Psyllid ID: psy6829

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------37
Protein Sequence
MNVLKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIATGALRSSPVQSLYAESNIPPLSVRRDKLLFNYVVKLYGCPLNPMHKILFGNVDSFNITPNKPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSCQ
Secondary Structure (PSIPRED)
ccHHHHHHcccccccHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHcccccHHHHHHHHHHHHHHHccccEEEEEEccccccccccHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHHHHHccccHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHccccccHHHHHccccccccccccccccccccccccccccccccccccHHHHHHcHHHHcccccEEEEEccccccccEEEEEEEcccEEEEEcccccHHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHcccccHHHHHHcccccccccc
Coil and Loop (DISEMBL)
MNVLKIVSNKNYGLHRQTLLKLYQSYVspiidygssiyssAKDHIinklnpvhhngiriatgalrsspvqslyaesnipplsvrrdKLLFNYVVKLygcplnpmhkilfgnvdsfnitpnkplplkirFNCIREVSAVLKntkvvpysqgfppwysdfpvvdlslygsktiqntscavyaggsAKSYILNNINSIFTAELLALVFCLdsvknrpdvntlIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKscgkkvaflwcpshtgisgneIVDRAtrqldgaefvnlsspadlISVGKKYIHEKWQKSWSDLtnnklkcvkptigpwnvsdcnnryeEVVLTRVRIghtrlthsylftrsdppscq
Flexible Loop (DISEMBL)
mnvlkivsnknyglhRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIATGALRSSPVQSLYAesnipplsvrRDKLLFNYVVKLYGCPLNPMHKILFGNVDSFNITPNKPLPLKIRFNCIREVSAVLKNTKvvpysqgfppwysDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVkptigpwnvsdcnnRYEEVVLTRVRIghtrlthsylftrsdppscq
Low Complexity Region (SEG)
MNVLKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIATGALRSSPVQSLYAESNIPPLSVRRDKLLFNYVVKLYGCPLNPMHKILFGNVDSFNITPNKPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSCQ
Disordered region (IsUnstruct)
***LKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIATGALRSSPVQSLYAESNIPPLSVRRDKLLFNYVVKLYGCPLNPMHKILFGNVDSFNITPNKPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFT********
Disordered Region (DISOPRED)
MNVLKI*SNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIATGALRSSPVQSLYAESNIPPLSVRRDKLLFNYVVKLYGCPLNPMHKILFGNVDSFNITPNKPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSC*
Disordered Region (DISEMBL)
MNVLKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIATGALRSSPVQSLYAESNIPPLSVRRDKLLFNYVVKLYGCPLNPMHKILFGNVDSFNITPNKPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFT********
Disordered Region (DISPRO)
MNVLKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIATGALRSSPVQSLYAESNIPPLSVRRDKLLFNYVVKLYGCPLNPMHKILFGN*******PNKPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSD***C*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNVLKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIATGALRSSPVQSLYAESNIPPLSVRRDKLLFNYVVKLYGCPLNPMHKILFGNVDSFNITPNKPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSCQ
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	369
427791807	1212	Putative tick transposon, partial [Rhipi	0.997	0.303	0.328	2e-50
427791321	1210	Putative tick transposon, partial [Rhipi	0.997	0.304	0.328	3e-50
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.994	0.300	0.312	4e-47
427791063	1035	Putative tick transposon, partial [Rhipi	0.983	0.350	0.304	3e-44
427798889	1199	Putative tick transposon, partial [Rhipi	0.991	0.305	0.293	6e-41
427798887	1199	Putative tick transposon, partial [Rhipi	0.983	0.302	0.296	2e-40
427798885	1199	Putative tick transposon, partial [Rhipi	0.986	0.303	0.294	5e-40
443710566	377	hypothetical protein CAPTEDRAFT_186063 [	0.869	0.851	0.292	6e-37
427778603	1397	Putative tick transposon [Rhipicephalus	0.983	0.259	0.272	9e-36
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.547	0.428	0.356	7e-30

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

 Score =  205 bits (522), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 133/405 (32%), Positives = 198/405 (48%), Gaps = 37/405 (9%)

Query: 1    MNVLKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIA 60
            +N+LK++S+K++G  R  LL++Y+S V  I+DYG  +Y SA++  I +L+PVH+ G+R++
Sbjct: 745  LNLLKVLSHKHWGSDRLCLLRIYRSIVRSILDYGCVVYGSARESYIRRLDPVHNLGLRLS 804

Query: 61   TGALRSSPVQSLYAESNIPPLSVRRDKLLFNYVVKLYGCPLNPMHKILFGNVDSFNITPN 120
            +GA R+SPV+SLY + N PPLS RR  L  +YV+++   P +  + I        +    
Sbjct: 805  SGAYRTSPVESLYVDCNEPPLSHRRASLTLSYVLRIRSSPQHICYDIATRCSSRLHYLNK 864

Query: 121  KPL--PLKIRFNCIREVSAVLKNT-KVVPYSQGFPPWYSDFPVVDLSLY----------- 166
              L  PL +RF        + + T  V       PPW+    + D+SL            
Sbjct: 865  SNLIKPLLLRFEEYCRTYVISEETLDVARKPPRIPPWFDLAQLCDISLSHINKKVTPPEL 924

Query: 167  ---------------------GSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVF 205
                                 GSKT  +    +  G SA S  +    SIFTAE+ AL  
Sbjct: 925  IIQEFRALQEKYRDYAEFYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYALYE 984

Query: 206  CLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPS 265
                +        +I  DS+SAL ++  K+   PL+  ILN    + S    + F W PS
Sbjct: 985  AARKIIAGKHKKAIIYTDSLSALKALHIKSECEPLVGDILNMV-LINSKVISMRFCWVPS 1043

Query: 266  HTGISGNEIVDRATRQLDGAEFVNLSSP-ADLISVGKKYIHEKWQKSWSDLTNNKLKCVK 324
            H GI GNE  D+            +  P  D     +  +  KWQ+ W   T+NKL  VK
Sbjct: 1044 HVGIPGNEKADKCASLAAHKTLTKIRIPLKDSQRTIRLALLAKWQQQWDSCTSNKLHLVK 1103

Query: 325  PTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSCQ 369
            PT+G W       R+ EV+L R+RIGHT LTH++L T+ + P C+
Sbjct: 1104 PTLGEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCE 1148

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 =  205 bits (522), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 133/405 (32%), Positives = 198/405 (48%), Gaps = 37/405 (9%)

Query: 1    MNVLKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIA 60
            +N+LK++S+K++G  R  LL++Y+S V  I+DYG  +Y SA++  I +L+PVH+ G+R++
Sbjct: 742  LNLLKVLSHKHWGSDRLCLLRIYRSIVRSILDYGCVVYGSARESYIRRLDPVHNLGLRLS 801

Query: 61   TGALRSSPVQSLYAESNIPPLSVRRDKLLFNYVVKLYGCPLNPMHKILFGNVDSFNITPN 120
            +GA R+SPV+SLY + N PPLS RR  L  +YV+++   P +  + I        +    
Sbjct: 802  SGAYRTSPVESLYVDCNEPPLSHRRASLTLSYVLRIRSSPQHICYDIATRCSSRLHYLNK 861

Query: 121  KPL--PLKIRFNCIREVSAVLKNT-KVVPYSQGFPPWYSDFPVVDLSLY----------- 166
              L  PL +RF        + + T  V       PPW+    + D+SL            
Sbjct: 862  SNLIKPLLLRFEEYCRTYVISEETLDVARKPPRIPPWFDLAQLCDISLSHINKKVTPPEL 921

Query: 167  ---------------------GSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVF 205
                                 GSKT  +    +  G SA S  +    SIFTAE+ AL  
Sbjct: 922  IIQEFRALQEKYRDYAEFYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYALYE 981

Query: 206  CLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPS 265
                +        +I  DS+SAL ++  K+   PL+  ILN    + S    + F W PS
Sbjct: 982  AARKIIAGKHKKAIIYTDSLSALKALHIKSECEPLVGDILNMV-LINSKVISMRFCWVPS 1040

Query: 266  HTGISGNEIVDRATRQLDGAEFVNLSSP-ADLISVGKKYIHEKWQKSWSDLTNNKLKCVK 324
            H GI GNE  D+            +  P  D     +  +  KWQ+ W   T+NKL  VK
Sbjct: 1041 HVGIPGNEKADKCASLAAHKTLTKIRIPLKDSQRTIRLALLAKWQQQWDSCTSNKLHLVK 1100

Query: 325  PTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSCQ 369
            PT+G W       R+ EV+L R+RIGHT LTH++L T+ + P C+
Sbjct: 1101 PTLGEWKNCRHQERFIEVILCRLRIGHTHLTHNFLLTKEEQPMCE 1145

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  194 bits (494), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 127/406 (31%), Positives = 196/406 (48%), Gaps = 39/406 (9%)

Query: 1    MNVLKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIA 60
            +N+L+++S+ ++G  R TLL LY+S +   +DYGS IY +A+   +  L P+ +  +R+ 
Sbjct: 763  LNILRVLSHTDWGADRDTLLLLYRSLIRSKLDYGSIIYGAARKSYLKILEPIQNAALRLC 822

Query: 61   TGALRSSPVQSLYAESNIPPLSVRRDKLLFNYVVKLYGCPLNPMHKILFG--NVDSFNIT 118
             GA R+SP+ SL+ E+   P+ +R  KL   Y+VKL   P NP    +F    V+ +N  
Sbjct: 823  LGAFRTSPIPSLHVEAGELPMDIRMKKLAMQYIVKLKSNPTNPAFDSIFNPTEVELYNRR 882

Query: 119  PN--KPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLY---------- 166
            PN  +PL L++R   I+ ++  +     +   Q  PPW  + P ++LSL           
Sbjct: 883  PNVIQPLGLRMR-EPIQNLTQPIDQISKIETPQN-PPWLMNKPKLNLSLLNFKKENTDPS 940

Query: 167  ----------------------GSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALV 204
                                  GSK     +CA        S  L +  SIFTAEL A++
Sbjct: 941  ILQVHFRELQESYGDCGTIYTDGSKMEGKVACACSFRNKTISRRLPDGCSIFTAELHAIL 1000

Query: 205  FCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCP 264
              L +VK       +I  DS SAL ++    T IPL+   L     + +  + V F+W P
Sbjct: 1001 LALMAVKASERSKFIICSDSKSALQALGRMKTDIPLVHKSLKLLDLITADRRDVTFIWVP 1060

Query: 265  SHTGISGNEIVDR-ATRQLDGAEFVNLSSPADLISVGKKYIHEKWQKSWSDLTNNKLKCV 323
            SH GI GNE  DR A R L+ A        +DL        + +WQ  W   T++KL+ +
Sbjct: 1061 SHVGIEGNEAADREAKRALNHAVSGTQIPYSDLRQSIASATYREWQNRWEAETHSKLRQI 1120

Query: 324  KPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSCQ 369
               +     S    R     ++R+RIGHT +THS++  R +PP C+
Sbjct: 1121 VADVRWRPTSKGLTRRGSTTMSRLRIGHTYITHSFVLKREEPPLCE 1166

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

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

 Score =  185 bits (470), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 125/410 (30%), Positives = 196/410 (47%), Gaps = 47/410 (11%)

