Citrus Sinensis ID: 039495

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------
Protein Sequence
IVARLDTKYFLWGVFRDVKSNHILHESHRELPSLVSAMEYVCDGPAAMDNAEVTDMVVDMEGGKIVGPVDVVVSKELYGKACGSHEKGDVNPATETMLSEPKQGQKSNSSDLFTGRSEKIKFKISSARPLSKGKLVNSMIDADCPPGFEKIHRPNSRICWMPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQPLGSLAVFDTPPYALAPIFQKDSTGIVQTRSH
Secondary Structure (PSIPRED)
cccccccEEEEEHHHcccccccccccccccccHHHHHHHHHcccccccccHHHccEEEEccccEEEEEccEEEEHHHHHHHccccccccccHHHHHHHHHHcccHHHHHHcccccccccEEEEHHcccccccccEEEEccccccccccccccccccccccccccccEEEEEEccccccccccEEEEEEEEEccccEEEEEccccccccHHHHHHHHHHHHHHHHHHHcccEEEEEEccHHHHHHHccccccccHHHHHHHHHHHHHcccccEEEEEEcccccHHHHHHHHHHHccccccEEEEccccccHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEccEEEEEHHEcccccccEEcccHcHccHHHHHHHHHcccccccccccEccEEEEcccccEEccEEEEEEHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccEEEEEEccccccccccccEEEEEEcccccEEEEEccccccccHHHHHHHHHHHHHHHHHHccccEEEEEccHHHHHHHHHcccccccHHHHHHHHHHHHHHccccEEEEEEEccccHHHHHHHHHHHHcccccEEEccccHHHHHHHHHHHccccEEcccc
Coil and Loop (DISEMBL)
ivarldtkYFLWGVFrdvksnhilheshreLPSLVSAMEyvcdgpaamdnaeVTDMVVdmeggkivgpVDVVVSKElygkacgshekgdvnpatetmlsepkqgqksnssdlftgrsekikfkissarplskgklvnsmidadcppgfekihrpnsricwmppptnwvklniegsssraqgsagaggivrdesgkwilgysknlgtsnsLASELWALYHGLNLVWERGFRKVLVECNsheavkclelpasfldpnraLILSCREYLCRNWDCKLQLILREANSCANWLAAhcenqplgslavfdtppyalapifqkdstgivqtrsh
Flexible Loop (DISEMBL)
ivarldtkyflwgVFRDVKSNHILHESHRELPSLVSAMEYVCDGPAAMDNAEVTDMVVDMEGGKIVGPVDVVVSKELYGKacgshekgdvnpatetmlsepkqgqksnssdlftgrsekikfkissarplskgklvNSMIDADCPPGFEKIHRPNSRICWMPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKClelpasfldpNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQPLGSLAVFDTPPYALapifqkdstgivqtrsh
Low Complexity Region (SEG)
IVARLDTKYFLWGVFRDVKSNHILHESHRELPSLVSAMEYVCDGPAAMDNAEVTDMVVDMEGGKIVGPVDVVVSKELYGKACGSHEKGDVNPATETMLSEPKQGQKSNSSDLFTGRSEKIKFKISSARPLSKGKLVNSMIDADCPPGFEKIHRPNSRICWMPPPTNWVKLNIEgsssraqgsagaggIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQPLGSLAVFDTPPYALAPIFQKDSTGIVQTRSH
Disordered region (IsUnstruct)
***RLDTKYFLWGVFRDVKSNHILHESHRELPSLVSAMEYVCDGPAAMDNAEVTDMVVDMEGGKIVGPVDVVVSKELYGKAC*******************************************************SMIDADCPPGFEKIHRPNSRICWMPPPTNWVKLNI**************GIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQPLGSLAVFDTPPYALAPIFQK***********
Disordered Region (DISOPRED)
**ARLDTKYFLWGVFRDVKSNHILHESHRELPSLVSAMEYVCDGPAAMDNAEVTDMVVDMEGGKIVGPVDVVVSKELYGKACGSHEKGDVNPATETMLSEPKQGQKSNSSDLFTGRSEKIKFKISSARPLSKGKLVNS***********************PPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQPLGSLAVFDTPPYALAPIFQKDSTGIVQTR**
Disordered Region (DISEMBL)
IVARLDTKYFLWGVFRDVKSNHILHESHRELPSLVSAMEYVCDGPAAMDNAEVTDMVVDMEGGKIVGPVDVVVSKELYGKACGSHEKGDVNPATET**************DLFTGRSEKIKFKISSARPLSKGKLVNSMIDADCPPGFEKIHRPNSRICWMPPPTNWVKLNIEGS***********GIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQPLGSLAVFDTPPYALAPIFQKDST********
Disordered Region (DISPRO)
IVARLDTKYFLWGVFRDVKSNHILHESHRELPSLVSAMEYVCDGPAAMDNAEVTDMVVDMEGGKIVGPVDVVVSKELYGKACGSHEKGDVNPATETMLSEPKQGQKSNSSDLFTGRSEKIKFKISSARPLSKGKLVNSM****************SRICWMPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQPLGSLAVFDTPPYALAPIFQKDSTGIVQ****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
IVARLDTKYFLWGVFRDVKSNHILHESHRELPSLVSAMEYVCDGPAAMDNAEVTDMVVDMEGGKIVGPVDVVVSKELYGKACGSHEKGDVNPATETMLSEPKQGQKSNSSDLFTGRSEKIKFKISSARPLSKGKLVNSMIDADCPPGFEKIHRPNSRICWMPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQPLGSLAVFDTPPYALAPIFQKDSTGIVQTRSH
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	327	2.2.26 [Sep-21-2011]
P0C2F6	620	Putative ribonuclease H p	no	no	0.611	0.322	0.302	2e-21

>sp|P0C2F6|RNHX1_ARATH Putative ribonuclease H protein At1g65750 OS=Arabidopsis thaliana GN=At1g65750 PE=3 SV=1

 Score =  103 bits (256), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 63/208 (30%), Positives = 106/208 (50%), Gaps = 8/208 (3%)

Query: 118 EKIKFKISSARPLSKGKLVNSMIDADCPPGFEKIHRPNSRICWMPPPTNWVKLNIEGSSS 177
           +++KF    A  + +    N ++    P       R    I W+ P   WVK+N +G+S 
Sbjct: 417 DRVKFVKEWAVEVYRAHSGNVLVGITQP-------RVERMIGWVSPCVGWVKVNTDGASR 469

Query: 178 RAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECN 237
              G A AGG++RD +G W  G+S N+G  ++  +ELW +Y+GL   WE+   +V +E +
Sbjct: 470 GNPGLASAGGVLRDCTGAWCGGFSLNIGRCSAPQAELWGVYYGLYFAWEKKVPRVELEVD 529

Query: 238 SHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQPL 297
           S   V  L+   S   P   L+  C  +L ++W  ++  + REAN  A+ LA +  +  L
Sbjct: 530 SEVIVGFLKTGISDSHPLSFLVRLCHGFLQKDWLVRIVHVYREANRLADGLANYAFSLSL 589

Query: 298 GSLAVFDTPPYALAPIFQKDSTGIVQTR 325
           G    FD  P A++ + ++D+ G  + R
Sbjct: 590 G-FHSFDLVPDAMSSLLREDTLGSTRPR 616


  Database: swissprot
    Posted date:  Mar 23, 2013  2:32 AM
  Number of letters in database: 191,569,459
  Number of sequences in database:  539,616
  
Lambda     K      H
   0.317    0.133    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 129,586,992
Number of Sequences: 539616
Number of extensions: 5445868
Number of successful extensions: 11378
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 11376
Number of HSP's gapped (non-prelim): 5
length of query: 327
length of database: 191,569,459
effective HSP length: 118
effective length of query: 209
effective length of database: 127,894,771
effective search space: 26730007139
effective search space used: 26730007139
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (28.1 bits)

Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 1EC: .EC: 2EC: 6EC: .EC: 4

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	327
297797059	352	hypothetical protein ARALYDRAFT_496261 [	0.519	0.482	0.379	1e-30
297789220	203	hypothetical protein ARALYDRAFT_359504 [	0.519	0.837	0.379	6e-30
240256469	657	nucleic acid binding protein [Arabidopsi	0.504	0.251	0.372	4e-28
224093782	245	predicted protein [Populus trichocarpa]	0.529	0.706	0.378	8e-27
224141789	245	predicted protein [Populus trichocarpa]	0.529	0.706	0.372	9e-27
224108063	245	predicted protein [Populus trichocarpa]	0.529	0.706	0.378	1e-26
9759309	676	non-LTR retroelement reverse transcripta	0.495	0.239	0.343	1e-22
404481706	153	RnaseH (mitochondrion) [Malus x domestic	0.440	0.941	0.413	3e-22
87116463	1898	unnamed protein product [Ipomoea batatas	0.510	0.087	0.345	1e-21
4544460	321	putative non-LTR retroelement reverse tr	0.654	0.666	0.293	1e-21

>gi|297797059|ref|XP_002866414.1| hypothetical protein ARALYDRAFT_496261 [Arabidopsis lyrata subsp. lyrata] gi|297312249|gb|EFH42673.1| hypothetical protein ARALYDRAFT_496261 [Arabidopsis lyrata subsp. lyrata]

 Score =  139 bits (351), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 69/182 (37%), Positives = 103/182 (56%), Gaps = 12/182 (6%)

Query: 141 DADCPPGFEKIHRPNSRICWMPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGY 200
           +   PPGFEKI        W PP   +VKLNI+G+S+     +G+ GIVRD+SGKW+ GY
Sbjct: 183 ETSLPPGFEKI--------WTPP---FVKLNIQGTSNPLSDLSGSAGIVRDQSGKWVFGY 231

Query: 201 SKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALIL 260
            +   +   +A+ L A+YHGL  +W+ GFR++ +E  S E +  L   +S     + L+ 
Sbjct: 232 IRCHRSIPEVAAGLLAIYHGLKFLWDSGFRRIHLETTSFEIINALTTRSSLFCKRKTLLG 291

Query: 261 SCREYLCRNWDCKLQLILREANSCANWLAAHCENQPLGSLAVFDTPPYALAPIFQKDSTG 320
           SC++ + + W+C +  I +E NSCA WLA   E QP   L  F+ PP  L  + +KD   
Sbjct: 292 SCKDMILKEWECDIYHISKEQNSCAEWLAKRSEEQP-QELVFFEYPPRGLVDLLEKDRLA 350

Query: 321 IV 322
            +
Sbjct: 351 AI 352

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297789220|ref|XP_002862599.1| hypothetical protein ARALYDRAFT_359504 [Arabidopsis lyrata subsp. lyrata] gi|297308223|gb|EFH38857.1| hypothetical protein ARALYDRAFT_359504 [Arabidopsis lyrata subsp. lyrata]

 Score =  137 bits (346), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 69/182 (37%), Positives = 102/182 (56%), Gaps = 12/182 (6%)

Query: 141 DADCPPGFEKIHRPNSRICWMPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGY 200
           +   PPGFEKI        W PP    VKLNI+G+S+     +G+ GIVRD+SGKW+ GY
Sbjct: 34  ETSLPPGFEKI--------WTPP---LVKLNIQGTSNPLSDLSGSAGIVRDQSGKWVFGY 82

Query: 201 SKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALIL 260
            +   +   +A+ L A+YHGL  +W+ GFR++ +E  S E +  L   +S     + L+ 
Sbjct: 83  IRCHRSIPEVAAGLLAIYHGLKFLWDSGFRRIHLETTSFEIINALTTRSSLFCKRKTLLG 142

Query: 261 SCREYLCRNWDCKLQLILREANSCANWLAAHCENQPLGSLAVFDTPPYALAPIFQKDSTG 320
           SC++ + + W+C +  I +E NSCA WLA   E QP   L  F+ PP  L  + +KD   
Sbjct: 143 SCKDMILKEWECDIYHISKEQNSCAEWLAKRSEEQP-QELVFFEYPPRGLVDLLEKDRLA 201

Query: 321 IV 322
            +
Sbjct: 202 AI 203

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|240256469|ref|NP_200917.4| nucleic acid binding protein [Arabidopsis thaliana] gi|9759455|dbj|BAB10371.1| unnamed protein product [Arabidopsis thaliana] gi|332010037|gb|AED97420.1| nucleic acid binding protein [Arabidopsis thaliana]

 Score =  131 bits (330), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 66/177 (37%), Positives = 98/177 (55%), Gaps = 12/177 (6%)

