI~  119 (160)
                      +...+|||||+. +++| +|+|++..... ....+ ..+|||+||+.||++||+..      ..++.|+|||+|++++|+
T Consensus         7 ~~~t~ytDGs~~-~n~~~g~~g~~~~~~~~~~~~~-~~~TNn~aEl~Avi~aL~~~------~~~v~I~TDS~yvi~~i~   78 (110)
T d1s1ta1           7 GAETFYVDGAAN-RETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS------GLEVNIVTDSQYALGIIQ   78 (110)
T ss_dssp             TSEEEEEEEEEE-TTTTEEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS------CSEEEEEECCHHHHHHHH
T ss_pred             CCcEEEEeCCCC-CCCCCcEEEEEEecCCeEEEec-ccCcHHHHHHHHHHHHHHhC------CCeEEEEEehHHHHHHHh
Confidence            356899999984 4445 45666664433 33344 45899999999999999743      357999999999999999


Q ss_pred             cCCCCCchhhhhhhHHHHHHhhhccceeeccccC
Q psy7630         120 SVHLNSCPALEASNDIVGTLCSVLNKIKTNCCPY  153 (160)
Q Consensus       120 ~~~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~p~  153 (160)
                      .+......  ..-.+|...+. ..++|.+.||||
T Consensus        79 ~~~~~~~~--~l~~~il~~l~-~~~~v~i~WVpg  109 (110)
T d1s1ta1          79 AQPDQSES--ELVNQIIEQLI-KKEKVYLAWVPA  109 (110)
T ss_dssp             HCCSEESC--HHHHHHHHHHH-HCSEEEEEECCS
T ss_pred             cCccccch--HHHHHHHHHHh-cCCceEEEEeCC
Confidence            88654433  33345555553 368999999998

>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=99.78  E-value=3.5e-19  Score=130.34  Aligned_cols=102  Identities=24%  Similarity=0.158  Sum_probs=72.1

Q ss_pred             eEEEEeeCCCCCCCCC-eEEEEEEecccc-eeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhhcc
Q psy7630          43 WLHIYTDGSLINPEDG-AGAGIFCELFSF-YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMNS  120 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~G-aG~gi~~~~~~~-~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI~~  120 (160)
                      ...||||||+. +++| +|+|+++..... ...++ .+||++||+.||++||++.      ..++.|+|||+++++.+++
T Consensus         7 ~~t~YTDGS~~-~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~~------~~~i~I~tDS~~v~~~~~~   78 (126)
T d1mu2a1           7 AETFYTDGSCN-RQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTDS------GPKVNIIVDSQYVMGIVAS   78 (126)
T ss_dssp             CEEEEEEEEEC-TTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHTS------CSEEEEEESCHHHHHHHHT
T ss_pred             CcEEEEcCCCC-CCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhccC------CcceEEEechHHHHHHHhc
Confidence            57899999984 3334 566766655443 34444 5899999999999998753      4579999999999999998


Q ss_pred             CCCCCchhhhhhhHHHHHHhhhccceeeccccCcc
Q psy7630         121 VHLNSCPALEASNDIVGTLCSVLNKIKTNCCPYSR  155 (160)
Q Consensus       121 ~~~~~~~~~~~~~~I~~~~~~~~~~~~~~~~p~~~  155 (160)
                      +...... ....+.|..+..  ..+|.|.||||-.
T Consensus        79 ~~~~~~~-~~~~~~~~~~~~--~~~v~~~wV~gH~  110 (126)
T d1mu2a1          79 QPTESES-KIVNQIIEEMIK--KEAIYVAWVPAHK  110 (126)
T ss_dssp             CCSEESC-HHHHHHHHHHHH--CSEEEEEECCSSS
T ss_pred             CCccccc-hHHHHHHHHhhh--cceeEEEEEeCCC
Confidence            7543322 123344444443  3589999999853

>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=99.72  E-value=4.8e-18  Score=126.31  Aligned_cols=105  Identities=13%  Similarity=0.124  Sum_probs=71.8

Q ss_pred             eEEEEeeCCCCCCCCC-eEEEEEEecccc---eeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhh
Q psy7630          43 WLHIYTDGSLINPEDG-AGAGIFCELFSF---YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPM  118 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~G-aG~gi~~~~~~~---~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI  118 (160)
                      .+.||||||+. +++| +|+|+++...+.   .....+.+||++||+.||++||+++.    ....+.|+|||++++++|
T Consensus         3 ~i~iytDGs~~-~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~----~~~~i~i~tds~~~~~~~   77 (147)
T d1rila_           3 RVALFTDGACL-GNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALK----EPCEVDLYTDSHYLKKAF   77 (147)
T ss_dssp             CCCEEEEEEES-STTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCC----SCCEEEEECCCHHHHHHH
T ss_pred             EEEEEEccCCC-CCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhcc----CCceEEEecchhhhhccc
Confidence            58999999996 4556 678887744331   22223457999999999999998762    245799999999999998


