Psyllid ID: psy8736

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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
Protein Sequence
MNTSSKEAWSKVKRILDYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAFKSSPIKSILSEAGEPPLSSRREILTCNYLLNTLRDPRHLHFNLIKNDNVNLHQEIQIGFFELAQKFPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSREQVSLTRLRIGHTNLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRSPNDLYACLSNDENSVLEFLKKSKIKL
Secondary Structure (PSIPRED)
ccccccHHHccccccccHHHHHHHHHHHHHHHHHHccEEcccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHcccccccEEccccccccccccccEEcccccEEccccccccHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHccHHHHHHHccccccccccccccccccccccccccccHHHHHHHHcHHHHHccccccHHHHccccHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccHHHHHHHHHHHHHHHHHHcHHEcccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHHcccccEEEEccccccccEEEEEEEccccEEEEccccccHHHHHHHHHHHHHHHHHHccccccccccEEEEcccHHHHcccccEEEEEEEEccccccHHHHHccccccccccccccEEEEEEEEEcHHHHHHcccccHHHHccccHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
MNTSSKEAWSKVKRILDYKTLLQLYRSYIRSKLDYASIVyssasdsslkVLDTVHHQGVRLAlgafksspiksilseagepplssrreiLTCNYLlntlrdprhlhfnlikndnvnlHQEIQIGFFELaqkfpnykqiftdasknehsvssafcceetkfsvkldpriSICNAELISIQYAISFIIsttplqvptpkfvlySDSLSALQSREQVSLTRLrightnlthvhlmkrepppecdtcncrltVKHLLKYCNKyhnirspndlyaclsndenSVLEFLKKSKIKL
Flexible Loop (DISEMBL)
mntsskeawskvkrildyKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLAlgafksspikSILSeagepplssrrEILTCNYLLNTLRDPRHLHFNLIKNDNVNLHQEIQIGFFELAQKFPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSREQVSLTRLRIGHTNLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRSPNDLYACLSNdensvleflkkskikl
Low Complexity Region (SEG)
MNTSSKEAWSKVKRILDYKTLLQLYRSYIRSKLdyasivyssasdssLKVLDTVHHQGVRLALGAFKSSPIKSILSEAGEPPLSSRREILTCNYLLNTLRDPRHLHFNLIKNDNVNLHQEIQIGFFELAQKFPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSREQVSLTRLRIGHTNLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRSPNDLYACLSNDENSVLEFLKKSKIKL
Disordered region (IsUnstruct)
********WSKVKRILDYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAFKS******************REILTCNYLLNTLRDPRHLHFNLIKNDNVNLHQEIQIGFFELAQKFPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSREQVSLTRLRIGHTNLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRSPNDLYACLSNDENSVLEF********
Disordered Region (DISOPRED)
****S**AWSKVKRILDYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAFKSSPIKSILSEAGEPPLSSRREILTCNYLLNTLRDPRHLHFNLIKNDNVNLHQEIQIGFFELAQKFPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSREQVSLTRLRIGHTNLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRSPNDLYACLSNDENSVLEFLKKSKIK*
Disordered Region (DISEMBL)
**********KVKRILDYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAFKSSPIKSILSEAGEPPLSSRREILTCNYLLNTLRDPRHLHFNLIKNDNVNLHQEIQIGFFELAQKFPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSREQVSLTRLRIGHTNLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRSPNDLYACLSNDENSVLEFLKKSKIKL
Disordered Region (DISPRO)
***SSKEAWSKVKRILDYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAFKSSPIKSILSEAGEPPLSSRREILTCNYLLNTLRDPRHLHFNLIKNDNVNLHQEIQIGFFELAQKFPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSREQVSLTRLRIGHTNLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRSPNDLYACLSNDENSVLEFLKKSKIKL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNTSSKEAWSKVKRILDYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAFKSSPIKSILSEAGEPPLSSRREILTCNYLLNTLRDPRHLHFNLIKNDNVNLHQEIQIGFFELAQKFPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSREQVSLTRLRIGHTNLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRSPNDLYACLSNDENSVLEFLKKSKIKL
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	290
328697220	1915	PREDICTED: hypothetical protein LOC10016	0.662	0.100	0.350	2e-22
427791807	1212	Putative tick transposon, partial [Rhipi	0.651	0.155	0.289	3e-20
427791321	1210	Putative tick transposon, partial [Rhipi	0.651	0.156	0.289	3e-20
427791981	1060	Putative tick transposon, partial [Rhipi	0.375	0.102	0.447	3e-19
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.651	0.154	0.329	4e-17
427791063	1035	Putative tick transposon, partial [Rhipi	0.651	0.182	0.279	5e-16
427798889	1199	Putative tick transposon, partial [Rhipi	0.672	0.162	0.299	8e-16
443710566	377	hypothetical protein CAPTEDRAFT_186063 [	0.703	0.541	0.268	2e-15
328697366	891	PREDICTED: hypothetical protein LOC10057	0.637	0.207	0.326	2e-14
427791653	947	Putative tick transposon, partial [Rhipi	0.303	0.092	0.454	2e-14

>gi|328697220|ref|XP_001949504.2| PREDICTED: hypothetical protein LOC100162931 [Acyrthosiphon pisum]

 Score =  112 bits (280), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 82/234 (35%), Positives = 119/234 (50%), Gaps = 42/234 (17%)

Query: 19   KTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAFKSSPIKSILSEA 78
            +TLL+++ ++I SKLDY + ++SSA  + LK+L+T+H+ G+RL++GAF+SSPIKSIL+ A
Sbjct: 799  QTLLKIHEAFILSKLDYGAPIFSSAKHTKLKILETIHNSGIRLSIGAFRSSPIKSILNIA 858

Query: 79   GEPPLSSRREILTCNYLLNTLRDPR-HLH-----FN--LIKND----------------- 113
            G P L  R    T        R P+ H+H     FN   IK D                 
Sbjct: 859  GIPSLEVRWREQTHKLAARISRSPQNHIHHPKHTFNHTFIKYDLENIIPYEKPLCPPWQF 918

Query: 114  ----NVNLHQE---------IQIGFFELAQKFPNYKQIFTDASKNEHSVSSAFCCEETKF 160
                N++LHQ           +  F ++         I+TDAS  E  V  A  C+ET  
Sbjct: 919  SMNINIDLHQFPKNSTCPHIFKNAFRDICSHTHPQTHIYTDASIIEGRVGMAIICDETTI 978

Query: 161  SVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSREQV 214
              KL  + SI  AE ++I  AI F IS    ++      ++SDSLSAL S + +
Sbjct: 979  QWKLSDKCSIYTAETLAILKAIEFTIS----EINDSNITIFSDSLSALTSLQNL 1028

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  105 bits (261), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 74/256 (28%), Positives = 120/256 (46%), Gaps = 67/256 (26%)

Query: 17   DYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAFKSSPIKSILS 76
            D   LL++YRS +RS LDY  +VY SA +S ++ LD VH+ G+RL+ GA+++SP++S+  
Sbjct: 759  DRLCLLRIYRSIVRSILDYGCVVYGSARESYIRRLDPVHNLGLRLSSGAYRTSPVESLYV 818

Query: 77   EAGEPPLSSRREILTCNYLLNTLRDPRHLHFNLIKNDNVNLH------------------ 118
            +  EPPLS RR  LT +Y+L     P+H+ +++    +  LH                  
Sbjct: 819  DCNEPPLSHRRASLTLSYVLRIRSSPQHICYDIATRCSSRLHYLNKSNLIKPLLLRFEEY 878

Query: 119  --------QEIQIG--------FFELAQ----------------------------KFPN 134
                    + + +         +F+LAQ                            K+ +
Sbjct: 879  CRTYVISEETLDVARKPPRIPPWFDLAQLCDISLSHINKKVTPPELIIQEFRALQEKYRD 938

Query: 135  YKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVP 194
            Y + +TD SK    V       E+ FSV++   ISI  AE+ ++  A   II+       
Sbjct: 939  YAEFYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYALYEAARKIIAGK----- 993

Query: 195  TPKFVLYSDSLSALQS 210
              K ++Y+DSLSAL++
Sbjct: 994  HKKAIIYTDSLSALKA 1009

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 =  104 bits (260), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 74/256 (28%), Positives = 120/256 (46%), Gaps = 67/256 (26%)

Query: 17   DYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAFKSSPIKSILS 76
            D   LL++YRS +RS LDY  +VY SA +S ++ LD VH+ G+RL+ GA+++SP++S+  
Sbjct: 756  DRLCLLRIYRSIVRSILDYGCVVYGSARESYIRRLDPVHNLGLRLSSGAYRTSPVESLYV 815

Query: 77   EAGEPPLSSRREILTCNYLLNTLRDPRHLHFNLIKNDNVNLH------------------ 118
            +  EPPLS RR  LT +Y+L     P+H+ +++    +  LH                  
Sbjct: 816  DCNEPPLSHRRASLTLSYVLRIRSSPQHICYDIATRCSSRLHYLNKSNLIKPLLLRFEEY 875

Query: 119  --------QEIQIG--------FFELAQ----------------------------KFPN 134
                    + + +         +F+LAQ                            K+ +
Sbjct: 876  CRTYVISEETLDVARKPPRIPPWFDLAQLCDISLSHINKKVTPPELIIQEFRALQEKYRD 935

Query: 135  YKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVP 194
            Y + +TD SK    V       E+ FSV++   ISI  AE+ ++  A   II+       
Sbjct: 936  YAEFYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYALYEAARKIIAGK----- 990

Query: 195  TPKFVLYSDSLSALQS 210
              K ++Y+DSLSAL++
Sbjct: 991  HKKAIIYTDSLSALKA 1006

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  101 bits (252), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 51/114 (44%), Positives = 72/114 (63%), Gaps = 5/114 (4%)

Query: 5   SKEAWSKVKRILDYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALG 64
           S++ W       D K LL +YRS +RSKLDY SI+Y SA DS LK LD VH++G+RLA G
Sbjct: 798 SRKRWGS-----DRKCLLHIYRSLVRSKLDYGSIIYGSARDSYLKRLDPVHNKGLRLATG 852

Query: 65  AFKSSPIKSILSEAGEPPLSSRREILTCNYLLNTLRDPRHLHFNLIKNDNVNLH 118
           A+++SPI S+ +E+ EP L  RR  L   Y+L     P H+ ++++   +  LH
Sbjct: 853 AYRTSPIPSLYAESNEPSLEYRRTQLMFTYVLKVRSSPDHICYSIVTRSDQRLH 906

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 = 94.7 bits (234), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 84/255 (32%), Positives = 114/255 (44%), Gaps = 66/255 (25%)

Query: 17   DYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAFKSSPIKSILS 76
            D  TLL LYRS IRSKLDY SI+Y +A  S LK+L+ + +  +RL LGAF++SPI S+  
Sbjct: 777  DRDTLLLLYRSLIRSKLDYGSIIYGAARKSYLKILEPIQNAALRLCLGAFRTSPIPSLHV 836

Query: 77   EAGEPPLSSRREILTCNYLLNTLRDPRHLHFNLIKN----------DNV----------- 115
            EAGE P+  R + L   Y++    +P +  F+ I N           NV           
Sbjct: 837  EAGELPMDIRMKKLAMQYIVKLKSNPTNPAFDSIFNPTEVELYNRRPNVIQPLGLRMREP 896

Query: 116  --NLHQEI-QIGFFELAQKFP-------------NYKQ---------------------- 137
              NL Q I QI   E  Q  P             N+K+                      
Sbjct: 897  IQNLTQPIDQISKIETPQNPPWLMNKPKLNLSLLNFKKENTDPSILQVHFRELQESYGDC 956

Query: 138  --IFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPT 195
              I+TD SK E  V+ A        S +L    SI  AEL +I  A+  + ++       
Sbjct: 957  GTIYTDGSKMEGKVACACSFRNKTISRRLPDGCSIFTAELHAILLALMAVKASE-----R 1011

Query: 196  PKFVLYSDSLSALQS 210
             KF++ SDS SALQ+
Sbjct: 1012 SKFIICSDSKSALQA 1026

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 = 91.3 bits (225), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 71/254 (27%), Positives = 116/254 (45%), Gaps = 65/254 (25%)

Query: 17  DYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAFKSSPIKSILS 76
           D K L+ +Y+S +R++LDY S+VY SA+ S+LK+LD +HH G+RLA GAF++SP++S+  
Sbjct: 617 DRKCLMDIYKSLVRTRLDYGSVVYHSAAPSALKILDPIHHLGIRLATGAFRTSPVQSLYV 676

Query: 77  EAGEPPLSSRREILTCNYLLN--------------------------TLRDPRHLHF-NL 109
           E+ +  L  +R  ++  Y L                           ++R P  L   +L
Sbjct: 677 ESNQWSLHLQRSYMSFVYFLKVKAEKEHPAHSTVNDLSSSVLYHNRPSVRQPYSLRVRDL 736

Query: 110 IKNDNVNLHQ------------------EIQIGFFELAQKFPN---------------YK 136
            +   ++LH+                  E  + F ++ +  P+               + 
Sbjct: 737 AEEMGLSLHEHSLMARAAYLPPWQWQLIECDVSFEQVTKHAPHAHIYTYFLELQHKYTFP 796

Query: 137 QIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTP 196
           + FTDASK   SVS A        +  L    SI  AE  +I  A+  I      Q+  P
Sbjct: 797 EFFTDASKFNSSVSYAAVGPSFSDAGVLHQNTSIFTAEAYAIFVAVKHI-----EQLKLP 851

Query: 197 KFVLYSDSLSALQS 210
             V+Y+DSLS +++
Sbjct: 852 SAVIYTDSLSVVKA 865

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 = 90.5 bits (223), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 80/267 (29%), Positives = 117/267 (43%), Gaps = 72/267 (26%)

Query: 5    SKEAWSKVKRILDYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALG 64
            S+  W       D K L+ LY+S IR++LDY +I+Y SAS ++LK+LD VHH G+RL+ G
Sbjct: 776  SRTTWGS-----DKKCLMNLYKSLIRTRLDYGAIIYQSASPTALKMLDPVHHLGIRLSTG 830

Query: 65   AFKSSPIKSILSEAGEPPLSSRREI-----------------------LTCNYLLNT--- 98
            AF++SP++S+  E+ E  L  +R                         L+C+ L      
Sbjct: 831  AFRTSPVESLYVESNEWSLHLQRSYMSFLYYIKVNADKEHPSHSTINDLSCSTLFENRPS 890

Query: 99   --------LRD--------------------PRHLHFNLIKND----NVNLHQ---EIQI 123
                    +RD                    P    + LI  D     V  H     I+ 
Sbjct: 891  LKPPYSLRVRDLAEQTGLPLFEHRLMAPAAYPPPWQWQLIDCDVSFMEVTKHAPIAHIRT 950

Query: 124  GFFELAQKFPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAIS 183
             F EL  K+ N    +TDASK+  SVS A        +  L P  SI  AE  +I  A+ 
Sbjct: 951  YFLELQHKY-NCPAFYTDASKSHTSVSYAAVGPSFSAAGALHPNTSIFTAEAYAILAAVK 1009

Query: 184  FIISTTPLQVPTPKFVLYSDSLSALQS 210
             I      ++   K V+Y+DSLS +++
Sbjct: 1010 HI-----RELKLQKAVIYTDSLSVVKA 1031

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 = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 75/279 (26%), Positives = 122/279 (43%), Gaps = 75/279 (26%)

Query: 17  DYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAFKSSPIKSILS 76
           D + L +L+RS +RS+LDY +IVY SA  S L+ L  + +Q  RL LGAF+ SP+ S+ +
Sbjct: 6   DREVLFRLFRSLLRSRLDYGAIVYGSARISYLERLKPIQNQAFRLCLGAFRISPVTSLHT 65

Query: 77  EAGEPPLSSRREILTCNYLLNTLRD---PRHLHFNLIKNDNVNLHQ-------------- 119
           EA E P++ R+++L+  + L    D   P H       ND   L +              
Sbjct: 66  EANEMPMAIRQKLLSVQFALRVCSDTTNPAHQCIFNYNNDRFYLSKPNAIRPLALRIKED 125

Query: 120 ---------------------------EIQIGFFELAQKF--PNY--------------- 135
                                      E+ I      +K   PNY               
Sbjct: 126 LQTICPDIKAITPNQLFNIPYWLLRPPELDISLIHFGKKTANPNYTLKNEFYNLMDKYPD 185

Query: 136 -KQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVP 194
            K IFTD SK++ +V+     +     ++L    SI +AEL++I   ++ +  +   Q  
Sbjct: 186 HKVIFTDGSKSDSAVACFATADNLSIQIRLPDSASIFSAELLAIYQVLTLLECSANDQ-- 243

Query: 195 TPKFVLYSDSLSALQSREQVSLTRLRIGHTNLTHVHLMK 233
             +F++ +DSLS+LQ+          IG+ N+ H ++ K
Sbjct: 244 -QQFLIATDSLSSLQA----------IGNFNIKHPYVFK 271

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|328697366|ref|XP_003240318.1| PREDICTED: hypothetical protein LOC100575042 [Acyrthosiphon pisum]

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/202 (32%), Positives = 103/202 (50%), Gaps = 17/202 (8%)

Query: 14  RILDYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAFKSSPIKS 73
           R  + K LL +Y+S I SK+ Y S +Y++A  + LK+LD +H++G+RLA+GAF++S   S
Sbjct: 40  RGANQKPLLSIYKSLILSKIKYGSQIYNTAKPNLLKILDPIHNEGIRLAIGAFRTSSTDS 99

Query: 74  ILSEAGEPPLSSRREILTCNYLLNTLRDPRHLHFNLIKNDNVNLHQEIQIGFFELAQKFP 133
           IL+ AGE PL  +R+  T  Y+         + +  I ++    H    I          
Sbjct: 100 ILNYAGELPLQLQRDQDTLAYITKRKSTTNRIGYKAIFDN----HAASPINM-------- 147

Query: 134 NYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQV 193
            +K+   DASK+EH V  A   ++T    KL    SI +AE  +I   +    +     +
Sbjct: 148 EHKKKPLDASKSEHGVGFAVVKDDTIIQHKLPEITSIFSAENYAIFEGVKLANT-----L 202

Query: 194 PTPKFVLYSDSLSALQSREQVS 215
            T   +L SDSLS L + +  S
Sbjct: 203 ETNDILLISDSLSTLLAFKNTS 224

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427791653|gb|JAA61278.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score = 85.9 bits (211), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 40/88 (45%), Positives = 61/88 (69%)

Query: 17  DYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAFKSSPIKSILS 76
           D K LL LYRS +R++LDY +I+Y SA+ ++LK+LD VHH G+RL+ GAF++SP++S+  
Sbjct: 776 DKKCLLNLYRSLVRTRLDYGAIIYQSATPTALKMLDPVHHLGIRLSTGAFRTSPVESLYV 835

Query: 77  EAGEPPLSSRREILTCNYLLNTLRDPRH 104
           E+ E  L  +R +L+  Y L    +  H
Sbjct: 836 ESNEWSLHLQRSLLSFVYYLKVNAEKEH 863

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

---

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

No EC number assignment, probably not an enzyme!

