Citrus Sinensis ID: 041278

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-
Protein Sequence
MVLVWFLVMLYVMHIVLKRMLSMSFINAPMHGKYMIVKEIFFWIWELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKRLLPPWFLTHRWNN
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccEEEEEEcccHHHHHHcccccccEEccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEccccccccccEEEccccc
Coil and Loop (DISEMBL)
MVLVWFLVMLYVMHIVLKRMLSmsfinapmhgkYMIVKEIFFWIWELTAFATKLIAIILAIEHASIRDWTMLwiecdspltvhlcnkrllppwflthrwnn
Flexible Loop (DISEMBL)
MVLVWFLVMLYVMHIVLKRMLSMSFINAPMHGKYMIVKEIFFWIWELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKRllppwflthrwnn
Low Complexity Region (SEG)
MVLVWFLVMLYVMHIVLKRMLSMSFINAPMHGKYMIVKEIFFWIWELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKRLLPPWFLTHRWNN
Disordered region (IsUnstruct)
*VLVWFLVMLYVMHIVLKRMLSMSFINAPMHGKYMIVKEIFFWIWELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKRLLPPWFLTHRW**
Disordered Region (DISOPRED)
MVLVWFLVMLYVMHIVLKRMLSMSFINAPMHGKYMIVKEIFFWIWELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKRLLPPWFLTHRWN*
Disordered Region (DISEMBL)
MVLVWFLVMLYVMHIVLKRMLSMSFINAPMHGKYMIVKEIFFWIWELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKRLLPPWFLTHRWNN
Disordered Region (DISPRO)
MVLVWFLVMLYVMHIVLKRMLSMSFINAPMHGKYMIVKEIFFWIWELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKRLLPPWFLTHRWNN
Transmembrane Helix (TMHMM)
iHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSoooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVLVWFLVMLYVMHIVLKRMLSMSFINAPMHGKYMIVKEIFFWIWELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKRLLPPWFLTHRWNN
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 Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

No confident hit detected by STRING

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	101
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	98.43
PRK13907	128	rnhA ribonuclease H; Provisional	97.73
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	97.1
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	96.97
PRK07708	219	hypothetical protein; Validated	96.2
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	95.52
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	94.77
KOG3752	371	consensus Ribonuclease H [Replication, recombinati	94.64
PRK06548	161	ribonuclease H; Provisional	92.31
PRK00203	150	rnhA ribonuclease H; Reviewed	90.04
PRK08719	147	ribonuclease H; Reviewed	88.68
PF11204	81	DUF2985: Protein of unknown function (DUF2985); In	86.86

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

Probab=98.43  E-value=4.6e-07  Score=55.92  Aligned_cols=47  Identities=23%  Similarity=0.188  Sum_probs=38.1

Q ss_pred             hHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhCCCcccccc
Q 041278           49 AFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKRLLPPWFL   95 (101)
Q Consensus        49 aL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn~slVPW~L   95 (101)
                      ++.+|+.|...|++.|.+.|++++++||||+.++.++++..-.+..+
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~   47 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSEL   47 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCC
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccc
Confidence            46899999999999999999999999999999999998886554443

>PRK13907 rnhA ribonuclease H; Provisional

Probab=97.73  E-value=4.4e-05  Score=51.92  Aligned_cols=44  Identities=14%  Similarity=0.242  Sum_probs=41.1

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhCC
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKR   88 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn~   88 (101)
                      +..+...+|+.|.+.|++.|.+.|.+++.+++||++|+..+++.
T Consensus        37 ~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~   80 (128)
T PRK13907         37 GTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE   80 (128)
T ss_pred             cccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHH
Confidence            56789999999999999999999999999999999999999764

>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=97.10  E-value=0.0012  Score=40.71  Aligned_cols=46  Identities=22%  Similarity=0.064  Sum_probs=42.3

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhCCCc
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKRLL   90 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn~sl   90 (101)
                      ...+.+.+|+.|...|++.+.+.+-+++.++|||..++..+++...
T Consensus        37 ~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~~   82 (130)
T cd06222          37 GNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWYE   82 (130)
T ss_pred             CCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcccc
Confidence            4668899999999999999999999999999999999999987643

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.