Query: 1    MNVLKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIA 60
            MN+LKI+S+  +G  R+ L+ +Y+S V   +DYGS +Y SA    +  L+P+HH GIR+A
Sbjct: 603  MNILKILSHTTWGSDRKCLMDIYKSLVRTRLDYGSVVYHSAAPSALKILDPIHHLGIRLA 662

Query: 61   TGALRSSPVQSLYAESNIPPLSVRRDKLLFNYVVKLYGCPLNPMHK--------ILFGNV 112
            TGA R+SPVQSLY ESN   L ++R  + F Y +K+     +P H         +L+ N 
Sbjct: 663  TGAFRTSPVQSLYVESNQWSLHLQRSYMSFVYFLKVKAEKEHPAHSTVNDLSSSVLYHNR 722

Query: 113  DSFNITPNKPLPLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLY------ 166
             S      +P  L++R +   E+   L    ++  +   PPW       D+S        
Sbjct: 723  PSVR----QPYSLRVR-DLAEEMGLSLHEHSLMARAAYLPPWQWQLIECDVSFEQVTKHA 777

Query: 167  ------------------------GSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLA 202
                                     SK   + S A      + + +L+   SIFTAE  A
Sbjct: 778  PHAHIYTYFLELQHKYTFPEFFTDASKFNSSVSYAAVGPSFSDAGVLHQNTSIFTAEAYA 837

Query: 203  LVFCLDSVKNRPDVNTLIVCDSMSALTSIAN-KNTSIPLIAHILNTWHTLKSCGKKVAFL 261
            +   +  ++     + +I  DS+S + ++   K    P++A + +   T+ +  + V   
Sbjct: 838  IFVAVKHIEQLKLPSAVIYTDSLSVVKALKTLKKHKNPVLASLYSLLCTVYALKQHVVVC 897

Query: 262  WCPSHTGISGNEIVDR-ATRQLDGAEFVNLSSPA-DLISVGKKYIHEKWQKSWSDLTNNK 319
            W P H  I GN + D+ A    + A    L+ PA DL  + K+ +   WQ  W   T NK
Sbjct: 898  WVPGHREIQGNVLADQLAASAHENAAHTFLAIPALDLKPLLKRKLRAYWQSIWDTQTQNK 957

Query: 320  LKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSCQ 369
            L  +KP +G W  +   +R  E+ LTR+R GHT  TH+YL + +DPP C+
Sbjct: 958  LHAIKPQLGEWPPAS-KSRRTEITLTRLRTGHTHTTHAYLLSGNDPPRCE 1006

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 =  174 bits (441), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 119/405 (29%), Positives = 196/405 (48%), Gaps = 39/405 (9%)

Query: 1    MNVLKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIA 60
            MN+LK++S   +G  ++ L+ LY+S +   +DYG+ IY SA    +  L+PVHH GIR++
Sbjct: 769  MNILKVLSRTTWGSDKKCLMNLYKSLIRTRLDYGAIIYQSASPTALKMLDPVHHLGIRLS 828

Query: 61   TGALRSSPVQSLYAESNIPPLSVRRDKLLFNYVVKLYGCPLNPMHKILFGNVDSFNITPN 120
            TGA R+SPV+SLY ESN   L ++R  + F Y +K+     +P H  +  ++    +  N
Sbjct: 829  TGAFRTSPVESLYVESNEWSLHLQRSYMSFLYYIKVNADKEHPSHSTI-NDLSCSTLFEN 887

Query: 121  KPL---PLKIRFNCIREVSAV-LKNTKVVPYSQGFPPWYSDF--------------PVVD 162
            +P    P  +R   + E + + L   +++  +   PPW                  P+  
Sbjct: 888  RPSLKPPYSLRVRDLAEQTGLPLFEHRLMAPAAYPPPWQWQLIDCDVSFMEVTKHAPIAH 947

Query: 163  LSLYGSKTIQNTSCAVYAGGSAKSYI----------------LNNINSIFTAELLALVFC 206
            +  Y  +     +C  +   ++KS+                 L+   SIFTAE  A++  
Sbjct: 948  IRTYFLELQHKYNCPAFYTDASKSHTSVSYAAVGPSFSAAGALHPNTSIFTAEAYAILAA 1007

Query: 207  LDSVKNRPDVNTLIVCDSMSALTSIAN-KNTSIPLIAHILNTWHTLKSCGKKVAFLWCPS 265
            +  ++       +I  DS+S + ++   K    P++  + +   T+ +  + V   W P 
Sbjct: 1008 VKHIRELKLQKAVIYTDSLSVVKALKTLKKHRNPVLVSLYSLLCTIYTSKQHVVVCWVPG 1067

Query: 266  HTGISGNEIVDR-ATRQLDGAEFVNLSSPA-DLISVGKKYIHEKWQKSWSDLTNNKLKCV 323
            H  I GN + D+ A    D +   +++ PA DL    K+ I   WQ +W   T+NKL  +
Sbjct: 1068 HREIQGNVMADQLAVSAHDSSANTSIAIPALDLKPYLKRKIRAYWQSTWDRQTHNKLHVI 1127

Query: 324  KPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSC 368
            KP +G W      +RY EV LTR+R GHT  TH+YL +  D P C
Sbjct: 1128 KPQLGHWP-PISKSRYTEVTLTRLRTGHTHSTHAYLLSGGDAPFC 1171

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427798887|gb|JAA64895.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  172 bits (437), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 121/408 (29%), Positives = 200/408 (49%), Gaps = 45/408 (11%)

Query: 1    MNVLKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIA 60
            MN+LK++S   +G  ++ L+ LY+S +   +DYG+ IY SA    +  L+PVHH GIR++
Sbjct: 769  MNILKVLSRTTWGSDKKCLMNLYKSLIRTRLDYGAIIYQSASPTALKMLDPVHHLGIRLS 828

Query: 61   TGALRSSPVQSLYAESNIPPLSVRRDKLLFNYVVKLYGCPLNPMHKILFGNVDSFNITPN 120
            TGA R+SPV+SLY ESN   L ++R  + F Y +K+     +P H  +  ++ S  +  N
Sbjct: 829  TGAFRTSPVESLYVESNEWSLHLQRSYMSFLYYLKVNADKEHPSHSTI-NDLSSSTLFEN 887

Query: 121  KPL---PLKIRFNCIREVSAV-LKNTKVVPYSQGFPPWYSDF--------------PVVD 162
            +P    P  +R   + E + + L   +++  +   PPW                  P+  
Sbjct: 888  RPSLRPPYSLRVRGLAEETGLPLFEHRLMAPAAYPPPWQWQLIDCDVSFMEVTKHAPIAH 947

Query: 163  LSLYGSKTIQNTSCAVYAGGSAKSYI----------------LNNINSIFTAELLALVFC 206
            +  Y  +     +C  +   ++KS+                 L+   SIFTAE  A++  
Sbjct: 948  IRTYFLELQHKYNCPAFYTDASKSHTSVSYAAVGPSFSAAGALHPNTSIFTAEAYAILAA 1007

Query: 207  LDSVKNRPDVNTLIVCDSMSALTSI----ANKNTSIPLIAHILNTWHTLKSCGKKVAFLW 262
            +  ++       +I  DS+S + ++     +KN+ +  +  ++ T +T K   + V   W
Sbjct: 1008 VKHIRELKLQKAVIYTDSLSVVKALKTLKKHKNSILVSLYSLVCTVYTAK---QHVVVCW 1064

Query: 263  CPSHTGISGNEIVDR-ATRQLDGAEFVNLSSPA-DLISVGKKYIHEKWQKSWSDLTNNKL 320
             P H  I GN + D  A    D +   +++ PA DL  + K+ +   WQ +W   T+NKL
Sbjct: 1065 VPGHREIQGNVMADHLAASTHDCSANTSIAIPALDLKPLLKRKLRAYWQSTWDQQTHNKL 1124

Query: 321  KCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSC 368
              +KP +G W      +RY EV LTR+R GHT  TH+YL +  D P C
Sbjct: 1125 HVIKPQLGHWP-PISKSRYTEVTLTRLRTGHTHSTHAYLLSGGDAPFC 1171

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427798885|gb|JAA64894.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  171 bits (433), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 120/407 (29%), Positives = 197/407 (48%), Gaps = 43/407 (10%)

Query: 1    MNVLKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIA 60
            MN+LK++S   +G  ++ L+ LY+S +   +DYG+ IY SA    +  L+P+HH GIR++
Sbjct: 769  MNILKVLSRTTWGSDKKCLMNLYKSLIRTCLDYGAIIYQSASPTALKMLDPIHHLGIRLS 828

Query: 61   TGALRSSPVQSLYAESNIPPLSVRRDKLLFNYVVKLYGCPLNPMHKILFGNVDSFNITPN 120
            TGA  +SPV+SLY ESN   L ++R  + F Y +K+     +P H  +  ++ S  +  N
Sbjct: 829  TGAFCTSPVESLYVESNEWSLQLQRSYMSFLYYLKVNADKEHPSHSTI-NDLSSSTLFEN 887

Query: 121  KPL---PLKIRFNCIREVSAV-LKNTKVVPYSQGFPPWYSDF--------------PVVD 162
            +P    P  +R   + E + + L   +++  +   PPW                  P+  
Sbjct: 888  RPSLRPPYSLRVRGLAEETGLPLFEHRLMAPAAYPPPWQWQLIDCDVSFMEVTKHAPIAH 947

Query: 163  LSLYGSKTIQNTSCAVYAGGSAKSY----------------ILNNINSIFTAELLALVFC 206
            +  Y  +     +C  +   ++KS+                +L+   SIFTAE  A++  
Sbjct: 948  IRTYFLELQHKYNCPAFYTDASKSHTSVSYAAVGPSFSDAGVLHPNTSIFTAEAYAILAA 1007

Query: 207  LDSVKNRPDVNTLIVCDSMS---ALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWC 263
            +  ++       +I  DS+S   AL ++     SI  +  + +   TL +  + V   W 
Sbjct: 1008 VKHIRELKLQKAVIYTDSLSVVKALKTLKKHKNSI--LVSLYSLVCTLYTAKQHVVVCWV 1065

Query: 264  PSHTGISGNEIVDR-ATRQLDGAEFVNLSSPA-DLISVGKKYIHEKWQKSWSDLTNNKLK 321
            P H  I GN + D  A    D +   +++ PA DL  + K+ +   WQ +W   T+NKL 
Sbjct: 1066 PGHREIQGNVMADHLAASTHDCSANTSIAIPALDLKPLLKRKLRAYWQSTWDQQTHNKLH 1125

Query: 322  CVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSC 368
             +KP +G W      +RY EV LTR+R GHT  TH+YL +  D P C
Sbjct: 1126 VIKPQLGHWP-PISKSRYTEVTLTRLRTGHTHSTHAYLLSGGDAPFC 1171

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  161 bits (407), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 106/363 (29%), Positives = 167/363 (46%), Gaps = 42/363 (11%)

Query: 11  NYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIATGALRSSPVQ 70
           N+G  R+ L +L++S +   +DYG+ +Y SA+   + +L P+ +   R+  GA R SPV 
Sbjct: 2   NWGADREVLFRLFRSLLRSRLDYGAIVYGSARISYLERLKPIQNQAFRLCLGAFRISPVT 61

