Psyllid ID: psy5610

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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-------
Protein Sequence
MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLHQIKLENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVISVKHILTDCQTHSNIRAPLNLSSTLLSCLKDNDISPILEFLRRTQIKI
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHHccccccccEEEEEEcHHHHHHHHHccccccHHHHHHHHHHHHccccccEEEEEEcccccccccHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccHHccccccHHHHccccccccHHHHcccccHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHHHHHHcccccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHcccHHHHHHHcccccccccccccccccEEEEEEccHHHHHHHHHHccccHHHHHcccccHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIfslnpiagEIRDLILTNKSKLNVRFiwvpshvgiagNEEADRLAKEAltsthptinkipipdykaysKRKILSAWNSEWHNLQNNKLHQiklenkpwnppylinrkeqVSLTRLRIGHTNTTHihlmkkenppicvpcgcvisvkhiltdcqthsniraplnLSSTLLsclkdndispILEFLRRTQIKI
Flexible Loop (DISEMBL)
MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEaltsthptinkipipdykaYSKRKILSAWNSEWHNLQNNKLHQIKLENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVISVKHILTDCQTHSNIRAPLNLSSTLLSClkdndispileflrrtqiki
Low Complexity Region (SEG)
MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLHQIKLENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVISVKHILTDCQTHSNIRAPLNLSSTLLSCLKDNDISPILEFLRRTQIKI
Disordered region (IsUnstruct)
****VLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLHQIKLENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVISVKHILTDCQTHSNIRAPLNLSSTLLSCLKDNDISPILEFLR******
Disordered Region (DISOPRED)
MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFS**PIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLHQIKLENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVISVKHILTDCQTHSNIRAPLNL***LL*CLKDNDISPILEFLRRTQIKI
Disordered Region (DISEMBL)
MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLHQIKLENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVISVKHILTDCQTHSNIRAPLNLSSTLLSCLKDNDISPILEFLRRTQIKI
Disordered Region (DISPRO)
*ATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLHQIKLENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVISVKHILTDCQTHSNIRAPLNLSSTLLSCLKDNDISPILEFLRRTQIKI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLHQIKLENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVISVKHILTDCQTHSNIRAPLNLSSTLLSCLKDNDISPILEFLRRTQIKI
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	237
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.683	0.620	0.452	7e-30
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.683	0.322	0.447	1e-29
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.843	0.424	0.376	7e-29
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.928	0.180	0.355	2e-28
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.827	0.493	0.387	2e-27
443724607	397	hypothetical protein CAPTEDRAFT_208903 [	0.683	0.408	0.429	6e-26
427798889	1199	Putative tick transposon, partial [Rhipi	0.827	0.163	0.391	1e-24
427791321	1210	Putative tick transposon, partial [Rhipi	0.691	0.135	0.402	1e-24
427791807	1212	Putative tick transposon, partial [Rhipi	0.691	0.135	0.402	1e-24
443733872	400	hypothetical protein CAPTEDRAFT_197082 [	0.573	0.34	0.408	3e-24

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

 Score =  136 bits (342), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 77/170 (45%), Positives = 103/170 (60%), Gaps = 8/170 (4%)

Query: 33  ICSDSLSALQTLQNIFSLNPIAGEI--RDLILTNKSKLNVRFIWVPSHVGIAGNEEADRL 90
           ICSDSLS+L  L N    +P    I  +   L  K KL V FIW PSHVGI GNE ADRL
Sbjct: 96  ICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKL-VVFIWCPSHVGILGNEVADRL 154

Query: 91  AKEALTSTHPTINKIPIP--DYKAYSKRKILSAWNSEWHNLQNNKLHQIKLENKPWNPPY 148
           AK+AL      + K+P+P  DYK+  +  + S W +EW    +NKLH I+     W    
Sbjct: 155 AKQALVMP---VTKLPLPHTDYKSPIRSYVKSLWQNEWDEETDNKLHSIQPVISEWKQGP 211

Query: 149 LINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVISVKHILTDC 198
            I+R+ ++ L R RIGH++ TH +L+++E  P C+PC  ++SVKHIL DC
Sbjct: 212 QIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLSVKHILIDC 261

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 =  135 bits (341), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 76/170 (44%), Positives = 103/170 (60%), Gaps = 8/170 (4%)

Query: 33  ICSDSLSALQTLQNIFSLNPIAGEI--RDLILTNKSKLNVRFIWVPSHVGIAGNEEADRL 90
           ICSDSLS+L  L N    +P    I  +   L  K KL V FIW PSHVGI GNE ADRL
Sbjct: 142 ICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKL-VVFIWCPSHVGILGNEVADRL 200

Query: 91  AKEALTSTHPTINKIPIP--DYKAYSKRKILSAWNSEWHNLQNNKLHQIKLENKPWNPPY 148
           AK+AL      + K+P+P  DYK+  +  + S W +EW    +NKLH I+     W    
Sbjct: 201 AKQALVMP---VTKLPLPHTDYKSPIRSYVKSLWQNEWDEETDNKLHSIQPVISEWKQGP 257

Query: 149 LINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVISVKHILTDC 198
            I+R+ ++ L R RIGH++ TH +L+++E  P C+PC  +++VKHIL DC
Sbjct: 258 QIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILIDC 307

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  133 bits (334), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 78/207 (37%), Positives = 116/207 (56%), Gaps = 7/207 (3%)

Query: 1   MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDL 60
           M+    E+ AIL A+        +N    + VICSDSLSA+  +  +   +P   ++   
Sbjct: 53  MSVFTSEIIAILSALR---CVEADNEQHQF-VICSDSLSAIMAIHGMDVRHPYVLQVLYA 108

Query: 61  I--LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKI 118
           I  ++ + K+ V F+W PSHVGI GNE AD LAKEAL+ST+     +P  D +   K+ I
Sbjct: 109 IKSISQQEKIVV-FMWCPSHVGIPGNEMADTLAKEALSSTNLAELPVPASDLRCLIKKYI 167

Query: 119 LSAWNSEWHNLQNNKLHQIKLENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKEN 178
            S W  EW    +NKLH I     PW P     R+E++ L R+RIGHT+ TH ++ + ++
Sbjct: 168 RSRWQHEWDEQHSNKLHSIHPTIGPWPPCQREKRREEIVLARIRIGHTHYTHDYIPRGDD 227

Query: 179 PPICVPCGCVISVKHILTDCQTHSNIR 205
              CV C C ++V+HI+ +C    +IR
Sbjct: 228 QTECVACVCPLTVQHIIIECADFLHIR 254

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  132 bits (331), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 80/225 (35%), Positives = 122/225 (54%), Gaps = 5/225 (2%)

Query: 8    LTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGE-IRDLILTNKS 66
             TA L AI  ++ A +    R+  +ICSDS SALQ L  + +  P+  + ++ L L    
Sbjct: 992  FTAELHAILLALMA-VKASERSKFIICSDSKSALQALGRMKTDIPLVHKSLKLLDLITAD 1050

Query: 67   KLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWNSEW 126
            + +V FIWVPSHVGI GNE ADR AK AL     +  +IP  D +          W + W
Sbjct: 1051 RRDVTFIWVPSHVGIEGNEAADREAKRALNHA-VSGTQIPYSDLRQSIASATYREWQNRW 1109

Query: 127  HNLQNNKLHQIKLENKPWNP-PYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPC 185
                ++KL QI  + + W P    + R+   +++RLRIGHT  TH  ++K+E PP+C  C
Sbjct: 1110 EAETHSKLRQIVADVR-WRPTSKGLTRRGSTTMSRLRIGHTYITHSFVLKREEPPLCEYC 1168

Query: 186  GCVISVKHILTDCQTHSNIRAPLNLSSTLLSCLKDNDISPILEFL 230
               ++V+HIL DC  + ++RA    ++ L +   + D   +L F+
Sbjct: 1169 DSRLTVEHILVDCPRYQDVRAKHFRATNLKTLFNNVDPGKVLGFI 1213

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

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

 Score =  128 bits (321), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 79/204 (38%), Positives = 111/204 (54%), Gaps = 8/204 (3%)

Query: 33  ICSDSLSALQTLQNIFSLNPIAGEI--RDLILTNKSKLNVRFIWVPSHVGIAGNEEADRL 90
           ICSDSLS+L  L N    +P    I  +   L  K K  V FIW PSHVGI GNE ADR 
Sbjct: 191 ICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGK-KVVFIWCPSHVGILGNEVADRQ 249

Query: 91  AKEALTSTHPTINKIPIP--DYKAYSKRKILSAWNSEWHNLQNNKLHQIKLENKPWNPPY 148
           AK+AL      + K+P+P  DYK+  +  + S W +EW    +NKLH I+     W    
Sbjct: 250 AKQALVMP---VTKLPLPHTDYKSPIRSYVKSLWQNEWDGETDNKLHIIQPVISEWKQGP 306

Query: 149 LINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVISVKHILTDCQTHSNIRAPL 208
            I+R+ ++ L   RIGH++ TH +L+++E  P C+PC  +++VKHIL DC      R   
Sbjct: 307 QIDRRGEIVLACARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILIDCIDFEISRRKY 366

Query: 209 NLSSTLLSCLKDNDISPILEFLRR 232
               ++    +D   S IL +L+ 
Sbjct: 367 FNVFSMRQLFEDTHPSKILLYLKE 390

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  123 bits (309), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 73/170 (42%), Positives = 100/170 (58%), Gaps = 8/170 (4%)

Query: 33  ICSDSLSALQTLQNIFSLNPIAGEI--RDLILTNKSKLNVRFIWVPSHVGIAGNEEADRL 90
           ICSDSLS+L  L N    +P    I  +   L  K KL V FIW PSHVGI GNE ADRL
Sbjct: 191 ICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKL-VVFIWCPSHVGILGNEVADRL 249

Query: 91  AKEALTSTHPTINKIPIP--DYKAYSKRKILSAWNSEWHNLQNNKLHQIKLENKPWNPPY 148
           AK+AL      + K+P+P  DYK+  +  + S   +EW    +NKLH I+     W    
Sbjct: 250 AKQALVMP---VTKLPLPHTDYKSPIRSYVKSLRQNEWDEETDNKLHTIQPVISEWKQGP 306

Query: 149 LINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVISVKHILTDC 198
            I+R+ ++ L    IGH++ TH +L+++E  P C+PC  +++VKHIL DC
Sbjct: 307 QIDRRGEIVLACACIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILIDC 356

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 =  119 bits (297), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 79/202 (39%), Positives = 109/202 (53%), Gaps = 6/202 (2%)