Query: 141 DADCPPGFEKIHRPNSRICWMPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGY 200
           +A  PPGFEKI        W PP    VKLNI+G+S+       + GIVRD+SGKW+ GY
Sbjct: 488 EASVPPGFEKI--------WTPP---LVKLNIQGTSNPLSDLTRSAGIVRDQSGKWVFGY 536

Query: 201 SKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALIL 260
            +   +   + + L A+Y GL  +W+ GFR++ +E  S E +  L   +S    ++ L+ 
Sbjct: 537 IRCHKSIPEVVAGLLAIYQGLKYLWDSGFRRIHLETTSFEIINALTTKSSLFCKSKTLLG 596

Query: 261 SCREYLCRNWDCKLQLILREANSCANWLAAHCENQPLGSLAVFDTPPYALAPIFQKD 317
           +C++ + + W+C +  I +E NSCA WLA   E QP   L  F+ PP  L    +KD
Sbjct: 597 ACKDMILKEWECDIYHISKEQNSCAEWLAKRSEEQP-QELVFFEYPPRGLMDFLEKD 652

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224093782|ref|XP_002309989.1| predicted protein [Populus trichocarpa] gi|222852892|gb|EEE90439.1| predicted protein [Populus trichocarpa]

 Score =  127 bits (319), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 67/177 (37%), Positives = 102/177 (57%), Gaps = 4/177 (2%)

Query: 153 RPNSRICWMPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLAS 212
           + ++++ W  P    +KLN++G S    G AGAGG++RD  G WI G+++N+G  +S+ +
Sbjct: 69  KEDTQVGWKYPQEERIKLNVDGCSKGNPGVAGAGGVIRDHLGAWIGGFARNIGICSSVNA 128

Query: 213 ELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDC 272
           ELWA+Y GL L W+RGFRKV +E +S   V  +   +  +D N  +I+  +  L R+W+ 
Sbjct: 129 ELWAVYVGLQLAWDRGFRKVDLESDSKVVVGLINGDSVRVDRNYNIIMQIKGMLGRDWEV 188

Query: 273 KLQLILREANSCANWLAAHCENQPL---GSLAVFDTPPYALAPIFQKDSTGIVQTRS 326
               + REAN  A+WLA +   + L   GS  V + PP  L P+   D  G   TRS
Sbjct: 189 TTYHVYREANCVADWLANYGLTRDLLDRGS-DVLEEPPSGLYPLLYYDLIGSTVTRS 244

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224141789|ref|XP_002324246.1| predicted protein [Populus trichocarpa] gi|222865680|gb|EEF02811.1| predicted protein [Populus trichocarpa]

 Score =  127 bits (318), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 66/177 (37%), Positives = 104/177 (58%), Gaps = 4/177 (2%)

Query: 153 RPNSRICWMPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLAS 212
           + ++++ W  P    +KLN++G S    G AGAGG++R+  G WI G+++N+   +S+ +
Sbjct: 69  KEDTQVGWKYPQEERIKLNVDGCSKGNPGVAGAGGVIREHLGAWIGGFARNIDICSSVNA 128

Query: 213 ELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDC 272
           ELWA+Y GL L W+RGFRKV +E +S   V  +   +  +D N  +I+  ++ L R+W+ 
Sbjct: 129 ELWAVYVGLQLAWDRGFRKVDLESDSKVVVGLINGDSVRVDRNYNIIMQIKDMLGRDWEV 188

Query: 273 KLQLILREANSCANWLAAHCENQPL---GSLAVFDTPPYALAPIFQKDSTGIVQTRS 326
               + REAN  A+WLA +  ++ L   GS  V + PP  L P+F  D  G   TRS
Sbjct: 189 TTYHVYREANCVADWLANYGLSRDLLDRGS-DVLEEPPSGLYPLFYYDLIGSTGTRS 244

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224108063|ref|XP_002314708.1| predicted protein [Populus trichocarpa] gi|222863748|gb|EEF00879.1| predicted protein [Populus trichocarpa]

 Score =  126 bits (316), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 67/177 (37%), Positives = 102/177 (57%), Gaps = 4/177 (2%)

Query: 153 RPNSRICWMPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLAS 212
           + ++++ W  P    +KLN++G S    G AGAGG++RD  G WI G+++N+G  +S+ +
Sbjct: 69  KEDTQVGWKYPQEERIKLNVDGCSKGNPGVAGAGGVIRDHLGAWIGGFARNIGICSSVNA 128

Query: 213 ELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDC 272
           ELWA+Y GL L W+RGFRKV +E +S   V  +   +  +D N  +I+  +  L RNW+ 
Sbjct: 129 ELWAVYVGLQLAWDRGFRKVDLESDSKVVVGLINGDSVRVDRNYNIIMQIKGMLGRNWEV 188

Query: 273 KLQLILREANSCANWLAAHCENQPL---GSLAVFDTPPYALAPIFQKDSTGIVQTRS 326
               + REAN  A+WLA +   + L   GS  V +  P  L P+   D  G + TRS
Sbjct: 189 TTYHVYREANCVADWLANYGLTRDLLDRGS-DVLEELPSGLYPLLYYDLIGSIVTRS 244

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|9759309|dbj|BAB09815.1| non-LTR retroelement reverse transcriptase-like [Arabidopsis thaliana]

 Score =  113 bits (282), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 56/163 (34%), Positives = 92/163 (56%), Gaps = 1/163 (0%)

Query: 158 ICWMPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWAL 217
           I W  P   WV +N +G+S    G A AGG++RDE G W++G++ N+G  ++  +ELW +
Sbjct: 506 IAWRKPAEGWVTMNTDGASHGNPGQATAGGVIRDEHGSWLVGFALNIGVCSAPLAELWGV 565

Query: 218 YHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLI 277
           Y+GL + WERG+R+V +E +S   V  L+       P   L+  C  ++ ++W  ++  +
Sbjct: 566 YYGLVVAWERGWRRVRLEVDSALVVGFLQSGIGDSHPLAFLVRLCHGFISKDWIVRITHV 625

Query: 278 LREANSCANWLAAHCENQPLGSLAVFDTPPYALAPIFQKDSTG 320
            REAN  A+ LA +    P G L + D+ P  ++ I  +D  G
Sbjct: 626 YREANRLADGLANYAFTLPFGFL-LLDSCPEHVSSILLEDVMG 667

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|404481706|ref|YP_006666138.1| RnaseH (mitochondrion) [Malus x domestica] gi|401661941|emb|CBX33402.1| rnaseH (mitochondrion) [Malus x domestica]

 Score =  112 bits (279), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 60/145 (41%), Positives = 79/145 (54%), Gaps = 1/145 (0%)

Query: 181 GSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHE 240
           GS GAGG++RD +G WI G++ NLG    +A+ELW L+ GL L W RGFR V VE +S  
Sbjct: 6   GSIGAGGLLRDNNGNWISGFTANLGKGKIIAAELWGLFFGLRLAWMRGFRSVEVEVDSAT 65

Query: 241 AVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQPLGSL 300
            V  +    + L P   LI  C+ YL  +W CKL  I RE N  A++LA+      LG  
Sbjct: 66  VVTLVNQQDNSLHPLHTLIRGCQAYLKMDWHCKLSHIYREKNFSADYLASIGLTYDLGYF 125

Query: 301 AVFDTPPYALAPIFQKDSTGIVQTR 325
               +PP    P   +DS G  + R
Sbjct: 126 ES-QSPPPGCIPFLFEDSLGYARPR 149

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|87116463|dbj|BAE79384.1| unnamed protein product [Ipomoea batatas]

 Score =  109 bits (273), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 58/168 (34%), Positives = 90/168 (53%), Gaps = 1/168 (0%)

Query: 158  ICWMPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWAL 217
            + W PP   + KLN +G+       A AGG++R+E+G W+ GY+ N+GT+NS  +ELW L
Sbjct: 1730 VVWSPPAAGFTKLNSDGACKSHSHLASAGGLLRNENGLWVAGYTCNIGTANSFLAELWGL 1789

Query: 218  YHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLI 277
              GL L   RGF K++ E +S   V+ L            L+  C+  L    + K+  I
Sbjct: 1790 REGLLLAKNRGFTKLIAETDSEAVVQVLRKDGPVTPDASILVKDCKLLLDHFQEIKVTHI 1849

Query: 278  LREANSCANWLAAHCENQPLGSLAVFDTPPYALAPIFQKDSTGIVQTR 325
            LRE N CA++LA   ++   G+  + + PP  L    Q+D+ G+  +R
Sbjct: 1850 LREGNQCADFLANLGQSSSWGT-TILERPPDDLRIFLQRDAIGLASSR 1896

Source: Ipomoea batatas

Species: Ipomoea batatas

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|4544460|gb|AAD22368.1| putative non-LTR retroelement reverse transcriptase [Arabidopsis thaliana]

 Score =  109 bits (273), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 115/225 (51%), Gaps = 11/225 (4%)

Query: 104 GQKSNSSDLFTGRS---EKIKFKISSARPLSKGKLVNSMIDADCPPGFEKIHRPNSRICW 160
           G K    ++F G     +++KF    A  ++   + N+ +  +      ++ R    + W
Sbjct: 101 GWKWRCGNIFGGNGKCRDRVKFIKDLAEEVA---IANAFVKGNEV----RVSRVERLVSW 153

Query: 161 MPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHG 220
           + P   WVKLN +G+S    G A AGG++RD +G WI G++ N+G  ++  +ELW +Y+G
Sbjct: 154 VSPEDGWVKLNTDGASRGNPGFATAGGVLRDHNGAWIGGFAVNIGVCSAPLAELWGVYYG 213

Query: 221 LNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLILRE 280
           L + W RG R+V +E +S   V  L    +   P   L+  C ++L + W  ++  + RE
Sbjct: 214 LFIAWGRGARRVELEVDSKMVVGFLTTGIADSHPLSFLLRLCYDFLSKGWIVRISHVYRE 273

Query: 281 ANSCANWLAAHCENQPLGSLAVFDTPPYALAPIFQKDSTGIVQTR 325
           AN  A+ LA +  +  LG L + ++ P  ++ I   D  G+   R
Sbjct: 274 ANRLADGLANYAFSLSLG-LHLLESRPDVVSSILLDDVAGVSYPR 317

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	327
TAIR|locus:2159481	657	AT5G61090 [Arabidopsis thalian	0.504	0.251	0.355	7.3e-28
TAIR|locus:504954956	258	AT5G42905 [Arabidopsis thalian	0.510	0.647	0.265	5.1e-12
TAIR|locus:2065330	365	AT2G02650 [Arabidopsis thalian	0.437	0.391	0.296	1.7e-08
TAIR|locus:2039129	160	AT2G46460 [Arabidopsis thalian	0.474	0.968	0.269	6.5e-08
TAIR|locus:4010713531	138	AT1G47497 [Arabidopsis thalian	0.388	0.920	0.276	4.8e-06
TAIR|locus:2090215	343	AT3G25270 [Arabidopsis thalian	0.256	0.244	0.321	8.4e-06
TAIR|locus:504955536	141	AT4G09775 [Arabidopsis thalian	0.253	0.588	0.317	1e-05
TAIR|locus:2058379	221	AT2G04420 [Arabidopsis thalian	0.284	0.420	0.281	3.7e-05
TAIR|locus:1006230762	257	AT1G04625 [Arabidopsis thalian	0.400	0.509	0.273	0.00038

TAIR|locus:2159481 AT5G61090 [Arabidopsis thaliana (taxid:3702)]

 Score = 302 (111.4 bits), Expect = 7.3e-28, Sum P(2) = 7.3e-28
 Identities = 63/177 (35%), Positives = 92/177 (51%)

Query:   141 DADCPPGFEKIHRPNSRICWMPPPTNWVKLNIEXXXXXXXXXXXXXXIVRDESGKWILGY 200
             +A  PPGFEKI        W PP    VKLNI+              IVRD+SGKW+ GY
Sbjct:   488 EASVPPGFEKI--------WTPP---LVKLNIQGTSNPLSDLTRSAGIVRDQSGKWVFGY 536

Query:   201 SKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALIL 260
              +   +   + + L A+Y GL  +W+ GFR++ +E  S E +  L   +S    ++ L+ 
Sbjct:   537 IRCHKSIPEVVAGLLAIYQGLKYLWDSGFRRIHLETTSFEIINALTTKSSLFCKSKTLLG 596

Query:   261 SCREYLCRNWDCKLQLILREANSCANWLAAHCENQPLGSLAVFDTPPYALAPIFQKD 317
             +C++ + + W+C +  I +E NSCA WLA   E QP   L  F+ PP  L    +KD
Sbjct:   597 ACKDMILKEWECDIYHISKEQNSCAEWLAKRSEEQPQ-ELVFFEYPPRGLMDFLEKD 652

