Psyllid ID: psy4967

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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-------340-------350----
Protein Sequence
MNQGVRLALGAFKSSPIPSILSEAGEPPLSYRREILTCNYLFNTQRNPKHFLSPLLTDDSLQQLYERKSSYEKPLRIRGKLLLEKYGIDHLDFLSPSPQTSAPWLIEPPPVDYSLRKFNKDTDSKEEINISFQELLQKTPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLQEIKLENKPWNPPYLILYYKNEIHSLIHISHFIVHTLIALKEYLPE
Secondary Structure (PSIPRED)
cHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccEEEEcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccEEEEEcccHHHHHHHcccccccHHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHccccccccHHHccccHHHHHccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccEEEEEccccccccEEEEEEEcccEEEEccccccHHHHHHHHHHHHHHHHHHHHcccccccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHcccccEEEEEEEccccccc
Coil and Loop (DISEMBL)
MNQGVRLALgafksspipsilseagepplsyrrEILTCnylfntqrnpkhflsplltddSLQQLYErkssyekplRIRGKLLLEKygidhldflspspqtsapwliepppvdyslrkfnkdtdskEEINISFQELLqktpdstvvytdaskndvavssafcsqdtkfssrlhplLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIfslnpiagEIRDLILTNKSKLNVRFiwvpshvgiagNEEADRLAKEAltsthptinkipipdykaysKRKILSAWNSEWHNLQNNKLQEiklenkpwnppyliLYYKNEIHSLIHISHFIVHTLIALKEYLPE
Flexible Loop (DISEMBL)
MNQGVRlalgafksspipsilseagepplSYRREILTCNYLFNTQRNPKHFLSPLLTDDSLQQLYErkssyekplriRGKLLLEKYGIDHLDFLSPSPQTSAPWLIEPPPVDYSLRKFNKDTDSKEEINISFQELLQKTPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEaltsthptinkipipdykaYSKRKILSAWNSEWHNLQNNKLQEIKLENKPWNPPYLILYYKNEIHSLIHISHFIVHTLIALKEYLPE
Low Complexity Region (SEG)
MNQGVRLALGAFKSSPIPSILSEAGEPPLSYRREILTCNYLFNTQRNPKHFLSPLLTDDSLQQLYERKSSYEKPLRIRGKLLLEKYGIDHLDFLSPSPQTSAPWLIEPPPVDYSLRKFNKDTDSKEEINISFQELLQKTPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLQEIKLENKPWNPPYLILYYKNEIHSLIHISHFIVHTLIALKEYLPE
Disordered region (IsUnstruct)
****************************LSYRREILTCNYLFNTQRNPKHFLSPLLTDDSLQQLYERKSSYEKPLRIRGKLLLEKYGIDHLDFLS*******PWLIE**********************ISFQELL*****STVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLQEIKLENKPWNPPYLILYYKNEIHSLIHISHFIVHTLIALKEY***
Disordered Region (DISOPRED)
*NQGVRLALGAFKSSPIPSILSEAGEPPLSYRREILTCNYLFNTQRNPKHFLSPLLTDDSLQQLYERKSSYEKPLRIRGKLLLEKYGIDHLDFLSPSPQTSAPWLIEPPPVDYSLRKFNKDTDSKEEINISFQELLQKTPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLQEIKLENKPWNPPYLILYYKNEIHSLIHISHFIVHTLIAL******
Disordered Region (DISEMBL)
MNQGVRLALGAFKSSPIPSILSEAGEPPLSYRREILTCNYLFNTQRNPKHFLSPLLTDDSLQQLYERKSSYEKPLRIRGKLLLEKYGIDHLDFLSPSPQTSAPWLIEPPPVDYSLRKFNKDTDSKEEINISFQELLQKTPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLQEIKLENKPWNPPYLILYYKNEIHSLIHISHFIVHTLIALKEYLPE
Disordered Region (DISPRO)
MNQGVRLALGAFKSSPIPSILSEAGEPPLSYRREILTCNYLFNTQRNPKHFLSPLLTDDSLQQLYERKSSYEKPLRIRGKLLLEKYGIDHLDFLSPSPQTSAPWLIEPPPVDYSLRKFNKDTDSKEEINISFQELLQKTPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLQEIKLENKPWNPPYLILYYKNEIHSLIHISHFIVHTLIALKE****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNQGVRLALGAFKSSPIPSILSEAGEPPLSYRREILTCNYLFNTQRNPKHFLSPLLTDDSLQQLYERKSSYEKPLRIRGKLLLEKYGIDHLDFLSPSPQTSAPWLIEPPPVDYSLRKFNKDTDSKEEINISFQELLQKTPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLQEIKLENKPWNPPYLILYYKNEIHSLIHISHFIVHTLIALKEYLPE
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	354
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.968	0.280	0.327	1e-37
427791807	1212	Putative tick transposon, partial [Rhipi	0.968	0.283	0.324	2e-37
427791321	1210	Putative tick transposon, partial [Rhipi	0.870	0.254	0.339	2e-37
443710566	377	hypothetical protein CAPTEDRAFT_186063 [	0.872	0.819	0.334	7e-32
443713753	266	hypothetical protein CAPTEDRAFT_215116 [	0.638	0.849	0.365	1e-27
427798889	1199	Putative tick transposon, partial [Rhipi	0.875	0.258	0.325	3e-27
427792011	1121	Putative tick transposon, partial [Rhipi	0.850	0.268	0.313	9e-26
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.531	0.399	0.379	3e-24
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.567	0.400	0.397	7e-24
443700898	300	hypothetical protein CAPTEDRAFT_212630,	0.782	0.923	0.316	7e-24

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

 Score =  163 bits (412), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 117/357 (32%), Positives = 183/357 (51%), Gaps = 14/357 (3%)

Query: 2    NQGVRLALGAFKSSPIPSILSEAGEPPLSYRREILTCNYLFNTQRNPKHFLSPLLTDDSL 61
            N  +RL LGAF++SPIPS+  EAGE P+  R + L   Y+   + NP +     + + + 
Sbjct: 816  NAALRLCLGAFRTSPIPSLHVEAGELPMDIRMKKLAMQYIVKLKSNPTNPAFDSIFNPTE 875

Query: 62   QQLYERKSSYEKPLRIRGKLLLEKYG--IDHLDFLSPSPQTSAPWLIEPPPVDYSLRKFN 119
             +LY R+ +  +PL +R +  ++     ID +  +  +PQ + PWL+  P ++ SL  F 
Sbjct: 876  VELYNRRPNVIQPLGLRMREPIQNLTQPIDQISKIE-TPQ-NPPWLMNKPKLNLSLLNFK 933

Query: 120  KDTDSKEEINISFQELLQKTPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICN 179
            K+      + + F+EL +   D   +YTD SK +  V+ A   ++   S RL    SI  
Sbjct: 934  KENTDPSILQVHFRELQESYGDCGTIYTDGSKMEGKVACACSFRNKTISRRLPDGCSIFT 993

Query: 180  AELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE-IRDLILTN 238
            AEL AIL A+  ++ A      R+  +ICSDS SALQ L  + +  P+  + ++ L L  
Sbjct: 994  AELHAILLAL-MAVKAS----ERSKFIICSDSKSALQALGRMKTDIPLVHKSLKLLDLIT 1048

Query: 239  KSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNS 298
              + +V FIWVPSHVGI GNE ADR AK AL     +  +IP  D +          W +
Sbjct: 1049 ADRRDVTFIWVPSHVGIEGNEAADREAKRALNHA-VSGTQIPYSDLRQSIASATYREWQN 1107

Query: 299  EWHNLQNNKLQEIKLENKPWNPPYLILYYKNE-IHSLIHISH-FIVHTLIALKEYLP 353
             W    ++KL++I + +  W P    L  +     S + I H +I H+ +  +E  P
Sbjct: 1108 RWEAETHSKLRQI-VADVRWRPTSKGLTRRGSTTMSRLRIGHTYITHSFVLKREEPP 1163

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

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

 Score =  162 bits (410), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 116/357 (32%), Positives = 173/357 (48%), Gaps = 14/357 (3%)

Query: 2    NQGVRLALGAFKSSPIPSILSEAGEPPLSYRREILTCNYLFNTQRNPKHFLSPLLTDDSL 61
            N G+RL+ GA+++SP+ S+  +  EPPLS+RR  LT +Y+   + +P+H    + T  S 
Sbjct: 798  NLGLRLSSGAYRTSPVESLYVDCNEPPLSHRRASLTLSYVLRIRSSPQHICYDIATRCSS 857

Query: 62   QQLYERKSSYEKPLRIRGKLLLEKYGI--DHLDFLSPSPQTSAPWLIEPPPVDYSLRKFN 119
            +  Y  KS+  KPL +R +     Y I  + LD     P+   PW       D SL   N
Sbjct: 858  RLHYLNKSNLIKPLLLRFEEYCRTYVISEETLDVARKPPRI-PPWFDLAQLCDISLSHIN 916

Query: 120  KDTDSKEEINISFQELLQKTPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICN 179
            K     E I   F+ L +K  D    YTD SK    V     + ++ FS R+   +SI  
Sbjct: 917  KKVTPPELIIQEFRALQEKYRDYAEFYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFT 976

Query: 180  AELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNK 239
            AE+ A+  A    I+           +I +DSLSAL+ L       P+ G+I +++L N 
Sbjct: 977  AEVYALYEAARKIIAGKHKKA-----IIYTDSLSALKALHIKSECEPLVGDILNMVLINS 1031

Query: 240  SKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIP--DYKAYSKRKILSAWN 297
              +++RF WVPSHVGI GNE+AD+ A  A    H T+ KI IP  D +   +  +L+ W 
Sbjct: 1032 KVISMRFCWVPSHVGIPGNEKADKCASLA---AHKTLTKIRIPLKDSQRTIRLALLAKWQ 1088

Query: 298  SEWHNLQNNKLQEIKLENKPWNPPYLILYYKNEIHSLIHISH-FIVHTLIALKEYLP 353
             +W +  +NKL  +K     W        +   I   + I H  + H  +  KE  P
Sbjct: 1089 QQWDSCTSNKLHLVKPTLGEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQP 1145

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 =  162 bits (410), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 109/321 (33%), Positives = 162/321 (50%), Gaps = 13/321 (4%)

Query: 2    NQGVRLALGAFKSSPIPSILSEAGEPPLSYRREILTCNYLFNTQRNPKHFLSPLLTDDSL 61
            N G+RL+ GA+++SP+ S+  +  EPPLS+RR  LT +Y+   + +P+H    + T  S 
Sbjct: 795  NLGLRLSSGAYRTSPVESLYVDCNEPPLSHRRASLTLSYVLRIRSSPQHICYDIATRCSS 854

Query: 62   QQLYERKSSYEKPLRIRGKLLLEKYGI--DHLDFLSPSPQTSAPWLIEPPPVDYSLRKFN 119
            +  Y  KS+  KPL +R +     Y I  + LD     P+   PW       D SL   N
Sbjct: 855  RLHYLNKSNLIKPLLLRFEEYCRTYVISEETLDVARKPPRI-PPWFDLAQLCDISLSHIN 913

Query: 120  KDTDSKEEINISFQELLQKTPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICN 179
            K     E I   F+ L +K  D    YTD SK    V     + ++ FS R+   +SI  
Sbjct: 914  KKVTPPELIIQEFRALQEKYRDYAEFYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFT 973

Query: 180  AELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNK 239
            AE+ A+  A    I+           +I +DSLSAL+ L       P+ G+I +++L N 
Sbjct: 974  AEVYALYEAARKIIAGKHKKA-----IIYTDSLSALKALHIKSECEPLVGDILNMVLINS 1028

Query: 240  SKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIP--DYKAYSKRKILSAWN 297
              +++RF WVPSHVGI GNE+AD+ A  A    H T+ KI IP  D +   +  +L+ W 
Sbjct: 1029 KVISMRFCWVPSHVGIPGNEKADKCASLA---AHKTLTKIRIPLKDSQRTIRLALLAKWQ 1085

Query: 298  SEWHNLQNNKLQEIKLENKPW 318
             +W +  +NKL  +K     W
Sbjct: 1086 QQWDSCTSNKLHLVKPTLGEW 1106

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443710566|gb|ELU04776.1| hypothetical protein CAPTEDRAFT_186063 [Capitella teleta]

 Score =  144 bits (362), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 108/323 (33%), Positives = 167/323 (51%), Gaps = 14/323 (4%)

Query: 2   NQGVRLALGAFKSSPIPSILSEAGEPPLSYRREILTCNY---LFNTQRNPKHFLSPLLTD 58
           NQ  RL LGAF+ SP+ S+ +EA E P++ R+++L+  +   + +   NP H       +
Sbjct: 45  NQAFRLCLGAFRISPVTSLHTEANEMPMAIRQKLLSVQFALRVCSDTTNPAHQCIFNYNN 104

Query: 59  DSLQQLYERKSSYEKPLRIRGKLLLEKYGIDHLDFLSPSPQTSAP-WLIEPPPVDYSLRK 117
           D   + Y  K +  +PL +R K  L+    D +  ++P+   + P WL+ PP +D SL  
Sbjct: 105 D---RFYLSKPNAIRPLALRIKEDLQTICPD-IKAITPNQLFNIPYWLLRPPELDISLIH 160