Query: 9    TAILFAIHFSISA---HLNNVNRAYLVICSDSLSALQTLQNIFS-LNPIAGEIRDLILT- 63
            T+I  A  ++I A   H+  +     VI +DSLS ++ L+ +    NP+   +  L+ T 
Sbjct: 994  TSIFTAEAYAILAAVKHIRELKLQKAVIYTDSLSVVKALKTLKKHRNPVLVSLYSLLCTI 1053

Query: 64   NKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSAWN 123
              SK +V   WVP H  I GN  AD+LA  A  S+  T   IP  D K Y KRKI + W 
Sbjct: 1054 YTSKQHVVVCWVPGHREIQGNVMADQLAVSAHDSSANTSIAIPALDLKPYLKRKIRAYWQ 1113

Query: 124  SEWHNLQNNKLHQIKLENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICV 183
            S W    +NKLH IK +   W PP   +R  +V+LTRLR GHT++TH +L+   + P C 
Sbjct: 1114 STWDRQTHNKLHVIKPQLGHW-PPISKSRYTEVTLTRLRTGHTHSTHAYLLSGGDAPFCD 1172

Query: 184  PCGCVISVKHILTDCQTHSNIR 205
             CG  ++V HIL  C+    IR
Sbjct: 1173 KCGEPLTVIHILIQCRGLDAIR 1194

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 =  119 bits (297), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 68/169 (40%), Positives = 97/169 (57%), Gaps = 5/169 (2%)

Query: 32   VICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLA 91
            +I +DSLSAL+ L       P+ G+I +++L N   +++RF WVPSHVGI GNE+AD+ A
Sbjct: 995  IIYTDSLSALKALHIKSECEPLVGDILNMVLINSKVISMRFCWVPSHVGIPGNEKADKCA 1054

Query: 92   KEALTSTHPTINKIPIP--DYKAYSKRKILSAWNSEWHNLQNNKLHQIKLENKPWNPPYL 149
              A    H T+ KI IP  D +   +  +L+ W  +W +  +NKLH +K     W     
Sbjct: 1055 SLA---AHKTLTKIRIPLKDSQRTIRLALLAKWQQQWDSCTSNKLHLVKPTLGEWKNCRH 1111

Query: 150  INRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVISVKHILTDC 198
              R  +V L RLRIGHT+ TH  L+ KE  P+C  C   +++ HIL  C
Sbjct: 1112 QERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCEKCQEPLTLIHILILC 1160

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 =  119 bits (297), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 68/169 (40%), Positives = 97/169 (57%), Gaps = 5/169 (2%)

Query: 32   VICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLA 91
            +I +DSLSAL+ L       P+ G+I +++L N   +++RF WVPSHVGI GNE+AD+ A
Sbjct: 998  IIYTDSLSALKALHIKSECEPLVGDILNMVLINSKVISMRFCWVPSHVGIPGNEKADKCA 1057

Query: 92   KEALTSTHPTINKIPIP--DYKAYSKRKILSAWNSEWHNLQNNKLHQIKLENKPWNPPYL 149
              A    H T+ KI IP  D +   +  +L+ W  +W +  +NKLH +K     W     
Sbjct: 1058 SLA---AHKTLTKIRIPLKDSQRTIRLALLAKWQQQWDSCTSNKLHLVKPTLGEWKNCRH 1114

Query: 150  INRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVISVKHILTDC 198
              R  +V L RLRIGHT+ TH  L+ KE  P+C  C   +++ HIL  C
Sbjct: 1115 QERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCEKCQEPLTLIHILILC 1163

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443733872|gb|ELU18078.1| hypothetical protein CAPTEDRAFT_197082 [Capitella teleta]

 Score =  117 bits (294), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 56/137 (40%), Positives = 84/137 (61%), Gaps = 1/137 (0%)

Query: 62  LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKRKILSA 121
           L +K  +++   W PSHVG+ GNE AD LAKEAL+ T  TI +IP  D+K  +       
Sbjct: 93  LLHKKGIDLVMTWCPSHVGVMGNERADLLAKEALSFTTCTI-RIPSSDFKPITHEFYKEK 151

Query: 122 WNSEWHNLQNNKLHQIKLENKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPI 181
           W  +W + Q NKL+ I+     W       R+E++ L R RIGH++ TH +L+++E PP+
Sbjct: 152 WQEQWSSEQENKLYCIQPTLGKWAKSSREIRREEIVLARARIGHSHLTHGYLLRREMPPV 211

Query: 182 CVPCGCVISVKHILTDC 198
           C+PC  ++S+KHI  +C
Sbjct: 212 CIPCQNILSIKHIFIEC 228

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

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)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	237
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.818	0.399	0.279	6.8e-10

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

 Score = 162 (62.1 bits), Expect = 6.8e-10, P = 6.8e-10
 Identities = 60/215 (27%), Positives = 102/215 (47%)

Query:     5 VLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNP---IAGEIRDLI 61
             V EL  IL A+   +   + +      VI +D+ + LQ L+N  S +    +   I  L 
Sbjct:   223 VAELQGILLALVIILQRQMQHA-----VIFTDNQATLQALRNPGSQSGQYILEAIIMALN 277

Query:    62 LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKR--KIL 119
                K+ LNV F W+P+H G+ GNE+ADR AKEA        ++  +    A  +R  +++
Sbjct:   278 KGRKAGLNVHFRWIPAHRGVEGNEQADRRAKEATGWRRIRGHRGRMTIRSAVKRRAHEVV 337

Query:   120 SA-WNSEWHNLQNNK-LHQIKLE--NKPWNPPYLINRKEQVSLTRLRIGHTNTTHIHLMK 175
             +A W ++W +  + + L+++      K       ++R     + ++R G     H +L +
Sbjct:   338 NARWENDWKSCHHGRELYELTPTPTRKVLRVHQDLHRALSTIIVQMRTGKIGLRH-YLYQ 396

Query:   176 KENPPI----CVPCG-CVISVKHILTDCQTHSNIR 205
             +  P +    C  CG    SV+HIL  C T S +R
Sbjct:   397 RGVPDVPNSDC-QCGRATQSVRHILLACPTFSGLR 430


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        0.320   0.134   0.403    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      237       237   0.00090  113 3  11 22  0.40    33
                                                     32  0.43    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  614 (65 KB)
  Total size of DFA:  198 KB (2112 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:  22.43u 0.06s 22.49t   Elapsed:  00:00:18
  Total cpu time:  22.43u 0.06s 22.49t   Elapsed:  00:00:19
  Start:  Thu Aug 15 12:34:07 2013   End:  Thu Aug 15 12:34:26 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	LOW CONFIDENCE prediction!
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	237
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	4e-23
pfam00075	126	pfam00075, RNase_H, RNase H	6e-13
cd09277	133	cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI	2e-09
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	6e-09
cd09278	139	cd09278, RNase_HI_prokaryote_like, RNase HI family	2e-06
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	1e-05
cd09279	128	cd09279, RNase_HI_archaeal_like, RNAse HI family t	3e-04
PRK00203	150	PRK00203, rnhA, ribonuclease H; Reviewed	0.001
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	0.001
pfam13456	88	pfam13456, RVT_3, Reverse transcriptase-like	0.003

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

 Score = 90.4 bits (225), Expect = 4e-23
 Identities = 37/89 (41%), Positives = 47/89 (52%), Gaps = 4/89 (4%)

Query: 7   ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIR-DLILTNK 65
           EL AIL A+     A         + I SDS +AL+ L++  S +P+   IR  +     
Sbjct: 41  ELLAILEALQL---ALREGRRARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELAN 97

Query: 66  SKLNVRFIWVPSHVGIAGNEEADRLAKEA 94
             + VR  WVP H GI GNE ADRLAKEA
Sbjct: 98  HGVKVRLHWVPGHSGIEGNERADRLAKEA 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 = 63.4 bits (155), Expect = 6e-13
 Identities = 29/95 (30%), Positives = 38/95 (40%), Gaps = 15/95 (15%)

Query: 5   VLELTAILFAIHFSISAHLNNVNRAYLVICSDSL----SALQTLQNIFSLNPIAGEIRDL 60
             EL A++ A+       +N        I +DS                  PI  EI +L
Sbjct: 42  RAELLALIEALEALSGQKVN--------IYTDSQYVIGGITNGWPTKSESKPIKNEIWEL 93

Query: 61  ILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
           +     K  V   WVP H GI GNE AD+LAK+  
Sbjct: 94  LQ---KKHKVYIQWVPGHSGIPGNELADKLAKQGA 125

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

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

 Score = 53.7 bits (130), Expect = 2e-09
 Identities = 16/45 (35%), Positives = 25/45 (55%)

Query: 51  NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
                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|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 = 53.0 bits (128), Expect = 6e-09
 Identities = 32/108 (29%), Positives = 49/108 (45%), Gaps = 24/108 (22%)

Query: 7   ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTL--------QNIFSLNPIAGEI- 57
           EL A++ A+   I      + +  LVI +DS   +  +        +N +  +   G+  
Sbjct: 47  ELRAVIHALRL-IKEVGEGLTK--LVIATDSEYVVNGVTEWIPKWKKNGWKTS--KGKPV 101

Query: 58  --RDLIL--------TNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
             +DLI           +  + V+F  VP H GI GNEEADRLAK+  
Sbjct: 102 ANKDLIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGA 149

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

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

 Score = 45.6 bits (109), Expect = 2e-06
 Identities = 14/29 (48%), Positives = 16/29 (55%)

Query: 66  SKLNVRFIWVPSHVGIAGNEEADRLAKEA 94
           +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|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 27/90 (30%), Positives = 42/90 (46%), Gaps = 10/90 (11%)

Query: 7   ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN-IFSLNPIAGEIRDLILTNK 65
           EL A+L A+   ++  L       L+I +DS   +  + +           + D++L   
Sbjct: 43  ELLALLEAL--ELALDLGLKK---LIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLS 97

Query: 66  SKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
             +++RF  VP      GNE ADRLAKEA 
Sbjct: 98  KFIDIRFEHVPRE----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|187703 cd09279, RNase_HI_archaeal_like, RNAse HI family that includes Archaeal RNase HI

 Score = 39.0 bits (92), Expect = 3e-04
 Identities = 24/95 (25%), Positives = 38/95 (40%), Gaps = 17/95 (17%)

Query: 7   ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF-----SLNPIAGEIRDLI 61
           E  A++  +  ++   +       L I  DS   +  +Q  +      L P   E R+L+
Sbjct: 46  EYEALIAGLELALELGIKK-----LEIYGDSQLVVNQIQGEYEVKNERLAPYLEEARELL 100

Query: 62  LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALT 96
              K    V   W+P       N+EAD LA +AL 
Sbjct: 101 ---KKFEEVEIKWIPRE----ENKEADALANQALD 128