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:504954956 AT5G42905 [Arabidopsis thaliana (taxid:3702)]

 Score = 177 (67.4 bits), Expect = 5.1e-12, P = 5.1e-12
 Identities = 47/177 (26%), Positives = 82/177 (46%)

Query:   104 GQKSNSSDLF---TGRSEKIKFKISSARPLSKGKLVNSMIDADCPPGFEKIHRPNSRICW 160
             G K   S++F   T   +++KF       + +  L N+++ +  P    ++ R    I W
Sbjct:    88 GWKWRCSNIFGENTKCRDRVKFVKEWVVEVYRAHLGNALVGSTQP----RVER---LIGW 140

Query:   161 MPPPTNWVKLNIEXXXXXXXXXXXXXXIVRDESGKWILGYSKNLGTSNSLASELWALYHG 220
             + P   WVK+N +              ++RD  G W  G+S N+G  ++  +ELW +Y+G
Sbjct:   141 VLPCVGWVKVNTDGASRGNPGLASAGGVLRDCEGAWCGGFSLNIGRCSAQHAELWGVYYG 200

Query:   221 LNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLI 277
             L   WE+   +V +E +S   V  L+   S   P   L+  C  +L ++W   L L+
Sbjct:   201 LYFAWEKKVPRVELEVDSEAIVGFLKTGISDSHPLSFLVRLCHNFLQKDWRILLGLL 257

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

TAIR|locus:2065330 AT2G02650 [Arabidopsis thaliana (taxid:3702)]

 Score = 154 (59.3 bits), Expect = 1.7e-08, P = 1.7e-08
 Identities = 45/152 (29%), Positives = 66/152 (43%)

Query:   160 WMPPPTNWVKLNIEXXXXXXXXXXXXXXIVRDESGKWIL-GYSKNLGTSNSLASELWALY 218
             W PPP  WVK N +               +R+ +G  +L G +K   ++ SL +E     
Sbjct:   206 WNPPPEGWVKCNFDSGYTQGSPYTRSGWTIRECNGHIVLCGNAKLQSSTCSLHAEALGFL 265

Query:   219 HGLNLVWERGFRKVLVECNSHEAVKCLELPA--SFLDPNRALILSCREYLCRNWDCKLQL 276
             H L ++W  G R V  E +S   V  +      S L     LI   R ++ +   C L+ 
Sbjct:   266 HALQVIWAHGLRYVWFESDSKSLVTLINNGEDHSLLG---TLIYDIRHWMLKLPYCSLEF 322

Query:   277 ILREANSCANWLAAHCE-NQPLGSLAVFDTPP 307
             + RE NS A+ LA+H     PL     + TPP
Sbjct:   323 VNRERNSAADALASHVHARDPL--FQSYTTPP 352

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2039129 AT2G46460 [Arabidopsis thaliana (taxid:3702)]

 Score = 129 (50.5 bits), Expect = 6.5e-08, P = 6.5e-08
 Identities = 44/163 (26%), Positives = 72/163 (44%)

Query:   160 WMPPPTNWVKLNIEXXXXXXXXXXXXXXIVRDESGKWI-LGYSKNLGTSNSLASELWALY 218
             W  PP  W K N +              I+RDESG+++  G +    TSN+L SE  AL 
Sbjct:     3 WTRPPHGWKKCNYDGSYNREMPSKAGW-IIRDESGQFVSAGQATGNHTSNALESEFQALL 61

Query:   219 HGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLIL 278
               +   W  G RK+  E ++ E ++ L    S  D     I   + +  R  +C+   I 
Sbjct:    62 ITMQSCWSHGHRKIWFEGDNREVMEILNRRKSRFDIFN-WIRDVQAWKQRFQECRFTWIN 120

Query:   279 REANSCANWLA-AHC-ENQPLGSLAVFDTPPYALAPIFQKDST 319
             R+ N  A+ LA +H  +N+       +D  P  ++   Q +++
Sbjct:   121 RKQNKPADILAKSHLPQNE---QFKFYDYIPIVISSALQLENS 160

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:4010713531 AT1G47497 [Arabidopsis thaliana (taxid:3702)]

 Score = 112 (44.5 bits), Expect = 4.8e-06, P = 4.8e-06
 Identities = 37/134 (27%), Positives = 64/134 (47%)

Query:   188 IVRDESGKWI-LGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLE 246
             ++RDESG+++  G +    TSN+L SE  AL   +   W  G RK+  E ++ E ++ L 
Sbjct:     8 VIRDESGQFVGAGQATGNHTSNALESEFQALLIAMQSCWSHGHRKIWFEGDNREVMEILN 67

Query:   247 LPASFLDPNRALILSCREYLCRNWDCKLQLILREANSCANWLA-AHC-ENQPLGSLAVFD 304
                S  D     I   + +  R  +C+   I R+ N  A+ LA +H  +N+       +D
Sbjct:    68 RRKSRFDTFN-WIRDVQAWKQRFQECRFTWINRKQNKPADILAKSHLPQNE---QFKFYD 123

Query:   305 TPPYALAPIFQKDS 318
               P  ++   Q ++
Sbjct:   124 YIPIVISSALQLEN 137

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2090215 AT3G25270 [Arabidopsis thaliana (taxid:3702)]

 Score = 130 (50.8 bits), Expect = 8.4e-06, P = 8.4e-06
 Identities = 28/87 (32%), Positives = 46/87 (52%)

Query:   156 SRICWMPPPTNWVKLNIEXXXXXXXXXXXXXXIVRDESGKWILGYSKNLG--TSNSLASE 213
             +R  W  PP+ W+K N +              ++RDE+G + +G  + +G  TS+SL SE
Sbjct:   182 ARTKWQRPPSTWIKYNYDGAFNHQTRNAKAGWLMRDENGVY-MGSGQAIGSTTSDSLESE 240

Query:   214 LWALYHGLNLVWERGFRKVLVECNSHE 240
               AL   +   W +G+RKV+ E +S +
Sbjct:   241 FQALIIAMQHAWSQGYRKVIFEGDSKQ 267

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:504955536 AT4G09775 [Arabidopsis thaliana (taxid:3702)]

 Score = 109 (43.4 bits), Expect = 1.0e-05, P = 1.0e-05
 Identities = 27/85 (31%), Positives = 40/85 (47%)

Query:   153 RPNSRIC-WMPPPTNWVKLNIEXXXXXXXXXXXXXXIVRDESGKWI-LGYSKNLGTSNSL 210
             RP+ R   W PPP  ++K N +              I+RD +G  I  G +K   + ++L
Sbjct:    54 RPSGRSKEWSPPPEGYLKCNFDSGYVQGRDYTSTCWIIRDSNGHVIHSGCAKLQQSYSAL 113

Query:   211 ASELWALYHGLNLVWERGFRKVLVE 235
              +E     H L +VW RG+R V  E
Sbjct:   114 QAEALGFLHALQMVWIRGYRYVWFE 138

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2058379 AT2G04420 [Arabidopsis thaliana (taxid:3702)]

 Score = 120 (47.3 bits), Expect = 3.7e-05, P = 3.7e-05
 Identities = 27/96 (28%), Positives = 48/96 (50%)

Query:   152 HRPNSRICWMPPPTNWVKLNIEXXXXXXXXXXXXXXIVRDESGKWILGYSKNLG--TSNS 209
             +R ++   W  PP  W+K N +              ++RD+ G +  G ++ +G   +N+
Sbjct:    55 NRESTHQKWEQPPMGWIKCNYDGSFNYRTQQTNSGWLIRDDKG-FYKGAAQAVGGTMNNA 113

Query:   210 LASELWALYHGLNLVWERGFRKVLVECNSHEAVKCL 245
             L SEL AL   +   W +G+RKV+ E +S +  + L
Sbjct:   114 LESELQALVMAMQHTWSQGYRKVIFEGDSKQVEELL 149

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

TAIR|locus:1006230762 AT1G04625 [Arabidopsis thaliana (taxid:3702)]

 Score = 113 (44.8 bits), Expect = 0.00038, P = 0.00038
 Identities = 38/139 (27%), Positives = 63/139 (45%)

Query:   154 PNSRICWMPPPTNWVKLNIEXXXXXXXXXXXXXXIVRDESGKWILGYSKNLG--TSNSLA 211
             P + + W  PP  W K N +              ++RD+ G + LG +  +G  T+N + 
Sbjct:    77 PTANL-WTTPPIGWTKCNYDGTYHSNAPSKAGW-LLRDDRGTF-LGAAHAIGSITTNPME 133

Query:   212 SELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPAS-FLDPNRALILSCREYLCRNW 270
             SEL AL   +   W RG+RK+  E ++ E  + +   +S F   N    +S   +  +  
Sbjct:   134 SELQALVMAMQHCWSRGYRKIYFEGDNKEVSEIVNGRSSNFAVFNWIRDISA--WRSKFE 191

Query:   271 DCKLQLILREANSCANWLA 289
             +CK     R +N  A+ LA
Sbjct:   192 ECKFTWTRRFSNMAADALA 210


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.134   0.422    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      327       313   0.00081  116 3  11 22  0.40    34
                                                     33  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  9
  No. of states in DFA:  622 (66 KB)
  Total size of DFA:  257 KB (2136 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  25.01u 0.16s 25.17t   Elapsed:  00:00:01
  Total cpu time:  25.01u 0.16s 25.17t   Elapsed:  00:00:01
  Start:  Sat May 11 03:57:24 2013   End:  Sat May 11 03:57:25 2013

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	327
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	6e-26
pfam13456	88	pfam13456, RVT_3, Reverse transcriptase-like	6e-14
cd09279	128	cd09279, RNase_HI_archaeal_like, RNAse HI family t	3e-06

>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 = 99.7 bits (249), Expect = 6e-26
 Identities = 35/119 (29%), Positives = 58/119 (48%)

Query: 171 NIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFR 230
           N +GS     G AGAGG++RD  G W+   S ++  + +  +EL AL   L L  + G +
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60

Query: 231 KVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLILREANSCANWLA 289
           K+++E +S   V  +   +     N  L+      L +  D + + + RE N  A+ LA
Sbjct: 61  KLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPREGNEVADRLA 119

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|205634 pfam13456, RVT_3, Reverse transcriptase-like

 Score = 66.1 bits (162), Expect = 6e-14
 Identities = 24/82 (29%), Positives = 38/82 (46%)

Query: 210 LASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRN 269
           L +E  AL  GL L  E G R+++VE +S   V+ ++          AL+   R+ L + 
Sbjct: 3   LEAEAEALLEGLQLALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLKKF 62

Query: 270 WDCKLQLILREANSCANWLAAH 291
               +  + RE N  A+ LA  
Sbjct: 63  DSVSVSHVPRECNRVADALAKL 84

This domain is found in plants and appears to be part of a retrotransposon. Length = 88

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

 Score = 45.6 bits (109), Expect = 3e-06
 Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 4/74 (5%)

Query: 168 VKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLG--TSNSLASELWALYHGLNLVW 225
             L  +G+S    G AGAG +++   G+ +L  S  LG   +N+ A E  AL  GL L  
Sbjct: 1   WTLYFDGASRGNPGPAGAGIVIKSPDGE-VLEQSIPLGFPATNNEA-EYEALIAGLELAL 58

Query: 226 ERGFRKVLVECNSH 239
           E G +K+ +  +S 
Sbjct: 59  ELGIKKLEIYGDSQ 72

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	327
PRK13907	128	rnhA ribonuclease H; Provisional	99.92
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.84
PRK07708	219	hypothetical protein; Validated	99.84
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.8
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.8
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.79
PRK00203	150	rnhA ribonuclease H; Reviewed	99.63
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.63
PRK08719	147	ribonuclease H; Reviewed	99.62
PRK06548	161	ribonuclease H; Provisional	99.6
KOG3752	371	consensus Ribonuclease H [Replication, recombinati	98.79
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	95.23

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.92  E-value=5.4e-25  Score=183.79  Aligned_cols=127  Identities=21%  Similarity=0.197  Sum_probs=115.4

Q ss_pred             cEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhc
Q 039495          167 WVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLE  246 (327)
Q Consensus       167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~  246 (327)
                      ++++|||||+..+++.+|+|+|+||..|.+...  ...+..|+++||++|+++||+.|.+.|+++|+|+|||++|+++++
T Consensus         1 ~~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~--~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~   78 (128)
T PRK13907          1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQLS--LPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVE   78 (128)
T ss_pred             CEEEEEeeCCCCCCCccEEEEEEEECCeeEEEE--ecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHh
Confidence            479999999999999999999999999877643  234567999999999999999999999999999999999999999