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

Probab=96.97  E-value=0.001  Score=49.88  Aligned_cols=42  Identities=21%  Similarity=0.022  Sum_probs=39.2

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhh
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCN   86 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFk   86 (101)
                      +.+|.=.+|+.|++.|+|.|.+.|..++.|.|||++|+.++.
T Consensus        39 ~~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~   80 (154)
T COG0328          39 GRTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGIT   80 (154)
T ss_pred             ecccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHH
Confidence            356777899999999999999999999999999999999987

>PRK07708 hypothetical protein; Validated

Probab=96.20  E-value=0.0069  Score=46.78  Aligned_cols=43  Identities=9%  Similarity=0.017  Sum_probs=39.2

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHhCCcc--eeeccchhHHHHHhhCC
Q 041278           46 ELTAFATKLIAIILAIEHASIRDWTM--LWIECDSPLTVHLCNKR   88 (101)
Q Consensus        46 ~anaL~aEL~gam~AiE~A~~~gW~n--LWLEsDS~LVvlAFkn~   88 (101)
                      ..|.-.+|+.|.+.|++.|.+.|.++  +.+++||++|+..++..
T Consensus       115 ~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~  159 (219)
T PRK07708        115 IYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGE  159 (219)
T ss_pred             cccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCC
Confidence            46888999999999999999999987  89999999999998654

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=95.52  E-value=0.019  Score=45.75  Aligned_cols=43  Identities=21%  Similarity=0.104  Sum_probs=38.9

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhC
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNK   87 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn   87 (101)
                      +.+|.-.+|+.|.+.|++.|.+.|-+++.+++||++|+....+
T Consensus        41 ~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i~~   83 (372)
T PRK07238         41 GRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSG   83 (372)
T ss_pred             CCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHhCC
Confidence            4556678999999999999999999999999999999999765

>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=94.77  E-value=0.052  Score=35.87  Aligned_cols=39  Identities=28%  Similarity=0.221  Sum_probs=32.4

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhC
Q 041278           46 ELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNK   87 (101)
Q Consensus        46 ~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn   87 (101)
                      ..+...+||.|++.|++ +. .. ..+.+-|||+.++.+..+
T Consensus        37 ~~s~~~aEl~Ai~~AL~-~~-~~-~~v~I~tDS~~v~~~l~~   75 (132)
T PF00075_consen   37 GQSNNRAELQAIIEALK-AL-EH-RKVTIYTDSQYVLNALNK   75 (132)
T ss_dssp             SECHHHHHHHHHHHHHH-TH-ST-SEEEEEES-HHHHHHHHT
T ss_pred             ccchhhhheehHHHHHH-Hh-hc-ccccccccHHHHHHHHHH
Confidence            45778999999999999 65 33 999999999999997765

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 Ribonuclease H [Replication, recombination and repair]

Probab=94.64  E-value=0.043  Score=46.57  Aligned_cols=41  Identities=24%  Similarity=0.193  Sum_probs=37.9

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHh
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLC   85 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAF   85 (101)
                      |..+.+.+||.|++.|+|.|.+++=+++-+-|||..++.+.
T Consensus       252 g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~l  292 (371)
T KOG3752|consen  252 GRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINSL  292 (371)
T ss_pred             CcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHHH
Confidence            56689999999999999999999999999999999998765

>PRK06548 ribonuclease H; Provisional

Probab=92.31  E-value=0.14  Score=38.17  Aligned_cols=40  Identities=18%  Similarity=0.069  Sum_probs=33.3

Q ss_pred             hhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhC
Q 041278           47 LTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNK   87 (101)
Q Consensus        47 anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn   87 (101)
                      .|.=.+||.|++.|+|.+. .+=..+-+-|||+.|+.++..
T Consensus        40 ~TNnraEl~Aii~aL~~~~-~~~~~v~I~TDS~yvi~~i~~   79 (161)
T PRK06548         40 ATNNIAELTAVRELLIATR-HTDRPILILSDSKYVINSLTK   79 (161)
T ss_pred             CCHHHHHHHHHHHHHHhhh-cCCceEEEEeChHHHHHHHHH
Confidence            5677899999999998654 344579999999999999974

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=90.04  E-value=0.43  Score=33.76  Aligned_cols=40  Identities=20%  Similarity=0.045  Sum_probs=33.3

