Psyllid ID: psy5302

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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-------330---
Protein Sequence
RNPNHFLSSLLTDHSLQQLYERKSSFEKPLRIRGKLLLEKYGIEYLDFLSPAPQTSAPWLIEPPVVDYSLRKFNKNTDPKEEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVMSVKHIHINRLPNLL
Secondary Structure (PSIPRED)
cccccccccccccccHHHHHHHcccccccHHHHHHHHHHHHcccccccccccccccccccccccEEEccccccccccccHHHHHHHHHHHHHHcccccEEEEEccccccccccEEEEEcccEEEEEccccccHHHHHHHHHHHHHHHHHHHHcccccccEEEEEcccHHHHHHHcccccccHHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHccccccHHHHcccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccHHHHHHHcccccccHHHHHHHHHHHccccHHcccccccccccccccccccEcccccccccccccHHHHHHHHHHHHHHcccccEEEEEccccccccEEEEEEEcccEEEEccccccHHHHHHHHHHHHHHHHHHHHHccccccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHcccccHHHHHHcccccccccccccccccEEEEEEccccccc
Coil and Loop (DISEMBL)
RNPNHFLSSLLTDHSLQQLYErkssfekplRIRGKLLLEKYGIeyldflspapqtsapwlieppvvdyslrkfnkntdpkeEINISFQELLqqvpvdstviytdasktdvavssafcsqdikfSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSirfiwvpshvgiagNEEADRLAKEAltsthptinkipipdykaysKRKILTSWNSEWhnlqnnklheikvenkpwnppylinrkeqVSLTRLRIGHTNTTHihlmkkenppicvpcgcvmsvkhihinrlpnll
Flexible Loop (DISEMBL)
rnpnhflsslltdhslQQLYerkssfekplriRGKLLLEKYGIEYLDFLSPAPQTSAPWLIEPPVVDYSLRKFNKNTDPKEEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEaltsthptinkipipdykaYSKRKILTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRLRIGHTNTthihlmkkenpPICVPCGCVMSVKHIHINRLPNLL
Low Complexity Region (SEG)
RNPNHFLSSLLTDHSLQQLYERKSSFEKPLRIRGKLLLEKYGIEYLDFLSPAPQTSAPWLIEPPVVDYSLRKFNKNTDPKEEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVMSVKHIHINRLPNLL
Disordered region (IsUnstruct)
*************************FEKPLRIRGKLLLEKYGIEYLDFLSPAPQTSAPWLIEPPVVDYSLRKFNKNTDPKEEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVMSVKHIHINRL****
Disordered Region (DISOPRED)
***NHFLSSLLTDHSLQQL***********RIRGKLLLEKYGIEYLDFLSPAPQTSAPWLIEPPVVDYSLRKFNKNTDPKEEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVMSVKHIHINRLPNLL
Disordered Region (DISEMBL)
RNPNHFLSSLLTDHSLQQLYERKSSFEKPLRIRGKLLLEKYGIEYLDFLSPAPQTSAPWLIEPPVVDYSLRKFNKNTDPKEEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVMSVKHIHINRLPNLL
Disordered Region (DISPRO)
*****FLSSLLTDHSLQQLYERKSSFEKPLRIRGKLLLEKYGIEYLDFLSPAPQTSAPWLIEPPVVDYSLRKFNKNTDPKEEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVMSVKHIHINRLPNLL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
RNPNHFLSSLLTDHSLQQLYERKSSFEKPLRIRGKLLLEKYGIEYLDFLSPAPQTSAPWLIEPPVVDYSLRKFNKNTDPKEEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVMSVKHIHINRLPNLL
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	333	2.2.26 [Sep-21-2011]
P11204	1146	Pol polyprotein OS=Equine	yes	N/A	0.372	0.108	0.25	0.0008
P32542	1146	Pol polyprotein OS=Equine	yes	N/A	0.372	0.108	0.25	0.0008

>sp|P11204|POL_EIAV9 Pol polyprotein OS=Equine infectious anemia virus (isolate 1369) GN=pol PE=1 SV=1

 Score = 45.1 bits (105), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 33/132 (25%), Positives = 53/132 (40%), Gaps = 8/132 (6%)

Query: 91  LQQVPVDSTVIYTDASKTDVAVSSAFCSQDIKFSTRLHSLLSICNAELTSILFAIHFLLS 150
           L + P     IYTD  K +    +A+ + + +   +    ++   AE  +I  A+     
Sbjct: 613 LVEEPTSGITIYTDGGKQNGEGIAAYVTSNGRTKQKRLGPVTHQVAERMAIQMALEDTRD 672

Query: 151 SCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSIRFIWVPSHVG 210
             +N        I +DS    + +     L    S    +I   + K  + F WVP H G
Sbjct: 673 KQVN--------IVTDSYYCWKNITEGLGLEGPQSPWWPIIQNIREKEIVYFAWVPGHKG 724

Query: 211 IAGNEEADRLAK 222
           I GN+ AD  AK
Sbjct: 725 ICGNQLADEAAK 736

During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.
Equus caballus (taxid: 9796)
EC: 3EC: .EC: 1EC: .EC: 1EC: 3EC: .EC: 2

>sp|P32542|POL_EIAVC Pol polyprotein OS=Equine infectious anemia virus (isolate CL22) GN=pol PE=1 SV=1

 Score = 45.1 bits (105), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 33/132 (25%), Positives = 53/132 (40%), Gaps = 8/132 (6%)

Query: 91  LQQVPVDSTVIYTDASKTDVAVSSAFCSQDIKFSTRLHSLLSICNAELTSILFAIHFLLS 150
           L + P     IYTD  K +    +A+ + + +   +    ++   AE  +I  A+     
Sbjct: 613 LVEEPTSGITIYTDGGKQNGEGIAAYVTSNGRTKQKRLGPVTHQVAERMAIQMALEDTRD 672

Query: 151 SCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSIRFIWVPSHVG 210
             +N        I +DS    + +     L    S    +I   + K  + F WVP H G
Sbjct: 673 KQVN--------IVTDSYYCWKNITEGLGLEGPQSPWWPIIQNIREKEIVYFAWVPGHKG 724

Query: 211 IAGNEEADRLAK 222
           I GN+ AD  AK
Sbjct: 725 ICGNQLADEAAK 736

During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.

Equus caballus (taxid: 9796)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 2

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	333
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.873	0.579	0.376	3e-41
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.759	0.969	0.394	9e-39
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.717	0.507	0.380	3e-37
427791807	1212	Putative tick transposon, partial [Rhipi	0.945	0.259	0.352	1e-36
427791321	1210	Putative tick transposon, partial [Rhipi	0.945	0.260	0.352	1e-36
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.897	0.244	0.352	1e-35
427778603	1397	Putative tick transposon [Rhipicephalus	0.939	0.224	0.325	9e-33
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.765	0.642	0.358	1e-32
427798889	1199	Putative tick transposon, partial [Rhipi	0.942	0.261	0.343	1e-31
443724607	397	hypothetical protein CAPTEDRAFT_208903 [	0.765	0.642	0.365	1e-31

>gi|443693558|gb|ELT94903.1| hypothetical protein CAPTEDRAFT_189741, partial [Capitella teleta]

 Score =  175 bits (443), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 120/319 (37%), Positives = 172/319 (53%), Gaps = 28/319 (8%)

Query: 19  LYERKSSFEKPLRIRGKLLLEKYGIEYLDFLSP-AP---QTSAPWLIEPPVVDYSLRKFN 74
            Y  K SF +PL  R +  LE          +P AP       PW + PP VD S+ KF 
Sbjct: 6   FYTSKPSFIRPLLYRTEEALESV------ITAPIAPFKISDVPPWKLRPPEVDTSISKFL 59

Query: 75  KNTDPKEEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQDIKFSTRLHSLLSIC 134
           K+  P   +   F  L+ + P     IYTD SK++ AV+ AF     +    L + +SI 
Sbjct: 60  KDQHPALFLKQEFYNLIDKYP--GINIYTDGSKSNNAVACAFTCSTYQIQFGLPTQMSIY 117

Query: 135 NAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNP----IASEIRNL 190
            AEL +I  A+ F+    + +  Q  F ICSDSLS+L  L N    +P    I ++  NL
Sbjct: 118 TAELIAIEQALIFI--ETVKDEDQ--FNICSDSLSSLTALSNCDITHPYLLSILTKQNNL 173

Query: 191 ILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIP--DYKAYSKRKI 248
           +   K KL + FIW PSHVGI GNE ADRLAK+AL      + K+P+P  DYK+  +  +
Sbjct: 174 V--RKGKLVV-FIWCPSHVGILGNEVADRLAKQALVMP---VTKLPLPHTDYKSPIRSYV 227

Query: 249 LTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKEN 308
            + W +EW    +NKLH I+     W     I+R+ ++ L R RIGH++ TH +L+++E 
Sbjct: 228 KSLWQNEWDEETDNKLHSIQPVISEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREV 287

Query: 309 PPICVPCGCVMSVKHIHIN 327
            P C+PC  +++VKHI I+
Sbjct: 288 APFCIPCQSLLTVKHILID 306

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443695973|gb|ELT96755.1| hypothetical protein CAPTEDRAFT_23017, partial [Capitella teleta]

 Score =  167 bits (422), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 107/271 (39%), Positives = 154/271 (56%), Gaps = 18/271 (6%)

Query: 63  PPVVDYSLRKFNKNTDPKEEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQDIK 122
           PP VD S+ KF K+  P   +   F  L+ + P     IYTD SK++ AV+ AF     +
Sbjct: 2   PPEVDTSISKFLKDQHPALFLKQEFYNLIDKYP--GINIYTDGSKSNDAVACAFTCSTYQ 59

Query: 123 FSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNP 182
               L + +SI  AEL +I  A+ F+    + +  Q  F ICSDSLS+L  L N    +P
Sbjct: 60  IQFGLPAQMSIYTAELIAIEQALIFI--ETVKDEDQ--FNICSDSLSSLTALSNCDITHP 115

Query: 183 ----IASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIP 238
               I ++  NL+   K KL + FIW PSHVGI GNE ADRLAK+AL      + K+P+P
Sbjct: 116 YLLSILTKQNNLV--RKGKLVV-FIWCPSHVGILGNEVADRLAKQALVMP---VTKLPLP 169

Query: 239 --DYKAYSKRKILTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRLRIGHT 296
             DYK+  +  + + W +EW    +NKLH I+     W     I+R+ ++ L R RIGH+
Sbjct: 170 HTDYKSPIRSYVKSLWQNEWDEETDNKLHSIQPVISEWKQGPQIDRRGEIVLARARIGHS 229

Query: 297 NTTHIHLMKKENPPICVPCGCVMSVKHIHIN 327
           + TH +L+++E  P C+PC  ++SVKHI I+
Sbjct: 230 HLTHGYLLRREVAPFCIPCQSLLSVKHILID 260

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443721618|gb|ELU10867.1| hypothetical protein CAPTEDRAFT_200496, partial [Capitella teleta]

 Score =  161 bits (408), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 94/247 (38%), Positives = 142/247 (57%), Gaps = 8/247 (3%)

Query: 83  INISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQDIKFSTRLHSLLSICNAELTSIL 142
           I   F + L + P DSTV YTD SK++ +V+ +F S  +K   +L   +S+  +E+ +IL
Sbjct: 6   IRSEFADALDRYP-DSTVFYTDGSKSEDSVACSFFSSRLKLKMKLPVQMSVFTSEIIAIL 64

Query: 143 FAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLI--LENKSKLSI 200
            A+  + +   NE  Q  FVICSDSLSA+  +  +   +P   ++   I  +  + K+ +
Sbjct: 65  SALRCVEAD--NEQHQ--FVICSDSLSAIMAIHGMDVRHPYVLQVLYAIKSISQQEKIVV 120

Query: 201 RFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILTSWNSEWHNLQ 260
            F+W PSHVGI GNE AD LAKEAL+ST+     +P  D +   K+ I + W  EW    
Sbjct: 121 -FMWCPSHVGIPGNEMADTLAKEALSSTNLAELPVPASDLRCLIKKYIRSRWQHEWDEQH 179

Query: 261 NNKLHEIKVENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVMS 320
           +NKLH I     PW P     R+E++ L R+RIGHT+ TH ++ + ++   CV C C ++
Sbjct: 180 SNKLHSIHPTIGPWPPCQREKRREEIVLARIRIGHTHYTHDYIPRGDDQTECVACVCPLT 239

Query: 321 VKHIHIN 327
           V+HI I 
Sbjct: 240 VQHIIIE 246

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|427791807|gb|JAA61355.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  159 bits (403), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 116/329 (35%), Positives = 164/329 (49%), Gaps = 14/329 (4%)

Query: 2    NPNHFLSSLLTDHSLQQLYERKSSFEKPLRIRGKLLLEKYGI--EYLDFLSPAPQTSAPW 59
            +P H    + T  S +  Y  KS+  KPL +R +     Y I  E LD     P+   PW
Sbjct: 843  SPQHICYDIATRCSSRLHYLNKSNLIKPLLLRFEEYCRTYVISEETLDVARKPPRI-PPW 901

Query: 60   LIEPPVVDYSLRKFNKNTDPKEEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQ 119
                 + D SL   NK   P E I   F+ L Q+   D    YTD SKT   V     + 
Sbjct: 902  FDLAQLCDISLSHINKKVTPPELIIQEFRAL-QEKYRDYAEFYTDGSKTRDHVGIGIVTG 960

Query: 120  DIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFS 179
            +  FS R+   +SI  AE+ ++  A   +++    +H +A  +I +DSLSAL+ L     
Sbjct: 961  ESAFSVRVPQCISIFTAEVYALYEAARKIIA---GKHKKA--IIYTDSLSALKALHIKSE 1015

Query: 180  LNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIP- 238
              P+  +I N++L N   +S+RF WVPSHVGI GNE+AD+ A  A    H T+ KI IP 
Sbjct: 1016 CEPLVGDILNMVLINSKVISMRFCWVPSHVGIPGNEKADKCASLA---AHKTLTKIRIPL 1072

Query: 239  -DYKAYSKRKILTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRLRIGHTN 297
             D +   +  +L  W  +W +  +NKLH +K     W       R  +V L RLRIGHT+
Sbjct: 1073 KDSQRTIRLALLAKWQQQWDSCTSNKLHLVKPTLGEWKNCRHQERFIEVILCRLRIGHTH 1132