Q ss_pred             CCCCCCCchhhhHHHHHHHhccCCccceeeccCcccHHHHHHHHHHhhC
Q 039495          247 LPASFLDPNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQ  295 (327)
Q Consensus       247 ~~~~~~s~~~~li~eI~~ll~~f~~v~~~hI~R~~N~~AD~LAk~A~~~  295 (327)
                      +.......+..++++++.++..|..+.+.|++|++|..||.||+.|+..
T Consensus        79 ~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         79 KEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAILQ  127 (128)
T ss_pred             HHHhcChhHHHHHHHHHHHHhcCCceEEEEcCchhchhHHHHHHHHHhc
Confidence            9776556788999999999999999999999999999999999999753

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.84  E-value=1.8e-20  Score=183.07  Aligned_cols=137  Identities=22%  Similarity=0.225  Sum_probs=121.9

Q ss_pred             cEEEEEeeeecCCCCceeEEEEEEcCCCc-eEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhh
Q 039495          167 WVKLNIEGSSSRAQGSAGAGGIVRDESGK-WILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCL  245 (327)
Q Consensus       167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~-~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i  245 (327)
                      .+++|||||+.++++.+|+|+|++|++|. ++..++..++..|+++||+.||+.||+++.+.|.++|+|++||++|++.+
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i   81 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQM   81 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHh
Confidence            37899999999999999999999999764 55666677777899999999999999999999999999999999999999


Q ss_pred             cCCCCCC-CchhhhHHHHHHHhccCCccceeeccCcccHHHHHHHHHHhhCCCCCeEEec
Q 039495          246 ELPASFL-DPNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQPLGSLAVFD  304 (327)
Q Consensus       246 ~~~~~~~-s~~~~li~eI~~ll~~f~~v~~~hI~R~~N~~AD~LAk~A~~~~~~~~~~~~  304 (327)
                      ++.+... ..+..++.+++.++++|..+.+.||+|++|..||.||+.|+..... .+|++
T Consensus        82 ~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~a~~~~~~-~~~~~  140 (372)
T PRK07238         82 SGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMDAAAG-GEPWG  140 (372)
T ss_pred             CCCCccCChHHHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHHHHHhhcc-CCCcc
Confidence            9987544 4577889999999999999999999999999999999999987763 35654

>PRK07708 hypothetical protein; Validated

Probab=99.84  E-value=4.1e-20  Score=168.22  Aligned_cols=135  Identities=16%  Similarity=0.112  Sum_probs=114.1

Q ss_pred             CCCCcEEEEEeeeecCCCCceeEEEEEEcCCCceEe--ccccccC-CccchHHHHHHHHHhhHHHHhhCceE--EEEEEc
Q 039495          163 PPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWIL--GYSKNLG-TSNSLASELWALYHGLNLVWERGFRK--VLVECN  237 (327)
Q Consensus       163 P~~g~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~--~~~~~~~-~~s~~~AE~~Al~~AL~~A~~~g~~~--Vi~EsD  237 (327)
                      +.++.+++|||||+..+++.+|+|+|++++.|....  ..+..++ ..|+++||+.|++.||+.|.++|+++  |+|++|
T Consensus        69 ~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~D  148 (219)
T PRK07708         69 EEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGD  148 (219)
T ss_pred             cCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEec
Confidence            334569999999999999999999999998776443  3334454 47999999999999999999999976  899999


Q ss_pred             cHhhHHhhcCCCCCCC-chhhhHHHHHHHhccCC-ccceeeccCcccHHHHHHHHHHhhCCC
Q 039495          238 SHEAVKCLELPASFLD-PNRALILSCREYLCRNW-DCKLQLILREANSCANWLAAHCENQPL  297 (327)
Q Consensus       238 S~~VV~~i~~~~~~~s-~~~~li~eI~~ll~~f~-~v~~~hI~R~~N~~AD~LAk~A~~~~~  297 (327)
                      |++|++++++.+.... .+..+.+.++.++++|. .+.+.||+|++|..||.||+.|++...
T Consensus       149 SqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~Al~~~~  210 (219)
T PRK07708        149 SQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQALEGTV  210 (219)
T ss_pred             cHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHHHHhcCC
Confidence            9999999999876554 45678888888888775 478899999999999999999998654

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

Probab=99.80  E-value=1.9e-19  Score=138.68  Aligned_cols=86  Identities=35%  Similarity=0.475  Sum_probs=76.6

Q ss_pred             chHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhcCCCCCCCchhhhHHHHHHHhccCCccceeeccCcccHHHHHH
Q 039495          209 SLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLILREANSCANWL  288 (327)
Q Consensus       209 ~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~~~~~~~s~~~~li~eI~~ll~~f~~v~~~hI~R~~N~~AD~L  288 (327)
                      |++||++|++.||++|.++|+++|+|||||+.+|+++++.....+.+..++.+|+.++..|+++.+.||+|++|..||.|
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~A~~L   80 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPREQNKVADAL   80 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GGGSHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChHHhHHHHHH
Confidence            58999999999999999999999999999999999999998777799999999999999999999999999999999999


Q ss_pred             HHHHhh
Q 039495          289 AAHCEN  294 (327)
Q Consensus       289 Ak~A~~  294 (327)
                      ||.|++
T Consensus        81 A~~a~~   86 (87)
T PF13456_consen   81 AKFALS   86 (87)
T ss_dssp             HHHHHH
T ss_pred             HHHHhh
Confidence            999976

>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=99.80  E-value=1.1e-18  Score=140.53  Aligned_cols=125  Identities=26%  Similarity=0.251  Sum_probs=112.5

Q ss_pred             EEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhcCC
Q 039495          169 KLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELP  248 (327)
Q Consensus       169 K~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~~~  248 (327)
                      +||+|||+....+.+|+|+++++..+.............+++++|++|+..||+.+...+.+++.|++||+.+++.+++.
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~   80 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGW   80 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcc
Confidence            58999999988899999999999999888766555566799999999999999999999999999999999999999987


Q ss_pred             CC-CCCchhhhHHHHHHHhccCCccceeeccC----cccHHHHHHHHHHh
Q 039495          249 AS-FLDPNRALILSCREYLCRNWDCKLQLILR----EANSCANWLAAHCE  293 (327)
Q Consensus       249 ~~-~~s~~~~li~eI~~ll~~f~~v~~~hI~R----~~N~~AD~LAk~A~  293 (327)
                      .. ....+..++.+++.++..+..+.+.|++|    +.|..||.||+.++
T Consensus        81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            65 34567788899999988889999999999    99999999999874

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=99.79  E-value=5e-19  Score=151.80  Aligned_cols=127  Identities=22%  Similarity=0.185  Sum_probs=108.2

Q ss_pred             cEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhc
Q 039495          167 WVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLE  246 (327)
Q Consensus       167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~  246 (327)
                      .+.+|+|||+.+++|.+|+|+|++...+..  ..+.....+|++++|++|+++||+.+.+.+...|.++|||++|++.|+
T Consensus         3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~--~~s~~~~~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~   80 (154)
T COG0328           3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEK--ELSGGEGRTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGIT   80 (154)
T ss_pred             ceEEEecCccCCCCCCceEEEEEEcCCceE--EEeeeeecccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHH
Confidence            478999999999999999999999666665  333344478999999999999999999999999999999999999999


Q ss_pred             CCC----C---------CCCchhhhHHHHHHHhccCCccceeecc----CcccHHHHHHHHHHhhCC
Q 039495          247 LPA----S---------FLDPNRALILSCREYLCRNWDCKLQLIL----REANSCANWLAAHCENQP  296 (327)
Q Consensus       247 ~~~----~---------~~s~~~~li~eI~~ll~~f~~v~~~hI~----R~~N~~AD~LAk~A~~~~  296 (327)
                       .+    .         .+-....+++++.+++..+..+.+.||+    +..|+.||.||+.+....
T Consensus        81 -~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          81 -RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             -HHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence             22    1         1122346799999999999899999998    889999999999998754

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.63  E-value=2.8e-15  Score=128.89  Aligned_cols=126  Identities=18%  Similarity=0.090  Sum_probs=98.4

Q ss_pred             cEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhc
Q 039495          167 WVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLE  246 (327)
Q Consensus       167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~  246 (327)
                      .+.+|||||+..+++.+|+|+|+...++...  ++...+..|++.||++|+..||+.+.+  ...|.|.|||+++++.|+
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~--~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~   78 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKE--LSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGIT   78 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEE--EecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHH
Confidence            3789999999999999999999987554432  233345679999999999999998765  357999999999999998


Q ss_pred             C--------CCC----CCCchhhhHHHHHHHhccCCccceeecc----CcccHHHHHHHHHHhhCCC
Q 039495          247 L--------PAS----FLDPNRALILSCREYLCRNWDCKLQLIL----REANSCANWLAAHCENQPL  297 (327)
Q Consensus       247 ~--------~~~----~~s~~~~li~eI~~ll~~f~~v~~~hI~----R~~N~~AD~LAk~A~~~~~  297 (327)
                      +        ...    .+-....++++|.+++.. ..+.|.||+    ++.|..||.||+.|.....
T Consensus        79 ~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~  144 (150)
T PRK00203         79 EWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAEEAT  144 (150)
T ss_pred             HHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence            5        111    122345678888888765 578888888    7779999999999987543

>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=99.63  E-value=3.5e-15  Score=123.95  Aligned_cols=119  Identities=24%  Similarity=0.296  Sum_probs=94.3

Q ss_pred             cEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhc
Q 039495          167 WVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLE  246 (327)
Q Consensus       167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~  246 (327)
                      -+.+++|||+..+++.+|+|+++.+.  .   .++..++..|++.||++|+.+||+ +...  +++.|.|||+.+++.++
T Consensus         3 ~~~iytDgS~~~~~~~~~~g~v~~~~--~---~~~~~~~~~s~~~aEl~Ai~~AL~-~~~~--~~v~I~tDS~~v~~~l~   74 (132)
T PF00075_consen    3 AIIIYTDGSCRPNPGKGGAGYVVWGG--R---NFSFRLGGQSNNRAELQAIIEALK-ALEH--RKVTIYTDSQYVLNALN   74 (132)
T ss_dssp             SEEEEEEEEECTTTTEEEEEEEEETT--E---EEEEEEESECHHHHHHHHHHHHHH-THST--SEEEEEES-HHHHHHHH
T ss_pred             cEEEEEeCCccCCCCceEEEEEEECC--e---EEEecccccchhhhheehHHHHHH-Hhhc--ccccccccHHHHHHHHH
Confidence            37899999999999999999977433  2   222333467999999999999999 5422  99999999999999888


Q ss_pred             C-----CCCCCCchhhhHHHHHHHhccCCccceeeccCc-----ccHHHHHHHHHHh
Q 039495          247 L-----PASFLDPNRALILSCREYLCRNWDCKLQLILRE-----ANSCANWLAAHCE  293 (327)
Q Consensus       247 ~-----~~~~~s~~~~li~eI~~ll~~f~~v~~~hI~R~-----~N~~AD~LAk~A~  293 (327)
                      .     ..........++.++.+++.....+.|.||+.+     .|..||.|||.|+
T Consensus        75 ~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   75 KWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             THHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             HhccccccccccccccchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence            8     443333333577888888877888999999998     6889999999986

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 ....

