Psyllid ID: psy15595

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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-
Protein Sequence
MHHNSTNPNFKRINNPPYKVLYENSTKLNPTVGIQRELLMNDIPFHKVILQREPKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTGDLKNVSLNLHEVERNRIICHIFGSWLSIIRV
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccEEEEEcccccccccEEEEEEccccEEEEEEccccccHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHcccccccEEEEEEcccccEEccccccEEEEEc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccHHHHHHccccccccccHHHHHHHHccccccEEcccccccccccccccEEEEEcHcccccccHHHHHHHHHHHHHHHcccccEEEEccccccccEEEEEEEccccEEEEEEccccccHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHcccEEEEEEEcccccEEEEEcccEEEEEEc
Coil and Loop (DISEMBL)
mhhnstnpnfkrinnppykvlyenstklnptvGIQRELlmndipfhkvilqrepkeswlhkkpscnlsltlykkdgmphqVFQQEFQRNMNENYGDFVQVytdgsksdssvgcafvipqlhivkkqtlnpkssifHAELLAISDAVSTIksqsigeaVIISDSLSALQAISsmshsnplvQSIHEeistgdlknvsLNLHEVERNRIICHIFGSWLSIIRV
Flexible Loop (DISEMBL)
mhhnstnpnfkrinnppYKVLYENSTKLNPTVGIQRELLMNDIPFHKVILQrepkeswlhkkpSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTGDLKNVSLNLHEVERNRIichifgswlsiirv
Low Complexity Region (SEG)
MHHNSTNPNFKRINNPPYKVLYENSTKLNPTVGIQRELLMNDIPFHKVILQREPKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTGDLKNVSLNLHEVERNRIICHIFGSWLSIIRV
Disordered region (IsUnstruct)
****************PYKVLYENSTKLNPTVGIQRELLMNDIPFHKVILQREPKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQ**************IH*EISTGDLKNVSLNLHEVERNRIICHIFGSWLSII**
Disordered Region (DISOPRED)
********NFKRINNPPYKVLYENSTKLNPTVGIQRELL************REPKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTGDLKNVSLNLHEVERNRIICHIFGSWLSIIRV
Disordered Region (DISEMBL)
********NFKRINNPPYKVLYENSTKLNPTVGIQRELLMNDIPFHKVILQREPKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTGDLKNVSLNLHEVERNRIICHIFGSWLSIIRV
Disordered Region (DISPRO)
********NFKRINNPPYKVLYENSTKLNPTVGIQRELLMNDIPFHKVILQREPKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTGDLKNVSLNLHEVERNRIICHIFGSWLSIIRV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MHHNSTNPNFKRINNPPYKVLYENSTKLNPTVGIQRELLMNDIPFHKVILQREPKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEISTGDLKNVSLNLHEVERNRIICHIFGSWLSIIRV
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	221
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.877	0.158	0.346	1e-16
443708866	213	hypothetical protein CAPTEDRAFT_187709 [	0.592	0.615	0.357	2e-10
443734745	252	hypothetical protein CAPTEDRAFT_216906 [	0.619	0.543	0.349	2e-10
443723447	225	hypothetical protein CAPTEDRAFT_187673 [	0.556	0.546	0.362	5e-10
443710566	377	hypothetical protein CAPTEDRAFT_186063 [	0.619	0.363	0.349	5e-10
443700898	300	hypothetical protein CAPTEDRAFT_212630,	0.619	0.456	0.342	6e-10
427791321	1210	Putative tick transposon, partial [Rhipi	0.547	0.1	0.351	1e-09
427791807	1212	Putative tick transposon, partial [Rhipi	0.547	0.099	0.351	1e-09
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.542	0.239	0.348	8e-09
427791981	1060	Putative tick transposon, partial [Rhipi	0.588	0.122	0.370	9e-09

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

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/202 (34%), Positives = 100/202 (49%), Gaps = 8/202 (3%)

Query: 1    MHHNSTNPNFKRINNPPYKVLYENSTKLNPTVGIQ-RELLMN-DIPFHKVILQREPKES- 57
            +  N TNP F  I NP    LY     +   +G++ RE + N   P  ++     P+   
Sbjct: 858  LKSNPTNPAFDSIFNPTEVELYNRRPNVIQPLGLRMREPIQNLTQPIDQISKIETPQNPP 917

Query: 58   WLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVI 117
            WL  KP  NLSL  +KK+     + Q  F R + E+YGD   +YTDGSK +  V CA   
Sbjct: 918  WLMNKPKLNLSLLNFKKENTDPSILQVHF-RELQESYGDCGTIYTDGSKMEGKVACACSF 976

Query: 118  PQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSN 177
                I ++  L    SIF AEL AI  A+  +K+    + +I SDS SALQA+  M    
Sbjct: 977  RNKTISRR--LPDGCSIFTAELHAILLALMAVKASERSKFIICSDSKSALQALGRMKTDI 1034

Query: 178  PLVQSIHE--EISTGDLKNVSL 197
            PLV    +  ++ T D ++V+ 
Sbjct: 1035 PLVHKSLKLLDLITADRRDVTF 1056

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|443708866|gb|ELU03797.1| hypothetical protein CAPTEDRAFT_187709 [Capitella teleta]

 Score = 72.0 bits (175), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 49/137 (35%), Positives = 76/137 (55%), Gaps = 6/137 (4%)

Query: 58  WLHKKPSCNLSLTLY-KKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFV 116
           WL + P  ++SL  + KK   P+   + EF  N+ + Y D   ++TDGSKSDS+V C+  
Sbjct: 78  WLLRPPELDISLIHFGKKTTNPNYTLKNEFY-NLMDKYPDHKVIFTDGSKSDSAVACSAT 136

Query: 117 IPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEA--VIISDSLSALQAISSMS 174
              L I  +  L   +SIF AELLAI   ++ ++  +  +   +I +DSLS+LQAI + +
Sbjct: 137 ADNLRIQIR--LPDSASIFSAELLAIYQVLTLLECSANDQQQFLIATDSLSSLQAIGNFN 194

Query: 175 HSNPLVQSIHEEISTGD 191
             +P V  I  E+   D
Sbjct: 195 IKHPYVFKILTEVYICD 211

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443734745|gb|ELU18611.1| hypothetical protein CAPTEDRAFT_216906 [Capitella teleta]

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 50/143 (34%), Positives = 79/143 (55%), Gaps = 6/143 (4%)

Query: 58  WLHKKPSCNLSLTLY-KKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFV 116
           WL + P  ++SL  + KK   P+   + EF  N+ + Y D   ++TDGSKSDS+V C+  
Sbjct: 78  WLLRPPELDISLIHFGKKTANPNYTLRNEFY-NLMDKYPDHKVIFTDGSKSDSAVACSAT 136

Query: 117 IPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEA--VIISDSLSALQAISSMS 174
              L I  +  L   +SIF AELLAI   ++ ++  +  +   +I +DSLS+LQAI + +
Sbjct: 137 ADNLRIQIR--LPDSASIFSAELLAIYQVLTLLECSANDQQQFLIATDSLSSLQAIGNFN 194

Query: 175 HSNPLVQSIHEEISTGDLKNVSL 197
             +P V  I E+ +    K + L
Sbjct: 195 IKHPYVFKILEKCTLLHKKGIYL 217

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443723447|gb|ELU11866.1| hypothetical protein CAPTEDRAFT_187673 [Capitella teleta]

 Score = 70.5 bits (171), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 46/127 (36%), Positives = 69/127 (54%), Gaps = 4/127 (3%)

Query: 58  WLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVI 117
           W   +P  +LSLT +KKD       + EF+  ++  Y D    YTDGSKS+ SV C+F  
Sbjct: 37  WHLVQPEVDLSLTSFKKDSKSALTIRSEFEDALD-RYPDSTLFYTDGSKSEDSVACSFFS 95

Query: 118 PQLHIVKKQTLNPKSSIFHAELLAISDAVSTIK-SQSIGEAVIISDSLSALQAISSMSHS 176
            +L +  K  L  + S+F +EL+AI  A+  ++      + VI SD+LSA+ AI  M   
Sbjct: 96  NRLRL--KMKLPVQMSVFTSELIAILSALKCVEVDNEQHQFVICSDALSAIMAIHGMDVR 153

Query: 177 NPLVQSI 183
           +P V  +
Sbjct: 154 HPYVLKV 160

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 70.5 bits (171), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 50/143 (34%), Positives = 78/143 (54%), Gaps = 6/143 (4%)

Query: 58  WLHKKPSCNLSLTLY-KKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFV 116
           WL + P  ++SL  + KK   P+   + EF  N+ + Y D   ++TDGSKSDS+V C   
Sbjct: 147 WLLRPPELDISLIHFGKKTANPNYTLKNEFY-NLMDKYPDHKVIFTDGSKSDSAVACFAT 205

Query: 117 IPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEA--VIISDSLSALQAISSMS 174
              L I  +  L   +SIF AELLAI   ++ ++  +  +   +I +DSLS+LQAI + +
Sbjct: 206 ADNLSIQIR--LPDSASIFSAELLAIYQVLTLLECSANDQQQFLIATDSLSSLQAIGNFN 263

Query: 175 HSNPLVQSIHEEISTGDLKNVSL 197
             +P V  I E+ +    K + L
Sbjct: 264 IKHPYVFKILEKCTLLHKKGIYL 286

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 = 70.1 bits (170), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 49/143 (34%), Positives = 79/143 (55%), Gaps = 6/143 (4%)

Query: 58  WLHKKPSCNLSLTLY-KKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFV 116
           WL + P  ++SL  + KK   P+   + EF  N+ + Y D   ++TDGSKSDS+V C+  
Sbjct: 78  WLLRPPELDISLIHFGKKTANPNYTLRNEFY-NLMDKYPDHKVIFTDGSKSDSAVACSAT 136

