Psyllid ID: psy17738

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310------
Protein Sequence
MRSAIDYTSMYRQINQIPRRNAYTWCSAEQVMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQALHLETNEPPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNKKINTINVFLEEKFPLFKKIHTLTHPPPPPWTLDTPDLNFQLHIFTKKITSSPIIKSNFLAILQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAISNIYTIQNQLITNIQTLNQGGFKCEILANTKTERLHMVLS
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHcccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccHHHccccccccHHHHHHHHHHHHHccccEEEEEcccccccccccEEEcccccEEEEEEccccccccHHHHHHHHHHHHHHccccccccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHccccccccccHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHcccccccHHHHccHHHccccccHHHHHHHHHHHccccccccccccccccccccccccccEEEEccccccccccHHHHHHHHHHHHHHccccEEEEEccccccccEEEEEEEccccEEEEEEccccccHHHHHHHHHHHHHHHHHHccccccccEEEEEccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHcccHHHHHHHEEcc
Coil and Loop (DISEMBL)
mrsaidytSMYRQInqiprrnaytwCSAEQVMELFGDLYLHTIDIIKvlnpdasennlkilNPIQNQCLRlatgafcttpiqalhletnepplEIRRKILTFNYaakvtsvpqhpcykllmfpkYVQNYKNKKINTINVFLeekfplfkkihtlthpppppwtldtpdlnfQLHIftkkitsspiiKSNFLAILQNYETHVRiytdgskdeenagcafvipdrnitkmfsldpkssifACELYAIYAALEYlhhpnnntveNYVIISDSQAALQAISNIYTIQNQLITNIQTLNQGGFKCEILANTKTERLHMVLS
Flexible Loop (DISEMBL)
mrsaidytsmyrqinqiprrNAYTWCSAEQVMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQAlhletneppLEIRRKILTFNYAAKvtsvpqhpcyKLLMFPKYVQNYKNKKINTINVFLEEKFPLFKKIHTLTHPPPPPWTLDTPDLNFQLHIFTKKITSSPIIKSNFLAILQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAISNIYTIQNQLITNIQTLNQGGFKCEIlantkterlhmvls
Low Complexity Region (SEG)
MRSAIDYTSMYRQINQIPRRNAYTWCSAEQVMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQALHLETNEPPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNKKINTINVFLEEKFPLFKKIhtlthpppppwtldtpdlNFQLHIFTKKITSSPIIKSNFLAILQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAISNIYTIQNQLITNIQTLNQGGFKCEILANTKTERLHMVLS
Disordered region (IsUnstruct)
*****DYTSMYRQINQIPRRNAYTWCSAEQVMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQALHLETNEPPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNKKINTINVFLEEKFPLFKKIHT*************PDLNFQLHIFTKKITSSPIIKSNFLAILQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAISNIYTIQNQLITNIQTLNQGGFKCEILANTKT********
Disordered Region (DISOPRED)
********SMYRQINQIPRRNAYTWCSAEQVMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQALHLETNEPPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNKKINTINVFLEEKFPLFKKIHTLTHPPPPPWTLDTPDLNFQLHIFTKKITSSPIIKSNFLAILQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAISN*****NQLITNIQTLNQGGFKCEILANTKTERLHMVL*
Disordered Region (DISEMBL)
MRSAIDYTSMYRQINQIPRRNAYTWCSAEQVMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQALHLETNEPPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNKKINTINVFLEEKFPLFKKIHTLTHPPPPPWTLDTPDLNFQLHIFTKKITSSPIIKSNFLAILQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAISNIYTIQNQLITNIQTLNQGGFKCEILANTKTERLHMVLS
Disordered Region (DISPRO)
MRSAIDYTSMYRQINQIPRRNAYTWCSAEQVMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQALHLETNEPPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNKKINTINVFLEEKFPLFKKIHTLTHPPPPPWTLDTPDLNFQLHIFTKKITSSPIIKSNFLAILQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAISNIYTIQNQLITNIQTLNQGGFKCEILANTKTERLHMVLS
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRSAIDYTSMYRQINQIPRRNAYTWCSAEQVMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQALHLETNEPPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNKKINTINVFLEEKFPLFKKIHTLTHPPPPPWTLDTPDLNFQLHIFTKKITSSPIIKSNFLAILQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAISNIYTIQNQLITNIQTLNQGGFKCEILANTKTERLHMVLS
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	316
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.781	0.202	0.338	9e-29
443710566	377	hypothetical protein CAPTEDRAFT_186063 [	0.775	0.649	0.322	6e-23
427791981	1060	Putative tick transposon, partial [Rhipi	0.768	0.229	0.317	1e-22
427798885	1199	Putative tick transposon, partial [Rhipi	0.819	0.216	0.294	3e-22
427792011	1121	Putative tick transposon, partial [Rhipi	0.825	0.232	0.291	2e-21
427791807	1212	Putative tick transposon, partial [Rhipi	0.753	0.196	0.300	2e-21
427791321	1210	Putative tick transposon, partial [Rhipi	0.753	0.196	0.300	3e-21
427798887	1199	Putative tick transposon, partial [Rhipi	0.819	0.216	0.287	9e-21
427798889	1199	Putative tick transposon, partial [Rhipi	0.819	0.216	0.283	4e-20
328697220	1915	PREDICTED: hypothetical protein LOC10016	0.784	0.129	0.288	3e-16