>PRK08719 ribonuclease H; Reviewed

Probab=99.62  E-value=3.9e-15  Score=127.74  Aligned_cols=123  Identities=21%  Similarity=0.229  Sum_probs=97.9

Q ss_pred             cEEEEEeeeecCCCC---ceeEEEEEEcCCCceEeccccccC-CccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhH
Q 039495          167 WVKLNIEGSSSRAQG---SAGAGGIVRDESGKWILGYSKNLG-TSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAV  242 (327)
Q Consensus       167 ~lK~NvDgS~~~~~~---~aG~G~ViRD~~G~~l~~~~~~~~-~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV  242 (327)
                      .+++|||||+..+++   ++|+|+++.+.+|..+...+..+. ..|++.||+.|+..||+.+.+..    .|.|||++++
T Consensus         4 ~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~~----~i~tDS~yvi   79 (147)
T PRK08719          4 SYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDGD----VIYSDSDYCV   79 (147)
T ss_pred             eEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCCC----EEEechHHHH
Confidence            478999999988766   789999999988876543333343 46999999999999999987653    7999999999


Q ss_pred             Hhhc--------CCCC----CCCchhhhHHHHHHHhccCCccceeeccC----cccHHHHHHHHHHhh
Q 039495          243 KCLE--------LPAS----FLDPNRALILSCREYLCRNWDCKLQLILR----EANSCANWLAAHCEN  294 (327)
Q Consensus       243 ~~i~--------~~~~----~~s~~~~li~eI~~ll~~f~~v~~~hI~R----~~N~~AD~LAk~A~~  294 (327)
                      +.++        +.+.    .+-.+..+++.|..+.+ ...++|.||++    ..|..||.||+.|..
T Consensus        80 ~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         80 RGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             HHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            9995        3322    22335678888888876 56789999999    569999999999864

>PRK06548 ribonuclease H; Provisional

Probab=99.60  E-value=1.4e-14  Score=125.92  Aligned_cols=123  Identities=19%  Similarity=0.159  Sum_probs=95.7

Q ss_pred             cEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhc
Q 039495          167 WVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLE  246 (327)
Q Consensus       167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~  246 (327)
                      .+.+|||||+.++++.+|+|+++.+. + .   .....+..|++.||++|+++||+.+. .+..+|.|.|||+++++.++
T Consensus         5 ~~~IytDGa~~gnpg~~G~g~~~~~~-~-~---~~g~~~~~TNnraEl~Aii~aL~~~~-~~~~~v~I~TDS~yvi~~i~   78 (161)
T PRK06548          5 EIIAATDGSSLANPGPSGWAWYVDEN-T-W---DSGGWDIATNNIAELTAVRELLIATR-HTDRPILILSDSKYVINSLT   78 (161)
T ss_pred             EEEEEEeeccCCCCCceEEEEEEeCC-c-E---EccCCCCCCHHHHHHHHHHHHHHhhh-cCCceEEEEeChHHHHHHHH
Confidence            38999999999999999999999753 2 1   12333457999999999999998554 45568999999999999999


Q ss_pred             C--------CC----CCCCchhhhHHHHHHHhccCCccceeeccC----cccHHHHHHHHHHhhCC
Q 039495          247 L--------PA----SFLDPNRALILSCREYLCRNWDCKLQLILR----EANSCANWLAAHCENQP  296 (327)
Q Consensus       247 ~--------~~----~~~s~~~~li~eI~~ll~~f~~v~~~hI~R----~~N~~AD~LAk~A~~~~  296 (327)
                      .        .+    ..+-....|+++|..++... .++|.||+-    ..|..||.||+.+....
T Consensus        79 ~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~-~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~  143 (161)
T PRK06548         79 KWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENR-NIRMSWVNAHTGHPLNEAADSLARQAANNF  143 (161)
T ss_pred             HHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcC-ceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence            3        22    12224578999999988763 677877654    56999999999998643

>KOG3752 consensus Ribonuclease H [Replication, recombination and repair]

Probab=98.79  E-value=4.7e-08  Score=94.04  Aligned_cols=127  Identities=20%  Similarity=0.144  Sum_probs=92.9

Q ss_pred             CCcEEEEEeeeecCC---CCceeEEEEEEcCCCceEeccccc-c-CCccchHHHHHHHHHhhHHHHhhCceEEEEEEccH
Q 039495          165 TNWVKLNIEGSSSRA---QGSAGAGGIVRDESGKWILGYSKN-L-GTSNSLASELWALYHGLNLVWERGFRKVLVECNSH  239 (327)
Q Consensus       165 ~g~lK~NvDgS~~~~---~~~aG~G~ViRD~~G~~l~~~~~~-~-~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~  239 (327)
                      .+.+.+|+||++..+   ..++|+|+.+=+..-.   ..+.. . +..|++.||+.|+.+||+.|++....+|+|.|||+
T Consensus       210 ~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~---N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~  286 (371)
T KOG3752|consen  210 IEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHEL---NVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSE  286 (371)
T ss_pred             ccceEEEecCccccCCCCCCcceeEEeeCCCCcc---cccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechH
Confidence            345789999999875   3568888877553211   11222 2 56799999999999999999999999999999999


Q ss_pred             hhHHhhcC-------------CCCC----CCchhhhHHHHHHHhcc--CCccceeeccC----cccHHHHHHHHHHhh
Q 039495          240 EAVKCLEL-------------PASF----LDPNRALILSCREYLCR--NWDCKLQLILR----EANSCANWLAAHCEN  294 (327)
Q Consensus       240 ~VV~~i~~-------------~~~~----~s~~~~li~eI~~ll~~--f~~v~~~hI~R----~~N~~AD~LAk~A~~  294 (327)
                      +++++|+.             ...+    .......+.++.+|.+.  ...+++.||+-    ..|..||.||+.+..
T Consensus       287 ~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~  364 (371)
T KOG3752|consen  287 YFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGST  364 (371)
T ss_pred             HHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence            99999983             1111    01123466777777766  35677777765    469999999999843

>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.23  E-value=0.028  Score=55.64  Aligned_cols=116  Identities=17%  Similarity=0.119  Sum_probs=83.6

Q ss_pred             CCceeEEEEEEcC-CCceEeccccccC---CccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhcCCCCCCC--
Q 039495          180 QGSAGAGGIVRDE-SGKWILGYSKNLG---TSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELPASFLD--  253 (327)
Q Consensus       180 ~~~aG~G~ViRD~-~G~~l~~~~~~~~---~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~~~~~~~s--  253 (327)
                      ...+|.|+.+.|. +....+.......   ..++.+||++|+..+|..+.++|+.++.+.+|+..+...+.+......  
T Consensus        16 ~~~~g~~vai~d~~d~~~~f~~k~~~~~~~~~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~~~~~~~~   95 (384)
T KOG1812|consen   16 ILLAGFGVAICDEHDDDLLFQMKASDHDSDSITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGREKPEQHR   95 (384)
T ss_pred             hhcccCceeeeccccHHHHHHhhcCcccccccchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhhhhHHHHH
Confidence            3568889999885 5555443333322   258999999999999999999999999999998888887776654333  


Q ss_pred             chhhhHHHHHHHhccCCccceeeccCc-ccHHHHHHHHHHhhC
Q 039495          254 PNRALILSCREYLCRNWDCKLQLILRE-ANSCANWLAAHCENQ  295 (327)
Q Consensus       254 ~~~~li~eI~~ll~~f~~v~~~hI~R~-~N~~AD~LAk~A~~~  295 (327)
                      .+..+..+.+.+...+....-..+++. ....|-.||+.+...
T Consensus        96 ~~~~l~~~v~~~r~~l~~~~~i~~~~~~d~~~~~~lA~e~i~s  138 (384)
T KOG1812|consen   96 KIVLLVELVQRIREQLTSSEPILVPKNADIKFAYKLAREAIVS  138 (384)
T ss_pred             HHHHHHHHHHHHHHHhhcccceecccchhhHHHHHHHHHhhcc
Confidence            355666666666666655555556554 456688999999874

---

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	327
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	2e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 49.1 bits (116), Expect = 1e-06
 Identities = 49/341 (14%), Positives = 96/341 (28%), Gaps = 85/341 (24%)

Query: 1   IVARLDTKY---FLWGVFRDVKSNHILHESHRELPSLVSAMEYVCDGPAAMDNAEVTDMV 57
            V   D K        +    + +HI+        +L      +      M    V   V
Sbjct: 29  FVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLR-LFWTLLSKQEEM----VQKFV 83

Query: 58  VDMEGGKIVGPVDVVVSKELYGKACGSHEKGDVNPATETMLSEPKQGQKSNSSDLFTGRS 117
            ++              +  Y       +     P+  T +   ++ +  N + +F   +
Sbjct: 84  EEVL-------------RINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN 130

Query: 118 -------EKIKFKISSARPLSKGKLVNSMIDADCPPGFEKIHRPNSRICWMPPPTNWVKL 170
                   K++  +   RP +K  L++ +       G  K                   +
Sbjct: 131 VSRLQPYLKLRQALLELRP-AKNVLIDGV------LGSGK----------------TW-V 166

Query: 171 NIEGSSSRAQGSAGAGGIVRDESGKWI-LGYSKNLGTSNSLASELWALYHGLNLVW-ERG 228
            ++   S          I       W+ L    N  +  ++   L  L + ++  W  R 
Sbjct: 167 ALDVCLSYKVQCKMDFKIF------WLNLK---NCNSPETVLEMLQKLLYQIDPNWTSRS 217

Query: 229 FRKVLVECNSHEAVKCL-ELPASFLDPNRALILSCREYLCRN-WD----------CKLQL 276
                ++   H     L  L  S    N  L+L        N  +          CK+ L
Sbjct: 218 DHSSNIKLRIHSIQAELRRLLKSKPYENCLLVL-------LNVQNAKAWNAFNLSCKILL 270

Query: 277 ILREANSCANWL-AAHCENQPLGSLAVFDTPPYALAPIFQK 316
             R      ++L AA   +  L   ++  TP    + +  K
Sbjct: 271 TTRFK-QVTDFLSAATTTHISLDHHSMTLTPDEVKS-LLLK 309

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

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 28/125 (22%), Positives = 49/125 (39%), Gaps = 4/125 (3%)

Query: 168 VKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLG--TSNSLASELWALYHGLNLVW 225
           V +  +G S    G AG G +V       +L  SK      +N++A E   L  GL+   
Sbjct: 4   VVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVA-EYRGLIAGLDDAV 62

Query: 226 ERGFRKVLVECNSHEAVKCLELPASFLDPN-RALILSCREYLCRNWDCKLQLILREANSC 284
           + G  +  V  +S   V+ +        P+   L +  +    +      + + R  N+ 
Sbjct: 63  KLGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTY 122

Query: 285 ANWLA 289
           A+ LA
Sbjct: 123 ADRLA 127

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	327
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.92
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.92
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.9
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.84
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.81
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.81
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.8
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.78
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.78
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.73
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.72
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.71
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.63
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.56
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.52
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.46

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

Probab=99.92  E-value=1.7e-24  Score=180.22  Aligned_cols=129  Identities=20%  Similarity=0.185  Sum_probs=117.3

Q ss_pred             cEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCce----EEEEEEccHhhH
Q 039495          167 WVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFR----KVLVECNSHEAV  242 (327)
Q Consensus       167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~----~Vi~EsDS~~VV  242 (327)
                      .+++|||||+.++++.+|+|+++++++|..+...+...+..|+++||++|+++||+.|.+.+.+    +|+|+|||++++
T Consensus         3 ~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~vi   82 (140)
T 3u3g_D            3 KIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIV   82 (140)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEEEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHHH
T ss_pred             eEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCCCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHHH
Confidence            4899999999999999999999999999988777766667899999999999999999999999    999999999999


Q ss_pred             HhhcCCCCCC-CchhhhHHHHHHH-hccCCccceeeccCcccHHHHHHHHHHhhC
Q 039495          243 KCLELPASFL-DPNRALILSCREY-LCRNWDCKLQLILREANSCANWLAAHCENQ  295 (327)
Q Consensus       243 ~~i~~~~~~~-s~~~~li~eI~~l-l~~f~~v~~~hI~R~~N~~AD~LAk~A~~~  295 (327)
                      +++++.+... ..+..++.+|+++ +.+|..+.|.||+|++|+.||.||+.|+..
T Consensus        83 ~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D           83 RQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEAIDK  137 (140)
T ss_dssp             HHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCGGGGHHHHHHHHHHHHH
T ss_pred             HHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCchhhHHHHHHHHHHHHh
Confidence            9999976433 3567789999999 888999999999999999999999999864

>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=99.92  E-value=1.5e-24  Score=181.36  Aligned_cols=130  Identities=18%  Similarity=0.189  Sum_probs=116.2

Q ss_pred             cEEEEEeeeecCCCCceeEEEEEEcCC-CceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhh
Q 039495          167 WVKLNIEGSSSRAQGSAGAGGIVRDES-GKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCL  245 (327)
Q Consensus       167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~-G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i  245 (327)
                      .+++|||||+.++++.+|+|+++++++ |.++...+...+..|+++||++|++.||+++.+.|.++|+|+|||+++++++
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~i   82 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQM   82 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCCCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHHH
Confidence            379999999999999999999999987 6776666666677899999999999999999999999999999999999999