Query: 117 IPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEA--VIISDSLSALQAISSMS 174
              L I  +  L   +SIF AELLAI   ++ ++  +  +   +I +DSLS+LQAI + +
Sbjct: 137 ADNLRIQIR--LPDSASIFSAELLAIYQVLTLLECSANDQQQFLIATDSLSSLQAIGNFN 194

Query: 175 HSNPLVQSIHEEISTGDLKNVSL 197
             +P V  I ++ +    K + L
Sbjct: 195 IKHPYVFKILQKCTLLHKKGIYL 217

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 69.3 bits (168), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 45/128 (35%), Positives = 66/128 (51%), Gaps = 7/128 (5%)

Query: 58   WLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVI 117
            W      C++SL+   K   P ++  QEF R + E Y D+ + YTDGSK+   VG   V 
Sbjct: 898  WFDLAQLCDISLSHINKKVTPPELIIQEF-RALQEKYRDYAEFYTDGSKTRDHVGIGIVT 956

Query: 118  PQ--LHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSH 175
             +    +   Q +    SIF AE+ A+ +A   I +    +A+I +DSLSAL+A+   S 
Sbjct: 957  GESAFSVRVPQCI----SIFTAEVYALYEAARKIIAGKHKKAIIYTDSLSALKALHIKSE 1012

Query: 176  SNPLVQSI 183
              PLV  I
Sbjct: 1013 CEPLVGDI 1020

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 45/128 (35%), Positives = 66/128 (51%), Gaps = 7/128 (5%)

Query: 58   WLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVI 117
            W      C++SL+   K   P ++  QEF R + E Y D+ + YTDGSK+   VG   V 
Sbjct: 901  WFDLAQLCDISLSHINKKVTPPELIIQEF-RALQEKYRDYAEFYTDGSKTRDHVGIGIVT 959

Query: 118  PQ--LHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSH 175
             +    +   Q +    SIF AE+ A+ +A   I +    +A+I +DSLSAL+A+   S 
Sbjct: 960  GESAFSVRVPQCI----SIFTAEVYALYEAARKIIAGKHKKAIIYTDSLSALKALHIKSE 1015

Query: 176  SNPLVQSI 183
              PLV  I
Sbjct: 1016 CEPLVGDI 1023

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 66.2 bits (160), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 45/129 (34%), Positives = 73/129 (56%), Gaps = 9/129 (6%)

Query: 58  WLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGCAFVI 117
           W  + P  + S++ + KD  P    +QEF   +++  G  + +YTDGSKS+++V CAF  
Sbjct: 44  WKLRPPEVDTSISKFLKDQHPALFLKQEFYNLIDKYPG--INIYTDGSKSNNAVACAFTC 101

Query: 118 PQLHIVKKQTLNPKSSIFHAELLAISDA---VSTIKSQSIGEAVIISDSLSALQAISSMS 174
               I  +  L  + SI+ AEL+AI  A   + T+K +   +  I SDSLS+L A+S+  
Sbjct: 102 STYQI--QFGLPTQMSIYTAELIAIEQALIFIETVKDED--QFNICSDSLSSLTALSNCD 157

Query: 175 HSNPLVQSI 183
            ++P + SI
Sbjct: 158 ITHPYLLSI 166

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|427791981|gb|JAA61442.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score = 66.2 bits (160), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 50/135 (37%), Positives = 71/135 (52%), Gaps = 5/135 (3%)

Query: 42   DIPFHKVILQREPKE--SWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQ 99
            +IP   + + + P+    W       + SLT  KK G P +   QEF R + E Y  F +
Sbjct: 929  NIPNEALSIAKRPRSLAPWSDFSMFLDFSLTHIKKQGTPREHILQEF-RTLQEKYHTFNE 987

Query: 100  VYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVI 159
             YTDGSK+ + VG + V      V +  L    S++ AE  A+  AV  I + +  +AVI
Sbjct: 988  FYTDGSKASAYVGSSVVGEIYEEVVR--LPQFVSVYTAECYALWIAVRNIINSNHKKAVI 1045

Query: 160  ISDSLSALQAISSMS 174
             SDSLSAL+A+SS S
Sbjct: 1046 FSDSLSALRALSSQS 1060

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

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

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	221
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	2e-22
pfam00075	126	pfam00075, RNase_H, RNase H	2e-06
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	9e-05
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	0.002

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

 Score = 88.1 bits (219), Expect = 2e-22
 Identities = 37/105 (35%), Positives = 53/105 (50%), Gaps = 3/105 (2%)

Query: 99  QVYTDGSKSDSSVGCAFVIPQLHIVKKQ-TLNPKSSIFHAELLAISDAVSTIKSQSIG-- 155
            +YTDGSK +   G  F I +   + +   L P  S+F AELLAI +A+     +     
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 156 EAVIISDSLSALQAISSMSHSNPLVQSIHEEISTGDLKNVSLNLH 200
           +  I SDS +AL+A+ S   S+PLV  I + I       V + LH
Sbjct: 61  KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLH 105

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 = 45.3 bits (108), Expect = 2e-06
 Identities = 26/95 (27%), Positives = 41/95 (43%), Gaps = 11/95 (11%)

Query: 100 VYTDGS--KSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEA 157
           VYTDGS   +    G  +V        K    P ++   AELLA+ +A+  +  Q +   
Sbjct: 6   VYTDGSCNGNPGPGGAGYVTDGGKQRSKP--LPGTTNQRAELLALIEALEALSGQKV--- 60

Query: 158 VIISDSLSALQAISSM----SHSNPLVQSIHEEIS 188
            I +DS   +  I++     S S P+   I E + 
Sbjct: 61  NIYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQ 95

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|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 = 40.4 bits (95), Expect = 9e-05
 Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 5/92 (5%)

Query: 101 YTDGSKSDSS--VGCAFVIPQLH---IVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIG 155
            TDGS   +    G   V+       +       P ++   AELLA+ +A+       + 
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60

Query: 156 EAVIISDSLSALQAISSMSHSNPLVQSIHEEI 187
           + +I +DS   +  I+S S        +  +I
Sbjct: 61  KLIIETDSKYVVDLINSWSKGWKKNNLLLWDI 92

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

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 4/71 (5%)

Query: 100 VYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVI 159
           V+TDGS      G A V     +++  TL   +S   AEL+A+  A+   K + +    I
Sbjct: 2   VFTDGSSFVRKAGYAVVTGP-DVLEIATLPYGTSAQRAELIALIRALELAKGKPVN---I 57

Query: 160 ISDSLSALQAI 170
            +DS  A   +
Sbjct: 58  YTDSAYAFGIL 68

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	221
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.56
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.48
PRK13907	128	rnhA ribonuclease H; Provisional	99.46
PRK08719	147	ribonuclease H; Reviewed	99.41
PRK00203	150	rnhA ribonuclease H; Reviewed	99.39
PRK06548	161	ribonuclease H; Provisional	99.36
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.28
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.16
PRK07708	219	hypothetical protein; Validated	99.14
KOG3752|consensus	371		99.06
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	98.79
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	92.5

>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=99.56  E-value=9.9e-15  Score=113.79  Aligned_cols=107  Identities=22%  Similarity=0.232  Sum_probs=78.7

Q ss_pred             CceEEEecCCCCC--CceeEEEEEeeCCeEEEEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHhC-
Q psy15595         96 DFVQVYTDGSKSD--SSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS-  172 (221)
Q Consensus        96 ~~~~IYTDGSK~~--~~vG~Avi~~~~~~~~~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~n-  172 (221)
                      +.+.||||||...  +..|+|+++... ....+.++ ..|++.||++||.+||+.+   ....++|+|||++++..|.. 
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~-~~~~~~~~-~~s~~~aEl~Ai~~AL~~~---~~~~v~I~tDS~~v~~~l~~~   76 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGG-RNFSFRLG-GQSNNRAELQAIIEALKAL---EHRKVTIYTDSQYVLNALNKW   76 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETT-EEEEEEEE-SECHHHHHHHHHHHHHHTH---STSEEEEEES-HHHHHHHHTH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECC-eEEEeccc-ccchhhhheehHHHHHHHh---hcccccccccHHHHHHHHHHh
Confidence            4689999999654  345777766433 34455666 8889999999999999944   33999999999999998876 


Q ss_pred             ----CCC-C--c-hHHHHHHHHHHhccccCceEEEEEEecCcch--hhh
Q psy15595        173 ----MSH-S--N-PLVQSIHEEISTGDLKNVSLNLHEVERNRII--CHI  211 (221)
Q Consensus       173 ----~~~-~--~-~ii~~I~~~i~~l~~~gi~V~l~WV~r~~~~--~~~  211 (221)
                          ... .  . ++...|.+++    .++..|.|+|||...-.  +|+
T Consensus        77 ~~~~~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~  121 (132)
T PF00075_consen   77 LHGNGWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNE  121 (132)
T ss_dssp             HHHTTSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHH
T ss_pred             ccccccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHH
Confidence                221 1  2 5666666666    55888999999988554  444

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 ....