Query: 298  TTHIHLMKKENPPICVPCGCVMSVKHIHI 326
             TH  L+ KE  P+C  C   +++ HI I
Sbjct: 1133 LTHNFLLTKEEQPMCEKCQEPLTLIHILI 1161

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427791321|gb|JAA61112.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  159 bits (403), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 116/329 (35%), Positives = 164/329 (49%), Gaps = 14/329 (4%)

Query: 2    NPNHFLSSLLTDHSLQQLYERKSSFEKPLRIRGKLLLEKYGI--EYLDFLSPAPQTSAPW 59
            +P H    + T  S +  Y  KS+  KPL +R +     Y I  E LD     P+   PW
Sbjct: 840  SPQHICYDIATRCSSRLHYLNKSNLIKPLLLRFEEYCRTYVISEETLDVARKPPRI-PPW 898

Query: 60   LIEPPVVDYSLRKFNKNTDPKEEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQ 119
                 + D SL   NK   P E I   F+ L Q+   D    YTD SKT   V     + 
Sbjct: 899  FDLAQLCDISLSHINKKVTPPELIIQEFRAL-QEKYRDYAEFYTDGSKTRDHVGIGIVTG 957

Query: 120  DIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFS 179
            +  FS R+   +SI  AE+ ++  A   +++    +H +A  +I +DSLSAL+ L     
Sbjct: 958  ESAFSVRVPQCISIFTAEVYALYEAARKIIA---GKHKKA--IIYTDSLSALKALHIKSE 1012

Query: 180  LNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIP- 238
              P+  +I N++L N   +S+RF WVPSHVGI GNE+AD+ A  A    H T+ KI IP 
Sbjct: 1013 CEPLVGDILNMVLINSKVISMRFCWVPSHVGIPGNEKADKCASLA---AHKTLTKIRIPL 1069

Query: 239  -DYKAYSKRKILTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRLRIGHTN 297
             D +   +  +L  W  +W +  +NKLH +K     W       R  +V L RLRIGHT+
Sbjct: 1070 KDSQRTIRLALLAKWQQQWDSCTSNKLHLVKPTLGEWKNCRHQERFIEVILCRLRIGHTH 1129

Query: 298  TTHIHLMKKENPPICVPCGCVMSVKHIHI 326
             TH  L+ KE  P+C  C   +++ HI I
Sbjct: 1130 LTHNFLLTKEEQPMCEKCQEPLTLIHILI 1158

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|125901787|gb|ABN58714.1| pol-like protein [Biomphalaria glabrata]

 Score =  156 bits (395), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 111/315 (35%), Positives = 171/315 (54%), Gaps = 16/315 (5%)

Query: 18   QLYERKSSFEKPLRIRGKLLLEKYGIEYLDFLSP--APQTSAPWLIEPPVVDYSLRKFNK 75
            +LY R+ +  +PL +R +  ++    + +D +S    PQ + PWL+  P ++ SL  F K
Sbjct: 877  ELYNRRPNVIQPLGLRMREPIQNL-TQPIDQISKIETPQ-NPPWLMNKPKLNLSLLNFKK 934

Query: 76   -NTDPKEEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQDIKFSTRLHSLLSIC 134
             NTDP   + + F+EL Q+   D   IYTD SK +  V+ A   ++   S RL    SI 
Sbjct: 935  ENTDP-SILQVHFREL-QESYGDCGTIYTDGSKMEGKVACACSFRNKTISRRLPDGCSIF 992

Query: 135  NAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASE-IRNLILE 193
             AEL +IL A+  + +S      ++ F+ICSDS SALQ L  + +  P+  + ++ L L 
Sbjct: 993  TAELHAILLALMAVKAS-----ERSKFIICSDSKSALQALGRMKTDIPLVHKSLKLLDLI 1047

Query: 194  NKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILTSWN 253
               +  + FIWVPSHVGI GNE ADR AK AL     +  +IP  D +          W 
Sbjct: 1048 TADRRDVTFIWVPSHVGIEGNEAADREAKRALNHA-VSGTQIPYSDLRQSIASATYREWQ 1106

Query: 254  SEWHNLQNNKLHEIKVENKPWNP-PYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPIC 312
            + W    ++KL +I V +  W P    + R+   +++RLRIGHT  TH  ++K+E PP+C
Sbjct: 1107 NRWEAETHSKLRQI-VADVRWRPTSKGLTRRGSTTMSRLRIGHTYITHSFVLKREEPPLC 1165

Query: 313  VPCGCVMSVKHIHIN 327
              C   ++V+HI ++
Sbjct: 1166 EYCDSRLTVEHILVD 1180

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|427778603|gb|JAA54753.1| Putative tick transposon [Rhipicephalus pulchellus]

 Score =  147 bits (370), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 106/326 (32%), Positives = 157/326 (48%), Gaps = 13/326 (3%)

Query: 5    HFLSSLLTDHSLQQLYERKSSFEKPLRIRGKLLLEKYGIEYLDFLSPAPQTSA--PWLIE 62
            H   +L+ D S  QLY  + S   P  +  + ++EK  I + D L    Q     PW   
Sbjct: 1016 HPCKALMNDVSTTQLYINRPSISPPFPLAIRPVVEKLKIHFED-LQEIDQVEVIPPWKQC 1074

Query: 63   PPVVDYSLRKFNKNTDPKEEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQDIK 122
            P + D+S +   K T P   I   F  L  +    S   ++D SK+  +VS A   +   
Sbjct: 1075 PIICDWSFKDLKKKTAPNALIQQHFLALEHKY--RSAAFFSDGSKSQTSVSCAAYGESFS 1132

Query: 123  FSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQ-NVFSLN 181
             +  LH+  SI  AE   IL     L+   + +H     +I +DSLS +  L     S N
Sbjct: 1133 DAKTLHAHTSIFTAEAYGIL-----LIVEHIKQHMIRRSIIYTDSLSVVTALSCGKCSKN 1187

Query: 182  PIASEIRNLILENKSK-LSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDY 240
            P+ +++ N + E  ++ LSI   WVP H GI GNE  D+ A+EA +     I+ +P  D 
Sbjct: 1188 PVFNKLLNNMHEAYNQNLSIVLCWVPGHAGITGNEMVDKNAREAASRHTIDISSVPGVDL 1247

Query: 241  KAYSKRKILTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRLRIGHTNTTH 300
                +R + + W  EW    +NKLH +K       P  L NR  +V+L RLRIGHT  TH
Sbjct: 1248 NPVVRRGLRSHWQVEWDKQVDNKLHLVKPHLSKVLPQKL-NRFTEVTLARLRIGHTYATH 1306

Query: 301  IHLMKKENPPICVPCGCVMSVKHIHI 326
             HL+   +PP C+ CG  +++ H+ I
Sbjct: 1307 KHLLTGTDPPTCIHCGETLTILHVLI 1332

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443712830|gb|ELU05953.1| hypothetical protein CAPTEDRAFT_202466 [Capitella teleta]

 Score =  146 bits (369), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 99/276 (35%), Positives = 149/276 (53%), Gaps = 21/276 (7%)

Query: 61  IEPPVVDYSLRKFNKNTDPK---EEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFC 117
           + P +V YS  K    T  +   +  N  F  L+ + P     IYTD SK++  V+ AF 
Sbjct: 92  VGPDMVHYSFLKHLPCTAQQIVVDAFNHEFYNLIDKYP--GINIYTDGSKSNDTVACAFT 149

Query: 118 SQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNV 177
               +    L + +SI  AEL +I  A+ F+    + +  Q  F ICSDSLS+L  L N 
Sbjct: 150 CSTYQIQFGLPAQMSIYTAELIAIEQALIFI--ETVKDEDQ--FNICSDSLSSLTALSNC 205

Query: 178 FSLNP----IASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTIN 233
              +P    I ++  NL+ + K    + FIW PSHVGI GNE ADR AK+AL      + 
Sbjct: 206 DITHPYLLSILTKQNNLVRKGKK---VVFIWCPSHVGILGNEVADRQAKQALVMP---VT 259

Query: 234 KIPIP--DYKAYSKRKILTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRL 291
           K+P+P  DYK+  +  + + W +EW    +NKLH I+     W     I+R+ ++ L   
Sbjct: 260 KLPLPHTDYKSPIRSYVKSLWQNEWDGETDNKLHIIQPVISEWKQGPQIDRRGEIVLACA 319

Query: 292 RIGHTNTTHIHLMKKENPPICVPCGCVMSVKHIHIN 327
           RIGH++ TH +L+++E  P C+PC  +++VKHI I+
Sbjct: 320 RIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILID 355

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|427798889|gb|JAA64896.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  142 bits (359), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 113/329 (34%), Positives = 159/329 (48%), Gaps = 15/329 (4%)

Query: 2    NPNHFLSSLLTDHSLQQLYERKSSFEKPLRIRGKLLLEKYGIEYLDFLSPAPQTSAP-WL 60
            +P+H   S + D S   L+E + S + P  +R + L E+ G+   +    AP    P W 
Sbjct: 870  HPSH---STINDLSCSTLFENRPSLKPPYSLRVRDLAEQTGLPLFEHRLMAPAAYPPPWQ 926

Query: 61   IEPPVVDYSLRKFNKNTDPKEEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFCSQD 120
             +    D S  +  K+  P   I   F EL  Q   +    YTDASK+  +VS A     
Sbjct: 927  WQLIDCDVSFMEVTKHA-PIAHIRTYFLEL--QHKYNCPAFYTDASKSHTSVSYAAVGPS 983

Query: 121  IKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFS- 179
               +  LH   SI  AE  +IL A+  +    L +      VI +DSLS ++ L+ +   
Sbjct: 984  FSAAGALHPNTSIFTAEAYAILAAVKHIRELKLQKA-----VIYTDSLSVVKALKTLKKH 1038

Query: 180  LNPIASEIRNLILE-NKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIP 238
             NP+   + +L+     SK  +   WVP H  I GN  AD+LA  A  S+  T   IP  
Sbjct: 1039 RNPVLVSLYSLLCTIYTSKQHVVVCWVPGHREIQGNVMADQLAVSAHDSSANTSIAIPAL 1098

Query: 239  DYKAYSKRKILTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRLRIGHTNT 298
            D K Y KRKI   W S W    +NKLH IK +   W PP   +R  +V+LTRLR GHT++
Sbjct: 1099 DLKPYLKRKIRAYWQSTWDRQTHNKLHVIKPQLGHW-PPISKSRYTEVTLTRLRTGHTHS 1157

Query: 299  THIHLMKKENPPICVPCGCVMSVKHIHIN 327
            TH +L+   + P C  CG  ++V HI I 
Sbjct: 1158 THAYLLSGGDAPFCDKCGEPLTVIHILIQ 1186

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443724607|gb|ELU12531.1| hypothetical protein CAPTEDRAFT_208903 [Capitella teleta]

 Score =  142 bits (359), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 101/276 (36%), Positives = 151/276 (54%), Gaps = 21/276 (7%)

Query: 61  IEPPVVDYSLRKFNKNTDPK---EEINISFQELLQQVPVDSTVIYTDASKTDVAVSSAFC 117
           + P +V YS  K    T  +   +  N  F  L+ + P     IYTD SK++ AV+ AF 
Sbjct: 92  VGPDMVHYSFLKHLPCTAQQIVVDAFNHEFYNLIDKYP--GINIYTDGSKSNDAVACAFT 149

Query: 118 SQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNV 177
               +    L + +SI  AEL +I  A+ F+ +  + +  Q  F ICSDSLS+L  L N 
Sbjct: 150 CSTYQIQFGLPAQMSIYTAELIAIEQALIFIET--MKDEDQ--FNICSDSLSSLTALSNC 205

Query: 178 FSLNP----IASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTIN 233
              +P    I ++  NL+   K KL + FIW PSHVGI GNE ADRLAK+AL      + 
Sbjct: 206 DITHPYLLSILTKQNNLV--RKGKLVV-FIWCPSHVGILGNEVADRLAKQALVMP---VT 259

Query: 234 KIPIP--DYKAYSKRKILTSWNSEWHNLQNNKLHEIKVENKPWNPPYLINRKEQVSLTRL 291
           K+P+P  DYK+  +  + +   +EW    +NKLH I+     W     I+R+ ++ L   
Sbjct: 260 KLPLPHTDYKSPIRSYVKSLRQNEWDEETDNKLHTIQPVISEWKQGPQIDRRGEIVLACA 319

Query: 292 RIGHTNTTHIHLMKKENPPICVPCGCVMSVKHIHIN 327
            IGH++ TH +L+++E  P C+PC  +++VKHI I+
Sbjct: 320 CIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILID 355

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

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	333
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.687	0.471	0.262	3.6e-08

ASPGD|ASPL0000075333 AN10625 [Emericella nidulans (taxid:162425)]

 Score = 154 (59.3 bits), Expect = 3.6e-08, P = 3.6e-08
 Identities = 67/255 (26%), Positives = 122/255 (47%)

Query:    88 QELLQQVPVDSTVIYTDASKTDVAV-SSAFCSQD-IKFSTRL--HSLLSICNAELTSILF 143
             + +L + P     +YTD S  +  V ++A C +  I  S+ +   S  ++  AEL  IL 
Sbjct:   173 RNILNRAP-RPIALYTDGSGINGRVGAAAICPKYLISRSSYMGQQSESTVYVAELQGILL 231

Query:   144 AIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNP---IASEIRNLILENKSKLSI 200
             A+  +L   + +H     VI +D+ + LQ L+N  S +    + + I  L    K+ L++
Sbjct:   232 ALVIILQRQM-QHA----VIFTDNQATLQALRNPGSQSGQYILEAIIMALNKGRKAGLNV 286

Query:   201 RFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKR--KILTS-WNSEWH 257
              F W+P+H G+ GNE+ADR AKEA        ++  +    A  +R  +++ + W ++W 
Sbjct:   287 HFRWIPAHRGVEGNEQADRRAKEATGWRRIRGHRGRMTIRSAVKRRAHEVVNARWENDWK 346

Query:   258 NLQNNK-LHEIKVE--NKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPI--- 311
             +  + + L+E+      K       ++R     + ++R G     H +L ++  P +   
Sbjct:   347 SCHHGRELYELTPTPTRKVLRVHQDLHRALSTIIVQMRTGKIGLRH-YLYQRGVPDVPNS 405