Query: 118 FNKDT-DSKEEINISFQELLQKTPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLS 176
           F K T +    +   F  L+ K PD  V++TD SK+D AV+    + +     RL    S
Sbjct: 161 FGKKTANPNYTLKNEFYNLMDKYPDHKVIFTDGSKSDSAVACFATADNLSIQIRLPDSAS 220

Query: 177 ICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRD-LI 235
           I +AEL AI + +   +    N+  +   +I +DSLS+LQ + N    +P   +I +   
Sbjct: 221 IFSAELLAI-YQVLTLLECSANDQQQ--FLIATDSLSSLQAIGNFNIKHPYVFKILEKCT 277

Query: 236 LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSA 295
           L +K  + +   W PSHVG+ GNE AD LAKEAL+ T  TI +IP  D+K  +       
Sbjct: 278 LLHKKGIYLVMAWCPSHVGVMGNERADLLAKEALSFTTCTI-RIPSSDFKPITHEFFKEK 336

Query: 296 WNSEWHNLQNNKLQEIKLENKPW 318
           W  +W + Q NKL  I+     W
Sbjct: 337 WQEQWSSEQENKLYCIQPTLGKW 359

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443713753|gb|ELU06453.1| hypothetical protein CAPTEDRAFT_215116 [Capitella teleta]

 Score =  130 bits (326), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 88/241 (36%), Positives = 125/241 (51%), Gaps = 15/241 (6%)

Query: 89  DHLDFLSPSPQT------SAPWLIEPPPVDYSLRKFNKDTDSKEEINISFQELLQKTPDS 142
           DH+D +  SP T      + PW +  P VD SL    KD+ S   I   F++ L   P S
Sbjct: 16  DHMDTVGSSPVTHHVIPETPPWHLVQPEVDLSLTFSKKDSMSALTIRSEFEDALDSYPVS 75

Query: 143 TVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNR 202
           TV YTD SK++ +V+ +F S   K   +L   +S+  +E+ AIL A+       L   N 
Sbjct: 76  TVFYTDGSKSEDSVARSFFSSRLKLKMKLPVQMSVFTSEIIAILSALKC-----LEADNE 130

Query: 203 AY-LVICSDSLSALQTLQNIFSLNPIAGEIRDLI--LTNKSKLNVRFIWVPSHVGIAGNE 259
            +  VICSDSLSA+  +  +   +P   ++   I  ++ + K+ V F+W PSHVGI GNE
Sbjct: 131 QHQFVICSDSLSAIMAIHGMDVHHPYVLQVLYAIKSISQQEKI-VVFMWCPSHVGIPGNE 189

Query: 260 EADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLQEIKLENKPWN 319
            A  LA++AL+ST+     +P  D +   K+ I S W  EW    NNKL  I     PW 
Sbjct: 190 MAHTLAEKALSSTNLAELPVPASDLRGLIKKYIRSQWQHEWEEQHNNKLHSIHPTIGPWP 249

Query: 320 P 320
           P
Sbjct: 250 P 250

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 =  129 bits (323), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 104/320 (32%), Positives = 149/320 (46%), Gaps = 10/320 (3%)

Query: 4    GVRLALGAFKSSPIPSILSEAGEPPLSYRREILTCNYLFNTQRNPKHFLSPLLTDDSLQQ 63
            G+RL+ GAF++SP+ S+  E+ E  L  +R  ++  Y      + +H     + D S   
Sbjct: 824  GIRLSTGAFRTSPVESLYVESNEWSLHLQRSYMSFLYYIKVNADKEHPSHSTINDLSCST 883

Query: 64   LYERKSSYEKPLRIRGKLLLEKYGIDHLDFLSPSPQT-SAPWLIEPPPVDYSLRKFNKDT 122
            L+E + S + P  +R + L E+ G+   +    +P     PW  +    D S  +  K  
Sbjct: 884  LFENRPSLKPPYSLRVRDLAEQTGLPLFEHRLMAPAAYPPPWQWQLIDCDVSFMEVTKHA 943

Query: 123  DSKEEINISFQELLQKTPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAEL 182
                 I   F EL  K  +    YTDASK+  +VS A        +  LHP  SI  AE 
Sbjct: 944  -PIAHIRTYFLELQHKY-NCPAFYTDASKSHTSVSYAAVGPSFSAAGALHPNTSIFTAEA 1001

Query: 183  TAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFS-LNPIAGEIRDLILT-NKS 240
             AIL A+      H+  +     VI +DSLS ++ L+ +    NP+   +  L+ T   S
Sbjct: 1002 YAILAAV-----KHIRELKLQKAVIYTDSLSVVKALKTLKKHRNPVLVSLYSLLCTIYTS 1056

Query: 241  KLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEW 300
            K +V   WVP H  I GN  AD+LA  A  S+  T   IP  D K Y KRKI + W S W
Sbjct: 1057 KQHVVVCWVPGHREIQGNVMADQLAVSAHDSSANTSIAIPALDLKPYLKRKIRAYWQSTW 1116

Query: 301  HNLQNNKLQEIKLENKPWNP 320
                +NKL  IK +   W P
Sbjct: 1117 DRQTHNKLHVIKPQLGHWPP 1136

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427792011|gb|JAA61457.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  124 bits (310), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 97/309 (31%), Positives = 142/309 (45%), Gaps = 8/309 (2%)

Query: 4    GVRLALGAFKSSPIPSILSEAGEPPLSYRREILTCNYLFNTQRNPKHFLSPLLTDDSLQQ 63
            G+RLA GAF++SP+ S+  EA E P+   RE  T  Y       P H  + L+ D S  +
Sbjct: 818  GIRLATGAFRTSPVSSLYVEANEWPMQLEREYCTLMYTLKVTSIPTHPCAKLVADTSALR 877

Query: 64   LYERKSSYEKPLRIRGKLLLEKYGIDHLDFL-SPSPQTSAPWLIEPPPVDYSLRKFNKDT 122
             +E++ S  KP  +       +  I       +PS +   PW       D S    +K  
Sbjct: 878  FFEKRPSLSKPFSLTCTATAAQAEIPLQQVAKAPSMEWLPPWEKTRIKCDMSFCHIDKQR 937

Query: 123  DSKEEINISFQELLQKTPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAEL 182
              +  I   F  L  K       YTDASK   +VS+A    +   S RL+   SI  AE 
Sbjct: 938  HPRAAIQQHFLSLQYKYRGCHQFYTDASKTRDSVSAAAVGPEFTTSERLNVHTSIFTAEA 997

Query: 183  TAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF-SLNPIAGEI-RDLILTNKS 240
             AIL AI + ++   +N+ ++  VI +DSLS ++ L     + NP+  ++ + L    ++
Sbjct: 998  YAILIAIKYILN---HNITKS--VIFTDSLSVVRALHTGKPNKNPVLCDVEKQLTNAYRN 1052

Query: 241  KLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEW 300
               +   WVP H GI GNE AD  A  A   ++  +N +P  D KA   R +   W  EW
Sbjct: 1053 TSEITVCWVPGHAGIDGNERADACAAVAAQKSNLDVNSVPYQDLKALVHRNLRERWQKEW 1112

Query: 301  HNLQNNKLQ 309
                NNKL 
Sbjct: 1113 DLETNNKLH 1121

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  119 bits (297), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 74/195 (37%), Positives = 106/195 (54%), Gaps = 7/195 (3%)

Query: 128 INISFQELLQKTPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILF 187
           I   F + L + PDSTV YTD SK++ +V+ +F S   K   +L   +S+  +E+ AIL 
Sbjct: 6   IRSEFADALDRYPDSTVFYTDGSKSEDSVACSFFSSRLKLKMKLPVQMSVFTSEIIAILS 65

Query: 188 AIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLI--LTNKSKLNVR 245
           A+        +N    + VICSDSLSA+  +  +   +P   ++   I  ++ + K+ V 
Sbjct: 66  ALR---CVEADNEQHQF-VICSDSLSAIMAIHGMDVRHPYVLQVLYAIKSISQQEKIVV- 120

Query: 246 FIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQN 305
           F+W PSHVGI GNE AD LAKEAL+ST+     +P  D +   K+ I S W  EW    +
Sbjct: 121 FMWCPSHVGIPGNEMADTLAKEALSSTNLAELPVPASDLRCLIKKYIRSRWQHEWDEQHS 180

Query: 306 NKLQEIKLENKPWNP 320
           NKL  I     PW P
Sbjct: 181 NKLHSIHPTIGPWPP 195

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  117 bits (294), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 85/214 (39%), Positives = 111/214 (51%), Gaps = 13/214 (6%)

Query: 103 PWLIEPPPVDYSLRKFNKDTDSKEEINISFQELLQKTPDSTVVYTDASKNDVAVSSAFCS 162
           PW + PP VD S+ KF KD      +   F  L+ K P    +YTD SK++ AV+ AF  
Sbjct: 43  PWKLRPPEVDTSISKFLKDQHPALFLKQEFYNLIDKYP-GINIYTDGSKSNNAVACAFTC 101

Query: 163 QDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF 222
              +    L   +SI  AEL AI  A+ F  +      +     ICSDSLS+L  L N  
Sbjct: 102 STYQIQFGLPTQMSIYTAELIAIEQALIFIETVK----DEDQFNICSDSLSSLTALSNCD 157

Query: 223 SLNPIAGEI--RDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIP 280
             +P    I  +   L  K KL V FIW PSHVGI GNE ADRLAK+AL      + K+P
Sbjct: 158 ITHPYLLSILTKQNNLVRKGKL-VVFIWCPSHVGILGNEVADRLAKQALVM---PVTKLP 213

Query: 281 IP--DYKAYSKRKILSAWNSEWHNLQNNKLQEIK 312
           +P  DYK+  +  + S W +EW    +NKL  I+
Sbjct: 214 LPHTDYKSPIRSYVKSLWQNEWDEETDNKLHSIQ 247

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443700898|gb|ELT99633.1| hypothetical protein CAPTEDRAFT_212630, partial [Capitella teleta]

 Score =  117 bits (293), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 92/291 (31%), Positives = 150/291 (51%), Gaps = 14/291 (4%)

Query: 28  PLSYRREILTCNY---LFNTQRNPKHFLSPLLTDDSLQQLYERKSSYEKPLRIRGKLLLE 84
           P++ R+++L+  +   + +   NP H       +D   + Y  K +  +PL +R K  L+
Sbjct: 2   PMTIRQKLLSVQFALRVCSDTTNPAHQCIFNYNND---RFYLSKPNAIRPLALRIKEDLQ 58

Query: 85  KYGIDHLDFLSPSPQTSAP-WLIEPPPVDYSLRKFNKDT-DSKEEINISFQELLQKTPDS 142
               D +  ++P+   + P WL+ PP +D SL  F K T +    +   F  L+ K PD 
Sbjct: 59  TICPD-IKAITPNQLFNIPYWLLRPPELDISLIHFGKKTANPNYTLRNEFYNLMDKYPDH 117

Query: 143 TVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNR 202
            V++TD SK+D AV+ +  + + +   RL    SI +AEL AI + +   +    N+  +
Sbjct: 118 KVIFTDGSKSDSAVACSATADNLRIQIRLPDSASIFSAELLAI-YQVLTLLECSANDQQQ 176

Query: 203 AYLVICSDSLSALQTLQNIFSLNPIAGEI-RDLILTNKSKLNVRFIWVPSHVGIAGNEEA 261
              +I +DSLS+LQ + N    +P   +I +   L +K  + +   W PSHVG+ GNE A
Sbjct: 177 --FLIATDSLSSLQAIGNFNIKHPYVFKILQKCTLLHKKGIYLVMAWCPSHVGVMGNERA 234

Query: 262 DRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLQEIK 312
           D LAKEAL+ T  TI ++P  D+K  +       W  +W + Q NKL  I+
Sbjct: 235 DLLAKEALSFTTCTI-RVPSSDFKPITHEFYKEKWQEQWSSEQENKLYCIQ 284

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	354
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.621	0.452	0.261	4.3e-08

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

 Score = 154 (59.3 bits), Expect = 4.3e-08, P = 4.3e-08
 Identities = 64/245 (26%), Positives = 113/245 (46%)

Query:   121 DTDSKEEINISFQELLQKTPDSTVVYTDASK-NDVAVSSAFC-----SQDTKFSSRLHPL 174
             D D++  I  + + +L + P    +YTD S  N    ++A C     S+ +    +    
Sbjct:   162 DGDAETAIE-THRNILNRAPRPIALYTDGSGINGRVGAAAICPKYLISRSSYMGQQSEST 220

Query:   175 LSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNP---IAGEI 231
             + +  AEL  IL A+   +   + +      VI +D+ + LQ L+N  S +    +   I
Sbjct:   221 VYV--AELQGILLALVIILQRQMQHA-----VIFTDNQATLQALRNPGSQSGQYILEAII 273

Query:   232 RDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKR- 290
               L    K+ LNV F W+P+H G+ GNE+ADR AKEA        ++  +    A  +R 
Sbjct:   274 MALNKGRKAGLNVHFRWIPAHRGVEGNEQADRRAKEATGWRRIRGHRGRMTIRSAVKRRA 333

