Psyllid ID: psy10247

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-----
Protein Sequence
MRENQTPPWIIASPTIIYLLNENKKSLIPQQARNSFLEFKSQNLDSLFIFTDGTKTATNTGFAYVSGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWLENQLYERNKLREIKKDIKTWKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAPPECRTCGVVLTIKHILTQCKAYAALRRKWKLESTMEKILQDDHDIVLRCINNNRY
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccHHHHHHHHHHHHccccccEEEEEccccccccEEEEEEEcccccEEEcccccccHHHHHHHHHHHHHHHHHHcHHccccccEEEEEcccHHHHHHHHccccccHHHHHHHHHHHHHHcccccEEEEEccccccccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEccccccccccccccccHHHHHHHHHHccccccHHHHccccccccccccccccccccccccccccHHHHHHccccccHHHHccccHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccEEEEcccHHHccccHHHHHHHHHHHHHHccccEEEEEccccccccEEEEEEEccccEEcccccccHHHHHHHHHHHHHHHHHHHHccccccccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccEccccccccccccccccccHHHHHHHHHHccccccHHHHHcccccccccccccccccHEEEEEccHHHHHHHHHHccHHHHHHHcccccHHHHHHHccccc
Coil and Loop (DISEMBL)
mrenqtppwiiasPTIIYLLNenkkslipqQARNSFLefksqnldslfiftdgtktatntgfayvsgdlcqtyrlnplssiftAESLAILKCLEYIMSLVIvdnfnfrsviicsdsrssLEALRTQFTLNEISFNILCTVHQLKArdinikflwipshcgivenervDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWLENQLYERNKLREIKKDIKTWKTVHWRNRRDEIAVCRLRIGhtkltqeylfkkdappecrtcgvVLTIKHILTQCKAYAALRRKWKLESTMEKILQDDHDIVLRCINNNRY
Flexible Loop (DISEMBL)
mrenqtppwiiasPTIIYLLNENKKSLIPQQARNSFLEFKSQNLDSLFIFTDGTKTATNTGFAYVSGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQSKKtilnewktdwlenqlyernklreikkdiktwktvhwrnrrdeiavcrlrightkltqeylfkkdappeCRTCGVVLTIKHILTQCKAYAALRRKWKLESTMEkilqddhdivlrcinnnry
Low Complexity Region (SEG)
MRENQTPPWIIASPTIIYLLNENKKSLIPQQARNSFLEFKSQNLDSLFIFTDGTKTATNTGFAYVSGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWLENQLYERNKLREIKKDIKTWKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAPPECRTCGVVLTIKHILTQCKAYAALRRKWKLESTMEKILQDDHDIVLRCINNNRY
Disordered region (IsUnstruct)
*******PWIIASPTIIYLLNENKKSLIPQQARNSFLEFKSQNLDSLFIFTDGTKTATNTGFAYVSGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWLENQLYERNKLREIKKDIKTWKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAPPECRTCGVVLTIKHILTQCKAYAALRRKWKLESTMEKILQDDHDIVLRCIN****
Disordered Region (DISOPRED)
*RENQTPPWIIASPTIIYLLNENKKSLIPQQARNSFLEFKSQNLDSLFIFTDGTKTATNTGFAYVSGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWLENQLYERNKLREIKKDIKTWKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAPPECRTCGVVLTIKHILTQCKAYAALRRKWKLESTMEKILQDDHDIVLRCINNN**
Disordered Region (DISEMBL)
MRENQTPPWIIASPTIIYLLNENKKSLIPQQARNSFLEFKSQNLDSLFIFTDGTKTATNTGFAYVSGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWLENQLYERNKLREIKKDIKTWKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAPPECRTCGVVLTIKHILTQCKAYAALRRKWKLESTMEKILQDDHDIVLRCINNNRY
Disordered Region (DISPRO)
****QTPPWIIASPTIIYLLNENKKSLIPQQARNSFLEFKSQNLDSLFIFTDGTKTATNTGFAYVSGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWLENQLYERNKLREIKKDIKTWKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAPPECRTCGVVLTIKHILTQCKAYAALRRKWKLESTMEKILQDDHDIVLRCINNNR*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRENQTPPWIIASPTIIYLLNENKKSLIPQQARNSFLEFKSQNLDSLFIFTDGTKTATNTGFAYVSGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWLENQLYERNKLREIKKDIKTWKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAPPECRTCGVVLTIKHILTQCKAYAALRRKWKLESTMEKILQDDHDIVLRCINNNRY
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	315
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.873	0.225	0.321	2e-29
427791807	1212	Putative tick transposon, partial [Rhipi	0.866	0.225	0.315	4e-28
427791321	1210	Putative tick transposon, partial [Rhipi	0.882	0.229	0.310	4e-28
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.793	0.530	0.307	1e-26
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.822	0.515	0.314	4e-26
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.771	0.612	0.330	5e-26
443724607	397	hypothetical protein CAPTEDRAFT_208903 [	0.758	0.602	0.337	6e-25
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.695	0.839	0.343	2e-24
427791063	1035	Putative tick transposon, partial [Rhipi	0.758	0.230	0.316	1e-23
427798889	1199	Putative tick transposon, partial [Rhipi	0.768	0.201	0.309	5e-23

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

 Score =  135 bits (341), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 92/286 (32%), Positives = 139/286 (48%), Gaps = 11/286 (3%)

Query: 5    QTPPWIIASPTI-IYLLNENKKSLIPQQARNSFLEFKSQNLDSLFIFTDGTKTATNTGFA 63
            Q PPW++  P + + LLN  K++  P   +  F E +    D   I+TDG+K       A
Sbjct: 914  QNPPWLMNKPKLNLSLLNFKKENTDPSILQVHFRELQESYGDCGTIYTDGSKMEGKVACA 973

Query: 64   YVSGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEAL 123
                +   + RL    SIFTAE  AIL      ++L+ V        IICSDS+S+L+AL
Sbjct: 974  CSFRNKTISRRLPDGCSIFTAELHAIL------LALMAVKASERSKFIICSDSKSALQAL 1027

Query: 124  RTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSV 183
                T   +    L  +  + A   ++ F+W+PSH GI  NE  D+ AK ++   +  + 
Sbjct: 1028 GRMKTDIPLVHKSLKLLDLITADRRDVTFIWVPSHVGIEGNEAADREAKRALNHAVSGTQ 1087

Query: 184  VVKDVIIQS-KKTILNEWKTDWLENQLYERNKLREIKKDIKTWKTVHWRNRRDEIAVCRL 242
            +    + QS       EW+  W   +    +KLR+I  D++   T     RR    + RL
Sbjct: 1088 IPYSDLRQSIASATYREWQNRW---EAETHSKLRQIVADVRWRPTSKGLTRRGSTTMSRL 1144

Query: 243  RIGHTKLTQEYLFKKDAPPECRTCGVVLTIKHILTQCKAYAALRRK 288
            RIGHT +T  ++ K++ PP C  C   LT++HIL  C  Y  +R K
Sbjct: 1145 RIGHTYITHSFVLKREEPPLCEYCDSRLTVEHILVDCPRYQDVRAK 1190

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

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

 Score =  131 bits (330), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 90/285 (31%), Positives = 140/285 (49%), Gaps = 12/285 (4%)

Query: 7    PPWI-IASPTIIYLLNENKKSLIPQQARNSFLEFKSQNLDSLFIFTDGTKTATNTGFAYV 65
            PPW  +A    I L + NKK   P+     F   + +  D    +TDG+KT  + G   V
Sbjct: 899  PPWFDLAQLCDISLSHINKKVTPPELIIQEFRALQEKYRDYAEFYTDGSKTRDHVGIGIV 958

Query: 66   SGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRT 125
            +G+   + R+    SIFTAE  A+ +    I++         +  II +DS S+L+AL  
Sbjct: 959  TGESAFSVRVPQCISIFTAEVYALYEAARKIIA------GKHKKAIIYTDSLSALKALHI 1012

Query: 126  QFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLK-SVV 184
            +     +  +IL  V  + ++ I+++F W+PSH GI  NE+ D+ A  + +  L K  + 
Sbjct: 1013 KSECEPLVGDILNMV-LINSKVISMRFCWVPSHVGIPGNEKADKCASLAAHKTLTKIRIP 1071

Query: 185  VKDVIIQSKKTILNEWKTDWLENQLYERNKLREIKKDIKTWKTVHWRNRRDEIAVCRLRI 244
            +KD     +  +L +W+  W        NKL  +K  +  WK    + R  E+ +CRLRI
Sbjct: 1072 LKDSQRTIRLALLAKWQQQW---DSCTSNKLHLVKPTLGEWKNCRHQERFIEVILCRLRI 1128

Query: 245  GHTKLTQEYLFKKDAPPECRTCGVVLTIKHILTQCKAYAALRRKW 289
            GHT LT  +L  K+  P C  C   LT+ HIL  C      R+K+
Sbjct: 1129 GHTHLTHNFLLTKEEQPMCEKCQEPLTLIHILILCPNIETQRQKY 1173

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 =  131 bits (330), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 90/290 (31%), Positives = 142/290 (48%), Gaps = 12/290 (4%)

Query: 2    RENQTPPWI-IASPTIIYLLNENKKSLIPQQARNSFLEFKSQNLDSLFIFTDGTKTATNT 60
            +  + PPW  +A    I L + NKK   P+     F   + +  D    +TDG+KT  + 
Sbjct: 891  KPPRIPPWFDLAQLCDISLSHINKKVTPPELIIQEFRALQEKYRDYAEFYTDGSKTRDHV 950

Query: 61   GFAYVSGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSL 120
            G   V+G+   + R+    SIFTAE  A+ +    I++         +  II +DS S+L
Sbjct: 951  GIGIVTGESAFSVRVPQCISIFTAEVYALYEAARKIIA------GKHKKAIIYTDSLSAL 1004

Query: 121  EALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLL 180
            +AL  +     +  +IL  V  + ++ I+++F W+PSH GI  NE+ D+ A  + +  L 
Sbjct: 1005 KALHIKSECEPLVGDILNMV-LINSKVISMRFCWVPSHVGIPGNEKADKCASLAAHKTLT 1063

Query: 181  K-SVVVKDVIIQSKKTILNEWKTDWLENQLYERNKLREIKKDIKTWKTVHWRNRRDEIAV 239
            K  + +KD     +  +L +W+  W        NKL  +K  +  WK    + R  E+ +
Sbjct: 1064 KIRIPLKDSQRTIRLALLAKWQQQW---DSCTSNKLHLVKPTLGEWKNCRHQERFIEVIL 1120

Query: 240  CRLRIGHTKLTQEYLFKKDAPPECRTCGVVLTIKHILTQCKAYAALRRKW 289
            CRLRIGHT LT  +L  K+  P C  C   LT+ HIL  C      R+K+
Sbjct: 1121 CRLRIGHTHLTHNFLLTKEEQPMCEKCQEPLTLIHILILCPNIETQRQKY 1170

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  126 bits (317), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 80/260 (30%), Positives = 127/260 (48%), Gaps = 10/260 (3%)

Query: 33  RNSFLEFKSQNLDSLFIFTDGTKTATNTGFAYVSGDLCQTYRLNPLSSIFTAESLAILKC 92
           R+ F +   +  DS   +TDG+K+  +   ++ S  L    +L    S+FT+E +AIL  
Sbjct: 7   RSEFADALDRYPDSTVFYTDGSKSEDSVACSFFSSRLKLKMKLPVQMSVFTSEIIAILSA 66

Query: 93  LEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKF 152
           L      V  DN   +  +ICSDS S++ A+      +     +L  +  +  ++  + F
Sbjct: 67  LR----CVEADNEQHQ-FVICSDSLSAIMAIHGMDVRHPYVLQVLYAIKSISQQEKIVVF 121

Query: 153 LWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVK--DVIIQSKKTILNEWKTDWLENQLY 210
           +W PSH GI  NE  D  AK ++ +  L  + V   D+    KK I + W+ +W E    
Sbjct: 122 MWCPSHVGIPGNEMADTLAKEALSSTNLAELPVPASDLRCLIKKYIRSRWQHEWDEQH-- 179

Query: 211 ERNKLREIKKDIKTWKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAPPECRTCGVVL 270
             NKL  I   I  W       RR+EI + R+RIGHT  T +Y+ + D   EC  C   L
Sbjct: 180 -SNKLHSIHPTIGPWPPCQREKRREEIVLARIRIGHTHYTHDYIPRGDDQTECVACVCPL 238

Query: 271 TIKHILTQCKAYAALRRKWK 290
           T++HI+ +C  +  +R + K
Sbjct: 239 TVQHIIIECADFLHIRYRDK 258

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 =  124 bits (312), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 90/286 (31%), Positives = 138/286 (48%), Gaps = 27/286 (9%)

Query: 4   NQTPPWIIASPTII-----YLLNENKKSLIPQQARNSFLEFKSQNLDSLFIFTDGTKTAT 58
           +  PPW +  P +      +L +++    + Q+  N   ++   N     I+TDG+K+  
Sbjct: 39  SDVPPWKLRPPEVDTSISKFLKDQHPALFLKQEFYNLIDKYPGIN-----IYTDGSKSNN 93

Query: 59  NTGFAYVSGDLCQTYR----LNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICS 114
               A+     C TY+    L    SI+TAE +AI + L +I ++   D FN     ICS
Sbjct: 94  AVACAFT----CSTYQIQFGLPTQMSIYTAELIAIEQALIFIETVKDEDQFN-----ICS 144

Query: 115 DSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNS 174
           DS SSL AL      +    +IL   + L  +   + F+W PSH GI+ NE  D+ AK +
Sbjct: 145 DSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQA 204

Query: 175 IYAQLLK-SVVVKDVIIQSKKTILNEWKTDWLENQLYERNKLREIKKDIKTWKTVHWRNR 233
           +   + K  +   D     +  + + W+ +W E      NKL  I+  I  WK     +R
Sbjct: 205 LVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDEET---DNKLHSIQPVISEWKQGPQIDR 261

Query: 234 RDEIAVCRLRIGHTKLTQEYLFKKDAPPECRTCGVVLTIKHILTQC 279
           R EI + R RIGH+ LT  YL +++  P C  C  +LT+KHIL  C
Sbjct: 262 RGEIVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILIDC 307

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  124 bits (312), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 86/260 (33%), Positives = 129/260 (49%), Gaps = 17/260 (6%)

Query: 49  IFTDGTKTATNTGFAYVSGDLCQTYR----LNPLSSIFTAESLAILKCLEYIMSLVIVDN 104
           I+TDG+K+      A+     C TY+    L    SI+TAE +AI + L +I ++   D 
Sbjct: 133 IYTDGSKSNDTVACAFT----CSTYQIQFGLPAQMSIYTAELIAIEQALIFIETVKDEDQ 188

Query: 105 FNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVEN 164
           FN     ICSDS SSL AL      +    +IL   + L  +   + F+W PSH GI+ N
Sbjct: 189 FN-----ICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKKVVFIWCPSHVGILGN 243

Query: 165 ERVDQAAKNSIYAQLLK-SVVVKDVIIQSKKTILNEWKTDWLENQLYERNKLREIKKDIK 223
           E  D+ AK ++   + K  +   D     +  + + W+ +W        NKL  I+  I 
Sbjct: 244 EVADRQAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDGE---TDNKLHIIQPVIS 300

Query: 224 TWKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAPPECRTCGVVLTIKHILTQCKAYA 283
            WK     +RR EI +   RIGH+ LT  YL +++  P C  C  +LT+KHIL  C  + 
Sbjct: 301 EWKQGPQIDRRGEIVLACARIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILIDCIDFE 360

Query: 284 ALRRKWKLESTMEKILQDDH 303
             RRK+    +M ++ +D H
Sbjct: 361 ISRRKYFNVFSMRQLFEDTH 380

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 =  120 bits (302), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 89/264 (33%), Positives = 129/264 (48%), Gaps = 25/264 (9%)

Query: 49  IFTDGTKTATNTGFAYVSGDLCQTYR----LNPLSSIFTAESLAILKCLEYIMSLVIVDN 104
           I+TDG+K+      A+     C TY+    L    SI+TAE +AI + L +I ++   D 
Sbjct: 133 IYTDGSKSNDAVACAFT----CSTYQIQFGLPAQMSIYTAELIAIEQALIFIETMKDEDQ 188

Query: 105 FNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVEN 164
           FN     ICSDS SSL AL      +    +IL   + L  +   + F+W PSH GI+ N
Sbjct: 189 FN-----ICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGN 243

Query: 165 ERVDQAAKNSIYAQL----LKSVVVKDVIIQSKKTI-LNEWKTDWLENQLYERNKLREIK 219
           E  D+ AK ++   +    L     K  I    K++  NEW  +         NKL  I+
Sbjct: 244 EVADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLRQNEWDEE-------TDNKLHTIQ 296

Query: 220 KDIKTWKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAPPECRTCGVVLTIKHILTQC 279
             I  WK     +RR EI +    IGH+ LT  YL +++  P C  C  +LT+KHIL  C
Sbjct: 297 PVISEWKQGPQIDRRGEIVLACACIGHSHLTHGYLLRREVAPFCIPCQSLLTVKHILIDC 356

Query: 280 KAYAALRRKWKLESTMEKILQDDH 303
             +   RRK+   S+M ++ +D H
Sbjct: 357 IDFEISRRKYFNVSSMRQLFEDTH 380

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  119 bits (298), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 81/236 (34%), Positives = 119/236 (50%), Gaps = 17/236 (7%)

Query: 49  IFTDGTKTATNTGFAYVSGDLCQTYR----LNPLSSIFTAESLAILKCLEYIMSLVIVDN 104
           I+TDG+K+      A+     C TY+    L    SI+TAE +AI + L +I ++   D 
Sbjct: 38  IYTDGSKSNDAVACAFT----CSTYQIQFGLPAQMSIYTAELIAIEQALIFIETVKDEDQ 93

Query: 105 FNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVEN 164
           FN     ICSDS SSL AL      +    +IL   + L  +   + F+W PSH GI+ N
Sbjct: 94  FN-----ICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIWCPSHVGILGN 148

Query: 165 ERVDQAAKNSIYAQLLK-SVVVKDVIIQSKKTILNEWKTDWLENQLYERNKLREIKKDIK 223
           E  D+ AK ++   + K  +   D     +  + + W+ +W E      NKL  I+  I 
Sbjct: 149 EVADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDEET---DNKLHSIQPVIS 205

Query: 224 TWKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAPPECRTCGVVLTIKHILTQC 279
            WK     +RR EI + R RIGH+ LT  YL +++  P C  C  +L++KHIL  C
Sbjct: 206 EWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIPCQSLLSVKHILIDC 261

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|427791063|gb|JAA60983.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  117 bits (292), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 82/259 (31%), Positives = 126/259 (48%), Gaps = 20/259 (7%)

Query: 36   FLEFKSQNLDSLFIFTDGTKTATNTGFAYVSGDLCQTYRLNPLSSIFTAESLAILKCLEY 95
            FLE + +     F FTD +K  ++  +A V         L+  +SIFTAE+ AI   +++
Sbjct: 786  FLELQHKYTFPEF-FTDASKFNSSVSYAAVGPSFSDAGVLHQNTSIFTAEAYAIFVAVKH 844

Query: 96   IMSLVIVDNFNFRSVIICSDSRSSLEALRT----QFTLNEISFNILCTVHQLKARDINIK 151
            I      +     S +I +DS S ++AL+T    +  +    +++LCTV+ LK    ++ 
Sbjct: 845  I------EQLKLPSAVIYTDSLSVVKALKTLKKHKNPVLASLYSLLCTVYALKQ---HVV 895

Query: 152  FLWIPSHCGIVENERVDQ--AAKNSIYAQLLKSVVVKDVIIQSKKTILNEWKTDWLENQL 209
              W+P H  I  N   DQ  A+ +   A    ++   D+    K+ +   W++ W     
Sbjct: 896  VCWVPGHREIQGNVLADQLAASAHENAAHTFLAIPALDLKPLLKRKLRAYWQSIW---DT 952

Query: 210  YERNKLREIKKDIKTWKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAPPECRTCGVV 269
              +NKL  IK  +  W     ++RR EI + RLR GHT  T  YL   + PP C  CG  
Sbjct: 953  QTQNKLHAIKPQLGEWPPAS-KSRRTEITLTRLRTGHTHTTHAYLLSGNDPPRCERCGEP 1011

Query: 270  LTIKHILTQCKAYAALRRK 288
            LT+ HIL QC    A+RRK
Sbjct: 1012 LTVLHILIQCNELDAMRRK 1030

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  114 bits (286), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 81/262 (30%), Positives = 133/262 (50%), Gaps = 20/262 (7%)

Query: 33   RNSFLEFKSQNLDSLFIFTDGTKTATNTGFAYVSGDLCQTYRLNPLSSIFTAESLAILKC 92
            R  FLE + +     F +TD +K+ T+  +A V         L+P +SIFTAE+ AIL  
Sbjct: 949  RTYFLELQHKYNCPAF-YTDASKSHTSVSYAAVGPSFSAAGALHPNTSIFTAEAYAILAA 1007

Query: 93   LEYIMSLVIVDNFNFRSVIICSDSRSSLEALRT-QFTLNEIS---FNILCTVHQLKARDI 148
            +++I  L        +  +I +DS S ++AL+T +   N +    +++LCT++  K    
Sbjct: 1008 VKHIREL------KLQKAVIYTDSLSVVKALKTLKKHRNPVLVSLYSLLCTIYTSKQ--- 1058

Query: 149  NIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVKDVIIQS--KKTILNEWKTDWLE 206
            ++   W+P H  I  N   DQ A ++  +    S+ +  + ++   K+ I   W++ W +
Sbjct: 1059 HVVVCWVPGHREIQGNVMADQLAVSAHDSSANTSIAIPALDLKPYLKRKIRAYWQSTW-D 1117

Query: 207  NQLYERNKLREIKKDIKTWKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAPPECRTC 266
             Q +  NKL  IK  +  W  +  ++R  E+ + RLR GHT  T  YL      P C  C
Sbjct: 1118 RQTH--NKLHVIKPQLGHWPPIS-KSRYTEVTLTRLRTGHTHSTHAYLLSGGDAPFCDKC 1174

Query: 267  GVVLTIKHILTQCKAYAALRRK 288
            G  LT+ HIL QC+   A+R+K
Sbjct: 1175 GEPLTVIHILIQCRGLDAIRKK 1196

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	315
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.730	0.473	0.236	2.4e-11

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

 Score = 181 (68.8 bits), Expect = 2.4e-11, P = 2.4e-11
 Identities = 61/258 (23%), Positives = 128/258 (49%)

Query:    49 IFTDGTKTATNTGFAYVSGDLCQTYRLNPLSSIFT-AESLAILKCLEYIM-SLVIVDNFN 106
             ++TDG+      G A +    C  Y ++  S +   +ES   +  L+ I+ +LVI+    
Sbjct:   185 LYTDGSGINGRVGAAAI----CPKYLISRSSYMGQQSESTVYVAELQGILLALVIILQRQ 240

Query:   107 FRSVIICSDSRSSLEALRTQFTLNE--ISFNILCTVHQLKARDINIKFLWIPSHCGIVEN 164
              +  +I +D++++L+ALR   + +   I   I+  +++ +   +N+ F WIP+H G+  N
Sbjct:   241 MQHAVIFTDNQATLQALRNPGSQSGQYILEAIIMALNKGRKAGLNVHFRWIPAHRGVEGN 300

Query:   165 ERVDQAAKNSIYAQLLKS----VVVKDVIIQSKKTILN-EWKTDWLE----NQLYERNKL 215
             E+ D+ AK +   + ++     + ++  + +    ++N  W+ DW       +LYE    
Sbjct:   301 EQADRRAKEATGWRRIRGHRGRMTIRSAVKRRAHEVVNARWENDWKSCHHGRELYELTPT 360