>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=99.48  E-value=9.7e-13  Score=97.91  Aligned_cols=102  Identities=21%  Similarity=0.170  Sum_probs=78.3

Q ss_pred             EEEecCCCCCC--ceeEEEEEeeCCeEEEE---EcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHhCC
Q psy15595         99 QVYTDGSKSDS--SVGCAFVIPQLHIVKKQ---TLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSM  173 (221)
Q Consensus        99 ~IYTDGSK~~~--~vG~Avi~~~~~~~~~~---kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~n~  173 (221)
                      .+|||||...+  ++|+|++..+.+....+   ......|++.||+.|++.||+++...+..++.|+|||+.++..+.+.
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~   80 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGW   80 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcc
Confidence            48999999875  68888888555433222   22257899999999999999999988899999999999999999976


Q ss_pred             CC--Cc---hHHHHHHHHHHhccccCceEEEEEEec
Q psy15595        174 SH--SN---PLVQSIHEEISTGDLKNVSLNLHEVER  204 (221)
Q Consensus       174 ~~--~~---~ii~~I~~~i~~l~~~gi~V~l~WV~r  204 (221)
                      ..  ..   .+...|++.+    .++..+.++||+|
T Consensus        81 ~~~~~~~~~~~~~~i~~~~----~~~~~~~i~~v~~  112 (130)
T cd06222          81 YEGKPVKNVDLWQRLLALL----KRFHKVRFEWVPG  112 (130)
T ss_pred             ccCCChhhHHHHHHHHHHH----hCCCeEEEEEcCC
Confidence            53  22   3444444433    5667899999999

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

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.46  E-value=1.3e-12  Score=102.96  Aligned_cols=107  Identities=14%  Similarity=0.108  Sum_probs=77.1

Q ss_pred             eEEEecCCCCCC--ceeEEEEEeeCCeEEEEE-cCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHhCCC
Q psy15595         98 VQVYTDGSKSDS--SVGCAFVIPQLHIVKKQT-LNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMS  174 (221)
Q Consensus        98 ~~IYTDGSK~~~--~vG~Avi~~~~~~~~~~k-L~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~n~~  174 (221)
                      ++||||||...+  ..|+|+++.+.+-..... ....+|...||++|++.||+.+...+..++.|+|||+.++..++...
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~   81 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEY   81 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHH
Confidence            579999998764  588898885554322222 23457899999999999999999998899999999999999998643


Q ss_pred             C-CchHHHHHHHHHHhccccCceEEEEEEecC
Q psy15595        175 H-SNPLVQSIHEEISTGDLKNVSLNLHEVERN  205 (221)
Q Consensus       175 ~-~~~ii~~I~~~i~~l~~~gi~V~l~WV~r~  205 (221)
                      . ...+...+++....+ .+-..+.+.||+|.
T Consensus        82 ~~~~~~~~l~~~~~~l~-~~f~~~~~~~v~r~  112 (128)
T PRK13907         82 AKNKMFAPLLEEALQYI-KSFDLFFIKWIPSS  112 (128)
T ss_pred             hcChhHHHHHHHHHHHH-hcCCceEEEEcCch
Confidence            2 223333333333333 33345678999994

>PRK08719 ribonuclease H; Reviewed

Probab=99.41  E-value=3.6e-12  Score=104.58  Aligned_cols=102  Identities=24%  Similarity=0.277  Sum_probs=70.9

Q ss_pred             CceEEEecCCCCCCc-----eeEEEEEeeC--CeE--EEEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHH
Q psy15595         96 DFVQVYTDGSKSDSS-----VGCAFVIPQL--HIV--KKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSA  166 (221)
Q Consensus        96 ~~~~IYTDGSK~~~~-----vG~Avi~~~~--~~~--~~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~Sa  166 (221)
                      +.+.||||||+..++     .|+|+++.+.  ...  ....+...+|..+||+.||..||+.+.+.    .+|+|||+.+
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yv   78 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYC   78 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHH
Confidence            568999999997653     4888876443  222  33345566899999999999999998653    3799999999


Q ss_pred             HHHHh--------CCCC-C-------chHHHHHHHHHHhccccCceEEEEEEecCc
Q psy15595        167 LQAIS--------SMSH-S-------NPLVQSIHEEISTGDLKNVSLNLHEVERNR  206 (221)
Q Consensus       167 L~aI~--------n~~~-~-------~~ii~~I~~~i~~l~~~gi~V~l~WV~r~~  206 (221)
                      +++|.        |... .       .++.+.|..    +..+ ..|.|+||++-.
T Consensus        79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~----l~~~-~~i~~~~VkgH~  129 (147)
T PRK08719         79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDE----LRAR-KYVEVEKVTAHS  129 (147)
T ss_pred             HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHH----HhCC-CcEEEEEecCCC
Confidence            99993        3221 1       233444433    3333 458999998743

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.39  E-value=5.2e-12  Score=103.03  Aligned_cols=102  Identities=21%  Similarity=0.216  Sum_probs=72.5

Q ss_pred             ceEEEecCCCCCC--ceeEEEEEeeCCeEEEE-EcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHhC-
Q psy15595         97 FVQVYTDGSKSDS--SVGCAFVIPQLHIVKKQ-TLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS-  172 (221)
Q Consensus        97 ~~~IYTDGSK~~~--~vG~Avi~~~~~~~~~~-kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~n-  172 (221)
                      .+.||||||+..+  ..|+|+++...+....+ ......|...||++|+.+||+.+..  ...+.|+|||+++++.|.. 
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w   80 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEW   80 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHH
Confidence            4789999999864  47788777544433222 2235678999999999999998854  4679999999999999984 


Q ss_pred             --------CCC-------CchHHHHHHHHHHhccccCceEEEEEEecC
Q psy15595        173 --------MSH-------SNPLVQSIHEEISTGDLKNVSLNLHEVERN  205 (221)
Q Consensus       173 --------~~~-------~~~ii~~I~~~i~~l~~~gi~V~l~WV~r~  205 (221)
                              +..       ..++.+.|..++..     ..|.|.||+--
T Consensus        81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-----~~v~~~wV~~H  123 (150)
T PRK00203         81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-----HQIKWHWVKGH  123 (150)
T ss_pred             HHHHHHcCCcccCCCccccHHHHHHHHHHhcc-----CceEEEEecCC
Confidence                    111       12455666554432     46899999843

>PRK06548 ribonuclease H; Provisional

Probab=99.36  E-value=9.2e-12  Score=103.97  Aligned_cols=100  Identities=17%  Similarity=0.220  Sum_probs=71.2

Q ss_pred             CceEEEecCCCCCC--ceeEEEEEeeCCeEEEEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHh--
Q psy15595         96 DFVQVYTDGSKSDS--SVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAIS--  171 (221)
Q Consensus        96 ~~~~IYTDGSK~~~--~vG~Avi~~~~~~~~~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~--  171 (221)
                      ..+.||||||+..+  ..|.|+++.+... . ..-....|...||++|+++||+.+. .....++|+|||++++++|.  
T Consensus         4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~-~-~g~~~~~TNnraEl~Aii~aL~~~~-~~~~~v~I~TDS~yvi~~i~~W   80 (161)
T PRK06548          4 NEIIAATDGSSLANPGPSGWAWYVDENTW-D-SGGWDIATNNIAELTAVRELLIATR-HTDRPILILSDSKYVINSLTKW   80 (161)
T ss_pred             CEEEEEEeeccCCCCCceEEEEEEeCCcE-E-ccCCCCCCHHHHHHHHHHHHHHhhh-cCCceEEEEeChHHHHHHHHHH
Confidence            45899999999875  4788888853321 1 1112457899999999999998664 34457999999999999998  


Q ss_pred             -------CCCC-------CchHHHHHHHHHHhccccCceEEEEEEe
Q psy15595        172 -------SMSH-------SNPLVQSIHEEISTGDLKNVSLNLHEVE  203 (221)
Q Consensus       172 -------n~~~-------~~~ii~~I~~~i~~l~~~gi~V~l~WV~  203 (221)
                             +++.       +.++.+.|..++..   .  .|.|+||+
T Consensus        81 ~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~---~--~v~~~wVk  121 (161)
T PRK06548         81 VYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN---R--NIRMSWVN  121 (161)
T ss_pred             HHHHHHCCCcccCCCccccHHHHHHHHHHHhc---C--ceEEEEEe
Confidence                   3322       23566666555442   2  58999996

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

Probab=99.28  E-value=2.3e-11  Score=101.08  Aligned_cols=108  Identities=18%  Similarity=0.146  Sum_probs=76.8

Q ss_pred             CceEEEecCCCCCC--ceeEEEEEeeCCeE--EEEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHh
Q psy15595         96 DFVQVYTDGSKSDS--SVGCAFVIPQLHIV--KKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAIS  171 (221)
Q Consensus        96 ~~~~IYTDGSK~~~--~vG~Avi~~~~~~~--~~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~  171 (221)
                      ..+.||||||+..+  ..|.|+|....+..  .+..+. .+|...||++|+.+||+++.+.+...+.|+|||+.+++.|.
T Consensus         2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~   80 (154)
T COG0328           2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGIT   80 (154)
T ss_pred             CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHH
Confidence            35789999999976  36677776433332  233344 89999999999999999999989999999999999999998


Q ss_pred             CC----CCCc--------hHHHHHHHHHHhccccCceEEEEEEec
Q psy15595        172 SM----SHSN--------PLVQSIHEEISTGDLKNVSLNLHEVER  204 (221)
Q Consensus       172 n~----~~~~--------~ii~~I~~~i~~l~~~gi~V~l~WV~r  204 (221)
                      .+    ....        --...+-..+..+..+--.|.++||+.
T Consensus        81 ~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkg  125 (154)
T COG0328          81 RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKG  125 (154)
T ss_pred             HHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeC
Confidence            33    1111        012233333444444444689999984

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.16  E-value=4.9e-10  Score=103.24  Aligned_cols=105  Identities=12%  Similarity=0.100  Sum_probs=77.0