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

 Score =  133 bits (335), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 88/260 (33%), Positives = 136/260 (52%), Gaps = 13/260 (5%)

Query: 29   EQVMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQALHLET 88
            + ++ L+  L    +D   ++   A ++ LKIL PIQN  LRL  GAF T+PI +LH+E 
Sbjct: 779  DTLLLLYRSLIRSKLDYGSIIYGAARKSYLKILEPIQNAALRLCLGAFRTSPIPSLHVEA 838

Query: 89   NEPPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNKKINTIN-VFLEEKFPL 147
             E P++IR K L   Y  K+ S P +P +  +  P  V+ Y N++ N I  + L  + P+
Sbjct: 839  GELPMDIRMKKLAMQYIVKLKSNPTNPAFDSIFNPTEVELY-NRRPNVIQPLGLRMREPI 897

Query: 148  ------FKKIHTLTHPPPPPWTLDTPDLNFQLHIFTKKITSSPIIKSNFLAILQNYETHV 201
                    +I  +  P  PPW ++ P LN  L  F K+ T   I++ +F  + ++Y    
Sbjct: 898  QNLTQPIDQISKIETPQNPPWLMNKPKLNLSLLNFKKENTDPSILQVHFRELQESYGDCG 957

Query: 202  RIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVE 261
             IYTDGSK E    CA    ++ I++   L    SIF  EL+AI  AL  +     +   
Sbjct: 958  TIYTDGSKMEGKVACACSFRNKTISR--RLPDGCSIFTAELHAILLALMAVKASERS--- 1012

Query: 262  NYVIISDSQAALQAISNIYT 281
             ++I SDS++ALQA+  + T
Sbjct: 1013 KFIICSDSKSALQALGRMKT 1032

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

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

 Score =  114 bits (285), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 87/270 (32%), Positives = 134/270 (49%), Gaps = 25/270 (9%)

Query: 25  WCSAEQVM-ELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQA 83
           W +  +V+  LF  L    +D   ++   A  + L+ L PIQNQ  RL  GAF  +P+ +
Sbjct: 3   WGADREVLFRLFRSLLRSRLDYGAIVYGSARISYLERLKPIQNQAFRLCLGAFRISPVTS 62

Query: 84  LHLETNEPPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNKK--------IN 135
           LH E NE P+ IR+K+L+  +A +V S   +P ++ +       NY N +        I 
Sbjct: 63  LHTEANEMPMAIRQKLLSVQFALRVCSDTTNPAHQCIF------NYNNDRFYLSKPNAIR 116

Query: 136 TINVFLEEKF----PLFKKIHTLTHPPPPPWTLDTPDLNFQLHIFTKKITSSP--IIKSN 189
            + + ++E      P  K I        P W L  P+L+  L  F KK T++P   +K+ 
Sbjct: 117 PLALRIKEDLQTICPDIKAITPNQLFNIPYWLLRPPELDISLIHFGKK-TANPNYTLKNE 175

Query: 190 FLAILQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAAL 249
           F  ++  Y  H  I+TDGSK +    C F   D N++    L   +SIF+ EL AIY  L
Sbjct: 176 FYNLMDKYPDHKVIFTDGSKSDSAVAC-FATAD-NLSIQIRLPDSASIFSAELLAIYQVL 233

Query: 250 EYLHHPNNNTVENYVIISDSQAALQAISNI 279
             L    N+  + ++I +DS ++LQAI N 
Sbjct: 234 TLLECSANDQ-QQFLIATDSLSSLQAIGNF 262

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score =  113 bits (283), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 85/268 (31%), Positives = 130/268 (48%), Gaps = 25/268 (9%)