Query:   216 REIKKDIKTWKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAP--P--ECRTCG-VVL 270
                +K ++  + +H   R     + ++R G   L + YL+++  P  P  +C+ CG    
Sbjct:   361 -PTRKVLRVHQDLH---RALSTIIVQMRTGKIGL-RHYLYQRGVPDVPNSDCQ-CGRATQ 414

Query:   271 TIKHILTQCKAYAALRRK 288
             +++HIL  C  ++ LR +
Sbjct:   415 SVRHILLACPTFSGLREE 432


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        0.322   0.135   0.408    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      315       315   0.00082  116 3  11 22  0.49    33
                                                     33  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  617 (66 KB)
  Total size of DFA:  241 KB (2129 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  29.57u 0.07s 29.64t   Elapsed:  00:00:03
  Total cpu time:  29.57u 0.07s 29.64t   Elapsed:  00:00:03
  Start:  Thu Aug 15 13:34:48 2013   End:  Thu Aug 15 13:34:51 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	3.1.26.4	LOW CONFIDENCE prediction!
3rd Layer	3.1.26	0.691

---

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	315
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	8e-30
pfam00075	126	pfam00075, RNase_H, RNase H	2e-12
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	7e-05
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	9e-05
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	0.002

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

 Score =  109 bits (275), Expect = 8e-30
 Identities = 42/128 (32%), Positives = 70/128 (54%), Gaps = 7/128 (5%)

Query: 48  FIFTDGTKTATNTGFAYV---SGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDN 104
            I+TDG+K    TG  +     G + ++Y+L P  S+F AE LAIL+ L+      + + 
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLA----LREG 56

Query: 105 FNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVEN 164
              R + I SDS+++L+ALR+  + + +   I   + +L    + ++  W+P H GI  N
Sbjct: 57  RRARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGN 116

Query: 165 ERVDQAAK 172
           ER D+ AK
Sbjct: 117 ERADRLAK 124

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 = 63.0 bits (154), Expect = 2e-12
 Identities = 31/137 (22%), Positives = 54/137 (39%), Gaps = 17/137 (12%)

Query: 45  DSLFIFTDG--TKTATNTGFAYVSGDLCQTYRLNPLSSIFTAESLAI---LKCLEYIMSL 99
           +++ ++TDG         G  YV+    Q  +  P ++   AE LA+   L+ L      
Sbjct: 2   EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALEALSG---- 57

Query: 100 VIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHC 159
                   + V I +DS+  +  +   +     S  I   + +L  +   +   W+P H 
Sbjct: 58  --------QKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQKKHKVYIQWVPGHS 109

Query: 160 GIVENERVDQAAKNSIY 176
           GI  NE  D+ AK    
Sbjct: 110 GIPGNELADKLAKQGAS 126

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

 Score = 42.0 bits (99), Expect = 7e-05
 Identities = 23/102 (22%), Positives = 43/102 (42%), Gaps = 20/102 (19%)

Query: 84  AESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISF--------- 134
           AE  A+++ LE +  L          V + +DS+  +E + T++ +              
Sbjct: 46  AELRALIEALEALKEL------GACEVTLYTDSKYVVEGI-TRWIVKWKKNGWKTADKKP 98

Query: 135 ----NILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAK 172
               ++   + +L  R   + + W+  H G  ENER DQ A+
Sbjct: 99  VKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140

Length = 154

>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 = 41.2 bits (97), Expect = 9e-05
 Identities = 24/100 (24%), Positives = 48/100 (48%), Gaps = 10/100 (10%)

Query: 76  NPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFN 135
            P ++   AE LA+L+ LE  + L        + +II +DS+  ++ + +     + +  
Sbjct: 34  IPAATNNEAELLALLEALELALDL------GLKKLIIETDSKYVVDLINSWSKGWKKNNL 87

Query: 136 ILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSI 175
           +L  +  L ++ I+I+F  +P       NE  D+ AK + 
Sbjct: 88  LLWDILLLLSKFIDIRFEHVPREG----NEVADRLAKEAA 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|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 = 37.6 bits (88), Expect = 0.002
 Identities = 24/114 (21%), Positives = 38/114 (33%), Gaps = 38/114 (33%)

Query: 84  AESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFN-------- 135
           AE  A++  L  I             ++I +DS         ++ +N ++          
Sbjct: 46  AELRAVIHALRLIKE----VGEGLTKLVIATDS---------EYVVNGVTEWIPKWKKNG 92

Query: 136 --------------ILCTVHQLK---ARDINIKFLWIPSHCGIVENERVDQAAK 172
                         I      L+    R I +KF  +P H GI  NE  D+ AK
Sbjct: 93  WKTSKGKPVANKDLIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	315
PRK06548	161	ribonuclease H; Provisional	99.9
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.9
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.9
PRK08719	147	ribonuclease H; Reviewed	99.89
PRK00203	150	rnhA ribonuclease H; Reviewed	99.88
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.79
PRK13907	128	rnhA ribonuclease H; Provisional	99.76
KOG3752|consensus	371		99.73
PRK07708	219	hypothetical protein; Validated	99.67
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.54
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.35
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	96.48
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	92.95
.; GO: 0004523 ribonuclease H activity" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF00336">PF00336	245	DNA_pol_viral_C: DNA polymerase (viral) C-terminal	83.09

>PRK06548 ribonuclease H; Provisional

Probab=99.90  E-value=4.8e-23  Score=171.36  Aligned_cols=126  Identities=21%  Similarity=0.288  Sum_probs=94.5

Q ss_pred             CCceEEEEcCCCCC--CCeeEEEE-ECCeeeEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHHHH
Q psy10247         44 LDSLFIFTDGTKTA--TNTGFAYV-SGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSL  120 (315)
Q Consensus        44 ~~~~~iytDGS~~~--~~~G~a~v-~~~~~~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~al  120 (315)
                      +..+.||||||+..  +..|+|++ ....... .....+|++.|||.||+.||+.+.       .....|.|+|||++|+
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~-g~~~~~TNnraEl~Aii~aL~~~~-------~~~~~v~I~TDS~yvi   74 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDS-GGWDIATNNIAELTAVRELLIATR-------HTDRPILILSDSKYVI   74 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCCcEEc-cCCCCCCHHHHHHHHHHHHHHhhh-------cCCceEEEEeChHHHH
Confidence            45699999999885  35888888 3322111 223468999999999999998652       1345799999999999


Q ss_pred             HHHhc--------cccc---cHHH-HHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhhc
Q psy10247        121 EALRT--------QFTL---NEIS-FNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQ  178 (315)
Q Consensus       121 ~~l~~--------~~~~---~~~~-~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~~  178 (315)
                      ++++.        .+.+   .++. +++++++..+.+. ..|+|.|||||+|.+|||.||+||++|+...
T Consensus        75 ~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~  143 (161)
T PRK06548         75 NSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNF  143 (161)
T ss_pred             HHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence            99985        2222   2333 5666666666554 4799999999999999999999999998654

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

Probab=99.90  E-value=6.1e-23  Score=167.92  Aligned_cols=127  Identities=24%  Similarity=0.292  Sum_probs=100.3

Q ss_pred             CceEEEEcCCCCC--CCeeEEEE--ECCee--eEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHH
Q psy10247         45 DSLFIFTDGTKTA--TNTGFAYV--SGDLC--QTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRS  118 (315)
Q Consensus        45 ~~~~iytDGS~~~--~~~G~a~v--~~~~~--~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~  118 (315)
                      ..+.||||||+..  |..|+|+|  .+...  .+.... .+||++||++|++.||+.+.      ..+...|.|+|||++
T Consensus         2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~------~~~~~~v~l~tDS~y   74 (154)
T COG0328           2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALK------ELGACEVTLYTDSKY   74 (154)
T ss_pred             CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHH------hcCCceEEEEecHHH
Confidence            4689999999985  45888887  33322  333344 89999999999999999994      357899999999999


Q ss_pred             HHHHHhcccc---c--------cH-HHHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhhc
Q psy10247        119 SLEALRTQFT---L--------NE-ISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQ  178 (315)
Q Consensus       119 al~~l~~~~~---~--------~~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~~  178 (315)
                      |+++|.....   .        .| -..+++.++..+......|.+.|||||+|.++||+||+||+.|+...
T Consensus        75 v~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          75 VVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             HHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            9999983311   1        12 13467777777777777999999999999999999999999998765

>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=99.90  E-value=2.1e-23  Score=168.86  Aligned_cols=118  Identities=34%  Similarity=0.517  Sum_probs=89.8

Q ss_pred             CceEEEEcCCCCC--CCeeEEEE-ECCeeeEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHHHHH
Q psy10247         45 DSLFIFTDGTKTA--TNTGFAYV-SGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLE  121 (315)
Q Consensus        45 ~~~~iytDGS~~~--~~~G~a~v-~~~~~~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~al~  121 (315)
                      ..+.||||||+..  +..|+|++ ..+...+..++ ..|++.|||.||..||+.+ .        ...++|+|||+++++
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--------~~~v~I~tDS~~v~~   71 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL-E--------HRKVTIYTDSQYVLN   71 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH-S--------TSEEEEEES-HHHHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh-h--------cccccccccHHHHHH
Confidence            4789999999774  33566665 44444445555 8899999999999999943 2        389999999999999


Q ss_pred             HHhc-----ccccc----HHHHHHHHHHHHHhhcCCcEEEEEeCCCCCC-chhhhhcHHHHHhHh
Q psy10247        122 ALRT-----QFTLN----EISFNILCTVHQLKARDINIKFLWIPSHCGI-VENERVDQAAKNSIY  176 (315)
Q Consensus       122 ~l~~-----~~~~~----~~~~~i~~~~~~l~~~~~~v~~~WVpgH~g~-~gNe~AD~lAk~a~~  176 (315)
                      .+..     .+...    ++..+|...   + ..+.+|.|.|||||+|+ .||+.||+|||+|+.
T Consensus        72 ~l~~~~~~~~~~~~~~~~~i~~~i~~~---~-~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~~  132 (132)
T PF00075_consen   72 ALNKWLHGNGWKKTSNGRPIKNEIWEL---L-SRGIKVRFRWVPGHSGVPQGNERADRLAKEAAQ  132 (132)
T ss_dssp             HHHTHHHHTTSBSCTSSSBHTHHHHHH---H-HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHhccccccccccccccchhheeec---c-ccceEEeeeeccCcCCCchhHHHHHHHHHHhcC
Confidence            8887     33222    344455532   2 55899999999999999 799999999999873

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

>PRK08719 ribonuclease H; Reviewed

Probab=99.89  E-value=9.1e-23  Score=168.12  Aligned_cols=121  Identities=23%  Similarity=0.349  Sum_probs=91.7

Q ss_pred             CceEEEEcCCCCCC-----CeeEEEE--EC--Cee--eEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEE
Q psy10247         45 DSLFIFTDGTKTAT-----NTGFAYV--SG--DLC--QTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIIC  113 (315)
Q Consensus        45 ~~~~iytDGS~~~~-----~~G~a~v--~~--~~~--~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~  113 (315)
                      +.++||||||+..+     .+|+|++  +.  ...  ....+...+|++.||+.|++.||+.+..       .   .+|+
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~-------~---~~i~   72 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARD-------G---DVIY   72 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCC-------C---CEEE
Confidence            57899999999643     2588876  32  222  3334555689999999999999999832       1   3799


Q ss_pred             eCCHHHHHHH--------hcccccc---HH-HHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHh
Q psy10247        114 SDSRSSLEAL--------RTQFTLN---EI-SFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIY  176 (315)
Q Consensus       114 sDS~~al~~l--------~~~~~~~---~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~  176 (315)
                      |||++|++++        .+++..+   ++ -..++..+..+.+ ..+|+|.|||||+|++|||.||+||++|+.
T Consensus        73 tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         73 SDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             echHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            9999999999        4455432   22 2456666666655 577999999999999999999999999874