Query:   291 -KILSA-WNSEWHNLQNNKLQEIKLENKPWNPPYLILYYKNEIHSLIHISHFIVHT-LIA 347
              ++++A W ++W +  + +  E+  E  P  P   +L    ++H  +      + T  I 
Sbjct:   334 HEVVNARWENDWKSCHHGR--EL-YELTP-TPTRKVLRVHQDLHRALSTIIVQMRTGKIG 389

Query:   348 LKEYL 352
             L+ YL
Sbjct:   390 LRHYL 394


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        0.317   0.134   0.395    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      354       354   0.00079  117 3  11 22  0.41    34
                                                     34  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:  617 (66 KB)
  Total size of DFA:  243 KB (2131 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:01
  No. of threads or processors used:  24
  Search cpu time:  33.84u 0.09s 33.93t   Elapsed:  00:00:30
  Total cpu time:  33.84u 0.09s 33.93t   Elapsed:  00:00:31
  Start:  Thu Aug 15 12:37:05 2013   End:  Thu Aug 15 12:37:36 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	354
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	8e-30
pfam00075	126	pfam00075, RNase_H, RNase H	6e-16
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	2e-10
cd09277	133	cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI	7e-09
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	5e-07
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	1e-06
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	3e-05
cd09279	128	cd09279, RNase_HI_archaeal_like, RNAse HI family t	5e-05
pfam13456	88	pfam13456, RVT_3, Reverse transcriptase-like	1e-04
PRK00203	150	PRK00203, rnhA, ribonuclease H; Reviewed	8e-04
cd09275	120	cd09275, RNase_HI_RT_DIRS1, DIRS1 family of RNase	0.001
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	0.001

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

 Score =  110 bits (277), Expect = 8e-30
 Identities = 49/129 (37%), Positives = 64/129 (49%), Gaps = 7/129 (5%)

Query: 144 VVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSIC---NAELTAILFAIHFSISAHLNNV 200
           V+YTD SK +    + F        SR + L   C   +AEL AIL A+     A     
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQL---ALREGR 57

Query: 201 NRAYLVICSDSLSALQTLQNIFSLNPIAGEIR-DLILTNKSKLNVRFIWVPSHVGIAGNE 259
               + I SDS +AL+ L++  S +P+   IR  +       + VR  WVP H GI GNE
Sbjct: 58  RARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNE 117

Query: 260 EADRLAKEA 268
            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 = 73.1 bits (180), Expect = 6e-16
 Identities = 41/137 (29%), Positives = 56/137 (40%), Gaps = 19/137 (13%)

Query: 140 PDSTVVYTDAS--KNDVAVSSAFCSQDTK-FSSRLHPLLSICNAELTAILFAIHFSISAH 196
           P++  VYTD S   N     + + +   K  S  L P  +   AEL A++ A+       
Sbjct: 1   PEAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPL-PGTTNQRAELLALIEALEALSGQK 59

Query: 197 LNNVNRAYLVICSDSL----SALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSH 252
           +N        I +DS                  PI  EI +L+     K  V   WVP H
Sbjct: 60  VN--------IYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQ---KKHKVYIQWVPGH 108

Query: 253 VGIAGNEEADRLAKEAL 269
            GI GNE AD+LAK+  
Sbjct: 109 SGIPGNELADKLAKQGA 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|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 = 58.0 bits (141), Expect = 2e-10
 Identities = 33/109 (30%), Positives = 50/109 (45%), Gaps = 24/109 (22%)

Query: 180 AELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTL--------QNIFSLNPIAGEI 231
           AEL A++ A+   I      + +  LVI +DS   +  +        +N +  +   G+ 
Sbjct: 46  AELRAVIHALRL-IKEVGEGLTK--LVIATDSEYVVNGVTEWIPKWKKNGWKTS--KGKP 100

Query: 232 ---RDLIL--------TNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 269
              +DLI           +  + V+F  VP H GI GNEEADRLAK+  
Sbjct: 101 VANKDLIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGA 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|187701 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus

 Score = 53.3 bits (129), Expect = 7e-09
 Identities = 16/45 (35%), Positives = 25/45 (55%)

Query: 225 NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 269
                E ++ +   K K+ + 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|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 = 47.7 bits (114), Expect = 5e-07
 Identities = 29/98 (29%), Positives = 45/98 (45%), Gaps = 10/98 (10%)

Query: 173 PLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN-IFSLNPIAGEI 231
           P  +   AEL A+L A+   ++  L       L+I +DS   +  + +           +
Sbjct: 35  PAATNNEAELLALLEAL--ELALDLGLKK---LIIETDSKYVVDLINSWSKGWKKNNLLL 89

Query: 232 RDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 269
            D++L     +++RF  VP      GNE ADRLAKEA 
Sbjct: 90  WDILLLLSKFIDIRFEHVPRE----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|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in prokaryotes

 Score = 47.1 bits (113), Expect = 1e-06
 Identities = 14/29 (48%), Positives = 16/29 (55%)

Query: 240 SKLNVRFIWVPSHVGIAGNEEADRLAKEA 268
           +K  V + 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|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term repeat retroelements

 Score = 43.0 bits (102), Expect = 3e-05
 Identities = 34/147 (23%), Positives = 50/147 (34%), Gaps = 33/147 (22%)

Query: 144 VVYTDASK-NDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNR 202
            V+TD S     A  +     D    + L    S   AEL A++ A+  +    +N    
Sbjct: 1   TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKGKPVN---- 56

Query: 203 AYLVICSDSLSALQTLQNI---------FSLNPIAG--EIRDLI----LTNKSKLNVRFI 247
               I +DS  A   L  +          +  PIA    I  L             V  I
Sbjct: 57  ----IYTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKP----VAVI 108

Query: 248 WVPSHVG-----IAGNEEADRLAKEAL 269
            + +H G       GN  AD+ A++A 
Sbjct: 109 HIRAHSGLPGPLALGNARADQAARQAA 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|187703 cd09279, RNase_HI_archaeal_like, RNAse HI family that includes Archaeal RNase HI

 Score = 42.1 bits (100), Expect = 5e-05
 Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 17/96 (17%)

Query: 180 AELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF-----SLNPIAGEIRDL 234
           AE  A++  +  ++   +       L I  DS   +  +Q  +      L P   E R+L
Sbjct: 45  AEYEALIAGLELALELGIKK-----LEIYGDSQLVVNQIQGEYEVKNERLAPYLEEAREL 99

Query: 235 ILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALT 270
           +   K    V   W+P       N+EAD LA +AL 
Sbjct: 100 L---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|205634 pfam13456, RVT_3, Reverse transcriptase-like

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 27/96 (28%), Positives = 40/96 (41%), Gaps = 16/96 (16%)

Query: 180 AELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNI-FSLNPIAG---EIRDLI 235
           AE  A+L  +  ++   +       L++ SDS   +Q +Q    + + +A    EIR L+
Sbjct: 5   AEAEALLEGLQLALELGIRR-----LIVESDSQLVVQQIQGEYEARSRLAALLREIRKLL 59

Query: 236 LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS 271
               S   V    VP       N  AD LAK A  S
Sbjct: 60  KKFDS---VSVSHVPRE----CNRVADALAKLASAS 88

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

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

 Score = 39.0 bits (92), Expect = 8e-04
 Identities = 9/26 (34%), Positives = 13/26 (50%)

Query: 243 NVRFIWVPSHVGIAGNEEADRLAKEA 268
            +++ WV  H G   NE  D LA+  
Sbjct: 114 QIKWHWVKGHAGHPENERCDELARAG 139

Length = 150

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

 Score = 38.4 bits (90), Expect = 0.001
 Identities = 33/126 (26%), Positives = 49/126 (38%), Gaps = 16/126 (12%)

Query: 144 VVYTDASKNDVAVSSAFCSQ--DTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVN 201
           V++TDAS +      A  S        S       I   EL A+L A+     A L+N  
Sbjct: 1   VLFTDASLSGWG---AVLSGSWAQGLWSAEERNKHINFLELLAVLLALQ-HWGARLSN-- 54

Query: 202 RAYLVICSDSLSALQTL--QNIFSLNPIAGEIRDLIL-TNKSKLNVRFIWVPSHVGIAGN 258
           R  LV   D+ +A+  +  Q       +    R L+L   +  + +R   +P       N
Sbjct: 55  RKVLVRS-DNTTAVAYINRQGGTRSPELLALARQLVLWCEERNIWLRARHIPG----VLN 109

Query: 259 EEADRL 264
             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|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and repair]

 Score = 38.5 bits (90), Expect = 0.001
 Identities = 15/37 (40%), Positives = 19/37 (51%)

Query: 232 RDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEA 268
            +L    K    V + WV  H G   NE AD+LA+EA
Sbjct: 106 EELDELLKRHELVFWEWVKGHAGHPENERADQLAREA 142

Length = 154

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	354
PRK06548	161	ribonuclease H; Provisional	99.88
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.88
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	99.87
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.75
KOG3752|consensus	371		99.74
PRK13907	128	rnhA ribonuclease H; Provisional	99.69
PRK07708	219	hypothetical protein; Validated	99.64
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.46
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.17
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	90.05

>PRK06548 ribonuclease H; Provisional

Probab=99.88  E-value=3.5e-22  Score=170.03  Aligned_cols=121  Identities=27%  Similarity=0.281  Sum_probs=90.4

Q ss_pred             CCcEEEEeCCCCCCC--CceEEEE-eCCeeeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHH
Q psy4967         140 PDSTVVYTDASKNDV--AVSSAFC-SQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQ  216 (354)
Q Consensus       140 ~~~~~iytDGS~~~~--~~G~a~~-~~~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~  216 (354)
                      +..++||||||+..+  ..|+|++ .+....+... ...||+.|||.|++.||+.+     . .....|.|+|||++|++
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~-~~~TNnraEl~Aii~aL~~~-----~-~~~~~v~I~TDS~yvi~   75 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGW-DIATNNIAELTAVRELLIAT-----R-HTDRPILILSDSKYVIN   75 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCC-CCCCHHHHHHHHHHHHHHhh-----h-cCCceEEEEeChHHHHH
Confidence            456899999999853  4788877 3322223222 35799999999999999866     2 23457999999999999


Q ss_pred             Hhcc---------cCCCC-------hhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         217 TLQN---------IFSLN-------PIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       217 ~i~~---------~~~~~-------~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      ++..         +...+       +++++|..++.    ...|+|.|||||+|++|||.||+||++|+..
T Consensus        76 ~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~----~~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~  142 (161)
T PRK06548         76 SLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLME----NRNIRMSWVNAHTGHPLNEAADSLARQAANN  142 (161)
T ss_pred             HHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHh----cCceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence            9994         22222       24444444443    3579999999999999999999999999977

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

Probab=99.88  E-value=3e-22  Score=167.62  Aligned_cols=122  Identities=21%  Similarity=0.238  Sum_probs=95.7

Q ss_pred             CcEEEEeCCCCCC--CCceEEEE--eCC-e-eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHH
Q psy4967         141 DSTVVYTDASKND--VAVSSAFC--SQD-T-KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSA  214 (354)
Q Consensus       141 ~~~~iytDGS~~~--~~~G~a~~--~~~-~-~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~a  214 (354)
                      ..+.||||||+..  |-.|+|+|  .+. . ..+..+. .+||+.||+.|++.||+.+     ...+...|.|+|||++|
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-RTTNNRAELRALIEALEAL-----KELGACEVTLYTDSKYV   75 (154)
T ss_pred             CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHH-----HhcCCceEEEEecHHHH
Confidence            3589999999985  34777776  332 2 3455555 7899999999999999999     44688999999999999


Q ss_pred             HHHhcccCC----CC------------hhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         215 LQTLQNIFS----LN------------PIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       215 l~~i~~~~~----~~------------~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      +++|..+..    ..            .+++++.++..   ....|.+.|||||.|.++||.||+||+.|++.
T Consensus        76 ~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~---~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~  145 (154)
T COG0328          76 VEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLK---RHELVFWEWVKGHAGHPENERADQLAREAARA  145 (154)
T ss_pred             HHHHHHHHhhccccCccccccCccccHHHHHHHHHHHh---hCCeEEEEEeeCCCCChHHHHHHHHHHHHHHh
Confidence            999985411    11            23555555544   35699999999999999999999999999987

>PRK08719 ribonuclease H; Reviewed

Probab=99.88  E-value=5.4e-22  Score=167.41  Aligned_cols=121  Identities=21%  Similarity=0.259  Sum_probs=87.6

Q ss_pred             CcEEEEeCCCCCCCC-----ceEEEE--eC--Ce--eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEe
Q psy4967         141 DSTVVYTDASKNDVA-----VSSAFC--SQ--DT--KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICS  209 (354)
Q Consensus       141 ~~~~iytDGS~~~~~-----~G~a~~--~~--~~--~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~s  209 (354)
                      +.++||||||+..++     .|+|++  ..  ..  ..+..+....|++.||+.|++.||+.+.     ..    ..|+|
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~-----~~----~~i~t   73 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYAR-----DG----DVIYS   73 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcC-----CC----CEEEe
Confidence            468999999997542     477776  32  22  3445566667999999999999999983     21    37999