---

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	290
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	2e-10

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

 Score = 57.3 bits (139), Expect = 2e-10
 Identities = 28/91 (30%), Positives = 40/91 (43%), Gaps = 9/91 (9%)

Query: 137 QIFTDASKNEHSVSSAFCC---EETKFSVKLDPRISICNAELISIQYAISFIISTTPLQV 193
            I+TD SK E    + F          S KL P  S+ +AEL++I  A+   +       
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALRE---GR 57

Query: 194 PTPKFVLYSDSLSA---LQSREQVSLTRLRI 221
              K  ++SDS +A   L+S    S   LRI
Sbjct: 58  RARKITIFSDSQAALKALRSPRSSSPLVLRI 88

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	290
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	98.4
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	98.03
PRK08719	147	ribonuclease H; Reviewed	97.96
PRK00203	150	rnhA ribonuclease H; Reviewed	97.9
KOG3752|consensus	371		97.88
PRK06548	161	ribonuclease H; Provisional	97.84
PRK13907	128	rnhA ribonuclease H; Provisional	97.77
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	97.43
PRK07708	219	hypothetical protein; Validated	96.94
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	96.7
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	96.44
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	91.61

>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=98.40  E-value=4e-07  Score=73.21  Aligned_cols=115  Identities=17%  Similarity=0.175  Sum_probs=70.5

Q ss_pred             CCeEEeecCCCC--CCceeEEEEec-CccceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhhh
Q psy8736         134 NYKQIFTDASKN--EHSVSSAFCCE-ETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS  210 (290)
Q Consensus       134 ~~~~iyTDgSk~--~~~~G~av~~~-~~~~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~~  210 (290)
                      ..+.||||||..  .+..|+|++.. +.+....++ ..+.+.||+.|+.+||+ .. .     . .++.|++||..++..
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~-~-----~-~~v~I~tDS~~v~~~   72 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALK-AL-E-----H-RKVTIYTDSQYVLNA   72 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHH-TH-S-----T-SEEEEEES-HHHHHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHH-Hh-h-----c-ccccccccHHHHHHH
Confidence            467899999953  33335554433 333445556 89999999999999999 54 3     2 689999999999874


Q ss_pred             hhh-hhhhhhccCCcc--cccccccccCCCCCCCCCCcccchhehhhhccc-hhhccC
Q psy8736         211 REQ-VSLTRLRIGHTN--LTHVHLMKREPPPECDTCNCRLTVKHLLKYCNK-YHNIRS  264 (290)
Q Consensus       211 r~~-~~l~rlRtGH~~--l~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~-~~~~R~  264 (290)
                      -.. ......+.-+..  +-+ .++     ..+ ..+....+.||.-||.. ..|++.
T Consensus        73 l~~~~~~~~~~~~~~~~~i~~-~i~-----~~~-~~~~~v~~~~V~~H~~~~~~N~~a  123 (132)
T PF00075_consen   73 LNKWLHGNGWKKTSNGRPIKN-EIW-----ELL-SRGIKVRFRWVPGHSGVPQGNERA  123 (132)
T ss_dssp             HHTHHHHTTSBSCTSSSBHTH-HHH-----HHH-HHSSEEEEEESSSSSSSHHHHHHH
T ss_pred             HHHhccccccccccccccchh-hee-----ecc-ccceEEeeeeccCcCCCchhHHHH
Confidence            222 111122211111  111 111     112 23677999999999999 576653

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

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

Probab=98.03  E-value=2e-05  Score=61.11  Aligned_cols=69  Identities=19%  Similarity=0.238  Sum_probs=52.4

Q ss_pred             EEeecCCCCCC--ceeEEEEecCcc--ce---eccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhh
Q psy8736         137 QIFTDASKNEH--SVSSAFCCEETK--FS---VKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ  209 (290)
Q Consensus       137 ~iyTDgSk~~~--~~G~av~~~~~~--~~---~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~  209 (290)
                      .+|||||...+  +.|++++..+..  ..   .......+++.+|+.|++.|++.+...     ...++.|++||..++.
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~-----~~~~i~i~~Ds~~~~~   75 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALEL-----GGKKVNIYTDSQYVIN   75 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhC-----CCceEEEEECHHHHHH
Confidence            37999998654  577776655543  11   122257899999999999999999865     7789999999998766


Q ss_pred             h
Q psy8736         210 S  210 (290)
Q Consensus       210 ~  210 (290)
                      .
T Consensus        76 ~   76 (130)
T cd06222          76 A   76 (130)
T ss_pred             H
Confidence            5

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.

>PRK08719 ribonuclease H; Reviewed

Probab=97.96  E-value=2.3e-05  Score=65.12  Aligned_cols=117  Identities=14%  Similarity=0.113  Sum_probs=69.5

Q ss_pred             CCeEEeecCCCCCCc-----eeEEEEe--cCcc----ceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEe
Q psy8736         134 NYKQIFTDASKNEHS-----VSSAFCC--EETK----FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYS  202 (290)
Q Consensus       134 ~~~~iyTDgSk~~~~-----~G~av~~--~~~~----~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~s  202 (290)
                      ..+.||||||...++     .|+|++.  ++..    ....+....+-..||+.|+..||+.+.+.         ..|++
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~---------~~i~t   73 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG---------DVIYS   73 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC---------CEEEe
Confidence            457899999986443     3666654  3322    23345556789999999999999988642         27999


Q ss_pred             cchhhhhhhhhhhhhhhccC-----Cccc--ccccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736         203 DSLSALQSREQVSLTRLRIG-----HTNL--THVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS  264 (290)
Q Consensus       203 Ds~saL~~r~~~~l~rlRtG-----H~~l--~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~  264 (290)
                      ||+-++..-.. -+.+++.+     ....  +.. |+..-+ ...  .....++.||.-|+....|++.
T Consensus        74 DS~yvi~~i~~-~~~~W~~~~w~~s~g~~v~n~d-l~~~i~-~l~--~~~~i~~~~VkgH~g~~~Ne~a  137 (147)
T PRK08719         74 DSDYCVRGFNE-WLDTWKQKGWRKSDKKPVANRD-LWQQVD-ELR--ARKYVEVEKVTAHSGIEGNEAA  137 (147)
T ss_pred             chHHHHHHHHH-HHHHHHhCCcccCCCcccccHH-HHHHHH-HHh--CCCcEEEEEecCCCCChhHHHH
Confidence            99987765321 11222221     1111  111 111000 011  1245889999999888777654

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=97.90  E-value=3.7e-05  Score=63.97  Aligned_cols=119  Identities=13%  Similarity=0.061  Sum_probs=67.3

Q ss_pred             CeEEeecCCCCCC--ceeEEEEec--Cccc-eeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhh
Q psy8736         135 YKQIFTDASKNEH--SVSSAFCCE--ETKF-SVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ  209 (290)
Q Consensus       135 ~~~iyTDgSk~~~--~~G~av~~~--~~~~-~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~  209 (290)
                      .+.||||||...+  ..|++++..  +... ........+...||+.|+..||+.+.+       ...+.|++||+.++.
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~-------~~~v~I~tDS~yvi~   75 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE-------PCEVTLYTDSQYVRQ   75 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC-------CCeEEEEECHHHHHH
Confidence            3689999998633  356665543  3221 122233566778999999999997753       246899999997776


Q ss_pred             hhhhhhhhh-----hccCCc-ccccccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736         210 SREQVSLTR-----LRIGHT-NLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS  264 (290)
Q Consensus       210 ~r~~~~l~r-----lRtGH~-~l~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~  264 (290)
                      .-.. -+.+     +++..+ ...+.-|+..-+ -..  -.....+.||.-|+....|++.
T Consensus        76 ~i~~-w~~~Wk~~~~~~~~g~~v~n~dl~~~i~-~l~--~~~~v~~~wV~~H~~~~~N~~A  132 (150)
T PRK00203         76 GITE-WIHGWKKNGWKTADKKPVKNVDLWQRLD-AAL--KRHQIKWHWVKGHAGHPENERC  132 (150)
T ss_pred             HHHH-HHHHHHHcCCcccCCCccccHHHHHHHH-HHh--ccCceEEEEecCCCCCHHHHHH
Confidence            5331 1111     121111 111110110000 000  1145899999999988877665

>KOG3752|consensus

Probab=97.88  E-value=4.4e-05  Score=71.43  Aligned_cols=70  Identities=24%  Similarity=0.187  Sum_probs=58.4

Q ss_pred             eEEeecCCCCCC-----ceeEEEEecCcc---ceeccC-CCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchh
Q psy8736         136 KQIFTDASKNEH-----SVSSAFCCEETK---FSVKLD-PRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLS  206 (290)
Q Consensus       136 ~~iyTDgSk~~~-----~~G~av~~~~~~---~~~~l~-~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~s  206 (290)
                      ..+|||||...+     .+|.+||.++..   ....+. ...+-|.||+.|+.+||+.+++.     +..++.|.+||.-
T Consensus       213 ~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~-----~~~kv~I~TDS~~  287 (371)
T KOG3752|consen  213 QVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSK-----NINKVVIRTDSEY  287 (371)
T ss_pred             eEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhc-----CCCcEEEEechHH
Confidence            679999997653     489999988764   566665 77899999999999999999986     6779999999986


Q ss_pred             hhhh
Q psy8736         207 ALQS  210 (290)
Q Consensus       207 aL~~  210 (290)
                      .+..
T Consensus       288 ~i~~  291 (371)
T KOG3752|consen  288 FINS  291 (371)
T ss_pred             HHHH
Confidence            6554

>PRK06548 ribonuclease H; Provisional

Probab=97.84  E-value=7.2e-05  Score=63.11  Aligned_cols=121  Identities=14%  Similarity=0.068  Sum_probs=69.5

Q ss_pred             CCeEEeecCCCCCC--ceeEEEEecCccceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhhhh
Q psy8736         134 NYKQIFTDASKNEH--SVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSR  211 (290)
Q Consensus       134 ~~~~iyTDgSk~~~--~~G~av~~~~~~~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~~r  211 (290)
                      ..+.|||||+...+  ..|.|+|..+......-....+--.||+.|+..||+.+..      ...++.|+|||.-++..-
T Consensus         4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~------~~~~v~I~TDS~yvi~~i   77 (161)
T PRK06548          4 NEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH------TDRPILILSDSKYVINSL   77 (161)
T ss_pred             CEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc------CCceEEEEeChHHHHHHH
Confidence            45789999997533  3677777654322222223456677999999999985542      334699999999887663