Q ss_pred             eEEEecCCCCCC--ceeEEEEEeeCC---eEE--EEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHH
Q psy15595         98 VQVYTDGSKSDS--SVGCAFVIPQLH---IVK--KQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAI  170 (221)
Q Consensus        98 ~~IYTDGSK~~~--~vG~Avi~~~~~---~~~--~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI  170 (221)
                      +.||||||...+  ..|+|+++.+.+   ...  ...++ .+|...||+.|++.||+++.+.+..++.|++||+.+++.+
T Consensus         3 ~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i   81 (372)
T PRK07238          3 VVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQM   81 (372)
T ss_pred             EEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHh
Confidence            689999999876  588888885542   112  22344 6778899999999999999999889999999999999999


Q ss_pred             hCCC-CCc-hHHHHHHHHHHhccccCceEEEEEEec
Q psy15595        171 SSMS-HSN-PLVQSIHEEISTGDLKNVSLNLHEVER  204 (221)
Q Consensus       171 ~n~~-~~~-~ii~~I~~~i~~l~~~gi~V~l~WV~r  204 (221)
                      .... ..+ .+...+.++ ..+..+.-.|.+.||+|
T Consensus        82 ~~~~~~~~~~l~~~~~~i-~~l~~~f~~~~i~~v~r  116 (372)
T PRK07238         82 SGRWKVKHPDMKPLAAQA-RELASQFGRVTYTWIPR  116 (372)
T ss_pred             CCCCccCChHHHHHHHHH-HHHHhcCCceEEEECCc
Confidence            8533 233 343333333 33334445689999999

>PRK07708 hypothetical protein; Validated

Probab=99.14  E-value=6.4e-10  Score=96.98  Aligned_cols=107  Identities=15%  Similarity=0.135  Sum_probs=77.1

Q ss_pred             CCceEEEecCCCCC--CceeEEEEEeeC--CeEE----EEEcCCCCchhHHHHHHHHHHHHHhhhcCCCc--EEEEeCcH
Q psy15595         95 GDFVQVYTDGSKSD--SSVGCAFVIPQL--HIVK----KQTLNPKSSIFHAELLAISDAVSTIKSQSIGE--AVIISDSL  164 (221)
Q Consensus        95 ~~~~~IYTDGSK~~--~~vG~Avi~~~~--~~~~----~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~--i~I~SDS~  164 (221)
                      ++.+.+|+|||...  +++|+|+++.+.  ....    ...+...+|...||+.|++.||+.+.+.+.+.  +.|++||+
T Consensus        71 p~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSq  150 (219)
T PRK07708         71 PHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQ  150 (219)
T ss_pred             CCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccH
Confidence            35699999999754  357777777432  2221    12466668999999999999999999987665  89999999


Q ss_pred             HHHHHHhCCC-CCc----hHHHHHHHHHHhccccCceEEEEEEec
Q psy15595        165 SALQAISSMS-HSN----PLVQSIHEEISTGDLKNVSLNLHEVER  204 (221)
Q Consensus       165 SaL~aI~n~~-~~~----~ii~~I~~~i~~l~~~gi~V~l~WV~r  204 (221)
                      .+++.+.... ..+    .+...+..++   +...+.+.+.||+|
T Consensus       151 lVi~qi~g~wk~~~~~l~~y~~~i~~l~---~~~~l~~~~~~VpR  192 (219)
T PRK07708        151 VVLNQLAGEWPCYDEHLNHWLDRIEQKL---KQLKLTPVYEPISR  192 (219)
T ss_pred             HHHHHhCCCceeCChhHHHHHHHHHHHH---hhCCceEEEEECCc
Confidence            9999998542 333    3334444443   34455688999999

>KOG3752|consensus

Probab=99.06  E-value=8.9e-10  Score=102.11  Aligned_cols=108  Identities=22%  Similarity=0.222  Sum_probs=83.8

Q ss_pred             CCceEEEecCCCCCC-----ceeEEEEEeeCCe-EEEEEcC-CCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHH
Q psy15595         95 GDFVQVYTDGSKSDS-----SVGCAFVIPQLHI-VKKQTLN-PKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSAL  167 (221)
Q Consensus        95 ~~~~~IYTDGSK~~~-----~vG~Avi~~~~~~-~~~~kL~-~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL  167 (221)
                      .+...+|||||...+     .+|+||+.++... .....+. .-.+.+.||+.||.+||+-|.+.+..+++|.|||+..+
T Consensus       210 ~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i  289 (371)
T KOG3752|consen  210 IEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFI  289 (371)
T ss_pred             ccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHH
Confidence            344899999999875     4999999966644 4566665 67789999999999999999999999999999999999


Q ss_pred             HHHhCCCC-----------Cc----------hHHHHHHHHHHhccccCceEEEEEEec
Q psy15595        168 QAISSMSH-----------SN----------PLVQSIHEEISTGDLKNVSLNLHEVER  204 (221)
Q Consensus       168 ~aI~n~~~-----------~~----------~ii~~I~~~i~~l~~~gi~V~l~WV~r  204 (221)
                      ++|+.+-.           .+          +....+.++...+  .+..|.+.||+=
T Consensus       290 ~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~--~~~~vq~~~V~G  345 (371)
T KOG3752|consen  290 NSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEI--SNKKVQQEYVGG  345 (371)
T ss_pred             HHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhh--ccCceEEEEecC
Confidence            99974321           11          2344455555554  577899999974

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

Probab=98.79  E-value=2.4e-08  Score=72.03  Aligned_cols=73  Identities=23%  Similarity=0.204  Sum_probs=52.6

Q ss_pred             hHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHhCCC-CCchHHHHHHHHHHhccccCceEEEEEEecCcch
Q psy15595        135 FHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMS-HSNPLVQSIHEEISTGDLKNVSLNLHEVERNRII  208 (221)
Q Consensus       135 ftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~n~~-~~~~ii~~I~~~i~~l~~~gi~V~l~WV~r~~~~  208 (221)
                      ..||++|++.||+++.+.+.++++|.|||+.++..|+... ..+.+...++++...++. ...+.++||+|..-.
T Consensus         2 ~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~-~~~~~~~~i~r~~N~   75 (87)
T PF13456_consen    2 LEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDR-FWNVSVSHIPREQNK   75 (87)
T ss_dssp             HHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCC-CSCEEEEE--GGGSH
T ss_pred             cHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhcc-ccceEEEEEChHHhH
Confidence            5799999999999999999999999999999999998663 334444444444443333 567899999998644

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

Probab=92.50  E-value=0.68  Score=38.06  Aligned_cols=54  Identities=22%  Similarity=0.192  Sum_probs=36.0

Q ss_pred             CceEEEecCCCCCCceeEEEEEee---CCeE--E---EEEc--CCCCchhHHHHHHHHHHHHHhhh
Q psy15595         96 DFVQVYTDGSKSDSSVGCAFVIPQ---LHIV--K---KQTL--NPKSSIFHAELLAISDAVSTIKS  151 (221)
Q Consensus        96 ~~~~IYTDGSK~~~~vG~Avi~~~---~~~~--~---~~kL--~~~~SIftAEl~AI~~AL~~~~~  151 (221)
                      ..+++|+|||+  .+.|+.++...   ....  .   ..|+  -...||=.-|++|++.|.+++..
T Consensus        80 ~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~  143 (159)
T PF05380_consen   80 VELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT  143 (159)
T ss_pred             eeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence            46899999994  45666665532   1111  1   1122  13459999999999999999755

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	221
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.67
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.65
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.62
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.56
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.52
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.5
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.5
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.5
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.49
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.44
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.4
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.28
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.23
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.2
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.14
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.08
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	83.94

>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=99.67  E-value=7.1e-16  Score=120.62  Aligned_cols=107  Identities=17%  Similarity=0.172  Sum_probs=80.9

Q ss_pred             ceEEEecCCCCCC--ceeEEEEEeeCC---eE-E-EEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHH
Q psy15595         97 FVQVYTDGSKSDS--SVGCAFVIPQLH---IV-K-KQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQA  169 (221)
Q Consensus        97 ~~~IYTDGSK~~~--~vG~Avi~~~~~---~~-~-~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~a  169 (221)
                      .+.||||||+..+  ..|+|+++.+.+   .. . ...+ ..+|.+.||+.|++.||+++.+.+..++.|+|||+.+++.
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~   81 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAI-GRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQ   81 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccC-CCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHH
Confidence            5789999998865  588888885542   22 2 2233 4788999999999999999999888999999999999999


Q ss_pred             HhCC-CCCchHHHHHHHHHHhccccCceEEEEEEec
Q psy15595        170 ISSM-SHSNPLVQSIHEEISTGDLKNVSLNLHEVER  204 (221)
Q Consensus       170 I~n~-~~~~~ii~~I~~~i~~l~~~gi~V~l~WV~r  204 (221)
                      +... ...+.....+...+..+..+...|.|+||+|
T Consensus        82 i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~  117 (141)
T 3hst_B           82 MSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR  117 (141)
T ss_dssp             HTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG
T ss_pred             HhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC
Confidence            9963 3444433333334444555567899999997

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

Probab=99.65  E-value=6.1e-16  Score=124.60  Aligned_cols=107  Identities=22%  Similarity=0.287  Sum_probs=82.7

Q ss_pred             CCceEEEecCCCCCCc-----eeEEEEEeeCCe-EEEEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHH
Q psy15595         95 GDFVQVYTDGSKSDSS-----VGCAFVIPQLHI-VKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQ  168 (221)
Q Consensus        95 ~~~~~IYTDGSK~~~~-----vG~Avi~~~~~~-~~~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~  168 (221)
                      .+.+.||||||+..++     +|+|+++.+.+. .....++..+|.+.||++|+++||+.+...+..+++|+|||+++++
T Consensus         5 ~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~   84 (154)
T 2qkb_A            5 GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTIN   84 (154)
T ss_dssp             TTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHH
T ss_pred             CCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHh
Confidence            3578999999998653     799998854322 2445676678999999999999999998888899999999999999