Query: 25   WCSAEQ-VMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQA 83
            W S  + ++ ++  L    +D   ++   A ++ LK L+P+ N+ LRLATGA+ T+PI +
Sbjct: 802  WGSDRKCLLHIYRSLVRSKLDYGSIIYGSARDSYLKRLDPVHNKGLRLATGAYRTSPIPS 861

Query: 84   LHLETNEPPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNK--KINTINVFL 141
            L+ E+NEP LE RR  L F Y  KV S P H CY ++       +Y NK   I  + +  
Sbjct: 862  LYAESNEPSLEYRRTQLMFTYVLKVRSSPDHICYSIVTRSDQRLHYANKPNAIKPLILRF 921

Query: 142  EEKFPLFKKIHTLTHPPP-----------PPWTLDTPDLNFQLHIFTKKITSSPIIKSNF 190
            EEKF      H L  P              PW+  +  L+F L    K+ T    I   F
Sbjct: 922  EEKF------HALNIPNEALSIAKRPRSLAPWSDFSMFLDFSLTHIKKQGTPREHILQEF 975

Query: 191  LAILQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALE 250
              + + Y T    YTDGSK     G + V       ++  L    S++  E YA++ A+ 
Sbjct: 976  RTLQEKYHTFNEFYTDGSKASAYVGSSVV--GEIYEEVVRLPQFVSVYTAECYALWIAVR 1033

Query: 251  YLHHPNNNTVENYVIISDSQAALQAISN 278
             + + N+   +  VI SDS +AL+A+S+
Sbjct: 1034 NIINSNH---KKAVIFSDSLSALRALSS 1058

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 =  112 bits (279), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 83/282 (29%), Positives = 142/282 (50%), Gaps = 23/282 (8%)

Query: 24   TWCSAEQ-VMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQ 82
            TW S ++ +M L+  L    +D   ++   AS   LK+L+PI +  +RL+TGAFCT+P++
Sbjct: 779  TWGSDKKCLMNLYKSLIRTCLDYGAIIYQSASPTALKMLDPIHHLGIRLSTGAFCTSPVE 838

Query: 83   ALHLETNEPPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNK-------KIN 135
            +L++E+NE  L+++R  ++F Y  KV +  +HP +  +        ++N+        + 
Sbjct: 839  SLYVESNEWSLQLQRSYMSFLYYLKVNADKEHPSHSTINDLSSSTLFENRPSLRPPYSLR 898

Query: 136  TINVFLEEKFPLFKKIHTLTHPP--PPPWTLDTPDLNFQLHIFTKKITSSPI--IKSNFL 191
               +  E   PLF+  H L  P   PPPW     D +      TK    +PI  I++ FL
Sbjct: 899  VRGLAEETGLPLFE--HRLMAPAAYPPPWQWQLIDCDVSFMEVTKH---APIAHIRTYFL 953

Query: 192  AILQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEY 251
             +   Y      YTD SK   +   A V P  + +    L P +SIF  E YAI AA++ 
Sbjct: 954  ELQHKYNCPA-FYTDASKSHTSVSYAAVGP--SFSDAGVLHPNTSIFTAEAYAILAAVK- 1009

Query: 252  LHHPNNNTVENYVIISDSQAALQAISNIYTIQNQLITNIQTL 293
              H     ++  VI +DS + ++A+  +   +N ++ ++ +L
Sbjct: 1010 --HIRELKLQKAVIYTDSLSVVKALKTLKKHKNSILVSLYSL 1049

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427792011|gb|JAA61457.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  109 bits (272), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 81/278 (29%), Positives = 142/278 (51%), Gaps = 17/278 (6%)

Query: 24   TWCSAEQ-VMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQ 82
            +W + ++ +M LF  L    ++   ++   AS+  +K+L+P+ +  +RLATGAF T+P+ 
Sbjct: 773  SWGTDKKCLMSLFNSLIKSRLNYGCIVYQSASKTAVKMLDPVYHLGIRLATGAFRTSPVS 832

Query: 83   ALHLETNEPPLEIRRKILTFNYAAKVTSVPQHPCYKLL-------MFPKYVQNYKNKKIN 135
            +L++E NE P+++ R+  T  Y  KVTS+P HPC KL+        F K     K   + 
Sbjct: 833  SLYVEANEWPMQLEREYCTLMYTLKVTSIPTHPCAKLVADTSALRFFEKRPSLSKPFSLT 892