Q ss_pred             hh-h---hhhhhccCCcc--cccccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736         212 EQ-V---SLTRLRIGHTN--LTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS  264 (290)
Q Consensus       212 ~~-~---~l~rlRtGH~~--l~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~  264 (290)
                      .. .   .-+.+|+.-+.  .|.... ..-+ .....  ..+++.||--|+....|++.
T Consensus        78 ~~W~~~Wk~~gWk~s~G~pV~N~dL~-~~l~-~l~~~--~~v~~~wVkgHsg~~gNe~a  132 (161)
T PRK06548         78 TKWVYSWKMRKWRKADGKPVLNQEII-QEID-SLMEN--RNIRMSWVNAHTGHPLNEAA  132 (161)
T ss_pred             HHHHHHHHHCCCcccCCCccccHHHH-HHHH-HHHhc--CceEEEEEecCCCCHHHHHH
Confidence            21 0   01122221111  111111 0000 01111  24788999999988888876

>PRK13907 rnhA ribonuclease H; Provisional

Probab=97.77  E-value=8.6e-05  Score=59.80  Aligned_cols=70  Identities=10%  Similarity=0.083  Sum_probs=51.2

Q ss_pred             eEEeecCCCCC--CceeEEEEecCccce--ec-cCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhhh
Q psy8736         136 KQIFTDASKNE--HSVSSAFCCEETKFS--VK-LDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS  210 (290)
Q Consensus       136 ~~iyTDgSk~~--~~~G~av~~~~~~~~--~~-l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~~  210 (290)
                      +.||||||...  +..|+|++..+....  .. .....+-..||..|++.||+.+.+.     +...+.|++||+-.+..
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~-----g~~~v~i~sDS~~vi~~   76 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEH-----NYNIVSFRTDSQLVERA   76 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhC-----CCCEEEEEechHHHHHH
Confidence            47999999653  346777776555421  11 1234677899999999999999986     55679999999977655

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

Probab=97.43  E-value=0.00058  Score=57.05  Aligned_cols=116  Identities=16%  Similarity=0.040  Sum_probs=70.5

Q ss_pred             CeEEeecCCCCC-Cc-eeEEEEe--cCccc--eeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhh
Q psy8736         135 YKQIFTDASKNE-HS-VSSAFCC--EETKF--SVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSAL  208 (290)
Q Consensus       135 ~~~iyTDgSk~~-~~-~G~av~~--~~~~~--~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL  208 (290)
                      .+.|||||+... +| -|.|+|.  .+...  ..... .++--.+|+.|+++||+.+.+.     +...+.|++||+-+.
T Consensus         3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~-----~~~~v~l~tDS~yv~   76 (154)
T COG0328           3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKEL-----GACEVTLYTDSKYVV   76 (154)
T ss_pred             ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhc-----CCceEEEEecHHHHH
Confidence            468999999753 23 3444443  33332  22333 6778889999999999999985     677899999999776


Q ss_pred             hhhhhhhhhhhccCCcccccccccccCCCCCCC-----------CCCcccchhehhhhccchhhccC
Q psy8736         209 QSREQVSLTRLRIGHTNLTHVHLMKREPPPECD-----------TCNCRLTVKHLLKYCNKYHNIRS  264 (290)
Q Consensus       209 ~~r~~~~l~rlRtGH~~l~h~~l~~~~~~p~C~-----------~c~~~~tv~Hil~~Cp~~~~~R~  264 (290)
                      ..-.     ++..+  +...++. ...-.|.|.           .-.....++||.-|-....|+|.
T Consensus        77 ~~i~-----~w~~~--w~~~~w~-~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~Nera  135 (154)
T COG0328          77 EGIT-----RWIVK--WKKNGWK-TADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERA  135 (154)
T ss_pred             HHHH-----HHHhh--ccccCcc-ccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHH
Confidence            6433     22111  1111111 011112211           11235688888888888888886

>PRK07708 hypothetical protein; Validated

Probab=96.94  E-value=0.0054  Score=54.36  Aligned_cols=73  Identities=12%  Similarity=0.109  Sum_probs=51.2

Q ss_pred             CCCeEEeecCCCC--CCceeEEEEec--Cccce------eccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCC--cEEE
Q psy8736         133 PNYKQIFTDASKN--EHSVSSAFCCE--ETKFS------VKLDPRISICNAELISIQYAISFIISTTPLQVPTP--KFVL  200 (290)
Q Consensus       133 ~~~~~iyTDgSk~--~~~~G~av~~~--~~~~~------~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~--~~~I  200 (290)
                      ++...+|+|||-.  .++.|+|++..  .....      ..++...+--.||..|++.||+.+.+.     +.+  .+.|
T Consensus        71 p~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~-----g~~~~~V~I  145 (219)
T PRK07708         71 PHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEEL-----GVKHEPVTF  145 (219)
T ss_pred             CCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHc-----CCCcceEEE
Confidence            5568999999964  34466665543  33222      245555788889999999999999986     333  3789


Q ss_pred             Eecchhhhhh
Q psy8736         201 YSDSLSALQS  210 (290)
Q Consensus       201 ~sDs~saL~~  210 (290)
                      ++||+-.+..
T Consensus       146 ~~DSqlVi~q  155 (219)
T PRK07708        146 RGDSQVVLNQ  155 (219)
T ss_pred             EeccHHHHHH
Confidence            9999866543

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=96.70  E-value=0.0057  Score=58.21  Aligned_cols=68  Identities=9%  Similarity=0.009  Sum_probs=49.1

Q ss_pred             eEEeecCCCCCC--ceeEEEEecCcc-------ceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchh
Q psy8736         136 KQIFTDASKNEH--SVSSAFCCEETK-------FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLS  206 (290)
Q Consensus       136 ~~iyTDgSk~~~--~~G~av~~~~~~-------~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~s  206 (290)
                      +.||||||...+  ..|+|++..+.+       ....++ .++...||..|++.||+.+.+.     +..++.|++||.-
T Consensus         3 ~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~-----g~~~v~i~~DS~l   76 (372)
T PRK07238          3 VVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAEL-----GATEVEVRMDSKL   76 (372)
T ss_pred             EEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhC-----CCCeEEEEeCcHH
Confidence            579999997543  356666654432       112333 4566789999999999999986     5668999999987


Q ss_pred             hhh
Q psy8736         207 ALQ  209 (290)
Q Consensus       207 aL~  209 (290)
                      .+.
T Consensus        77 vi~   79 (372)
T PRK07238         77 VVE   79 (372)
T ss_pred             HHH
Confidence            654

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

Probab=96.44  E-value=0.0013  Score=49.34  Aligned_cols=42  Identities=29%  Similarity=0.389  Sum_probs=30.0

Q ss_pred             hccCCccc-ccccc--cccCCCCCCCCCC-cccchhehhhhccchh
Q psy8736         219 LRIGHTNL-THVHL--MKREPPPECDTCN-CRLTVKHLLKYCNKYH  260 (290)
Q Consensus       219 lRtGH~~l-~h~~l--~~~~~~p~C~~c~-~~~tv~Hil~~Cp~~~  260 (290)
                      +|.-|.+| +...|  .+...++.|..|+ ..||++|++++||...
T Consensus        38 W~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~   83 (86)
T PF13966_consen   38 WRALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR   83 (86)
T ss_pred             eeeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCcc
Confidence            34445555 22333  4456789999887 5999999999999754

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

Probab=91.61  E-value=0.31  Score=35.39  Aligned_cols=35  Identities=20%  Similarity=0.220  Sum_probs=29.2

Q ss_pred             hHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhhh
Q psy8736         171 CNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS  210 (290)
Q Consensus       171 ftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~~  210 (290)
                      ..||+.|++.|++.+++.     +-.++.+.+||...+..
T Consensus         2 ~~aE~~al~~al~~a~~~-----g~~~i~v~sDs~~vv~~   36 (87)
T PF13456_consen    2 LEAEALALLEALQLAWEL-----GIRKIIVESDSQLVVDA   36 (87)
T ss_dssp             HHHHHHHHHHHHHHHHCC-----T-SCEEEEES-HHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHC-----CCCEEEEEecCcccccc
Confidence            469999999999999987     77899999999987664

---

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	290
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-04

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

 Score = 48.3 bits (114), Expect = 2e-06
 Identities = 43/269 (15%), Positives = 85/269 (31%), Gaps = 79/269 (29%)

Query: 13  KRILDYKTLLQLYRSYIRSKLDYASIVYSSASDSSLKVLDTVHHQGVRLALGAF-KSSPI 71
           + I D       ++     KL       ++  +SSL VL+   ++ +   L  F  S+ I
Sbjct: 335 ESIRDGLATWDNWKHVNCDKL-------TTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI 387

Query: 72  KSILSEA--GEPPLSSRREILT--CNYLLNTLRDPR-------HLHFNL-IKNDN-VNLH 118
            +IL      +   S    ++     Y L   + P+        ++  L +K +N   LH
Sbjct: 388 PTILLSLIWFDVIKSDVMVVVNKLHKYSL-VEKQPKESTISIPSIYLELKVKLENEYALH 446

Query: 119 QEI--------------------------QIGF----FELAQKFPNYKQIFTD----ASK 144
           + I                           IG      E  ++   ++ +F D      K
Sbjct: 447 RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQK 506

Query: 145 NEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDS 204
             H  S+A+    +  +     +            Y   +I    P          Y   
Sbjct: 507 IRHD-STAWNASGSILNTLQQLKF-----------YK-PYICDNDP---------KYERL 544