Q ss_pred             HHhCC---------C-------CCchHHHHHHHHHHhccccCceEEEEEEecCc
Q psy15595        169 AISSM---------S-------HSNPLVQSIHEEISTGDLKNVSLNLHEVERNR  206 (221)
Q Consensus       169 aI~n~---------~-------~~~~ii~~I~~~i~~l~~~gi~V~l~WV~r~~  206 (221)
                      .|..+         .       ...++.+.|..++.     +..|.|+||+|-.
T Consensus        85 ~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~-----~~~v~~~~V~~H~  133 (154)
T 2qkb_A           85 GITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ-----GMDIQWMHVPGHS  133 (154)
T ss_dssp             HHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT-----TCEEEEEECCTTS
T ss_pred             hhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc-----CCceEEEEccCCC
Confidence            99862         1       11356666665544     3569999999843

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

Probab=99.62  E-value=1.6e-15  Score=117.83  Aligned_cols=112  Identities=15%  Similarity=0.148  Sum_probs=79.3

Q ss_pred             CceEEEecCCCCCC--ceeEEEEEeeC--CeE-E-EEEcCCCCchhHHHHHHHHHHHHHhhhcCCC----cEEEEeCcHH
Q psy15595         96 DFVQVYTDGSKSDS--SVGCAFVIPQL--HIV-K-KQTLNPKSSIFHAELLAISDAVSTIKSQSIG----EAVIISDSLS  165 (221)
Q Consensus        96 ~~~~IYTDGSK~~~--~vG~Avi~~~~--~~~-~-~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~----~i~I~SDS~S  165 (221)
                      ..+.||||||+..+  ..|+|+++.+.  +.. . ...+ ..+|.+.||+.|++.||+++.+.+..    ++.|+|||+.
T Consensus         2 ~~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~   80 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYI-GETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSEL   80 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEE-EEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHH
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeC-CCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHH
Confidence            35799999999865  58888888553  222 2 2233 35789999999999999999887777    9999999999


Q ss_pred             HHHHHhCCC-CCc-hHHHHHHHHHHhccccCceEEEEEEecCcchhhh
Q psy15595        166 ALQAISSMS-HSN-PLVQSIHEEISTGDLKNVSLNLHEVERNRIICHI  211 (221)
Q Consensus       166 aL~aI~n~~-~~~-~ii~~I~~~i~~l~~~gi~V~l~WV~r~~~~~~~  211 (221)
                      +++.+.... ..+ ++...+..+......+...|.|+||+|   .+|+
T Consensus        81 vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~---~~N~  125 (140)
T 3u3g_D           81 IVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPR---EKNA  125 (140)
T ss_dssp             HHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCG---GGGH
T ss_pred             HHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCc---hhhH
Confidence            999999643 233 344333333332022334689999997   4554

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

Probab=99.56  E-value=2.6e-14  Score=113.80  Aligned_cols=100  Identities=21%  Similarity=0.234  Sum_probs=77.7

Q ss_pred             CceEEEecCCCCCC--ceeEEEEEeeCCeEE--EEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHh
Q psy15595         96 DFVQVYTDGSKSDS--SVGCAFVIPQLHIVK--KQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAIS  171 (221)
Q Consensus        96 ~~~~IYTDGSK~~~--~vG~Avi~~~~~~~~--~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~  171 (221)
                      +.+.||||||+..+  ..|+|+++.+.+...  +..+ ..+|...||++|++.||+.+.+  ..+++|+|||+++++.|.
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~   79 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMN   79 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHH
Confidence            56899999998875  488898886655332  2233 4678999999999999999875  579999999999999998


Q ss_pred             C-C----------------CCCchHHHHHHHHHHhccccCceEEEEEEe
Q psy15595        172 S-M----------------SHSNPLVQSIHEEISTGDLKNVSLNLHEVE  203 (221)
Q Consensus       172 n-~----------------~~~~~ii~~I~~~i~~l~~~gi~V~l~WV~  203 (221)
                      . +                -...++.+.|..++..     ..|.|+||+
T Consensus        80 ~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~-----~~v~~~~V~  123 (146)
T 3h08_A           80 EGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTL-----HRVTFHKVK  123 (146)
T ss_dssp             SSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHH-----SEEEEEECC
T ss_pred             HHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhh-----CceEEEEcC
Confidence            7 2                1124677777777664     359999998

>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=99.52  E-value=7.8e-15  Score=118.00  Aligned_cols=106  Identities=16%  Similarity=0.106  Sum_probs=81.1

Q ss_pred             CceEEEecCCCCCCceeEEEEEeeCCeEE--EE-Ec--CC--CCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHH
Q psy15595         96 DFVQVYTDGSKSDSSVGCAFVIPQLHIVK--KQ-TL--NP--KSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQ  168 (221)
Q Consensus        96 ~~~~IYTDGSK~~~~vG~Avi~~~~~~~~--~~-kL--~~--~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~  168 (221)
                      +.+.||||||+..+.+|+|+++.+.+...  .. .+  +.  .+|++.||++|++.||+++.+.+. ++.|+|||+...+
T Consensus         5 ~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i~~   83 (147)
T 2kq2_A            5 TEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGIAF   83 (147)
T ss_dssp             SCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTHHH
T ss_pred             CeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHHHH
Confidence            56899999999997799999886554332  22 22  22  358999999999999999887777 9999999998888


Q ss_pred             HHhC-CCCCchHHHHHHHHHHhccccCceEEEEEEecC
Q psy15595        169 AISS-MSHSNPLVQSIHEEISTGDLKNVSLNLHEVERN  205 (221)
Q Consensus       169 aI~n-~~~~~~ii~~I~~~i~~l~~~gi~V~l~WV~r~  205 (221)
                      .+.+ +..........++++..+..   .|.|+||++-
T Consensus        84 w~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~gH  118 (147)
T 2kq2_A           84 WATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVKAH  118 (147)
T ss_dssp             HTTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCCCC
T ss_pred             HHhCCCccCCcchHHHHHHHHHhcC---CeeEEEecCc
Confidence            7774 33445566667777777655   6899999964

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

Probab=99.50  E-value=9.9e-14  Score=112.61  Aligned_cols=101  Identities=20%  Similarity=0.216  Sum_probs=75.5

Q ss_pred             CceEEEecCCCCCC--ceeEEEEEeeCCeEE--EEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHh
Q psy15595         96 DFVQVYTDGSKSDS--SVGCAFVIPQLHIVK--KQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAIS  171 (221)
Q Consensus        96 ~~~~IYTDGSK~~~--~vG~Avi~~~~~~~~--~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~  171 (221)
                      ..+.||||||+..+  ..|+|+++.+.+...  ...+ ..+|...||+.|++.||+.+...  .++.|+|||+++++.|.
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~~--~~v~I~tDS~~vi~~i~   81 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKEP--CKIILTSDSQYMRQGIM   81 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSSC--CEEEEEECCHHHHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhccC--CeEEEEeCHHHHHHHHH
Confidence            45899999999864  478888886554322  2233 35789999999999999998643  89999999999999998


Q ss_pred             C---------CC-------CCchHHHHHHHHHHhccccCceEEEEEEec
Q psy15595        172 S---------MS-------HSNPLVQSIHEEISTGDLKNVSLNLHEVER  204 (221)
Q Consensus       172 n---------~~-------~~~~ii~~I~~~i~~l~~~gi~V~l~WV~r  204 (221)
                      .         +.       ...++.+.|..++..     ..|.|+||+.
T Consensus        82 ~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~-----~~v~~~wV~g  125 (158)
T 2e4l_A           82 TWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQL-----HQIDWRWVKG  125 (158)
T ss_dssp             THHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTT-----SEEEEEECCT
T ss_pred             HHHHHHHHccccccCCCcccCHHHHHHHHHHHcc-----CcEEEEEccC
Confidence            7         11       123666666665542     4799999984

>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=99.50  E-value=1.4e-13  Score=113.44  Aligned_cols=109  Identities=17%  Similarity=0.092  Sum_probs=77.7

Q ss_pred             ceEEEecCCCCC--CceeEEEEEeeCCeE-EEEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHhCC
Q psy15595         97 FVQVYTDGSKSD--SSVGCAFVIPQLHIV-KKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSM  173 (221)
Q Consensus        97 ~~~IYTDGSK~~--~~vG~Avi~~~~~~~-~~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~n~  173 (221)
                      .+.||||||+..  +..|+|+++...+.. ....++..+|++.||++|+..||+++   ...++.|+|||+++++.|-..
T Consensus        23 ~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~iw~~   99 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATAHVH   99 (165)
T ss_dssp             SEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHHHSC
T ss_pred             CEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhhhcc
Confidence            489999999984  346777655334332 23356778899999999999999999   368999999999999999421


Q ss_pred             CC-----CchHHHHHHHHHHhccccCceEEEEEEecCc------chhhhc
Q psy15595        174 SH-----SNPLVQSIHEEISTGDLKNVSLNLHEVERNR------IICHIF  212 (221)
Q Consensus       174 ~~-----~~~ii~~I~~~i~~l~~~gi~V~l~WV~r~~------~~~~~~  212 (221)
                      ..     ..++.+.+   +..+. ++..|.|+||++-.      ..||+.
T Consensus       100 ~~g~~v~n~dl~~~l---~~~l~-~~~~v~~~wVkgH~g~~~~~~~gNe~  145 (165)
T 3p1g_A          100 SEGREIKNKNEILAL---LKALF-LPKRLSIIHCPGHQKGNSAEARGNRM  145 (165)
T ss_dssp             CCSCCCSSHHHHHHH---HHHTT-SBSEEEEEECCSSCCSCSHHHHHHHH
T ss_pred             cCCCcccCHHHHHHH---HHHHh-cCCceEEEEecCCCCCCcCcchHHHH
Confidence            11     12444444   33333 46789999999876      566653