Q ss_pred             cCCCCCC-CchhhhHHHHHHHhccCCccceeeccCcccHHHHHHHHHHhhCC
Q 039495          246 ELPASFL-DPNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQP  296 (327)
Q Consensus       246 ~~~~~~~-s~~~~li~eI~~ll~~f~~v~~~hI~R~~N~~AD~LAk~A~~~~  296 (327)
                      ++.+... ..+..++.+|+.++..|..+.|.||+|++|..||.||+.|+...
T Consensus        83 ~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~~~N~~AD~LA~~a~~~~  134 (141)
T 3hst_B           83 SGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLANDAMDAA  134 (141)
T ss_dssp             TTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCGGGCHHHHHHHHHHHHHH
T ss_pred             hCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCCcccHHHHHHHHHHHHHh
Confidence            9975433 34667888999999989999999999999999999999998743

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

Probab=99.90  E-value=3e-23  Score=176.03  Aligned_cols=129  Identities=16%  Similarity=0.113  Sum_probs=113.0

Q ss_pred             cEEEEEeeeec-CCCCceeE-EEEEEcCCCceEeccccccC----CccchHHHHHHHHHhhHHHHhhCceEEEEEEccHh
Q 039495          167 WVKLNIEGSSS-RAQGSAGA-GGIVRDESGKWILGYSKNLG----TSNSLASELWALYHGLNLVWERGFRKVLVECNSHE  240 (327)
Q Consensus       167 ~lK~NvDgS~~-~~~~~aG~-G~ViRD~~G~~l~~~~~~~~----~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~  240 (327)
                      ++++|||||+. ++++.+|+ |+++++ +|..+..++...+    ..|+++||++|++.||+.|.+.|.++|+|+|||++
T Consensus         1 m~~iy~DGs~~~~n~g~~G~~G~vi~~-~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~   79 (149)
T 2ehg_A            1 MIIGYFDGLCEPKNPGGIATFGFVIYL-DNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQL   79 (149)
T ss_dssp             CCEEEEEEEEESSSSSSEEEEEEEEEC-SSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHH
T ss_pred             CEEEEEeeccCCCCCChheEEEEEEEE-CCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHH
Confidence            47999999999 79999997 999999 8888765544443    67999999999999999999999999999999999


Q ss_pred             hHHhhcCCCCCC-CchhhhHHHHHHHhccCCccceeeccCcccHHHHHHHHHHhhCCC
Q 039495          241 AVKCLELPASFL-DPNRALILSCREYLCRNWDCKLQLILREANSCANWLAAHCENQPL  297 (327)
Q Consensus       241 VV~~i~~~~~~~-s~~~~li~eI~~ll~~f~~v~~~hI~R~~N~~AD~LAk~A~~~~~  297 (327)
                      +++++++.+... ..+..++++++.++..| .+.|.||+|+.|..||.||+.|.....
T Consensus        80 vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~~~N~~AD~LA~~a~~~~~  136 (149)
T 2ehg_A           80 VIKQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPREENKEADRLSRVAYELVR  136 (149)
T ss_dssp             HHHHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCGGGCHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCCcccHHHHHHHHHHHHhhc
Confidence            999999975432 35778999999999888 699999999999999999999987543

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

Probab=99.84  E-value=1.6e-20  Score=160.45  Aligned_cols=131  Identities=15%  Similarity=0.084  Sum_probs=107.5

Q ss_pred             CCCCCcEEEEEeeeecCCCC---ceeEEEEEEcCCCceEecccccc-CCccchHHHHHHHHHhhHHHHhhCceEEEEEEc
Q 039495          162 PPPTNWVKLNIEGSSSRAQG---SAGAGGIVRDESGKWILGYSKNL-GTSNSLASELWALYHGLNLVWERGFRKVLVECN  237 (327)
Q Consensus       162 ~P~~g~lK~NvDgS~~~~~~---~aG~G~ViRD~~G~~l~~~~~~~-~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsD  237 (327)
                      +|+.+++++|||||+.++++   .+|+|+++++..+..+.   ..+ +..|++.||++|++.||+.+.+.+.++|+|+||
T Consensus         2 ~~~~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~---~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tD   78 (154)
T 2qkb_A            2 SHMGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVG---IRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTN   78 (154)
T ss_dssp             CEETTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEE---EECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEES
T ss_pred             CCCCCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEE---eecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEEC
Confidence            56778999999999998765   48999999986554332   223 357999999999999999999999999999999


Q ss_pred             cHhhHHhhcC--------CCC----CCCchhhhHHHHHHHhccCCccceeeccCc----ccHHHHHHHHHHhhCC
Q 039495          238 SHEAVKCLEL--------PAS----FLDPNRALILSCREYLCRNWDCKLQLILRE----ANSCANWLAAHCENQP  296 (327)
Q Consensus       238 S~~VV~~i~~--------~~~----~~s~~~~li~eI~~ll~~f~~v~~~hI~R~----~N~~AD~LAk~A~~~~  296 (327)
                      |+++++.|++        .+.    .+..+..++++|..++..+ .+.|.||+++    .|+.||.||+.|+...
T Consensus        79 S~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~~-~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           79 SMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGM-DIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             CHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTTC-EEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             cHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcCC-ceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            9999999987        111    2234567899999988865 5999999985    5999999999998753

>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=99.81  E-value=1e-19  Score=155.31  Aligned_cols=125  Identities=18%  Similarity=0.153  Sum_probs=103.5

Q ss_pred             CCCCCcEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhh
Q 039495          162 PPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEA  241 (327)
Q Consensus       162 ~P~~g~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~V  241 (327)
                      .|+.+.+++|||||+.++++.+|+|+|+++..+..+     ..+..|++.||++|++.||+.+   + .+|.|+|||+++
T Consensus         7 ~P~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~-----~~~~~Tnn~aEl~A~i~AL~~~---~-~~v~i~tDS~~v   77 (150)
T 3qio_A            7 EPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVV-----TLTDTTNQKTELQAIYLALQDS---G-LEVNIVTDSQYA   77 (150)
T ss_dssp             SCCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEE-----EESSCCHHHHHHHHHHHHHHHS---C-SEEEEEESCHHH
T ss_pred             CCCCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEE-----eCCCCCHHHHHHHHHHHHHHhC---C-CcEEEEeCcHHH
Confidence            578899999999999999999999999998654332     2456799999999999999974   3 899999999999


Q ss_pred             HHhhcCC------------CCCCCchhhhHHHHHHHhccCCccceeeccCcc----cHHHHHHHHHHhhC
Q 039495          242 VKCLELP------------ASFLDPNRALILSCREYLCRNWDCKLQLILREA----NSCANWLAAHCENQ  295 (327)
Q Consensus       242 V~~i~~~------------~~~~s~~~~li~eI~~ll~~f~~v~~~hI~R~~----N~~AD~LAk~A~~~  295 (327)
                      ++.+++-            ...+.....+++++.+++.++..+.|.||+++.    |+.||.||+.|+..
T Consensus        78 ~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           78 LGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            9999862            112234567888888877788899999999998    99999999999865

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

Probab=99.81  E-value=5.3e-20  Score=159.52  Aligned_cols=132  Identities=19%  Similarity=0.148  Sum_probs=105.0

Q ss_pred             cCCCCCcEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHh
Q 039495          161 MPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHE  240 (327)
Q Consensus       161 ~~P~~g~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~  240 (327)
                      +||+.+.+++|||||+.++++.+|+|+|+++..+....  +...+..|++.||++|++.||+.+.+.  .+|.|+|||++
T Consensus         2 ~p~~m~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~--~~~~~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~   77 (166)
T 1ril_A            2 NPSPRKRVALFTDGACLGNPGPGGWAALLRFHAHEKLL--SGGEACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHY   77 (166)
T ss_dssp             ----CCCCCEEEEEEESSTTEEEEEEEEECBTTBCCEE--CCEEEEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHH
T ss_pred             CCCCCccEEEEECccccCCCCCEEEEEEEEECCEEEEE--ecCCCCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHH
Confidence            46777889999999999999999999999986554332  222345699999999999999988775  48999999999


Q ss_pred             hHHhhcCC---------CC----CCCchhhhHHHHHHHhccCCccceeecc----CcccHHHHHHHHHHhhCCC
Q 039495          241 AVKCLELP---------AS----FLDPNRALILSCREYLCRNWDCKLQLIL----REANSCANWLAAHCENQPL  297 (327)
Q Consensus       241 VV~~i~~~---------~~----~~s~~~~li~eI~~ll~~f~~v~~~hI~----R~~N~~AD~LAk~A~~~~~  297 (327)
                      +++.|++.         +.    .+.....+++++..++..+ .+.|.||+    |+.|..||.||+.|+....
T Consensus        78 vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~~-~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~  150 (166)
T 1ril_A           78 LKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPH-RVRFHFVKGHTGHPENERVDREARRQAQSQA  150 (166)
T ss_dssp             HHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTS-EEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             HHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhcC-eEEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence            99999982         21    1223456899999988764 88899888    8899999999999998655

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

Probab=99.80  E-value=1.2e-19  Score=153.43  Aligned_cols=125  Identities=19%  Similarity=0.106  Sum_probs=103.2

Q ss_pred             cEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhc
Q 039495          167 WVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLE  246 (327)
Q Consensus       167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~  246 (327)
                      .+++|||||+.++++.+|+|+++++...  ....+...+..|++.||+.|++.||+.+.+  ..+|.|+|||+++++.++
T Consensus         4 ~i~iytDGs~~~n~g~~g~G~v~~~~~~--~~~~~~~~~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~   79 (146)
T 3h08_A            4 TITIYTDGAASGNPGKGGWGALLMYGSS--RKEISGYDPATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMN   79 (146)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEEETTE--EEEEEEEEEEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHH
T ss_pred             eEEEEEecCCCCCCCceEEEEEEEECCe--eEEeecCCCCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHH
Confidence            4899999999999999999999998643  233344445679999999999999999986  589999999999999999


Q ss_pred             CC-------------CCCCCchhhhHHHHHHHhccCCccceeecc----CcccHHHHHHHHHHhhCC
Q 039495          247 LP-------------ASFLDPNRALILSCREYLCRNWDCKLQLIL----REANSCANWLAAHCENQP  296 (327)
Q Consensus       247 ~~-------------~~~~s~~~~li~eI~~ll~~f~~v~~~hI~----R~~N~~AD~LAk~A~~~~  296 (327)
                      +.             ...+.....+++++..++..+ .+.|.||+    |+.|+.||.||+.|+...
T Consensus        80 ~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~-~v~~~~V~gH~g~~~N~~AD~LA~~a~~~~  145 (146)
T 3h08_A           80 EGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLH-RVTFHKVKGHSDNPYNSRADELARLAIKEN  145 (146)
T ss_dssp             SSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHHS-EEEEEECCC-CCSHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhhC-ceEEEEcCCcCCcHhHHHHHHHHHHHHHhC
Confidence            82             122334567999999988865 68889998    999999999999998643

>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=99.78  E-value=5.1e-19  Score=151.45  Aligned_cols=126  Identities=20%  Similarity=0.160  Sum_probs=103.2

Q ss_pred             cEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhc
Q 039495          167 WVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLE  246 (327)
Q Consensus       167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~  246 (327)
                      .+++|||||+.++++.+|+|+++++..+...  .+...+..|++.||+.|++.||+.+.+.  .+|.|+|||+++++.|+
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~--~~~~~~~~tn~~aEl~A~~~aL~~~~~~--~~v~I~tDS~~vi~~i~   79 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKT--FSAGYTRTTNNRMELMAAIVALEALKEH--AEVILSTDSQYVRQGIT   79 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEE--EEEEEEEECHHHHHHHHHHHHHHTCCSC--CEEEEEECCHHHHHHHH
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEE--EecCCCCCcHHHHHHHHHHHHHHHhCcC--CcEEEEeCHHHHHHHHH
Confidence            4899999999999999999999998665432  2233455699999999999999999864  89999999999999999


Q ss_pred             C--------CCC----CCCchhhhHHHHHHHhccCCccceeecc----CcccHHHHHHHHHHhhCCC
Q 039495          247 L--------PAS----FLDPNRALILSCREYLCRNWDCKLQLIL----REANSCANWLAAHCENQPL  297 (327)
Q Consensus       247 ~--------~~~----~~s~~~~li~eI~~ll~~f~~v~~~hI~----R~~N~~AD~LAk~A~~~~~  297 (327)
                      +        .+.    .+.....+++++..++.. ..+.|.||+    |++|..||.||+.|...+.
T Consensus        80 ~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~-~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~  145 (155)
T 1jl1_A           80 QWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQ-HQIKWEWVKGHAGHPENERADELARAAAMNPT  145 (155)
T ss_dssp             TTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTT-CEEEEEECCSSTTCHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHhhcccccccCCccCCHHHHHHHHHHHcc-CceEEEEcCCCCCCHHHHHHHHHHHHHHhccc
Confidence            7        221    122346788999888875 488999999    8899999999999998654