Q ss_pred             CCHHHHHHhc--------ccCC-CCh--h-HHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhc
Q psy4967         210 DSLSALQTLQ--------NIFS-LNP--I-AGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALT  270 (354)
Q Consensus       210 DS~~al~~i~--------~~~~-~~~--~-~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~  270 (354)
                      ||++|++++.        +.+. ..+  + -.++.+.+..+.....|+|.|||||+|++|||.||+||++|++
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            9999999984        3222 211  1 1233333333334677999999999999999999999999975

>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=4.6e-22  Score=164.86  Aligned_cols=118  Identities=37%  Similarity=0.508  Sum_probs=91.3

Q ss_pred             CcEEEEeCCCCCC--CCceEEEE-eCCeeeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHHH
Q psy4967         141 DSTVVYTDASKND--VAVSSAFC-SQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQT  217 (354)
Q Consensus       141 ~~~~iytDGS~~~--~~~G~a~~-~~~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~~  217 (354)
                      +.+.||||||+..  +..|+|++ ..+...+..++ ..+++.||+.||..||+.+        ....+.|+|||++++..
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~--------~~~~v~I~tDS~~v~~~   72 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL--------EHRKVTIYTDSQYVLNA   72 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH--------STSEEEEEES-HHHHHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh--------hcccccccccHHHHHHH
Confidence            4689999999773  33466655 44445555566 7899999999999999943        23899999999999997


Q ss_pred             hcc-----cCC-C--C-hhHHHHHHHHHhhcCCCceEEEEeCCCCCC-ccchHHhHHHHHhhc
Q psy4967         218 LQN-----IFS-L--N-PIAGEIRDLILTNKSKLNVRFIWVPSHVGI-AGNEEADRLAKEALT  270 (354)
Q Consensus       218 i~~-----~~~-~--~-~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi-~gNe~AD~lAk~a~~  270 (354)
                      +..     ... .  . ++..++.+++.   .+..|.|+|||||+|+ .|||.||+|||+|+.
T Consensus        73 l~~~~~~~~~~~~~~~~~i~~~i~~~~~---~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~~  132 (132)
T PF00075_consen   73 LNKWLHGNGWKKTSNGRPIKNEIWELLS---RGIKVRFRWVPGHSGVPQGNERADRLAKEAAQ  132 (132)
T ss_dssp             HHTHHHHTTSBSCTSSSBHTHHHHHHHH---HSSEEEEEESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred             HHHhccccccccccccccchhheeeccc---cceEEeeeeccCcCCCchhHHHHHHHHHHhcC
Confidence            777     222 1  2 46677777774   4899999999999999 699999999999973

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

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.87  E-value=7.5e-22  Score=167.70  Aligned_cols=118  Identities=18%  Similarity=0.222  Sum_probs=89.3

Q ss_pred             cEEEEeCCCCCC--CCceEEEE--eCCe--eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHH
Q psy4967         142 STVVYTDASKND--VAVSSAFC--SQDT--KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSAL  215 (354)
Q Consensus       142 ~~~iytDGS~~~--~~~G~a~~--~~~~--~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al  215 (354)
                      .++||||||+..  +..|+|+|  .++.  ...... ...|++.|||.|++.||+.+     .  ....+.|+|||++++
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~-~~~TN~~aEL~Ai~~AL~~~-----~--~~~~v~I~tDS~yvi   74 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGE-ALTTNNRMELMAAIEALEAL-----K--EPCEVTLYTDSQYVR   74 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCC-CCCcHHHHHHHHHHHHHHHc-----C--CCCeEEEEECHHHHH
Confidence            489999999984  34777776  3322  223333 45789999999999999988     2  246799999999999


Q ss_pred             HHhccc---------CCCC-------hhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         216 QTLQNI---------FSLN-------PIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       216 ~~i~~~---------~~~~-------~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      ++|..+         ....       ++++++.+++    ....|.|.|||||+|++||+.||+|||+|+..
T Consensus        75 ~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~----~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~  142 (150)
T PRK00203         75 QGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAAL----KRHQIKWHWVKGHAGHPENERCDELARAGAEE  142 (150)
T ss_pred             HHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHh----ccCceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence            999863         1111       2344444443    34789999999999999999999999999987

>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=2e-17  Score=134.05  Aligned_cols=118  Identities=31%  Similarity=0.407  Sum_probs=91.3

Q ss_pred             EEEeCCCCCCC--CceEEEE--eC-C-ee-eeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHH
Q psy4967         144 VVYTDASKNDV--AVSSAFC--SQ-D-TK-FSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQ  216 (354)
Q Consensus       144 ~iytDGS~~~~--~~G~a~~--~~-~-~~-~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~  216 (354)
                      .+|||||...+  ++|+|++  +. + .. .........+++.+|+.|++.||+.+.     .....++.|++||+.++.
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~-----~~~~~~i~i~~Ds~~~~~   75 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELAL-----ELGGKKVNIYTDSQYVIN   75 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHH-----hCCCceEEEEECHHHHHH
Confidence            48999999865  6888877  32 2 11 122222567999999999999999994     457899999999999999


Q ss_pred             HhcccCC-CC----hhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhh
Q psy4967         217 TLQNIFS-LN----PIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL  269 (354)
Q Consensus       217 ~i~~~~~-~~----~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~  269 (354)
                      .+.+... ..    .++..+.+++   .....+.|.|||+|+|+.+|+.||.|||.|.
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    2344444444   2588999999999999999999999999874

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.

>KOG3752|consensus

Probab=99.74  E-value=1.1e-17  Score=156.24  Aligned_cols=125  Identities=28%  Similarity=0.244  Sum_probs=97.4

Q ss_pred             CcEEEEeCCCCCCC-----CceEEEE--eCC-eeeeecCC-CCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCC
Q psy4967         141 DSTVVYTDASKNDV-----AVSSAFC--SQD-TKFSSRLH-PLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDS  211 (354)
Q Consensus       141 ~~~~iytDGS~~~~-----~~G~a~~--~~~-~~~~~~l~-~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS  211 (354)
                      +..++|||||+..+     .+|+|++  ++. ...++++. ...++|.||+.|+..||+.+.     .....+|+|.|||
T Consensus       211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~-----~~~~~kv~I~TDS  285 (371)
T KOG3752|consen  211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKAR-----SKNINKVVIRTDS  285 (371)
T ss_pred             cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHH-----hcCCCcEEEEech
Confidence            35899999999863     4999998  332 35677775 788999999999999999994     4466799999999


Q ss_pred             HHHHHHhcccCCC-----------Ch----------hHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhc
Q psy4967         212 LSALQTLQNIFSL-----------NP----------IAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALT  270 (354)
Q Consensus       212 ~~al~~i~~~~~~-----------~~----------~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~  270 (354)
                      +++++.|+.|...           ++          .+.++.++.+.. ...+|.+.||+||.|+.|||.||.||+++..
T Consensus       286 ~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~-~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~  364 (371)
T KOG3752|consen  286 EYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEI-SNKKVQQEYVGGHSGILGNEMADALARKGST  364 (371)
T ss_pred             HHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhh-ccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence            9999999866321           11          223333443321 4689999999999999999999999999865


Q ss_pred             C
Q psy4967         271 S  271 (354)
Q Consensus       271 ~  271 (354)
                      .
T Consensus       365 ~  365 (371)
T KOG3752|consen  365 L  365 (371)
T ss_pred             h
Confidence            4

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.69  E-value=3.5e-16  Score=129.31  Aligned_cols=116  Identities=24%  Similarity=0.301  Sum_probs=88.3

Q ss_pred             EEEEeCCCCCC--CCceEEEE--eC-C-eeeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHH
Q psy4967         143 TVVYTDASKND--VAVSSAFC--SQ-D-TKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQ  216 (354)
Q Consensus       143 ~~iytDGS~~~--~~~G~a~~--~~-~-~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~  216 (354)
                      +.||||||+..  +..|+|+|  +. + ...++.. ...|++.||+.|++.||+.+.     ..+..++.|++||+.+++
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-GTMSNHEAEYHALLAALKYCT-----EHNYNIVSFRTDSQLVER   75 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecc-cccCCcHHHHHHHHHHHHHHH-----hCCCCEEEEEechHHHHH
Confidence            68999999985  45888887  32 2 2233333 457999999999999999994     446678999999999999


Q ss_pred             HhcccCCCC----hhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         217 TLQNIFSLN----PIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       217 ~i~~~~~~~----~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      .+++.....    ++++++..++.   ....+.|.|||+    +.|+.||.||+.|+..
T Consensus        76 ~~~~~~~~~~~~~~l~~~~~~l~~---~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         76 AVEKEYAKNKMFAPLLEEALQYIK---SFDLFFIKWIPS----SQNKVADELARKAILQ  127 (128)
T ss_pred             HHhHHHhcChhHHHHHHHHHHHHh---cCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence            999865432    34555555543   467788899995    6999999999999753

>PRK07708 hypothetical protein; Validated

Probab=99.64  E-value=3.5e-15  Score=133.76  Aligned_cols=128  Identities=19%  Similarity=0.228  Sum_probs=93.2

Q ss_pred             HHhcCCCcEEEEeCCCCC--CCCceEEEE--e--CCee----eeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCce
Q psy4967         135 LLQKTPDSTVVYTDASKN--DVAVSSAFC--S--QDTK----FSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAY  204 (354)
Q Consensus       135 ~~~~~~~~~~iytDGS~~--~~~~G~a~~--~--~~~~----~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~  204 (354)
                      .+...|+.+++|+|||..  ++++|+|+|  .  ++..    ....+....|++.||+.|++.||+.+...   ......
T Consensus        66 ~~~~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~---g~~~~~  142 (219)
T PRK07708         66 EVEEEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEEL---GVKHEP  142 (219)
T ss_pred             hhccCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHc---CCCcce
Confidence            345677889999999986  456888876  2  2222    12345556799999999999999999541   222335


Q ss_pred             EEEEeCCHHHHHHhcccCC-CChhH----HHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         205 LVICSDSLSALQTLQNIFS-LNPIA----GEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       205 i~I~sDS~~al~~i~~~~~-~~~~~----~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      |.|++||+.+++.+.+.+. .++..    ..+.++++.  ....+.+.|||    ...|+.||+||+.|+..
T Consensus       143 V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~--~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~  208 (219)
T PRK07708        143 VTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQ--LKLTPVYEPIS----RKQNKEADQLATQALEG  208 (219)
T ss_pred             EEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhh--CCceEEEEECC----chhhhHHHHHHHHHHhc
Confidence            9999999999999998764 44433    334444433  34457889998    67899999999999987

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.46  E-value=7.4e-13  Score=128.86  Aligned_cols=117  Identities=20%  Similarity=0.295  Sum_probs=88.3

Q ss_pred             cEEEEeCCCCCCC--CceEEEE--e--CC-e--eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCH
Q psy4967         142 STVVYTDASKNDV--AVSSAFC--S--QD-T--KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSL  212 (354)
Q Consensus       142 ~~~iytDGS~~~~--~~G~a~~--~--~~-~--~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~  212 (354)
                      .+.||||||+..+  ..|+|++  +  ++ .  ..+..++ .+|++.||+.|++.||+.+.     ..+...|.|++||+
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-RATNNVAEYRGLIAGLEAAA-----ELGATEVEVRMDSK   75 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHH-----hCCCCeEEEEeCcH
Confidence            3689999999854  5788876  3  22 1  2233344 67899999999999999994     44677999999999


Q ss_pred             HHHHHhcccCC-CCh----hHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         213 SALQTLQNIFS-LNP----IAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       213 ~al~~i~~~~~-~~~----~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      .+++.+.+... ++.    ++.++..+.+   ....|.|.|||+    .+|+.||.||+.|+..
T Consensus        76 lvi~~i~~~~~~~~~~l~~~~~~i~~l~~---~f~~~~i~~v~r----~~N~~AD~LA~~a~~~  132 (372)
T PRK07238         76 LVVEQMSGRWKVKHPDMKPLAAQARELAS---QFGRVTYTWIPR----ARNAHADRLANEAMDA  132 (372)
T ss_pred             HHHHHhCCCCccCChHHHHHHHHHHHHHh---cCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence            99999988654 333    2333444333   568899999994    7999999999999754

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

Probab=99.17  E-value=2.3e-10  Score=87.24  Aligned_cols=82  Identities=28%  Similarity=0.304  Sum_probs=63.2

Q ss_pred             hHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHHHhcccCC-CCh---hHHHHHHHHHhhcCCCceEEEEeCCC
Q psy4967         177 ICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFS-LNP---IAGEIRDLILTNKSKLNVRFIWVPSH  252 (354)
Q Consensus       177 ~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~~i~~~~~-~~~---~~~~i~~~~~~~~~~~~V~~~WVpgH  252 (354)
                      +..||+.|+..||+.+     ...+..+|.|+|||+.++..|++... .+.   ++.+|+.++   .....+.|.|||  
T Consensus         1 ~~~aE~~al~~al~~a-----~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~---~~~~~~~~~~i~--   70 (87)
T PF13456_consen    1 PLEAEALALLEALQLA-----WELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLL---DRFWNVSVSHIP--   70 (87)
T ss_dssp             HHHHHHHHHHHHHHHH-----HCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHH---CCCSCEEEEE----
T ss_pred             CcHHHHHHHHHHHHHH-----HHCCCCEEEEEecCccccccccccccccccccccchhhhhhh---ccccceEEEEEC--
Confidence            4689999999999999     56688999999999999999998753 333   344444444   358999999999  