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhC
Q 041278           46 ELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNK   87 (101)
Q Consensus        46 ~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn   87 (101)
                      ..|.-.+||.|++.|++.+.+.  ..+.+=|||+.++.++..
T Consensus        40 ~~TN~~aEL~Ai~~AL~~~~~~--~~v~I~tDS~yvi~~i~~   79 (150)
T PRK00203         40 LTTNNRMELMAAIEALEALKEP--CEVTLYTDSQYVRQGITE   79 (150)
T ss_pred             CCcHHHHHHHHHHHHHHHcCCC--CeEEEEECHHHHHHHHHH
Confidence            3456679999999999988654  579999999999998864

>PRK08719 ribonuclease H; Reviewed

Probab=88.68  E-value=0.39  Score=34.72  Aligned_cols=37  Identities=32%  Similarity=0.203  Sum_probs=32.3

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhh
Q 041278           46 ELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCN   86 (101)
Q Consensus        46 ~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFk   86 (101)
                      ..|.-.+||.|++.|+|.+.+.+    -+-|||++|+.+..
T Consensus        47 ~~Tnn~aEl~A~~~aL~~~~~~~----~i~tDS~yvi~~i~   83 (147)
T PRK08719         47 YTDNAELELLALIEALEYARDGD----VIYSDSDYCVRGFN   83 (147)
T ss_pred             CccHHHHHHHHHHHHHHHcCCCC----EEEechHHHHHHHH
Confidence            35888999999999999998764    59999999999983

>PF11204 DUF2985: Protein of unknown function (DUF2985); InterPro: IPR021369 This eukaryotic family of proteins has no known function

Probab=86.86  E-value=1  Score=31.09  Aligned_cols=69  Identities=22%  Similarity=0.250  Sum_probs=43.6

Q ss_pred             hcccccchhhHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHh--hCCCcccccccc
Q 041278           25 FINAPMHGKYMIVKEIFFWIWELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLC--NKRLLPPWFLTH   97 (101)
Q Consensus        25 ~~~~~~~~~~~i~~~~f~~ig~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAF--kn~slVPW~LRN   97 (101)
                      |+..||.  ++++.-.+.....+.++.=-++|.+.|+-.  .++=++.|+|.||+...-.|  ..-.+.||..|.
T Consensus         3 ~~~tP~g--~~i~iy~~~V~~~Ga~lfllL~g~~~~~~~--~~s~r~~WiEi~sQILnALF~v~g~gl~P~R~~d   73 (81)
T PF11204_consen    3 WVKTPMG--FAITIYGLNVVAWGAMLFLLLCGMLNAMCH--NKSPRDIWIEIDSQILNALFTVMGFGLHPWRFRD   73 (81)
T ss_pred             chhchhh--HHHHHHHHHHHHHHHHHHHHHHccchhccC--CCccceEEEEehhHHHHHHHHHHhhccccHHHHH
Confidence            4555653  233332233334455666566666655433  77788999999999887777  455678998775

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	101
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	98.0
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	97.95
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	97.64
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	97.51
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	96.56
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	96.26
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	96.17
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	96.05
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	95.99
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	95.94
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	95.48
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	94.59
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	93.39
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	91.79
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	88.91
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	86.68

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

Probab=98.00  E-value=5.6e-06  Score=54.72  Aligned_cols=43  Identities=19%  Similarity=0.052  Sum_probs=40.5

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhC
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNK   87 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn   87 (101)
                      +..|...+|+.|++.|+|.|.+.|.+++.++|||++|+..+++
T Consensus        42 ~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~i~~   84 (141)
T 3hst_B           42 GRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSG   84 (141)
T ss_dssp             EEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHHHTT
T ss_pred             CCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHHHhC
Confidence            4568899999999999999999999999999999999999987

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

Probab=97.95  E-value=7.3e-06  Score=53.59  Aligned_cols=44  Identities=23%  Similarity=0.102  Sum_probs=40.6