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

Probab=99.78  E-value=8.5e-19  Score=150.62  Aligned_cols=125  Identities=14%  Similarity=0.084  Sum_probs=102.4

Q ss_pred             CcEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhh
Q 039495          166 NWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCL  245 (327)
Q Consensus       166 g~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i  245 (327)
                      ..+++|||||+.++++.+|+|+|+++...  ....+...+..|++.||+.|++.||+.+.+.  .+|.|+|||+++++.|
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~--~~~~~~~~~~~tn~~aEl~A~~~AL~~~~~~--~~v~I~tDS~~vi~~i   80 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGH--TKEMSDGFSLTTNNRMELLAPIVALEALKEP--CKIILTSDSQYMRQGI   80 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTE--EEEEEEEEEEECHHHHHHHHHHHHHHTCSSC--CEEEEEECCHHHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCE--EEEEecCcCCCccHHHHHHHHHHHHHHhccC--CeEEEEeCHHHHHHHH
Confidence            35899999999999999999999998542  2223333455799999999999999998654  8999999999999999


Q ss_pred             cC--------CCC----CCCchhhhHHHHHHHhccCCccceeecc----CcccHHHHHHHHHHhhC
Q 039495          246 EL--------PAS----FLDPNRALILSCREYLCRNWDCKLQLIL----REANSCANWLAAHCENQ  295 (327)
Q Consensus       246 ~~--------~~~----~~s~~~~li~eI~~ll~~f~~v~~~hI~----R~~N~~AD~LAk~A~~~  295 (327)
                      ++        .+.    .+.....+++++..++.. ..+.|.||+    |++|..||.||+.|+..
T Consensus        81 ~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~-~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A           81 MTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQL-HQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             HTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTT-SEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHccccccCCCcccCHHHHHHHHHHHcc-CcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            88        332    223456788899998875 488999998    88999999999999986

>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=99.73  E-value=4.3e-17  Score=141.23  Aligned_cols=135  Identities=20%  Similarity=0.109  Sum_probs=105.3

Q ss_pred             ceecCCCCCcEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEc
Q 039495          158 ICWMPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECN  237 (327)
Q Consensus       158 ~~W~~P~~g~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsD  237 (327)
                      ....|.+...+++|||||+.+++|.+|+|+++++. |..+. .....+..|++.||++|++.||+.+   ...+|.|+||
T Consensus        14 l~~~P~~~~~i~iytDGs~~~npG~~g~G~vi~~~-~~~~~-~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tD   88 (165)
T 3p1g_A           14 LTDQPIPDADYTWYTDGSSFLQEGQRRAGAAVTTE-TEVIW-ARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTD   88 (165)
T ss_dssp             CBSSCCTTCSEEEEEEEEEEEETTEEEEEEEEECS-SCEEE-EEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEEC
T ss_pred             CCCCCCCCCCEEEEEEcccCCCCCceEEEEEEEEC-CEEEE-EecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEc
Confidence            34556666679999999999999999999999874 44432 2233455699999999999999998   3689999999


Q ss_pred             cHhhHHhhcCCC-CCCCchhhhHHHHHHHhccCCccceeeccCcc---------cHHHHHHHHHHhhCCC
Q 039495          238 SHEAVKCLELPA-SFLDPNRALILSCREYLCRNWDCKLQLILREA---------NSCANWLAAHCENQPL  297 (327)
Q Consensus       238 S~~VV~~i~~~~-~~~s~~~~li~eI~~ll~~f~~v~~~hI~R~~---------N~~AD~LAk~A~~~~~  297 (327)
                      |+++++.+.... ..+.....+++++...+..+..+.|.||+++.         |+.||.||+.|.....
T Consensus        89 S~~vi~~iw~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~~  158 (165)
T 3p1g_A           89 SRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAV  158 (165)
T ss_dssp             CHHHHHHHHSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhcccCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcCC
Confidence            999999984221 12233456777776666677899999999876         9999999999987543

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

Probab=99.72  E-value=4.6e-17  Score=141.06  Aligned_cols=127  Identities=19%  Similarity=0.064  Sum_probs=102.0

Q ss_pred             cEEEEEeeeecCCCCc-----eeEEEEEEcCC--CceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccH
Q 039495          167 WVKLNIEGSSSRAQGS-----AGAGGIVRDES--GKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSH  239 (327)
Q Consensus       167 ~lK~NvDgS~~~~~~~-----aG~G~ViRD~~--G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~  239 (327)
                      -+.+||||||.++++.     +|+|++++..+  ..+..+.....+..+++.||+.||..||+.+...+. +|.|.|||+
T Consensus         7 evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~~~-~v~I~TDS~   85 (165)
T 2lsn_A            7 EGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIPG-PVLVITDSF   85 (165)
T ss_dssp             SEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHSSS-CEEEEESCH
T ss_pred             eEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcCCC-eEEEEeChH
Confidence            4789999999999886     99999998543  344444444556678999999999999999887764 799999999


Q ss_pred             hhHHhhcC------------CCCCCCchhhhHHHHHHHhccCCccceeecc----------CcccHHHHHHHHHHhh
Q 039495          240 EAVKCLEL------------PASFLDPNRALILSCREYLCRNWDCKLQLIL----------REANSCANWLAAHCEN  294 (327)
Q Consensus       240 ~VV~~i~~------------~~~~~s~~~~li~eI~~ll~~f~~v~~~hI~----------R~~N~~AD~LAk~A~~  294 (327)
                      ++++.++.            ....+-....|++++.+++..+..+.|.||+          |+.|..||.||+++..
T Consensus        86 Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~  162 (165)
T 2lsn_A           86 YVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSY  162 (165)
T ss_dssp             HHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhhh
Confidence            99999974            1122234567899999988888899999998          5579999999999874

>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=99.71  E-value=1.1e-17  Score=142.16  Aligned_cols=127  Identities=11%  Similarity=-0.023  Sum_probs=94.3

Q ss_pred             CCCcEEEEEeeeecCCCCceeEEEEEEcCCCceEe-cc-ccccC---CccchHHHHHHHHHhhHHHHhhCceEEEEEEcc
Q 039495          164 PTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWIL-GY-SKNLG---TSNSLASELWALYHGLNLVWERGFRKVLVECNS  238 (327)
Q Consensus       164 ~~g~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~-~~-~~~~~---~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS  238 (327)
                      +.+.+++|||||+.+  +.+|+|+++++ +|.... .. ....+   ..|++.||++|++.||++|.+.+. +|.|+|||
T Consensus         3 ~~~~i~iytDGs~~~--g~~G~G~vi~~-~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS   78 (147)
T 2kq2_A            3 DRTEYDVYTDGSYVN--GQYAWAYAFVK-DGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDY   78 (147)
T ss_dssp             TTSCCEEECCCCCBT--TBCEEEEEEEE-TTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCC
T ss_pred             CCCeEEEEECCCCCC--CCcEEEEEEEE-CCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECc
Confidence            456789999999987  99999999998 555422 22 12212   359999999999999999999999 99999999


Q ss_pred             HhhHHhhcCCCCCCCchhhhHHHHHHHhccCC-ccceeecc----CcccHHHHHHHHHHhhCCC
Q 039495          239 HEAVKCLELPASFLDPNRALILSCREYLCRNW-DCKLQLIL----REANSCANWLAAHCENQPL  297 (327)
Q Consensus       239 ~~VV~~i~~~~~~~s~~~~li~eI~~ll~~f~-~v~~~hI~----R~~N~~AD~LAk~A~~~~~  297 (327)
                      +.+.+++++.+.....   .....+++..... .+.|.||+    ++.|+.||.||+.|+....
T Consensus        79 ~~i~~w~~~~w~~~~~---~~~~~~~l~~~l~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~  139 (147)
T 2kq2_A           79 AGIAFWATGEWKAKNE---FTQAYAKLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAKSALGIRD  139 (147)
T ss_dssp             STHHHHTTSSSSCCHH---HHHHHHCGGGGGSTTCCBCCCCCCCCCHHHHHHHHHHHHHHTCCC
T ss_pred             HHHHHHHhCCCccCCc---chHHHHHHHHHhcCCeeEEEecCcCCCcchHHHHHHHHHHHhccc
Confidence            9999999886543321   1122222222211 67888887    6779999999999998655

>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=99.63  E-value=3.5e-16  Score=132.26  Aligned_cols=102  Identities=18%  Similarity=0.224  Sum_probs=81.8

Q ss_pred             cCCCCCcEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHh
Q 039495          161 MPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHE  240 (327)
Q Consensus       161 ~~P~~g~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~  240 (327)
                      .||+.+++++|||||+.+++|.+|+|+|++ .+|..+... ..++..|++.||++|++.||+.+.+.++ +|.|+|||++
T Consensus         5 ~~~~~~~~~iy~DGa~~gNpG~~G~G~vl~-~~g~~~~~~-~~~~~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~   81 (142)
T 1zbf_A            5 AKEEIIWESLSVDVGSQGNPGIVEYKGVDT-KTGEVLFER-EPIPIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQT   81 (142)
T ss_dssp             ---CCCSSSEEEEEEECSSSEEEEEEEEET-TTCCEEEEC-CCEEEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHH
T ss_pred             CCCCCCeEEEEEeeccCCCCCCeEEEEEEE-eCCEEEEEe-cccCCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHH
Confidence            367778999999999999999999999999 678776533 3355679999999999999999999999 9999999999


Q ss_pred             hHHhhcCCCC-----CCCchhhhHHHHHHH
Q 039495          241 AVKCLELPAS-----FLDPNRALILSCREY  265 (327)
Q Consensus       241 VV~~i~~~~~-----~~s~~~~li~eI~~l  265 (327)
                      ||+++++...     .+.....+++.+.++
T Consensus        82 vi~w~~~~~~k~~~~~~v~n~dLw~~l~~~  111 (142)
T 1zbf_A           82 AIKWVKDKKAKSTLVRNEETALIWKLVDEA  111 (142)
T ss_dssp             HHHHHHHTCCCCCCCCSTTTHHHHHHHHHH
T ss_pred             HHHHHHcCCccCCCCCCcccHHHHHHHHHH
Confidence            9999998652     222345566665554

>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=99.56  E-value=1.2e-14  Score=147.70  Aligned_cols=122  Identities=16%  Similarity=0.125  Sum_probs=100.0

Q ss_pred             cCCCCCcEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHh
Q 039495          161 MPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHE  240 (327)
Q Consensus       161 ~~P~~g~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~  240 (327)
                      ..|..+.+++|+|||+.++++.+|+|+++++..+.     ....+..|++.||++|++.||+.    +..+|.|.|||++
T Consensus       430 ~~p~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~-----~~~~~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~  500 (555)
T 1mu2_A          430 GDPIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDK-----VKKLEQTTNQQAELEAFAMALTD----SGPKVNIIVDSQY  500 (555)
T ss_dssp             SSCCTTCEEEEEEEEECTTTCCEEEEEEETTSCEE-----EEEESSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHH
T ss_pred             CCCCCCceEEEEcccccCCCCCceEEEEEEeCCEe-----eccCCCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHH
Confidence            34667889999999999999999999999875432     22345679999999999999997    7789999999999


Q ss_pred             hHHhhcCCCCCCCchhhhHHHHHHHhccCCccceeeccCc----ccHHHHHHHHHHh
Q 039495          241 AVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLILRE----ANSCANWLAAHCE  293 (327)
Q Consensus       241 VV~~i~~~~~~~s~~~~li~eI~~ll~~f~~v~~~hI~R~----~N~~AD~LAk~A~  293 (327)
                      |++.+++-..  .....+++++.+++..+..+.+.||+++    +|+.||.||+.|+
T Consensus       501 v~~~i~~~~~--~~~~~l~~~~~~~~~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          501 VMGIVASQPT--ESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             HHHHHHTCCS--EESCHHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHHHHhcccc--cccHHHHHHHHHHhccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            9999997321  2345677777777777888999999884    6999999999874

>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=99.52  E-value=1.1e-14  Score=147.84  Aligned_cols=121  Identities=17%  Similarity=0.163  Sum_probs=96.3