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

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

 Score = 38.3 bits (90), Expect = 0.001
 Identities = 9/26 (34%), Positives = 13/26 (50%)

Query: 69  NVRFIWVPSHVGIAGNEEADRLAKEA 94
            +++ WV  H G   NE  D LA+  
Sbjct: 114 QIKWHWVKGHAGHPENERCDELARAG 139

Length = 150

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 15/37 (40%), Positives = 19/37 (51%)

Query: 58  RDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEA 94
            +L    K    V + WV  H G   NE AD+LA+EA
Sbjct: 106 EELDELLKRHELVFWEWVKGHAGHPENERADQLAREA 142

Length = 154

>gnl|CDD|205634 pfam13456, RVT_3, Reverse transcriptase-like

 Score = 35.6 bits (83), Expect = 0.003
 Identities = 26/97 (26%), Positives = 39/97 (40%), Gaps = 16/97 (16%)

Query: 5  VLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNI-FSLNPIAG---EIRDL 60
            E  A+L  +  ++   +       L++ SDS   +Q +Q    + + +A    EIR L
Sbjct: 4  EAEAEALLEGLQLALELGIRR-----LIVESDSQLVVQQIQGEYEARSRLAALLREIRKL 58

Query: 61 ILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS 97
          +    S   V    VP       N  AD LAK A  S
Sbjct: 59 LKKFDS---VSVSHVPRE----CNRVADALAKLASAS 88

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	237
PRK06548	161	ribonuclease H; Provisional	99.78
PRK08719	147	ribonuclease H; Reviewed	99.73
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.72
PRK00203	150	rnhA ribonuclease H; Reviewed	99.71
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.71
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.56
KOG3752|consensus	371		99.4
PRK13907	128	rnhA ribonuclease H; Provisional	99.38
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.31
PRK07708	219	hypothetical protein; Validated	99.17
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	98.99
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	96.87

>PRK06548 ribonuclease H; Provisional

Probab=99.78  E-value=1.3e-18  Score=136.78  Aligned_cols=91  Identities=29%  Similarity=0.333  Sum_probs=72.0

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhc---------ccC--CChHH-HHHHHHHHHhhcCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN---------IFS--LNPIA-GEIRDLILTNKSKL   68 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~---------~~~--~~~~~-~~i~~~~~~l~~~~   68 (237)
                      ++|++||+.|++.||+.+     . .....|.|+|||++++++++.         |+.  ..|+. +++.+.+..+.+..
T Consensus        40 ~TNnraEl~Aii~aL~~~-----~-~~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~  113 (161)
T PRK06548         40 ATNNIAELTAVRELLIAT-----R-HTDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENR  113 (161)
T ss_pred             CCHHHHHHHHHHHHHHhh-----h-cCCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcC
Confidence            479999999999999863     2 234579999999999999994         222  23444 45555555555566


Q ss_pred             cEEEEEecCCCCCcCChHHHHHHHHhhhc
Q psy5610          69 NVRFIWVPSHVGIAGNEEADRLAKEALTS   97 (237)
Q Consensus        69 ~v~~~wvp~H~g~~gNe~ad~~a~~a~~~   97 (237)
                      .|+|.|||||+|..|||.||.||++++..
T Consensus       114 ~v~~~wVkgHsg~~gNe~aD~LA~~aa~~  142 (161)
T PRK06548        114 NIRMSWVNAHTGHPLNEAADSLARQAANN  142 (161)
T ss_pred             ceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence            79999999999999999999999999877

>PRK08719 ribonuclease H; Reviewed

Probab=99.73  E-value=2.3e-17  Score=128.34  Aligned_cols=87  Identities=29%  Similarity=0.342  Sum_probs=67.4

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhc---------ccCCC--hHH-HHHHHHHHHhhcCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN---------IFSLN--PIA-GEIRDLILTNKSKL   68 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~---------~~~~~--~~~-~~i~~~~~~l~~~~   68 (237)
                      ++|++||+.|++.||+.+.     .    ...|+|||++++++++.         |...+  ++. .+++..+..+....
T Consensus        48 ~Tnn~aEl~A~~~aL~~~~-----~----~~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~  118 (147)
T PRK08719         48 TDNAELELLALIEALEYAR-----D----GDVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARK  118 (147)
T ss_pred             ccHHHHHHHHHHHHHHHcC-----C----CCEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCC
Confidence            3799999999999999952     2    13799999999999843         22221  222 34555556565667


Q ss_pred             cEEEEEecCCCCCcCChHHHHHHHHhhh
Q psy5610          69 NVRFIWVPSHVGIAGNEEADRLAKEALT   96 (237)
Q Consensus        69 ~v~~~wvp~H~g~~gNe~ad~~a~~a~~   96 (237)
                      +|+|.|||||+|++||+.||+||+.|+.
T Consensus       119 ~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719        119 YVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             cEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            7999999999999999999999999875

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

Probab=99.72  E-value=1.1e-17  Score=129.43  Aligned_cols=92  Identities=22%  Similarity=0.310  Sum_probs=72.7

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccC----CC-------hH-HHHHHHHHHHhhcC-
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFS----LN-------PI-AGEIRDLILTNKSK-   67 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~----~~-------~~-~~~i~~~~~~l~~~-   67 (237)
                      ++|++||+.|++.||+++     ...+...|.|+|||++++++|+.|..    .+       |+ ..++++.+..+.+. 
T Consensus        41 tTNNraEl~A~i~AL~~l-----~~~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~  115 (154)
T COG0328          41 TTNNRAELRALIEALEAL-----KELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRH  115 (154)
T ss_pred             ccChHHHHHHHHHHHHHH-----HhcCCceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhC
Confidence            589999999999999995     44577899999999999999995422    11       11 12344444444444 


Q ss_pred             CcEEEEEecCCCCCcCChHHHHHHHHhhhc
Q psy5610          68 LNVRFIWVPSHVGIAGNEEADRLAKEALTS   97 (237)
Q Consensus        68 ~~v~~~wvp~H~g~~gNe~ad~~a~~a~~~   97 (237)
                      ..|.+.|||||.|.++||.||+||+.++..
T Consensus       116 ~~v~~~WVkgH~g~~~NeraD~LA~~~~~~  145 (154)
T COG0328         116 ELVFWEWVKGHAGHPENERADQLAREAARA  145 (154)
T ss_pred             CeEEEEEeeCCCCChHHHHHHHHHHHHHHh
Confidence            489999999999999999999999999877

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.71  E-value=3.7e-17  Score=127.84  Aligned_cols=90  Identities=19%  Similarity=0.319  Sum_probs=69.8

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhccc---------C--CChHH-HHHHHHHHHhhcCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF---------S--LNPIA-GEIRDLILTNKSKL   68 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~---------~--~~~~~-~~i~~~~~~l~~~~   68 (237)
                      .+|++||+.|++.||+.+     .  ....+.|+|||++++++|..+.         .  ..++. .++.+.+.++....
T Consensus        41 ~TN~~aEL~Ai~~AL~~~-----~--~~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~  113 (150)
T PRK00203         41 TTNNRMELMAAIEALEAL-----K--EPCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRH  113 (150)
T ss_pred             CcHHHHHHHHHHHHHHHc-----C--CCCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhccC
Confidence            478999999999999984     2  2357999999999999999632         1  12332 23334444444556


Q ss_pred             cEEEEEecCCCCCcCChHHHHHHHHhhhc
Q psy5610          69 NVRFIWVPSHVGIAGNEEADRLAKEALTS   97 (237)
Q Consensus        69 ~v~~~wvp~H~g~~gNe~ad~~a~~a~~~   97 (237)
                      +|.|.|||||+|++||+.||+||++|...
T Consensus       114 ~v~~~wV~~H~~~~~N~~AD~lA~~a~~~  142 (150)
T PRK00203        114 QIKWHWVKGHAGHPENERCDELARAGAEE  142 (150)
T ss_pred             ceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence            79999999999999999999999999877

>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=99.71  E-value=2e-17  Score=126.05  Aligned_cols=84  Identities=42%  Similarity=0.649  Sum_probs=66.7

Q ss_pred             hhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcc-----cC-C--C-hHHHHHHHHHHHhhcCCcEEE
Q psy5610           2 ATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNI-----FS-L--N-PIAGEIRDLILTNKSKLNVRF   72 (237)
Q Consensus         2 ~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~-----~~-~--~-~~~~~i~~~~~~l~~~~~v~~   72 (237)
                      |+++||+.||..||+.     .   ....++|||||+++++.+..+     .. .  . ++..+|.+++   .....|.|
T Consensus        39 s~~~aEl~Ai~~AL~~-----~---~~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~---~~~~~v~~  107 (132)
T PF00075_consen   39 SNNRAELQAIIEALKA-----L---EHRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELL---SRGIKVRF  107 (132)
T ss_dssp             CHHHHHHHHHHHHHHT-----H---STSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHH---HHSSEEEE
T ss_pred             chhhhheehHHHHHHH-----h---hcccccccccHHHHHHHHHHhccccccccccccccchhheeecc---ccceEEee
Confidence            7899999999999995     2   128999999999999988872     21 1  1 4556666555   34677999


Q ss_pred             EEecCCCCC-cCChHHHHHHHHhhh
Q psy5610          73 IWVPSHVGI-AGNEEADRLAKEALT   96 (237)
Q Consensus        73 ~wvp~H~g~-~gNe~ad~~a~~a~~   96 (237)
                      .|||||+|+ .||+.||+|||+|+.
T Consensus       108 ~~V~~H~~~~~~N~~aD~lAk~a~~  132 (132)
T PF00075_consen  108 RWVPGHSGVPQGNERADRLAKEAAQ  132 (132)
T ss_dssp             EESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred             eeccCcCCCchhHHHHHHHHHHhcC
Confidence            999999999 699999999999863

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=99.56  E-value=4.1e-14  Score=105.24  Aligned_cols=90  Identities=32%  Similarity=0.420  Sum_probs=70.3

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccC-CC-hHHHHHHHHHHHhhcCCcEEEEEecCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFS-LN-PIAGEIRDLILTNKSKLNVRFIWVPSH   78 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~-~~-~~~~~i~~~~~~l~~~~~v~~~wvp~H   78 (237)
                      .|++.||+.|+..||+++     ...+...+.|++||+.+++.+.++.. .. .....+.++...+.....++|.|||+|
T Consensus        39 ~s~~~aEl~al~~al~~~-----~~~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h  113 (130)
T cd06222          39 TTNNRAELLALIEALELA-----LELGGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGH  113 (130)
T ss_pred             CcHHHHHHHHHHHHHHHH-----HhCCCceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCC
Confidence            478999999999999995     45678999999999999999998653 22 222233232222235667999999999