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.88  E-value=7.9e-22  Score=163.69  Aligned_cols=125  Identities=19%  Similarity=0.270  Sum_probs=91.7

Q ss_pred             ceEEEEcCCCCC--CCeeEEEE--ECCeeeEE-ecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHHHH
Q psy10247         46 SLFIFTDGTKTA--TNTGFAYV--SGDLCQTY-RLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSL  120 (315)
Q Consensus        46 ~~~iytDGS~~~--~~~G~a~v--~~~~~~~~-~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~al  120 (315)
                      .+.||||||+..  +..|+|+|  .++....+ ......|++.|||.|++.||+.+.        ....+.|+|||++++
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~--------~~~~v~I~tDS~yvi   74 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALK--------EPCEVTLYTDSQYVR   74 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcC--------CCCeEEEEECHHHHH
Confidence            589999999984  34788877  33322222 223478899999999999999872        246799999999999


Q ss_pred             HHHhcc--------ccc---cHHH-HHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhhcc
Q psy10247        121 EALRTQ--------FTL---NEIS-FNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQL  179 (315)
Q Consensus       121 ~~l~~~--------~~~---~~~~-~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~~~  179 (315)
                      ++|...        +..   .++. ..+++.+..+.. ...|.|.|||||+|++||+.||+||++|+..+.
T Consensus        75 ~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~  144 (150)
T PRK00203         75 QGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAGAEEAT  144 (150)
T ss_pred             HHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence            999862        221   1222 234444444433 378999999999999999999999999987643

>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=99.79  E-value=2.7e-18  Score=135.93  Aligned_cols=122  Identities=27%  Similarity=0.351  Sum_probs=93.5

Q ss_pred             EEEEcCCCCCC--CeeEEEE--ECCe--ee-EEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHHHH
Q psy10247         48 FIFTDGTKTAT--NTGFAYV--SGDL--CQ-TYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSL  120 (315)
Q Consensus        48 ~iytDGS~~~~--~~G~a~v--~~~~--~~-~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~al  120 (315)
                      .+|||||...+  ++|+|++  +...  .. ........+++.+|+.|++.||+.+.      ......+.|++||+.++
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~------~~~~~~i~i~~Ds~~~~   74 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELAL------ELGGKKVNIYTDSQYVI   74 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHH------hCCCceEEEEECHHHHH
Confidence            47999999864  6888887  3221  11 11222578999999999999999984      45789999999999999


Q ss_pred             HHHhcccc-ccHHHHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhH
Q psy10247        121 EALRTQFT-LNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSI  175 (315)
Q Consensus       121 ~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~  175 (315)
                      +.+++... .......+...+..+...+..+.|.|||+|+|..+|+.||.|||.|.
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          75 NALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             HHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            99998764 22223344444445556788999999999999999999999999873

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

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.76  E-value=1.6e-17  Score=134.07  Aligned_cols=121  Identities=21%  Similarity=0.244  Sum_probs=92.9

Q ss_pred             eEEEEcCCCCC--CCeeEEEE--ECCeeeEEe-cCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHHHHH
Q psy10247         47 LFIFTDGTKTA--TNTGFAYV--SGDLCQTYR-LNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLE  121 (315)
Q Consensus        47 ~~iytDGS~~~--~~~G~a~v--~~~~~~~~~-l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~al~  121 (315)
                      +.||||||+..  +..|+|+|  +.......+ .....|++.||+.|++.||+.+..      .+...+.|+|||+.+++
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~------~g~~~v~i~sDS~~vi~   75 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTE------HNYNIVSFRTDSQLVER   75 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHh------CCCCEEEEEechHHHHH
Confidence            67999999985  45888888  332221121 234679999999999999999953      45678999999999999


Q ss_pred             HHhccccccHHHHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhh
Q psy10247        122 ALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYA  177 (315)
Q Consensus       122 ~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~  177 (315)
                      .+++.+........++..+..+......+.|.|||.    +.|+.||.||++|...
T Consensus        76 ~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         76 AVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAILQ  127 (128)
T ss_pred             HHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence            999977544444556666666666777888999995    5999999999998753

>KOG3752|consensus

Probab=99.73  E-value=1.4e-17  Score=151.93  Aligned_cols=128  Identities=20%  Similarity=0.322  Sum_probs=98.0

Q ss_pred             CCceEEEEcCCCCCC-----CeeEEEE--EC-CeeeEEecC-CCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEe
Q psy10247         44 LDSLFIFTDGTKTAT-----NTGFAYV--SG-DLCQTYRLN-PLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICS  114 (315)
Q Consensus        44 ~~~~~iytDGS~~~~-----~~G~a~v--~~-~~~~~~~l~-~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~s  114 (315)
                      .+.+++|||||+..+     .+|+|++  ++ ....+..+. ..+++|.|||.||..||+.|.+      ....+++|.|
T Consensus       210 ~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~------~~~~kv~I~T  283 (371)
T KOG3752|consen  210 IEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARS------KNINKVVIRT  283 (371)
T ss_pred             ccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHh------cCCCcEEEEe
Confidence            455899999999863     4899998  22 345777775 7899999999999999999953      3566999999


Q ss_pred             CCHHHHHHHhccccc-----------cH-----H-HHHHHHHHHHHhh--cCCcEEEEEeCCCCCCchhhhhcHHHHHhH
Q psy10247        115 DSRSSLEALRTQFTL-----------NE-----I-SFNILCTVHQLKA--RDINIKFLWIPSHCGIVENERVDQAAKNSI  175 (315)
Q Consensus       115 DS~~al~~l~~~~~~-----------~~-----~-~~~i~~~~~~l~~--~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~  175 (315)
                      ||.+++++|+.+...           ++     + .+.....+..|.+  .+.+|++.||+||.|+.|||+||.||++++
T Consensus       284 DS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs  363 (371)
T KOG3752|consen  284 DSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGS  363 (371)
T ss_pred             chHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence            999999999764321           12     0 1123333444433  368999999999999999999999999985


Q ss_pred             hh
Q psy10247        176 YA  177 (315)
Q Consensus       176 ~~  177 (315)
                      ..
T Consensus       364 ~~  365 (371)
T KOG3752|consen  364 TL  365 (371)
T ss_pred             hh
Confidence            43

>PRK07708 hypothetical protein; Validated

Probab=99.67  E-value=1.5e-15  Score=132.96  Aligned_cols=141  Identities=16%  Similarity=0.178  Sum_probs=98.6

Q ss_pred             HHHHHHHHHHhhCCCceEEEEcCCCC--CCCeeEEEE--E--CCeee----EEecCCCCcHhHHHHHHHHHHHHHHHHhh
Q psy10247         31 QARNSFLEFKSQNLDSLFIFTDGTKT--ATNTGFAYV--S--GDLCQ----TYRLNPLSSIFTAESLAILKCLEYIMSLV  100 (315)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~iytDGS~~--~~~~G~a~v--~--~~~~~----~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~  100 (315)
                      +..+...++ ...|+.+.+|+|||+.  ++++|+|+|  .  ++...    ...++...|++.||+.|++.||+.+..  
T Consensus        59 ~~~~~~~~~-~~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e--  135 (219)
T PRK07708         59 ELKKLSKEV-EEEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEE--  135 (219)
T ss_pred             HHhhhhhhh-ccCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHH--
Confidence            344443333 3357789999999986  356788876  3  22221    123555689999999999999999964  


Q ss_pred             hhccCCcceEEEEeCCHHHHHHHhccccc-cHHHHHHHHHHHHH-hhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhhc
Q psy10247        101 IVDNFNFRSVIICSDSRSSLEALRTQFTL-NEISFNILCTVHQL-KARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQ  178 (315)
Q Consensus       101 ~~~~~~~~~i~I~sDS~~al~~l~~~~~~-~~~~~~i~~~~~~l-~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~~  178 (315)
                        .......|.|++||+.+++.+++.+.. .+....+...+..+ ......+.|.|||    +..|+.||+||++|....
T Consensus       136 --~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~  209 (219)
T PRK07708        136 --LGVKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGT  209 (219)
T ss_pred             --cCCCcceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcC
Confidence              222234599999999999999998754 34444444444433 3334568889998    678999999999999865


Q ss_pred             cc
Q psy10247        179 LL  180 (315)
Q Consensus       179 ~~  180 (315)
                      .+
T Consensus       210 ~~  211 (219)
T PRK07708        210 VI  211 (219)
T ss_pred             CC
Confidence            44

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.54  E-value=9.9e-14  Score=131.69  Aligned_cols=122  Identities=16%  Similarity=0.252  Sum_probs=93.6

Q ss_pred             ceEEEEcCCCCCC--CeeEEEE--EC--C-eee--EEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCC
Q psy10247         46 SLFIFTDGTKTAT--NTGFAYV--SG--D-LCQ--TYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDS  116 (315)
Q Consensus        46 ~~~iytDGS~~~~--~~G~a~v--~~--~-~~~--~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS  116 (315)
                      .+.||||||+..+  .+|+|++  +.  . ...  ...++ ..|++.||+.|++.||+.+..      .+.+.|.|++||
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~------~g~~~v~i~~DS   74 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAE------LGATEVEVRMDS   74 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHh------CCCCeEEEEeCc
Confidence            4789999998854  5788877  32  2 212  22233 778899999999999999953      467799999999


Q ss_pred             HHHHHHHhcccc-ccHHHHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhhc
Q psy10247        117 RSSLEALRTQFT-LNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQ  178 (315)
Q Consensus       117 ~~al~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~~  178 (315)
                      +.+++.+++.+. .++-...+...+..+.+....+.+.|||.    .+|+.||.||+.|....
T Consensus        75 ~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~~  133 (372)
T PRK07238         75 KLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDAA  133 (372)
T ss_pred             HHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHhh
Confidence            999999998775 33333445555666777778999999994    79999999999997643

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

Probab=99.35  E-value=5.4e-12  Score=94.11  Aligned_cols=86  Identities=24%  Similarity=0.291  Sum_probs=66.9

Q ss_pred             HhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHHHHHHHhccccccHHHHHHHHHHHHHhhcCCcEEEEEeCCCCC
Q psy10247         81 IFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCG  160 (315)
Q Consensus        81 ~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~al~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~g  160 (315)
                      +..||+.|+..||+.+      ...+.++|.|.|||+.+++.|++..........+...+..+.+...++.|.|||    
T Consensus         1 ~~~aE~~al~~al~~a------~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----   70 (87)
T PF13456_consen    1 PLEAEALALLEALQLA------WELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----   70 (87)
T ss_dssp             HHHHHHHHHHHHHHHH------HCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------
T ss_pred             CcHHHHHHHHHHHHHH------HHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----
Confidence            4689999999999999      456889999999999999999998543223345555666677778999999999    


Q ss_pred             CchhhhhcHHHHHhHh
Q psy10247        161 IVENERVDQAAKNSIY  176 (315)
Q Consensus       161 ~~gNe~AD~lAk~a~~  176 (315)
                      .++|..||.|||.|.+
T Consensus        71 r~~N~~A~~LA~~a~~   86 (87)
T PF13456_consen   71 REQNKVADALAKFALS   86 (87)
T ss_dssp             GGGSHHHHHHHHHHHH
T ss_pred             hHHhHHHHHHHHHHhh
Confidence            8999999999999864

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

Probab=96.48  E-value=0.0016  Score=48.42  Aligned_cols=31  Identities=26%  Similarity=0.417  Sum_probs=25.3

Q ss_pred             hhcCCCCCCCCCCCCc-cccccchhccccccH
Q psy10247        253 YLFKKDAPPECRTCGV-VLTIKHILTQCKAYA  283 (315)
Q Consensus       253 ~~~~~~~~p~C~~Cg~-~et~~H~l~~Cp~~~  283 (315)
                      .+.+...++.|+.|+. .||++|+|++||...
T Consensus        52 ~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~   83 (86)
T PF13966_consen   52 QRRGIQVDPICPLCGNEEETIEHLFFHCPFAR   83 (86)
T ss_pred             hccCCccCCccccCCCccccccceeccCcCcc
Confidence            3345577799999985 899999999999753