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

Probab=99.50  E-value=8.9e-14  Score=110.67  Aligned_cols=102  Identities=20%  Similarity=0.125  Sum_probs=76.5

Q ss_pred             eEEEecCCCC-C--CceeE-EEEEeeCCeE-EEE--EcC---CCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHH
Q psy15595         98 VQVYTDGSKS-D--SSVGC-AFVIPQLHIV-KKQ--TLN---PKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSAL  167 (221)
Q Consensus        98 ~~IYTDGSK~-~--~~vG~-Avi~~~~~~~-~~~--kL~---~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL  167 (221)
                      +.||||||.. .  +++|+ |+++.+.+.. ..+  .+.   ..+|.+.||+.|++.||+.+...+..++.|+|||+.++
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi   81 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVI   81 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHH
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHH
Confidence            5799999987 3  35775 8777543332 222  223   37889999999999999999988889999999999999


Q ss_pred             HHHhCCCC-C----chHHHHHHHHHHhccccCceEEEEEEec
Q psy15595        168 QAISSMSH-S----NPLVQSIHEEISTGDLKNVSLNLHEVER  204 (221)
Q Consensus       168 ~aI~n~~~-~----~~ii~~I~~~i~~l~~~gi~V~l~WV~r  204 (221)
                      +.+..+.. .    .++.+.|..++...     .|.|+||+|
T Consensus        82 ~~i~~~w~~~~~~~~~l~~~i~~l~~~~-----~v~~~~V~~  118 (149)
T 2ehg_A           82 KQMNGEYKVKAKRIIPLYEKAIELKKKL-----NATLIWVPR  118 (149)
T ss_dssp             HHHTTSSCCCCTTHHHHHHHHHHHHHHH-----TCEEEECCG
T ss_pred             HHHhCccccCCHHHHHHHHHHHHHHhcC-----CEEEEEcCC
Confidence            99987522 2    24555555555543     389999999

>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=99.49  E-value=1.1e-13  Score=111.90  Aligned_cols=101  Identities=19%  Similarity=0.225  Sum_probs=75.0

Q ss_pred             CceEEEecCCCCCC--ceeEEEEEeeCCeEE--EEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHh
Q psy15595         96 DFVQVYTDGSKSDS--SVGCAFVIPQLHIVK--KQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAIS  171 (221)
Q Consensus        96 ~~~~IYTDGSK~~~--~vG~Avi~~~~~~~~--~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~  171 (221)
                      ..+.||||||+..+  ..|+|+++.+.+...  ...+ ..+|.+.||+.|+..||+.+.+.  .++.|+|||+++++.|.
T Consensus         3 ~~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~~--~~v~I~tDS~~vi~~i~   79 (155)
T 1jl1_A            3 KQVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKEH--AEVILSTDSQYVRQGIT   79 (155)
T ss_dssp             CCEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCSC--CEEEEEECCHHHHHHHH
T ss_pred             ceEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCcC--CcEEEEeCHHHHHHHHH
Confidence            35789999999865  478888886544322  2233 46789999999999999998753  79999999999999998


Q ss_pred             CC---------CC-------CchHHHHHHHHHHhccccCceEEEEEEec
Q psy15595        172 SM---------SH-------SNPLVQSIHEEISTGDLKNVSLNLHEVER  204 (221)
Q Consensus       172 n~---------~~-------~~~ii~~I~~~i~~l~~~gi~V~l~WV~r  204 (221)
                      .+         ..       ..++.+.|..++.     ...|.|+||+.
T Consensus        80 ~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-----~~~v~~~wV~g  123 (155)
T 1jl1_A           80 QWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG-----QHQIKWEWVKG  123 (155)
T ss_dssp             TTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT-----TCEEEEEECCS
T ss_pred             HHHHHHhhcccccccCCccCCHHHHHHHHHHHc-----cCceEEEEcCC
Confidence            62         11       1356666655543     24799999983

>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=99.44  E-value=5.8e-13  Score=107.79  Aligned_cols=102  Identities=25%  Similarity=0.199  Sum_probs=74.9

Q ss_pred             CCceEEEecCCCCCC--ceeEEEEEeeCCeEEEEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHhC
Q psy15595         95 GDFVQVYTDGSKSDS--SVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS  172 (221)
Q Consensus        95 ~~~~~IYTDGSK~~~--~vG~Avi~~~~~~~~~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~n  172 (221)
                      .+.+.||||||+..+  ..|+|++..+... ....+ ..+|...||++|+..||+.+    ..+++|+|||+++++.|..
T Consensus        10 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~-~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i~~   83 (150)
T 3qio_A           10 VGAETFYVDGAANRETKLGKAGYVTNRGRQ-KVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIITQ   83 (150)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCE-EEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHHHH
T ss_pred             CCCEEEEEccCCCCCCCCeEEEEEEEcCCE-EEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHHHH
Confidence            467899999998765  3778887744332 22334 57889999999999999985    4899999999999999976


Q ss_pred             CC----------------CCchHHHHHHHHHHhccccCceEEEEEEecCc
Q psy15595        173 MS----------------HSNPLVQSIHEEISTGDLKNVSLNLHEVERNR  206 (221)
Q Consensus       173 ~~----------------~~~~ii~~I~~~i~~l~~~gi~V~l~WV~r~~  206 (221)
                      +.                ...++.+.+.+.+.    +...|.|+||++-.
T Consensus        84 w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~----~~~~v~~~wV~gH~  129 (150)
T 3qio_A           84 WIHNWKKRGWKTADKKPVKNVDLVNQIIEQLI----KKEKVYLAWVPAHK  129 (150)
T ss_dssp             HHHHHCC------------CHHHHHHHHHHHT----TCSEEEEEECCTTS
T ss_pred             HHHHHhhcCcCcCcCcccccHHHHHHHHHHHh----hcCceEEEEccCcC
Confidence            41                12345555544332    45689999999854

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

Probab=99.40  E-value=2.6e-13  Score=111.20  Aligned_cols=101  Identities=18%  Similarity=0.147  Sum_probs=74.4

Q ss_pred             CceEEEecCCCCCC--ceeEEEEEeeCCeEEEE--EcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHh
Q psy15595         96 DFVQVYTDGSKSDS--SVGCAFVIPQLHIVKKQ--TLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAIS  171 (221)
Q Consensus        96 ~~~~IYTDGSK~~~--~vG~Avi~~~~~~~~~~--kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~  171 (221)
                      ..+.||||||+..+  ..|+|+++.+.+....+  .+ ..+|.+.||++|++.||+.+...  .++.|+|||+++++.|.
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i~   83 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGE-ACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAFT   83 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEE-EEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHHH
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCC-CCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHHh
Confidence            35789999999865  47888888543322111  22 35789999999999999998654  58999999999999998


Q ss_pred             C----------CCC-------CchHHHHHHHHHHhccccCceEEEEEEec
Q psy15595        172 S----------MSH-------SNPLVQSIHEEISTGDLKNVSLNLHEVER  204 (221)
Q Consensus       172 n----------~~~-------~~~ii~~I~~~i~~l~~~gi~V~l~WV~r  204 (221)
                      .          +..       ..++.+.|..++..     ..|.|+||+.
T Consensus        84 ~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~-----~~v~~~wV~g  128 (166)
T 1ril_A           84 EGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP-----HRVRFHFVKG  128 (166)
T ss_dssp             SSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTT-----SEEECCCCCG
T ss_pred             hhHHHHHHhcccccccCCccCcHHHHHHHHHHHhc-----CeEEEEEeeC
Confidence            7          221       23566667666542     4799999983

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

Probab=99.28  E-value=2.2e-11  Score=100.46  Aligned_cols=102  Identities=20%  Similarity=0.230  Sum_probs=71.9

Q ss_pred             ceEEEecCCCCCC-c------eeEEEEEeeC----CeEEEEEcC-CCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcH
Q psy15595         97 FVQVYTDGSKSDS-S------VGCAFVIPQL----HIVKKQTLN-PKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSL  164 (221)
Q Consensus        97 ~~~IYTDGSK~~~-~------vG~Avi~~~~----~~~~~~kL~-~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~  164 (221)
                      .+.||||||+..+ +      .|+|+++...    .....+..+ ...+-..||+.|+..||+.+...+ .++.|+|||+
T Consensus         7 evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~~-~~v~I~TDS~   85 (165)
T 2lsn_A            7 EGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIP-GPVLVITDSF   85 (165)
T ss_dssp             SEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHSS-SCEEEEESCH
T ss_pred             eEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcCC-CeEEEEeChH
Confidence            4789999998865 2      7899987432    233444433 556678899999998888876644 5799999999


Q ss_pred             HHHHHHhCC---------CC-------CchHHHHHHHHHHhccccCceEEEEEEe
Q psy15595        165 SALQAISSM---------SH-------SNPLVQSIHEEISTGDLKNVSLNLHEVE  203 (221)
Q Consensus       165 SaL~aI~n~---------~~-------~~~ii~~I~~~i~~l~~~gi~V~l~WV~  203 (221)
                      ++++.|..+         ..       ..++.+.+.+++...    ..|.|+||+
T Consensus        86 Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~----~~v~~~~Vk  136 (165)
T 2lsn_A           86 YVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMK----PDITIQHEK  136 (165)
T ss_dssp             HHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHC----TTCEEEECC
T ss_pred             HHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCC----CCEEEEEEe
Confidence            999999631         11       236666666655432    258999997