Q ss_pred             CCCcCChHHHHHHHHhh
Q psy5610          79 VGIAGNEEADRLAKEAL   95 (237)
Q Consensus        79 ~g~~gNe~ad~~a~~a~   95 (237)
                      +|..+|+.||.||+.+.
T Consensus       114 ~~~~~n~~ad~la~~~~  130 (130)
T cd06222         114 SGIEGNERADALAKEAA  130 (130)
T ss_pred             CCCcchHHHHHHHHhhC
Confidence            99999999999999873

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=99.40  E-value=6.5e-13  Score=114.85  Aligned_cols=91  Identities=25%  Similarity=0.221  Sum_probs=69.4

Q ss_pred             hhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccC-----------CCh----HH--HHHHHHHHHh
Q psy5610           2 ATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFS-----------LNP----IA--GEIRDLILTN   64 (237)
Q Consensus         2 ~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~-----------~~~----~~--~~i~~~~~~l   64 (237)
                      +|++||+.||..||+.+     ...+..+++|.|||+.++++|+.|..           .++    ++  +.....+..|
T Consensus       255 tNnrAEl~Av~~ALkka-----~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l  329 (371)
T KOG3752|consen  255 TNNRAELIAAIEALKKA-----RSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDEL  329 (371)
T ss_pred             cccHHHHHHHHHHHHHH-----HhcCCCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHH
Confidence            68999999999999995     44466699999999999999997653           122    01  1222223333


Q ss_pred             hc---CCcEEEEEecCCCCCcCChHHHHHHHHhhhc
Q psy5610          65 KS---KLNVRFIWVPSHVGIAGNEEADRLAKEALTS   97 (237)
Q Consensus        65 ~~---~~~v~~~wvp~H~g~~gNe~ad~~a~~a~~~   97 (237)
                      .+   ..+|.+.|||||.|+.||++||.+|+++...
T Consensus       330 ~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~  365 (371)
T KOG3752|consen  330 EQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL  365 (371)
T ss_pred             HhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence            33   3679999999999999999999999998654

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.38  E-value=3.2e-12  Score=97.18  Aligned_cols=88  Identities=23%  Similarity=0.294  Sum_probs=66.4

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccCCChHHHHHHHHHHHhh-cCCcEEEEEecCCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNK-SKLNVRFIWVPSHV   79 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~~~~~~~~i~~~~~~l~-~~~~v~~~wvp~H~   79 (237)
                      ++|..||+.|++.||+.+     ...+...+.|++||+.+++.+++.....+....+.+.+..+. ....+.|.|||+  
T Consensus        39 ~tn~~AE~~All~aL~~a-----~~~g~~~v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r--  111 (128)
T PRK13907         39 MSNHEAEYHALLAALKYC-----TEHNYNIVSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPS--  111 (128)
T ss_pred             cCCcHHHHHHHHHHHHHH-----HhCCCCEEEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCc--
Confidence            578999999999999995     445667899999999999999985443332333333333333 344588899996  


Q ss_pred             CCcCChHHHHHHHHhhhc
Q psy5610          80 GIAGNEEADRLAKEALTS   97 (237)
Q Consensus        80 g~~gNe~ad~~a~~a~~~   97 (237)
                        ++|+.||.+|+.|...
T Consensus       112 --~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907        112 --SQNKVADELARKAILQ  127 (128)
T ss_pred             --hhchhHHHHHHHHHhc
Confidence              5999999999998753

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

Probab=99.31  E-value=2e-11  Score=85.79  Aligned_cols=85  Identities=25%  Similarity=0.198  Sum_probs=62.2

Q ss_pred             hhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhccc-CCChHHHHHHHHHHHhhcCCcEEEEEecCCCCC
Q psy5610           3 TSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF-SLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGI   81 (237)
Q Consensus         3 ~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~-~~~~~~~~i~~~~~~l~~~~~v~~~wvp~H~g~   81 (237)
                      |..||+.|++.||+.     +...+.+++.|+|||+.+++.|++.. ..+++...+.+....+.....+.|.|||    .
T Consensus         1 ~~~aE~~al~~al~~-----a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----r   71 (87)
T PF13456_consen    1 PLEAEALALLEALQL-----AWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----R   71 (87)
T ss_dssp             HHHHHHHHHHHHHHH-----HHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------G
T ss_pred             CcHHHHHHHHHHHHH-----HHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----h
Confidence            468999999999999     56678899999999999999999863 3333333333333333455679999999    8


Q ss_pred             cCChHHHHHHHHhhh
Q psy5610          82 AGNEEADRLAKEALT   96 (237)
Q Consensus        82 ~gNe~ad~~a~~a~~   96 (237)
                      ++|..||.|||.|..
T Consensus        72 ~~N~~A~~LA~~a~~   86 (87)
T PF13456_consen   72 EQNKVADALAKFALS   86 (87)
T ss_dssp             GGSHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHHHHhh
Confidence            999999999998863

>PRK07708 hypothetical protein; Validated

Probab=99.17  E-value=2.1e-10  Score=94.85  Aligned_cols=88  Identities=20%  Similarity=0.170  Sum_probs=68.5

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCc--eEEEEeccHHHHHHHhc-ccCCChHHHHHHHHHHHhhcCC--cEEEEEe
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRA--YLVICSDSLSALQTLQN-IFSLNPIAGEIRDLILTNKSKL--NVRFIWV   75 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~--~~~I~tDs~~~i~~l~~-~~~~~~~~~~i~~~~~~l~~~~--~v~~~wv   75 (237)
                      ++|+.||+.|++.||+.+..     .+.+  .|.|++||+.+++.+++ +...++..+.+.+.+..+.++.  .+.|.||
T Consensus       116 ~TNN~AEy~Ali~aL~~A~e-----~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~V  190 (219)
T PRK07708        116 YDNNEAEYAALYYAMQELEE-----LGVKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPI  190 (219)
T ss_pred             ccCcHHHHHHHHHHHHHHHH-----cCCCcceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEEC
Confidence            47899999999999999643     3433  48999999999999997 4455665666655555544333  4788999


Q ss_pred             cCCCCCcCChHHHHHHHHhhhc
Q psy5610          76 PSHVGIAGNEEADRLAKEALTS   97 (237)
Q Consensus        76 p~H~g~~gNe~ad~~a~~a~~~   97 (237)
                      |    ...|+.||.||++|...
T Consensus       191 p----R~~N~~AD~LAk~Al~~  208 (219)
T PRK07708        191 S----RKQNKEADQLATQALEG  208 (219)
T ss_pred             C----chhhhHHHHHHHHHHhc
Confidence            8    57899999999999987

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=98.99  E-value=2.8e-09  Score=95.15  Aligned_cols=88  Identities=19%  Similarity=0.292  Sum_probs=67.6

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhccc-CCChHHHHHHHHHHHhh-cCCcEEEEEecCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF-SLNPIAGEIRDLILTNK-SKLNVRFIWVPSH   78 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~-~~~~~~~~i~~~~~~l~-~~~~v~~~wvp~H   78 (237)
                      .+|+.||+.|++.||+.+     ...+...+.|++||+.+++.+.+.+ .+++-...+.+.+..+. ....++|.|||+ 
T Consensus        43 ~tnn~AE~~All~gL~~a-----~~~g~~~v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r-  116 (372)
T PRK07238         43 ATNNVAEYRGLIAGLEAA-----AELGATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR-  116 (372)
T ss_pred             CCchHHHHHHHHHHHHHH-----HhCCCCeEEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc-
Confidence            378899999999999995     4456779999999999999999743 34433333333344443 345699999995 


Q ss_pred             CCCcCChHHHHHHHHhhhc
Q psy5610          79 VGIAGNEEADRLAKEALTS   97 (237)
Q Consensus        79 ~g~~gNe~ad~~a~~a~~~   97 (237)
                         .+|+.||.||+.|...
T Consensus       117 ---~~N~~AD~LA~~a~~~  132 (372)
T PRK07238        117 ---ARNAHADRLANEAMDA  132 (372)
T ss_pred             ---hhhhHHHHHHHHHHHh
Confidence               7999999999999766

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

Probab=96.87  E-value=0.0006  Score=47.92  Aligned_cols=32  Identities=22%  Similarity=0.514  Sum_probs=26.8

Q ss_pred             ccccCCCCCCCCCCCCc-ccccccccccccccH
Q psy5610         171 IHLMKKENPPICVPCGC-VISVKHILTDCQTHS  202 (237)
Q Consensus       171 ~~r~~~~~~p~C~~Cg~-~et~~H~l~~Cp~~~  202 (237)
                      +.+.+...++.|..||. .||++|+++.||...
T Consensus        51 l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~   83 (86)
T PF13966_consen   51 LQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR   83 (86)
T ss_pred             hhccCCccCCccccCCCccccccceeccCcCcc
Confidence            45566778899999996 899999999999753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	237
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	1e-11
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	2e-09
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	3e-07
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	9e-07
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	3e-06
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	1e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	2e-05
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	2e-05
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	4e-05
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	5e-05
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	1e-04
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	6e-04
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	7e-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 = 59.7 bits (145), Expect = 1e-11
 Identities = 19/96 (19%), Positives = 31/96 (32%), Gaps = 9/96 (9%)

Query: 1   MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLN-PIAGEIRD 59
           M     E+ A L+A+  +    +       + I  D           +            
Sbjct: 48  MRNVAGEIAAALYAVKKASQLGVK------IRILHDYAGIAFWATGEWKAKNEFTQAYAK 101

Query: 60  LILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
           L+  N+ +    F  V +H G   N+  D  AK AL
Sbjct: 102 LM--NQYRGIYSFEKVKAHSGNEFNDYVDMKAKSAL 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 = 54.1 bits (130), Expect = 2e-09
 Identities = 21/94 (22%), Positives = 31/94 (32%), Gaps = 11/94 (11%)

Query: 7   ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKS 66
           EL A+  A+  +    LN      +   S    A   + +         EI  L+     
Sbjct: 67  ELIALTQALKMAEGKKLN------VYTDSRYAFATAHVHSEGREIKNKNEILALLKALFL 120

Query: 67  KLNVRFIWVPSHVG-----IAGNEEADRLAKEAL 95
              +  I  P H         GN  AD+ A+EA 
Sbjct: 121 PKRLSIIHCPGHQKGNSAEARGNRMADQAAREAA 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 = 47.6 bits (114), Expect = 3e-07
 Identities = 14/29 (48%), Positives = 21/29 (72%)

Query: 66  SKLNVRFIWVPSHVGIAGNEEADRLAKEA 94
             ++++++ VP H G  GNEEADRLA+E 
Sbjct: 120 QGMDIQWMHVPGHSGFIGNEEADRLAREG 148