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

Probab=92.95  E-value=0.59  Score=38.84  Aligned_cols=68  Identities=19%  Similarity=0.215  Sum_probs=40.3

Q ss_pred             CceEEEEcCCCCCCCeeEEEE--E---CCee-----eEEecC--CCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEE
Q psy10247         45 DSLFIFTDGTKTATNTGFAYV--S---GDLC-----QTYRLN--PLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVII  112 (315)
Q Consensus        45 ~~~~iytDGS~~~~~~G~a~v--~---~~~~-----~~~~l~--~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I  112 (315)
                      ..+++|+|+|..  +.|+.++  .   +...     ...++.  ...|+=+-||.|+..|.+.+.....-.......+++
T Consensus        80 ~~L~~F~DAS~~--aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~~~~l~~~~~~~~~  157 (159)
T PF05380_consen   80 VELHVFCDASES--AYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTVKKELDIEISQVVF  157 (159)
T ss_pred             eeeeEeeccccc--ceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHHHHHcCCCcceeEE
Confidence            468999999954  3444444  2   2211     111222  244899999999999998875432223345556655


Q ss_pred             Ee
Q psy10247        113 CS  114 (315)
Q Consensus       113 ~s  114 (315)
                      +|
T Consensus       158 wt  159 (159)
T PF05380_consen  158 WT  159 (159)
T ss_pred             eC
Confidence            43

>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein

Probab=83.09  E-value=1.5  Score=37.68  Aligned_cols=81  Identities=17%  Similarity=0.041  Sum_probs=47.7

Q ss_pred             cCCChHHHHHHHHHHHh-------hCCCceEEEEcCCCCCCCeeEEEEECCeeeEEecCCCCcHhHHHHHHHHHHHHHHH
Q psy10247         25 KSLIPQQARNSFLEFKS-------QNLDSLFIFTDGTKTATNTGFAYVSGDLCQTYRLNPLSSIFTAESLAILKCLEYIM   97 (315)
Q Consensus        25 ~~~~~~~~~~~~~~~~~-------~~~~~~~iytDGS~~~~~~G~a~v~~~~~~~~~l~~~~s~~~aEl~Ai~~aL~~~~   97 (315)
                      .+.-+..++..+-...-       +.+.--.||+|+.-    +|+|+..+.....+.....-.+..+||+|.-.|.-+. 
T Consensus        66 aF~FS~~Yk~~L~kqy~~l~pvarqr~~lc~VfaDATp----Tgwgi~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~-  140 (245)
T PF00336_consen   66 AFTFSPTYKAFLCKQYMNLYPVARQRPGLCQVFADATP----TGWGISITGQRMRGTFSKPLPIHTAELLAACLARLMS-  140 (245)
T ss_pred             eeecCHHHHHHHHHhhccccccccCCCCCCceeccCCC----CcceeeecCceeeeeecccccchHHHHHHHHHHHhcc-
Confidence            44445555555443221       24456789999886    4555552222222222235678999999997776554 


Q ss_pred             HhhhhccCCcceEEEEeCCHHHH
Q psy10247         98 SLVIVDNFNFRSVIICSDSRSSL  120 (315)
Q Consensus        98 ~~~~~~~~~~~~i~I~sDS~~al  120 (315)
                               ..++ |.|||..|+
T Consensus       141 ---------~~r~-l~tDnt~Vl  153 (245)
T PF00336_consen  141 ---------GARC-LGTDNTVVL  153 (245)
T ss_pred             ---------CCcE-EeecCcEEE
Confidence                     2333 999998766

The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity

---

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	315
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-07
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	5e-05
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	2e-04

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

 Score = 50.6 bits (120), Expect = 4e-07
 Identities = 39/257 (15%), Positives = 81/257 (31%), Gaps = 80/257 (31%)

Query: 89  ILKCLEYIMSLVIVDN---------FNFRS-VIICSDSRSSLEALRTQFTLNEISFNILC 138
           +LK   Y   L+++ N         FN    +++ +  +   + L    T +    +   
Sbjct: 237 LLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSM 296

Query: 139 TVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVK------DVIIQS 192
           T+   + + + +K+L                        Q L   V+        +I +S
Sbjct: 297 TLTPDEVKSLLLKYLDCR--------------------PQDLPREVLTTNPRRLSIIAES 336

Query: 193 KKTILNEWKTDWLENQLYERNKLRE-IKKDIKTWKTVHWRNRRDEIAVCRLRIGHTKLTQ 251
            +  L  W   W        +KL   I+  +   +   +R   D ++V            
Sbjct: 337 IRDGLATWDN-WKH---VNCDKLTTIIESSLNVLEPAEYRKMFDRLSV------------ 380

Query: 252 EYLFKKDAP-PECRTCGVVLTI----------KHILTQCKAYAALRRKWKLESTMEKILQ 300
              F   A  P      ++L++            ++ +   Y+ + ++ K EST+     
Sbjct: 381 ---FPPSAHIPT-----ILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPK-ESTIS---- 427

Query: 301 DDHDI--VLRCINNNRY 315
               I   L+    N Y
Sbjct: 428 -IPSIYLELKVKLENEY 443

>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 = 42.0 bits (99), Expect = 5e-05
 Identities = 8/33 (24%), Positives = 15/33 (45%)

Query: 143 LKARDINIKFLWIPSHCGIVENERVDQAAKNSI 175
           +        F  + +H G   N+ VD  AK+++
Sbjct: 103 MNQYRGIYSFEKVKAHSGNEFNDYVDMKAKSAL 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 = 40.2 bits (94), Expect = 2e-04
 Identities = 27/151 (17%), Positives = 50/151 (33%), Gaps = 22/151 (14%)

Query: 47  LFIFTDGTKTATN----TGFAYVSGD-LCQTYRLNPLSSIFTAESLAILKCLEYIMSLVI 101
              +TDG+          G A  +   +     L   +S   AE +A+ + L+       
Sbjct: 24  YTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEG--- 80

Query: 102 VDNFNFRSVIICSDSRSSLEALRTQFTLNEISFN--ILCTVHQLKARDINIKFLWIPSHC 159
                 + + + +DSR +           EI     IL  +  L      +  +  P H 
Sbjct: 81  ------KKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPK-RLSIIHCPGHQ 133

Query: 160 GIVE-----NERVDQAAKNSIYAQLLKSVVV 185
                    N   DQAA+ +    +L++  +
Sbjct: 134 KGNSAEARGNRMADQAAREAAMKAVLETSTL 164

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	315
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.92
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.91
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.9
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.9
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.9
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.89
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.89
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.87
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.86
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.84
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.83
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.8
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.78
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.78
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.43
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.23

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

Probab=99.92  E-value=1.4e-24  Score=179.86  Aligned_cols=128  Identities=20%  Similarity=0.356  Sum_probs=96.7

Q ss_pred             CCceEEEEcCCCCCCC-----eeEEEE--ECC-eeeEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeC
Q psy10247         44 LDSLFIFTDGTKTATN-----TGFAYV--SGD-LCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSD  115 (315)
Q Consensus        44 ~~~~~iytDGS~~~~~-----~G~a~v--~~~-~~~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sD  115 (315)
                      ++.+.||||||+..++     +|+|+|  ++. ...+..+...+|++.||+.|++.||+.+..      .+...|.|+||
T Consensus         5 ~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~------~~~~~v~i~tD   78 (154)
T 2qkb_A            5 GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKT------QNINKLVLYTN   78 (154)
T ss_dssp             TTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHH------TTCCEEEEEES
T ss_pred             CCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHh------CCCceEEEEEC
Confidence            5679999999987532     789988  222 223445655789999999999999999953      35689999999


Q ss_pred             CHHHHHHHhcc--------cccc---HH-HHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhhc
Q psy10247        116 SRSSLEALRTQ--------FTLN---EI-SFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQ  178 (315)
Q Consensus       116 S~~al~~l~~~--------~~~~---~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~~  178 (315)
                      |++|++.|.+.        +..+   ++ ...++..+..+.. +..|.|.|||||+|++|||.||+|||+|+..+
T Consensus        79 S~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           79 SMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             CHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             cHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            99999999873        2211   11 1334444444433 46799999999999999999999999998753

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

Probab=99.91  E-value=4.1e-24  Score=175.41  Aligned_cols=123  Identities=20%  Similarity=0.259  Sum_probs=89.8

Q ss_pred             CceEEEEcCCCCCC--CeeEEEE--ECCeee--EEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHH
Q psy10247         45 DSLFIFTDGTKTAT--NTGFAYV--SGDLCQ--TYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRS  118 (315)
Q Consensus        45 ~~~~iytDGS~~~~--~~G~a~v--~~~~~~--~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~  118 (315)
                      ..++||||||+..+  .+|+|+|  .++...  +..+ ..+|++.||+.|++.||+.+.      .  ...|.|+|||++
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~------~--~~~v~I~tDS~~   73 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALK------E--PARVQLYSDSAY   73 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCS------S--CCEEEEEESCHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcC------c--cCcEEEEeChHH
Confidence            57899999998864  3788887  444222  2223 368999999999999999982      2  589999999999


Q ss_pred             HHHHHhccc---------ccc---H-HHHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhh
Q psy10247        119 SLEALRTQF---------TLN---E-ISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYA  177 (315)
Q Consensus       119 al~~l~~~~---------~~~---~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~  177 (315)
                      |++.|.+.+         ..+   + ....++..+..+... .+|.|.|||||+|+++||.||+|||+|+..
T Consensus        74 vi~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~-~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A           74 LVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTL-HRVTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             HHHHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHH-SEEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhh-CceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence            999998831         110   1 112334333333332 579999999999999999999999999875

>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} SCOP: c.55.3.1 PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A

Probab=99.90  E-value=6.1e-24  Score=175.04  Aligned_cols=124  Identities=19%  Similarity=0.246  Sum_probs=92.0

Q ss_pred             CCCceEEEEcCCCCCC--CeeEEEE-ECCeeeEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHHH
Q psy10247         43 NLDSLFIFTDGTKTAT--NTGFAYV-SGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSS  119 (315)
Q Consensus        43 ~~~~~~iytDGS~~~~--~~G~a~v-~~~~~~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~a  119 (315)
                      .++.+.||||||+..+  ..|+|++ ..+......+ ..+|++.||+.|++.||+.+          ...|.|+|||+++
T Consensus         9 ~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~----------~~~v~i~tDS~~v   77 (150)
T 3qio_A            9 IVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----------GLEVNIVTDSQYA   77 (150)
T ss_dssp             CTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----------CSEEEEEESCHHH
T ss_pred             CCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC----------CCcEEEEeCcHHH
Confidence            4578999999998753  4788877 2222233344 47899999999999999875          3789999999999


Q ss_pred             HHHHhccc--------cc---cHH-HHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhh
Q psy10247        120 LEALRTQF--------TL---NEI-SFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYA  177 (315)
Q Consensus       120 l~~l~~~~--------~~---~~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~  177 (315)
                      +++|.++.        .+   .++ -..++..+..+...+.+|.|.|||||+|++|||.||+||++|+..
T Consensus        78 ~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           78 LGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            99998751        11   111 123444433333467899999999999999999999999998764

>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=99.90  E-value=6.8e-25  Score=180.30  Aligned_cols=127  Identities=16%  Similarity=0.102  Sum_probs=96.6

Q ss_pred             CCCceEEEEcCCCCCCCeeEEEE--ECCee--eEE-ec--CC--CCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEE
Q psy10247         43 NLDSLFIFTDGTKTATNTGFAYV--SGDLC--QTY-RL--NP--LSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIIC  113 (315)
Q Consensus        43 ~~~~~~iytDGS~~~~~~G~a~v--~~~~~--~~~-~l--~~--~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~  113 (315)
                      +++.+.||||||+..+.+|+|+|  ..+..  .+. ..  +.  .+||+.||+.|++.||+.++.    .  +. .|.|+
T Consensus         3 ~~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~----~--~~-~v~I~   75 (147)
T 2kq2_A            3 DRTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQ----L--GV-KIRIL   75 (147)
T ss_dssp             TTSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHH----H--TC-CCCBS
T ss_pred             CCCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHH----C--CC-eEEEE
Confidence            35789999999999877899987  43332  222 22  21  368999999999999998864    2  34 89999