Query: 71  SLYAESNIPPLSVRRDKLLFNYVVKLYGCPLNPMHKILFG-NVDSFNIT-PNKPLPLKIR 128
           SL+ E+N  P+++R+  L   + +++     NP H+ +F  N D F ++ PN   PL +R
Sbjct: 62  SLHTEANEMPMAIRQKLLSVQFALRVCSDTTNPAHQCIFNYNNDRFYLSKPNAIRPLALR 121

Query: 129 FNCIREVSAVLKNTKVVPYSQGF--PPWYSDFPVVDLSLY-------------------- 166
                ++  +  + K +  +Q F  P W    P +D+SL                     
Sbjct: 122 IK--EDLQTICPDIKAITPNQLFNIPYWLLRPPELDISLIHFGKKTANPNYTLKNEFYNL 179

Query: 167 -------------GSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLAL--VFCLDSVK 211
                        GSK+    +C   A   +    L +  SIF+AELLA+  V  L    
Sbjct: 180 MDKYPDHKVIFTDGSKSDSAVACFATADNLSIQIRLPDSASIFSAELLAIYQVLTLLECS 239

Query: 212 NRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISG 271
                  LI  DS+S+L +I N N   P +  IL     L   G  +   WCPSH G+ G
Sbjct: 240 ANDQQQFLIATDSLSSLQAIGNFNIKHPYVFKILEKCTLLHKKGIYLVMAWCPSHVGVMG 299

Query: 272 NEIVDRATRQLDGAEFVNLSSP-ADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPW 330
           NE  D   ++        +  P +D   +  ++  EKWQ+ WS    NKL C++PT+G W
Sbjct: 300 NERADLLAKEALSFTTCTIRIPSSDFKPITHEFFKEKWQEQWSSEQENKLYCIQPTLGKW 359

Query: 331 NVS 333
             S
Sbjct: 360 AKS 362

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  157 bits (396), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 126/462 (27%), Positives = 202/462 (43%), Gaps = 99/462 (21%)

Query: 1    MNVLKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHIINKLNPVHHNGIRIA 60
            MN+LKI+S++++G  R  L+ L++S V   IDYGS IY SA    +  L+PV+H GIR+A
Sbjct: 862  MNLLKILSHQSWGTDRYCLITLFRSLVLSRIDYGSIIYQSASKTALKLLDPVYHLGIRLA 921

Query: 61   TGA-----------------------------------LRSSPVQSLYAES-------NI 78
             GA                                   L+  P +SL  +        N 
Sbjct: 922  LGAFRTSPVQSLYAESDQWPLDYQRTYLGVTYATRIMSLKQHPCKSLMNDVSTTQLYINR 981

Query: 79   P------PLSVR----RDKLLFNYVVKLYGCPLNPMHKILFGNVDSFNITPNKP-----L 123
            P      PL++R    + K+ F  + ++         K L  +V +  +  N+P      
Sbjct: 982  PSISPPFPLAIRPVVEKLKIHFEDLQEIDQVEXQHPCKALMNDVSTTQLYINRPSISPPF 1041

Query: 124  PLKIRFNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLY----------------- 166
            PL IR   + ++    ++ + +   +  PPW     + D S                   
Sbjct: 1042 PLAIR-PVVEKLKIHFEDLQEIDQVEVIPPWKQCPIICDWSFKDLKKKTAPNALIQQHFL 1100

Query: 167  --------------GSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKN 212
                          GSK+  + SCA Y    + +  L+   SIFTAE   ++  ++ +K 
Sbjct: 1101 ALEHKYRSAAFFSDGSKSQTSVSCAAYGESFSDAKTLHAHTSIFTAEAYGILLIVEHIKQ 1160

Query: 213  RPDVNTLIVCDSMSALTSIA-NKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISG 271
                 ++I  DS+S +T+++  K +  P+   +LN  H   +    +   W P H GI+G
Sbjct: 1161 HMIRRSIIYTDSLSVVTALSCGKCSKNPVFNKLLNNMHEAYNQNLSIVLCWVPGHAGITG 1220

Query: 272  NEIVDRATRQLDGAEFVNLSS--PADLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIG- 328
            NE+VD+  R+      +++SS    DL  V ++ +   WQ  W    +NKL  VKP +  
Sbjct: 1221 NEMVDKNAREAASRHTIDISSVPGVDLNPVVRRGLRSHWQVEWDKQVDNKLHLVKPHLSK 1280

Query: 329  --PWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDPPSC 368
              P  +    NR+ EV L R+RIGHT  TH +L T +DPP+C
Sbjct: 1281 VLPQKL----NRFTEVTLARLRIGHTYATHKHLLTGTDPPTC 1318

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 =  137 bits (346), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 73/205 (35%), Positives = 108/205 (52%), Gaps = 3/205 (1%)

Query: 167 GSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVC-DSM 225
           GSK+  + +C+ ++        L    S+FT+E++A++  L  V+   + +  ++C DS+
Sbjct: 27  GSKSEDSVACSFFSSRLKLKMKLPVQMSVFTSEIIAILSALRCVEADNEQHQFVICSDSL 86

Query: 226 SALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDR-ATRQLDG 284
           SA+ +I   +   P +  +L    ++    K V F+WCPSH GI GNE+ D  A   L  
Sbjct: 87  SAIMAIHGMDVRHPYVLQVLYAIKSISQQEKIVVFMWCPSHVGIPGNEMADTLAKEALSS 146

Query: 285 AEFVNLSSPA-DLISVGKKYIHEKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVV 343
                L  PA DL  + KKYI  +WQ  W +  +NKL  + PTIGPW       R EE+V
Sbjct: 147 TNLAELPVPASDLRCLIKKYIRSRWQHEWDEQHSNKLHSIHPTIGPWPPCQREKRREEIV 206

Query: 344 LTRVRIGHTRLTHSYLFTRSDPPSC 368
           L R+RIGHT  TH Y+    D   C
Sbjct: 207 LARIRIGHTHYTHDYIPRGDDQTEC 231

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	369
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.493	0.374	0.237	1.3e-05

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

 Score = 132 (51.5 bits), Expect = 1.3e-05, P = 1.3e-05
 Identities = 46/194 (23%), Positives = 80/194 (41%)

Query:   183 SAKSYILNNINS-IFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIP-- 239
             S  SY+     S ++ AEL  ++  L  +  R   + +I  D+ + L ++ N  +     
Sbjct:   208 SRSSYMGQQSESTVYVAELQGILLALVIILQRQMQHAVIFTDNQATLQALRNPGSQSGQY 267

Query:   240 LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSSPADLI-S 298
             ++  I+   +  +  G  V F W P+H G+ GNE  DR  ++  G   +        I S
Sbjct:   268 ILEAIIMALNKGRKAGLNVHFRWIPAHRGVEGNEQADRRAKEATGWRRIRGHRGRMTIRS 327

Query:   299 VGKKYIHE----KWQKSWSDLTNNKLK---CVKPTIGPWNVSDCNNRYEEVVLTRVRIGH 351
               K+  HE    +W+  W    + +        PT     V    +R    ++ ++R G 
Sbjct:   328 AVKRRAHEVVNARWENDWKSCHHGRELYELTPTPTRKVLRVHQDLHRALSTIIVQMRTGK 387

Query:   352 TRLTHSYLFTRSDP 365
               L H YL+ R  P
Sbjct:   388 IGLRH-YLYQRGVP 400


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.319   0.135   0.413    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      369       369   0.00085  117 3  11 22  0.39    34
                                                     34  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  617 (66 KB)
  Total size of DFA:  260 KB (2138 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:04
  No. of threads or processors used:  24
  Search cpu time:  29.84u 0.08s 29.92t   Elapsed:  00:00:37
  Total cpu time:  29.84u 0.08s 29.92t   Elapsed:  00:00:44
  Start:  Thu Aug 15 14:44:34 2013   End:  Thu Aug 15 14:45:18 2013

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	369
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	4e-24
pfam00075	126	pfam00075, RNase_H, RNase H	1e-10
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	9e-05

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

 Score = 95.8 bits (239), Expect = 4e-24
 Identities = 40/133 (30%), Positives = 58/133 (43%), Gaps = 14/133 (10%)

Query: 154 WYSDFPVVDLSLYGSKTIQNTSCAVYA--GGSA-KSYILNNINSIFTAELLALVFCLDSV 210
            Y+D         GSK    T         G+  +SY L    S+F AELLA++  L   
Sbjct: 2   IYTD---------GSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLA 52

Query: 211 KNRPD-VNTLIVC-DSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTG 268
                    + +  DS +AL ++ +  +S PL+  I      L + G KV   W P H+G
Sbjct: 53  LREGRRARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSG 112

Query: 269 ISGNEIVDRATRQ 281
           I GNE  DR  ++
Sbjct: 113 IEGNERADRLAKE 125

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 = 58.0 bits (141), Expect = 1e-10
 Identities = 30/93 (32%), Positives = 43/93 (46%), Gaps = 11/93 (11%)

Query: 193 NSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSI----ANKNTSIPLIAHILNTW 248
            +   AELLAL+  L+++  +  VN  I  DS   +  I      K+ S P+   I    
Sbjct: 38  TTNQRAELLALIEALEALSGQK-VN--IYTDSQYVIGGITNGWPTKSESKPIKNEIWE-- 92

Query: 249 HTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQ 281
             L     KV   W P H+GI GNE+ D+  +Q
Sbjct: 93  --LLQKKHKVYIQWVPGHSGIPGNELADKLAKQ 123

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

>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

 Score = 41.6 bits (98), Expect = 9e-05
 Identities = 21/92 (22%), Positives = 34/92 (36%), Gaps = 4/92 (4%)

Query: 190 NNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWH 249
               +   AELLAL+  L+   +      +I  DS   +  I + +        +L    
Sbjct: 34  IPAATNNEAELLALLEALELALDLGLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDIL 93

Query: 250 TLKSCGKKVAFLWCPSHTGISGNEIVDRATRQ 281
            L S    + F   P      GNE+ DR  ++
Sbjct: 94  LLLSKFIDIRFEHVPR----EGNEVADRLAKE 121

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	369
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.88
PRK06548	161	ribonuclease H; Provisional	99.88
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.86
PRK08719	147	ribonuclease H; Reviewed	99.86
PRK00203	150	rnhA ribonuclease H; Reviewed	99.85
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.75
PRK13907	128	rnhA ribonuclease H; Provisional	99.7
KOG3752|consensus	371		99.69
PRK07708	219	hypothetical protein; Validated	99.52
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.46
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.28

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

Probab=99.88  E-value=1.4e-22  Score=171.33  Aligned_cols=127  Identities=18%  Similarity=0.098  Sum_probs=105.0

Q ss_pred             CcccccccCCCCCCceEEEEE--eCCee--EEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcC
Q psy6829         159 PVVDLSLYGSKTIQNTSCAVY--AGGSA--KSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK  234 (369)
Q Consensus       159 ~~i~td~s~~~~~~~~G~a~~--~~~~~--~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~  234 (369)
                      ..||+||++..++|..|+|++  .++..  .+..+. .+||++||+.|++.||+.+.+.+...|.|+|||++|+++|..+
T Consensus         4 v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~w   82 (154)
T COG0328           4 VEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITRW   82 (154)
T ss_pred             eEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHHH
Confidence            349999999999888888877  33322  344445 8999999999999999999988899999999999999999854