Query:   312 -CVPCG-CVMSVKHI 324
              C  CG    SV+HI
Sbjct:   406 DC-QCGRATQSVRHI 419


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        0.319   0.133   0.400    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      333       333   0.00091  116 3  11 22  0.39    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:  1
  No. of states in DFA:  614 (65 KB)
  Total size of DFA:  244 KB (2132 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:  30.59u 0.16s 30.75t   Elapsed:  00:00:02
  Total cpu time:  30.59u 0.16s 30.75t   Elapsed:  00:00:02
  Start:  Thu Aug 15 12:53:10 2013   End:  Thu Aug 15 12:53:12 2013

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" 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 EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.26	0.691
3rd Layer	3.1.26.4	LOW CONFIDENCE prediction!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	333
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	2e-30
pfam00075	126	pfam00075, RNase_H, RNase H	2e-15
cd09277	133	cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI	1e-09
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	2e-08
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	6e-06
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	1e-05
cd09275	120	cd09275, RNase_HI_RT_DIRS1, DIRS1 family of RNase	4e-05
cd09279	128	cd09279, RNase_HI_archaeal_like, RNAse HI family t	3e-04
PRK00203	150	PRK00203, rnhA, ribonuclease H; Reviewed	0.001
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	0.001
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	0.003

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

 Score =  111 bits (280), Expect = 2e-30
 Identities = 49/129 (37%), Positives = 65/129 (50%), Gaps = 7/129 (5%)

Query: 100 VIYTDASKTDVAVSSAFCSQDIKFSTRLHSLLSIC---NAELTSILFAIHFLLSSCLNEH 156
           VIYTD SK +    + F        +R + L   C   +AEL +IL A+   L       
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 157 TQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSK-LSIRFIWVPSHVGIAGNE 215
                 I SDS +AL+ L++  S +P+   IR  I E  +  + +R  WVP H GI GNE
Sbjct: 61  K---ITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNE 117

Query: 216 EADRLAKEA 224
            ADRLAKEA
Sbjct: 118 RADRLAKEA 126

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

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

 Score = 71.1 bits (175), Expect = 2e-15
 Identities = 29/91 (31%), Positives = 44/91 (48%), Gaps = 9/91 (9%)

Query: 136 AELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILE-N 194
           AEL +++ A+  L    +N        I +DS   +  + N +     +  I+N I E  
Sbjct: 43  AELLALIEALEALSGQKVN--------IYTDSQYVIGGITNGWPTKSESKPIKNEIWELL 94

Query: 195 KSKLSIRFIWVPSHVGIAGNEEADRLAKEAL 225
           + K  +   WVP H GI GNE AD+LAK+  
Sbjct: 95  QKKHKVYIQWVPGHSGIPGNELADKLAKQGA 125

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

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

 Score = 55.6 bits (135), Expect = 1e-09
 Identities = 17/45 (37%), Positives = 25/45 (55%)

Query: 181 NPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEAL 225
                E +  + + K K+ I F+ V +H G   NE AD+LAK+AL
Sbjct: 89  KEGTKEYKEFMDKIKKKIKISFVKVKAHSGDKYNELADKLAKKAL 133

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability. Some bacteria distinguished from other bacterial RNase HI in the presence of a hybrid binding domain (HBD) at the N-terminus which is commonly present at the N-termini of eukaryotic RNase HI. It has been reported that this domain is required for dimerization and processivity of RNase HI upon binding to RNA-DNA hybrids. Length = 133

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

 Score = 52.6 bits (127), Expect = 2e-08
 Identities = 30/107 (28%), Positives = 48/107 (44%), Gaps = 20/107 (18%)

Query: 136 AELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTL--------QNVFSL---NPIA 184
           AEL +++ A+  +             VI +DS   +  +        +N +      P+A
Sbjct: 46  AELRAVIHALRLIKEVGEGLTK---LVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVA 102

Query: 185 -----SEIRNLILE-NKSKLSIRFIWVPSHVGIAGNEEADRLAKEAL 225
                 E+  L+ E  +  + ++F  VP H GI GNEEADRLAK+  
Sbjct: 103 NKDLIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGA 149

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

>gnl|CDD|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in prokaryotes

 Score = 44.8 bits (107), Expect = 6e-06
 Identities = 13/29 (44%), Positives = 16/29 (55%)

Query: 196 SKLSIRFIWVPSHVGIAGNEEADRLAKEA 224
           +K  + + WV  H G  GNE AD LA  A
Sbjct: 109 AKHQVTWHWVKGHAGHPGNERADELANAA 137

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. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability. Length = 139

>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 = 43.5 bits (103), Expect = 1e-05
 Identities = 28/91 (30%), Positives = 40/91 (43%), Gaps = 10/91 (10%)

Query: 136 AELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILE-N 194
           AEL ++L A+   L+  L        +I +DS   +  + +        + +   IL   
Sbjct: 42  AELLALLEAL--ELALDLGLKK---LIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLL 96

Query: 195 KSKLSIRFIWVPSHVGIAGNEEADRLAKEAL 225
              + IRF  VP      GNE ADRLAKEA 
Sbjct: 97  SKFIDIRFEHVPRE----GNEVADRLAKEAA 123

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|187699 cd09275, RNase_HI_RT_DIRS1, DIRS1 family of RNase HI in long-term repeat retroelements

 Score = 42.3 bits (100), Expect = 4e-05
 Identities = 27/126 (21%), Positives = 48/126 (38%), Gaps = 16/126 (12%)

Query: 100 VIYTDASKTDVAVSSAFCSQ--DIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHT 157
           V++TDAS +      A  S        +       I   EL ++L A+    +   N   
Sbjct: 1   VLFTDASLSGWG---AVLSGSWAQGLWSAEERNKHINFLELLAVLLALQHWGARLSNRKV 57

Query: 158 QACFVICSDSLSALQTL--QNVFSLNPIASEIRNLILE-NKSKLSIRFIWVPSHVGIAGN 214
               ++ SD+ +A+  +  Q       + +  R L+L   +  + +R   +P       N
Sbjct: 58  ----LVRSDNTTAVAYINRQGGTRSPELLALARQLVLWCEERNIWLRARHIPG----VLN 109

Query: 215 EEADRL 220
             ADRL
Sbjct: 110 VAADRL 115

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. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 120

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

 Score = 39.8 bits (94), Expect = 3e-04
 Identities = 27/113 (23%), Positives = 42/113 (37%), Gaps = 21/113 (18%)

Query: 121 IKFSTRLHSLLSICN--AELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVF 178
           ++ S  L    +  N  AE  +++  +   L     E       I  DS   +  +Q  +
Sbjct: 30  LEQSIPLGFPAT--NNEAEYEALIAGLELAL-----ELGIKKLEIYGDSQLVVNQIQGEY 82

Query: 179 -----SLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALT 226
                 L P   E R L+   K    +   W+P       N+EAD LA +AL 
Sbjct: 83  EVKNERLAPYLEEARELL---KKFEEVEIKWIPRE----ENKEADALANQALD 128

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

>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed

 Score = 38.7 bits (91), Expect = 0.001
 Identities = 10/26 (38%), Positives = 13/26 (50%)

Query: 199 SIRFIWVPSHVGIAGNEEADRLAKEA 224
            I++ WV  H G   NE  D LA+  
Sbjct: 114 QIKWHWVKGHAGHPENERCDELARAG 139

Length = 150

>gnl|CDD|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term repeat retroelements

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 29/146 (19%), Positives = 51/146 (34%), Gaps = 31/146 (21%)

Query: 100 VIYTDASKTDVAVSSAFCS-QDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQ 158
            ++TD S        A  +  D+     L    S   AEL +++ A+       +N    
Sbjct: 1   TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKGKPVN---- 56

Query: 159 ACFVICSDSLSALQTLQNV--------------FSLNPIASEIRNLILENKSKLSIRFIW 204
               I +DS  A   L  +               +L  +  +++  I   K    +  I 
Sbjct: 57  ----IYTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKP---VAVIH 109

Query: 205 VPSHVG-----IAGNEEADRLAKEAL 225
           + +H G       GN  AD+ A++A 
Sbjct: 110 IRAHSGLPGPLALGNARADQAARQAA 135

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 eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 135

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

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 12/21 (57%), Positives = 14/21 (66%)

Query: 204 WVPSHVGIAGNEEADRLAKEA 224
           WV  H G   NE AD+LA+EA
Sbjct: 122 WVKGHAGHPENERADQLAREA 142

Length = 154

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	333
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.89
PRK06548	161	ribonuclease H; Provisional	99.89
PRK08719	147	ribonuclease H; Reviewed	99.88
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.88
PRK00203	150	rnhA ribonuclease H; Reviewed	99.88
KOG3752|consensus	371		99.75
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.75
PRK13907	128	rnhA ribonuclease H; Provisional	99.69
PRK07708	219	hypothetical protein; Validated	99.66
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.46
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.24
COG3341	225	Predicted double-stranded RNA/RNA-DNA hybrid bindi	97.08
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	96.36

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

Probab=99.89  E-value=9.9e-23  Score=167.95  Aligned_cols=123  Identities=22%  Similarity=0.234  Sum_probs=96.5

Q ss_pred             CcEEEEecCCCC--CCCcceEEe--cCc--eeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHH
Q psy5302          97 DSTVIYTDASKT--DVAVSSAFC--SQD--IKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSA  170 (333)
Q Consensus        97 ~~~~iytDGS~~--~~~~G~g~~--~~~--~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~  170 (333)
                      ..+.||||||+.  +|..|+|+|  .+.  ...+.... .+|+++||+.|++.||+.+.+.+..   .  |.|+|||++|
T Consensus         2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~---~--v~l~tDS~yv   75 (154)
T COG0328           2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGAC---E--VTLYTDSKYV   75 (154)
T ss_pred             CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCc---e--EEEEecHHHH
Confidence            358999999975  455788877  232  23455555 8999999999999999999985543   4  9999999999


Q ss_pred             HHHHcCCCCC----------------chHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCC
Q psy5302         171 LQTLQNVFSL----------------NPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTST  228 (333)
Q Consensus       171 ~~~l~~~~~~----------------~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~  228 (333)
                      +++|..|..+                .++++++.+++   .....|.+.|||||+|.++||+||+||+.|+...
T Consensus        76 ~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~---~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          76 VEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELL---KRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             HHHHHHHHhhccccCccccccCccccHHHHHHHHHHH---hhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            9999855221                12455555554   5555899999999999999999999999998765

>PRK06548 ribonuclease H; Provisional

Probab=99.89  E-value=1.5e-22  Score=169.68  Aligned_cols=122  Identities=25%  Similarity=0.237  Sum_probs=90.0

Q ss_pred             CCcEEEEecCCCCC--CCcceEEe-cCceeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHHH
Q psy5302          96 VDSTVIYTDASKTD--VAVSSAFC-SQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQ  172 (333)
Q Consensus        96 ~~~~~iytDGS~~~--~~~G~g~~-~~~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~~  172 (333)
                      +..+.||||||+..  +..|+|++ .+....+.. ....|++.|||.|++.||+.+....      ..|.|+|||++|++
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~-~~~~TNnraEl~Aii~aL~~~~~~~------~~v~I~TDS~yvi~   75 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGG-WDIATNNIAELTAVRELLIATRHTD------RPILILSDSKYVIN   75 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccC-CCCCCHHHHHHHHHHHHHHhhhcCC------ceEEEEeChHHHHH
Confidence            34599999999864  44788877 322222222 2368999999999999998654321      23999999999999


Q ss_pred             HHcC---------CCCC-------chHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCC
Q psy5302         173 TLQN---------VFSL-------NPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTST  228 (333)
Q Consensus       173 ~l~~---------~~~~-------~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~  228 (333)
                      ++..         |...       .+++++|..++    ....|.|.|||||+|++|||.||+||++|+...
T Consensus        76 ~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~----~~~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~  143 (161)
T PRK06548         76 SLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLM----ENRNIRMSWVNAHTGHPLNEAADSLARQAANNF  143 (161)
T ss_pred             HHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHH----hcCceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence            9983         3322       23555555554    234799999999999999999999999999765

>PRK08719 ribonuclease H; Reviewed

Probab=99.88  E-value=3.3e-22  Score=166.21  Aligned_cols=121  Identities=22%  Similarity=0.263  Sum_probs=87.7

Q ss_pred             CcEEEEecCCCCCCC-----cceEEe--c--Cce--eEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEe
Q psy5302          97 DSTVIYTDASKTDVA-----VSSAFC--S--QDI--KFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICS  165 (333)
Q Consensus        97 ~~~~iytDGS~~~~~-----~G~g~~--~--~~~--~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~s  165 (333)
                      ..++||||||+..++     .|+|++  .  +..  ..+..+....|++.||+.|++.||+.+..       .  ..|+|
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~-------~--~~i~t   73 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARD-------G--DVIYS   73 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCC-------C--CEEEe
Confidence            568999999986433     488876  2  232  24455656689999999999999999854       2  57999


Q ss_pred             CcHHHHHHHcC---------CCCCch--H-HHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhc
Q psy5302         166 DSLSALQTLQN---------VFSLNP--I-ASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALT  226 (333)
Q Consensus       166 Ds~~~~~~l~~---------~~~~~~--~-~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~  226 (333)
                      ||++|+++++.         |....+  + -.++++.+........|+|.|||||+|++|||.||+||++|+.
T Consensus        74 DS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         74 DSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             chHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            99999999842         222211  1 1233333332223567999999999999999999999999975

>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=99.88  E-value=1.6e-22  Score=165.23  Aligned_cols=117  Identities=38%  Similarity=0.529  Sum_probs=90.4

Q ss_pred             CcEEEEecCCCCC--CCcceEEe-cCceeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHHHH
Q psy5302          97 DSTVIYTDASKTD--VAVSSAFC-SQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQT  173 (333)
Q Consensus        97 ~~~~iytDGS~~~--~~~G~g~~-~~~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~~~  173 (333)
                      ..++||||||+..  +..|+|++ .++...+..++ ..+++.|||.||..||+ +.. . .   .  +.|+|||++++..
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~~-~-~---~--v~I~tDS~~v~~~   72 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALK-ALE-H-R---K--VTIYTDSQYVLNA   72 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHH-THS-T-S---E--EEEEES-HHHHHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHH-Hhh-c-c---c--ccccccHHHHHHH
Confidence            4689999999653  33566665 33345555566 88999999999999999 442 2 2   3  9999999999998


Q ss_pred             HcC-----CC-CC--c-hHHHHHHHHHHhhcCCCceEEEEecCCCCC-ccchhhhHHHHHHh
Q psy5302         174 LQN-----VF-SL--N-PIASEIRNLILENKSKLSIRFIWVPSHVGI-AGNEEADRLAKEAL  225 (333)
Q Consensus       174 l~~-----~~-~~--~-~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~-~gNe~AD~lAk~a~  225 (333)
                      +..     .. ..  . ++..+|++++   ..+..|.|.|||||+|+ .||+.||+|||+|+
T Consensus        73 l~~~~~~~~~~~~~~~~~i~~~i~~~~---~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   73 LNKWLHGNGWKKTSNGRPIKNEIWELL---SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HHTHHHHTTSBSCTSSSBHTHHHHHHH---HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             HHHhccccccccccccccchhheeecc---ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence            777     22 11  2 4777888887   44788999999999999 69999999999987

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 ....