Q ss_pred             eCCHHHHHHHhcccccc-HHHHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhhcc
Q psy10247        114 SDSRSSLEALRTQFTLN-EISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQL  179 (315)
Q Consensus       114 sDS~~al~~l~~~~~~~-~~~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~~~  179 (315)
                      |||+.+.+.+.+.+..+ +....+...++.+..   +|.|.|||||+|++|||.||+|||+|+....
T Consensus        76 tDS~~i~~w~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~  139 (147)
T 2kq2_A           76 HDYAGIAFWATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALGIRD  139 (147)
T ss_dssp             SCCSTHHHHTTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHTCCC
T ss_pred             ECcHHHHHHHhCCCccCCcchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHhccc
Confidence            99999998888877654 233334433344432   8999999999999999999999999997654

>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=99.90  E-value=1.9e-23  Score=174.54  Aligned_cols=126  Identities=19%  Similarity=0.203  Sum_probs=92.4

Q ss_pred             CceEEEEcCCCC--CCCeeEEEE--EC-CeeeEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHHH
Q psy10247         45 DSLFIFTDGTKT--ATNTGFAYV--SG-DLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSS  119 (315)
Q Consensus        45 ~~~~iytDGS~~--~~~~G~a~v--~~-~~~~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~a  119 (315)
                      ..+.||||||+.  ++..|+|++  .+ ...........+||+.||+.|++.||+.+         ....+.|+|||+++
T Consensus        22 ~~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---------~~~~v~I~tDS~~v   92 (165)
T 3p1g_A           22 ADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---------EGKKLNVYTDSRYA   92 (165)
T ss_dssp             CSEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---------BTSEEEEEECCHHH
T ss_pred             CCEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---------cCceEEEEEchHHH
Confidence            359999999997  444677765  33 33333345568899999999999999987         26799999999999


Q ss_pred             HHHHhccccccHH-HHHHHHHH-HHHhhcCCcEEEEEeCCCCC-----CchhhhhcHHHHHhHhhccc
Q psy10247        120 LEALRTQFTLNEI-SFNILCTV-HQLKARDINIKFLWIPSHCG-----IVENERVDQAAKNSIYAQLL  180 (315)
Q Consensus       120 l~~l~~~~~~~~~-~~~i~~~~-~~l~~~~~~v~~~WVpgH~g-----~~gNe~AD~lAk~a~~~~~~  180 (315)
                      ++.+-......++ -..++..+ ..+ ..+.+|.|.|||||+|     +.|||.||+|||+|+..+.+
T Consensus        93 i~~iw~~~~g~~v~n~dl~~~l~~~l-~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~~~  159 (165)
T 3p1g_A           93 FATAHVHSEGREIKNKNEILALLKAL-FLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVL  159 (165)
T ss_dssp             HHHHHSCCCSCCCSSHHHHHHHHHHT-TSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HhhhhcccCCCcccCHHHHHHHHHHH-hcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcCCC
Confidence            9998321111121 12323222 333 3578999999999999     99999999999999987644

>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ...

Probab=99.89  E-value=2.3e-23  Score=172.71  Aligned_cols=126  Identities=20%  Similarity=0.303  Sum_probs=94.1

Q ss_pred             CceEEEEcCCCCCC--CeeEEEE--ECCee--eEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHH
Q psy10247         45 DSLFIFTDGTKTAT--NTGFAYV--SGDLC--QTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRS  118 (315)
Q Consensus        45 ~~~~iytDGS~~~~--~~G~a~v--~~~~~--~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~  118 (315)
                      ..+.||||||+..+  .+|+|+|  ..+..  .+..+ ..+|++.||+.|++.||+.+.      .  ...|.|+|||++
T Consensus         3 ~~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~------~--~~~v~I~tDS~~   73 (155)
T 1jl1_A            3 KQVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALK------E--HAEVILSTDSQY   73 (155)
T ss_dssp             CCEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCC------S--CCEEEEEECCHH
T ss_pred             ceEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhC------c--CCcEEEEeCHHH
Confidence            46899999999853  4788887  33322  22223 367899999999999999983      2  379999999999


Q ss_pred             HHHHHhc--------ccccc---HH-HHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhhccc
Q psy10247        119 SLEALRT--------QFTLN---EI-SFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLL  180 (315)
Q Consensus       119 al~~l~~--------~~~~~---~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~~~~  180 (315)
                      |++.|.+        .+.++   ++ -..++..+..+.. ...|.|.|||||+|++||+.||+||++|+..+.+
T Consensus        74 vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  146 (155)
T 1jl1_A           74 VRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAAAMNPTL  146 (155)
T ss_dssp             HHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             HHHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHHc-cCceEEEEcCCCCCCHHHHHHHHHHHHHHhccch
Confidence            9999987        22211   11 1234444444443 4689999999999999999999999999987654

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

Probab=99.89  E-value=3.3e-23  Score=172.26  Aligned_cols=125  Identities=24%  Similarity=0.333  Sum_probs=92.9

Q ss_pred             CceEEEEcCCCCCC--CeeEEEE--ECCee--eEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHH
Q psy10247         45 DSLFIFTDGTKTAT--NTGFAYV--SGDLC--QTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRS  118 (315)
Q Consensus        45 ~~~~iytDGS~~~~--~~G~a~v--~~~~~--~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~  118 (315)
                      ..+.||||||+..+  .+|+|+|  +++..  .+..+ ..+|++.||+.|++.||+.+      ..  ...|.|+|||++
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~------~~--~~~v~I~tDS~~   75 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEAL------KE--PCKIILTSDSQY   75 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTC------SS--CCEEEEEECCHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHh------cc--CCeEEEEeCHHH
Confidence            46899999999853  4788887  44322  22223 35799999999999999987      22  389999999999


Q ss_pred             HHHHHhc--------ccccc---HH-HHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhh-cc
Q psy10247        119 SLEALRT--------QFTLN---EI-SFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYA-QL  179 (315)
Q Consensus       119 al~~l~~--------~~~~~---~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~-~~  179 (315)
                      |++.|.+        .+..+   ++ -..++..+..+.. ...|.|.|||||+|+++|+.||+||++|+.. +.
T Consensus        76 vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~~  148 (158)
T 2e4l_A           76 MRQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQ-LHQIDWRWVKGHAGHAENERCDQLARAAAEANPT  148 (158)
T ss_dssp             HHHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHT-TSEEEEEECCTTCCCHHHHHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHc-cCcEEEEEccCCCCchhHHHHHHHHHHHHHhchh
Confidence            9999988        33211   11 1234444444433 3689999999999999999999999999987 44

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

Probab=99.87  E-value=1.2e-22  Score=170.08  Aligned_cols=125  Identities=20%  Similarity=0.206  Sum_probs=92.1

Q ss_pred             CceEEEEcCCCCCC--CeeEEEE--ECCee--eEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHH
Q psy10247         45 DSLFIFTDGTKTAT--NTGFAYV--SGDLC--QTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRS  118 (315)
Q Consensus        45 ~~~~iytDGS~~~~--~~G~a~v--~~~~~--~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~  118 (315)
                      ..+.||||||+..+  .+|+|+|  +.+..  .+... ..+|++.||+.|++.||+.+.      .  ...|.|+|||++
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~Ai~~AL~~~~------~--~~~v~I~tDS~~   77 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGE-ACTTNNRMELKAAIEGLKALK------E--PCEVDLYTDSHY   77 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEE-EEECHHHHHHHHHHHHHHSCC------S--CCEEEEECCCHH
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCC-CCCcHHHHHHHHHHHHHHHhc------c--CCeEEEEeChHH
Confidence            57899999999853  4788887  33221  11122 367899999999999999872      2  358999999999


Q ss_pred             HHHHHhcc---------cccc---HH-HHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhhcc
Q psy10247        119 SLEALRTQ---------FTLN---EI-SFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQL  179 (315)
Q Consensus       119 al~~l~~~---------~~~~---~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~~~  179 (315)
                      |++.|.+.         +..+   ++ -..++..+..+.. ...|.|.|||||+|+++|+.||+|||+|+....
T Consensus        78 vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~  150 (166)
T 1ril_A           78 LKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA-PHRVRFHFVKGHTGHPENERVDREARRQAQSQA  150 (166)
T ss_dssp             HHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT-TSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             HHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHh-cCeEEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence            99999982         2211   11 1234444444443 368999999999999999999999999998754

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

Probab=99.86  E-value=1e-21  Score=163.78  Aligned_cols=127  Identities=15%  Similarity=0.132  Sum_probs=90.3

Q ss_pred             CCceEEEEcCCCCC--CC-----eeEEEE--E-CC---eeeEEec-CCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcce
Q psy10247         44 LDSLFIFTDGTKTA--TN-----TGFAYV--S-GD---LCQTYRL-NPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRS  109 (315)
Q Consensus        44 ~~~~~iytDGS~~~--~~-----~G~a~v--~-~~---~~~~~~l-~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~  109 (315)
                      .-.++||||||+..  +.     +|+|+|  . +.   ....+.. ....+++.||+.|+..||+.++.       ....
T Consensus         5 ~~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~-------~~~~   77 (165)
T 2lsn_A            5 QYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALK-------IPGP   77 (165)
T ss_dssp             CCSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHH-------SSSC
T ss_pred             CceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhc-------CCCe
Confidence            45689999999874  22     789987  2 22   2233333 24678889999999999988754       3457


Q ss_pred             EEEEeCCHHHHHHHhcc--------ccc---cHH-HHHHHHHHHHHhhcCCcEEEEEeCCCCCC------chhhhhcHHH
Q psy10247        110 VIICSDSRSSLEALRTQ--------FTL---NEI-SFNILCTVHQLKARDINIKFLWIPSHCGI------VENERVDQAA  171 (315)
Q Consensus       110 i~I~sDS~~al~~l~~~--------~~~---~~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~g~------~gNe~AD~lA  171 (315)
                      |.|+|||++|+++|..+        +.+   .++ -..++..+..+.....+|.|.|||||+|.      +|||+||+||
T Consensus        78 v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA  157 (165)
T 2lsn_A           78 VLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLA  157 (165)
T ss_dssp             EEEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHH
T ss_pred             EEEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHH
Confidence            99999999999999752        211   121 12344444444445578999999999995      6899999999


Q ss_pred             HHhHhh
Q psy10247        172 KNSIYA  177 (315)
Q Consensus       172 k~a~~~  177 (315)
                      ++|+..
T Consensus       158 ~~gA~~  163 (165)
T 2lsn_A          158 TQGSYV  163 (165)
T ss_dssp             HHHHHH
T ss_pred             HHhhhh
Confidence            999854

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

Probab=99.84  E-value=1.5e-20  Score=152.35  Aligned_cols=122  Identities=20%  Similarity=0.315  Sum_probs=91.5

Q ss_pred             CceEEEEcCCCCCC--CeeEEEE--E--CCee--eEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcc----eEEE
Q psy10247         45 DSLFIFTDGTKTAT--NTGFAYV--S--GDLC--QTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFR----SVII  112 (315)
Q Consensus        45 ~~~~iytDGS~~~~--~~G~a~v--~--~~~~--~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~----~i~I  112 (315)
                      ..+.||||||+..+  .+|+|++  +  +...  .+..+ ..+|++.||+.|++.||+.+..      .+.+    +|.|
T Consensus         2 ~~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~------~~~~~~~~~v~i   74 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYI-GETTNNVAEYEALIRALEDLQM------FGDKLVDMEVEV   74 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEE-EEECHHHHHHHHHHHHHHHHGG------GGGGGTTCEEEE
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeC-CCCchHHHHHHHHHHHHHHHHH------cCCCCCCceEEE
Confidence            36899999999753  5888887  3  2222  12223 3579999999999999999943      3455    9999