>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=99.23  E-value=3.7e-11  Score=114.47  Aligned_cols=101  Identities=24%  Similarity=0.190  Sum_probs=76.5

Q ss_pred             CCceEEEecCCCCCC--ceeEEEEEeeCCeEEEEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHhC
Q psy15595         95 GDFVQVYTDGSKSDS--SVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS  172 (221)
Q Consensus        95 ~~~~~IYTDGSK~~~--~vG~Avi~~~~~~~~~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~n  172 (221)
                      .+.+.||||||+..+  ..|+|++....+ .....+ ..+|.+.||+.|++.||+.+    ..++.|+|||+.+++.|..
T Consensus       437 ~~~~~iytDGs~~~n~g~~g~g~v~~~~~-~~~~~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~  510 (557)
T 2zd1_A          437 VGAETFYVDGAANRETKLGKAGYVTNKGR-QKVVPL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQA  510 (557)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEETTSC-EEEEEE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTT
T ss_pred             CCCEEEEEccCCCCCCCceEEEEEEECCc-EEEecC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhc
Confidence            456899999998765  267777774333 222333 57889999999999999998    5799999999999999997


Q ss_pred             CCCC--chHHHHHHHHHHhccccCceEEEEEEecC
Q psy15595        173 MSHS--NPLVQSIHEEISTGDLKNVSLNLHEVERN  205 (221)
Q Consensus       173 ~~~~--~~ii~~I~~~i~~l~~~gi~V~l~WV~r~  205 (221)
                      +...  .++.+.+.+.+..    ...|.|+||++.
T Consensus       511 ~~~~~~~~l~~~~~~~l~~----~~~v~~~wV~~H  541 (557)
T 2zd1_A          511 QPDKSESELVNQIIEQLIK----KEKVYLAWVPAH  541 (557)
T ss_dssp             CCSEESSHHHHHHHHHHHH----CSEEEEEECCSS
T ss_pred             CCccCCHHHHHHHHHHHhc----CCCEEEEEcCCC
Confidence            6543  5677666554433    237999999994

>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=99.20  E-value=7.9e-11  Score=112.17  Aligned_cols=101  Identities=24%  Similarity=0.212  Sum_probs=77.1

Q ss_pred             CCceEEEecCCCCCCc--eeEEEEEeeCCeEEEEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHhC
Q psy15595         95 GDFVQVYTDGSKSDSS--VGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS  172 (221)
Q Consensus        95 ~~~~~IYTDGSK~~~~--vG~Avi~~~~~~~~~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~n  172 (221)
                      .+.+.||||||+..++  .|+|++....+.. ...+ ..+|...||+.|++.||+.    +..++.|+|||+.+++.|..
T Consensus       434 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~-~~~~-~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~  507 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDK-VKKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVAS  507 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEE-EEEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHT
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCCEe-eccC-CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhc
Confidence            4568999999988653  7888887544322 2333 4678999999999999998    56899999999999999997


Q ss_pred             CCC--CchHHHHHHHHHHhccccCceEEEEEEecC
Q psy15595        173 MSH--SNPLVQSIHEEISTGDLKNVSLNLHEVERN  205 (221)
Q Consensus       173 ~~~--~~~ii~~I~~~i~~l~~~gi~V~l~WV~r~  205 (221)
                      +..  ..++.+.+.+.+..    +..|.++||++.
T Consensus       508 ~~~~~~~~l~~~~~~~~~~----~~~v~~~wV~~H  538 (555)
T 1mu2_A          508 QPTESESKIVNQIIEEMIK----KEAIYVAWVPAH  538 (555)
T ss_dssp             CCSEESCHHHHHHHHHHHH----CSEEEEEECCSS
T ss_pred             ccccccHHHHHHHHHHhcc----CCcEEEEEEECC
Confidence            653  35676665555443    456999999984

>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=99.14  E-value=6.7e-11  Score=95.44  Aligned_cols=100  Identities=15%  Similarity=0.061  Sum_probs=74.5

Q ss_pred             CceEEEecCCCCCC--ceeEEEEEeeCCeEEEEEc-CCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHhC
Q psy15595         96 DFVQVYTDGSKSDS--SVGCAFVIPQLHIVKKQTL-NPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS  172 (221)
Q Consensus        96 ~~~~IYTDGSK~~~--~vG~Avi~~~~~~~~~~kL-~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~n  172 (221)
                      +.+.||||||+..+  ..|+|++....+....... ...+|...||++|++.||+.+.+.+. ++.|+|||+.++..+++
T Consensus        10 ~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~~~   88 (142)
T 1zbf_A           10 IWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWVKD   88 (142)
T ss_dssp             CSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHHHH
T ss_pred             CeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccCCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHHHc
Confidence            56789999999865  4789988843222222211 12578999999999999999988766 99999999999999985


Q ss_pred             CCC---------CchHHHHHHHHHHhccccCce
Q psy15595        173 MSH---------SNPLVQSIHEEISTGDLKNVS  196 (221)
Q Consensus       173 ~~~---------~~~ii~~I~~~i~~l~~~gi~  196 (221)
                      ...         ..++-+.|......++....+
T Consensus        89 ~~~k~~~~~~v~n~dLw~~l~~~~~w~~~~~~~  121 (142)
T 1zbf_A           89 KKAKSTLVRNEETALIWKLVDEAEEWLNTHTYE  121 (142)
T ss_dssp             TCCCCCCCCSTTTHHHHHHHHHHHHHHHHCCCC
T ss_pred             CCccCCCCCCcccHHHHHHHHHHHHHHhhCCCc
Confidence            431         236777777777766666544

>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=99.08  E-value=1.4e-10  Score=93.16  Aligned_cols=98  Identities=15%  Similarity=0.118  Sum_probs=69.7

Q ss_pred             CceEEEecCCCCCC--ceeEEEEEeeCCeE--EEEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHh
Q psy15595         96 DFVQVYTDGSKSDS--SVGCAFVIPQLHIV--KKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAIS  171 (221)
Q Consensus        96 ~~~~IYTDGSK~~~--~vG~Avi~~~~~~~--~~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~  171 (221)
                      +...||||||+..+  ..|.|+|+...+..  ....+ ..+|...||++|+..||+.+.+.+.. +.|+|||+.+++.|.
T Consensus         4 ~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~-~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi~   81 (134)
T 4htu_A            4 IWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWVK   81 (134)
T ss_dssp             CSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHHH
T ss_pred             cceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCC-CCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHHH
Confidence            44679999999876  37775555333222  22223 36889999999999999999886544 899999999999998


Q ss_pred             CCCC---------CchHHHHHHHHHHhccccCc
Q psy15595        172 SMSH---------SNPLVQSIHEEISTGDLKNV  195 (221)
Q Consensus       172 n~~~---------~~~ii~~I~~~i~~l~~~gi  195 (221)
                      +...         ..++-+.+..+...|+....
T Consensus        82 ~~~~kt~~~~~vkN~dLw~~ld~~~~~l~~~~~  114 (134)
T 4htu_A           82 DKKAKSTLVRNEETALIWKLVDEAEEWLNTHTY  114 (134)
T ss_dssp             HTCCCCCCCCSSTTHHHHHHHHHHHHHHHHCCC
T ss_pred             cCCcccCCCCCccCHHHHHHHHHHHHHHHhCCC
Confidence            5322         23777777766665555543

>1rw3_A POL polyprotein; RNA and DNA dependent DNA polymerase, reverse transcriptase, transferase, replication; 3.00A {Moloney murine leukemia virus} SCOP: e.8.1.2

Probab=83.94  E-value=0.14  Score=46.93  Aligned_cols=75  Identities=9%  Similarity=-0.021  Sum_probs=47.4

Q ss_pred             CCceEEEecCCCCCCceeEEEEEeeCC---eEEEE---EcC---CCCchhHHHHHHHHHHHHHhhh-cCCCcEEEEeCcH
Q psy15595         95 GDFVQVYTDGSKSDSSVGCAFVIPQLH---IVKKQ---TLN---PKSSIFHAELLAISDAVSTIKS-QSIGEAVIISDSL  164 (221)
Q Consensus        95 ~~~~~IYTDGSK~~~~vG~Avi~~~~~---~~~~~---kL~---~~~SIftAEl~AI~~AL~~~~~-~~~~~i~I~SDS~  164 (221)
                      .....+|||||..  ++| |++....+   ....|   ++.   ...|++..|++||..|++.... .....++|+||+.
T Consensus       344 ~~~~~l~~DAS~~--~~g-avL~q~~~~~~~~i~y~Sk~l~~~e~~ys~~ekEllAi~~a~~~~~~yl~g~~~~v~tDh~  420 (455)
T 1rw3_A          344 TKPFELFVDEKQG--YAK-GVLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVIKAPHA  420 (455)
T ss_dssp             CCTTSCEEEEEEC--SSS-BEECCBCTTTTCCCCCCCBCSCSSCSSSCCSSHHHHHHHHHHHHHHGGGCSSCEEEECSSC
T ss_pred             CCcEEEEEeccCC--cce-eEEEEecCCcEEEEEEEcccCCccccccchHHHHHHHHHHHHHHHHHHcCCCcEEEEecCh
Confidence            3446899999843  344 34432110   11111   222   3467899999999999988755 3457999999996


Q ss_pred             HHHHHHhCC
Q psy15595        165 SALQAISSM  173 (221)
Q Consensus       165 SaL~aI~n~  173 (221)
                       ++..+.+.
T Consensus       421 -~~~~l~~~  428 (455)
T 1rw3_A          421 -VEALVKQP  428 (455)
T ss_dssp             -TTTTSSST
T ss_pred             -HHHHhCCC
Confidence             66555544

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	221
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.53
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.5
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.35
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.31
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.31