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.88  E-value=3.9e-22  Score=166.94  Aligned_cols=120  Identities=19%  Similarity=0.215  Sum_probs=90.4

Q ss_pred             cEEEEecCCCCC--CCcceEEe--cCc-e-eEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHH
Q psy5302          98 STVIYTDASKTD--VAVSSAFC--SQD-I-KFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSAL  171 (333)
Q Consensus        98 ~~~iytDGS~~~--~~~G~g~~--~~~-~-~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~  171 (333)
                      .+.||||||+..  +..|+|+|  .++ . ..+... ...|++.|||.|++.||+.+...  .   .  |.|+|||++++
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~-~~~TN~~aEL~Ai~~AL~~~~~~--~---~--v~I~tDS~yvi   74 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGE-ALTTNNRMELMAAIEALEALKEP--C---E--VTLYTDSQYVR   74 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCC-CCCcHHHHHHHHHHHHHHHcCCC--C---e--EEEEECHHHHH
Confidence            489999999864  34778876  222 2 223333 46789999999999999987542  1   3  99999999999


Q ss_pred             HHHcCC---------CCC-------chHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCCC
Q psy5302         172 QTLQNV---------FSL-------NPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTH  229 (333)
Q Consensus       172 ~~l~~~---------~~~-------~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~~  229 (333)
                      ++|..|         ...       .+++++|.+++    ....|.|.|||||+|++||+.||+|||+|+....
T Consensus        75 ~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~----~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~  144 (150)
T PRK00203         75 QGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAAL----KRHQIKWHWVKGHAGHPENERCDELARAGAEEAT  144 (150)
T ss_pred             HHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHh----ccCceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence            999863         211       13556666554    3368999999999999999999999999998763

>KOG3752|consensus

Probab=99.75  E-value=4.5e-18  Score=156.37  Aligned_cols=126  Identities=27%  Similarity=0.287  Sum_probs=98.0

Q ss_pred             CCcEEEEecCCCCCC-----CcceEEe--cC-ceeEEeecC-CCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeC
Q psy5302          96 VDSTVIYTDASKTDV-----AVSSAFC--SQ-DIKFSTRLH-SLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSD  166 (333)
Q Consensus        96 ~~~~~iytDGS~~~~-----~~G~g~~--~~-~~~~~~~l~-~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sD  166 (333)
                      .+..++|||||+..+     .+|+|++  ++ ....++.+. ..+++|.|||.|+..||+.+.+....   +  ++|.||
T Consensus       210 ~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~---k--v~I~TD  284 (371)
T KOG3752|consen  210 IEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNIN---K--VVIRTD  284 (371)
T ss_pred             ccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCC---c--EEEEec
Confidence            344899999997642     3899988  32 345677765 78999999999999999999886654   4  999999


Q ss_pred             cHHHHHHHcCCCCC-----------ch----------HHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHh
Q psy5302         167 SLSALQTLQNVFSL-----------NP----------IASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEAL  225 (333)
Q Consensus       167 s~~~~~~l~~~~~~-----------~~----------~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~  225 (333)
                      |+.++++|+.|.+.           ++          .+..+.++++. ....+|.+.||+||.|+.|||+||.||++++
T Consensus       285 S~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~-~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs  363 (371)
T KOG3752|consen  285 SEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQE-ISNKKVQQEYVGGHSGILGNEMADALARKGS  363 (371)
T ss_pred             hHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhh-hccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence            99999999876542           11          33444444411 1468999999999999999999999999986


Q ss_pred             cC
Q psy5302         226 TS  227 (333)
Q Consensus       226 ~~  227 (333)
                      ..
T Consensus       364 ~~  365 (371)
T KOG3752|consen  364 TL  365 (371)
T ss_pred             hh
Confidence            54

>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=99.75  E-value=3e-17  Score=131.24  Aligned_cols=118  Identities=31%  Similarity=0.389  Sum_probs=90.6

Q ss_pred             EEEecCCCCCC--CcceEEe--cC-c-ee-EEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHHH
Q psy5302         100 VIYTDASKTDV--AVSSAFC--SQ-D-IK-FSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQ  172 (333)
Q Consensus       100 ~iytDGS~~~~--~~G~g~~--~~-~-~~-~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~~  172 (333)
                      .+|||||...+  ++|+|++  +. . .. .........+++.+|+.|++.||+.+......   .  +.|++||+.++.
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~---~--i~i~~Ds~~~~~   75 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGK---K--VNIYTDSQYVIN   75 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCc---e--EEEEECHHHHHH
Confidence            48999998654  6888877  22 2 22 22222257899999999999999999865544   4  999999999999


Q ss_pred             HHcCCCC-Cc----hHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHh
Q psy5302         173 TLQNVFS-LN----PIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEAL  225 (333)
Q Consensus       173 ~l~~~~~-~~----~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~  225 (333)
                      .++++.. ..    .++..+.+++   .....+.|.|||+|+|..+|+.||.|||+|.
T Consensus        76 ~~~~~~~~~~~~~~~~~~~i~~~~---~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          76 ALTGWYEGKPVKNVDLWQRLLALL---KRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             HhhccccCCChhhHHHHHHHHHHH---hCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            9998764 11    2445555544   5678899999999999999999999999874

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

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.69  E-value=3.8e-16  Score=127.20  Aligned_cols=116  Identities=23%  Similarity=0.326  Sum_probs=89.0

Q ss_pred             EEEEecCCCCC--CCcceEEe--cC-c-eeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHHH
Q psy5302          99 TVIYTDASKTD--VAVSSAFC--SQ-D-IKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQ  172 (333)
Q Consensus        99 ~~iytDGS~~~--~~~G~g~~--~~-~-~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~~  172 (333)
                      +.||||||...  +..|+|+|  +. + ...++.. ...+++.||+.|++.||+.+...+..   .  +.|+|||+.++.
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~-~~~tn~~AE~~All~aL~~a~~~g~~---~--v~i~sDS~~vi~   75 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPL-GTMSNHEAEYHALLAALKYCTEHNYN---I--VSFRTDSQLVER   75 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecc-cccCCcHHHHHHHHHHHHHHHhCCCC---E--EEEEechHHHHH
Confidence            67999999764  45889987  32 2 2233322 35789999999999999999987765   4  999999999999


Q ss_pred             HHcCCCCCc----hHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcC
Q psy5302         173 TLQNVFSLN----PIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTS  227 (333)
Q Consensus       173 ~l~~~~~~~----~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~  227 (333)
                      .+++.....    ++++++..++   .....+.|.|||.    +.|+.||.||++|...
T Consensus        76 ~~~~~~~~~~~~~~l~~~~~~l~---~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         76 AVEKEYAKNKMFAPLLEEALQYI---KSFDLFFIKWIPS----SQNKVADELARKAILQ  127 (128)
T ss_pred             HHhHHHhcChhHHHHHHHHHHHH---hcCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence            999855432    3555555554   5566788899995    6999999999999753

>PRK07708 hypothetical protein; Validated

Probab=99.66  E-value=2.7e-15  Score=132.41  Aligned_cols=141  Identities=17%  Similarity=0.187  Sum_probs=99.1

Q ss_pred             ChHHHHHHHHHHHhhCCCCcEEEEecCCCC--CCCcceEEe--c--Ccee----EEeecCCCcchHHHHHHHHHHHHHHH
Q psy5302          79 PKEEINISFQELLQQVPVDSTVIYTDASKT--DVAVSSAFC--S--QDIK----FSTRLHSLLSICNAELTSILFAIHFL  148 (333)
Q Consensus        79 ~~~~a~~~~~~~~~~~~~~~~~iytDGS~~--~~~~G~g~~--~--~~~~----~~~~l~~~~s~~~AEl~Ai~~al~~~  148 (333)
                      +.+|.++...++  ...++.+++|+|||..  ++.+|+|++  .  +...    ....++...+++.||+.|++.||+.+
T Consensus        56 ~~k~~~~~~~~~--~~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A  133 (219)
T PRK07708         56 SLKELKKLSKEV--EEEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQEL  133 (219)
T ss_pred             eHHHHhhhhhhh--ccCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHH
Confidence            444555444443  2334679999999975  456888876  2  2222    12345556899999999999999999


Q ss_pred             hhhccCcCCcceEEEEeCcHHHHHHHcCCC-CCchHHHHHHHHHHh--hcCCCceEEEEecCCCCCccchhhhHHHHHHh
Q psy5302         149 LSSCLNEHTQACFVICSDSLSALQTLQNVF-SLNPIASEIRNLILE--NKSKLSIRFIWVPSHVGIAGNEEADRLAKEAL  225 (333)
Q Consensus       149 ~~~~~~~~~~~~i~I~sDs~~~~~~l~~~~-~~~~~~~~i~~~~~~--~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~  225 (333)
                      ...+.+   ...|.|++||+.+++.+++.. ..++....+.+.+..  ......+.|.|||    +..|+.||+||++|+
T Consensus       134 ~e~g~~---~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al  206 (219)
T PRK07708        134 EELGVK---HEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQAL  206 (219)
T ss_pred             HHcCCC---cceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHH
Confidence            997765   234899999999999998854 344444444333322  2334457889998    788999999999999


Q ss_pred             cCC
Q psy5302         226 TST  228 (333)
Q Consensus       226 ~~~  228 (333)
                      ...
T Consensus       207 ~~~  209 (219)
T PRK07708        207 EGT  209 (219)
T ss_pred             hcC
Confidence            865

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.46  E-value=7.6e-13  Score=126.87  Aligned_cols=118  Identities=18%  Similarity=0.271  Sum_probs=89.1

Q ss_pred             cEEEEecCCCCC--CCcceEEe--c--Cc-e--eEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcH
Q psy5302          98 STVIYTDASKTD--VAVSSAFC--S--QD-I--KFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSL  168 (333)
Q Consensus        98 ~~~iytDGS~~~--~~~G~g~~--~--~~-~--~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~  168 (333)
                      .+.||||||...  +.+|+|++  +  +. .  .....++ ..|++.||+.|++.||+.+.+.+.+   .  |.|++||+
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~---~--v~i~~DS~   75 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGAT---E--VEVRMDSK   75 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCC---e--EEEEeCcH
Confidence            378999999764  45888877  3  22 2  2233344 6788999999999999999987765   4  99999999


Q ss_pred             HHHHHHcCCCC-Cch----HHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCC
Q psy5302         169 SALQTLQNVFS-LNP----IASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTST  228 (333)
Q Consensus       169 ~~~~~l~~~~~-~~~----~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~  228 (333)
                      .++..+++... ++.    ++.++.++   ......|.|.|||    ..+|+.||.||+.|....
T Consensus        76 lvi~~i~~~~~~~~~~l~~~~~~i~~l---~~~f~~~~i~~v~----r~~N~~AD~LA~~a~~~~  133 (372)
T PRK07238         76 LVVEQMSGRWKVKHPDMKPLAAQAREL---ASQFGRVTYTWIP----RARNAHADRLANEAMDAA  133 (372)
T ss_pred             HHHHHhCCCCccCChHHHHHHHHHHHH---HhcCCceEEEECC----chhhhHHHHHHHHHHHhh
Confidence            99999987543 333    23334443   3566789999999    489999999999997655

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

Probab=99.24  E-value=7.4e-11  Score=88.70  Aligned_cols=82  Identities=26%  Similarity=0.333  Sum_probs=65.4

Q ss_pred             hHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHHHHHcCCCCC-c---hHHHHHHHHHHhhcCCCceEEEEecCC
Q psy5302         133 ICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSL-N---PIASEIRNLILENKSKLSIRFIWVPSH  208 (333)
Q Consensus       133 ~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~~~l~~~~~~-~---~~~~~i~~~~~~~~~~~~v~~~wVp~H  208 (333)
                      +..||+.|+..||+.+.+.+..   +  |.|.|||+.++..+++.... +   .++..|..++   .....+.|.|||  
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~---~--i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~---~~~~~~~~~~i~--   70 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIR---K--IIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLL---DRFWNVSVSHIP--   70 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-S---C--EEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHH---CCCSCEEEEE----
T ss_pred             CcHHHHHHHHHHHHHHHHCCCC---E--EEEEecCccccccccccccccccccccchhhhhhh---ccccceEEEEEC--
Confidence            4689999999999999998876   5  99999999999999887432 2   3566666665   668899999999  


Q ss_pred             CCCccchhhhHHHHHHhc
Q psy5302         209 VGIAGNEEADRLAKEALT  226 (333)
Q Consensus       209 ~g~~gNe~AD~lAk~a~~  226 (333)
                        .++|..||.|||.|..
T Consensus        71 --r~~N~~A~~LA~~a~~   86 (87)
T PF13456_consen   71 --REQNKVADALAKFALS   86 (87)
T ss_dssp             --GGGSHHHHHHHHHHHH
T ss_pred             --hHHhHHHHHHHHHHhh
Confidence              8999999999999864

>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]

Probab=97.08  E-value=0.00084  Score=58.13  Aligned_cols=171  Identities=8%  Similarity=0.017  Sum_probs=107.0