Q ss_pred             CCC-----------cH-HHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCCC
Q psy6829         235 NTS-----------IP-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE  286 (369)
Q Consensus       235 ~~~-----------~~-~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~~  286 (369)
                      ...           .| -..++++.+.++.++...|.+.|||||+|.++||.||+||+.|+...
T Consensus        83 ~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          83 IVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             HhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            111           12 24578888888877777999999999999999999999999998775

>PRK06548 ribonuclease H; Provisional

Probab=99.88  E-value=5.1e-22  Score=170.68  Aligned_cols=124  Identities=22%  Similarity=0.197  Sum_probs=97.0

Q ss_pred             cccccccCCCCCCceEEEEEeCCe-eEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhc-----
Q psy6829         160 VVDLSLYGSKTIQNTSCAVYAGGS-AKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN-----  233 (369)
Q Consensus       160 ~i~td~s~~~~~~~~G~a~~~~~~-~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~-----  233 (369)
                      .|||||++..++|..|+|++..+. ..+.. ...+||+.|||.|++.||+.+.. ....+.|+|||++|++++..     
T Consensus         7 ~IytDGa~~gnpg~~G~g~~~~~~~~~~g~-~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~~~W   84 (161)
T PRK06548          7 IAATDGSSLANPGPSGWAWYVDENTWDSGG-WDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWVYSW   84 (161)
T ss_pred             EEEEeeccCCCCCceEEEEEEeCCcEEccC-CCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHHHHH
Confidence            399999999988999999884322 22222 23689999999999999986643 34679999999999999994     


Q ss_pred             ----CCCCc--HH-HHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCCC
Q psy6829         234 ----KNTSI--PL-IAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE  286 (369)
Q Consensus       234 ----~~~~~--~~-~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~~  286 (369)
                          +...+  ++ .+++++.+..+... ..|.|.|||||+|++|||.||+||++|+...
T Consensus        85 k~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~  143 (161)
T PRK06548         85 KMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNF  143 (161)
T ss_pred             HHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence                32222  33 36777777777654 4799999999999999999999999998764

>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=99.86  E-value=9.6e-22  Score=164.43  Aligned_cols=116  Identities=26%  Similarity=0.333  Sum_probs=88.5

Q ss_pred             cccccccCCCCCCceEEEEE-eCCeeEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhc-----
Q psy6829         160 VVDLSLYGSKTIQNTSCAVY-AGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN-----  233 (369)
Q Consensus       160 ~i~td~s~~~~~~~~G~a~~-~~~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~-----  233 (369)
                      .||||||+..+++..|+|++ .++...+..++ ..+++.||+.||..||+.+ .  ...+.|+|||++++..+..     
T Consensus         5 ~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v~~~l~~~~~~~   80 (132)
T PF00075_consen    5 IIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYVLNALNKWLHGN   80 (132)
T ss_dssp             EEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHHHHHHHTHHHHT
T ss_pred             EEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHHHHHHHHhcccc
Confidence            38999998766555555554 44445555666 8999999999999999944 3  4999999999999998877     


Q ss_pred             CCCCc----HHHHHHHHHHHHHhhCCCeEEEEEecCCCCC-ccchHHhHHHhhhh
Q psy6829         234 KNTSI----PLIAHILNTWHTLKSCGKKVAFLWCPSHTGI-SGNEIVDRATRQLD  283 (369)
Q Consensus       234 ~~~~~----~~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi-~gNe~AD~lAk~a~  283 (369)
                      .....    ++..+|++.+    ..+..|.|.|||||+|+ .|||.||+|||+|+
T Consensus        81 ~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   81 GWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             TSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             ccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence            22211    3445555433    45789999999999999 69999999999986

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=99.86  E-value=4.5e-21  Score=163.32  Aligned_cols=119  Identities=18%  Similarity=0.208  Sum_probs=90.5

Q ss_pred             ccccccCCCCCC---ceEEEEE--eC--Ce--eEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHh
Q psy6829         161 VDLSLYGSKTIQ---NTSCAVY--AG--GS--AKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSI  231 (369)
Q Consensus       161 i~td~s~~~~~~---~~G~a~~--~~--~~--~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l  231 (369)
                      |||||++..+++   ..|+|++  ..  +.  ..+..+....|+++||+.|+..||+.+.+.    ..|+|||++|++++
T Consensus         7 iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yvi~~i   82 (147)
T PRK08719          7 IYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYCVRGF   82 (147)
T ss_pred             EEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHHHHHH
Confidence            999999976544   3455554  33  22  244456566899999999999999998753    37999999999999


Q ss_pred             h--------cCCCCc---HH-HHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhC
Q psy6829         232 A--------NKNTSI---PL-IAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDG  284 (369)
Q Consensus       232 ~--------~~~~~~---~~-~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~  284 (369)
                      .        +.+..+   ++ ..++++.+..+.+ ...|.|.|||||+|++|||.||+||++|+.
T Consensus        83 ~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         83 NEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             HHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            4        333222   22 3567777777765 567999999999999999999999999875

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.85  E-value=8.6e-21  Score=162.72  Aligned_cols=125  Identities=15%  Similarity=0.134  Sum_probs=93.9

Q ss_pred             cccccccCCCCCCceEEEEE--eCCeeEEE-ecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcC--
Q psy6829         160 VVDLSLYGSKTIQNTSCAVY--AGGSAKSY-ILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK--  234 (369)
Q Consensus       160 ~i~td~s~~~~~~~~G~a~~--~~~~~~~~-~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~--  234 (369)
                      .||||||+..+++..|+|++  .++....+ ......|++.|||.|+..||+.+.+  ...+.|+|||++++++|..+  
T Consensus         5 ~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w~~   82 (150)
T PRK00203          5 EIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEWIH   82 (150)
T ss_pred             EEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHHHH
Confidence            38999999877777777776  33333222 2234689999999999999998865  46799999999999999862  


Q ss_pred             -------CCCc--HH-HHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCCCC
Q psy6829         235 -------NTSI--PL-IAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEF  287 (369)
Q Consensus       235 -------~~~~--~~-~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~~~  287 (369)
                             ...+  ++ ..++++.+..+.. ...|.|.|||||+|++|||.||+|||+|+..+.
T Consensus        83 ~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~  144 (150)
T PRK00203         83 GWKKNGWKTADKKPVKNVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAGAEEAT  144 (150)
T ss_pred             HHHHcCCcccCCCccccHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence                   1111  22 2345555555543 368999999999999999999999999987653

>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner

Probab=99.75  E-value=3.6e-17  Score=133.70  Aligned_cols=123  Identities=22%  Similarity=0.198  Sum_probs=96.3

Q ss_pred             ccccccCCCCCCceEEEEE--eCCe--eEE-EecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcCC
Q psy6829         161 VDLSLYGSKTIQNTSCAVY--AGGS--AKS-YILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN  235 (369)
Q Consensus       161 i~td~s~~~~~~~~G~a~~--~~~~--~~~-~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~~  235 (369)
                      +|+|||.....++.|+|++  +.+.  ... .......+++.+|+.|+..||+.+...+..++.|++||+.++..+.+..
T Consensus         2 ~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~   81 (130)
T cd06222           2 IYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWY   81 (130)
T ss_pred             EEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhccc
Confidence            6899998877788888887  2221  111 1222578999999999999999998888999999999999999999876


Q ss_pred             C-CcHHHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhh
Q psy6829         236 T-SIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLD  283 (369)
Q Consensus       236 ~-~~~~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~  283 (369)
                      . .......++..+..+...+..+.|.|||+|+|+.+|+.||.|||+|.
T Consensus        82 ~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          82 EGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             cCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            4 22233444444445545678999999999999999999999999873

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=99.70  E-value=1.6e-16  Score=132.48  Aligned_cols=120  Identities=18%  Similarity=0.101  Sum_probs=96.2

Q ss_pred             ccccccCCCCCCceEEEEE--eCCee--EEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcCCC
Q psy6829         161 VDLSLYGSKTIQNTSCAVY--AGGSA--KSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT  236 (369)
Q Consensus       161 i~td~s~~~~~~~~G~a~~--~~~~~--~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~~~  236 (369)
                      ||+||++...++..|+|++  +.+..  ..+.. ...|+..||+.|++.||+.+...+..++.|+|||+.+++.+++...
T Consensus         4 iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~-~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~~   82 (128)
T PRK13907          4 VYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPL-GTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEYA   82 (128)
T ss_pred             EEEeeCCCCCCCccEEEEEEEECCeeEEEEecc-cccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHHh
Confidence            8999999988888888887  32222  22223 3679999999999999999999888899999999999999998665


Q ss_pred             CcHHHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCC
Q psy6829         237 SIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGA  285 (369)
Q Consensus       237 ~~~~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~  285 (369)
                      .......+++.+..+..+...+.|.|||.    ++|+.||.||++|...
T Consensus        83 ~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         83 KNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAILQ  127 (128)
T ss_pred             cChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence            44445566666666767777888999997    5999999999998753

>KOG3752|consensus

Probab=99.69  E-value=7.4e-17  Score=152.05  Aligned_cols=125  Identities=24%  Similarity=0.189  Sum_probs=100.1

Q ss_pred             cccccccCCCC---CCceEEEEEeCC---eeEEEecC-CCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhh
Q psy6829         160 VVDLSLYGSKT---IQNTSCAVYAGG---SAKSYILN-NINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIA  232 (369)
Q Consensus       160 ~i~td~s~~~~---~~~~G~a~~~~~---~~~~~~l~-~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~  232 (369)
                      .|||||+++.+   ...+|+|||.++   ...++++. ...|++.|||.||..||+-+.+....+++|.|||++++++|+
T Consensus       214 vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~l~  293 (371)
T KOG3752|consen  214 VVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINSLT  293 (371)
T ss_pred             EEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHHHH
Confidence            39999998863   578999999542   34677774 789999999999999999999988889999999999999998


Q ss_pred             cCCCC-----------cH------HHHHHHHHHHHHhhC--CCeEEEEEecCCCCCccchHHhHHHhhhhC
Q psy6829         233 NKNTS-----------IP------LIAHILNTWHTLKSC--GKKVAFLWCPSHTGISGNEIVDRATRQLDG  284 (369)
Q Consensus       233 ~~~~~-----------~~------~~~~i~~~~~~l~~~--~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~  284 (369)
                      .|...           ++      ..+..+..+++|.+.  +..|.+.|||||.|+.|||+||.||++++.
T Consensus       294 ~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~  364 (371)
T KOG3752|consen  294 LWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGST  364 (371)
T ss_pred             HHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence            65321           11      123444555555443  589999999999999999999999998754

>PRK07708 hypothetical protein; Validated

Probab=99.52  E-value=1.7e-13  Score=124.06  Aligned_cols=124  Identities=14%  Similarity=0.024  Sum_probs=92.6