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCc----ceeeccchhHHHHHhhCC
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWT----MLWIECDSPLTVHLCNKR   88 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~----nLWLEsDS~LVvlAFkn~   88 (101)
                      +..|...+|+.|++.|+|.|.+.|.+    ++.++|||++|+..+++.
T Consensus        41 ~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~vi~~i~~~   88 (140)
T 3u3g_D           41 GETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQMQGV   88 (140)
T ss_dssp             EEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHHHHHHTTS
T ss_pred             CCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHHHHHhCCC
Confidence            45688899999999999999999999    999999999999999873

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

Probab=97.64  E-value=6.4e-05  Score=50.88  Aligned_cols=43  Identities=19%  Similarity=0.107  Sum_probs=40.0

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhCC
Q 041278           46 ELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKR   88 (101)
Q Consensus        46 ~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn~   88 (101)
                      ..|...+|+.|++.|+|.|.+.|.+++.++|||++|+...++.
T Consensus        45 ~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi~~i~~~   87 (149)
T 2ehg_A           45 NSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQMNGE   87 (149)
T ss_dssp             TCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHHHHHTTS
T ss_pred             CccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHHHHHhCc
Confidence            5678899999999999999999999999999999999998764

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

Probab=97.51  E-value=0.0001  Score=50.69  Aligned_cols=43  Identities=21%  Similarity=0.128  Sum_probs=39.8

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhC
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNK   87 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn   87 (101)
                      |..|...+||.|++.|+|.|.+.+-+.+.+.|||++|+.++.+
T Consensus        46 ~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~~i~~   88 (154)
T 2qkb_A           46 GRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTINGITN   88 (154)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHHHHHT
T ss_pred             CCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHhhhhh
Confidence            3568899999999999999999999999999999999999875

>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=96.56  E-value=0.0016  Score=45.85  Aligned_cols=43  Identities=14%  Similarity=0.027  Sum_probs=38.5

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhCC
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKR   88 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn~   88 (101)
                      +..|.-.+|+.|++.|+|.|.+.+. .+-+.|||++|+...++.
T Consensus        47 ~~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~~~~   89 (142)
T 1zbf_A           47 PIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWVKDK   89 (142)
T ss_dssp             EEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHHHHT
T ss_pred             CCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHHHcC
Confidence            4568889999999999999999998 999999999999976553

>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=96.26  E-value=0.0015  Score=45.14  Aligned_cols=41  Identities=20%  Similarity=0.140  Sum_probs=36.4

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhC
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNK   87 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn   87 (101)
                      +..|...+||.|++.|+|.|.+.  ..+.+.|||++|+.++++
T Consensus        40 ~~~tn~~aEl~A~~~aL~~~~~~--~~v~I~tDS~~vi~~i~~   80 (155)
T 1jl1_A           40 TRTTNNRMELMAAIVALEALKEH--AEVILSTDSQYVRQGITQ   80 (155)
T ss_dssp             EEECHHHHHHHHHHHHHHTCCSC--CEEEEEECCHHHHHHHHT
T ss_pred             CCCcHHHHHHHHHHHHHHHhCcC--CcEEEEeCHHHHHHHHHH
Confidence            34578899999999999999864  899999999999999876

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

Probab=96.17  E-value=0.0025  Score=44.32  Aligned_cols=40  Identities=20%  Similarity=0.088  Sum_probs=35.4

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhC
Q 041278           46 ELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNK   87 (101)
Q Consensus        46 ~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn   87 (101)
                      ..|...+||.|++.|+|.+.+.  ..+.+.|||++|+.++.+
T Consensus        43 ~~tn~~aEl~A~~~AL~~~~~~--~~v~I~tDS~~vi~~i~~   82 (158)
T 2e4l_A           43 LTTNNRMELLAPIVALEALKEP--CKIILTSDSQYMRQGIMT   82 (158)
T ss_dssp             EECHHHHHHHHHHHHHHTCSSC--CEEEEEECCHHHHHHHHT
T ss_pred             CCccHHHHHHHHHHHHHHhccC--CeEEEEeCHHHHHHHHHH
Confidence            4577899999999999998654  899999999999998876

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

Probab=96.05  E-value=0.0031  Score=42.56  Aligned_cols=40  Identities=23%  Similarity=0.141  Sum_probs=35.6