Q ss_pred             CCCCCCCCCCCCCCccccccccccCCCCChHHHHHHHHHHHh----hCCCCcEEEEecCCCC--CCCcceEEecCce--e
Q psy5302          51 PAPQTSAPWLIEPPVVDYSLRKFNKNTDPKEEINISFQELLQ----QVPVDSTVIYTDASKT--DVAVSSAFCSQDI--K  122 (333)
Q Consensus        51 ~~p~~~ppW~~~~~~v~~~~~~~~k~~~~~~~a~~~~~~~~~----~~~~~~~~iytDGS~~--~~~~G~g~~~~~~--~  122 (333)
                      +.|+++..|.+|..+|.+..++.+|++.+.|+|...+..-+.    ....+.+.-+.+|+..  ++..++-++.+..  .
T Consensus        14 R~tGIyktW~Ec~~qVkGy~ga~YKsf~s~EeA~a~~~g~i~~~tp~~~~e~~i~~~~G~y~~~p~t~~~k~yr~k~~~~   93 (225)
T COG3341          14 RKTGIYKTWDECEKQVKGYPGAKYKSFKSYEEAEAYCEGNIESVTPYLDFEYIISWAKGDYDAKPGTQEFKEYRGKCTIE   93 (225)
T ss_pred             cccceeccHHHHHHHhcCCCcccccccccHHHHHHHhccCccccCcccchhccceeccCCccccCCCcceeEEecccccc
Confidence            579999999999999999999999999999999966552111    1123445667778753  2223333332211  1


Q ss_pred             -----EEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEE----eCcHHHHHHHcCCCCC-chHHHHHHHHHH
Q psy5302         123 -----FSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVIC----SDSLSALQTLQNVFSL-NPIASEIRNLIL  192 (333)
Q Consensus       123 -----~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~----sDs~~~~~~l~~~~~~-~~~~~~i~~~~~  192 (333)
                           ..... ...++..+|.+|++.+|+.+.....+    +.++++    .||++...-+.+-... ..+... .+.. 
T Consensus        94 ~~~lt~~~~~-~~~~n~s~d~la~ly~~~~~~~~~nr----k~~i~y~~~~~ds~a~~k~~k~~~~~k~~~~~~-~e~~-  166 (225)
T COG3341          94 YSWLTESSEF-SIKSNDSGDVLAKLYGLRYEVPLDNR----KSVINYLTPGNDSWAYFKYVKDKCETKVNLLKD-REFF-  166 (225)
T ss_pred             ceeeeeeccc-ccccCchHHHHHHhccccccccccCc----cceeeccCCcchhHHHHHHHhhhhhhHHHHHHh-HHhh-
Confidence                 11111 23456689999999999998875433    224446    6888777666543311 111111 1110 


Q ss_pred             hhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCC
Q psy5302         193 ENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTST  228 (333)
Q Consensus       193 ~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~  228 (333)
                      ....+....+.|+--|.++.-+..++.++.......
T Consensus       167 ~~~~~v~h~~k~i~~~~~~~~~~~~~s~~~~~~k~~  202 (225)
T COG3341         167 SIGKGVFHDEKDINIHIWIFESKKGNSHVYNTSKKE  202 (225)
T ss_pred             hccchhhhhhhhcccccccchhhhhhhhhhchhhhh
Confidence            012234566788999999988888888887766655

>PF13966 zf-RVT: zinc-binding in reverse transcriptase

Probab=96.36  E-value=0.0024  Score=47.96  Aligned_cols=40  Identities=20%  Similarity=0.347  Sum_probs=29.3

Q ss_pred             eecccccc---cccccCCCCCCCCCCCCC-ccccceeccccCCC
Q psy5302         292 RIGHTNTT---HIHLMKKENPPICVPCGC-VMSVKHIHINRLPN  331 (333)
Q Consensus       292 RTGH~~l~---~~~r~~~~~~~~C~~Cg~-~et~~H~l~~Cp~~  331 (333)
                      +.-|..+.   -+.+.+...++.|..|+. .||++|+|++||..
T Consensus        39 ~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a   82 (86)
T PF13966_consen   39 RALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFA   82 (86)
T ss_pred             eeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCc
Confidence            34445542   234556667799999995 89999999999975

---

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	333
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	4e-10
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	1e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	4e-07
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	2e-06
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	3e-05
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	5e-05
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	5e-05
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	7e-05
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	7e-05
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	2e-04
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	5e-04
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	7e-04
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	8e-04

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A Length = 147

 Score = 56.6 bits (137), Expect = 4e-10
 Identities = 17/91 (18%), Positives = 28/91 (30%), Gaps = 9/91 (9%)

Query: 136 AELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLN-PIASEIRNLILEN 194
            E+ + L+A+       +         I  D           +            L+  N
Sbjct: 53  GEIAAALYAVKKASQLGVK------IRILHDYAGIAFWATGEWKAKNEFTQAYAKLM--N 104

Query: 195 KSKLSIRFIWVPSHVGIAGNEEADRLAKEAL 225
           + +    F  V +H G   N+  D  AK AL
Sbjct: 105 QYRGIYSFEKVKAHSGNEFNDYVDMKAKSAL 135

>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 Length = 165

 Score = 55.6 bits (134), Expect = 1e-09
 Identities = 22/95 (23%), Positives = 33/95 (34%), Gaps = 11/95 (11%)

Query: 136 AELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENK 195
           AEL ++  A+       LN +T       S    A   + +        +EI  L+    
Sbjct: 66  AELIALTQALKMAEGKKLNVYT------DSRYAFATAHVHSEGREIKNKNEILALLKALF 119

Query: 196 SKLSIRFIWVPSHVG-----IAGNEEADRLAKEAL 225
               +  I  P H         GN  AD+ A+EA 
Sbjct: 120 LPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAA 154

>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 = 53.7 bits (128), Expect = 4e-08
 Identities = 48/321 (14%), Positives = 108/321 (33%), Gaps = 75/321 (23%)

Query: 6   FLSSLLTDHSLQQLYERKSSFEKPLRIRGKLLLEKYGIEYLDFLSPAPQTSAPWLIEP-- 63
              S+L+   +  +   K +    LR+   LL ++  +    F+    + +  +L+ P  
Sbjct: 41  MPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEM-VQKFVEEVLRINYKFLMSPIK 99

Query: 64  -----PVVDYSL------------RKFNKNTDPKEEINISFQELLQQV-PVDSTVIY--T 103
                P +   +            + F K    + +  +  ++ L ++ P  + +I    
Sbjct: 100 TEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVL 159

Query: 104 DASKTDVAVSSAFCSQDIKFSTRLHSLLSICNAELTSILFAIHFL-LSSC-----LNEHT 157
            + KT VA+         K   ++               F I +L L +C     + E  
Sbjct: 160 GSGKTWVALDVC---LSYKVQCKMD--------------FKIFWLNLKNCNSPETVLEML 202

Query: 158 QA-CFVICSDSLSALQTLQNV-FSLNPIASEIRNLILENKSK---LSIRFIWVPSHVG-- 210
           Q   + I  +  S      N+   ++ I +E+R L+     +   L +  +         
Sbjct: 203 QKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAF 262

Query: 211 --------IAGNEE-ADRLAKEALTSTHPTINKIPIPDYKAYSKRKILTSWNSEWHNLQN 261
                       ++  D L+  A T+TH +++   +       K  +L     ++ + + 
Sbjct: 263 NLSCKILLTTRFKQVTDFLS--AATTTHISLDHHSMTLTPDEVK-SLL----LKYLDCRP 315

Query: 262 NKL-HEIKVENKPWNPPYLIN 281
             L  E+   N     P  ++
Sbjct: 316 QDLPREVLTTN-----PRRLS 331

>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 = 46.4 bits (109), Expect = 1e-05
 Identities = 35/196 (17%), Positives = 65/196 (33%), Gaps = 60/196 (30%)

Query: 1   RNPNHFLSSLLTDHSLQQLYERKSSFEKPLRIRGKLLLEKYGIEYLDFLSPAPQTSAPWL 60
           + P     S+    S+    + K   E  L    + +++ Y I         P+T     
Sbjct: 419 KQPKESTISI---PSIYLELKVKLENEYALH---RSIVDHYNI---------PKTFDSDD 463

Query: 61  IEPPVVD-YSLRKFN------KNTDPKEEINISFQELL-------QQVPVDSTVIYTDAS 106
           + PP +D Y    ++      KN +  E + + F+ +        Q++  DST      S
Sbjct: 464 LIPPYLDQYF---YSHIGHHLKNIEHPERMTL-FRMVFLDFRFLEQKIRHDSTAWNASGS 519

Query: 107 KTDVAV-----SSAFCSQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACF 161
             +            C  D K+   ++++L               FL    + E+     
Sbjct: 520 ILNTLQQLKFYKPYICDNDPKYERLVNAIL--------------DFLPK--IEEN----- 558

Query: 162 VICSDSLSALQ-TLQN 176
           +ICS     L+  L  
Sbjct: 559 LICSKYTDLLRIALMA 574

>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A* Length = 154

 Score = 48.0 bits (115), Expect = 4e-07
 Identities = 15/29 (51%), Positives = 20/29 (68%)

Query: 196 SKLSIRFIWVPSHVGIAGNEEADRLAKEA 224
             + I+++ VP H G  GNEEADRLA+E 
Sbjct: 120 QGMDIQWMHVPGHSGFIGNEEADRLAREG 148

>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A Length = 150

 Score = 46.0 bits (110), Expect = 2e-06
 Identities = 12/29 (41%), Positives = 16/29 (55%)

Query: 196 SKLSIRFIWVPSHVGIAGNEEADRLAKEA 224
            K  +   WVP+H GI GNE+ D+L    
Sbjct: 116 KKEKVYLAWVPAHKGIGGNEQVDKLVSAG 144

>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 ... Length = 155

 Score = 42.5 bits (101), Expect = 3e-05
 Identities = 13/48 (27%), Positives = 18/48 (37%), Gaps = 7/48 (14%)

Query: 192 LENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPD 239
                +  I++ WV  H G   NE AD LA+ A            + D
Sbjct: 108 DAALGQHQIKWEWVKGHAGHPENERADELARAA-------AMNPTLED 148

>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum} Length = 146

 Score = 41.7 bits (99), Expect = 5e-05
 Identities = 11/34 (32%), Positives = 15/34 (44%)

Query: 191 ILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEA 224
           IL+  +   + F  V  H     N  AD LA+ A
Sbjct: 108 ILKLTTLHRVTFHKVKGHSDNPYNSRADELARLA 141

>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A Length = 166

 Score = 42.2 bits (100), Expect = 5e-05
 Identities = 15/51 (29%), Positives = 19/51 (37%), Gaps = 4/51 (7%)

Query: 192 LENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKA 242
           L   +   +RF +V  H G   NE  DR A+    S      K P P    
Sbjct: 113 LLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQS----QAKTPCPPRAP 159

>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* ... Length = 557

 Score = 43.6 bits (103), Expect = 7e-05
 Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 14/87 (16%)

Query: 136 AELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQN--VFSLNPIASEIRNLILE 193
            EL +I  A+         + +     I +DS  AL  +Q     S + + ++I   I +
Sbjct: 479 TELQAIYLAL---------QDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQI---IEQ 526

Query: 194 NKSKLSIRFIWVPSHVGIAGNEEADRL 220
              K  +   WVP+H GI GNE+ D+L
Sbjct: 527 LIKKEKVYLAWVPAHKGIGGNEQVDKL 553

>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A Length = 158

 Score = 41.4 bits (98), Expect = 7e-05
 Identities = 12/33 (36%), Positives = 16/33 (48%)

Query: 192 LENKSKLSIRFIWVPSHVGIAGNEEADRLAKEA 224
            +      I + WV  H G A NE  D+LA+ A
Sbjct: 110 DKAAQLHQIDWRWVKGHAGHAENERCDQLARAA 142

>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A Length = 149

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 8/47 (17%)

Query: 179 SLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEAL 225
            + P+  +   L      KL+   IWVP       N+EADRL++ A 
Sbjct: 94  RIIPLYEKAIELK----KKLNATLIWVPR----EENKEADRLSRVAY 132

>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism} Length = 140

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 6/46 (13%)

Query: 180 LNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEAL 225
           L    ++I ++      K+      V  H+    N  AD L  EA+
Sbjct: 96  LKEKFAKIAHI------KMERVPNLVFVHIPREKNARADELVNEAI 135

>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 Length = 555

 Score = 40.1 bits (94), Expect = 7e-04
 Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 163 ICSDSLSALQTLQN--VFSLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRL 220
           I  DS   +  + +    S + I ++I   I E   K +I   WVP+H GI GN+E D L
Sbjct: 494 IIVDSQYVMGIVASQPTESESKIVNQI---IEEMIKKEAIYVAWVPAHKGIGGNQEVDHL 550

>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 = 38.0 bits (89), Expect = 8e-04
 Identities = 18/95 (18%), Positives = 33/95 (34%), Gaps = 17/95 (17%)

Query: 136 AELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVF-----SLNPIASEIRNL 190
           AE   ++  +   +     E       +  DS   ++ +   +      L  +  + + L
Sbjct: 49  AEYRGLIAGLDDAVKLGATE-----AAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQAL 103

Query: 191 ILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEAL 225
                    I + WVP       N  ADRLA +A+
Sbjct: 104 A---SQFRRINYEWVPRA----RNTYADRLANDAM 131

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	333
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.92
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.9
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.9
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.89
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.89
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.89
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.89
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.88
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.86
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.8
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.8
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.79
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.79
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.77
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.34
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.11
3bsu_A	53	Ribonuclease H1, RNAse H1; RNAse H, RNA/DNA hybrid	90.94
1qhk_A	47	RNAse HI, protein (ribonuclease HI); ribonuclease	90.68

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

Probab=99.92  E-value=3.5e-25  Score=185.12  Aligned_cols=125  Identities=25%  Similarity=0.346  Sum_probs=98.0

Q ss_pred             CCCcEEEEecCCCCCCC-----cceEEe--cC-ceeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeC
Q psy5302          95 PVDSTVIYTDASKTDVA-----VSSAFC--SQ-DIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSD  166 (333)
Q Consensus        95 ~~~~~~iytDGS~~~~~-----~G~g~~--~~-~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sD  166 (333)
                      +.+.++||||||+..++     +|+|+|  ++ ....+..+...+|++.||+.|++.||+.+......   .  |.|+||
T Consensus         4 ~~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~---~--v~i~tD   78 (154)
T 2qkb_A            4 MGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNIN---K--LVLYTN   78 (154)
T ss_dssp             ETTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCC---E--EEEEES
T ss_pred             CCCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCc---e--EEEEEC
Confidence            35679999999986432     688887  32 22345566557899999999999999999876543   4  999999


Q ss_pred             cHHHHHHHcCCC---------C-------CchHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCC
Q psy5302         167 SLSALQTLQNVF---------S-------LNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTST  228 (333)
Q Consensus       167 s~~~~~~l~~~~---------~-------~~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~  228 (333)
                      |+++++.|..|.         .       ..+++++|.+++    .+..|.|.|||||+|++|||.||+|||+|+..+
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 SMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLT----QGMDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             CHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHH----TTCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             cHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHH----cCCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            999999998742         1       124666776665    246799999999999999999999999998764