Q ss_pred             cccccccCCCCCCceEEEEE--e--CCeeE----EEecCCCCchHHHHHHHHHHHHHHhhcCCCCc--EEEEeCcHHHHH
Q psy6829         160 VVDLSLYGSKTIQNTSCAVY--A--GGSAK----SYILNNINSIFTAELLALVFCLDSVKNRPDVN--TLIVCDSMSALT  229 (369)
Q Consensus       160 ~i~td~s~~~~~~~~G~a~~--~--~~~~~----~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~--i~I~tDS~~al~  229 (369)
                      .+|+||+...++++.|+|++  .  ++...    ...++...|++.||+.|++.||+.+.+.+.++  |.|++||+.+++
T Consensus        75 ~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~  154 (219)
T PRK07708         75 LVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLN  154 (219)
T ss_pred             EEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHH
Confidence            39999998776766777665  3  22221    12455568999999999999999999876554  899999999999


Q ss_pred             HhhcCCC-CcHHHHHHHHHHHHHhhCC-CeEEEEEecCCCCCccchHHhHHHhhhhCCCC
Q psy6829         230 SIANKNT-SIPLIAHILNTWHTLKSCG-KKVAFLWCPSHTGISGNEIVDRATRQLDGAEF  287 (369)
Q Consensus       230 ~l~~~~~-~~~~~~~i~~~~~~l~~~~-~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~~~  287 (369)
                      .+.+.+. .++..+.+.+.+..+.++. ..+.|.|||    ...|+.||+||++|+....
T Consensus       155 qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~  210 (219)
T PRK07708        155 QLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTV  210 (219)
T ss_pred             HhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCC
Confidence            9998654 3444555555555554443 347888998    4689999999999998644

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.46  E-value=5.7e-13  Score=130.88  Aligned_cols=120  Identities=15%  Similarity=0.151  Sum_probs=96.2

Q ss_pred             ccccccCCCCCCceEEEEE--eC--Cee---EEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhc
Q psy6829         161 VDLSLYGSKTIQNTSCAVY--AG--GSA---KSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN  233 (369)
Q Consensus       161 i~td~s~~~~~~~~G~a~~--~~--~~~---~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~  233 (369)
                      ||+||++..+++..|+|++  +.  +..   ....++ ..|++.||+.|++.||+.+.+.+..++.|++||+.+++.+.+
T Consensus         5 i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i~~   83 (372)
T PRK07238          5 VEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSG   83 (372)
T ss_pred             EEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHhCC
Confidence            8999999988887788877  32  211   223344 678889999999999999999888999999999999999988


Q ss_pred             CCC-CcHHHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCC
Q psy6829         234 KNT-SIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGA  285 (369)
Q Consensus       234 ~~~-~~~~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~  285 (369)
                      ... +++-...+.+.+..+.+++..+.|.|||.    .+|+.||.||+.|...
T Consensus        84 ~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~  132 (372)
T PRK07238         84 RWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA  132 (372)
T ss_pred             CCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence            654 34444555566667777788999999996    6999999999998754

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

Probab=99.28  E-value=1.7e-11  Score=94.34  Aligned_cols=86  Identities=17%  Similarity=0.131  Sum_probs=67.5

Q ss_pred             hHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcCCCCcHHHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchH
Q psy6829         195 IFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEI  274 (369)
Q Consensus       195 ~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~  274 (369)
                      +..||+.|+..||+.+.+.+.+++.|.|||+.+++.|++..........+...+..+......+.|.|||    .++|..
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~~   76 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----REQNKV   76 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------GGGSHH
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----hHHhHH
Confidence            4689999999999999999999999999999999999987543223445555556676778899999999    589999


Q ss_pred             HhHHHhhhhC
Q psy6829         275 VDRATRQLDG  284 (369)
Q Consensus       275 AD~lAk~a~~  284 (369)
                      ||.|||.|..
T Consensus        77 A~~LA~~a~~   86 (87)
T PF13456_consen   77 ADALAKFALS   86 (87)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHhh
Confidence            9999998864

---

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	369
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	2e-05
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	1e-04
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	4e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04

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

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 12/90 (13%), Positives = 24/90 (26%), Gaps = 7/90 (7%)

Query: 190 NNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN--TSIPLIAHILNT 247
                    E+ A ++ +        V   I+ D    +   A                 
Sbjct: 45  AATMRNVAGEIAAALYAVKKASQLG-VKIRILHDYAG-IAFWATGEWKAKNEFTQAYAKL 102

Query: 248 WHTLKSCGKKVAFLWCPSHTGISGNEIVDR 277
            +  +      +F    +H+G   N+ VD 
Sbjct: 103 MNQYR---GIYSFEKVKAHSGNEFNDYVDM 129

>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 = 41.0 bits (96), Expect = 1e-04
 Identities = 22/91 (24%), Positives = 38/91 (41%), Gaps = 11/91 (12%)

Query: 198 AELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKK 257
           AEL+AL   L   +    +N  +  DS  A  + A+ ++    I +       LK+    
Sbjct: 66  AELIALTQALKMAE-GKKLN--VYTDSRYAF-ATAHVHSEGREIKNKNEILALLKALFLP 121

Query: 258 --VAFLWCPSHTG-----ISGNEIVDRATRQ 281
             ++ + CP H         GN + D+A R+
Sbjct: 122 KRLSIIHCPGHQKGNSAEARGNRMADQAARE 152

>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ... Length = 557

 Score = 41.3 bits (97), Expect = 4e-04
 Identities = 29/84 (34%), Positives = 40/84 (47%), Gaps = 14/84 (16%)

Query: 198 AELLALVFCL-DSVKNRPDVNTLIVCDSMSALTSIANK--NTSIPLIAHILNTWHTLKSC 254
            EL A+   L DS     +VN  IV DS  AL  I  +   +   L+  I+      +  
Sbjct: 479 TELQAIYLALQDS---GLEVN--IVTDSQYALGIIQAQPDKSESELVNQIIE-----QLI 528

Query: 255 GKKVAFL-WCPSHTGISGNEIVDR 277
            K+  +L W P+H GI GNE VD+
Sbjct: 529 KKEKVYLAWVPAHKGIGGNEQVDK 552

>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 = 41.4 bits (96), Expect = 5e-04
 Identities = 52/308 (16%), Positives = 100/308 (32%), Gaps = 99/308 (32%)

Query: 4   LKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHI----------INKLNPVH 53
           LK +  +   L R+ L        +P     S I  S +D +           +KL  + 
Sbjct: 308 LKYLDCRPQDLPREVLT------TNPRRL--SIIAESIRDGLATWDNWKHVNCDKLTTI- 358

Query: 54  HNGIRIATGALRSSPVQSLYAE-------SNIPP--LSV-----------------RRDK 87
              I  +   L  +  + ++         ++IP   LS+                  +  
Sbjct: 359 ---IESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYS 415

Query: 88  LL----FNYVVKLYGCPLN---------PMHKILFGNVDSFNIT----PNKPLPLKIR-- 128
           L+        + +    L           +H+ +   VD +NI      +  +P  +   
Sbjct: 416 LVEKQPKESTISIPSIYLELKVKLENEYALHRSI---VDHYNIPKTFDSDDLIPPYLDQY 472

Query: 129 -FNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSA--- 184
            ++ I      LKN +       F   + DF  ++      + I++ S A  A GS    
Sbjct: 473 FYSHI---GHHLKNIEHPERMTLFRMVFLDFRFLE------QKIRHDSTAWNASGSILNT 523

Query: 185 -------KSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIA--NKN 235
                  K YI +N    +   + A+      +   P +   ++C   + L  IA   ++
Sbjct: 524 LQQLKFYKPYICDNDP-KYERLVNAI------LDFLPKIEENLICSKYTDLLRIALMAED 576

Query: 236 TSIPLIAH 243
            +I   AH
Sbjct: 577 EAIFEEAH 584

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	369
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.88
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.88
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.87
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.86
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.86
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.86
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.85
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.85
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.82
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.8
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.79
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.75
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.75
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.74
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.31
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.14

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

Probab=99.88  E-value=1.2e-22  Score=173.82  Aligned_cols=125  Identities=22%  Similarity=0.221  Sum_probs=97.9

Q ss_pred             ccccccCCCCCC---ceEEEEEeC--C-eeEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcC
Q psy6829         161 VDLSLYGSKTIQ---NTSCAVYAG--G-SAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK  234 (369)
Q Consensus       161 i~td~s~~~~~~---~~G~a~~~~--~-~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~  234 (369)
                      ||||||+..+++   ..|+|++..  + ...+..+...+|++.||+.|++.||+.+.+.+..++.|+|||+++++.|.++
T Consensus        10 iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~~i~~~   89 (154)
T 2qkb_A           10 VYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTINGITNW   89 (154)
T ss_dssp             EEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHHHHHTH
T ss_pred             EEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHhhhhhh
Confidence            999999976543   478888832  2 2345566667899999999999999999887789999999999999999874


Q ss_pred             C---------CCc--H-HHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCCC
Q psy6829         235 N---------TSI--P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE  286 (369)
Q Consensus       235 ~---------~~~--~-~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~~  286 (369)
                      .         ..+  + ....+++.+..+.. +..|.|.|||||+|++|||.||+|||+|+..+
T Consensus        90 ~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~-~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           90 VQGWKKNGWKTSAGKEVINKEDFVALERLTQ-GMDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             HHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT-TCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHhccccccCCCccccHHHHHHHHHHHc-CCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            1         111  1 12345555555544 45799999999999999999999999998764

>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=99.88  E-value=1.3e-22  Score=172.58  Aligned_cols=121  Identities=23%  Similarity=0.226  Sum_probs=92.5

Q ss_pred             cccccccCCCCCCceEEEEEe-CCeeEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcCC---
Q psy6829         160 VVDLSLYGSKTIQNTSCAVYA-GGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN---  235 (369)
Q Consensus       160 ~i~td~s~~~~~~~~G~a~~~-~~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~~---  235 (369)
                      .|||||++..+++..|+|++. .+......+ ..+|++.||+.|+..||+.+    ..++.|+|||++++++|.++.   
T Consensus        14 ~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i~~w~~~W   88 (150)
T 3qio_A           14 TFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIITQWIHNW   88 (150)
T ss_dssp             EEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHHHHHHHHH
T ss_pred             EEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHHHHHHHHH
Confidence            499999999888777888773 222233344 47899999999999999986    489999999999999998752   


Q ss_pred             --------CCcH-HHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCC
Q psy6829         236 --------TSIP-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGA  285 (369)
Q Consensus       236 --------~~~~-~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~  285 (369)
                              ...+ ..+++++.+..+..++..|.|.|||||+|++|||.||+||++|+..
T Consensus        89 ~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           89 KKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             CC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             hhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence                    1111 1234444444333567899999999999999999999999999875

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

Probab=99.87  E-value=1.3e-22  Score=172.00  Aligned_cols=121  Identities=17%  Similarity=0.083  Sum_probs=90.7