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

 Score = 46.0 bits (110), Expect = 9e-07
 Identities = 13/29 (44%), Positives = 16/29 (55%)

Query: 66  SKLNVRFIWVPSHVGIAGNEEADRLAKEA 94
            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 = 46.3 bits (110), Expect = 3e-06
 Identities = 29/86 (33%), Positives = 41/86 (47%), Gaps = 14/86 (16%)

Query: 7   ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN--IFSLNPIAGEIRDLILTN 64
           EL AI  A+  S       VN     I +DS  AL  +Q     S + +  +I + ++  
Sbjct: 480 ELQAIYLALQDSGL----EVN-----IVTDSQYALGIIQAQPDKSESELVNQIIEQLI-- 528

Query: 65  KSKLNVRFIWVPSHVGIAGNEEADRL 90
             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 = 42.9 bits (102), Expect = 1e-05
 Identities = 11/29 (37%), Positives = 16/29 (55%)

Query: 66  SKLNVRFIWVPSHVGIAGNEEADRLAKEA 94
            +  +++ WV  H G   NE AD LA+ A
Sbjct: 112 GQHQIKWEWVKGHAGHPENERADELARAA 140

>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 = 44.5 bits (104), Expect = 2e-05
 Identities = 34/234 (14%), Positives = 68/234 (29%), Gaps = 67/234 (28%)

Query: 34  CSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFI-WVPSHVGIAGNEEADRLAK 92
           C D        ++I S      EI  +I++  +      + W    +     E   +  +
Sbjct: 35  CKD---VQDMPKSILS----KEEIDHIIMSKDAVSGTLRLFWT---LLSKQEEMVQKFVE 84

Query: 93  EALTSTHPTINKIPIPDYKAYSKRKILSAWNSEWHNLQNNKLHQIKLENKPWN-----PP 147
           E L             +YK      ++S   +E           I+  ++ +N       
Sbjct: 85  EVLR-----------INYKF-----LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAK 128

Query: 148 YLINRKEQV-----SLTRLRIGHTNTTHIHLMK------------KENPPICVPCGCV-- 188
           Y ++R +       +L  LR    N   I  +                   C     +  
Sbjct: 129 YNVSRLQPYLKLRQALLELR-PAKNVL-IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW 186

Query: 189 ISVKHILTDCQTHSNIRAPL-NLSSTL---LSCLKDNDISPILEF------LRR 232
           +++K+    C +   +   L  L   +    +   D+  +  L        LRR
Sbjct: 187 LNLKN----CNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRR 236

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 15/47 (31%), Positives = 18/47 (38%), Gaps = 4/47 (8%)

Query: 66  SKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKA 112
           +   VRF +V  H G   NE  DR A+    S      K P P    
Sbjct: 117 APHRVRFHFVKGHTGHPENERVDREARRQAQS----QAKTPCPPRAP 159

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

 Score = 42.1 bits (100), Expect = 2e-05
 Identities = 10/29 (34%), Positives = 12/29 (41%)

Query: 66  SKLNVRFIWVPSHVGIAGNEEADRLAKEA 94
           +   V F  V  H     N  AD LA+ A
Sbjct: 113 TLHRVTFHKVKGHSDNPYNSRADELARLA 141

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

 Score = 41.7 bits (99), Expect = 4e-05
 Identities = 11/29 (37%), Positives = 15/29 (51%)

Query: 66  SKLNVRFIWVPSHVGIAGNEEADRLAKEA 94
               + + WV  H G A NE  D+LA+ A
Sbjct: 114 QLHQIDWRWVKGHAGHAENERCDQLARAA 142

>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 = 42.8 bits (101), Expect = 5e-05
 Identities = 25/86 (29%), Positives = 37/86 (43%), Gaps = 14/86 (16%)

Query: 7   ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN--IFSLNPIAGEIRDLILTN 64
           EL A   A+  S       VN     I  DS   +  + +    S + I  +I + ++  
Sbjct: 477 ELEAFAMALTDSGP----KVN-----IIVDSQYVMGIVASQPTESESKIVNQIIEEMI-- 525

Query: 65  KSKLNVRFIWVPSHVGIAGNEEADRL 90
             K  +   WVP+H GI GN+E D L
Sbjct: 526 -KKEAIYVAWVPAHKGIGGNQEVDHL 550

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 13/70 (18%)

Query: 31  LVICSDSLSALQTLQNIF-----SLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNE 85
            +I  DS   ++ +   +      + P+  +  +L      KLN   IWVP       N+
Sbjct: 71  PIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELK----KKLNATLIWVPR----EENK 122

Query: 86  EADRLAKEAL 95
           EADRL++ A 
Sbjct: 123 EADRLSRVAY 132

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

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 15/94 (15%), Positives = 32/94 (34%), Gaps = 17/94 (18%)

Query: 7   ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF-----SLNPIAGEIRDLI 61
           E   ++  +  ++             +  DS   ++ +   +      L  +  + + L 
Sbjct: 50  EYRGLIAGLDDAVKLGATEAA-----VLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALA 104

Query: 62  LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
                   + + WVP       N  ADRLA +A+
Sbjct: 105 ---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 = 37.5 bits (88), Expect = 7e-04
 Identities = 11/46 (23%), Positives = 16/46 (34%), Gaps = 6/46 (13%)

Query: 50  LNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
           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	237
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.78
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.78
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.76
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.75
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.74
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.74
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.74
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.72
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.64
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.6
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.59
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.58
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.57
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.56
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	98.65
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	98.14

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

Probab=99.78  E-value=3.9e-19  Score=138.48  Aligned_cols=92  Identities=26%  Similarity=0.350  Sum_probs=71.8

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhccc---------CCC--hH-HHHHHHHHHHhhcCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF---------SLN--PI-AGEIRDLILTNKSKL   68 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~---------~~~--~~-~~~i~~~~~~l~~~~   68 (237)
                      ++|++||+.|++.||+.+     ...+..+|.|+|||+++++.|.++.         ..+  ++ ...+.+.+..+....
T Consensus        48 ~tn~~aEl~A~~~aL~~~-----~~~~~~~v~i~tDS~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~~  122 (154)
T 2qkb_A           48 QTNQRAEIHAACKAIEQA-----KTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGM  122 (154)
T ss_dssp             CCHHHHHHHHHHHHHHHH-----HHTTCCEEEEEESCHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTTC
T ss_pred             CchHHHHHHHHHHHHHHH-----HhCCCceEEEEECcHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcCC
Confidence            479999999999999995     3446789999999999999998742         111  11 123333344444556


Q ss_pred             cEEEEEecCCCCCcCChHHHHHHHHhhhc
Q psy5610          69 NVRFIWVPSHVGIAGNEEADRLAKEALTS   97 (237)
Q Consensus        69 ~v~~~wvp~H~g~~gNe~ad~~a~~a~~~   97 (237)
                      +|.|.|||||+|++||+.||+||++|+..
T Consensus       123 ~v~~~~V~~H~g~~~N~~AD~LA~~a~~~  151 (154)
T 2qkb_A          123 DIQWMHVPGHSGFIGNEEADRLAREGAKQ  151 (154)
T ss_dssp             EEEEEECCTTSSCHHHHHHHHHHHHHHTC
T ss_pred             ceEEEEccCCCCCHhHHHHHHHHHHHHHh
Confidence            79999999999999999999999999875

>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=99.78  E-value=5.3e-19  Score=137.11  Aligned_cols=88  Identities=28%  Similarity=0.409  Sum_probs=68.1

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhccc-----------CCChHH-H-HHHHHHHHhhcC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF-----------SLNPIA-G-EIRDLILTNKSK   67 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~-----------~~~~~~-~-~i~~~~~~l~~~   67 (237)
                      ++|++||+.|++.||+.     .    ..++.|+|||++++++|++|.           ...++. . .+.+++..+.+.
T Consensus        47 ~Tnn~aEl~A~i~AL~~-----~----~~~v~i~tDS~~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~  117 (150)
T 3qio_A           47 TTNQKTELQAIYLALQD-----S----GLEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKK  117 (150)
T ss_dssp             CCHHHHHHHHHHHHHHH-----S----CSEEEEEESCHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHTTC
T ss_pred             CCHHHHHHHHHHHHHHh-----C----CCcEEEEeCcHHHHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhc
Confidence            47999999999999998     2    379999999999999999862           111221 1 223333344456


Q ss_pred             CcEEEEEecCCCCCcCChHHHHHHHHhhhc
Q psy5610          68 LNVRFIWVPSHVGIAGNEEADRLAKEALTS   97 (237)
Q Consensus        68 ~~v~~~wvp~H~g~~gNe~ad~~a~~a~~~   97 (237)
                      .+|.|.|||||+|++|||.||+||++|+..
T Consensus       118 ~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A          118 EKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             SEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             CceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            679999999999999999999999999865

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

Probab=99.76  E-value=6.3e-19  Score=136.04  Aligned_cols=85  Identities=24%  Similarity=0.227  Sum_probs=66.3

Q ss_pred             hhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhc-cc-----------CC-----ChHHHHHHHHHHHh
Q psy5610           2 ATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN-IF-----------SL-----NPIAGEIRDLILTN   64 (237)
Q Consensus         2 ~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~-~~-----------~~-----~~~~~~i~~~~~~l   64 (237)
                      +|++||+.|++.||+.+     ..  ..++.|+|||+++++.|++ |.           ..     .++.+.+.+++   
T Consensus        43 Tnn~aEl~A~~~AL~~~-----~~--~~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~---  112 (146)
T 3h08_A           43 TNNRMELMAAIKGLEAL-----KE--PARVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLT---  112 (146)
T ss_dssp             CHHHHHHHHHHHHHHTC-----SS--CCEEEEEESCHHHHHHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHH---
T ss_pred             cHHHHHHHHHHHHHHhc-----Cc--cCcEEEEeChHHHHHHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHH---
Confidence            68999999999999994     32  4799999999999999987 31           01     12333333333   


Q ss_pred             hcCCcEEEEEecCCCCCcCChHHHHHHHHhhhc
Q psy5610          65 KSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS   97 (237)
Q Consensus        65 ~~~~~v~~~wvp~H~g~~gNe~ad~~a~~a~~~   97 (237)
                       ...+|.|.|||||+|++||+.||+||++|+..
T Consensus       113 -~~~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A          113 -TLHRVTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             -HHSEEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             -hhCceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence             34579999999999999999999999999865

>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=99.75  E-value=1.6e-19  Score=139.68  Aligned_cols=90  Identities=21%  Similarity=0.126  Sum_probs=73.3