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

Probab=99.90  E-value=2.4e-24  Score=178.45  Aligned_cols=119  Identities=19%  Similarity=0.135  Sum_probs=91.7

Q ss_pred             CcEEEEecCCCCCC--CcceEEe--cCce--eEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHH
Q psy5302          97 DSTVIYTDASKTDV--AVSSAFC--SQDI--KFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSA  170 (333)
Q Consensus        97 ~~~~iytDGS~~~~--~~G~g~~--~~~~--~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~  170 (333)
                      ..++||||||+..+  ..|+|++  .++.  ..+..+ ..+|++.||+.|++.||+.+.+  ..   .  |.|+|||++|
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~--~~---~--v~I~tDS~~v   74 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALKE--PA---R--VQLYSDSAYL   74 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CC---E--EEEEESCHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcCc--cC---c--EEEEeChHHH
Confidence            56999999997653  3788877  3332  233333 3689999999999999999875  22   3  9999999999


Q ss_pred             HHHHcC-CC----------------CCchHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcC
Q psy5302         171 LQTLQN-VF----------------SLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTS  227 (333)
Q Consensus       171 ~~~l~~-~~----------------~~~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~  227 (333)
                      +..|.. |.                ...++++++.+++.    ...|.|.|||||+|+++||.||+|||+|+..
T Consensus        75 i~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~----~~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A           75 VNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTT----LHRVTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             HHHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHH----HSEEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHh----hCceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence            999988 31                12347777777763    2469999999999999999999999999864

>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=99.90  E-value=7.8e-24  Score=175.93  Aligned_cols=121  Identities=21%  Similarity=0.310  Sum_probs=93.2

Q ss_pred             hCCCCcEEEEecCCCCC--CCcceEEe--cCceeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcH
Q psy5302          93 QVPVDSTVIYTDASKTD--VAVSSAFC--SQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSL  168 (333)
Q Consensus        93 ~~~~~~~~iytDGS~~~--~~~G~g~~--~~~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~  168 (333)
                      .+..+.+.||||||+..  +..|+|++  ++. ...+.+ ..+|++.||+.|++.||+.+   . .   .  |.|+|||+
T Consensus         7 ~P~~~~~~iytDGs~~~n~g~~g~G~v~~~~~-~~~~~~-~~~Tnn~aEl~A~i~AL~~~---~-~---~--v~i~tDS~   75 (150)
T 3qio_A            7 EPIVGAETFYVDGAANRETKLGKAGYVTNRGR-QKVVTL-TDTTNQKTELQAIYLALQDS---G-L---E--VNIVTDSQ   75 (150)
T ss_dssp             SCCTTCEEEEEEEEECTTTCCEEEEEEETTSC-EEEEEE-SSCCHHHHHHHHHHHHHHHS---C-S---E--EEEEESCH
T ss_pred             CCCCCCEEEEEccCCCCCCCCeEEEEEEEcCC-EEEEeC-CCCCHHHHHHHHHHHHHHhC---C-C---c--EEEEeCcH
Confidence            45567899999999753  33778877  332 223333 46899999999999999985   1 2   3  99999999


Q ss_pred             HHHHHHcCCC----------------CCchHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcC
Q psy5302         169 SALQTLQNVF----------------SLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTS  227 (333)
Q Consensus       169 ~~~~~l~~~~----------------~~~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~  227 (333)
                      +++++|..|.                ...++++++.+++   .....|.|.|||||+|++|||.||+||++|+..
T Consensus        76 ~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l---~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           76 YALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQL---IKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHHHHHHHHHCC------------CHHHHHHHHHHH---TTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHH---hhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            9999998762                1123556555544   467899999999999999999999999999875

>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=99.89  E-value=4.3e-24  Score=177.03  Aligned_cols=127  Identities=17%  Similarity=0.103  Sum_probs=96.7

Q ss_pred             CCCcEEEEecCCCCCCCcceEEe--c-Cce-eEEe-ec--CC--CcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEe
Q psy5302          95 PVDSTVIYTDASKTDVAVSSAFC--S-QDI-KFST-RL--HS--LLSICNAELTSILFAIHFLLSSCLNEHTQACFVICS  165 (333)
Q Consensus        95 ~~~~~~iytDGS~~~~~~G~g~~--~-~~~-~~~~-~l--~~--~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~s  165 (333)
                      +++.++||||||+..+.+|+|+|  . +.. ..+. +.  +.  ..|++.||+.|++.||+.+.+.+.+      |.|+|
T Consensus         3 ~~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~~------v~I~t   76 (147)
T 2kq2_A            3 DRTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGVK------IRILH   76 (147)
T ss_dssp             TTSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTCC------CCBSS
T ss_pred             CCCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCCe------EEEEE
Confidence            45779999999998877899987  3 332 2333 22  22  3699999999999999998775443      99999


Q ss_pred             CcHHHHHHHcC-CCCCchHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCCC
Q psy5302         166 DSLSALQTLQN-VFSLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTH  229 (333)
Q Consensus       166 Ds~~~~~~l~~-~~~~~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~~  229 (333)
                      ||+.+...+.+ |....+....+.+++.....  .|.|.|||||+|++|||+||+|||+|+....
T Consensus        77 DS~~i~~w~~~~w~~~~~~~~~~~~l~~~l~~--~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~  139 (147)
T 2kq2_A           77 DYAGIAFWATGEWKAKNEFTQAYAKLMNQYRG--IYSFEKVKAHSGNEFNDYVDMKAKSALGIRD  139 (147)
T ss_dssp             CCSTHHHHTTSSSSCCHHHHHHHHCGGGGGST--TCCBCCCCCCCCCHHHHHHHHHHHHHHTCCC
T ss_pred             CcHHHHHHHhCCCccCCcchHHHHHHHHHhcC--CeeEEEecCcCCCcchHHHHHHHHHHHhccc
Confidence            99987765554 44455555666666633222  8999999999999999999999999998773

>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=99.89  E-value=2.2e-23  Score=175.60  Aligned_cols=121  Identities=20%  Similarity=0.157  Sum_probs=91.4

Q ss_pred             CcEEEEecCCCC--CCCcceEEe--c-CceeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHH
Q psy5302          97 DSTVIYTDASKT--DVAVSSAFC--S-QDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSAL  171 (333)
Q Consensus        97 ~~~~iytDGS~~--~~~~G~g~~--~-~~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~  171 (333)
                      ..+.||||||+.  +|..|+|++  . +.......+...+|++.||+.|++.||+.+.   .     ..|.|+|||++++
T Consensus        22 ~~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~---~-----~~v~I~tDS~~vi   93 (165)
T 3p1g_A           22 ADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAE---G-----KKLNVYTDSRYAF   93 (165)
T ss_dssp             CSEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHTB---T-----SEEEEEECCHHHH
T ss_pred             CCEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHcc---C-----ceEEEEEchHHHH
Confidence            359999999986  455778765  3 3332222456678999999999999999982   2     2399999999999


Q ss_pred             HHHcCCCC-----CchHHHHHHHHHHhhcCCCceEEEEecCCCC-----CccchhhhHHHHHHhcCC
Q psy5302         172 QTLQNVFS-----LNPIASEIRNLILENKSKLSIRFIWVPSHVG-----IAGNEEADRLAKEALTST  228 (333)
Q Consensus       172 ~~l~~~~~-----~~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g-----~~gNe~AD~lAk~a~~~~  228 (333)
                      +++-....     ..++++++.+.+   ..+..|.|.|||||+|     ++|||+||+|||+|+...
T Consensus        94 ~~iw~~~~g~~v~n~dl~~~l~~~l---~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~  157 (165)
T 3p1g_A           94 ATAHVHSEGREIKNKNEILALLKAL---FLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKA  157 (165)
T ss_dssp             HHHHSCCCSCCCSSHHHHHHHHHHT---TSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhcccCCCcccCHHHHHHHHHHH---hcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcC
Confidence            99821111     123455554433   4678999999999999     999999999999999876

>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=99.89  E-value=1.6e-23  Score=175.11  Aligned_cols=120  Identities=20%  Similarity=0.258  Sum_probs=92.5

Q ss_pred             CcEEEEecCCCCCC--CcceEEe--cCc--eeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHH
Q psy5302          97 DSTVIYTDASKTDV--AVSSAFC--SQD--IKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSA  170 (333)
Q Consensus        97 ~~~~iytDGS~~~~--~~G~g~~--~~~--~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~  170 (333)
                      ..+.||||||+..+  .+|+|++  ..+  ...+..+ ...|++.||+.|++.||+.+...  .   .  |.|+|||+++
T Consensus         3 ~~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~~--~---~--v~I~tDS~~v   74 (155)
T 1jl1_A            3 KQVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKEH--A---E--VILSTDSQYV   74 (155)
T ss_dssp             CCEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCSC--C---E--EEEEECCHHH
T ss_pred             ceEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCcC--C---c--EEEEeCHHHH
Confidence            35899999998643  3788877  322  2233333 36789999999999999998752  2   3  9999999999


Q ss_pred             HHHHcCCC---------C-------CchHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCC
Q psy5302         171 LQTLQNVF---------S-------LNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTST  228 (333)
Q Consensus       171 ~~~l~~~~---------~-------~~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~  228 (333)
                      ++.|..|.         .       ..++++.|.+++    ....|.|.|||||+|++||+.||+|||+|+..+
T Consensus        75 i~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~----~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~  144 (155)
T 1jl1_A           75 RQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAAL----GQHQIKWEWVKGHAGHPENERADELARAAAMNP  144 (155)
T ss_dssp             HHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHT----TTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHH----ccCceEEEEcCCCCCCHHHHHHHHHHHHHHhcc
Confidence            99998731         1       124566666554    346899999999999999999999999999876

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

Probab=99.89  E-value=2.3e-23  Score=174.81  Aligned_cols=119  Identities=23%  Similarity=0.248  Sum_probs=92.3

Q ss_pred             CcEEEEecCCCCC--CCcceEEe--cCce--eEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHH
Q psy5302          97 DSTVIYTDASKTD--VAVSSAFC--SQDI--KFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSA  170 (333)
Q Consensus        97 ~~~~iytDGS~~~--~~~G~g~~--~~~~--~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~  170 (333)
                      ..+.||||||+..  +.+|+|+|  .++.  ..+..+ ...|++.||+.|++.||+.+...  .   .  |.|+|||++|
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~~--~---~--v~I~tDS~~v   76 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKEP--C---K--IILTSDSQYM   76 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSSC--C---E--EEEEECCHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhccC--C---e--EEEEeCHHHH
Confidence            4689999999864  34788877  3322  233333 35799999999999999988542  2   3  9999999999


Q ss_pred             HHHHcCC---------CC-------CchHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcC
Q psy5302         171 LQTLQNV---------FS-------LNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTS  227 (333)
Q Consensus       171 ~~~l~~~---------~~-------~~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~  227 (333)
                      ++.|..|         ..       ..++++.|.+++    ....|.|.|||||+|+++|+.||+|||+|+..
T Consensus        77 i~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~----~~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A           77 RQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAA----QLHQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             HHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHH----TTSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHH----ccCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            9999882         11       124666776665    23689999999999999999999999999987

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

Probab=99.88  E-value=3.5e-23  Score=174.99  Aligned_cols=120  Identities=17%  Similarity=0.130  Sum_probs=93.1

Q ss_pred             CcEEEEecCCCCCC--CcceEEe--cCc-e-eEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHH
Q psy5302          97 DSTVIYTDASKTDV--AVSSAFC--SQD-I-KFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSA  170 (333)
Q Consensus        97 ~~~~iytDGS~~~~--~~G~g~~--~~~-~-~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~  170 (333)
                      ..++||||||+..+  ..|+|+|  .++ . ..+... ...|++.||+.|++.||+.+...       ..|.|+|||+++
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~Ai~~AL~~~~~~-------~~v~I~tDS~~v   78 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGE-ACTTNNRMELKAAIEGLKALKEP-------CEVDLYTDSHYL   78 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEE-EEECHHHHHHHHHHHHHHSCCSC-------CEEEEECCCHHH
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCC-CCCcHHHHHHHHHHHHHHHhccC-------CeEEEEeChHHH
Confidence            57899999998643  3788877  322 1 222222 35799999999999999987653       139999999999


Q ss_pred             HHHHcC----------CCCC-------chHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCC
Q psy5302         171 LQTLQN----------VFSL-------NPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTST  228 (333)
Q Consensus       171 ~~~l~~----------~~~~-------~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~  228 (333)
                      +..|..          |...       .++++.|.+++    ....|.|.|||||+|+++|+.||+|||+|+...
T Consensus        79 i~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~----~~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~  149 (166)
T 1ril_A           79 KKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAM----APHRVRFHFVKGHTGHPENERVDREARRQAQSQ  149 (166)
T ss_dssp             HHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH----TTSEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             HHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHH----hcCeEEEEEeeCCCCchhHHHHHHHHHHHHHHh
Confidence            999998          3221       24677777665    235899999999999999999999999999877

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

Probab=99.86  E-value=6.7e-22  Score=166.35  Aligned_cols=122  Identities=18%  Similarity=0.140  Sum_probs=89.4

Q ss_pred             CCcEEEEecCCCCC--CC-----cceEEe--c-C-c--eeEEeec-CCCcchHHHHHHHHHHHHHHHhhhccCcCCcceE
Q psy5302          96 VDSTVIYTDASKTD--VA-----VSSAFC--S-Q-D--IKFSTRL-HSLLSICNAELTSILFAIHFLLSSCLNEHTQACF  161 (333)
Q Consensus        96 ~~~~~iytDGS~~~--~~-----~G~g~~--~-~-~--~~~~~~l-~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i  161 (333)
                      ...++||||||+..  +.     .|+|+|  . + .  ....+.. ....+.+.||+.|+..||+.+......      |
T Consensus         5 ~~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~~~~------v   78 (165)
T 2lsn_A            5 QYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIPGP------V   78 (165)
T ss_dssp             CCSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHSSSC------E
T ss_pred             CceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcCCCe------E
Confidence            45689999999753  32     788887  2 2 1  2223332 245678889999998888887664433      9