Q ss_pred             EeCCHHHHHHHhccccc-cHHHHHHHHHHHHH-hhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhh
Q psy10247        113 CSDSRSSLEALRTQFTL-NEISFNILCTVHQL-KARDINIKFLWIPSHCGIVENERVDQAAKNSIYA  177 (315)
Q Consensus       113 ~sDS~~al~~l~~~~~~-~~~~~~i~~~~~~l-~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~  177 (315)
                      +|||+++++.+++.+.. ++....++..+..+ .+....|.|.|||    .++|+.||+|||+|+..
T Consensus        75 ~tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~----~~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D           75 RMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIP----REKNARADELVNEAIDK  137 (140)
T ss_dssp             EESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECC----GGGGHHHHHHHHHHHHH
T ss_pred             EeChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcC----chhhHHHHHHHHHHHHh
Confidence            99999999999997742 33233344455555 5556799999999    58999999999999865

>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=99.83  E-value=3.7e-20  Score=150.42  Aligned_cols=124  Identities=15%  Similarity=0.240  Sum_probs=95.2

Q ss_pred             CceEEEEcCCCCCC--CeeEEEE--EC---CeeeEEe-cCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCC
Q psy10247         45 DSLFIFTDGTKTAT--NTGFAYV--SG---DLCQTYR-LNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDS  116 (315)
Q Consensus        45 ~~~~iytDGS~~~~--~~G~a~v--~~---~~~~~~~-l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS  116 (315)
                      ..+.||||||+..+  .+|+|+|  +.   .....++ ....+|++.||+.|++.||+.+..      .+..+|.|+|||
T Consensus         2 ~~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~------~~~~~v~i~tDS   75 (141)
T 3hst_B            2 VKVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVK------LGATEAAVLMDS   75 (141)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEEEECHHHHHHHHHHHHHHHHHH------HTCSEEEEEESC
T ss_pred             cEEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCCCCchHHHHHHHHHHHHHHHHH------CCCceEEEEeCh
Confidence            35899999998853  5788877  32   2222221 123789999999999999999954      356899999999


Q ss_pred             HHHHHHHhcccc-ccHHHHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhhc
Q psy10247        117 RSSLEALRTQFT-LNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQ  178 (315)
Q Consensus       117 ~~al~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~~  178 (315)
                      +++++.+++.+. .++....+...+..+...+..|.|.|||    .++|+.||+|||+|+...
T Consensus        76 ~~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~----~~~N~~AD~LA~~a~~~~  134 (141)
T 3hst_B           76 KLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVP----RARNTYADRLANDAMDAA  134 (141)
T ss_dssp             HHHHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECC----GGGCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcC----CcccHHHHHHHHHHHHHh
Confidence            999999999764 3343445555666676677999999999    489999999999998753

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

Probab=99.80  E-value=1.7e-19  Score=148.27  Aligned_cols=121  Identities=17%  Similarity=0.263  Sum_probs=89.4

Q ss_pred             eEEEEcCCCCC---CCeeE-EEE--E-CCeeeEEe--cC---CCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEe
Q psy10247         47 LFIFTDGTKTA---TNTGF-AYV--S-GDLCQTYR--LN---PLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICS  114 (315)
Q Consensus        47 ~~iytDGS~~~---~~~G~-a~v--~-~~~~~~~~--l~---~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~s  114 (315)
                      +.||||||+.+   +++|+ |++  + +.....++  ++   ..+|++.||+.|++.||+.+..      .+..+|.|+|
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~------~g~~~v~i~t   75 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLR------LGISSPIIKG   75 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHH------HTCCSCEEEE
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHH------cCCCEEEEEe
Confidence            67999999872   45775 876  3 33322222  22   3789999999999999999954      2567899999


Q ss_pred             CCHHHHHHHhcccccc-HHHHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhhc
Q psy10247        115 DSRSSLEALRTQFTLN-EISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQ  178 (315)
Q Consensus       115 DS~~al~~l~~~~~~~-~~~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~~  178 (315)
                      ||+++++.+++.+..+ +....++..+..+.+.. +|.|.|||+    .+|+.||+||++|+...
T Consensus        76 DS~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~----~~N~~AD~LA~~a~~~~  135 (149)
T 2ehg_A           76 DSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPR----EENKEADRLSRVAYELV  135 (149)
T ss_dssp             SCHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCG----GGCHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCC----cccHHHHHHHHHHHHhh
Confidence            9999999999986532 33344444444444333 599999998    49999999999998764

>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B

Probab=99.78  E-value=3.7e-19  Score=175.72  Aligned_cols=116  Identities=25%  Similarity=0.292  Sum_probs=89.8

Q ss_pred             CCceEEEEcCCCCCC--CeeEEEE--ECCeeeEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHHH
Q psy10247         44 LDSLFIFTDGTKTAT--NTGFAYV--SGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSS  119 (315)
Q Consensus        44 ~~~~~iytDGS~~~~--~~G~a~v--~~~~~~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~a  119 (315)
                      ++.+.||||||+..+  ..|+|++  .++ ...... ..+||+.||+.|++.||+.          ....+.|+|||++|
T Consensus       434 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~-~~~~~~-~~~TNn~aEl~A~i~aL~~----------~~~~v~I~tDS~~v  501 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKEGKAGYVTDRGK-DKVKKL-EQTTNQQAELEAFAMALTD----------SGPKVNIIVDSQYV  501 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSC-EEEEEE-SSCCHHHHHHHHHHHHHHT----------SCSEEEEEESCHHH
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCC-EeeccC-CCCCHHHHHHHHHHHHHHc----------CCCeEEEEEehHHH
Confidence            567999999998854  3788877  333 223333 4789999999999999986          25789999999999


Q ss_pred             HHHHhcccc--ccHHHHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhH
Q psy10247        120 LEALRTQFT--LNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSI  175 (315)
Q Consensus       120 l~~l~~~~~--~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~  175 (315)
                      +++++++..  ..++.+++..   .+ ..+..|.|.|||||+|++|||.||+||++|+
T Consensus       502 ~~~i~~~~~~~~~~l~~~~~~---~~-~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          502 MGIVASQPTESESKIVNQIIE---EM-IKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             HHHHHTCCSEESCHHHHHHHH---HH-HHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             HHHHhcccccccHHHHHHHHH---Hh-ccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            999998542  2355554442   22 2367899999999999999999999999874

>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...

Probab=99.78  E-value=2.1e-19  Score=177.59  Aligned_cols=116  Identities=24%  Similarity=0.287  Sum_probs=87.8

Q ss_pred             CCceEEEEcCCCCCC--CeeEEEE-ECCeeeEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHHHH
Q psy10247         44 LDSLFIFTDGTKTAT--NTGFAYV-SGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSL  120 (315)
Q Consensus        44 ~~~~~iytDGS~~~~--~~G~a~v-~~~~~~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~al  120 (315)
                      ++.+.||||||+..+  .+|+|++ ..+....... ..+||+.||+.|++.||+.+          ...+.|+|||++|+
T Consensus       437 ~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~----------~~~v~I~tDS~~vi  505 (557)
T 2zd1_A          437 VGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS----------GLEVNIVTDSQYAL  505 (557)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS----------CSEEEEEECCHHHH
T ss_pred             CCCEEEEEccCCCCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC----------CCcEEEEeChHHHH
Confidence            467999999998743  3778877 2222222333 47899999999999999987          46899999999999


Q ss_pred             HHHhccccc--cHHHHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHh
Q psy10247        121 EALRTQFTL--NEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNS  174 (315)
Q Consensus       121 ~~l~~~~~~--~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a  174 (315)
                      ++++++...  .++.+++.   +.+.. ..+|.|.|||||+|++|||.||+||++|
T Consensus       506 ~~i~~~~~~~~~~l~~~~~---~~l~~-~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          506 GIIQAQPDKSESELVNQII---EQLIK-KEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             HHHTTCCSEESSHHHHHHH---HHHHH-CSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             HHHhcCCccCCHHHHHHHH---HHHhc-CCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            999986554  35555544   23333 4689999999999999999999999986

>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE motif, hydrolase; 1.50A {Bacillus halodurans} SCOP: c.55.3.1 PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A 2g8f_A 2g8v_A 2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A* 2r7y_A*

Probab=99.43  E-value=5.7e-14  Score=113.94  Aligned_cols=117  Identities=14%  Similarity=0.036  Sum_probs=82.7

Q ss_pred             CCCceEEEEcCCCCC--CCeeEEEE---ECCeee-EEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCC
Q psy10247         43 NLDSLFIFTDGTKTA--TNTGFAYV---SGDLCQ-TYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDS  116 (315)
Q Consensus        43 ~~~~~~iytDGS~~~--~~~G~a~v---~~~~~~-~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS  116 (315)
                      ++..+.||||||+..  +.+|+|+|   ++.... +..++ .+||+.||++|++.||+.+..      ... .|.|+|||
T Consensus         8 ~~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~-~~TNN~aEl~A~i~aL~~~~~------~~~-~v~i~tDS   79 (142)
T 1zbf_A            8 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKE------RNS-RKPIYSNS   79 (142)
T ss_dssp             CCCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEE-EECHHHHHHHHHHHHHHHHHH------TTC-CCCEEESC
T ss_pred             CCCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccC-CcCcHHHHHHHHHHHHHHHHh------CCC-eEEEEEeh
Confidence            456789999999874  45789988   222221 11222 579999999999999999954      233 89999999


Q ss_pred             HHHHHHHhccccc-c--------HHHHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcH
Q psy10247        117 RSSLEALRTQFTL-N--------EISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQ  169 (315)
Q Consensus       117 ~~al~~l~~~~~~-~--------~~~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~  169 (315)
                      ++|++.+++.+.. +        ++.+.|.....-+..  ..+....|+-|++.-||..||.
T Consensus        80 ~~vi~w~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~--~~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A           80 QTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNT--HTYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             HHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHHH--CCCCCCEEECCHHHHCSCTTCC
T ss_pred             HHHHHHHHcCCccCCCCCCcccHHHHHHHHHHHHHHhh--CCCceeEEEeccCccCcCcccc
Confidence            9999999987731 1        244444433333443  4556667888888899999983

>4htu_A Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine, W-C base PAIR, wobble base PAIR, D helix; HET: DNA UCL; 1.49A {Bacillus halodurans} PDB: 3d0p_A* 4hue_A* 4huf_A* 4hug_A* 1zbf_A 1zbi_A 2g8u_A 3uld_A* 3ey1_A* 3twh_A* 2g8f_A 2g8v_A 2g8w_A 2g8i_A 2g8h_A 2g8k_A 3i8d_A* 2r7y_A* 1zbl_A

Probab=99.23  E-value=1.6e-11  Score=97.83  Aligned_cols=75  Identities=19%  Similarity=0.211  Sum_probs=55.6

Q ss_pred             CCceEEEEcCCCCC--CCeeEEEE--E-CCe-eeEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCH
Q psy10247         44 LDSLFIFTDGTKTA--TNTGFAYV--S-GDL-CQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSR  117 (315)
Q Consensus        44 ~~~~~iytDGS~~~--~~~G~a~v--~-~~~-~~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~  117 (315)
                      +....||||||+..  +..|+|+|  . +.. .....+ ..+||+.||++|++.||+.+.+      ... .+.|+|||+
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~-~~tTNN~aEl~A~i~aL~~l~~------~~~-~v~i~tDSq   74 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKE------RNS-RKPIYSNSQ   74 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEE-EEECHHHHHHHHHHHHHHHHHH------TTC-CCCEEESCH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCC-CCCchHHHHHHHHHHHHHHHHh------CCC-CEEEEcchH
Confidence            56778999999874  34788544  3 222 222233 3789999999999999999954      122 389999999


Q ss_pred             HHHHHHhcc
Q psy10247        118 SSLEALRTQ  126 (315)
Q Consensus       118 ~al~~l~~~  126 (315)
                      +|++.+.+.
T Consensus        75 yVi~wi~~~   83 (134)
T 4htu_A           75 TAIKWVKDK   83 (134)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHcC
Confidence            999999874