Q ss_pred             ccCCC-----CCch--------hhhhhhHHHHHHhhhccceeeccccCc
Q psy7630         119 NSVHL-----NSCP--------ALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       119 ~~~~~-----~~~~--------~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      ..+..     +...        -.+.-+.|..++  ..++|+|.||||-
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~--~~~~v~~~wVkgH  124 (147)
T d1rila_          78 TEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAM--APHRVRFHFVKGH  124 (147)
T ss_dssp             HSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH--TTSEEECCCCCGG
T ss_pred             cccchhhhhhccccccccccchhHHHHHHHHHHh--hhcccceEEccCC
Confidence            76421     1110        012234454444  3568999999985

>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=99.71  E-value=4.7e-18  Score=125.61  Aligned_cols=105  Identities=19%  Similarity=0.154  Sum_probs=72.9

Q ss_pred             eEEEEeeCCCCCCCCC-eEEEEEEeccc--c-eeecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhh
Q psy7630          43 WLHIYTDGSLINPEDG-AGAGIFCELFS--F-YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPM  118 (160)
Q Consensus        43 ~i~IYTDGSk~ng~~G-aG~gi~~~~~~--~-~~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI  118 (160)
                      .++||||||+. +++| +|+|+++...+  . .....+.+||++||+.||+.||+++.    ....+.|+|||++++..+
T Consensus         2 ~I~IYtDGS~~-~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~----~~~~i~i~tds~~~i~~~   76 (152)
T d1jl1a_           2 QVEIFTAGSAL-GNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALK----EHAEVILSTDSQYVRQGI   76 (152)
T ss_dssp             CEEEEEEEEES-STTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCC----SCCEEEEEECCHHHHHHH
T ss_pred             EEEEEEeCCCC-CCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhc----ccceEEEeecceeeEEcc
Confidence            58999999995 5556 78898875443  1 11222458999999999999999873    245699999999999999


Q ss_pred             ccCCC---------CCc---hhhhhhhHHHHHHhhhccceeeccccCc
Q psy7630         119 NSVHL---------NSC---PALEASNDIVGTLCSVLNKIKTNCCPYS  154 (160)
Q Consensus       119 ~~~~~---------~~~---~~~~~~~~I~~~~~~~~~~~~~~~~p~~  154 (160)
                      ..+..         ...   .-.+..+.|..++.  ..+|+|+||||-
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~--~~~V~~~wV~gH  122 (152)
T d1jl1a_          77 TQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQIKWEWVKGH  122 (152)
T ss_dssp             HTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT--TCEEEEEECCSS
T ss_pred             cchhhHhHhccchhcccCeeecHHHHHHHHHHhh--cceeEEEEeccc
Confidence            76521         000   11223444544443  348999999985

>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=99.64  E-value=8.1e-17  Score=121.66  Aligned_cols=73  Identities=22%  Similarity=0.119  Sum_probs=57.4

Q ss_pred             EEEeeCCCCCCCCC-eEEEEEEecccc-e---eecCCCcchHHHHHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHhhc
Q psy7630          45 HIYTDGSLINPEDG-AGAGIFCELFSF-Y---KRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIHPMN  119 (160)
Q Consensus        45 ~IYTDGSk~ng~~G-aG~gi~~~~~~~-~---~~L~~~~Sn~~AEl~AI~~AL~~i~~~~~~~~~i~I~SDSqsaI~aI~  119 (160)
                      .||||||| .|+|| +|+|+++...+. .   -.+ +.+|||+||+.|++.||+.+.+.   ..++.|+|||+++++.++
T Consensus         6 sIy~DGa~-~GNPGp~g~g~v~~~~~~~~~~sg~~-~~~TNN~aEl~A~i~aL~~~~~~---~~~i~I~tDS~yvi~wv~   80 (132)
T d1zbfa1           6 SLSVDVGS-QGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKER---NSRKPIYSNSQTAIKWVK   80 (132)
T ss_dssp             SEEEEEEE-CSSSEEEEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHHT---TCCCCEEESCHHHHHHHH
T ss_pred             eEEEeecC-CCCCchheEEEEEEcCCEEEEEEcCc-CccchHHHHHHHHHHHHHHhhcC---CceEEEEeccHHHHHHHH
Confidence            49999999 58889 777877654432 1   122 45899999999999999999542   357999999999999998


Q ss_pred             cCC
Q psy7630         120 SVH  122 (160)
Q Consensus       120 ~~~  122 (160)
                      +|.
T Consensus        81 ~~~   83 (132)
T d1zbfa1          81 DKK   83 (132)
T ss_dssp             HTC
T ss_pred             hCc
Confidence            764