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhc-ccCCChHHHHHHHHHHHhhcCCcEEEEEecCCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN-IFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHV   79 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~-~~~~~~~~~~i~~~~~~l~~~~~v~~~wvp~H~   79 (237)
                      ++|++||+.|++.||++++.     .+. +|.|+|||+.+.+.+.+ |...++....+.+++.++..  +|.|.|||||+
T Consensus        48 ~tNn~aEl~A~~~AL~~a~~-----~~~-~v~I~tDS~~i~~w~~~~w~~~~~~~~~~~~l~~~l~~--~v~~~wV~gH~  119 (147)
T 2kq2_A           48 MRNVAGEIAAALYAVKKASQ-----LGV-KIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMNQYRG--IYSFEKVKAHS  119 (147)
T ss_dssp             TCTTHHHHHHHHHHHHHHHH-----HTC-CCCBSSCCSTHHHHTTSSSSCCHHHHHHHHCGGGGGST--TCCBCCCCCCC
T ss_pred             ccHHHHHHHHHHHHHHHHHH-----CCC-eEEEEECcHHHHHHHhCCCccCCcchHHHHHHHHHhcC--CeeEEEecCcC
Confidence            47999999999999999643     234 89999999988877765 44444555666677666644  89999999999


Q ss_pred             CCcCChHHHHHHHHhhhcC
Q psy5610          80 GIAGNEEADRLAKEALTST   98 (237)
Q Consensus        80 g~~gNe~ad~~a~~a~~~~   98 (237)
                      |++|||.||+||++|+...
T Consensus       120 g~~~Ne~AD~LA~~a~~~~  138 (147)
T 2kq2_A          120 GNEFNDYVDMKAKSALGIR  138 (147)
T ss_dssp             CCHHHHHHHHHHHHHHTCC
T ss_pred             CCcchHHHHHHHHHHHhcc
Confidence            9999999999999999874

>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=99.74  E-value=3e-18  Score=133.61  Aligned_cols=91  Identities=22%  Similarity=0.369  Sum_probs=70.9

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhccc---------CC--ChHH-HHHHHHHHHhhcCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF---------SL--NPIA-GEIRDLILTNKSKL   68 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~---------~~--~~~~-~~i~~~~~~l~~~~   68 (237)
                      ++|++||+.|++.||+.+     ..  ..++.|+|||+++++.|.+|.         ..  .++. ..+...+..+....
T Consensus        42 ~tn~~aEl~A~~~aL~~~-----~~--~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~  114 (155)
T 1jl1_A           42 TTNNRMELMAAIVALEAL-----KE--HAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQH  114 (155)
T ss_dssp             ECHHHHHHHHHHHHHHTC-----CS--CCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTC
T ss_pred             CcHHHHHHHHHHHHHHHh-----Cc--CCcEEEEeCHHHHHHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHHccC
Confidence            368999999999999994     32  379999999999999999731         11  1221 23344444444556


Q ss_pred             cEEEEEecCCCCCcCChHHHHHHHHhhhcC
Q psy5610          69 NVRFIWVPSHVGIAGNEEADRLAKEALTST   98 (237)
Q Consensus        69 ~v~~~wvp~H~g~~gNe~ad~~a~~a~~~~   98 (237)
                      .|.|.|||||+|++||+.||+||++|+..+
T Consensus       115 ~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~  144 (155)
T 1jl1_A          115 QIKWEWVKGHAGHPENERADELARAAAMNP  144 (155)
T ss_dssp             EEEEEECCSSTTCHHHHHHHHHHHHHHHSC
T ss_pred             ceEEEEcCCCCCCHHHHHHHHHHHHHHhcc
Confidence            899999999999999999999999999873

>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=99.74  E-value=4.1e-18  Score=134.01  Aligned_cols=89  Identities=26%  Similarity=0.222  Sum_probs=70.5

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccCCChHH--HHHHHHHHHhhcCCcEEEEEecCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIA--GEIRDLILTNKSKLNVRFIWVPSH   78 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~~~~~~--~~i~~~~~~l~~~~~v~~~wvp~H   78 (237)
                      ++|++||+.|++.||+.     +   ...++.|||||+++++++-....+.++.  ..+++++..+..+.+|.|.|||||
T Consensus        61 ~Tnn~aEl~Ai~~AL~~-----~---~~~~v~I~tDS~~vi~~iw~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH  132 (165)
T 3p1g_A           61 TSAQRAELIALTQALKM-----A---EGKKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGH  132 (165)
T ss_dssp             CCHHHHHHHHHHHHHHH-----T---BTSEEEEEECCHHHHHHHHSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSS
T ss_pred             CcHHHHHHHHHHHHHHH-----c---cCceEEEEEchHHHHhhhhcccCCCcccCHHHHHHHHHHHhcCCceEEEEecCC
Confidence            47899999999999999     3   2579999999999999983212222221  234455555556678999999999


Q ss_pred             CC-----CcCChHHHHHHHHhhhc
Q psy5610          79 VG-----IAGNEEADRLAKEALTS   97 (237)
Q Consensus        79 ~g-----~~gNe~ad~~a~~a~~~   97 (237)
                      +|     +.|||.||+||++|+..
T Consensus       133 ~g~~~~~~~gNe~AD~LA~~aa~~  156 (165)
T 3p1g_A          133 QKGNSAEARGNRMADQAAREAAMK  156 (165)
T ss_dssp             CCSCSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcCcchHHHHHHHHHHHHHhc
Confidence            99     99999999999999987

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

Probab=99.74  E-value=4.5e-18  Score=133.01  Aligned_cols=89  Identities=22%  Similarity=0.337  Sum_probs=69.2

Q ss_pred             hhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhccc---------CC--ChHH-HHHHHHHHHhhcCCc
Q psy5610           2 ATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF---------SL--NPIA-GEIRDLILTNKSKLN   69 (237)
Q Consensus         2 ~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~---------~~--~~~~-~~i~~~~~~l~~~~~   69 (237)
                      +|++||+.|++.||+.+     ..  ..+|.|+|||+++++.|.+|.         ..  .++. ..+...+..+.....
T Consensus        45 tn~~aEl~A~~~AL~~~-----~~--~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~  117 (158)
T 2e4l_A           45 TNNRMELLAPIVALEAL-----KE--PCKIILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQLHQ  117 (158)
T ss_dssp             CHHHHHHHHHHHHHHTC-----SS--CCEEEEEECCHHHHHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTTSE
T ss_pred             ccHHHHHHHHHHHHHHh-----cc--CCeEEEEeCHHHHHHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHccCc
Confidence            68999999999999994     32  289999999999999998821         11  1211 233333444445568


Q ss_pred             EEEEEecCCCCCcCChHHHHHHHHhhhc
Q psy5610          70 VRFIWVPSHVGIAGNEEADRLAKEALTS   97 (237)
Q Consensus        70 v~~~wvp~H~g~~gNe~ad~~a~~a~~~   97 (237)
                      |.|.|||||+|++||+.||+||++|+..
T Consensus       118 v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A          118 IDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             EEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             EEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            9999999999999999999999999987

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

Probab=99.72  E-value=5.4e-18  Score=133.63  Aligned_cols=91  Identities=21%  Similarity=0.295  Sum_probs=70.1

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhc----------ccCCC--hHH-HHHHHHHHHhhcC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN----------IFSLN--PIA-GEIRDLILTNKSK   67 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~----------~~~~~--~~~-~~i~~~~~~l~~~   67 (237)
                      ++|++||+.|++.||+.+     ..  ..+|.|+|||+++++.|.+          +...+  ++. ..+...+..+...
T Consensus        46 ~Tnn~aEl~Ai~~AL~~~-----~~--~~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~  118 (166)
T 1ril_A           46 TTNNRMELKAAIEGLKAL-----KE--PCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP  118 (166)
T ss_dssp             ECHHHHHHHHHHHHHHSC-----CS--CCEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTT
T ss_pred             CcHHHHHHHHHHHHHHHh-----cc--CCeEEEEeChHHHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhc
Confidence            378999999999999984     32  2589999999999999998          22211  111 2333334444445


Q ss_pred             CcEEEEEecCCCCCcCChHHHHHHHHhhhcC
Q psy5610          68 LNVRFIWVPSHVGIAGNEEADRLAKEALTST   98 (237)
Q Consensus        68 ~~v~~~wvp~H~g~~gNe~ad~~a~~a~~~~   98 (237)
                      ..|.|.|||||+|++||+.||+||++|+...
T Consensus       119 ~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~  149 (166)
T 1ril_A          119 HRVRFHFVKGHTGHPENERVDREARRQAQSQ  149 (166)
T ss_dssp             SEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             CeEEEEEeeCCCCchhHHHHHHHHHHHHHHh
Confidence            6899999999999999999999999999883

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

Probab=99.64  E-value=5.3e-16  Score=121.83  Aligned_cols=89  Identities=17%  Similarity=0.236  Sum_probs=59.6

Q ss_pred             hhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhccc---------C--CChHH--HHHHHHHHHhhcCCc
Q psy5610           3 TSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF---------S--LNPIA--GEIRDLILTNKSKLN   69 (237)
Q Consensus         3 ~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~---------~--~~~~~--~~i~~~~~~l~~~~~   69 (237)
                      +..||+.|+..||+.++.      ...+|.|+|||++++++|+.|.         .  +.|+.  ..++.+...+....+
T Consensus        56 e~~Aei~Al~~al~~al~------~~~~v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~  129 (165)
T 2lsn_A           56 AQMAEIAAVEFACKKALK------IPGPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPD  129 (165)
T ss_dssp             HHHHHHHHHHHHHHHHHH------SSSCEEEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHHHHhc------CCCeEEEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCC
Confidence            345555555555555322      3357999999999999997642         1  11221  122233333345668


Q ss_pred             EEEEEecCCCCC------cCChHHHHHHHHhhhc
Q psy5610          70 VRFIWVPSHVGI------AGNEEADRLAKEALTS   97 (237)
Q Consensus        70 v~~~wvp~H~g~------~gNe~ad~~a~~a~~~   97 (237)
                      |.|.|||||+|.      +|||.||+||++|+..
T Consensus       130 v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~~  163 (165)
T 2lsn_A          130 ITIQHEKGHQPTNTSIHTEGNALADKLATQGSYV  163 (165)
T ss_dssp             CEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEeCCCCccCCCCChHHHHHHHHHHHhhhh
Confidence            999999999995      5899999999999854

>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=99.60  E-value=4.7e-15  Score=113.10  Aligned_cols=88  Identities=19%  Similarity=0.248  Sum_probs=70.4