Q ss_pred             CCCccchHHhHHHHHhhc
Q psy4967         253 VGIAGNEEADRLAKEALT  270 (354)
Q Consensus       253 ~gi~gNe~AD~lAk~a~~  270 (354)
                        .++|..||.|||.|.+
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

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

Probab=90.05  E-value=1.3  Score=37.75  Aligned_cols=65  Identities=22%  Similarity=0.259  Sum_probs=38.6

Q ss_pred             cEEEEeCCCCCCCCceEEEE--e---CCee-----eeecC-C-CCCchHHHHHHHHHHHHHHHHHhc-cccCCCceEEEE
Q psy4967         142 STVVYTDASKNDVAVSSAFC--S---QDTK-----FSSRL-H-PLLSICNAELTAILFAIHFSISAH-LNNVNRAYLVIC  208 (354)
Q Consensus       142 ~~~iytDGS~~~~~~G~a~~--~---~~~~-----~~~~l-~-~~~t~~~AEl~Ai~~aL~~~~~~~-~~~~~~~~i~I~  208 (354)
                      .+++|+|+|.  .+.|+.+|  .   +...     ...++ + ...|+-+-||.|+..|.+++.... ........+.++
T Consensus        81 ~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~~~~l~~~~~~~~~w  158 (159)
T PF05380_consen   81 ELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTVKKELDIEISQVVFW  158 (159)
T ss_pred             eeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHHHHHcCCCcceeEEe
Confidence            6899999994  35565554  1   2211     11112 1 234999999999999999885431 122344555544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	354
1mu2_A	555	Crystal Structure Of Hiv-2 Reverse Transcriptase Le		7e-04
2ykn_A	562	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		7e-04
2ykm_A	562	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		8e-04

>pdb|1MU2|A Chain A, Crystal Structure Of Hiv-2 Reverse Transcriptase Length = 555

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 29/142 (20%), Positives = 58/142 (40%), Gaps = 8/142 (5%)
Query: 128 INISFQELLQKTPDSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILF 187
           + ++F  +    P +   YTD S N  +          +   ++  L    N +     F
Sbjct: 422 VRLAFNLVGDPIPGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAF 481
Query: 188 AIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFI 247
           A+  + S    N+     ++ S  +  +   Q   S + I  +I + ++  ++   +   
Sbjct: 482 AMALTDSGPKVNI-----IVDSQYVMGIVASQPTESESKIVNQIIEEMIKKEA---IYVA 533
Query: 248 WVPSHVGIAGNEEADRLAKEAL 269
           WVP+H GI GN+E D L  + +
Sbjct: 534 WVPAHKGIGGNQEVDHLVSQGI 555

>pdb|2YKN|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti) Length = 562

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 38/143 (26%), Positives = 55/143 (38%), Gaps = 16/143 (11%)
Query: 136 LQKTP--DSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSI 193
           L+K P   +   Y D + N             K   ++ PL +  N +    L AI+ ++
Sbjct: 429 LEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTQ--LQAIYLAL 486
Query: 194 SAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILTNKSKLNVRFIWVP 250
                 VN     I +DS  AL     I    P   E   +  +I     K  V   WVP
Sbjct: 487 QDSGLEVN-----IVTDSQYAL----GIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVP 537
Query: 251 SHVGIAGNEEADRLAKEALTSTH 273
           +H GI GNE+ D+L    +   H
Sbjct: 538 AHKGIGGNEQVDKLVSAGIRHHH 560

>pdb|2YKM|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti) Length = 562

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 38/143 (26%), Positives = 55/143 (38%), Gaps = 16/143 (11%)
Query: 136 LQKTP--DSTVVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSI 193
           L+K P   +   Y D + N             K   ++ PL +  N +    L AI+ ++
Sbjct: 429 LEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTQ--LQAIYLAL 486
Query: 194 SAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE---IRDLILTNKSKLNVRFIWVP 250
                 VN     I +DS  AL     I    P   E   +  +I     K  V   WVP
Sbjct: 487 QDSGLEVN-----IVTDSQYAL----GIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVP 537
Query: 251 SHVGIAGNEEADRLAKEALTSTH 273
           +H GI GNE+ D+L    +   H
Sbjct: 538 AHKGIGGNEQVDKLVSAGIRHHH 560

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	354
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	8e-12
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	1e-10
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	2e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	7e-07
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	4e-06
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	1e-05
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	2e-05
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	2e-05
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	3e-05
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	5e-05
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	5e-05
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	1e-04
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	6e-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 = 61.2 bits (149), Expect = 8e-12
 Identities = 25/139 (17%), Positives = 42/139 (30%), Gaps = 18/139 (12%)

Query: 141 DSTVVYTDASKND-------VAVSSAFCSQDTKFSSRLHPLLSICN--AELTAILFAIHF 191
               VYTD S  +         V       +     +     ++ N   E+ A L+A+  
Sbjct: 5   TEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKK 64

Query: 192 SISAHLNNVNRAYLVICSDSLSALQTLQNIFSLN-PIAGEIRDLILTNKSKLNVRFIWVP 250
           +    +       + I  D           +            L+  N+ +    F  V 
Sbjct: 65  ASQLGVK------IRILHDYAGIAFWATGEWKAKNEFTQAYAKLM--NQYRGIYSFEKVK 116

Query: 251 SHVGIAGNEEADRLAKEAL 269
           +H G   N+  D  AK AL
Sbjct: 117 AHSGNEFNDYVDMKAKSAL 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 = 58.7 bits (142), Expect = 1e-10
 Identities = 28/136 (20%), Positives = 45/136 (33%), Gaps = 16/136 (11%)

Query: 144 VVYTD--ASKND---VAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLN 198
             YTD  +   +    A ++     +  ++  L    S   AEL A+  A+  +    LN
Sbjct: 25  TWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKKLN 84

Query: 199 NVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVG---- 254
                 +   S    A   + +         EI  L+        +  I  P H      
Sbjct: 85  ------VYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSA 138

Query: 255 -IAGNEEADRLAKEAL 269
              GN  AD+ A+EA 
Sbjct: 139 EARGNRMADQAAREAA 154

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

 Score = 49.1 bits (118), Expect = 2e-07
 Identities = 14/29 (48%), Positives = 21/29 (72%)

Query: 240 SKLNVRFIWVPSHVGIAGNEEADRLAKEA 268
             ++++++ VP H G  GNEEADRLA+E 
Sbjct: 120 QGMDIQWMHVPGHSGFIGNEEADRLAREG 148

>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 = 51.8 bits (123), Expect = 2e-07
 Identities = 56/381 (14%), Positives = 114/381 (29%), Gaps = 87/381 (22%)

Query: 23  EAGEPPLSYRREILTCNY-LFNTQRNPKH---FLSPLLTDDSLQQLYERKSSYEKPLRIR 78
           E GE    Y+ +IL+     F    + K        +L+ + +  +   K +    LR+ 
Sbjct: 10  ETGEHQYQYK-DILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLF 68

Query: 79  GKLLLEKYGIDHLDFLSPSPQTSAPWLIEP-------PPVDYSL------------RKFN 119
             LL ++  +    F+    + +  +L+ P       P +   +            + F 
Sbjct: 69  WTLLSKQEEMVQ-KFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFA 127

Query: 120 KDTDSKEEINISFQELLQK-TPDSTV-----------VYTDASKNDVAVSSAFC------ 161
           K   S+ +  +  ++ L +  P   V                      V           
Sbjct: 128 KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWL 187

Query: 162 --SQDTKFSSRLHPLLSIC---NAELTAILFAIHFSISAHLNNVNRA--YLVICSDSLSA 214
                    + L  L  +    +   T+       +I   ++++      L+      + 
Sbjct: 188 NLKNCNSPETVLEMLQKLLYQIDPNWTS-RSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246

Query: 215 LQTLQNIFS---LNPIAGEIRDLILT-NKSKLNVRFIWVPSHVGIAG------------- 257
           L  L N+ +    N      + L+ T  K   +       +H+ +               
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL 306

Query: 258 -----NEEADRLAKEALTSTHP-TINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLQEI 311
                +     L +E LT T+P  ++ I      A S R  L+ W+  W ++  +KL  I
Sbjct: 307 LLKYLDCRPQDLPREVLT-TNPRRLSII------AESIRDGLATWD-NWKHVNCDKLTTI 358

Query: 312 ---KLENKPWNPPYLILYYKN 329
               L      P      +  
Sbjct: 359 IESSLNV--LEPAEYRKMFDR 377

>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 = 47.2 bits (113), Expect = 7e-07
 Identities = 13/29 (44%), Positives = 16/29 (55%)

Query: 240 SKLNVRFIWVPSHVGIAGNEEADRLAKEA 268
            K  V   WVP+H GI GNE+ D+L    
Sbjct: 116 KKEKVYLAWVPAHKGIGGNEQVDKLVSAG 144

>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 = 47.5 bits (113), Expect = 4e-06
 Identities = 29/87 (33%), Positives = 41/87 (47%), Gaps = 14/87 (16%)

Query: 180 AELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN--IFSLNPIAGEIRDLILT 237
            EL AI  A+  S       VN     I +DS  AL  +Q     S + +  +I + ++ 
Sbjct: 479 TELQAIYLALQDSGL----EVN-----IVTDSQYALGIIQAQPDKSESELVNQIIEQLI- 528

Query: 238 NKSKLNVRFIWVPSHVGIAGNEEADRL 264
              K  V   WVP+H GI GNE+ D+L
Sbjct: 529 --KKEKVYLAWVPAHKGIGGNEQVDKL 553

>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 = 44.0 bits (105), Expect = 1e-05
 Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 7/44 (15%)

Query: 240 SKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPD 283
            +  +++ WV  H G   NE AD LA+ A            + D
Sbjct: 112 GQHQIKWEWVKGHAGHPENERADELARAA-------AMNPTLED 148

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

 Score = 43.2 bits (103), Expect = 2e-05
 Identities = 10/29 (34%), Positives = 12/29 (41%)

Query: 240 SKLNVRFIWVPSHVGIAGNEEADRLAKEA 268
           +   V F  V  H     N  AD LA+ A
Sbjct: 113 TLHRVTFHKVKGHSDNPYNSRADELARLA 141

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

 Score = 43.3 bits (103), Expect = 2e-05
 Identities = 15/47 (31%), Positives = 18/47 (38%), Gaps = 4/47 (8%)

Query: 240 SKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKA 286
           +   VRF +V  H G   NE  DR A+    S      K P P    
Sbjct: 117 APHRVRFHFVKGHTGHPENERVDREARRQAQS----QAKTPCPPRAP 159

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

 Score = 42.9 bits (102), Expect = 3e-05
 Identities = 11/29 (37%), Positives = 15/29 (51%)

Query: 240 SKLNVRFIWVPSHVGIAGNEEADRLAKEA 268
               + + WV  H G A NE  D+LA+ A
Sbjct: 114 QLHQIDWRWVKGHAGHAENERCDQLARAA 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 = 42.0 bits (99), Expect = 5e-05
 Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 18/95 (18%)

Query: 180 AELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF-----SLNPIAGEIRDL 234
           AE + ++  +       +  +  +  +I  DS   ++ +   +      + P+  +  +L
Sbjct: 51  AEYSGLICLME-----TMLRLGISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIEL 105

Query: 235 ILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 269
                 KLN   IWVP       N+EADRL++ A 
Sbjct: 106 K----KKLNATLIWVPR----EENKEADRLSRVAY 132

>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 = 44.0 bits (104), Expect = 5e-05
 Identities = 26/87 (29%), Positives = 38/87 (43%), Gaps = 14/87 (16%)

Query: 180 AELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN--IFSLNPIAGEIRDLILT 237
           AEL A   A+  S       VN     I  DS   +  + +    S + I  +I + ++ 
Sbjct: 476 AELEAFAMALTDSGP----KVN-----IIVDSQYVMGIVASQPTESESKIVNQIIEEMI- 525

Query: 238 NKSKLNVRFIWVPSHVGIAGNEEADRL 264
              K  +   WVP+H GI GN+E D L
Sbjct: 526 --KKEAIYVAWVPAHKGIGGNQEVDHL 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 = 40.7 bits (96), Expect = 1e-04
 Identities = 16/95 (16%), Positives = 33/95 (34%), Gaps = 17/95 (17%)

Query: 180 AELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF-----SLNPIAGEIRDL 234
           AE   ++  +  ++             +  DS   ++ +   +      L  +  + + L
Sbjct: 49  AEYRGLIAGLDDAVKLGATEAA-----VLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQAL 103

Query: 235 ILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 269
                    + + WVP       N  ADRLA +A+
Sbjct: 104 A---SQFRRINYEWVPRA----RNTYADRLANDAM 131

>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 = 6e-04
 Identities = 11/46 (23%), Positives = 16/46 (34%), Gaps = 6/46 (13%)

Query: 224 LNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 269
           L     +I  +      K+      V  H+    N  AD L  EA+
Sbjct: 96  LKEKFAKIAHI------KMERVPNLVFVHIPREKNARADELVNEAI 135

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	354
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.91
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.9
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.89
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.89
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.88
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.88
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.88
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.86
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.85
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.79
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.78
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.78
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.78
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.76
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.3
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.09