---

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	315
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	1e-06
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	8e-04
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	8e-04

>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 = 44.9 bits (105), Expect = 1e-06
 Identities = 26/129 (20%), Positives = 44/129 (34%), Gaps = 14/129 (10%)

Query: 49  IFTDG--TKTATNTGFAYVSGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFN 106
            +TDG   + +      YV+       +    ++   AE  A    L             
Sbjct: 10  FYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTDSGP-------- 61

Query: 107 FRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENER 166
              V I  DS+  +  + +Q    E    I+  + +   +   I   W+P+H GI  N+ 
Sbjct: 62  --KVNIIVDSQYVMGIVASQP--TESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQE 117

Query: 167 VDQAAKNSI 175
           VD      I
Sbjct: 118 VDHLVSQGI 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 = 36.9 bits (84), Expect = 8e-04
 Identities = 23/139 (16%), Positives = 44/139 (31%), Gaps = 9/139 (6%)

Query: 49  IFTDG--TKTATNTGFAYV---SGDLCQTYRLNPLSSIFTAESLAILKCLEYI----MSL 99
           +FTDG         G+A +                ++    E  A ++ L+ +       
Sbjct: 6   LFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCEVD 65

Query: 100 VIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHC 159
           +  D+   +            +          +    L     L      ++F ++  H 
Sbjct: 66  LYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHT 125

Query: 160 GIVENERVDQAAKNSIYAQ 178
           G  ENERVD+ A+    +Q
Sbjct: 126 GHPENERVDREARRQAQSQ 144

>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 = 36.9 bits (84), Expect = 8e-04
 Identities = 24/141 (17%), Positives = 44/141 (31%), Gaps = 8/141 (5%)

Query: 49  IFTDGT--KTATNTGFAYV---SGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVD 103
           IFT G+        G+  +    G           ++    E +A +  LE +     V 
Sbjct: 5   IFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAEVI 64

Query: 104 NFNFRSVIICSDSRSSLEALRTQF---TLNEISFNILCTVHQLKARDINIKFLWIPSHCG 160
                  +    ++      +  +       +    L            IK+ W+  H G
Sbjct: 65  LSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAG 124

Query: 161 IVENERVDQAAKNSIYAQLLK 181
             ENER D+ A+ +     L+
Sbjct: 125 HPENERADELARAAAMNPTLE 145

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	315
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.92
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.89
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.88
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.77
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.57

>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=99.92  E-value=3.2e-25  Score=175.67  Aligned_cols=116  Identities=22%  Similarity=0.243  Sum_probs=86.8

Q ss_pred             CCceEEEEcCCCCCC--CeeEEEE-ECCeeeEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHHHH
Q psy10247         44 LDSLFIFTDGTKTAT--NTGFAYV-SGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSL  120 (315)
Q Consensus        44 ~~~~~iytDGS~~~~--~~G~a~v-~~~~~~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~al  120 (315)
                      ++...+|||||+..+  ..|+|++ ..+......++ ..|++.|||.||++||+..          ...+.|+|||++|+
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~~----------~~~i~I~tDS~~v~   73 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTDS----------GPKVNIIVDSQYVM   73 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHTS----------CSEEEEEESCHHHH
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhccC----------CcceEEEechHHHH
Confidence            456899999998753  3566666 22233334443 6799999999999998753          56899999999999


Q ss_pred             HHHhcccccc--HHHHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHh
Q psy10247        121 EALRTQFTLN--EISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNS  174 (315)
Q Consensus       121 ~~l~~~~~~~--~~~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a  174 (315)
                      +.+++.+...  .....   .+..+. ...+|.|.|||||+|+.|||.||+||++|
T Consensus        74 ~~~~~~~~~~~~~~~~~---~~~~~~-~~~~v~~~wV~gH~g~~gNe~AD~LA~~a  125 (126)
T d1mu2a1          74 GIVASQPTESESKIVNQ---IIEEMI-KKEAIYVAWVPAHKGIGGNQEVDHLVSQG  125 (126)
T ss_dssp             HHHHTCCSEESCHHHHH---HHHHHH-HCSEEEEEECCSSSCCTTHHHHHHHHHTT
T ss_pred             HHHhcCCccccchHHHH---HHHHhh-hcceeEEEEEeCCCCCcchHHHHHHHHhh
Confidence            9999976532  22222   223333 34689999999999999999999999987

>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=99.89  E-value=1.9e-23  Score=170.22  Aligned_cols=130  Identities=20%  Similarity=0.303  Sum_probs=94.2

Q ss_pred             ceEEEEcCCCCCC--CeeEEEE--ECCeeeEEec-CCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHHHH
Q psy10247         46 SLFIFTDGTKTAT--NTGFAYV--SGDLCQTYRL-NPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSL  120 (315)
Q Consensus        46 ~~~iytDGS~~~~--~~G~a~v--~~~~~~~~~l-~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~al  120 (315)
                      .|.||||||+..+  .+|+|+|  .++....+.. ...+|++.||++|++.||+++.        ....+.|++||++++
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~--------~~~~i~i~tds~~~i   73 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALK--------EHAEVILSTDSQYVR   73 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCC--------SCCEEEEEECCHHHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhc--------ccceEEEeecceeeE
Confidence            4889999998754  4788877  4443322221 2467899999999999998762        467899999999999


Q ss_pred             HHHhcccc--------c---cHH-HHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhhccccCCC
Q psy10247        121 EALRTQFT--------L---NEI-SFNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVV  184 (315)
Q Consensus       121 ~~l~~~~~--------~---~~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~~~~~~~~  184 (315)
                      ..+.....        .   .++ -..+...+..+. ...+|+|+|||||+|++|||.||+|||+|+..+.+.+.+
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~-~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~d~~  148 (152)
T d1jl1a_          74 QGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAAL-GQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTG  148 (152)
T ss_dssp             HHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHT-TTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCCTT
T ss_pred             EcccchhhHhHhccchhcccCeeecHHHHHHHHHHh-hcceeEEEEecccCCCccHHHHHHHHHHHHhCCCCCccC
Confidence            98865431        1   011 112333333332 356899999999999999999999999999988776543

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

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

Probab=99.88  E-value=7.2e-24  Score=172.16  Aligned_cols=125  Identities=19%  Similarity=0.193  Sum_probs=89.4

Q ss_pred             CceEEEEcCCCCCC--CeeEEEE--ECC-eeeEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHHH
Q psy10247         45 DSLFIFTDGTKTAT--NTGFAYV--SGD-LCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSS  119 (315)
Q Consensus        45 ~~~~iytDGS~~~~--~~G~a~v--~~~-~~~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~a  119 (315)
                      ..++||||||+..+  .+|+|+|  ..+ ..........+|++.||+.||+.||+.+.        ....+.|++||+++
T Consensus         2 ~~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~--------~~~~i~i~tds~~~   73 (147)
T d1rila_           2 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALK--------EPCEVDLYTDSHYL   73 (147)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCC--------SCCEEEEECCCHHH
T ss_pred             CEEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhcc--------CCceEEEecchhhh
Confidence            35889999998864  3788877  222 22222222356999999999999998762        46789999999999


Q ss_pred             HHHHhcccc---------c---cHHH-HHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhcHHHHHhHhhc
Q psy10247        120 LEALRTQFT---------L---NEIS-FNILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQ  178 (315)
Q Consensus       120 l~~l~~~~~---------~---~~~~-~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~~~  178 (315)
                      ++.+.....         .   .++. ..++..+..+. ...+|+|.|||||+|++|||.||+|||+|+...
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~-~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_          74 KKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAM-APHRVRFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             HHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH-TTSEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             hccccccchhhhhhccccccccccchhHHHHHHHHHHh-hhcccceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence            998866321         1   1111 22333333333 357899999999999999999999999998753

>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=99.77  E-value=4.9e-19  Score=135.96  Aligned_cols=100  Identities=22%  Similarity=0.274  Sum_probs=73.6

Q ss_pred             CCceEEEEcCCCCCC--CeeEEEE-ECCeeeEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHHHH
Q psy10247         44 LDSLFIFTDGTKTAT--NTGFAYV-SGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSL  120 (315)
Q Consensus        44 ~~~~~iytDGS~~~~--~~G~a~v-~~~~~~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~al  120 (315)
                      ++..++|||||+..+  ..|+|++ ..+......+. .+||+.|||.||+.||+..          ...+.|+|||++|+
T Consensus         6 ~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~~-~~TNn~aEl~Avi~aL~~~----------~~~v~I~TDS~yvi   74 (110)
T d1s1ta1           6 VGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLALQDS----------GLEVNIVTDSQYAL   74 (110)
T ss_dssp             TTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHHS----------CSEEEEEECCHHHH
T ss_pred             CCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEecc-cCcHHHHHHHHHHHHHHhC----------CCeEEEEEehHHHH
Confidence            567889999997653  3566666 22333444443 6799999999999999743          46799999999999


Q ss_pred             HHHhccccc--cHHHHHHHHHHHHHhhcCCcEEEEEeCCC
Q psy10247        121 EALRTQFTL--NEISFNILCTVHQLKARDINIKFLWIPSH  158 (315)
Q Consensus       121 ~~l~~~~~~--~~~~~~i~~~~~~l~~~~~~v~~~WVpgH  158 (315)
                      +++++....  .++.++|.   +.+. ....|.+.|||||
T Consensus        75 ~~i~~~~~~~~~~l~~~il---~~l~-~~~~v~i~WVpgH  110 (110)
T d1s1ta1          75 GIIQAQPDQSESELVNQII---EQLI-KKEKVYLAWVPAH  110 (110)
T ss_dssp             HHHHHCCSEESCHHHHHHH---HHHH-HCSEEEEEECCSS
T ss_pred             HHHhcCccccchHHHHHHH---HHHh-cCCceEEEEeCCC
Confidence            999997654  34555554   3333 3578999999999

>d1zbfa1 c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: BH0863-like Ribonuclease H
species: Bacillus halodurans [TaxId: 86665]

Probab=99.57  E-value=4.5e-16  Score=121.71  Aligned_cols=112  Identities=14%  Similarity=0.059  Sum_probs=79.0

Q ss_pred             EEEEcCCCCC--CCeeEEEE--E-CCeeeEEecCCCCcHhHHHHHHHHHHHHHHHHhhhhccCCcceEEEEeCCHHHHHH
Q psy10247         48 FIFTDGTKTA--TNTGFAYV--S-GDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEA  122 (315)
Q Consensus        48 ~iytDGS~~~--~~~G~a~v--~-~~~~~~~~l~~~~s~~~aEl~Ai~~aL~~~~~~~~~~~~~~~~i~I~sDS~~al~~  122 (315)
                      .||||||+..  |.+|+|+|  . +........-+.+|+++||++|++.||+.+..       ...++.|+|||++|++.
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~-------~~~~i~I~tDS~yvi~w   78 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKE-------RNSRKPIYSNSQTAIKW   78 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHH-------TTCCCCEEESCHHHHHH
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhc-------CCceEEEEeccHHHHHH
Confidence            3899999885  44888877  2 22222111114679999999999999999853       23578999999999999


Q ss_pred             Hhccccc---------cHHHHHHHHHHHHHhhcCCcEEEEEeCCCCCCchhhhhc
Q psy10247        123 LRTQFTL---------NEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERVD  168 (315)
Q Consensus       123 l~~~~~~---------~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~g~~gNe~AD  168 (315)
                      +.+....         ..+.+.|.+....+.  ...+.+.|++.|+..-||..||
T Consensus        79 v~~~~~kt~~~~~vkN~~l~~~i~~a~~~lk--~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          79 VKDKKAKSTLVRNEETALIWKLVDEAEEWLN--THTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             HHHTCCCCCCCCSTTTHHHHHHHHHHHHHHH--HCCCCCCEEECCHHHHCSCTTC
T ss_pred             HHhCceecCcCCCcccHHHHHHHHHHHHHHH--hCCcCceeEEecCcccccCCCC
Confidence            9875421         123333333323333  3568999999999999999998