Q ss_pred             EEEeCcHHHHHHHcCC---------CC-------CchHHHHHHHHHHhhcCCCceEEEEecCCCCC------ccchhhhH
Q psy5302         162 VICSDSLSALQTLQNV---------FS-------LNPIASEIRNLILENKSKLSIRFIWVPSHVGI------AGNEEADR  219 (333)
Q Consensus       162 ~I~sDs~~~~~~l~~~---------~~-------~~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~------~gNe~AD~  219 (333)
                      .|+|||++|+++|..|         ..       ..++++++.+++   .....|.|.|||||+|+      +|||+||+
T Consensus        79 ~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~---~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~  155 (165)
T 2lsn_A           79 LVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECL---SMKPDITIQHEKGHQPTNTSIHTEGNALADK  155 (165)
T ss_dssp             EEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHH---HHCTTCEEEECCSSSCSSSCHHHHHHHHHHH
T ss_pred             EEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHH---hCCCCEEEEEEeCCCCccCCCCChHHHHHHH
Confidence            9999999999999753         11       124677777766   33457999999999995      58999999


Q ss_pred             HHHHHhc
Q psy5302         220 LAKEALT  226 (333)
Q Consensus       220 lAk~a~~  226 (333)
                      ||++|+.
T Consensus       156 LA~~gA~  162 (165)
T 2lsn_A          156 LATQGSY  162 (165)
T ss_dssp             HHHHHHH
T ss_pred             HHHHhhh
Confidence            9999985

>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=99.80  E-value=3.8e-19  Score=145.79  Aligned_cols=121  Identities=17%  Similarity=0.160  Sum_probs=90.2

Q ss_pred             cEEEEecCCCCC--CCcceEEe--c---Cce--eEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcH
Q psy5302          98 STVIYTDASKTD--VAVSSAFC--S---QDI--KFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSL  168 (333)
Q Consensus        98 ~~~iytDGS~~~--~~~G~g~~--~---~~~--~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~  168 (333)
                      .++||||||+..  +.+|+|++  +   +..  ..+..+ ..+|++.||+.|++.||+.+...+..   +  |.|+|||+
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~---~--v~i~tDS~   76 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAI-GRATNNVAEYRGLIAGLDDAVKLGAT---E--AAVLMDSK   76 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHHTCS---E--EEEEESCH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccC-CCCchHHHHHHHHHHHHHHHHHCCCc---e--EEEEeChH
Confidence            589999999764  35788877  3   222  223333 36899999999999999999887654   4  99999999


Q ss_pred             HHHHHHcCC-CCCchHHHHHHHHHH-hhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCC
Q psy5302         169 SALQTLQNV-FSLNPIASEIRNLIL-ENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTST  228 (333)
Q Consensus       169 ~~~~~l~~~-~~~~~~~~~i~~~~~-~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~  228 (333)
                      ++++.+++. ...+..+..+.+.+. .......|.|.|||    .++|+.||+|||+|+...
T Consensus        77 ~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~----~~~N~~AD~LA~~a~~~~  134 (141)
T 3hst_B           77 LVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVP----RARNTYADRLANDAMDAA  134 (141)
T ss_dssp             HHHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECC----GGGCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcC----CcccHHHHHHHHHHHHHh
Confidence            999999984 344443333332222 23556899999999    499999999999998654

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

Probab=99.80  E-value=3e-19  Score=145.94  Aligned_cols=122  Identities=18%  Similarity=0.201  Sum_probs=88.8

Q ss_pred             CcEEEEecCCCCC--CCcceEEe--c--Cce--eEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcH
Q psy5302          97 DSTVIYTDASKTD--VAVSSAFC--S--QDI--KFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSL  168 (333)
Q Consensus        97 ~~~~iytDGS~~~--~~~G~g~~--~--~~~--~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~  168 (333)
                      ..+.||||||+..  +.+|+|++  +  +..  ..+..++ .+|++.||+.|++.||+.+...+.... ...|.|+|||+
T Consensus         2 ~~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~~~~~-~~~v~i~tDS~   79 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIG-ETTNNVAEYEALIRALEDLQMFGDKLV-DMEVEVRMDSE   79 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEE-EECHHHHHHHHHHHHHHHHGGGGGGGT-TCEEEEEESCH
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCC-CCchHHHHHHHHHHHHHHHHHcCCCCC-CceEEEEeChH
Confidence            3589999999864  34888877  3  332  2333333 579999999999999999987543100 11499999999


Q ss_pred             HHHHHHcCCCC-Cc-h---HHHHHHHH-HHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcC
Q psy5302         169 SALQTLQNVFS-LN-P---IASEIRNL-ILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTS  227 (333)
Q Consensus       169 ~~~~~l~~~~~-~~-~---~~~~i~~~-~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~  227 (333)
                      ++++.++++.. .+ .   ++.++.++ +   .....|.|.|||    .++|+.||+|||+|+..
T Consensus        80 ~vi~~i~~~~~~~~~~l~~~~~~i~~l~~---~~~~~v~~~~V~----~~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D           80 LIVRQMQGVYKVKEPTLKEKFAKIAHIKM---ERVPNLVFVHIP----REKNARADELVNEAIDK  137 (140)
T ss_dssp             HHHHHHTTSSCCCCGGGHHHHHHHHHHHH---HHCTTCEEEECC----GGGGHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCcccCCHHHHHHHHHHHHHhh---cCCCcEEEEEcC----chhhHHHHHHHHHHHHh
Confidence            99999998653 33 3   34444444 3   344589999999    59999999999999864

>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=99.79  E-value=2.9e-19  Score=178.27  Aligned_cols=116  Identities=23%  Similarity=0.284  Sum_probs=91.8

Q ss_pred             CCcEEEEecCCCCCC--CcceEEe--cCceeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHH
Q psy5302          96 VDSTVIYTDASKTDV--AVSSAFC--SQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSAL  171 (333)
Q Consensus        96 ~~~~~iytDGS~~~~--~~G~g~~--~~~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~  171 (333)
                      .+.++||||||+..+  ..|+|++  .++. .+..+ ..+|++.||+.|++.||+.    ..     ..+.|+|||++|+
T Consensus       434 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~-~~~~~-~~~TNn~aEl~A~i~aL~~----~~-----~~v~I~tDS~~v~  502 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKEGKAGYVTDRGKD-KVKKL-EQTTNQQAELEAFAMALTD----SG-----PKVNIIVDSQYVM  502 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCE-EEEEE-SSCCHHHHHHHHHHHHHHT----SC-----SEEEEEESCHHHH
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCCE-eeccC-CCCCHHHHHHHHHHHHHHc----CC-----CeEEEEEehHHHH
Confidence            456999999997643  3678877  3332 23333 3679999999999999998    22     2399999999999


Q ss_pred             HHHcCCCC--CchHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHh
Q psy5302         172 QTLQNVFS--LNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEAL  225 (333)
Q Consensus       172 ~~l~~~~~--~~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~  225 (333)
                      +.+++|..  +.++++++.+++   .....|.|.|||||+|++|||.||+||++|+
T Consensus       503 ~~i~~~~~~~~~~l~~~~~~~~---~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          503 GIVASQPTESESKIVNQIIEEM---IKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             HHHHTCCSEESCHHHHHHHHHH---HHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHHhcccccccHHHHHHHHHHh---ccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            99999864  446777777765   2357899999999999999999999999885

>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=99.79  E-value=2e-19  Score=179.44  Aligned_cols=116  Identities=23%  Similarity=0.330  Sum_probs=88.5

Q ss_pred             CCcEEEEecCCCCC--CCcceEEe-cCceeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHHH
Q psy5302          96 VDSTVIYTDASKTD--VAVSSAFC-SQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQ  172 (333)
Q Consensus        96 ~~~~~iytDGS~~~--~~~G~g~~-~~~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~~  172 (333)
                      .+.++||||||+..  +..|+|++ ..+....... ..+|++.||+.|++.||+.+    ..   .  +.|+|||++|++
T Consensus       437 ~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~----~~---~--v~I~tDS~~vi~  506 (557)
T 2zd1_A          437 VGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS----GL---E--VNIVTDSQYALG  506 (557)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS----CS---E--EEEEECCHHHHH
T ss_pred             CCCEEEEEccCCCCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC----CC---c--EEEEeChHHHHH
Confidence            45699999999753  33677877 3222222233 46899999999999999998    22   3  999999999999


Q ss_pred             HHcCCCCC--chHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHH
Q psy5302         173 TLQNVFSL--NPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEA  224 (333)
Q Consensus       173 ~l~~~~~~--~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a  224 (333)
                      .+.+|...  .+++.++.+.+   .....|.|.|||||+|++|||.||+||++|
T Consensus       507 ~i~~~~~~~~~~l~~~~~~~l---~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          507 IIQAQPDKSESELVNQIIEQL---IKKEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             HHTTCCSEESSHHHHHHHHHH---HHCSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             HHhcCCccCCHHHHHHHHHHH---hcCCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            99998764  46777776655   224589999999999999999999999986

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

Probab=99.77  E-value=7.9e-19  Score=145.53  Aligned_cols=117  Identities=19%  Similarity=0.234  Sum_probs=88.6

Q ss_pred             EEEEecCCCC---CCCcce-EEe--c-CceeE--EeecC---CCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeC
Q psy5302          99 TVIYTDASKT---DVAVSS-AFC--S-QDIKF--STRLH---SLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSD  166 (333)
Q Consensus        99 ~~iytDGS~~---~~~~G~-g~~--~-~~~~~--~~~l~---~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sD  166 (333)
                      +.||||||+.   ++.+|+ |++  + +....  +..++   ...|++.||+.|++.||+.+...+..   +  |.|+||
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~---~--v~i~tD   76 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGIS---S--PIIKGD   76 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCC---S--CEEEES
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCC---E--EEEEeC
Confidence            6899999986   245775 866  3 33322  22222   37899999999999999999887654   4  999999


Q ss_pred             cHHHHHHHcCCCC-Cc----hHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCC
Q psy5302         167 SLSALQTLQNVFS-LN----PIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTST  228 (333)
Q Consensus       167 s~~~~~~l~~~~~-~~----~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~  228 (333)
                      |+++++.++++.. .+    ++++++..++...    .|.|.|||+    ++|+.||+||++|+...
T Consensus        77 S~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~----~v~~~~V~~----~~N~~AD~LA~~a~~~~  135 (149)
T 2ehg_A           77 SQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKL----NATLIWVPR----EENKEADRLSRVAYELV  135 (149)
T ss_dssp             CHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHH----TCEEEECCG----GGCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHhCccccCCHHHHHHHHHHHHHHhcC----CEEEEEcCC----cccHHHHHHHHHHHHhh
Confidence            9999999999743 22    3556666555222    599999997    69999999999998765

>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=99.34  E-value=3.2e-13  Score=110.43  Aligned_cols=118  Identities=11%  Similarity=-0.010  Sum_probs=82.2

Q ss_pred             CCCCcEEEEecCCCCC--CCcceEEe---cCcee-EEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCc
Q psy5302          94 VPVDSTVIYTDASKTD--VAVSSAFC---SQDIK-FSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDS  167 (333)
Q Consensus        94 ~~~~~~~iytDGS~~~--~~~G~g~~---~~~~~-~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs  167 (333)
                      .....+.||||||+..  +.+|+|+|   ++... .+..++ ..|++.||+.|++.||+.+.+....      |.|+|||
T Consensus         7 ~~~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~-~~TNN~aEl~A~i~aL~~~~~~~~~------v~i~tDS   79 (142)
T 1zbf_A            7 EEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKERNSR------KPIYSNS   79 (142)
T ss_dssp             -CCCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEE-EECHHHHHHHHHHHHHHHHHHTTCC------CCEEESC
T ss_pred             CCCCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccC-CcCcHHHHHHHHHHHHHHHHhCCCe------EEEEEeh
Confidence            3446788999999753  44788887   23322 222333 5799999999999999999875433      9999999


Q ss_pred             HHHHHHHcCCCCC---------chHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhH
Q psy5302         168 LSALQTLQNVFSL---------NPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADR  219 (333)
Q Consensus       168 ~~~~~~l~~~~~~---------~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~  219 (333)
                      ++|+..+.+...+         .++++.+..+..- .....+....|+-|++.-||..||.
T Consensus        80 ~~vi~w~~~~~~k~~~~~~v~n~dLw~~l~~~~~w-~~~~~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A           80 QTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEW-LNTHTYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             HHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHH-HHHCCCCCCEEECCHHHHCSCTTCC
T ss_pred             HHHHHHHHcCCccCCCCCCcccHHHHHHHHHHHHH-HhhCCCceeEEEeccCccCcCcccc
Confidence            9999988876521         1355555444321 1223455666788999999999984

>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=99.11  E-value=8.7e-11  Score=94.35  Aligned_cols=76  Identities=12%  Similarity=0.051  Sum_probs=56.9

Q ss_pred             CCcEEEEecCCCC--CCCcceEEe--c-Cce-eEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHH
Q psy5302          96 VDSTVIYTDASKT--DVAVSSAFC--S-QDI-KFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLS  169 (333)
Q Consensus        96 ~~~~~iytDGS~~--~~~~G~g~~--~-~~~-~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~  169 (333)
                      +..+.||||||+.  +|..|+|+|  . +.. ..+..++ .+|++.||+.|++.||+.+.+....      +.|+|||++
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~~-~tTNN~aEl~A~i~aL~~l~~~~~~------v~i~tDSqy   75 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKERNSR------KPIYSNSQT   75 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEEE-EECHHHHHHHHHHHHHHHHHHTTCC------CCEEESCHH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCCC-CCchHHHHHHHHHHHHHHHHhCCCC------EEEEcchHH
Confidence            4567899999975  344788544  3 332 2333333 6899999999999999999876543      899999999


Q ss_pred             HHHHHcCCC
Q psy5302         170 ALQTLQNVF  178 (333)
Q Consensus       170 ~~~~l~~~~  178 (333)
                      |+..+.++.
T Consensus        76 Vi~wi~~~~   84 (134)
T 4htu_A           76 AIKWVKDKK   84 (134)
T ss_dssp             HHHHHHHTC
T ss_pred             HHHHHHcCC
Confidence            999888653

>3bsu_A Ribonuclease H1, RNAse H1; RNAse H, RNA/DNA hybrid; HET: DNA 5IU; 2.10A {Homo sapiens}

Probab=90.94  E-value=0.012  Score=38.93  Aligned_cols=37  Identities=14%  Similarity=-0.066  Sum_probs=33.1