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

Probab=99.91  E-value=2.2e-24  Score=182.87  Aligned_cols=123  Identities=27%  Similarity=0.329  Sum_probs=96.0

Q ss_pred             CCcEEEEeCCCCCCCC-----ceEEEE--eCC-eeeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCC
Q psy4967         140 PDSTVVYTDASKNDVA-----VSSAFC--SQD-TKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDS  211 (354)
Q Consensus       140 ~~~~~iytDGS~~~~~-----~G~a~~--~~~-~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS  211 (354)
                      ++.++||||||+..++     +|+|+|  .+. ...+..+...+|++.||+.|++.||+.+.     ..+..+|.|+|||
T Consensus         5 ~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~-----~~~~~~v~i~tDS   79 (154)
T 2qkb_A            5 GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAK-----TQNINKLVLYTNS   79 (154)
T ss_dssp             TTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHH-----HTTCCEEEEEESC
T ss_pred             CCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHH-----hCCCceEEEEECc
Confidence            3568999999997542     788888  222 23455565568999999999999999994     3467899999999


Q ss_pred             HHHHHHhcccC---------CC-------ChhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         212 LSALQTLQNIF---------SL-------NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       212 ~~al~~i~~~~---------~~-------~~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      ++++++|..+.         ..       .++++++.+++    .+..|.|.|||||+|++|||.||+|||+|+..
T Consensus        80 ~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~----~~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~  151 (154)
T 2qkb_A           80 MFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLT----QGMDIQWMHVPGHSGFIGNEEADRLAREGAKQ  151 (154)
T ss_dssp             HHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHH----TTCEEEEEECCTTSSCHHHHHHHHHHHHHHTC
T ss_pred             HHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHH----cCCceEEEEccCCCCCHhHHHHHHHHHHHHHh
Confidence            99999998741         11       12455555544    35679999999999999999999999999876

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

Probab=99.90  E-value=5.9e-24  Score=178.63  Aligned_cols=119  Identities=20%  Similarity=0.150  Sum_probs=92.5

Q ss_pred             CcEEEEeCCCCCCC--CceEEEE--eCCe--eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHH
Q psy4967         141 DSTVVYTDASKNDV--AVSSAFC--SQDT--KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSA  214 (354)
Q Consensus       141 ~~~~iytDGS~~~~--~~G~a~~--~~~~--~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~a  214 (354)
                      +.++||||||+..+  ..|+|++  .++.  ..+..++ .+|++.||+.|++.||+.+     ..  ..+|.|+|||+++
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~~-~~Tnn~aEl~A~~~AL~~~-----~~--~~~v~I~tDS~~v   74 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDP-ATTNNRMELMAAIKGLEAL-----KE--PARVQLYSDSAYL   74 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEE-EECHHHHHHHHHHHHHHTC-----SS--CCEEEEEESCHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCCC-CCcHHHHHHHHHHHHHHhc-----Cc--cCcEEEEeChHHH
Confidence            46899999999864  3788877  4432  2333333 5799999999999999988     32  5899999999999


Q ss_pred             HHHhcc-cC---------C-------CChhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         215 LQTLQN-IF---------S-------LNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       215 l~~i~~-~~---------~-------~~~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      ++.|.. +.         .       ..++++++.+++..    ..|.|.|||||+|++|||.||+|||+|+..
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 VNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTL----HRVTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             HHHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHH----SEEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhh----CceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence            999987 21         0       12366677776654    579999999999999999999999999875

>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=99.89  E-value=1.8e-23  Score=176.24  Aligned_cols=119  Identities=24%  Similarity=0.344  Sum_probs=90.3

Q ss_pred             CCcEEEEeCCCCCCC--CceEEEE-eCCeeeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHH
Q psy4967         140 PDSTVVYTDASKNDV--AVSSAFC-SQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQ  216 (354)
Q Consensus       140 ~~~~~iytDGS~~~~--~~G~a~~-~~~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~  216 (354)
                      ++.++||||||+..+  ..|+|++ ..+......+ ..+|++.||+.|++.||+.+         ..+|.|+|||+++++
T Consensus        10 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~---------~~~v~i~tDS~~v~~   79 (150)
T 3qio_A           10 VGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS---------GLEVNIVTDSQYALG   79 (150)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS---------CSEEEEEESCHHHHH
T ss_pred             CCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC---------CCcEEEEeCcHHHHH
Confidence            457999999999743  3777776 2222222333 46799999999999999875         378999999999999


Q ss_pred             HhcccC-----------C-----CChhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         217 TLQNIF-----------S-----LNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       217 ~i~~~~-----------~-----~~~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      +|..+.           .     ..++++++.+++   .....|.|.|||||+|++|||.||+||++|+..
T Consensus        80 ~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l---~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           80 IITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQL---IKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHHHHHCC------------CHHHHHHHHHHH---TTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHH---hhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            998752           0     112344443333   357899999999999999999999999999875

>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=8e-24  Score=178.03  Aligned_cols=125  Identities=19%  Similarity=0.116  Sum_probs=96.0

Q ss_pred             CCcEEEEeCCCCCCCCceEEEE--eCCe--eeee-cC--CC--CCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeC
Q psy4967         140 PDSTVVYTDASKNDVAVSSAFC--SQDT--KFSS-RL--HP--LLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSD  210 (354)
Q Consensus       140 ~~~~~iytDGS~~~~~~G~a~~--~~~~--~~~~-~l--~~--~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sD  210 (354)
                      ++.+.||||||+..+.+|+|+|  .++.  ..+. ..  +.  .+||+.||+.|++.||+.+++     .+. +|.|+||
T Consensus         4 ~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~-----~~~-~v~I~tD   77 (147)
T 2kq2_A            4 RTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQ-----LGV-KIRILHD   77 (147)
T ss_dssp             TSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHH-----HTC-CCCBSSC
T ss_pred             CCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHH-----CCC-eEEEEEC
Confidence            4578999999999977899987  3333  2233 22  22  368999999999999998853     234 8999999


Q ss_pred             CHHHHHHhcccCC-CChhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcCC
Q psy4967         211 SLSALQTLQNIFS-LNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTST  272 (354)
Q Consensus       211 S~~al~~i~~~~~-~~~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~~  272 (354)
                      |+.+.+.+.+.+. ..+....+.++++.+..  .|.|.|||||+|++|||.||+|||+|+...
T Consensus        78 S~~i~~w~~~~w~~~~~~~~~~~~l~~~l~~--~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~  138 (147)
T 2kq2_A           78 YAGIAFWATGEWKAKNEFTQAYAKLMNQYRG--IYSFEKVKAHSGNEFNDYVDMKAKSALGIR  138 (147)
T ss_dssp             CSTHHHHTTSSSSCCHHHHHHHHCGGGGGST--TCCBCCCCCCCCCHHHHHHHHHHHHHHTCC
T ss_pred             cHHHHHHHhCCCccCCcchHHHHHHHHHhcC--CeeEEEecCcCCCcchHHHHHHHHHHHhcc
Confidence            9988877766443 34455566666665433  899999999999999999999999999883

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

Probab=99.88  E-value=5.6e-23  Score=174.98  Aligned_cols=119  Identities=20%  Similarity=0.243  Sum_probs=91.7

Q ss_pred             CcEEEEeCCCCCCC--CceEEEE--eCCe--eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHH
Q psy4967         141 DSTVVYTDASKNDV--AVSSAFC--SQDT--KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSA  214 (354)
Q Consensus       141 ~~~~iytDGS~~~~--~~G~a~~--~~~~--~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~a  214 (354)
                      ..++||||||+..+  ..|+|+|  .++.  ..+..++ .+|++.||+.|++.||+.+     ..  ..+|.|+|||+++
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~-~~tn~~aEl~A~~~AL~~~-----~~--~~~v~I~tDS~~v   76 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGFS-LTTNNRMELLAPIVALEAL-----KE--PCKIILTSDSQYM   76 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEEE-EECHHHHHHHHHHHHHHTC-----SS--CCEEEEEECCHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCcC-CCccHHHHHHHHHHHHHHh-----cc--CCeEEEEeCHHHH
Confidence            46899999999853  3788877  3332  2233333 4789999999999999987     32  3899999999999


Q ss_pred             HHHhccc--------C-CC-------ChhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         215 LQTLQNI--------F-SL-------NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       215 l~~i~~~--------~-~~-------~~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      +++|..+        . ..       .++++++.+++    ....|.|.|||||+|++|||.||+|||+|+..
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        1 11       13455555554    34699999999999999999999999999986

>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=99.88  E-value=9.9e-23  Score=174.19  Aligned_cols=122  Identities=25%  Similarity=0.209  Sum_probs=90.7

Q ss_pred             cEEEEeCCCCC--CCCceEEEE--e-CCeeeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHH
Q psy4967         142 STVVYTDASKN--DVAVSSAFC--S-QDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQ  216 (354)
Q Consensus       142 ~~~iytDGS~~--~~~~G~a~~--~-~~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~  216 (354)
                      .+.||||||+.  +|..|+|++  . +.......++..+||+.||+.|++.||+.+        ...++.|+|||+++++
T Consensus        23 ~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~--------~~~~v~I~tDS~~vi~   94 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA--------EGKKLNVYTDSRYAFA   94 (165)
T ss_dssp             SEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT--------BTSEEEEEECCHHHHH
T ss_pred             CEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc--------cCceEEEEEchHHHHh
Confidence            58999999997  344677764  3 333222245567899999999999999988        2679999999999999


Q ss_pred             HhcccCCCChh--HHHHHHHHHhhcCCCceEEEEeCCCCC-----CccchHHhHHHHHhhcC
Q psy4967         217 TLQNIFSLNPI--AGEIRDLILTNKSKLNVRFIWVPSHVG-----IAGNEEADRLAKEALTS  271 (354)
Q Consensus       217 ~i~~~~~~~~~--~~~i~~~~~~~~~~~~V~~~WVpgH~g-----i~gNe~AD~lAk~a~~~  271 (354)
                      ++-......++  ...+++++..+..+..|.|.|||||+|     ++|||.||+|||+|+..
T Consensus        95 ~iw~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~  156 (165)
T 3p1g_A           95 TAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMK  156 (165)
T ss_dssp             HHHSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhcccCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhc
Confidence            98211111111  122333434444678999999999999     99999999999999988

>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=99.88  E-value=6.2e-23  Score=174.17  Aligned_cols=119  Identities=19%  Similarity=0.245  Sum_probs=91.3

Q ss_pred             CcEEEEeCCCCCCC--CceEEEE--eCCe--eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHH
Q psy4967         141 DSTVVYTDASKNDV--AVSSAFC--SQDT--KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSA  214 (354)
Q Consensus       141 ~~~~iytDGS~~~~--~~G~a~~--~~~~--~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~a  214 (354)
                      ..++||||||+..+  ..|+|+|  .++.  ..+..+ ..+|++.||+.|++.||+.+     ..  ..+|.|+|||+++
T Consensus         3 ~~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~-----~~--~~~v~I~tDS~~v   74 (155)
T 1jl1_A            3 KQVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEAL-----KE--HAEVILSTDSQYV   74 (155)
T ss_dssp             CCEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTC-----CS--CCEEEEEECCHHH
T ss_pred             ceEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHh-----Cc--CCcEEEEeCHHHH
Confidence            35899999999853  3788877  3332  233333 35789999999999999988     32  3799999999999


Q ss_pred             HHHhccc---------CCC-------ChhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         215 LQTLQNI---------FSL-------NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       215 l~~i~~~---------~~~-------~~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      ++.|..+         ...       .++++++.+++    ....|.|.|||||+|++|||.||+|||+|+..
T Consensus        75 i~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~----~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  143 (155)
T 1jl1_A           75 RQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAAL----GQHQIKWEWVKGHAGHPENERADELARAAAMN  143 (155)
T ss_dssp             HHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHT----TTCEEEEEECCSSTTCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHH----ccCceEEEEcCCCCCCHHHHHHHHHHHHHHhc
Confidence            9999873         111       12444444443    34689999999999999999999999999987

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

Probab=99.86  E-value=1.2e-22  Score=174.34  Aligned_cols=119  Identities=18%  Similarity=0.124  Sum_probs=91.3

Q ss_pred             CcEEEEeCCCCCCC--CceEEEE--eCCe--eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHH
Q psy4967         141 DSTVVYTDASKNDV--AVSSAFC--SQDT--KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSA  214 (354)
Q Consensus       141 ~~~~iytDGS~~~~--~~G~a~~--~~~~--~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~a  214 (354)
                      ..++||||||+..+  ..|+|+|  .++.  ..+... ..+|++.||+.|++.||+.+     ..  ...|.|+|||+++
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-ACTTNNRMELKAAIEGLKAL-----KE--PCEVDLYTDSHYL   78 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEE-EEECHHHHHHHHHHHHHHSC-----CS--CCEEEEECCCHHH
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCC-CCCcHHHHHHHHHHHHHHHh-----cc--CCeEEEEeChHHH
Confidence            35799999999854  3788877  3322  222222 35789999999999999987     32  3589999999999