Q ss_pred             ccccccCCCCCCceEEEEE--eCCee--EEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhc-CC
Q psy6829         161 VDLSLYGSKTIQNTSCAVY--AGGSA--KSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN-KN  235 (369)
Q Consensus       161 i~td~s~~~~~~~~G~a~~--~~~~~--~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~-~~  235 (369)
                      ||||||+..+++..|+|++  .++..  .+..++ .+|++.||+.|++.||+.+.+  ..++.|+|||++|++.|.+ +.
T Consensus         7 iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~~-~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~~~w~   83 (146)
T 3h08_A            7 IYTDGAASGNPGKGGWGALLMYGSSRKEISGYDP-ATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMNEGWL   83 (146)
T ss_dssp             EEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEE-EECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHHSSHH
T ss_pred             EEEecCCCCCCCceEEEEEEEECCeeEEeecCCC-CCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHHHHHH
Confidence            8999999988777888877  44432  223333 689999999999999999976  6899999999999999987 21


Q ss_pred             ---------CCc--H-HHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCC
Q psy6829         236 ---------TSI--P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGA  285 (369)
Q Consensus       236 ---------~~~--~-~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~  285 (369)
                               ..+  + ..+.+++.+..+... ..|.|.|||||+|++|||.||+|||+|+..
T Consensus        84 ~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~-~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A           84 KRWVKNGWKTAAKKPVENIDLWQEILKLTTL-HRVTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             HHHHHTTCC----CCCTTHHHHHHHHHHHHH-SEEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCccCCCCCcCCHHHHHHHHHHHhh-CceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence                     111  1 123344444444332 469999999999999999999999999864

>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=99.86  E-value=4.3e-22  Score=170.57  Aligned_cols=124  Identities=15%  Similarity=0.141  Sum_probs=96.0

Q ss_pred             ccccccCCCCCCceEEEEE--eCCee--EEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcC--
Q psy6829         161 VDLSLYGSKTIQNTSCAVY--AGGSA--KSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK--  234 (369)
Q Consensus       161 i~td~s~~~~~~~~G~a~~--~~~~~--~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~--  234 (369)
                      ||||||+..+++..|+|++  ..+..  .+..+ ..+|++.||+.|+..||+.+.+  ..++.|+|||+++++.|.++  
T Consensus         7 iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~--~~~v~I~tDS~~vi~~i~~w~~   83 (155)
T 1jl1_A            7 IFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQWIH   83 (155)
T ss_dssp             EEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHTTHH
T ss_pred             EEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc--CCcEEEEeCHHHHHHHHHHHHH
Confidence            8999999987777888877  33322  23333 3679999999999999999976  38999999999999999973  


Q ss_pred             ------C-CCc--HH-HHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCCCCC
Q psy6829         235 ------N-TSI--PL-IAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFV  288 (369)
Q Consensus       235 ------~-~~~--~~-~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~~~~  288 (369)
                            . ..+  ++ ...+++.+..+.. ...|.|.|||||+|++|||.||+|||+|+..+.+
T Consensus        84 ~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  146 (155)
T 1jl1_A           84 NWKKRGWKTADKKPVKNVDLWQRLDAALG-QHQIKWEWVKGHAGHPENERADELARAAAMNPTL  146 (155)
T ss_dssp             HHHHTTTBCTTSCBCTTHHHHHHHHHHTT-TCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             HHhhcccccccCCccCCHHHHHHHHHHHc-cCceEEEEcCCCCCCHHHHHHHHHHHHHHhccch
Confidence                  1 111  11 2345555555544 4689999999999999999999999999988764

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

Probab=99.86  E-value=6.4e-22  Score=170.00  Aligned_cols=123  Identities=17%  Similarity=0.163  Sum_probs=94.3

Q ss_pred             ccccccCCCCCCceEEEEE--eCCee--EEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhc---
Q psy6829         161 VDLSLYGSKTIQNTSCAVY--AGGSA--KSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN---  233 (369)
Q Consensus       161 i~td~s~~~~~~~~G~a~~--~~~~~--~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~---  233 (369)
                      ||||||+..+++..|+|++  .++..  .+..++ .+|++.||+.|+..||+.+.+  ..++.|+|||++|++.|.+   
T Consensus         9 iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~-~~tn~~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~~w~~   85 (158)
T 2e4l_A            9 IFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGFS-LTTNNRMELLAPIVALEALKE--PCKIILTSDSQYMRQGIMTWIH   85 (158)
T ss_dssp             EEEEEEESSSSEEEEEEEEEEETTEEEEEEEEEE-EECHHHHHHHHHHHHHHTCSS--CCEEEEEECCHHHHHHHHTHHH
T ss_pred             EEEcccccCCCCcEEEEEEEEECCEEEEEecCcC-CCccHHHHHHHHHHHHHHhcc--CCeEEEEeCHHHHHHHHHHHHH
Confidence            8999999987777888877  34332  223333 579999999999999999865  3899999999999999988   


Q ss_pred             -----CCC-Cc--H-HHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCC-CC
Q psy6829         234 -----KNT-SI--P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGA-EF  287 (369)
Q Consensus       234 -----~~~-~~--~-~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~-~~  287 (369)
                           ... .+  + ....+++.+..+.. ...|.|.|||||+|++|||.||+|||+|+.. +.
T Consensus        86 ~W~~n~~~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~~  148 (158)
T 2e4l_A           86 GWKKKGWMTSNRTPVKNVDLWKRLDKAAQ-LHQIDWRWVKGHAGHAENERCDQLARAAAEANPT  148 (158)
T ss_dssp             HHHHTTTBCTTSSBCTTHHHHHHHHHHHT-TSEEEEEECCTTCCCHHHHHHHHHHHHHHHSCCC
T ss_pred             HHHHccccccCCCcccCHHHHHHHHHHHc-cCcEEEEEccCCCCchhHHHHHHHHHHHHHhchh
Confidence                 221 11  1 12344444555544 4689999999999999999999999999987 44

>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=99.86  E-value=9.5e-22  Score=169.70  Aligned_cols=124  Identities=17%  Similarity=0.132  Sum_probs=91.5

Q ss_pred             cccccccCCCCCCceEEEEE--eCCee-EEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcCCC
Q psy6829         160 VVDLSLYGSKTIQNTSCAVY--AGGSA-KSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT  236 (369)
Q Consensus       160 ~i~td~s~~~~~~~~G~a~~--~~~~~-~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~~~  236 (369)
                      .||||||+..++|..|+|++  .++.. ....+...+||+.||+.|+..||+.+ .  ..++.|+|||+++++++-....
T Consensus        25 ~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~vi~~iw~~~~  101 (165)
T 3p1g_A           25 TWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA-E--GKKLNVYTDSRYAFATAHVHSE  101 (165)
T ss_dssp             EEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT-B--TSEEEEEECCHHHHHHHHSCCC
T ss_pred             EEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc-c--CceEEEEEchHHHHhhhhcccC
Confidence            39999999876666666654  44332 23345668899999999999999999 2  6899999999999999932111


Q ss_pred             CcHH-HHHHHHHH-HHHhhCCCeEEEEEecCCCC-----CccchHHhHHHhhhhCCCC
Q psy6829         237 SIPL-IAHILNTW-HTLKSCGKKVAFLWCPSHTG-----ISGNEIVDRATRQLDGAEF  287 (369)
Q Consensus       237 ~~~~-~~~i~~~~-~~l~~~~~~v~~~WvpgH~g-----i~gNe~AD~lAk~a~~~~~  287 (369)
                      ..++ ..+++..+ ..+ ..+..|.|.|||||+|     ++|||.||+|||+|+..+.
T Consensus       102 g~~v~n~dl~~~l~~~l-~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~~  158 (165)
T 3p1g_A          102 GREIKNKNEILALLKAL-FLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAV  158 (165)
T ss_dssp             SCCCSSHHHHHHHHHHT-TSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcccCHHHHHHHHHHH-hcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcCC
Confidence            1111 12333222 334 3578999999999999     9999999999999998754

>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=99.85  E-value=3.4e-22  Score=169.66  Aligned_cols=123  Identities=11%  Similarity=0.019  Sum_probs=93.8

Q ss_pred             cccccccCCCCCCceEEEEE--eCCee--EEE-ec--CC--CCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHH
Q psy6829         160 VVDLSLYGSKTIQNTSCAVY--AGGSA--KSY-IL--NN--INSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTS  230 (369)
Q Consensus       160 ~i~td~s~~~~~~~~G~a~~--~~~~~--~~~-~l--~~--~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~  230 (369)
                      .||||||+..  +.+|+|++  .++..  .+. ..  +.  .+||+.||+.|+..||+.+.+.+. +|.|+|||+.+.+.
T Consensus         8 ~iytDGs~~~--g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i~~w   84 (147)
T 2kq2_A            8 DVYTDGSYVN--GQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGIAFW   84 (147)
T ss_dssp             EEECCCCCBT--TBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTHHHH
T ss_pred             EEEECCCCCC--CCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHHHHH
Confidence            3999999987  55566655  44432  233 22  22  369999999999999999877656 99999999998888


Q ss_pred             hhcCCCC-cHHHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCCCCC
Q psy6829         231 IANKNTS-IPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFV  288 (369)
Q Consensus       231 l~~~~~~-~~~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~~~~  288 (369)
                      +.+.+.. .+....+.+.++++..   .|.|.|||||+|++|||.||+|||+|+..+.+
T Consensus        85 ~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  140 (147)
T 2kq2_A           85 ATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALGIRDL  140 (147)
T ss_dssp             TTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHTCCCT
T ss_pred             HhCCCccCCcchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHhcccc
Confidence            8775544 3444555555555533   79999999999999999999999999988654

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

Probab=99.85  E-value=1e-21  Score=170.04  Aligned_cols=124  Identities=18%  Similarity=0.069  Sum_probs=94.9

Q ss_pred             cccccccCCCCCCceEEEEEe--CCee--EEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhc--
Q psy6829         160 VVDLSLYGSKTIQNTSCAVYA--GGSA--KSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN--  233 (369)
Q Consensus       160 ~i~td~s~~~~~~~~G~a~~~--~~~~--~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~--  233 (369)
                      .||||||+..+++..|+|++.  ++..  .+... ..+|++.||+.|++.||+.+.+.  .+|.|+|||+++++.|.+  
T Consensus        10 ~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i~~~w   86 (166)
T 1ril_A           10 ALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGE-ACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAFTEGW   86 (166)
T ss_dssp             CEEEEEEESSTTEEEEEEEEECBTTBCCEECCEE-EEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHHHSSH
T ss_pred             EEEECccccCCCCCEEEEEEEEECCEEEEEecCC-CCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHHhhhH
Confidence            499999999887888888873  3322  22222 36799999999999999998763  589999999999999998  


Q ss_pred             --------CCCCc--H-HHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCCCC
Q psy6829         234 --------KNTSI--P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEF  287 (369)
Q Consensus       234 --------~~~~~--~-~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~~~  287 (369)
                              +...+  + ...++++.+..+.. ...|.|.|||||+|++|||.||+|||+|+....
T Consensus        87 ~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~  150 (166)
T 1ril_A           87 LEGWRKRGWRTAEGKPVKNRDLWEALLLAMA-PHRVRFHFVKGHTGHPENERVDREARRQAQSQA  150 (166)
T ss_dssp             HHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT-TSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             HHHHHhcccccccCCccCcHHHHHHHHHHHh-cCeEEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence                    22211  1 12345555555544 358999999999999999999999999998864