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhc-ccCCChHHHHHHHHHHHhhc-CCcEEEEEecCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN-IFSLNPIAGEIRDLILTNKS-KLNVRFIWVPSH   78 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~-~~~~~~~~~~i~~~~~~l~~-~~~v~~~wvp~H   78 (237)
                      ++|++||+.|++.||+.+.     ..+..++.|+|||+++++.+++ |...++....+.+.+..+.. ...|.|.|||+ 
T Consensus        44 ~tn~~aEl~A~~~aL~~a~-----~~~~~~v~i~tDS~~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~-  117 (141)
T 3hst_B           44 ATNNVAEYRGLIAGLDDAV-----KLGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR-  117 (141)
T ss_dssp             ECHHHHHHHHHHHHHHHHH-----HHTCSEEEEEESCHHHHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG-
T ss_pred             CchHHHHHHHHHHHHHHHH-----HCCCceEEEEeChHHHHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC-
Confidence            3789999999999999954     3456899999999999999997 44555544444444555544 46799999994 


Q ss_pred             CCCcCChHHHHHHHHhhhc
Q psy5610          79 VGIAGNEEADRLAKEALTS   97 (237)
Q Consensus        79 ~g~~gNe~ad~~a~~a~~~   97 (237)
                         ++|+.||+||++|...
T Consensus       118 ---~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B          118 ---ARNTYADRLANDAMDA  133 (141)
T ss_dssp             ---GGCHHHHHHHHHHHHH
T ss_pred             ---cccHHHHHHHHHHHHH
Confidence               8999999999999876

>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=99.59  E-value=3.3e-15  Score=138.38  Aligned_cols=83  Identities=25%  Similarity=0.366  Sum_probs=69.2

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccC--CChHHHHHHHHHHHhhcCCcEEEEEecCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFS--LNPIAGEIRDLILTNKSKLNVRFIWVPSH   78 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~--~~~~~~~i~~~~~~l~~~~~v~~~wvp~H   78 (237)
                      ++|++||+.|++.||+.         ...++.|+|||+++++.+++|..  ..++.+++.+.+   .....|.|.|||||
T Consensus       471 ~TNn~aEl~A~i~aL~~---------~~~~v~I~tDS~~v~~~i~~~~~~~~~~l~~~~~~~~---~~~~~v~~~wV~~H  538 (555)
T 1mu2_A          471 TTNQQAELEAFAMALTD---------SGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEM---IKKEAIYVAWVPAH  538 (555)
T ss_dssp             CCHHHHHHHHHHHHHHT---------SCSEEEEEESCHHHHHHHHTCCSEESCHHHHHHHHHH---HHCSEEEEEECCSS
T ss_pred             CCHHHHHHHHHHHHHHc---------CCCeEEEEEehHHHHHHHhcccccccHHHHHHHHHHh---ccCCcEEEEEEECC
Confidence            47999999999999988         34789999999999999998753  345555544443   34677999999999


Q ss_pred             CCCcCChHHHHHHHHhh
Q psy5610          79 VGIAGNEEADRLAKEAL   95 (237)
Q Consensus        79 ~g~~gNe~ad~~a~~a~   95 (237)
                      +|++|||.||+||++|+
T Consensus       539 ~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          539 KGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             SCCTTHHHHHHHHHTTC
T ss_pred             CCChhHHHHHHHHHhhC
Confidence            99999999999999874

>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=99.58  E-value=2.4e-15  Score=139.34  Aligned_cols=82  Identities=30%  Similarity=0.393  Sum_probs=66.5

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccCC--ChHHHHHHHHHHHhhcCCcEEEEEecCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSL--NPIAGEIRDLILTNKSKLNVRFIWVPSH   78 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~~--~~~~~~i~~~~~~l~~~~~v~~~wvp~H   78 (237)
                      ++|++||+.|++.||+.     +    ..++.|+|||++|++.++++...  .++.+++.+.   +....+|.|.|||||
T Consensus       474 ~TNn~aEl~Ai~~aL~~-----~----~~~v~I~tDS~~vi~~i~~~~~~~~~~l~~~~~~~---l~~~~~v~~~wV~~H  541 (557)
T 2zd1_A          474 TTNQKTELQAIYLALQD-----S----GLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQ---LIKKEKVYLAWVPAH  541 (557)
T ss_dssp             CCHHHHHHHHHHHHHHH-----S----CSEEEEEECCHHHHHHHTTCCSEESSHHHHHHHHH---HHHCSEEEEEECCSS
T ss_pred             CCHHHHHHHHHHHHHHh-----C----CCcEEEEeChHHHHHHHhcCCccCCHHHHHHHHHH---HhcCCCEEEEEcCCC
Confidence            47999999999999999     3    47899999999999999987653  4555554433   334568999999999


Q ss_pred             CCCcCChHHHHHHHHh
Q psy5610          79 VGIAGNEEADRLAKEA   94 (237)
Q Consensus        79 ~g~~gNe~ad~~a~~a   94 (237)
                      +|++|||.||+||++|
T Consensus       542 ~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          542 KGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             SCCTTCCGGGGCC---
T ss_pred             CCChhHHHHHHHHhcC
Confidence            9999999999999876

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

Probab=99.57  E-value=3.7e-15  Score=115.05  Aligned_cols=88  Identities=23%  Similarity=0.338  Sum_probs=66.6

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhccc-CCChHHHHHHHHHHHhhcCCcEEEEEecCCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF-SLNPIAGEIRDLILTNKSKLNVRFIWVPSHV   79 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~-~~~~~~~~i~~~~~~l~~~~~v~~~wvp~H~   79 (237)
                      ++|++||+.|++.||+.+.     ..+..++.|+|||+++++.++++. ..++....+.+.+..+....+|.|.|||+  
T Consensus        46 ~tnn~aEl~A~~~aL~~a~-----~~g~~~v~i~tDS~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~~v~~~~V~~--  118 (149)
T 2ehg_A           46 STNNVAEYSGLICLMETML-----RLGISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPR--  118 (149)
T ss_dssp             CCHHHHHHHHHHHHHHHHH-----HHTCCSCEEEESCHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHHTCEEEECCG--
T ss_pred             ccHHHHHHHHHHHHHHHHH-----HcCCCEEEEEeChHHHHHHHhCccccCCHHHHHHHHHHHHHHhcCCEEEEEcCC--
Confidence            4789999999999999964     345679999999999999999853 33332333333333332223699999998  


Q ss_pred             CCcCChHHHHHHHHhhhc
Q psy5610          80 GIAGNEEADRLAKEALTS   97 (237)
Q Consensus        80 g~~gNe~ad~~a~~a~~~   97 (237)
                        ++|+.||+||++|+..
T Consensus       119 --~~N~~AD~LA~~a~~~  134 (149)
T 2ehg_A          119 --EENKEADRLSRVAYEL  134 (149)
T ss_dssp             --GGCHHHHHHHHHHHHH
T ss_pred             --cccHHHHHHHHHHHHh
Confidence              5999999999999877

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

Probab=99.56  E-value=1.1e-14  Score=110.65  Aligned_cols=87  Identities=22%  Similarity=0.247  Sum_probs=66.0

Q ss_pred             hhhHHHHHHHHHHHHHhHHhhhhcCCCc----eEEEEeccHHHHHHHhccc-CCChHHHHHHHHHHHh--hcCCcEEEEE
Q psy5610           2 ATSVLELTAILFAIHFSISAHLNNVNRA----YLVICSDSLSALQTLQNIF-SLNPIAGEIRDLILTN--KSKLNVRFIW   74 (237)
Q Consensus         2 ~~~~AEl~ai~~al~~~~~~~~~~~~~~----~~~I~tDs~~~i~~l~~~~-~~~~~~~~i~~~~~~l--~~~~~v~~~w   74 (237)
                      +|++||+.|++.||+.+..     .+.+    ++.|+|||+++++.++++. ..++-...+.+.+..+  .....|.|.|
T Consensus        44 tn~~aEl~A~~~aL~~a~~-----~~~~~~~~~v~i~tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~  118 (140)
T 3u3g_D           44 TNNVAEYEALIRALEDLQM-----FGDKLVDMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVH  118 (140)
T ss_dssp             CHHHHHHHHHHHHHHHHGG-----GGGGGTTCEEEEEESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEE
T ss_pred             chHHHHHHHHHHHHHHHHH-----cCCCCCCceEEEEeChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEE
Confidence            7899999999999999643     3445    9999999999999999854 3443233333333333  3345899999


Q ss_pred             ecCCCCCcCChHHHHHHHHhhhc
Q psy5610          75 VPSHVGIAGNEEADRLAKEALTS   97 (237)
Q Consensus        75 vp~H~g~~gNe~ad~~a~~a~~~   97 (237)
                      ||    .++|+.||+||++|...
T Consensus       119 V~----~~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D          119 IP----REKNARADELVNEAIDK  137 (140)
T ss_dssp             CC----GGGGHHHHHHHHHHHHH
T ss_pred             cC----chhhHHHHHHHHHHHHh
Confidence            99    48999999999999764

>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=98.65  E-value=6.8e-09  Score=79.19  Aligned_cols=82  Identities=15%  Similarity=0.023  Sum_probs=56.8

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccCC----C-----hHHHHHHHHHHHhhcCCcEE
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSL----N-----PIAGEIRDLILTNKSKLNVR   71 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~~----~-----~~~~~i~~~~~~l~~~~~v~   71 (237)
                      ++|++||+.|++.||+.+.+     .+. ++.|+|||+++++.+++....    .     ++.+.+.++..-+. ...++
T Consensus        49 ~TNN~aEl~A~i~aL~~~~~-----~~~-~v~i~tDS~~vi~w~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~-~~~~~  121 (142)
T 1zbf_A           49 GTNNMGEFLAIVHGLRYLKE-----RNS-RKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLN-THTYE  121 (142)
T ss_dssp             ECHHHHHHHHHHHHHHHHHH-----TTC-CCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHH-HCCCC
T ss_pred             cCcHHHHHHHHHHHHHHHHh-----CCC-eEEEEEehHHHHHHHHcCCccCCCCCCcccHHHHHHHHHHHHHHh-hCCCc
Confidence            37999999999999999643     344 899999999999999975421    1     23333333322222 23455


Q ss_pred             EEEecCCCCCcCChHHHH
Q psy5610          72 FIWVPSHVGIAGNEEADR   89 (237)
Q Consensus        72 ~~wvp~H~g~~gNe~ad~   89 (237)
                      ...|..|++.-||..||.
T Consensus       122 ~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A          122 TPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             CCEEECCHHHHCSCTTCC
T ss_pred             eeEEEeccCccCcCcccc
Confidence            666777888889999883

>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=98.14  E-value=4.5e-06  Score=62.61  Aligned_cols=41  Identities=20%  Similarity=0.210  Sum_probs=34.2