Q ss_pred             HHHhcc----------cCCC-------ChhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         215 LQTLQN----------IFSL-------NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       215 l~~i~~----------~~~~-------~~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      ++.|..          +...       .++++++.+++.    ...|.|.|||||+|++|||.||+|||+|+..
T Consensus        79 i~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~----~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  148 (166)
T 1ril_A           79 KKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA----PHRVRFHFVKGHTGHPENERVDREARRQAQS  148 (166)
T ss_dssp             HHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT----TSEEECCCCCGGGSCTHHHHHHHHHHHHHTS
T ss_pred             HHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHh----cCeEEEEEeeCCCCchhHHHHHHHHHHHHHH
Confidence            999988          2221       135555555543    4699999999999999999999999999988

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

Probab=99.85  E-value=2.3e-21  Score=165.61  Aligned_cols=122  Identities=17%  Similarity=0.135  Sum_probs=89.9

Q ss_pred             CcEEEEeCCCCCCC--C-----ceEEEE--e-CC---eeeeecC-CCCCchHHHHHHHHHHHHHHHHHhccccCCCceEE
Q psy4967         141 DSTVVYTDASKNDV--A-----VSSAFC--S-QD---TKFSSRL-HPLLSICNAELTAILFAIHFSISAHLNNVNRAYLV  206 (354)
Q Consensus       141 ~~~~iytDGS~~~~--~-----~G~a~~--~-~~---~~~~~~l-~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~  206 (354)
                      ..++||||||+..+  .     .|+|+|  . +.   ....+.. ....+++.||+.|+..||+.+++      ...+|.
T Consensus         6 ~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~------~~~~v~   79 (165)
T 2lsn_A            6 YEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALK------IPGPVL   79 (165)
T ss_dssp             CSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHH------SSSCEE
T ss_pred             ceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhc------CCCeEE
Confidence            46899999999743  2     788887  2 22   2223332 24567888999999999888743      345799


Q ss_pred             EEeCCHHHHHHhccc---------CC-------CChhHHHHHHHHHhhcCCCceEEEEeCCCCCC------ccchHHhHH
Q psy4967         207 ICSDSLSALQTLQNI---------FS-------LNPIAGEIRDLILTNKSKLNVRFIWVPSHVGI------AGNEEADRL  264 (354)
Q Consensus       207 I~sDS~~al~~i~~~---------~~-------~~~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi------~gNe~AD~l  264 (354)
                      |+|||++++++|..+         ..       ..++++++.+++..   ...|.|.|||||+|+      +|||.||+|
T Consensus        80 I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~---~~~v~~~~VkgH~g~~~~~~~~gNe~AD~L  156 (165)
T 2lsn_A           80 VITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSM---KPDITIQHEKGHQPTNTSIHTEGNALADKL  156 (165)
T ss_dssp             EEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHH---CTTCEEEECCSSSCSSSCHHHHHHHHHHHH
T ss_pred             EEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhC---CCCEEEEEEeCCCCccCCCCChHHHHHHHH
Confidence            999999999999753         11       12366777666654   568999999999995      589999999


Q ss_pred             HHHhhcC
Q psy4967         265 AKEALTS  271 (354)
Q Consensus       265 Ak~a~~~  271 (354)
                      |++|+..
T Consensus       157 A~~gA~~  163 (165)
T 2lsn_A          157 ATQGSYV  163 (165)
T ss_dssp             HHHHHHH
T ss_pred             HHHhhhh
Confidence            9999854

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

Probab=99.79  E-value=3e-19  Score=148.03  Aligned_cols=118  Identities=19%  Similarity=0.255  Sum_probs=89.0

Q ss_pred             CcEEEEeCCCCCCC--CceEEEE--e--CCe--eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCc----eEEEE
Q psy4967         141 DSTVVYTDASKNDV--AVSSAFC--S--QDT--KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRA----YLVIC  208 (354)
Q Consensus       141 ~~~~iytDGS~~~~--~~G~a~~--~--~~~--~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~----~i~I~  208 (354)
                      ..++||||||+..+  ..|+|++  +  +..  ..+..++ .+|++.||+.|++.||+.+.     ..+..    +|.|+
T Consensus         2 ~~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~-----~~~~~~~~~~v~i~   75 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIG-ETTNNVAEYEALIRALEDLQ-----MFGDKLVDMEVEVR   75 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEE-EECHHHHHHHHHHHHHHHHG-----GGGGGGTTCEEEEE
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCC-CCchHHHHHHHHHHHHHHHH-----HcCCCCCCceEEEE
Confidence            35899999999853  4788877  3  222  2233333 47999999999999999994     33455    99999


Q ss_pred             eCCHHHHHHhcccCC-CCh----hHHHHHHH-HHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         209 SDSLSALQTLQNIFS-LNP----IAGEIRDL-ILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       209 sDS~~al~~i~~~~~-~~~----~~~~i~~~-~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      |||+++++.+.++.. .+.    ++.++.++ +.   ....|.|.|||    .++||.||+|||+|+..
T Consensus        76 tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~---~~~~v~~~~V~----~~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D           76 MDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKME---RVPNLVFVHIP----REKNARADELVNEAIDK  137 (140)
T ss_dssp             ESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHH---HCTTCEEEECC----GGGGHHHHHHHHHHHHH
T ss_pred             eChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhc---CCCcEEEEEcC----chhhHHHHHHHHHHHHh
Confidence            999999999998664 332    33445555 43   35699999999    59999999999999865

>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=99.78  E-value=6.9e-19  Score=178.16  Aligned_cols=116  Identities=25%  Similarity=0.363  Sum_probs=93.0

Q ss_pred             CCcEEEEeCCCCCCCC--ceEEEE--eCCeeeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHH
Q psy4967         140 PDSTVVYTDASKNDVA--VSSAFC--SQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSAL  215 (354)
Q Consensus       140 ~~~~~iytDGS~~~~~--~G~a~~--~~~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al  215 (354)
                      ++.++||||||+..++  .|+|++  .++. ....+ ..+||+.||+.|++.||+.         ....+.|+|||++|+
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---------SGPKVNIIVDSQYVM  502 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCE-EEEEE-SSCCHHHHHHHHHHHHHHT---------SCSEEEEEESCHHHH
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCCE-eeccC-CCCCHHHHHHHHHHHHHHc---------CCCeEEEEEehHHHH
Confidence            4569999999998543  677877  3332 23333 3579999999999999986         357899999999999


Q ss_pred             HHhcccCC--CChhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhh
Q psy4967         216 QTLQNIFS--LNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL  269 (354)
Q Consensus       216 ~~i~~~~~--~~~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~  269 (354)
                      +++.++..  ..++.+++.+++..   ...|.|.|||||+|++|||.||+|||+|+
T Consensus       503 ~~i~~~~~~~~~~l~~~~~~~~~~---~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          503 GIVASQPTESESKIVNQIIEEMIK---KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             HHHHTCCSEESCHHHHHHHHHHHH---CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHHhcccccccHHHHHHHHHHhcc---CCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            99998763  45677777666654   68899999999999999999999999985

>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=99.78  E-value=1e-18  Score=145.27  Aligned_cols=120  Identities=15%  Similarity=0.187  Sum_probs=89.5

Q ss_pred             cEEEEeCCCCCCC--CceEEEE--eC--C-e--eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCH
Q psy4967         142 STVVYTDASKNDV--AVSSAFC--SQ--D-T--KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSL  212 (354)
Q Consensus       142 ~~~iytDGS~~~~--~~G~a~~--~~--~-~--~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~  212 (354)
                      .++||||||+..+  ..|+|++  +.  + .  ..+..+ ..+|++.||+.|++.||+.+.+     .+..+|.|+|||+
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~-----~~~~~v~i~tDS~   76 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAI-GRATNNVAEYRGLIAGLDDAVK-----LGATEAAVLMDSK   76 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHH-----HTCSEEEEEESCH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccC-CCCchHHHHHHHHHHHHHHHHH-----CCCceEEEEeChH
Confidence            4799999999854  4788876  32  2 2  223333 3679999999999999999953     3568999999999


Q ss_pred             HHHHHhcccC-CCChhHHHHHHHHHh-hcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         213 SALQTLQNIF-SLNPIAGEIRDLILT-NKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       213 ~al~~i~~~~-~~~~~~~~i~~~~~~-~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      ++++.+.+.+ ..+.....+.+.+.. ......|.|.|||    .++|+.||+|||+|+..
T Consensus        77 ~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~----~~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B           77 LVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVP----RARNTYADRLANDAMDA  133 (141)
T ss_dssp             HHHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECC----GGGCHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcC----CcccHHHHHHHHHHHHH
Confidence            9999999854 344433333222222 2356899999999    48999999999999977

>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=99.78  E-value=3.6e-19  Score=180.29  Aligned_cols=116  Identities=26%  Similarity=0.363  Sum_probs=89.5

Q ss_pred             CCcEEEEeCCCCCCC--CceEEEE-eCCeeeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHH
Q psy4967         140 PDSTVVYTDASKNDV--AVSSAFC-SQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQ  216 (354)
Q Consensus       140 ~~~~~iytDGS~~~~--~~G~a~~-~~~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~  216 (354)
                      ++.++||||||+..+  ..|+|++ ..+....... ..+||+.||+.|++.||+.+         ..++.|+|||++|++
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---------GLEVNIVTDSQYALG  506 (557)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS---------CSEEEEEECCHHHHH
T ss_pred             CCCEEEEEccCCCCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC---------CCcEEEEeChHHHHH
Confidence            346899999998743  3677776 2222222233 35799999999999999987         468999999999999


Q ss_pred             HhcccCCC--ChhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHh
Q psy4967         217 TLQNIFSL--NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEA  268 (354)
Q Consensus       217 ~i~~~~~~--~~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a  268 (354)
                      ++.++...  .++++++.+.+..   ...|.|.|||||+|++|||.||+|||+|
T Consensus       507 ~i~~~~~~~~~~l~~~~~~~l~~---~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          507 IIQAQPDKSESELVNQIIEQLIK---KEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             HHTTCCSEESSHHHHHHHHHHHH---CSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             HHhcCCccCCHHHHHHHHHHHhc---CCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            99998754  4577766655554   5689999999999999999999999986

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

Probab=99.76  E-value=1.4e-18  Score=146.11  Aligned_cols=116  Identities=19%  Similarity=0.241  Sum_probs=88.3

Q ss_pred             EEEEeCCCCCC---CCceE-EEE--e-CCeee--eecCC---CCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeC
Q psy4967         143 TVVYTDASKND---VAVSS-AFC--S-QDTKF--SSRLH---PLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSD  210 (354)
Q Consensus       143 ~~iytDGS~~~---~~~G~-a~~--~-~~~~~--~~~l~---~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sD  210 (354)
                      +.||||||+.+   +.+|+ |++  + +....  +...+   ..+|++.||+.|++.||+.+..     .+..+|.|+||
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 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLR-----LGISSPIIKGD   76 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHH-----HTCCSCEEEES
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHH-----cCCCEEEEEeC
Confidence            68999999972   45775 866  3 33222  22222   3689999999999999999953     35679999999


Q ss_pred             CHHHHHHhcccCC-CC----hhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         211 SLSALQTLQNIFS-LN----PIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       211 S~~al~~i~~~~~-~~----~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      |+++++.+.++.. .+    ++++++..++..   . .|.|.|||+    ++|+.||+|||+|+..
T Consensus        77 S~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~---~-~v~~~~V~~----~~N~~AD~LA~~a~~~  134 (149)
T 2ehg_A           77 SQLVIKQMNGEYKVKAKRIIPLYEKAIELKKK---L-NATLIWVPR----EENKEADRLSRVAYEL  134 (149)
T ss_dssp             CHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHH---H-TCEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHhCccccCCHHHHHHHHHHHHHHhc---C-CEEEEEcCC----cccHHHHHHHHHHHHh
Confidence            9999999998754 22    355566666554   2 599999997    6999999999999987

>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=99.30  E-value=3.7e-13  Score=111.73  Aligned_cols=116  Identities=12%  Similarity=-0.036  Sum_probs=80.8

Q ss_pred             CCcEEEEeCCCCCC--CCceEEEE---eCCe-eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHH
Q psy4967         140 PDSTVVYTDASKND--VAVSSAFC---SQDT-KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLS  213 (354)
Q Consensus       140 ~~~~~iytDGS~~~--~~~G~a~~---~~~~-~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~  213 (354)
                      +..+.||||||+..  +..|+|+|   .+.. ..+..++ .+||+.||+.|++.||+.+.+     .+. +|.|+|||++
T Consensus         9 ~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~-~~TNN~aEl~A~i~aL~~~~~-----~~~-~v~i~tDS~~   81 (142)
T 1zbf_A            9 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKE-----RNS-RKPIYSNSQT   81 (142)
T ss_dssp             CCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEE-EECHHHHHHHHHHHHHHHHHH-----TTC-CCCEEESCHH
T ss_pred             CCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccC-CcCcHHHHHHHHHHHHHHHHh-----CCC-eEEEEEehHH
Confidence            34678999999974  34788887   2222 2223333 579999999999999999953     234 8999999999


Q ss_pred             HHHHhcccCCC---------ChhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhH
Q psy4967         214 ALQTLQNIFSL---------NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADR  263 (354)
Q Consensus       214 al~~i~~~~~~---------~~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~  263 (354)
                      +++.+.+...+         .++++.+..+..-+ ....++...|.-|++.-||.-||.
T Consensus        82 vi~w~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~-~~~~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A           82 AIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWL-NTHTYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             HHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHH-HHCCCCCCEEECCHHHHCSCTTCC
T ss_pred             HHHHHHcCCccCCCCCCcccHHHHHHHHHHHHHH-hhCCCceeEEEeccCccCcCcccc
Confidence            99999887621         12444444433221 234556666777888889999884