Query: 205 LSALQS-REQVSLTRLRIGHTNLTHVHLM 232
           ++A+     ++    +   +T+L  + LM
Sbjct: 545 VNAILDFLPKIEENLICSKYTDLLRIALM 573

>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 = 39.8 bits (92), Expect = 8e-04
 Identities = 60/332 (18%), Positives = 104/332 (31%), Gaps = 100/332 (30%)

Query: 16  LDYKTLLQLYRSYIRSKLDYASI------VYSSAS-DSSLKVLDTVHHQGVRLALGAFKS 68
             YK +L ++        D   +      + S    D  +   D V   G         S
Sbjct: 16  YQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAV--SGTLRLFWTLLS 73

Query: 69  SPIKSILSEAGEPPLSSRREILTCNY--LLNTL----RDP----------RHLHFN---L 109
              + ++ +  E       E+L  NY  L++ +    R P          R   +N   +
Sbjct: 74  KQ-EEMVQKFVE-------EVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV 125

Query: 110 IKNDNVN---LHQEIQIGFFELAQKFPNYKQIFTD----ASKNEHSVSSAFCCEETKFSV 162
               NV+    + +++    EL +   N   +  D    + K   +  +   C   K   
Sbjct: 126 FAKYNVSRLQPYLKLRQALLEL-RPAKN---VLIDGVLGSGK---TWVALDVCLSYKVQC 178

Query: 163 KLDPRI---SI--CN--AELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSREQVS 215
           K+D +I   ++  CN    ++ +   + + I         P +   SD  S ++ R    
Sbjct: 179 KMDFKIFWLNLKNCNSPETVLEMLQKLLYQI--------DPNWTSRSDHSSNIKLRIHSI 230

Query: 216 LTRLRIGHTNLTHVHLMKREPPPEC-----DTCN----------CR--LT-----VKHLL 253
              LR          L+K +P   C     +  N          C+  LT     V   L
Sbjct: 231 QAELR---------RLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFL 281

Query: 254 KYCNKYHNIRSPNDLYACLSNDENSVLEFLKK 285
                 H   S +     L+ DE  V   L K
Sbjct: 282 SAATTTH--ISLDHHSMTLTPDE--VKSLLLK 309

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	290
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	98.57
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	98.24
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	98.24
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	98.19
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	98.06
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	97.99
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	97.95
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	97.87
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	97.87
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	97.85
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	97.85
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	97.38
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	97.31
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	97.27
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	97.2
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	97.09

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

Probab=98.57  E-value=1.2e-07  Score=77.91  Aligned_cols=122  Identities=13%  Similarity=0.128  Sum_probs=77.0

Q ss_pred             CCeEEeecCCCCCCc-----eeEEEEecCcc---ceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecch
Q psy8736         134 NYKQIFTDASKNEHS-----VSSAFCCEETK---FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSL  205 (290)
Q Consensus       134 ~~~~iyTDgSk~~~~-----~G~av~~~~~~---~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~  205 (290)
                      +.+.||||||...++     .|+++|..+..   ....++..++.+.||+.|++.||+.+.+.     +..++.|++||+
T Consensus         6 ~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~-----~~~~v~i~tDS~   80 (154)
T 2qkb_A            6 DFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQ-----NINKLVLYTNSM   80 (154)
T ss_dssp             TEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHT-----TCCEEEEEESCH
T ss_pred             CeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhC-----CCceEEEEECcH
Confidence            457899999976432     78888876543   34456657899999999999999999875     567899999999


Q ss_pred             hhhhhhhhhh----hhhhcc--CCcccccccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736         206 SALQSREQVS----LTRLRI--GHTNLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS  264 (290)
Q Consensus       206 saL~~r~~~~----l~rlRt--GH~~l~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~  264 (290)
                      .++..-..-.    -+.+++  |...-+. -|+..-. ..+.  +-..++.||.-|+....|++.
T Consensus        81 ~vi~~i~~~~~~w~~~~w~~~~~~~~~n~-~l~~~i~-~l~~--~~~v~~~~V~~H~g~~~N~~A  141 (154)
T 2qkb_A           81 FTINGITNWVQGWKKNGWKTSAGKEVINK-EDFVALE-RLTQ--GMDIQWMHVPGHSGFIGNEEA  141 (154)
T ss_dssp             HHHHHHHTHHHHHHTTTSBCTTSSBCTTH-HHHHHHH-HHHT--TCEEEEEECCTTSSCHHHHHH
T ss_pred             HHHhhhhhhHHHHHhccccccCCCccccH-HHHHHHH-HHHc--CCceEEEEccCCCCCHhHHHH
Confidence            8776533211    011221  1111111 1111000 0111  234889999999877777665

>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=98.24  E-value=8.8e-07  Score=72.27  Aligned_cols=119  Identities=11%  Similarity=0.010  Sum_probs=72.0

Q ss_pred             CCeEEeecCCCCCCceeEEEEecC-cc---cee-cc--CC--CccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecc
Q psy8736         134 NYKQIFTDASKNEHSVSSAFCCEE-TK---FSV-KL--DP--RISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDS  204 (290)
Q Consensus       134 ~~~~iyTDgSk~~~~~G~av~~~~-~~---~~~-~l--~~--~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs  204 (290)
                      +.+.||||||...+..|+|+|..+ ..   ... +.  +.  ..+.+.||+.|++.||+.+.+.     +. ++.|++||
T Consensus         5 ~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~-----~~-~v~I~tDS   78 (147)
T 2kq2_A            5 TEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQL-----GV-KIRILHDY   78 (147)
T ss_dssp             SCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHH-----TC-CCCBSSCC
T ss_pred             CeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHC-----CC-eEEEEECc
Confidence            457899999998766788876643 22   122 22  22  2588999999999999998775     44 89999999


Q ss_pred             hhhhhhhhhhhhhhhccCCccccc-ccccccCCCCCCCCCCcccchhehhhhccchhhccCCCChhh
Q psy8736         205 LSALQSREQVSLTRLRIGHTNLTH-VHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRSPNDLYA  270 (290)
Q Consensus       205 ~saL~~r~~~~l~rlRtGH~~l~h-~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~~~~l~~  270 (290)
                      .....-..    ..+++-...... .-++..-.        ...++.||.-|+.+..|++.+.-.++
T Consensus        79 ~~i~~w~~----~~w~~~~~~~~~~~~l~~~l~--------~~v~~~wV~gH~g~~~Ne~AD~LA~~  133 (147)
T 2kq2_A           79 AGIAFWAT----GEWKAKNEFTQAYAKLMNQYR--------GIYSFEKVKAHSGNEFNDYVDMKAKS  133 (147)
T ss_dssp             STHHHHTT----SSSSCCHHHHHHHHCGGGGGS--------TTCCBCCCCCCCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHh----CCCccCCcchHHHHHHHHHhc--------CCeeEEEecCcCCCcchHHHHHHHHH
Confidence            64322100    011111100000 00121111        16889999999998888876333333

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

Probab=98.24  E-value=9.2e-07  Score=70.47  Aligned_cols=70  Identities=14%  Similarity=0.055  Sum_probs=51.5

Q ss_pred             CeEEeecCCCCCC--ceeEEEEecCcc------ceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCC----cEEEEe
Q psy8736         135 YKQIFTDASKNEH--SVSSAFCCEETK------FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTP----KFVLYS  202 (290)
Q Consensus       135 ~~~iyTDgSk~~~--~~G~av~~~~~~------~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~----~~~I~s  202 (290)
                      .+.||||||...+  ..|++++..+.+      ....+ ..++...||+.|++.||+.+.+.     +..    ++.|++
T Consensus         3 ~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~-----~~~~~~~~v~i~t   76 (140)
T 3u3g_D            3 KIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYI-GETTNNVAEYEALIRALEDLQMF-----GDKLVDMEVEVRM   76 (140)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEE-EEECHHHHHHHHHHHHHHHHGGG-----GGGGTTCEEEEEE
T ss_pred             eEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeC-CCCchHHHHHHHHHHHHHHHHHc-----CCCCCCceEEEEe
Confidence            4689999998643  467776664422      11222 34789999999999999999875     334    899999


Q ss_pred             cchhhhhh
Q psy8736         203 DSLSALQS  210 (290)
Q Consensus       203 Ds~saL~~  210 (290)
                      ||+.++..
T Consensus        77 DS~~vi~~   84 (140)
T 3u3g_D           77 DSELIVRQ   84 (140)
T ss_dssp             SCHHHHHH
T ss_pred             ChHHHHHH
Confidence            99988764

>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=98.19  E-value=1.6e-06  Score=69.42  Aligned_cols=70  Identities=10%  Similarity=-0.002  Sum_probs=51.8

Q ss_pred             CeEEeecCCCCCC--ceeEEEEecCcc-------ceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecch
Q psy8736         135 YKQIFTDASKNEH--SVSSAFCCEETK-------FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSL  205 (290)
Q Consensus       135 ~~~iyTDgSk~~~--~~G~av~~~~~~-------~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~  205 (290)
                      .+.||||||...+  ..|++++..+..       ....+ ..++...||+.|++.||+.+.+.     +..++.|++||+
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~-----~~~~v~i~tDS~   76 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAI-GRATNNVAEYRGLIAGLDDAVKL-----GATEAAVLMDSK   76 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHH-----TCSEEEEEESCH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccC-CCCchHHHHHHHHHHHHHHHHHC-----CCceEEEEeChH
Confidence            3679999997643  366666554321       12222 36788999999999999999986     567899999999


Q ss_pred             hhhhh
Q psy8736         206 SALQS  210 (290)
Q Consensus       206 saL~~  210 (290)
                      .++..
T Consensus        77 ~vv~~   81 (141)
T 3hst_B           77 LVVEQ   81 (141)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            88764