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

Probab=99.82  E-value=2.5e-20  Score=160.60  Aligned_cols=124  Identities=15%  Similarity=0.084  Sum_probs=90.3

Q ss_pred             cccccccCCCCCCc-----eEEEEEe--CC----eeEEEec-CCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHH
Q psy6829         160 VVDLSLYGSKTIQN-----TSCAVYA--GG----SAKSYIL-NNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSA  227 (369)
Q Consensus       160 ~i~td~s~~~~~~~-----~G~a~~~--~~----~~~~~~l-~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~a  227 (369)
                      .||||||+..++|+     .|+|++.  ++    ....+.. ....+++.||+.|+..||+.+.+. ..+|.|+|||++|
T Consensus         9 viYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~-~~~v~I~TDS~Yv   87 (165)
T 2lsn_A            9 VFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKI-PGPVLVITDSFYV   87 (165)
T ss_dssp             EEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHS-SSCEEEEESCHHH
T ss_pred             EEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcC-CCeEEEEeChHHH
Confidence            38999999987665     7888872  22    1233333 346788999999999999988765 4579999999999


Q ss_pred             HHHhhcCC---------CC--cHH-HHHHHHHHHHHhhCCCeEEEEEecCCCCC------ccchHHhHHHhhhhC
Q psy6829         228 LTSIANKN---------TS--IPL-IAHILNTWHTLKSCGKKVAFLWCPSHTGI------SGNEIVDRATRQLDG  284 (369)
Q Consensus       228 l~~l~~~~---------~~--~~~-~~~i~~~~~~l~~~~~~v~~~WvpgH~gi------~gNe~AD~lAk~a~~  284 (369)
                      +++|..+.         ..  .++ -.++++.+.++......|.|.|||||+|+      +|||.||+||++|+.
T Consensus        88 i~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~  162 (165)
T 2lsn_A           88 AESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSY  162 (165)
T ss_dssp             HHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             HhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhhh
Confidence            99997531         11  111 23444444444444568999999999995      589999999999874

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

Probab=99.80  E-value=4.4e-19  Score=148.85  Aligned_cols=121  Identities=14%  Similarity=0.158  Sum_probs=97.8

Q ss_pred             cccccccCCCCCCceEEEEE--eCC---ee--EEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhh
Q psy6829         160 VVDLSLYGSKTIQNTSCAVY--AGG---SA--KSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIA  232 (369)
Q Consensus       160 ~i~td~s~~~~~~~~G~a~~--~~~---~~--~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~  232 (369)
                      .|||||++..+++..|+|++  +.+   ..  .+..++ .+|++.||+.|++.||+.+.+.+..++.|+|||+++++.+.
T Consensus         5 ~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~i~   83 (141)
T 3hst_B            5 VIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIG-RATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMS   83 (141)
T ss_dssp             EEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEE-EECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHHHT
T ss_pred             EEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCC-CCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHHHh
Confidence            38999999888777888877  322   22  223333 78999999999999999998877899999999999999999


Q ss_pred             cCC-CCcHHHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCC
Q psy6829         233 NKN-TSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGA  285 (369)
Q Consensus       233 ~~~-~~~~~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~  285 (369)
                      +.+ ..++....+++.+..+..++..|.|.|||+    ++||.||+|||+|+..
T Consensus        84 ~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B           84 GRWKVKHPDLLKLYVQAQALASQFRRINYEWVPR----ARNTYADRLANDAMDA  133 (141)
T ss_dssp             TSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             CCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHHHHH
Confidence            854 344555566667777777788999999995    8999999999998865

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

Probab=99.79  E-value=3e-19  Score=149.37  Aligned_cols=120  Identities=13%  Similarity=0.078  Sum_probs=93.4

Q ss_pred             ccccccCCCCCCceEEEEE--e--CCee--EEEecCCCCchHHHHHHHHHHHHHHhhcCCCC----cEEEEeCcHHHHHH
Q psy6829         161 VDLSLYGSKTIQNTSCAVY--A--GGSA--KSYILNNINSIFTAELLALVFCLDSVKNRPDV----NTLIVCDSMSALTS  230 (369)
Q Consensus       161 i~td~s~~~~~~~~G~a~~--~--~~~~--~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~----~i~I~tDS~~al~~  230 (369)
                      ||||||+..+++..|+|++  +  ++..  .+..++ .+|++.||+.|+..||+.+.+.+.+    ++.|+|||+++++.
T Consensus         6 iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~vi~~   84 (140)
T 3u3g_D            6 IYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIG-ETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQ   84 (140)
T ss_dssp             EEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEE-EECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHHHHH
T ss_pred             EEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCC-CCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHHHHH
Confidence            8999999988888888887  2  2222  222333 5799999999999999999887666    99999999999999


Q ss_pred             hhcCCC-CcHHHHHHHHHHHHH-hhCCCeEEEEEecCCCCCccchHHhHHHhhhhCC
Q psy6829         231 IANKNT-SIPLIAHILNTWHTL-KSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGA  285 (369)
Q Consensus       231 l~~~~~-~~~~~~~i~~~~~~l-~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~  285 (369)
                      +.++.. .++....+++.+..+ ..+...|.|.|||+    ++||.||+|||+|+..
T Consensus        85 i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D           85 MQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPR----EKNARADELVNEAIDK  137 (140)
T ss_dssp             HTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCG----GGGHHHHHHHHHHHHH
T ss_pred             hCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCc----hhhHHHHHHHHHHHHh
Confidence            998664 333334455555555 55566899999994    8999999999998753

>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=99.75  E-value=2.3e-18  Score=175.98  Aligned_cols=113  Identities=21%  Similarity=0.264  Sum_probs=89.8

Q ss_pred             ccccccCCCCCCceEEEEE--eCCeeEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcCCCC-
Q psy6829         161 VDLSLYGSKTIQNTSCAVY--AGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTS-  237 (369)
Q Consensus       161 i~td~s~~~~~~~~G~a~~--~~~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~~~~-  237 (369)
                      ||||||+..+++..|+|++  .++ .....++ .+||+.||+.|+..||+.    ...++.|+|||++|++++.++... 
T Consensus       439 iytDGs~~~n~g~~g~G~v~~~~~-~~~~~~~-~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~~~~~~  512 (555)
T 1mu2_A          439 FYTDGSCNRQSKEGKAGYVTDRGK-DKVKKLE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQPTES  512 (555)
T ss_dssp             EEEEEEECTTTCCEEEEEEETTSC-EEEEEES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTCCSEE
T ss_pred             EEEcccccCCCCCceEEEEEEeCC-EeeccCC-CCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhcccccc
Confidence            8999999887776777777  333 2233333 689999999999999998    468999999999999999987643 


Q ss_pred             -cHHHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhh
Q psy6829         238 -IPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLD  283 (369)
Q Consensus       238 -~~~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~  283 (369)
                       .++.+++.+   .+ ..+..|.|.|||||+|++|||.||+|||+|+
T Consensus       513 ~~~l~~~~~~---~~-~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          513 ESKIVNQIIE---EM-IKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             SCHHHHHHHH---HH-HHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             cHHHHHHHHH---Hh-ccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence             345554443   22 2367899999999999999999999999885

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

Probab=99.75  E-value=4e-18  Score=144.67  Aligned_cols=120  Identities=14%  Similarity=0.108  Sum_probs=91.9

Q ss_pred             ccccccCC-CCCCceEE-EEE--eC-CeeEEE--ecC---CCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHH
Q psy6829         161 VDLSLYGS-KTIQNTSC-AVY--AG-GSAKSY--ILN---NINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTS  230 (369)
Q Consensus       161 i~td~s~~-~~~~~~G~-a~~--~~-~~~~~~--~l~---~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~  230 (369)
                      |||||++. .+++..|+ |++  ++ .....+  .++   ..+|++.||+.|+..||+.+.+.+..++.|+|||+++++.
T Consensus         4 iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi~~   83 (149)
T 2ehg_A            4 GYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQ   83 (149)
T ss_dssp             EEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHHHH
T ss_pred             EEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHHHH
Confidence            89999998 67777775 765  32 222222  233   3789999999999999999988778899999999999999


Q ss_pred             hhcCCCC-cHHHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCC
Q psy6829         231 IANKNTS-IPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGA  285 (369)
Q Consensus       231 l~~~~~~-~~~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~  285 (369)
                      +.++... ++....+++.+..+..+. .|.|.|||+    ++|+.||+|||+|+..
T Consensus        84 i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~----~~N~~AD~LA~~a~~~  134 (149)
T 2ehg_A           84 MNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPR----EENKEADRLSRVAYEL  134 (149)
T ss_dssp             HTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             HhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCC----cccHHHHHHHHHHHHh
Confidence            9997542 333445555555554444 599999998    5999999999999865

>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=99.74  E-value=2e-18  Score=176.62  Aligned_cols=113  Identities=26%  Similarity=0.323  Sum_probs=87.8

Q ss_pred             ccccccCCCCCCceEEEEEe-CCeeEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcCCCC--
Q psy6829         161 VDLSLYGSKTIQNTSCAVYA-GGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTS--  237 (369)
Q Consensus       161 i~td~s~~~~~~~~G~a~~~-~~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~~~~--  237 (369)
                      ||||||+..++|..|+|++. .+....... ..+||+.||+.|+..||+.+    ..++.|+|||++|++.+.++...  
T Consensus       442 iytDGs~~~n~g~~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~~~~~~~  516 (557)
T 2zd1_A          442 FYVDGAANRETKLGKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQPDKSE  516 (557)
T ss_dssp             EEEEEEECTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTTCCSEES
T ss_pred             EEEccCCCCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhcCCccCC
Confidence            89999998877777777773 222233333 36899999999999999998    57899999999999999998654  


Q ss_pred             cHHHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhh
Q psy6829         238 IPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQL  282 (369)
Q Consensus       238 ~~~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a  282 (369)
                      .++.+++.+   .+.. ...|.|.|||||+|++|||.||+||++|
T Consensus       517 ~~l~~~~~~---~l~~-~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          517 SELVNQIIE---QLIK-KEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             SHHHHHHHH---HHHH-CSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             HHHHHHHHH---HHhc-CCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            245555543   3333 4589999999999999999999999986

>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=99.31  E-value=6.7e-13  Score=111.21  Aligned_cols=114  Identities=15%  Similarity=0.068  Sum_probs=83.1

Q ss_pred             cccccccCCCCCCceEEEEEeC--CeeE--EEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcCC
Q psy6829         160 VVDLSLYGSKTIQNTSCAVYAG--GSAK--SYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN  235 (369)
Q Consensus       160 ~i~td~s~~~~~~~~G~a~~~~--~~~~--~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~~  235 (369)
                      .|||||++..++|..|+|++..  +...  +..++ .+||+.||+.|++.||+.+.+.+. ++.|+|||++|++.+++..
T Consensus        13 ~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~-~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~~~~~   90 (142)
T 1zbf_A           13 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWVKDKK   90 (142)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEE-EECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHHHHTC
T ss_pred             EEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccC-CcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHHHcCC
Confidence            4999999999889899999842  2222  12233 579999999999999999988655 9999999999999999876