>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=99.09  E-value=9.7e-11  Score=95.53  Aligned_cols=77  Identities=13%  Similarity=0.019  Sum_probs=56.5

Q ss_pred             CCCcEEEEeCCCCCCC--CceEEEE--e-CCe-eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCH
Q psy4967         139 TPDSTVVYTDASKNDV--AVSSAFC--S-QDT-KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSL  212 (354)
Q Consensus       139 ~~~~~~iytDGS~~~~--~~G~a~~--~-~~~-~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~  212 (354)
                      .++...||||||+..+  ..|+|+|  . +.. ..+..++ .+||+.||+.|++.||+.+.+     .+. .+.|+|||+
T Consensus         2 ep~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~~-~tTNN~aEl~A~i~aL~~l~~-----~~~-~v~i~tDSq   74 (134)
T 4htu_A            2 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKE-----RNS-RKPIYSNSQ   74 (134)
T ss_dssp             CCCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEEE-EECHHHHHHHHHHHHHHHHHH-----TTC-CCCEEESCH
T ss_pred             CccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCCC-CCchHHHHHHHHHHHHHHHHh-----CCC-CEEEEcchH
Confidence            3567789999999853  3778544  3 332 2333333 579999999999999999943     222 389999999


Q ss_pred             HHHHHhcccC
Q psy4967         213 SALQTLQNIF  222 (354)
Q Consensus       213 ~al~~i~~~~  222 (354)
                      +|++.|.++.
T Consensus        75 yVi~wi~~~~   84 (134)
T 4htu_A           75 TAIKWVKDKK   84 (134)
T ss_dssp             HHHHHHHHTC
T ss_pred             HHHHHHHcCC
Confidence            9999998753

---

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	354
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	5e-12
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	2e-07
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	3e-06
d1s1ta1	110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	9e-05

>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 = 60.3 bits (145), Expect = 5e-12
 Identities = 29/134 (21%), Positives = 51/134 (38%), Gaps = 16/134 (11%)

Query: 140 PDSTVVYTDAS--KNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHL 197
           P +   YTD S  +      + + +   K   +     +   AEL A   A+  S     
Sbjct: 5   PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTDSGPKV- 63

Query: 198 NNVNRAYLVICSDSLSALQTLQN--IFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGI 255
                    I  DS   +  + +    S + I  +I + ++  +    +   WVP+H GI
Sbjct: 64  --------NIIVDSQYVMGIVASQPTESESKIVNQIIEEMIKKE---AIYVAWVPAHKGI 112

Query: 256 AGNEEADRLAKEAL 269
            GN+E D L  + +
Sbjct: 113 GGNQEVDHLVSQGI 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 = 47.6 bits (112), Expect = 2e-07
 Identities = 21/136 (15%), Positives = 38/136 (27%), Gaps = 11/136 (8%)

Query: 144 VVYTD--ASKNDVAVSSAFCSQD---TKFSSRLHPLLSICNAELTAILFAIHFSISAHLN 198
            ++TD     N      A   +     K  S      +    EL A +  +         
Sbjct: 5   ALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCEV 64

Query: 199 NVNRAY------LVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSH 252
           ++                     +  +          ++ + +L   +   VRF +V  H
Sbjct: 65  DLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGH 124

Query: 253 VGIAGNEEADRLAKEA 268
            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 = 44.2 bits (103), Expect = 3e-06
 Identities = 11/26 (42%), Positives = 15/26 (57%)

Query: 243 NVRFIWVPSHVGIAGNEEADRLAKEA 268
            +++ WV  H G   NE AD LA+ A
Sbjct: 113 QIKWEWVKGHAGHPENERADELARAA 138

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

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

 Score = 39.2 bits (91), Expect = 9e-05
 Identities = 22/117 (18%), Positives = 40/117 (34%), Gaps = 16/117 (13%)

Query: 140 PDSTVVYTDAS--KNDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHL 197
             +   Y D +  +      + + +   +         +    EL AI  A+  S     
Sbjct: 6   VGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLE-- 63

Query: 198 NNVNRAYLVICSDSLSALQTLQNIF--SLNPIAGEIRDLILTNKSKLNVRFIWVPSH 252
                  + I +DS  AL  +Q     S + +  +I + +     K  V   WVP+H
Sbjct: 64  -------VNIVTDSQYALGIIQAQPDQSESELVNQIIEQL---IKKEKVYLAWVPAH 110

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	354
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.91
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.88
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	99.49

>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=9.7e-25  Score=176.96  Aligned_cols=117  Identities=26%  Similarity=0.371  Sum_probs=86.9

Q ss_pred             CCcEEEEeCCCCCCC-C-ceEEEE-eCCeeeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHH
Q psy4967         140 PDSTVVYTDASKNDV-A-VSSAFC-SQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQ  216 (354)
Q Consensus       140 ~~~~~iytDGS~~~~-~-~G~a~~-~~~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~  216 (354)
                      ++..++|||||+..+ + .|+|++ ..+......++ ..|++.|||.||++||+..         ...+.|+|||+++++
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~~---------~~~i~I~tDS~~v~~   74 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTDS---------GPKVNIIVDSQYVMG   74 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHTS---------CSEEEEEESCHHHHH
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhccC---------CcceEEEechHHHHH
Confidence            456799999998743 3 556665 33333334444 4699999999999998744         568999999999999


Q ss_pred             HhcccCCC--ChhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhh
Q psy4967         217 TLQNIFSL--NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL  269 (354)
Q Consensus       217 ~i~~~~~~--~~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~  269 (354)
                      .+.++...  ........+.+.   ....|.|.|||||+|++|||.||+||++|+
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~---~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          75 IVASQPTESESKIVNQIIEEMI---KKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             HHHTCCSEESCHHHHHHHHHHH---HCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHhcCCccccchHHHHHHHHhh---hcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            99987652  333333222222   357899999999999999999999999984

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

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

Probab=99.88  E-value=5.3e-24  Score=177.07  Aligned_cols=119  Identities=18%  Similarity=0.128  Sum_probs=88.2

Q ss_pred             cEEEEeCCCCCCC--CceEEEE--eCC-eeeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHH
Q psy4967         142 STVVYTDASKNDV--AVSSAFC--SQD-TKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQ  216 (354)
Q Consensus       142 ~~~iytDGS~~~~--~~G~a~~--~~~-~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~  216 (354)
                      .++||||||+.++  ..|+|+|  ..+ ...........|++.||+.|++.||+++       .....+.|++||++++.
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~-------~~~~~i~i~tds~~~~~   75 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKAL-------KEPCEVDLYTDSHYLKK   75 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSC-------CSCCEEEEECCCHHHHH
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhc-------cCCceEEEecchhhhhc
Confidence            5899999999864  3677776  222 2211112234699999999999999876       24678999999999999


Q ss_pred             HhcccCC----------C-------ChhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         217 TLQNIFS----------L-------NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       217 ~i~~~~~----------~-------~~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      ++.....          .       .++++++..+.    ....|.|.|||||+|++|||.||+|||+|+..
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~----~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~  143 (147)
T d1rila_          76 AFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAM----APHRVRFHFVKGHTGHPENERVDREARRQAQS  143 (147)
T ss_dssp             HHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH----TTSEEECCCCCGGGSCTHHHHHHHHHHHHHTS
T ss_pred             cccccchhhhhhccccccccccchhHHHHHHHHHHh----hhcccceEEccCCCCCcchHHHHHHHHHHHHH
Confidence            8865321          0       12445554433    46789999999999999999999999999987

>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=6.6e-23  Score=171.02  Aligned_cols=122  Identities=20%  Similarity=0.249  Sum_probs=88.4

Q ss_pred             cEEEEeCCCCCCC--CceEEEE--eCCe--eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHH
Q psy4967         142 STVVYTDASKNDV--AVSSAFC--SQDT--KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSAL  215 (354)
Q Consensus       142 ~~~iytDGS~~~~--~~G~a~~--~~~~--~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al  215 (354)
                      .|.||||||+.++  ..|+|+|  .++.  ..+... ...|++.||+.|++.||+++       .....+.|++||++++
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~-~~~tnn~aE~~Ai~~Al~~~-------~~~~~i~i~tds~~~i   73 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEAL-------KEHAEVILSTDSQYVR   73 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTC-------CSCCEEEEEECCHHHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEecccc-CcccHHHHHHhhhhhhhhhh-------cccceEEEeecceeeE
Confidence            4799999998854  3788876  4433  223333 34689999999999999876       2467899999999999


Q ss_pred             HHhcccCC---------CC--h-hHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967         216 QTLQNIFS---------LN--P-IAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS  271 (354)
Q Consensus       216 ~~i~~~~~---------~~--~-~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~  271 (354)
                      ..+..+..         ..  . ...++...+..+.....|.|+|||||+|++|||.||+|||+|+..
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~  141 (152)
T d1jl1a_          74 QGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMN  141 (152)
T ss_dssp             HHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTCHHHHHHHHHHHHHHHS
T ss_pred             EcccchhhHhHhccchhcccCeeecHHHHHHHHHHhhcceeEEEEecccCCCccHHHHHHHHHHHHhC
Confidence            88865421         11  1 011122222222356789999999999999999999999999998

>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=1.5e-18  Score=136.37  Aligned_cols=100  Identities=23%  Similarity=0.295  Sum_probs=75.8

Q ss_pred             CCcEEEEeCCCCCCC-C-ceEEEE-eCCeeeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHH
Q psy4967         140 PDSTVVYTDASKNDV-A-VSSAFC-SQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQ  216 (354)
Q Consensus       140 ~~~~~iytDGS~~~~-~-~G~a~~-~~~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~  216 (354)
                      ++..++|||||+..+ + .|+|++ ..+......+. .+||+.|||.||+.||+..         ..++.|+|||+++++
T Consensus         6 ~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~~-~~TNn~aEl~Avi~aL~~~---------~~~v~I~TDS~yvi~   75 (110)
T d1s1ta1           6 VGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLALQDS---------GLEVNIVTDSQYALG   75 (110)
T ss_dssp             TTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHHS---------CSEEEEEECCHHHHH
T ss_pred             CCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEecc-cCcHHHHHHHHHHHHHHhC---------CCeEEEEEehHHHHH
Confidence            456799999998743 3 555555 33333334443 4699999999999999744         457999999999999


Q ss_pred             HhcccCC--CChhHHHHHHHHHhhcCCCceEEEEeCCC
Q psy4967         217 TLQNIFS--LNPIAGEIRDLILTNKSKLNVRFIWVPSH  252 (354)
Q Consensus       217 ~i~~~~~--~~~~~~~i~~~~~~~~~~~~V~~~WVpgH  252 (354)
                      ++..+..  ..++++++.+.+..   ...|.+.|||||
T Consensus        76 ~i~~~~~~~~~~l~~~il~~l~~---~~~v~i~WVpgH  110 (110)
T d1s1ta1          76 IIQAQPDQSESELVNQIIEQLIK---KEKVYLAWVPAH  110 (110)
T ss_dssp             HHHHCCSEESCHHHHHHHHHHHH---CSEEEEEECCSS
T ss_pred             HHhcCccccchHHHHHHHHHHhc---CCceEEEEeCCC
Confidence            9998765  45677777666654   678999999999

>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=99.49  E-value=3.3e-15  Score=119.39  Aligned_cols=111  Identities=13%  Similarity=0.025  Sum_probs=79.7

Q ss_pred             EEEeCCCCCCC--CceEEEE--e-CCe-eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHHH
Q psy4967         144 VVYTDASKNDV--AVSSAFC--S-QDT-KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQT  217 (354)
Q Consensus       144 ~iytDGS~~~~--~~G~a~~--~-~~~-~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~~  217 (354)
                      .||||||+..+  ..|+|+|  . +.. ..+..+ ...||+.||+.|++.||+.+.+      ...++.|+|||++|+..
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~-~~~TNN~aEl~A~i~aL~~~~~------~~~~i~I~tDS~yvi~w   78 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKE------RNSRKPIYSNSQTAIKW   78 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHH------TTCCCCEEESCHHHHHH
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCc-CccchHHHHHHHHHHHHHHhhc------CCceEEEEeccHHHHHH
Confidence            48999999853  4888877  2 332 233334 3569999999999999999942      23578999999999999


Q ss_pred             hcccCCC---------ChhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHh
Q psy4967         218 LQNIFSL---------NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEAD  262 (354)
Q Consensus       218 i~~~~~~---------~~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD  262 (354)
                      +.++...         .++++.+.++..- .....+.+.||..|+..-||..||
T Consensus        79 v~~~~~kt~~~~~vkN~~l~~~i~~a~~~-lk~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          79 VKDKKAKSTLVRNEETALIWKLVDEAEEW-LNTHTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             HHHTCCCCCCCCSTTTHHHHHHHHHHHHH-HHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             HHhCceecCcCCCcccHHHHHHHHHHHHH-HHhCCcCceeEEecCcccccCCCC
Confidence            9876521         1244444333211 134678999999999999999998