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

Probab=98.06  E-value=2.8e-06  Score=68.89  Aligned_cols=119  Identities=16%  Similarity=0.058  Sum_probs=68.7

Q ss_pred             CCeEEeecCCCCCC--ceeEEEEecCcc----ceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhh
Q psy8736         134 NYKQIFTDASKNEH--SVSSAFCCEETK----FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSA  207 (290)
Q Consensus       134 ~~~~iyTDgSk~~~--~~G~av~~~~~~----~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~sa  207 (290)
                      +.+.||||||...+  ..|+|++..+..    ....+ ..++...||+.|++.||+.+.+       ..++.|++||+.+
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~-------~~~v~I~tDS~~v   74 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALKE-------PARVQLYSDSAYL   74 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS-------CCEEEEEESCHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcCc-------cCcEEEEeChHHH
Confidence            35789999997644  367776654432    12222 3577889999999999999863       3589999999987


Q ss_pred             hhhhhhhhhhhhc-----c--CCcccccccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736         208 LQSREQVSLTRLR-----I--GHTNLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS  264 (290)
Q Consensus       208 L~~r~~~~l~rlR-----t--GH~~l~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~  264 (290)
                      +..-..--+.+++     +  |..--+.. |+..-. ..+.  .-..++.||.-|+.+..|++.
T Consensus        75 i~~i~~~w~~~W~~~~w~~~~~~~v~n~~-l~~~~~-~~~~--~~~v~~~~V~gH~g~~~N~~A  134 (146)
T 3h08_A           75 VNAMNEGWLKRWVKNGWKTAAKKPVENID-LWQEIL-KLTT--LHRVTFHKVKGHSDNPYNSRA  134 (146)
T ss_dssp             HHHHHSSHHHHHHHTTCC----CCCTTHH-HHHHHH-HHHH--HSEEEEEECCC-CCSHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCccCCCCCcCCHH-HHHHHH-HHHh--hCceEEEEcCCcCCcHhHHHH
Confidence            7653320011111     1  11100111 100000 0001  124788899999888888775

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

Probab=97.99  E-value=1.3e-05  Score=64.96  Aligned_cols=70  Identities=9%  Similarity=0.018  Sum_probs=51.0

Q ss_pred             eEEeecCCCC--C-CceeE-EEEecC-cc--cee--ccC---CCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEec
Q psy8736         136 KQIFTDASKN--E-HSVSS-AFCCEE-TK--FSV--KLD---PRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSD  203 (290)
Q Consensus       136 ~~iyTDgSk~--~-~~~G~-av~~~~-~~--~~~--~l~---~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sD  203 (290)
                      +.+|||||..  + +..|+ +++..+ ..  ..+  .++   ...+...||+.|++.||+.+.+.     +..++.|++|
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~-----g~~~v~i~tD   76 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRL-----GISSPIIKGD   76 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHH-----TCCSCEEEES
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHc-----CCCEEEEEeC
Confidence            4799999976  2 34664 655443 22  111  222   36889999999999999999986     5678999999


Q ss_pred             chhhhhh
Q psy8736         204 SLSALQS  210 (290)
Q Consensus       204 s~saL~~  210 (290)
                      |+.++..
T Consensus        77 S~~vi~~   83 (149)
T 2ehg_A           77 SQLVIKQ   83 (149)
T ss_dssp             CHHHHHH
T ss_pred             hHHHHHH
Confidence            9987754

>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=97.95  E-value=6.2e-06  Score=67.72  Aligned_cols=119  Identities=17%  Similarity=0.116  Sum_probs=70.7

Q ss_pred             CeEEeecCCCCCC--ceeEEEEecCcc----ceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhh
Q psy8736         135 YKQIFTDASKNEH--SVSSAFCCEETK----FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSAL  208 (290)
Q Consensus       135 ~~~iyTDgSk~~~--~~G~av~~~~~~----~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL  208 (290)
                      .+.||||||...+  ..|+|++..+..    ....+ ...+...||+.|++.||+.+.+       ..++.|++||+.++
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~-------~~~v~I~tDS~~vi   75 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE-------HAEVILSTDSQYVR   75 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS-------CCEEEEEECCHHHH
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc-------CCcEEEEeCHHHHH
Confidence            4689999998643  367776654322    12222 3567889999999999998864       26899999999887


Q ss_pred             hhhhhhh----hhhhccCCc-ccccccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736         209 QSREQVS----LTRLRIGHT-NLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS  264 (290)
Q Consensus       209 ~~r~~~~----l~rlRtGH~-~l~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~  264 (290)
                      ..-..-+    -+.+++--+ ...+.-|+..-+ ..+.  ....++.||.-|+.+..|++.
T Consensus        76 ~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~-~l~~--~~~v~~~wV~gH~g~~~Ne~A  133 (155)
T 1jl1_A           76 QGITQWIHNWKKRGWKTADKKPVKNVDLWQRLD-AALG--QHQIKWEWVKGHAGHPENERA  133 (155)
T ss_dssp             HHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHH-HHTT--TCEEEEEECCSSTTCHHHHHH
T ss_pred             HHHHHHHHHHhhcccccccCCccCCHHHHHHHH-HHHc--cCceEEEEcCCCCCCHHHHHH
Confidence            6533210    011121100 111111111000 0111  136889999999988888876

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

Probab=97.87  E-value=1e-05  Score=67.25  Aligned_cols=120  Identities=13%  Similarity=-0.015  Sum_probs=69.7

Q ss_pred             CeEEeecCCCCCC--ceeEEEEecCcc--ceec-cCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhh
Q psy8736         135 YKQIFTDASKNEH--SVSSAFCCEETK--FSVK-LDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ  209 (290)
Q Consensus       135 ~~~iyTDgSk~~~--~~G~av~~~~~~--~~~~-l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~  209 (290)
                      .+.||||||...+  ..|+|+|..+..  ..+. .....+...||+.|++.||+.+.+       ..++.|++||+.++.
T Consensus         8 ~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~-------~~~v~I~tDS~~vi~   80 (166)
T 1ril_A            8 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE-------PCEVDLYTDSHYLKK   80 (166)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS-------CCEEEEECCCHHHHH
T ss_pred             cEEEEECccccCCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHhcc-------CCeEEEEeChHHHHH
Confidence            5689999998643  367777764322  1111 113577889999999999998753       248999999998775


Q ss_pred             hhhh-hhh----hhhccCCcc-cccccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736         210 SREQ-VSL----TRLRIGHTN-LTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS  264 (290)
Q Consensus       210 ~r~~-~~l----~rlRtGH~~-l~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~  264 (290)
                      .-.. -+-    +-+++.-+. ..+.-|+..-+ ..+.  ....++.||.-|+.+..|++.
T Consensus        81 ~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~-~l~~--~~~v~~~wV~gH~g~~~Ne~A  138 (166)
T 1ril_A           81 AFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALL-LAMA--PHRVRFHFVKGHTGHPENERV  138 (166)
T ss_dssp             HHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHH-HHHT--TSEEECCCCCGGGSCTHHHHH
T ss_pred             HHhhhHHHHHHhcccccccCCccCcHHHHHHHH-HHHh--cCeEEEEEeeCCCCchhHHHH
Confidence            4322 100    012221110 11111110000 0111  126889999999888888776

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

Probab=97.87  E-value=8.8e-06  Score=67.04  Aligned_cols=119  Identities=18%  Similarity=0.085  Sum_probs=69.9

Q ss_pred             CeEEeecCCCCCC--ceeEEEEecCcc----ceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhh
Q psy8736         135 YKQIFTDASKNEH--SVSSAFCCEETK----FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSAL  208 (290)
Q Consensus       135 ~~~iyTDgSk~~~--~~G~av~~~~~~----~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL  208 (290)
                      .+.||||||...+  ..|+|+|..+..    ....+ +..+...||+.|++.||+.+.+       ..++.|++||+.++
T Consensus         6 ~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~-------~~~v~I~tDS~~vi   77 (158)
T 2e4l_A            6 LIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKE-------PCKIILTSDSQYMR   77 (158)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS-------CCEEEEEECCHHHH
T ss_pred             eEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhcc-------CCeEEEEeCHHHHH
Confidence            4789999998643  367776654322    12223 3477889999999999998742       26899999999877


Q ss_pred             hhhhhhh----hhhhccCCcc-cccccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736         209 QSREQVS----LTRLRIGHTN-LTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS  264 (290)
Q Consensus       209 ~~r~~~~----l~rlRtGH~~-l~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~  264 (290)
                      ..-..-+    -+.+++..+. ..+.-|+..-. ..+.  +...++.||.-|+.+..|++.
T Consensus        78 ~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~-~l~~--~~~v~~~wV~gH~g~~~Ne~A  135 (158)
T 2e4l_A           78 QGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLD-KAAQ--LHQIDWRWVKGHAGHAENERC  135 (158)
T ss_dssp             HHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHH-HHHT--TSEEEEEECCTTCCCHHHHHH
T ss_pred             HHHHHHHHHHHHccccccCCCcccCHHHHHHHH-HHHc--cCcEEEEEccCCCCchhHHHH
Confidence            6532200    0112221110 11111110000 0111  136889999999988888876

>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=97.85  E-value=3.1e-05  Score=63.31  Aligned_cols=120  Identities=13%  Similarity=0.058  Sum_probs=69.3

Q ss_pred             CCCeEEeecCCCCCC-c-eeEEEEecCcc-ceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhh
Q psy8736         133 PNYKQIFTDASKNEH-S-VSSAFCCEETK-FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ  209 (290)
Q Consensus       133 ~~~~~iyTDgSk~~~-~-~G~av~~~~~~-~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~  209 (290)
                      ++.+.||||||...+ + .|++++..+.. ....+ ..++...||+.|+..||+..         ..++.|++||+.++.
T Consensus        10 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~---------~~~v~i~tDS~~v~~   79 (150)
T 3qio_A           10 VGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS---------GLEVNIVTDSQYALG   79 (150)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS---------CSEEEEEESCHHHHH
T ss_pred             CCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC---------CCcEEEEeCcHHHHH
Confidence            346899999997533 2 56666665543 23333 46888999999999999973         257999999998776