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhC
Q 041278           46 ELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNK   87 (101)
Q Consensus        46 ~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn   87 (101)
                      ..|.-.+||.|++.|+|.|.+  -..+.+.|||++|+.++++
T Consensus        41 ~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~~   80 (146)
T 3h08_A           41 ATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMNE   80 (146)
T ss_dssp             EECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHHS
T ss_pred             CCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHHH
Confidence            457778999999999999976  3789999999999999877

>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=95.99  E-value=0.0058  Score=42.07  Aligned_cols=38  Identities=18%  Similarity=0.127  Sum_probs=33.8

Q ss_pred             hhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHh
Q 041278           47 LTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLC   85 (101)
Q Consensus        47 anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAF   85 (101)
                      .|...+||.|++.|+|.|.+.|- .+.+.|||+.+..-.
T Consensus        48 ~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i~~w~   85 (147)
T 2kq2_A           48 MRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGIAFWA   85 (147)
T ss_dssp             TCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTHHHHT
T ss_pred             ccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHHHHHH
Confidence            47889999999999999999998 999999998777543

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

Probab=95.94  E-value=0.0027  Score=44.64  Aligned_cols=41  Identities=15%  Similarity=-0.065  Sum_probs=36.1

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhC
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNK   87 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn   87 (101)
                      +..|...+||.|++.|+|.+.+.  ..+.+.|||++|+.++.+
T Consensus        44 ~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i~~   84 (166)
T 1ril_A           44 ACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAFTE   84 (166)
T ss_dssp             EEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHHHS
T ss_pred             CCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHHhh
Confidence            34578899999999999998776  489999999999999877

>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=95.48  E-value=0.01  Score=42.18  Aligned_cols=41  Identities=15%  Similarity=0.015  Sum_probs=35.9

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhh
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCN   86 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFk   86 (101)
                      +..|.=.+|+.|++.|+|.+.+.+.+ +-+.|||++|+.-.+
T Consensus        41 ~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi~   81 (134)
T 4htu_A           41 PIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWVK   81 (134)
T ss_dssp             EEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHHH
Confidence            45677789999999999999998876 899999999998654

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

Probab=94.59  E-value=0.027  Score=40.26  Aligned_cols=42  Identities=21%  Similarity=0.081  Sum_probs=35.3

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhC
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNK   87 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn   87 (101)
                      +..+.+.||+.|...|+|.|.+.+ ..+-+-|||++|+.++..
T Consensus        52 nn~te~~Aei~Al~~al~~al~~~-~~v~I~TDS~Yvi~~it~   93 (165)
T 2lsn_A           52 GNHTAQMAEIAAVEFACKKALKIP-GPVLVITDSFYVAESANK   93 (165)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHHHSS-SCEEEEESCHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHHHHHHhcCC-CeEEEEeChHHHHhhhhh
Confidence            445778899999999999888776 579999999999999864

>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=93.39  E-value=0.05  Score=37.81  Aligned_cols=39  Identities=26%  Similarity=0.250  Sum_probs=34.2

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhC
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNK   87 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn   87 (101)
                      +..|.-.+||.|++.|+|.+   + ..+-+.|||++|+.+..+
T Consensus        45 ~~~Tnn~aEl~A~i~AL~~~---~-~~v~i~tDS~~v~~~i~~   83 (150)
T 3qio_A           45 TDTTNQKTELQAIYLALQDS---G-LEVNIVTDSQYALGIITQ   83 (150)
T ss_dssp             SSCCHHHHHHHHHHHHHHHS---C-SEEEEEESCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHhC---C-CcEEEEeCcHHHHHHHHH
Confidence            45677899999999999985   3 889999999999999875

>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=91.79  E-value=0.14  Score=36.43  Aligned_cols=37  Identities=24%  Similarity=0.197  Sum_probs=32.7

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHh
Q 041278           46 ELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLC   85 (101)
Q Consensus        46 ~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAF   85 (101)
                      ..|.-.+|+.|++.|+|.+   .-..+-+-|||++|+.++
T Consensus        60 ~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~i   96 (165)
T 3p1g_A           60 GTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATA   96 (165)
T ss_dssp             TCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhh
Confidence            4477899999999999999   247899999999999987

>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=88.91  E-value=0.27  Score=40.03  Aligned_cols=39  Identities=26%  Similarity=0.185  Sum_probs=34.6