Q ss_pred             cCCCCCcEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHh
Q 039495          161 MPPPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHE  240 (327)
Q Consensus       161 ~~P~~g~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~  240 (327)
                      ..|..+.+++++|||+.++++.+|+|+++++.....+     ..+..||+.||+.|++.||+.+    .++|.|.|||++
T Consensus       433 ~ep~~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~-----~~~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~  503 (557)
T 2zd1_A          433 KEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVV-----PLTNTTNQKTELQAIYLALQDS----GLEVNIVTDSQY  503 (557)
T ss_dssp             SSCCTTSCEEEEEEEECTTTCCEEEEEEETTSCEEEE-----EECSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHH
T ss_pred             cCCCCCCEEEEEccCCCCCCCceEEEEEEECCcEEEe-----cCCCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHH
Confidence            3466778999999999999999999999985443322     2356799999999999999988    689999999999


Q ss_pred             hHHhhcCCCCCCCchhhhHHHHHHHhccCCccceeeccCc----ccHHHHHHHHHH
Q 039495          241 AVKCLELPASFLDPNRALILSCREYLCRNWDCKLQLILRE----ANSCANWLAAHC  292 (327)
Q Consensus       241 VV~~i~~~~~~~s~~~~li~eI~~ll~~f~~v~~~hI~R~----~N~~AD~LAk~A  292 (327)
                      |++.+++....  ....++.++.+.+..+..+.+.||+++    +|+.||.||+.|
T Consensus       504 vi~~i~~~~~~--~~~~l~~~~~~~l~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          504 ALGIIQAQPDK--SESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             HHHHHTTCCSE--ESSHHHHHHHHHHHHCSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             HHHHHhcCCcc--CCHHHHHHHHHHHhcCCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            99999984332  234567777766666778999999995    599999999976

>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=99.46  E-value=8.2e-14  Score=116.30  Aligned_cols=96  Identities=20%  Similarity=0.262  Sum_probs=75.2

Q ss_pred             cEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhc
Q 039495          167 WVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLE  246 (327)
Q Consensus       167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~  246 (327)
                      ...+|||||+.+++|.+|+|+|+++ .|..+..+ ..++..|++.||++|+++||+.+.+.+.+ +.|+|||++|+++++
T Consensus         5 ~~~iytDGac~GNPGp~G~ggV~~~-~g~~~~~~-g~~~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi~   81 (134)
T 4htu_A            5 WESLSVDVGSQGNPGIVEYKGVDTK-TGEVLFER-EPIPIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWVK   81 (134)
T ss_dssp             SSSEEEEEEEETTTEEEEEEEEETT-TCCEEEEE-EEEEEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHHH
T ss_pred             ceEEEEeeccCCCCCCeEEEEEEEE-CCEEEEEe-cCCCCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHHH
Confidence            4579999999999999999999988 66655433 33556799999999999999999998876 899999999999998


Q ss_pred             CCCC-----CCCchhhhHHHHHHH
Q 039495          247 LPAS-----FLDPNRALILSCREY  265 (327)
Q Consensus       247 ~~~~-----~~s~~~~li~eI~~l  265 (327)
                      +..-     .+.....|++.+.++
T Consensus        82 ~~~~kt~~~~~vkN~dLw~~ld~~  105 (134)
T 4htu_A           82 DKKAKSTLVRNEETALIWKLVDEA  105 (134)
T ss_dssp             HTCCCCCCCCSSTTHHHHHHHHHH
T ss_pred             cCCcccCCCCCccCHHHHHHHHHH
Confidence            6321     112345555555543

---

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	327
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.62
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.6
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.57
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.43
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.37

>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=99.62  E-value=1.7e-15  Score=122.98  Aligned_cols=120  Identities=16%  Similarity=0.117  Sum_probs=89.7

Q ss_pred             CCCCcEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhH
Q 039495          163 PPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAV  242 (327)
Q Consensus       163 P~~g~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV  242 (327)
                      |-.|...+|||||+..+++.+|+|+++.+.....     ..++..|++.||+.|+++||+.    ...++.|.|||++++
T Consensus         3 p~~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~-----~~~~~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v~   73 (126)
T d1mu2a1           3 PIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKV-----KKLEQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVM   73 (126)
T ss_dssp             CCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEE-----EEESSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHH
T ss_pred             CCCCCcEEEEcCCCCCCCCcEEEEEEecCCCEEE-----EecCCCcchHHHHHHHHHHhcc----CCcceEEEechHHHH
Confidence            4557778999999999999999998886643322     2234569999999999998874    567899999999999


Q ss_pred             HhhcCCCCCCCchhhhHHHHHHHhccCCccceeeccC----cccHHHHHHHHHHh
Q 039495          243 KCLELPASFLDPNRALILSCREYLCRNWDCKLQLILR----EANSCANWLAAHCE  293 (327)
Q Consensus       243 ~~i~~~~~~~s~~~~li~eI~~ll~~f~~v~~~hI~R----~~N~~AD~LAk~A~  293 (327)
                      +++++...... ...+.+.+..+. ....+.|.||+.    ..|+.||.||++|+
T Consensus        74 ~~~~~~~~~~~-~~~~~~~~~~~~-~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          74 GIVASQPTESE-SKIVNQIIEEMI-KKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             HHHHTCCSEES-CHHHHHHHHHHH-HCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHHhcCCcccc-chHHHHHHHHhh-hcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            99998754322 222333344443 455778888775    56999999999874

>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=99.60  E-value=2.6e-15  Score=124.68  Aligned_cols=126  Identities=19%  Similarity=0.135  Sum_probs=97.3

Q ss_pred             cEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhc
Q 039495          167 WVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLE  246 (327)
Q Consensus       167 ~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~  246 (327)
                      .+++|||||+.++++++|+|+++++.+.....  +...+..|++.||++|+..||+++.  ....+.+.+||+.++..++
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~--~~~~~~~tnn~aE~~Ai~~Al~~~~--~~~~i~i~tds~~~i~~~~   77 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTF--SAGYTRTTNNRMELMAAIVALEALK--EHAEVILSTDSQYVRQGIT   77 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEE--EEEEEEECHHHHHHHHHHHHHHTCC--SCCEEEEEECCHHHHHHHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEe--ccccCcccHHHHHHhhhhhhhhhhc--ccceEEEeecceeeEEccc
Confidence            37999999999999999999999986655433  2334556899999999999998654  4567899999999999887


Q ss_pred             CCC------------CCCCchhhhHHHHHHHhccCCccceeecc----CcccHHHHHHHHHHhhCCC
Q 039495          247 LPA------------SFLDPNRALILSCREYLCRNWDCKLQLIL----REANSCANWLAAHCENQPL  297 (327)
Q Consensus       247 ~~~------------~~~s~~~~li~eI~~ll~~f~~v~~~hI~----R~~N~~AD~LAk~A~~~~~  297 (327)
                      ...            ..+.....++..+..++. ...++|.||+    +..|..||.||+.|...+.
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~-~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~  143 (152)
T d1jl1a_          78 QWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAAAMNPT  143 (152)
T ss_dssp             TTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCC
T ss_pred             chhhHhHhccchhcccCeeecHHHHHHHHHHhh-cceeEEEEecccCCCccHHHHHHHHHHHHhCCC
Confidence            421            112223456777777655 3478888888    7889999999999998665

>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=99.57  E-value=3.7e-15  Score=123.75  Aligned_cols=124  Identities=17%  Similarity=0.100  Sum_probs=95.8

Q ss_pred             EEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhcC
Q 039495          168 VKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLEL  247 (327)
Q Consensus       168 lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~~  247 (327)
                      +.+|||||+.++++.+|+|+++++........  ...+..|++.||+.|+.+||+.+.  ....+.+.+||+++++.++.
T Consensus         4 i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~--~~~~~~Tnn~aEl~Ai~~AL~~~~--~~~~i~i~tds~~~~~~~~~   79 (147)
T d1rila_           4 VALFTDGACLGNPGPGGWAALLRFHAHEKLLS--GGEACTTNNRMELKAAIEGLKALK--EPCEVDLYTDSHYLKKAFTE   79 (147)
T ss_dssp             CCEEEEEEESSTTEEEEEEEEECBTTBCCEEC--CEEEEECHHHHHHHHHHHHHHSCC--SCCEEEEECCCHHHHHHHHS
T ss_pred             EEEEEccCCCCCCCccEEEEEEEECCcceEEe--cccccccHHHHHHHHHHHHhhhcc--CCceEEEecchhhhhccccc
Confidence            68999999999999999999998776554432  223345999999999999998654  34679999999999998865


Q ss_pred             CC-------------CCCCchhhhHHHHHHHhccCCccceeecc----CcccHHHHHHHHHHhhCC
Q 039495          248 PA-------------SFLDPNRALILSCREYLCRNWDCKLQLIL----REANSCANWLAAHCENQP  296 (327)
Q Consensus       248 ~~-------------~~~s~~~~li~eI~~ll~~f~~v~~~hI~----R~~N~~AD~LAk~A~~~~  296 (327)
                      ..             ..+-....|++++..++.. ..+.|.||+    ++.|..||.||+.|....
T Consensus        80 ~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~~-~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_          80 GWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP-HRVRFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             SHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTT-SEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             cchhhhhhccccccccccchhHHHHHHHHHHhhh-cccceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence            21             1122345678888877654 467788776    789999999999998754

>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=99.43  E-value=3e-13  Score=107.44  Aligned_cols=107  Identities=18%  Similarity=0.183  Sum_probs=84.7

Q ss_pred             CCCCcEEEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhH
Q 039495          163 PPTNWVKLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAV  242 (327)
Q Consensus       163 P~~g~lK~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV  242 (327)
                      |-.+-..+|||||+..+++.+|+|+++.+.....     ..++..||+.||++|+++||+    .+..+|.|.|||++++
T Consensus         4 Pi~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~-----~~~~~~TNn~aEl~Avi~aL~----~~~~~v~I~TDS~yvi   74 (110)
T d1s1ta1           4 PIVGAETFYVDGAANRETKLGKAGYVTNRGRQKV-----VTLTDTTNQKTELQAIYLALQ----DSGLEVNIVTDSQYAL   74 (110)
T ss_dssp             CCTTSEEEEEEEEEETTTTEEEEEEEETTSCEEE-----EEESSCCHHHHHHHHHHHHHH----HSCSEEEEEECCHHHH
T ss_pred             CCCCCcEEEEeCCCCCCCCCcEEEEEEecCCeEE-----EecccCcHHHHHHHHHHHHHH----hCCCeEEEEEehHHHH
Confidence            5556678999999999999999998886643322     224456999999999999986    3567899999999999


Q ss_pred             HhhcCCCCCCCchhhhHHHHHHHhccCCccceeeccCc
Q 039495          243 KCLELPASFLDPNRALILSCREYLCRNWDCKLQLILRE  280 (327)
Q Consensus       243 ~~i~~~~~~~s~~~~li~eI~~ll~~f~~v~~~hI~R~  280 (327)
                      +.+++....  ....++.++.+.+..+..+.+.||+.+
T Consensus        75 ~~i~~~~~~--~~~~l~~~il~~l~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          75 GIIQAQPDQ--SESELVNQIIEQLIKKEKVYLAWVPAH  110 (110)
T ss_dssp             HHHHHCCSE--ESCHHHHHHHHHHHHCSEEEEEECCSS
T ss_pred             HHHhcCccc--cchHHHHHHHHHHhcCCceEEEEeCCC
Confidence            999986542  234577888887777889999999864

>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=99.37  E-value=2.7e-13  Score=110.77  Aligned_cols=77  Identities=19%  Similarity=0.246  Sum_probs=65.1

Q ss_pred             EEEEeeeecCCCCceeEEEEEEcCCCceEeccccccCCccchHHHHHHHHHhhHHHHhhCceEEEEEEccHhhHHhhcCC
Q 039495          169 KLNIEGSSSRAQGSAGAGGIVRDESGKWILGYSKNLGTSNSLASELWALYHGLNLVWERGFRKVLVECNSHEAVKCLELP  248 (327)
Q Consensus       169 K~NvDgS~~~~~~~aG~G~ViRD~~G~~l~~~~~~~~~~s~~~AE~~Al~~AL~~A~~~g~~~Vi~EsDS~~VV~~i~~~  248 (327)
                      .++||||+.+++|++|+|+|+.+......  .+..++..|+++||++|++.||+.+.+.+ .++.|+|||+++++++++.
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~--~sg~~~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~   82 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLF--EREPIPIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDK   82 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEE--ECCCEEEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHT
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEE--EEcCcCccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhC
Confidence            58999999999999999999876544433  33455667999999999999999999887 5799999999999999753