Q ss_pred             hhhhhh----hhhhccCCc-ccccccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736         210 SREQVS----LTRLRIGHT-NLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS  264 (290)
Q Consensus       210 ~r~~~~----l~rlRtGH~-~l~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~  264 (290)
                      .-..-.    -+-+++--+ ...+.-|+..-..-.+  -....++.||.-|+....|++.
T Consensus        80 ~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~--~~~~v~~~wV~gH~g~~~Ne~A  137 (150)
T 3qio_A           80 IITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLI--KKEKVYLAWVPAHKGIGGNEQV  137 (150)
T ss_dssp             HHHHHHHHHCC------------CHHHHHHHHHHHT--TCSEEEEEECCTTSCCHHHHHH
T ss_pred             HHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHh--hcCceEEEEccCcCCChhHHHH
Confidence            532110    011111111 0001111110000001  1356889999999988888775

>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=97.85  E-value=2.4e-05  Score=65.04  Aligned_cols=114  Identities=20%  Similarity=0.130  Sum_probs=68.9

Q ss_pred             CeEEeecCCCC--CCceeEEE--EecCccc-eeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhh
Q psy8736         135 YKQIFTDASKN--EHSVSSAF--CCEETKF-SVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ  209 (290)
Q Consensus       135 ~~~iyTDgSk~--~~~~G~av--~~~~~~~-~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~  209 (290)
                      .+.||||||..  .+..|+|+  +..+... ...++..++...||+.|+..||+.+ .       ..++.|++||+-++.
T Consensus        23 ~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~-~-------~~~v~I~tDS~~vi~   94 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA-E-------GKKLNVYTDSRYAFA   94 (165)
T ss_dssp             SEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT-B-------TSEEEEEECCHHHHH
T ss_pred             CEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc-c-------CceEEEEEchHHHHh
Confidence            47899999985  23245554  3333222 2245677899999999999999988 2       357999999998876


Q ss_pred             hhhhhhhhhhccCCcccccccccccCCCCCCCCCCcccchhehhhhcc-----chhhccC
Q psy8736         210 SREQVSLTRLRIGHTNLTHVHLMKREPPPECDTCNCRLTVKHLLKYCN-----KYHNIRS  264 (290)
Q Consensus       210 ~r~~~~l~rlRtGH~~l~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp-----~~~~~R~  264 (290)
                      .. +.  +  ..|..--+. -|+..-....+  -+...++.||.-|..     ...|++.
T Consensus        95 ~i-w~--~--~~g~~v~n~-dl~~~l~~~l~--~~~~v~~~wVkgH~g~~~~~~~gNe~A  146 (165)
T 3p1g_A           95 TA-HV--H--SEGREIKNK-NEILALLKALF--LPKRLSIIHCPGHQKGNSAEARGNRMA  146 (165)
T ss_dssp             HH-HS--C--CCSCCCSSH-HHHHHHHHHTT--SBSEEEEEECCSSCCSCSHHHHHHHHH
T ss_pred             hh-hc--c--cCCCcccCH-HHHHHHHHHHh--cCCceEEEEecCCCCCCcCcchHHHHH
Confidence            43 10  0  122111111 11110000011  245688999999887     6777765

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

Probab=97.38  E-value=0.00028  Score=58.58  Aligned_cols=70  Identities=14%  Similarity=0.127  Sum_probs=45.9

Q ss_pred             CeEEeecCCCCCC-c------eeEEEEecCcc------ceecc-CCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEE
Q psy8736         135 YKQIFTDASKNEH-S------VSSAFCCEETK------FSVKL-DPRISICNAELISIQYAISFIISTTPLQVPTPKFVL  200 (290)
Q Consensus       135 ~~~iyTDgSk~~~-~------~G~av~~~~~~------~~~~l-~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I  200 (290)
                      ...||||||...+ +      .|+++|.....      ..+.. .+..+-..||..|+..|++.+.+.      ..++.|
T Consensus         7 evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~------~~~v~I   80 (165)
T 2lsn_A            7 EGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKI------PGPVLV   80 (165)
T ss_dssp             SEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHS------SSCEEE
T ss_pred             eEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcC------CCeEEE
Confidence            3679999997532 2      67887754321      12222 234455678888888888877653      347999


Q ss_pred             Eecchhhhhh
Q psy8736         201 YSDSLSALQS  210 (290)
Q Consensus       201 ~sDs~saL~~  210 (290)
                      +|||.-++..
T Consensus        81 ~TDS~Yvi~~   90 (165)
T 2lsn_A           81 ITDSFYVAES   90 (165)
T ss_dssp             EESCHHHHHH
T ss_pred             EeChHHHHhh
Confidence            9999876654

>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=97.31  E-value=0.00031  Score=68.94  Aligned_cols=109  Identities=13%  Similarity=0.067  Sum_probs=67.1

Q ss_pred             CCeEEeecCCCCCC-c-eeEEEEecCcc-ceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhhh
Q psy8736         134 NYKQIFTDASKNEH-S-VSSAFCCEETK-FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS  210 (290)
Q Consensus       134 ~~~~iyTDgSk~~~-~-~G~av~~~~~~-~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~~  210 (290)
                      +.+.||||||...+ | .|+|++..+.. ..... ..++...||+.|++.||+.+         ..++.|++||+-++..
T Consensus       438 ~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~---------~~~v~I~tDS~~vi~~  507 (557)
T 2zd1_A          438 GAETFYVDGAANRETKLGKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS---------GLEVNIVTDSQYALGI  507 (557)
T ss_dssp             TSCEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS---------CSEEEEEECCHHHHHH
T ss_pred             CCEEEEEccCCCCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC---------CCcEEEEeChHHHHHH
Confidence            34789999997533 3 56666655433 23332 46789999999999999987         1369999999988765


Q ss_pred             hhhhhhhhhccC-CcccccccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736         211 REQVSLTRLRIG-HTNLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS  264 (290)
Q Consensus       211 r~~~~l~rlRtG-H~~l~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~  264 (290)
                      -..     .... +..+-..++ ..    ..  .....++.||.-|+....|++.
T Consensus       508 i~~-----~~~~~~~~l~~~~~-~~----l~--~~~~v~~~wV~~H~g~~~Ne~A  550 (557)
T 2zd1_A          508 IQA-----QPDKSESELVNQII-EQ----LI--KKEKVYLAWVPAHKGIGGNEQV  550 (557)
T ss_dssp             HTT-----CCSEESSHHHHHHH-HH----HH--HCSEEEEEECCSSSCCTTCCGG
T ss_pred             Hhc-----CCccCCHHHHHHHH-HH----Hh--cCCCEEEEEcCCCCCChhHHHH
Confidence            321     1110 000000000 00    00  0135788899888888877765

>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=97.27  E-value=0.00044  Score=55.97  Aligned_cols=69  Identities=13%  Similarity=0.160  Sum_probs=49.1

Q ss_pred             CCeEEeecCCCCC--CceeEEEEecCc-c-c--eeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhh
Q psy8736         134 NYKQIFTDASKNE--HSVSSAFCCEET-K-F--SVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSA  207 (290)
Q Consensus       134 ~~~~iyTDgSk~~--~~~G~av~~~~~-~-~--~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~sa  207 (290)
                      ....||||||...  +..|.++|.... . .  ...++ ..+-..||+.|++.||+.+.+.     .. ++.|++||+-+
T Consensus        10 ~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~-~~TNN~aEl~A~i~aL~~~~~~-----~~-~v~i~tDS~~v   82 (142)
T 1zbf_A           10 IWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKER-----NS-RKPIYSNSQTA   82 (142)
T ss_dssp             CSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEE-EECHHHHHHHHHHHHHHHHHHT-----TC-CCCEEESCHHH
T ss_pred             CeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccC-CcCcHHHHHHHHHHHHHHHHhC-----CC-eEEEEEehHHH
Confidence            4568999999753  236777776532 2 1  11222 4678889999999999999875     34 79999999866


Q ss_pred             hh
Q psy8736         208 LQ  209 (290)
Q Consensus       208 L~  209 (290)
                      +.
T Consensus        83 i~   84 (142)
T 1zbf_A           83 IK   84 (142)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>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=97.20  E-value=0.00046  Score=67.66  Aligned_cols=111  Identities=17%  Similarity=0.090  Sum_probs=67.3

Q ss_pred             CCeEEeecCCCCCCc--eeEEEEecCccceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhhhh
Q psy8736         134 NYKQIFTDASKNEHS--VSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSR  211 (290)
Q Consensus       134 ~~~~iyTDgSk~~~~--~G~av~~~~~~~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~~r  211 (290)
                      +.+.+|||||...++  .|+|++.............++...||+.|++.||+.   .      ..++.|++||+-++..-
T Consensus       435 ~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~TNn~aEl~A~i~aL~~---~------~~~v~I~tDS~~v~~~i  505 (555)
T 1mu2_A          435 GAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTD---S------GPKVNIIVDSQYVMGIV  505 (555)
T ss_dssp             TCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEESSCCHHHHHHHHHHHHHHT---S------CSEEEEEESCHHHHHHH
T ss_pred             CceEEEEcccccCCCCCceEEEEEEeCCEeeccCCCCCHHHHHHHHHHHHHHc---C------CCeEEEEEehHHHHHHH
Confidence            347899999976432  567766655432222234577889999999999987   1      35799999999877653