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhC
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNK   87 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn   87 (101)
                      +.+|.-.+|+.|++.|+|.|    =+.+-+-|||++|+.+.++
T Consensus       472 ~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~  510 (557)
T 2zd1_A          472 TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQA  510 (557)
T ss_dssp             CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhc
Confidence            34678899999999999999    3789999999999999976

>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=86.68  E-value=0.47  Score=38.59  Aligned_cols=38  Identities=18%  Similarity=0.160  Sum_probs=33.7

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhC
Q 041278           46 ELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNK   87 (101)
Q Consensus        46 ~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn   87 (101)
                      ..|.-.+|+.|++.|+|.    +-..+-+-|||++|+.+.++
T Consensus       470 ~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~  507 (555)
T 1mu2_A          470 QTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVAS  507 (555)
T ss_dssp             SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhc
Confidence            457779999999999998    55899999999999999976

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	101
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	94.01
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	93.63
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	93.42
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	80.89

>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=94.01  E-value=0.018  Score=39.26  Aligned_cols=41  Identities=15%  Similarity=0.041  Sum_probs=35.3

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhh
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCN   86 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFk   86 (101)
                      +..|.=.+|+.|++.|+|.+.+++ .++=+-|||++|+...+
T Consensus        40 ~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~   80 (132)
T d1zbfa1          40 PIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVK   80 (132)
T ss_dssp             EEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHH
T ss_pred             CccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHH
Confidence            455666999999999999999998 67889999999997654

>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=93.63  E-value=0.035  Score=35.15  Aligned_cols=40  Identities=18%  Similarity=0.129  Sum_probs=33.0

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhCC
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKR   88 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn~   88 (101)
                      +..|.-.+||.|++.|++.    .-..+.+-|||++|+.+.++.
T Consensus        40 ~~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v~~~~~~~   79 (126)
T d1mu2a1          40 EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQ   79 (126)
T ss_dssp             SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTC
T ss_pred             CCCcchHHHHHHHHHHhcc----CCcceEEEechHHHHHHHhcC
Confidence            3457788999999988875    446899999999999998764

>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=93.42  E-value=0.029  Score=35.98  Aligned_cols=40  Identities=25%  Similarity=0.203  Sum_probs=33.4

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhCC
Q 041278           45 WELTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKR   88 (101)
Q Consensus        45 g~anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn~   88 (101)
                      +..|.-.+||.|++.|+|.    +-..+-+=|||++|+.++...
T Consensus        41 ~~~TNn~aEl~Avi~aL~~----~~~~v~I~TDS~yvi~~i~~~   80 (110)
T d1s1ta1          41 TDTTNQKTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQ   80 (110)
T ss_dssp             SSCCHHHHHHHHHHHHHHH----SCSEEEEEECCHHHHHHHHHC
T ss_pred             ccCcHHHHHHHHHHHHHHh----CCCeEEEEEehHHHHHHHhcC
Confidence            4557779999999999874    567899999999999998753

>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=80.89  E-value=0.48  Score=29.94  Aligned_cols=46  Identities=17%  Similarity=0.081  Sum_probs=36.0

Q ss_pred             hhhHHHHHHHHHHHHHHHHHhCCcceeeccchhHHHHHhhCCCccccc
Q 041278           47 LTAFATKLIAIILAIEHASIRDWTMLWIECDSPLTVHLCNKRLLPPWF   94 (101)
Q Consensus        47 anaL~aEL~gam~AiE~A~~~gW~nLWLEsDS~LVvlAFkn~slVPW~   94 (101)
                      .|.-.+||.|++.|+|.+.  .-..+-+-|||..++..+.+.....|.
T Consensus        41 ~Tnn~aEl~Ai~~AL~~~~--~~~~i~i~tds~~~~~~~~~~~~~~~~   86 (147)
T d1rila_          41 TTNNRMELKAAIEGLKALK--EPCEVDLYTDSHYLKKAFTEGWLEGWR   86 (147)
T ss_dssp             ECHHHHHHHHHHHHHHSCC--SCCEEEEECCCHHHHHHHHSSHHHHHH
T ss_pred             ccHHHHHHHHHHHHhhhcc--CCceEEEecchhhhhccccccchhhhh
Confidence            3667899999999998754  446788999999999998776544443