Q ss_pred             CCCCCCCCCCCCCCccccccccccCCCCChHHHHHHH
Q psy5302          51 PAPQTSAPWLIEPPVVDYSLRKFNKNTDPKEEINISF   87 (333)
Q Consensus        51 ~~p~~~ppW~~~~~~v~~~~~~~~k~~~~~~~a~~~~   87 (333)
                      ..|+++..|.+|..+|+....+.+|++.+.+||...+
T Consensus        12 ~~~GIy~sW~ec~~qV~g~~ga~yK~F~t~~eA~~~l   48 (53)
T 3bsu_A           12 RKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFV   48 (53)
T ss_dssp             SSCEEESSHHHHHHHHTTCTTCEEEEESSHHHHHHHH
T ss_pred             CCCceECCHHHHHHHhcCCCCCccCCCCCHHHHHHHH
Confidence            4699999999999999999999999999999998543

>1qhk_A RNAse HI, protein (ribonuclease HI); ribonuclease HI N-terminal domain, hydrolase; NMR {Saccharomyces cerevisiae} SCOP: d.100.1.2

Probab=90.68  E-value=0.01  Score=38.21  Aligned_cols=35  Identities=14%  Similarity=0.001  Sum_probs=32.1

Q ss_pred             CCCCCCCCCCCCCCccccccccccCCCCChHHHHH
Q psy5302          51 PAPQTSAPWLIEPPVVDYSLRKFNKNTDPKEEINI   85 (333)
Q Consensus        51 ~~p~~~ppW~~~~~~v~~~~~~~~k~~~~~~~a~~   85 (333)
                      ..|+++..|.+|..+|++...+.+|++.+.+||..
T Consensus        10 ~~~GIy~sW~ec~~qV~g~~ga~yK~F~t~~eA~~   44 (47)
T 1qhk_A           10 RETGIYNTWNECKNQVDGYGGAIYKKFNSYEQAKS   44 (47)
T ss_dssp             SSCEEEEEHHHHHHHSSSCSSCCCEEESCHHHHHH
T ss_pred             CCCceECCHHHHHHHhcCCCCCccCCCCCHHHHHH
Confidence            46999999999999999999999999999999984

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	333
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	5e-10
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	1e-06
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	6e-06

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]} Length = 126

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 2 [TaxId: 11709]

 Score = 54.5 bits (130), Expect = 5e-10
 Identities = 26/131 (19%), Positives = 47/131 (35%), Gaps = 12/131 (9%)

Query: 97  DSTVIYTDAS--KTDVAVSSAFCSQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLN 154
            +   YTD S  +      + + +   K   +     +   AEL +              
Sbjct: 6   GAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFA---------MAL 56

Query: 155 EHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGN 214
             +     I  DS   +  + +  +    +  +  +I E   K +I   WVP+H GI GN
Sbjct: 57  TDSGPKVNIIVDSQYVMGIVASQPT-ESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGN 115

Query: 215 EEADRLAKEAL 225
           +E D L  + +
Sbjct: 116 QEVDHLVSQGI 126

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]} Length = 147

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Thermus thermophilus [TaxId: 274]

 Score = 45.7 bits (107), Expect = 1e-06
 Identities = 20/136 (14%), Positives = 42/136 (30%), Gaps = 11/136 (8%)

Query: 100 VIYTDASKTD---VAVSSAFCSQD--IKFSTRLHSLLSICNAELTSILFAIHFLLSSCL- 153
            ++TD +          +A        K  +   +  +    EL + +  +  L   C  
Sbjct: 5   ALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCEV 64

Query: 154 -----NEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSIRFIWVPSH 208
                + + +  F          +  +          ++   +L   +   +RF +V  H
Sbjct: 65  DLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGH 124

Query: 209 VGIAGNEEADRLAKEA 224
            G   NE  DR A+  
Sbjct: 125 TGHPENERVDREARRQ 140

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]} Length = 152

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Escherichia coli [TaxId: 562]

 Score = 43.5 bits (101), Expect = 6e-06
 Identities = 12/25 (48%), Positives = 15/25 (60%)

Query: 200 IRFIWVPSHVGIAGNEEADRLAKEA 224
           I++ WV  H G   NE AD LA+ A
Sbjct: 114 IKWEWVKGHAGHPENERADELARAA 138

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	333
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.91
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.89
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.88
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.76
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.52
d1qhka_	47	N-terminal domain of RNase HI {Baker's yeast (Sacc	87.69

>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=99.91  E-value=9.3e-25  Score=174.51  Aligned_cols=117  Identities=23%  Similarity=0.290  Sum_probs=85.8

Q ss_pred             CCcEEEEecCCCCC-CC-cceEEe-cCceeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHHH
Q psy5302          96 VDSTVIYTDASKTD-VA-VSSAFC-SQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQ  172 (333)
Q Consensus        96 ~~~~~iytDGS~~~-~~-~G~g~~-~~~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~~  172 (333)
                      ++..+||||||+.. ++ .|+|++ ..+......++ ..|++.|||.||+.||+..    .     +.+.|+|||++++.
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~~----~-----~~i~I~tDS~~v~~   74 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTDS----G-----PKVNIIVDSQYVMG   74 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHTS----C-----SEEEEEESCHHHHH
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhccC----C-----cceEEEechHHHHH
Confidence            45689999999754 33 556665 33333334443 5799999999999999753    1     23999999999999


Q ss_pred             HHcCCCCCc--hHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHh
Q psy5302         173 TLQNVFSLN--PIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEAL  225 (333)
Q Consensus       173 ~l~~~~~~~--~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~  225 (333)
                      .+.++...+  .....+.+.+   .....|.|.|||||+|++|||+||+||++|.
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~---~~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          75 IVASQPTESESKIVNQIIEEM---IKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             HHHTCCSEESCHHHHHHHHHH---HHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHhcCCccccchHHHHHHHHh---hhcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            999976532  3333322222   2346899999999999999999999999984

>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=99.89  E-value=2.4e-24  Score=176.64  Aligned_cols=120  Identities=17%  Similarity=0.143  Sum_probs=88.5

Q ss_pred             cEEEEecCCCCCC--CcceEEe---cCceeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHHH
Q psy5302          98 STVIYTDASKTDV--AVSSAFC---SQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQ  172 (333)
Q Consensus        98 ~~~iytDGS~~~~--~~G~g~~---~~~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~~  172 (333)
                      .|+||||||+..+  ..|+|+|   .+............|++.||+.|++.||+++...       ..+.|++||++++.
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~~-------~~i~i~tds~~~~~   75 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEP-------CEVDLYTDSHYLKK   75 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCSC-------CEEEEECCCHHHHH
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhccCC-------ceEEEecchhhhhc
Confidence            4899999998754  3678866   2222211112235699999999999999875431       23999999999999


Q ss_pred             HHcCCCC-----------------CchHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCC
Q psy5302         173 TLQNVFS-----------------LNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTST  228 (333)
Q Consensus       173 ~l~~~~~-----------------~~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~  228 (333)
                      .+..+..                 +.++++++..++    ....|.|.|||||+|++|||.||+|||+|+...
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~----~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_          76 AFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAM----APHRVRFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             HHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH----TTSEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             cccccchhhhhhccccccccccchhHHHHHHHHHHh----hhcccceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence            8866421                 123566666554    456899999999999999999999999999765

>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=99.88  E-value=3.1e-23  Score=170.55  Aligned_cols=119  Identities=21%  Similarity=0.238  Sum_probs=88.6

Q ss_pred             cEEEEecCCCCCC--CcceEEe--cCc-e-eEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHH
Q psy5302          98 STVIYTDASKTDV--AVSSAFC--SQD-I-KFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSAL  171 (333)
Q Consensus        98 ~~~iytDGS~~~~--~~G~g~~--~~~-~-~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~  171 (333)
                      .|.||||||+..+  .+|+|+|  .++ . ..+... ...|++.||+.|++.||+.+...       ..+.|++||++++
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~-~~~tnn~aE~~Ai~~Al~~~~~~-------~~i~i~tds~~~i   73 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKEH-------AEVILSTDSQYVR   73 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCSC-------CEEEEEECCHHHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEecccc-CcccHHHHHHhhhhhhhhhhccc-------ceEEEeecceeeE
Confidence            4899999997653  3788876  332 2 233333 35789999999999999876432       2399999999999


Q ss_pred             HHHcCCCC---------C-------chHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhhHHHHHHhcCC
Q psy5302         172 QTLQNVFS---------L-------NPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTST  228 (333)
Q Consensus       172 ~~l~~~~~---------~-------~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD~lAk~a~~~~  228 (333)
                      ..+..+..         .       .++++.+..+    .....|.|+|||||+|++|||+||+|||+|+..+
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~----~~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~  142 (152)
T d1jl1a_          74 QGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAA----LGQHQIKWEWVKGHAGHPENERADELARAAAMNP  142 (152)
T ss_dssp             HHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHH----TTTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSC
T ss_pred             EcccchhhHhHhccchhcccCeeecHHHHHHHHHH----hhcceeEEEEecccCCCccHHHHHHHHHHHHhCC
Confidence            88865532         1       1234444443    3456899999999999999999999999999877

>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=99.76  E-value=1.3e-18  Score=134.75  Aligned_cols=102  Identities=20%  Similarity=0.232  Sum_probs=75.0

Q ss_pred             CCCCcEEEEecCCCCC-CC-cceEEe-cCceeEEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHH
Q psy5302          94 VPVDSTVIYTDASKTD-VA-VSSAFC-SQDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSA  170 (333)
Q Consensus        94 ~~~~~~~iytDGS~~~-~~-~G~g~~-~~~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~  170 (333)
                      +-++..++|||||+.. ++ .|+|++ ..+......+. .+|++.|||.|++.||+..    .     .+|.|+|||++|
T Consensus         4 Pi~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~~-~~TNn~aEl~Avi~aL~~~----~-----~~v~I~TDS~yv   73 (110)
T d1s1ta1           4 PIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLALQDS----G-----LEVNIVTDSQYA   73 (110)
T ss_dssp             CCTTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHHS----C-----SEEEEEECCHHH
T ss_pred             CCCCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEecc-cCcHHHHHHHHHHHHHHhC----C-----CeEEEEEehHHH
Confidence            3456689999999653 33 556665 32233333443 5799999999999999742    1     239999999999


Q ss_pred             HHHHcCCCCC--chHHHHHHHHHHhhcCCCceEEEEecCC
Q psy5302         171 LQTLQNVFSL--NPIASEIRNLILENKSKLSIRFIWVPSH  208 (333)
Q Consensus       171 ~~~l~~~~~~--~~~~~~i~~~~~~~~~~~~v~~~wVp~H  208 (333)
                      +.+++.+...  ..+++++.+++   .....|.|.|||||
T Consensus        74 i~~i~~~~~~~~~~l~~~il~~l---~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          74 LGIIQAQPDQSESELVNQIIEQL---IKKEKVYLAWVPAH  110 (110)
T ss_dssp             HHHHHHCCSEESCHHHHHHHHHH---HHCSEEEEEECCSS
T ss_pred             HHHHhcCccccchHHHHHHHHHH---hcCCceEEEEeCCC
Confidence            9999997763  46787777666   23468999999999

>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=99.52  E-value=1.1e-15  Score=120.27  Aligned_cols=110  Identities=12%  Similarity=0.025  Sum_probs=79.6

Q ss_pred             EEecCCCC--CCCcceEEe---cCcee-EEeecCCCcchHHHHHHHHHHHHHHHhhhccCcCCcceEEEEeCcHHHHHHH
Q psy5302         101 IYTDASKT--DVAVSSAFC---SQDIK-FSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTL  174 (333)
Q Consensus       101 iytDGS~~--~~~~G~g~~---~~~~~-~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~~~~~l  174 (333)
                      ||||||+.  +|.+|+|+|   .+... .+..+ ...|++.||+.|++.||+.+.....    +  +.|+|||++|+..+
T Consensus         7 Iy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~-~~~TNN~aEl~A~i~aL~~~~~~~~----~--i~I~tDS~yvi~wv   79 (132)
T d1zbfa1           7 LSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERNS----R--KPIYSNSQTAIKWV   79 (132)
T ss_dssp             EEEEEEECSSSEEEEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHHTTC----C--CCEEESCHHHHHHH
T ss_pred             EEEeecCCCCCchheEEEEEEcCCEEEEEEcCc-CccchHHHHHHHHHHHHHHhhcCCc----e--EEEEeccHHHHHHH
Confidence            89999976  455888877   23332 33333 3679999999999999999987543    3  99999999999999


Q ss_pred             cCCCCC---------chHHHHHHHHHHhhcCCCceEEEEecCCCCCccchhhh
Q psy5302         175 QNVFSL---------NPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEAD  218 (333)
Q Consensus       175 ~~~~~~---------~~~~~~i~~~~~~~~~~~~v~~~wVp~H~g~~gNe~AD  218 (333)
                      .++...         .++++.+.++.. .-+...+.+.||+.|+..-||..||
T Consensus        80 ~~~~~kt~~~~~vkN~~l~~~i~~a~~-~lk~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          80 KDKKAKSTLVRNEETALIWKLVDEAEE-WLNTHTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             HHTCCCCCCCCSTTTHHHHHHHHHHHH-HHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             HhCceecCcCCCcccHHHHHHHHHHHH-HHHhCCcCceeEEecCcccccCCCC
Confidence            876532         124444443321 1234558889999999999999998

>d1qhka_ d.100.1.2 (A:) N-terminal domain of RNase HI {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: MbtH/L9 domain-like
superfamily: L9 N-domain-like
family: N-terminal domain of RNase HI
domain: N-terminal domain of RNase HI
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.69  E-value=0.01  Score=36.69  Aligned_cols=35  Identities=14%  Similarity=0.001  Sum_probs=31.8

Q ss_pred             CCCCCCCCCCCCCCccccccccccCCCCChHHHHH
Q psy5302          51 PAPQTSAPWLIEPPVVDYSLRKFNKNTDPKEEINI   85 (333)
Q Consensus        51 ~~p~~~ppW~~~~~~v~~~~~~~~k~~~~~~~a~~   85 (333)
                      ..|+++..|.+|.++|+....+..|++.+.+||++
T Consensus        10 ~~~GIy~~W~e~~~~V~g~~ga~~k~F~t~~eA~~   44 (47)
T d1qhka_          10 RETGIYNTWNECKNQVDGYGGAIYKKFNSYEQAKS   44 (47)
T ss_dssp             SSCEEEEEHHHHHHHSSSCSSCCCEEESCHHHHHH
T ss_pred             CCCCccCCHHHHHHHhcCCCCCeECCcCCHHHHHH
Confidence            46899999999999999999999999999999973