>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=99.53  E-value=3.6e-14  Score=108.05  Aligned_cols=100  Identities=26%  Similarity=0.200  Sum_probs=71.9

Q ss_pred             CCceEEEecCCCCCC-c-eeEEEEEeeCCeEEEEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHhC
Q psy15595         95 GDFVQVYTDGSKSDS-S-VGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS  172 (221)
Q Consensus        95 ~~~~~IYTDGSK~~~-~-vG~Avi~~~~~~~~~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~n  172 (221)
                      .+...+|||||+..+ + .|+|++..+. ......+ ..+|...||++||++||+.    ...++.|+|||++++.++..
T Consensus         6 ~~~~t~ytDGs~~~n~~~g~~g~~~~~~-~~~~~~~-~~~TNn~aEl~Avi~aL~~----~~~~v~I~TDS~yvi~~i~~   79 (110)
T d1s1ta1           6 VGAETFYVDGAANRETKLGKAGYVTNRG-RQKVVTL-TDTTNQKTELQAIYLALQD----SGLEVNIVTDSQYALGIIQA   79 (110)
T ss_dssp             TTSEEEEEEEEEETTTTEEEEEEEETTS-CEEEEEE-SSCCHHHHHHHHHHHHHHH----SCSEEEEEECCHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCCCcEEEEEEecC-CeEEEec-ccCcHHHHHHHHHHHHHHh----CCCeEEEEEehHHHHHHHhc
Confidence            355679999997654 3 4555555333 2333344 4678999999999999985    35689999999999999996


Q ss_pred             CCC--CchHHHHHHHHHHhccccCceEEEEEEec
Q psy15595        173 MSH--SNPLVQSIHEEISTGDLKNVSLNLHEVER  204 (221)
Q Consensus       173 ~~~--~~~ii~~I~~~i~~l~~~gi~V~l~WV~r  204 (221)
                      ...  ..++..+|.+.+...    -.|.++|||.
T Consensus        80 ~~~~~~~~l~~~il~~l~~~----~~v~i~WVpg  109 (110)
T d1s1ta1          80 QPDQSESELVNQIIEQLIKK----EKVYLAWVPA  109 (110)
T ss_dssp             CCSEESCHHHHHHHHHHHHC----SEEEEEECCS
T ss_pred             CccccchHHHHHHHHHHhcC----CceEEEEeCC
Confidence            543  457777766655432    3589999984

>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=99.50  E-value=5.6e-14  Score=107.82  Aligned_cols=99  Identities=25%  Similarity=0.230  Sum_probs=69.1

Q ss_pred             CCceEEEecCCCCCC-c-eeEEEEEeeCCeEEEEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHhC
Q psy15595         95 GDFVQVYTDGSKSDS-S-VGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISS  172 (221)
Q Consensus        95 ~~~~~IYTDGSK~~~-~-vG~Avi~~~~~~~~~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~n  172 (221)
                      .+...||||||+..+ + .|+|+++++.. .....++ .+|.++||+.||++||+.    ...++.|+|||+++++.+.+
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~~-~~~~~~~-~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v~~~~~~   78 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRGK-DKVKKLE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVAS   78 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSC-EEEEEES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHT
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCCC-EEEEecC-CCcchHHHHHHHHHHhcc----CCcceEEEechHHHHHHHhc
Confidence            345689999997654 3 55666664333 3334444 678999999999999986    35789999999999999997


Q ss_pred             CCCC--chHH-HHHHHHHHhccccCceEEEEEEec
Q psy15595        173 MSHS--NPLV-QSIHEEISTGDLKNVSLNLHEVER  204 (221)
Q Consensus       173 ~~~~--~~ii-~~I~~~i~~l~~~gi~V~l~WV~r  204 (221)
                      ....  .... +.++....     ...|.|+||+.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~-----~~~v~~~wV~g  108 (126)
T d1mu2a1          79 QPTESESKIVNQIIEEMIK-----KEAIYVAWVPA  108 (126)
T ss_dssp             CCSEESCHHHHHHHHHHHH-----CSEEEEEECCS
T ss_pred             CCccccchHHHHHHHHhhh-----cceeEEEEEeC
Confidence            6542  3333 33333322     24789999995

>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=99.35  E-value=1.6e-12  Score=100.90  Aligned_cols=101  Identities=19%  Similarity=0.187  Sum_probs=71.2

Q ss_pred             ceEEEecCCCCCC--ceeEEEEEeeCCeEEEEE-cCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHhCC
Q psy15595         97 FVQVYTDGSKSDS--SVGCAFVIPQLHIVKKQT-LNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSM  173 (221)
Q Consensus        97 ~~~IYTDGSK~~~--~vG~Avi~~~~~~~~~~k-L~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~n~  173 (221)
                      .+.||||||+.++  ..|+|+++.+.+....+. ....+|..+||++||..||+++..  ...+.|.|||+.++..+...
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~~--~~~i~i~tds~~~i~~~~~~   79 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQW   79 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHTT
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhcc--cceEEEeecceeeEEcccch
Confidence            3789999998876  488888886665544332 234567899999999999998643  56789999999999888533


Q ss_pred             C---------C-------CchHHHHHHHHHHhccccCceEEEEEEec
Q psy15595        174 S---------H-------SNPLVQSIHEEISTGDLKNVSLNLHEVER  204 (221)
Q Consensus       174 ~---------~-------~~~ii~~I~~~i~~l~~~gi~V~l~WV~r  204 (221)
                      .         .       ..++.+.|..+..     ...|.|+||+-
T Consensus        80 ~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~-----~~~V~~~wV~g  121 (152)
T d1jl1a_          80 IHNWKKRGWKTADKKPVKNVDLWQRLDAALG-----QHQIKWEWVKG  121 (152)
T ss_dssp             HHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT-----TCEEEEEECCS
T ss_pred             hhHhHhccchhcccCeeecHHHHHHHHHHhh-----cceeEEEEecc
Confidence            1         0       1234444444322     34799999983

>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=99.31  E-value=1.3e-12  Score=102.94  Aligned_cols=104  Identities=14%  Similarity=0.069  Sum_probs=77.3

Q ss_pred             EEEecCCCCCC--ceeEEEEEeeCCeEEEEEc-CCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHhCCCC
Q psy15595         99 QVYTDGSKSDS--SVGCAFVIPQLHIVKKQTL-NPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSH  175 (221)
Q Consensus        99 ~IYTDGSK~~~--~vG~Avi~~~~~~~~~~kL-~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~n~~~  175 (221)
                      .||||||+..+  ..|.|+|+...+....++- -..+|..+||++|+..||+++.+.+ .++.|+|||+.++..++++..
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~~   84 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKKA   84 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTCC
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCce
Confidence            48999999976  3788888755444433332 1467899999999999999997755 579999999999999985432


Q ss_pred             ---------CchHHHHHHHHHHhccccCceEEEEEEecC
Q psy15595        176 ---------SNPLVQSIHEEISTGDLKNVSLNLHEVERN  205 (221)
Q Consensus       176 ---------~~~ii~~I~~~i~~l~~~gi~V~l~WV~r~  205 (221)
                               ..++.+.|.+....++.+.  +.+.||.-+
T Consensus        85 kt~~~~~vkN~~l~~~i~~a~~~lk~h~--~~~~~~KW~  121 (132)
T d1zbfa1          85 KSTLVRNEETALIWKLVDEAEEWLNTHT--YETPILKWQ  121 (132)
T ss_dssp             CCCCCCSTTTHHHHHHHHHHHHHHHHCC--CCCCEEECC
T ss_pred             ecCcCCCcccHHHHHHHHHHHHHHHhCC--cCceeEEec
Confidence                     2467778887777777665  455666554

>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=99.31  E-value=6.9e-13  Score=103.51  Aligned_cols=100  Identities=17%  Similarity=0.097  Sum_probs=69.3

Q ss_pred             ceEEEecCCCCCC--ceeEEEEEeeCCe-EEEEEcCCCCchhHHHHHHHHHHHHHhhhcCCCcEEEEeCcHHHHHHHhCC
Q psy15595         97 FVQVYTDGSKSDS--SVGCAFVIPQLHI-VKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSM  173 (221)
Q Consensus        97 ~~~IYTDGSK~~~--~vG~Avi~~~~~~-~~~~kL~~~~SIftAEl~AI~~AL~~~~~~~~~~i~I~SDS~SaL~aI~n~  173 (221)
                      .+.||||||+..+  ..|+|+++...+. ...+.....+|..+||++||++||+++.  ....+.|+|||+.++..+...
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~--~~~~i~i~tds~~~~~~~~~~   80 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALK--EPCEVDLYTDSHYLKKAFTEG   80 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCC--SCCEEEEECCCHHHHHHHHSS
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhcc--CCceEEEecchhhhhcccccc
Confidence            4789999999876  3778887743332 2222223456899999999999999864  356899999999999988542


Q ss_pred             CC-----------------CchHHHHHHHHHHhccccCceEEEEEEe
Q psy15595        174 SH-----------------SNPLVQSIHEEISTGDLKNVSLNLHEVE  203 (221)
Q Consensus       174 ~~-----------------~~~ii~~I~~~i~~l~~~gi~V~l~WV~  203 (221)
                      ..                 ..++.+.|..+.   +  ...|.|+||+
T Consensus        81 ~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~---~--~~~v~~~wVk  122 (147)
T d1rila_          81 WLEGWRKRGWRTAEGKPVKNRDLWEALLLAM---A--PHRVRFHFVK  122 (147)
T ss_dssp             HHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH---T--TSEEECCCCC
T ss_pred             chhhhhhccccccccccchhHHHHHHHHHHh---h--hcccceEEcc
Confidence            10                 124555554433   2  3469999997