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcc
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNI   47 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~   47 (237)
                      ++|++||++|++.||+.+.+     .+. ++.|+|||+++++.|.++
T Consensus        43 tTNN~aEl~A~i~aL~~l~~-----~~~-~v~i~tDSqyVi~wi~~~   83 (134)
T 4htu_A           43 GTNNMGEFLAIVHGLRYLKE-----RNS-RKPIYSNSQTAIKWVKDK   83 (134)
T ss_dssp             ECHHHHHHHHHHHHHHHHHH-----TTC-CCCEEESCHHHHHHHHHT
T ss_pred             CchHHHHHHHHHHHHHHHHh-----CCC-CEEEEcchHHHHHHHHcC
Confidence            37999999999999999643     222 389999999999999874

---

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	237
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	5e-08
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	3e-06
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	6e-06

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

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

 Score = 48.0 bits (113), Expect = 5e-08
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 16  HFSISAHLNNVNRAYLVICSDSLSALQTLQN--IFSLNPIAGEIRDLILTNKSKLNVRFI 73
                A     +   + I  DS   +  + +    S + I  +I + ++  +    +   
Sbjct: 48  ELEAFAMALTDSGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIKKE---AIYVA 104

Query: 74  WVPSHVGIAGNEEADRLAKEAL 95
           WVP+H GI GN+E D L  + +
Sbjct: 105 WVPAHKGIGGNQEVDHLVSQGI 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 = 43.8 bits (102), Expect = 3e-06
 Identities = 11/26 (42%), Positives = 13/26 (50%)

Query: 69  NVRFIWVPSHVGIAGNEEADRLAKEA 94
            VRF +V  H G   NE  DR A+  
Sbjct: 115 RVRFHFVKGHTGHPENERVDREARRQ 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 = 42.7 bits (99), Expect = 6e-06
 Identities = 11/26 (42%), Positives = 15/26 (57%)

Query: 69  NVRFIWVPSHVGIAGNEEADRLAKEA 94
            +++ WV  H G   NE AD LA+ A
Sbjct: 113 QIKWEWVKGHAGHPENERADELARAA 138

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	237
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.81
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.7
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.67
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.46
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	98.96

>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=99.81  E-value=2.6e-20  Score=138.58  Aligned_cols=85  Identities=24%  Similarity=0.330  Sum_probs=67.0

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccCCChHHHHHHHHHHHhhcCCcEEEEEecCCCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSHVG   80 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~~~~~~~~i~~~~~~l~~~~~v~~~wvp~H~g   80 (237)
                      .+|++||+.||++||+.         ....+.|+|||+++++.+.++...+. ...+...+..+.....|.|.|||||+|
T Consensus        42 ~tnn~AEl~Ai~~al~~---------~~~~i~I~tDS~~v~~~~~~~~~~~~-~~~~~~~~~~~~~~~~v~~~wV~gH~g  111 (126)
T d1mu2a1          42 TTNQQAELEAFAMALTD---------SGPKVNIIVDSQYVMGIVASQPTESE-SKIVNQIIEEMIKKEAIYVAWVPAHKG  111 (126)
T ss_dssp             CCHHHHHHHHHHHHHHT---------SCSEEEEEESCHHHHHHHHTCCSEES-CHHHHHHHHHHHHCSEEEEEECCSSSC
T ss_pred             CcchHHHHHHHHHHhcc---------CCcceEEEechHHHHHHHhcCCcccc-chHHHHHHHHhhhcceeEEEEEeCCCC
Confidence            37899999999999987         34689999999999999998543211 112233344444566899999999999


Q ss_pred             CcCChHHHHHHHHhh
Q psy5610          81 IAGNEEADRLAKEAL   95 (237)
Q Consensus        81 ~~gNe~ad~~a~~a~   95 (237)
                      ++|||.||+||++|.
T Consensus       112 ~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1         112 IGGNQEVDHLVSQGI  126 (126)
T ss_dssp             CTTHHHHHHHHHTTC
T ss_pred             CcchHHHHHHHHhhC
Confidence            999999999999874

>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=99.70  E-value=6.2e-18  Score=128.70  Aligned_cols=90  Identities=21%  Similarity=0.290  Sum_probs=68.6

Q ss_pred             hhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccC------------CChHH-HHHHHHHHHhhcCC
Q psy5610           2 ATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFS------------LNPIA-GEIRDLILTNKSKL   68 (237)
Q Consensus         2 ~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~------------~~~~~-~~i~~~~~~l~~~~   68 (237)
                      +|++||+.|++.||+++     .  ....+.|++||+++++.+.....            ..++. .++...+..+....
T Consensus        42 Tnn~aEl~Ai~~AL~~~-----~--~~~~i~i~tds~~~~~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~~~  114 (147)
T d1rila_          42 TNNRMELKAAIEGLKAL-----K--EPCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPH  114 (147)
T ss_dssp             CHHHHHHHHHHHHHHSC-----C--SCCEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTS
T ss_pred             cHHHHHHHHHHHHhhhc-----c--CCceEEEecchhhhhccccccchhhhhhccccccccccchhHHHHHHHHHHhhhc
Confidence            78999999999999983     2  45689999999999998875321            11221 12223333444667


Q ss_pred             cEEEEEecCCCCCcCChHHHHHHHHhhhcC
Q psy5610          69 NVRFIWVPSHVGIAGNEEADRLAKEALTST   98 (237)
Q Consensus        69 ~v~~~wvp~H~g~~gNe~ad~~a~~a~~~~   98 (237)
                      +|+|.|||||+|++|||.||+||++|+...
T Consensus       115 ~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_         115 RVRFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             EEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             ccceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence            899999999999999999999999998873

>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=99.67  E-value=4.4e-17  Score=124.20  Aligned_cols=90  Identities=22%  Similarity=0.365  Sum_probs=68.7

Q ss_pred             hhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccC-----------CChHH-HHHHHHHHHhhcCCc
Q psy5610           2 ATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFS-----------LNPIA-GEIRDLILTNKSKLN   69 (237)
Q Consensus         2 ~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~-----------~~~~~-~~i~~~~~~l~~~~~   69 (237)
                      +|++||++|++.||+++     .  ....+.|++||++++..+..+..           ..++. ..+...+..+....+
T Consensus        41 tnn~aE~~Ai~~Al~~~-----~--~~~~i~i~tds~~~i~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~~~~  113 (152)
T d1jl1a_          41 TNNRMELMAAIVALEAL-----K--EHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ  113 (152)
T ss_dssp             CHHHHHHHHHHHHHHTC-----C--SCCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCE
T ss_pred             cHHHHHHhhhhhhhhhh-----c--ccceEEEeecceeeEEcccchhhHhHhccchhcccCeeecHHHHHHHHHHhhcce
Confidence            68999999999999983     2  45678999999999988875431           11111 123333344445668


Q ss_pred             EEEEEecCCCCCcCChHHHHHHHHhhhcC
Q psy5610          70 VRFIWVPSHVGIAGNEEADRLAKEALTST   98 (237)
Q Consensus        70 v~~~wvp~H~g~~gNe~ad~~a~~a~~~~   98 (237)
                      |+|+|||||+|++|||.||+||++|+..+
T Consensus       114 V~~~wV~gH~g~~gNe~AD~LAk~aa~~~  142 (152)
T d1jl1a_         114 IKWEWVKGHAGHPENERADELARAAAMNP  142 (152)
T ss_dssp             EEEEECCSSTTCHHHHHHHHHHHHHHHSC
T ss_pred             eEEEEecccCCCccHHHHHHHHHHHHhCC
Confidence            99999999999999999999999999873

>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=99.46  E-value=6e-14  Score=101.12  Aligned_cols=66  Identities=29%  Similarity=0.325  Sum_probs=52.3

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccC--CChHHHHHHHHHHHhhcCCcEEEEEecCC
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFS--LNPIAGEIRDLILTNKSKLNVRFIWVPSH   78 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~--~~~~~~~i~~~~~~l~~~~~v~~~wvp~H   78 (237)
                      .||++||+.||+.||+.         ....+.|+|||+++++++.++..  ..++..+|   +..+..+.+|.+.|||||
T Consensus        43 ~TNn~aEl~Avi~aL~~---------~~~~v~I~TDS~yvi~~i~~~~~~~~~~l~~~i---l~~l~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          43 TTNQKTELQAIYLALQD---------SGLEVNIVTDSQYALGIIQAQPDQSESELVNQI---IEQLIKKEKVYLAWVPAH  110 (110)
T ss_dssp             CCHHHHHHHHHHHHHHH---------SCSEEEEEECCHHHHHHHHHCCSEESCHHHHHH---HHHHHHCSEEEEEECCSS
T ss_pred             CcHHHHHHHHHHHHHHh---------CCCeEEEEEehHHHHHHHhcCccccchHHHHHH---HHHHhcCCceEEEEeCCC
Confidence            37999999999999987         34679999999999999998654  33444444   444445678999999999

>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=98.96  E-value=6.8e-11  Score=86.81  Aligned_cols=82  Identities=16%  Similarity=0.085  Sum_probs=59.3

Q ss_pred             ChhhHHHHHHHHHHHHHhHHhhhhcCCCceEEEEeccHHHHHHHhcccCC-----ChHHHHHHHHHHHh---hcCCcEEE
Q psy5610           1 MATSVLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSL-----NPIAGEIRDLILTN---KSKLNVRF   72 (237)
Q Consensus         1 ~~~~~AEl~ai~~al~~~~~~~~~~~~~~~~~I~tDs~~~i~~l~~~~~~-----~~~~~~i~~~~~~l---~~~~~v~~   72 (237)
                      ++|++||++|++.||+.+..     . ..++.|||||+++++.+.++.-.     ..--+.+.+++.++   .....+.+
T Consensus        42 ~TNN~aEl~A~i~aL~~~~~-----~-~~~i~I~tDS~yvi~wv~~~~~kt~~~~~vkN~~l~~~i~~a~~~lk~h~~~~  115 (132)
T d1zbfa1          42 GTNNMGEFLAIVHGLRYLKE-----R-NSRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYET  115 (132)
T ss_dssp             ECHHHHHHHHHHHHHHHHHH-----T-TCCCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHHHCCCCC
T ss_pred             cchHHHHHHHHHHHHHHhhc-----C-CceEEEEeccHHHHHHHHhCceecCcCCCcccHHHHHHHHHHHHHHHhCCcCc
Confidence            37899999999999999532     2 35799999999999999875421     11112333333332   23345889


Q ss_pred             EEecCCCCCcCChHHH
Q psy5610          73 IWVPSHVGIAGNEEAD   88 (237)
Q Consensus        73 ~wvp~H~g~~gNe~ad   88 (237)
                      .|+..|+..-||..||
T Consensus       116 ~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1         116 PILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CEEECCHHHHCSCTTC
T ss_pred             eeEEecCcccccCCCC
Confidence            9999999999999988