Q ss_pred             CC-c--------HHHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhH
Q psy6829         236 TS-I--------PLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDR  277 (369)
Q Consensus       236 ~~-~--------~~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~  277 (369)
                      .. +        ++.+.+.....-+..  ..+....|.-|++.-||..||.
T Consensus        91 ~k~~~~~~v~n~dLw~~l~~~~~w~~~--~~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A           91 AKSTLVRNEETALIWKLVDEAEEWLNT--HTYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             CCCCCCCSTTTHHHHHHHHHHHHHHHH--CCCCCCEEECCHHHHCSCTTCC
T ss_pred             ccCCCCCCcccHHHHHHHHHHHHHHhh--CCCceeEEEeccCccCcCcccc
Confidence            21 1        244444433333433  3455556677888889999984

>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=99.14  E-value=1.3e-10  Score=95.70  Aligned_cols=74  Identities=18%  Similarity=0.162  Sum_probs=58.3

Q ss_pred             cccccccCCCCCCceEEEEE--e-CCee-EEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcCC
Q psy6829         160 VVDLSLYGSKTIQNTSCAVY--A-GGSA-KSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN  235 (369)
Q Consensus       160 ~i~td~s~~~~~~~~G~a~~--~-~~~~-~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~~  235 (369)
                      .|||||++..++|..|+|++  . +... ....++ .+||+.||+.|++.||+.+.+.+. ++.|+|||++|++.|.++.
T Consensus         7 ~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~~-~tTNN~aEl~A~i~aL~~l~~~~~-~v~i~tDSqyVi~wi~~~~   84 (134)
T 4htu_A            7 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWVKDKK   84 (134)
T ss_dssp             SEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEEE-EECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHHHHTC
T ss_pred             EEEEeeccCCCCCCeEEEEEEEECCEEEEEecCCC-CCchHHHHHHHHHHHHHHHHhCCC-CEEEEcchHHHHHHHHcCC
Confidence            49999999999998999544  2 2222 223333 789999999999999999987543 3899999999999998753

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	369
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.89
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.87
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.86
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.69
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.52

>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=99.89  E-value=9.3e-24  Score=172.70  Aligned_cols=116  Identities=21%  Similarity=0.243  Sum_probs=89.3

Q ss_pred             CcccccccCCCCCCceEEEEEeC-CeeEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcCCCC
Q psy6829         159 PVVDLSLYGSKTIQNTSCAVYAG-GSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTS  237 (369)
Q Consensus       159 ~~i~td~s~~~~~~~~G~a~~~~-~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~~~~  237 (369)
                      +.||||||+..+.+..|+|++.. +......++ ..|++.||+.||.+||+..    ...+.|+|||++|++.+.++...
T Consensus         8 ~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~~----~~~i~I~tDS~~v~~~~~~~~~~   82 (126)
T d1mu2a1           8 ETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTDS----GPKVNIIVDSQYVMGIVASQPTE   82 (126)
T ss_dssp             EEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHTS----CSEEEEEESCHHHHHHHHTCCSE
T ss_pred             cEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhccC----CcceEEEechHHHHHHHhcCCcc
Confidence            34999999987777777777633 333444454 5799999999999999864    67899999999999999997654


Q ss_pred             c--HHHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhh
Q psy6829         238 I--PLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLD  283 (369)
Q Consensus       238 ~--~~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~  283 (369)
                      +  .....+   +..+. ....|.|.|||||+|++|||.||+||++|.
T Consensus        83 ~~~~~~~~~---~~~~~-~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          83 SESKIVNQI---IEEMI-KKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             ESCHHHHHH---HHHHH-HCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             ccchHHHHH---HHHhh-hcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            3  232222   23343 346899999999999999999999999984

>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=99.87  E-value=1.2e-22  Score=170.92  Aligned_cols=129  Identities=14%  Similarity=0.146  Sum_probs=96.4

Q ss_pred             ccccccCCCCCCceEEEEE--eCCeeEEEec-CCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcCCC-
Q psy6829         161 VDLSLYGSKTIQNTSCAVY--AGGSAKSYIL-NNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT-  236 (369)
Q Consensus       161 i~td~s~~~~~~~~G~a~~--~~~~~~~~~l-~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~~~-  236 (369)
                      ||||||+..+++..|+|++  .++....+.. ...+|++.||+.|+..||+++..  ...+.|+|||++++..+..+.. 
T Consensus         5 IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~~--~~~i~i~tds~~~i~~~~~~~~~   82 (152)
T d1jl1a_           5 IFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQWIHN   82 (152)
T ss_dssp             EEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHTTHHH
T ss_pred             EEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhcc--cceEEEeecceeeEEcccchhhH
Confidence            8999999887777787776  4443322221 24678999999999999998754  5678999999999998875421 


Q ss_pred             --------Cc--H-HHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCCCCCCCCC
Q psy6829         237 --------SI--P-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAEFVNLSS  292 (369)
Q Consensus       237 --------~~--~-~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~~~~~~~~  292 (369)
                              ..  + ...+++..+..+. ....|.|+|||||+|++|||.||+|||+|+..|.+.+.+
T Consensus        83 ~~~~~~~~~~~~~~~n~~~~~~i~~~~-~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~d~~  148 (152)
T d1jl1a_          83 WKKRGWKTADKKPVKNVDLWQRLDAAL-GQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTG  148 (152)
T ss_dssp             HHHTTTBCTTSCBCTTHHHHHHHHHHT-TTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCCTT
T ss_pred             hHhccchhcccCeeecHHHHHHHHHHh-hcceeEEEEecccCCCccHHHHHHHHHHHHhCCCCCccC
Confidence                    11  1 1123344444443 456899999999999999999999999999998776554

>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=99.86  E-value=1.1e-22  Score=170.54  Aligned_cols=124  Identities=16%  Similarity=0.060  Sum_probs=91.4

Q ss_pred             cccccccCCCCCCceEEEEE--eCCe-eEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcCCC
Q psy6829         160 VVDLSLYGSKTIQNTSCAVY--AGGS-AKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT  236 (369)
Q Consensus       160 ~i~td~s~~~~~~~~G~a~~--~~~~-~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~~~  236 (369)
                      .||||||+..+++..|+|++  ..+. ...+.....+|+++||+.|+..||+++..  ...+.|+|||+++++.+.....
T Consensus         5 ~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~--~~~i~i~tds~~~~~~~~~~~~   82 (147)
T d1rila_           5 ALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYLKKAFTEGWL   82 (147)
T ss_dssp             CEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHHHHHHHSSHH
T ss_pred             EEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhccC--CceEEEecchhhhhccccccch
Confidence            49999999887777777776  2322 22222223579999999999999998754  5789999999999998866321


Q ss_pred             ----------C--cHH-HHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHhHHHhhhhCCC
Q psy6829         237 ----------S--IPL-IAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE  286 (369)
Q Consensus       237 ----------~--~~~-~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD~lAk~a~~~~  286 (369)
                                .  .++ ..+++..+..+. ....|.|.|||||+|++|||.||+|||+|+.+.
T Consensus        83 ~~~~~~~~~~~~~~~v~n~dL~~~l~~~~-~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_          83 EGWRKRGWRTAEGKPVKNRDLWEALLLAM-APHRVRFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             HHHHHTTSBCTTSSBCTTHHHHHHHHHHH-TTSEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             hhhhhccccccccccchhHHHHHHHHHHh-hhcccceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence                      1  111 133444444553 456899999999999999999999999999874

>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=99.69  E-value=2.4e-17  Score=130.59  Aligned_cols=99  Identities=22%  Similarity=0.271  Sum_probs=74.9

Q ss_pred             CcccccccCCCCCCceEEEEEeC-CeeEEEecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcCCCC
Q psy6829         159 PVVDLSLYGSKTIQNTSCAVYAG-GSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTS  237 (369)
Q Consensus       159 ~~i~td~s~~~~~~~~G~a~~~~-~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~~~~  237 (369)
                      +.+|||||+..+++..|+|++.. +......++ .+||+.|||.||+.||+..    ..++.|+|||++|++++..+...
T Consensus         9 ~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~~-~~TNn~aEl~Avi~aL~~~----~~~v~I~TDS~yvi~~i~~~~~~   83 (110)
T d1s1ta1           9 ETFYVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQPDQ   83 (110)
T ss_dssp             EEEEEEEEEETTTTEEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHHHCCSE
T ss_pred             cEEEEeCCCCCCCCCcEEEEEEecCCeEEEecc-cCcHHHHHHHHHHHHHHhC----CCeEEEEEehHHHHHHHhcCccc
Confidence            34899999887766667766632 334444454 6799999999999999864    56899999999999999997654


Q ss_pred             --cHHHHHHHHHHHHHhhCCCeEEEEEecCC
Q psy6829         238 --IPLIAHILNTWHTLKSCGKKVAFLWCPSH  266 (369)
Q Consensus       238 --~~~~~~i~~~~~~l~~~~~~v~~~WvpgH  266 (369)
                        ..+.+++.+   .+. ....|.|.|||||
T Consensus        84 ~~~~l~~~il~---~l~-~~~~v~i~WVpgH  110 (110)
T d1s1ta1          84 SESELVNQIIE---QLI-KKEKVYLAWVPAH  110 (110)
T ss_dssp             ESCHHHHHHHH---HHH-HCSEEEEEECCSS
T ss_pred             cchHHHHHHHH---HHh-cCCceEEEEeCCC
Confidence              345666553   333 3568999999999

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

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

Probab=99.52  E-value=2e-15  Score=121.81  Aligned_cols=113  Identities=15%  Similarity=0.048  Sum_probs=84.2

Q ss_pred             cccccccCCCCCCceEEEEEeC--CeeEEE--ecCCCCchHHHHHHHHHHHHHHhhcCCCCcEEEEeCcHHHHHHhhcCC
Q psy6829         160 VVDLSLYGSKTIQNTSCAVYAG--GSAKSY--ILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN  235 (369)
Q Consensus       160 ~i~td~s~~~~~~~~G~a~~~~--~~~~~~--~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~i~I~tDS~~al~~l~~~~  235 (369)
                      .||+||++++++|..|+|++..  +....+  .+ ..+||+.||+.|++.||+.+.+.+ .++.|+|||++|++.+.++.
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~-~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~   83 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKK   83 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTC
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCc-CccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCc
Confidence            4999999999999999998832  222222  23 367999999999999999998754 67999999999999998765


Q ss_pred             CC-----c----HHHHHHHHHHHHHhhCCCeEEEEEecCCCCCccchHHh
Q psy6829         236 TS-----I----PLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVD  276 (369)
Q Consensus       236 ~~-----~----~~~~~i~~~~~~l~~~~~~v~~~WvpgH~gi~gNe~AD  276 (369)
                      ..     .    ++.+.+.++..-+.  ...+.+.|+..|+.--||..||
T Consensus        84 ~kt~~~~~vkN~~l~~~i~~a~~~lk--~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          84 AKSTLVRNEETALIWKLVDEAEEWLN--THTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CCCCCCCSTTTHHHHHHHHHHHHHHH--HCCCCCCEEECCHHHHCSCTTC
T ss_pred             eecCcCCCcccHHHHHHHHHHHHHHH--hCCcCceeEEecCcccccCCCC
Confidence            21     1    23333333222233  3468899999999999999998