Q ss_pred             hhhhhhhhccCCcccccccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736         212 EQVSLTRLRIGHTNLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS  264 (290)
Q Consensus       212 ~~~~l~rlRtGH~~l~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~  264 (290)
                      ..     ++++..    .-+++... ... ..+...++.||.-|+....|++.
T Consensus       506 ~~-----~~~~~~----~~l~~~~~-~~~-~~~~~v~~~wV~~H~g~~~Ne~A  547 (555)
T 1mu2_A          506 AS-----QPTESE----SKIVNQII-EEM-IKKEAIYVAWVPAHKGIGGNQEV  547 (555)
T ss_dssp             HT-----CCSEES----CHHHHHHH-HHH-HHCSEEEEEECCSSSCCTTHHHH
T ss_pred             hc-----cccccc----HHHHHHHH-HHh-ccCCcEEEEEEECCCCChhHHHH
Confidence            22     222210    00110000 000 01345788899888887777664

>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=97.09  E-value=0.00043  Score=55.45  Aligned_cols=70  Identities=13%  Similarity=0.187  Sum_probs=46.8

Q ss_pred             CCCeEEeecCCCC-CCc-eeE-EEEecCcc---ceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchh
Q psy8736         133 PNYKQIFTDASKN-EHS-VSS-AFCCEETK---FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLS  206 (290)
Q Consensus       133 ~~~~~iyTDgSk~-~~~-~G~-av~~~~~~---~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~s  206 (290)
                      +....|||||+.. +.| .|. +|+..+..   ....+ ..++--.||+.|++.||+.+.+.     .. ++.|++||+-
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~-~~tTNN~aEl~A~i~aL~~l~~~-----~~-~v~i~tDSqy   75 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKER-----NS-RKPIYSNSQT   75 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHT-----TC-CCCEEESCHH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCC-CCCchHHHHHHHHHHHHHHHHhC-----CC-CEEEEcchHH
Confidence            3456799999975 333 566 34433222   11122 25777889999999999999874     22 3799999986


Q ss_pred             hhh
Q psy8736         207 ALQ  209 (290)
Q Consensus       207 aL~  209 (290)
                      ++.
T Consensus        76 Vi~   78 (134)
T 4htu_A           76 AIK   78 (134)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            653

---

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	290
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	98.39
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	98.39
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	98.13
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	98.06
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	97.33

>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=98.39  E-value=2.9e-07  Score=69.84  Aligned_cols=69  Identities=17%  Similarity=0.171  Sum_probs=47.8

Q ss_pred             CCCeEEeecCCCC-CCce-eEEEEecCccceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhhh
Q psy8736         133 PNYKQIFTDASKN-EHSV-SSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS  210 (290)
Q Consensus       133 ~~~~~iyTDgSk~-~~~~-G~av~~~~~~~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~~  210 (290)
                      +....+|||||.. +++. |++++..+...........|...||+.|++.||+.         ...++.|+|||+-++..
T Consensus         6 ~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~~~~TNn~aEl~Avi~aL~~---------~~~~v~I~TDS~yvi~~   76 (110)
T d1s1ta1           6 VGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD---------SGLEVNIVTDSQYALGI   76 (110)
T ss_dssp             TTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEESSCCHHHHHHHHHHHHHHH---------SCSEEEEEECCHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEecccCcHHHHHHHHHHHHHHh---------CCCeEEEEEehHHHHHH
Confidence            3456899999964 4444 44455555443222234578889999999999973         23469999999988765

>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=98.39  E-value=3.2e-07  Score=70.92  Aligned_cols=110  Identities=16%  Similarity=0.108  Sum_probs=66.2

Q ss_pred             CCCeEEeecCCCC-CCc-eeEEEEecCccceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhhh
Q psy8736         133 PNYKQIFTDASKN-EHS-VSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS  210 (290)
Q Consensus       133 ~~~~~iyTDgSk~-~~~-~G~av~~~~~~~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~~  210 (290)
                      +....+|||||.. +++ .|++++..+....+......|.+.||+.|+++|++.         ...++.|++||+.++..
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~~~tnn~AEl~Ai~~al~~---------~~~~i~I~tDS~~v~~~   75 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTD---------SGPKVNIIVDSQYVMGI   75 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEESSCCHHHHHHHHHHHHHHT---------SCSEEEEEESCHHHHHH
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecCCCcchHHHHHHHHHHhcc---------CCcceEEEechHHHHHH
Confidence            3446899999965 444 445555655543333334578899999999999873         34579999999987754


Q ss_pred             hhhhhhhhhccCCcccccccc--cccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736         211 REQVSLTRLRIGHTNLTHVHL--MKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS  264 (290)
Q Consensus       211 r~~~~l~rlRtGH~~l~h~~l--~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~  264 (290)
                      -..     ..  +......+.  +..    .+.  ....++.||.-|+.+..|++.
T Consensus        76 ~~~-----~~--~~~~~~~~~~~~~~----~~~--~~~v~~~wV~gH~g~~gNe~A  118 (126)
T d1mu2a1          76 VAS-----QP--TESESKIVNQIIEE----MIK--KEAIYVAWVPAHKGIGGNQEV  118 (126)
T ss_dssp             HHT-----CC--SEESCHHHHHHHHH----HHH--CSEEEEEECCSSSCCTTHHHH
T ss_pred             Hhc-----CC--ccccchHHHHHHHH----hhh--cceeEEEEEeCCCCCcchHHH
Confidence            221     00  000000000  000    000  124678999999988887764

>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=98.13  E-value=3e-07  Score=72.78  Aligned_cols=120  Identities=16%  Similarity=0.071  Sum_probs=69.7

Q ss_pred             CeEEeecCCCCCC--ceeEEEEec--Ccccee-ccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhh
Q psy8736         135 YKQIFTDASKNEH--SVSSAFCCE--ETKFSV-KLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ  209 (290)
Q Consensus       135 ~~~iyTDgSk~~~--~~G~av~~~--~~~~~~-~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~  209 (290)
                      .+.||||||...+  ..|+|+|..  +....+ ...+..+...||+.|+..|++.+.       ....+.+.+||...+.
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~-------~~~~i~i~tds~~~i~   74 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALK-------EHAEVILSTDSQYVRQ   74 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCC-------SCCEEEEEECCHHHHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhc-------ccceEEEeecceeeEE
Confidence            4689999997654  256666543  322222 112345678899999999998754       3456889999987766


Q ss_pred             hhhhhhhhhhccCCcccc-----cccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736         210 SREQVSLTRLRIGHTNLT-----HVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS  264 (290)
Q Consensus       210 ~r~~~~l~rlRtGH~~l~-----h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~  264 (290)
                      .-........+.|.....     +..++..-+ ..+  -.-.+++.||.-||....|++.
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~-~~~--~~~~V~~~wV~gH~g~~gNe~A  131 (152)
T d1jl1a_          75 GITQWIHNWKKRGWKTADKKPVKNVDLWQRLD-AAL--GQHQIKWEWVKGHAGHPENERA  131 (152)
T ss_dssp             HHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHH-HHT--TTCEEEEEECCSSTTCHHHHHH
T ss_pred             cccchhhHhHhccchhcccCeeecHHHHHHHH-HHh--hcceeEEEEecccCCCccHHHH
Confidence            543322222222221110     000110000 001  1235889999999999998876

>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=98.06  E-value=1.2e-06  Score=69.13  Aligned_cols=121  Identities=12%  Similarity=-0.015  Sum_probs=69.0

Q ss_pred             CCeEEeecCCCCCC-c-eeEEEEecCcc---ceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhh
Q psy8736         134 NYKQIFTDASKNEH-S-VSSAFCCEETK---FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSAL  208 (290)
Q Consensus       134 ~~~~iyTDgSk~~~-~-~G~av~~~~~~---~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL  208 (290)
                      ..+.||||||...+ + .|+|+|.....   ........++...||+.|+++||+.+.       ....+.|++||..++
T Consensus         2 ~~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~-------~~~~i~i~tds~~~~   74 (147)
T d1rila_           2 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALK-------EPCEVDLYTDSHYLK   74 (147)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCC-------SCCEEEEECCCHHHH
T ss_pred             CEEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhcc-------CCceEEEecchhhhh
Confidence            35789999998654 3 56666543322   222223446788999999999998653       345789999999877


Q ss_pred             hhhhh-----hhhhhhccCCccc-ccccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736         209 QSREQ-----VSLTRLRIGHTNL-THVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS  264 (290)
Q Consensus       209 ~~r~~-----~~l~rlRtGH~~l-~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~  264 (290)
                      ..-..     ...+..++.+... .+.-|+..-. ..|.  .-...+.||.-|+....|++.
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~-~~~~--~~~v~~~wVkgHsg~~gNe~A  133 (147)
T d1rila_          75 KAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALL-LAMA--PHRVRFHFVKGHTGHPENERV  133 (147)
T ss_dssp             HHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHH-HHHT--TSEEECCCCCGGGSCTHHHHH
T ss_pred             ccccccchhhhhhccccccccccchhHHHHHHHH-HHhh--hcccceEEccCCCCCcchHHH
Confidence            54221     1111112211110 0000110000 0121  235788999999988887765

>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=97.33  E-value=0.00011  Score=56.73  Aligned_cols=65  Identities=15%  Similarity=0.173  Sum_probs=45.2

Q ss_pred             EEeecCCCC-CCc-eeEEEEecCccc----eeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhh
Q psy8736         137 QIFTDASKN-EHS-VSSAFCCEETKF----SVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSAL  208 (290)
Q Consensus       137 ~iyTDgSk~-~~~-~G~av~~~~~~~----~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL  208 (290)
                      .||||||.. +.| .|.++|......    ...+ ...+--.||+.|+..||+.+.+.      ..++.|+|||+=++
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~-~~~TNN~aEl~A~i~aL~~~~~~------~~~i~I~tDS~yvi   76 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKER------NSRKPIYSNSQTAI   76 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHHT------TCCCCEEESCHHHH
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCc-CccchHHHHHHHHHHHHHHhhcC------CceEEEEeccHHHH
Confidence            499999965 334 666666554431    1122 24566689999999999999764      34688999998554