Query: 136  TINVFLEEKFPLFKKIHTLTHPPPPPW--TLDTPDLNFQLHIFTKKITSSPIIKSNFLAI 193
                  + + PL +     +    PPW  T    D++F  HI  K+      I+ +FL++
Sbjct: 893  CTATAAQAEIPLQQVAKAPSMEWLPPWEKTRIKCDMSF-CHI-DKQRHPRAAIQQHFLSL 950

Query: 194  LQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLH 253
               Y    + YTD SK  ++   A V P+   T    L+  +SIF  E YAI  A++Y+ 
Sbjct: 951  QYKYRGCHQFYTDASKTRDSVSAAAVGPE--FTTSERLNVHTSIFTAEAYAILIAIKYIL 1008

Query: 254  HPNNNTVENYVIISDSQAALQAISNIYTIQNQLITNIQ 291
               N+ +   VI +DS + ++A+      +N ++ +++
Sbjct: 1009 ---NHNITKSVIFTDSLSVVRALHTGKPNKNPVLCDVE 1043

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  109 bits (272), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 77/256 (30%), Positives = 131/256 (51%), Gaps = 18/256 (7%)

Query: 31   VMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQALHLETNE 90
            ++ ++  +    +D   V+   A E+ ++ L+P+ N  LRL++GA+ T+P+++L+++ NE
Sbjct: 763  LLRIYRSIVRSILDYGCVVYGSARESYIRRLDPVHNLGLRLSSGAYRTSPVESLYVDCNE 822

Query: 91   PPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNKK--INTINVFLEE---KF 145
            PPL  RR  LT +Y  ++ S PQH CY +        +Y NK   I  + +  EE    +
Sbjct: 823  PPLSHRRASLTLSYVLRIRSSPQHICYDIATRCSSRLHYLNKSNLIKPLLLRFEEYCRTY 882

Query: 146  PLFKKIHTLTHPPP--PPWTLDTPDL-NFQLHIFTKKITSSPIIKSNFLAILQNYETHVR 202
             + ++   +   PP  PPW  D   L +  L    KK+T   +I   F A+ + Y  +  
Sbjct: 883  VISEETLDVARKPPRIPPW-FDLAQLCDISLSHINKKVTPPELIIQEFRALQEKYRDYAE 941

Query: 203  IYTDGSKDEENAGCAFVIPDRNITKMFSLD-PKS-SIFACELYAIYAALEYLHHPNNNTV 260
             YTDGSK  ++ G   V  +      FS+  P+  SIF  E+YA+Y A   +    +   
Sbjct: 942  FYTDGSKTRDHVGIGIVTGE----SAFSVRVPQCISIFTAEVYALYEAARKIIAGKHKKA 997

Query: 261  ENYVIISDSQAALQAI 276
               +I +DS +AL+A+
Sbjct: 998  ---IIYTDSLSALKAL 1010

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 =  108 bits (271), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 77/256 (30%), Positives = 131/256 (51%), Gaps = 18/256 (7%)

Query: 31   VMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQALHLETNE 90
            ++ ++  +    +D   V+   A E+ ++ L+P+ N  LRL++GA+ T+P+++L+++ NE
Sbjct: 760  LLRIYRSIVRSILDYGCVVYGSARESYIRRLDPVHNLGLRLSSGAYRTSPVESLYVDCNE 819

Query: 91   PPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNKK--INTINVFLEE---KF 145
            PPL  RR  LT +Y  ++ S PQH CY +        +Y NK   I  + +  EE    +
Sbjct: 820  PPLSHRRASLTLSYVLRIRSSPQHICYDIATRCSSRLHYLNKSNLIKPLLLRFEEYCRTY 879

Query: 146  PLFKKIHTLTHPPP--PPWTLDTPDL-NFQLHIFTKKITSSPIIKSNFLAILQNYETHVR 202
             + ++   +   PP  PPW  D   L +  L    KK+T   +I   F A+ + Y  +  
Sbjct: 880  VISEETLDVARKPPRIPPW-FDLAQLCDISLSHINKKVTPPELIIQEFRALQEKYRDYAE 938

Query: 203  IYTDGSKDEENAGCAFVIPDRNITKMFSLD-PKS-SIFACELYAIYAALEYLHHPNNNTV 260
             YTDGSK  ++ G   V  +      FS+  P+  SIF  E+YA+Y A   +    +   
Sbjct: 939  FYTDGSKTRDHVGIGIVTGE----SAFSVRVPQCISIFTAEVYALYEAARKIIAGKHKKA 994

Query: 261  ENYVIISDSQAALQAI 276
               +I +DS +AL+A+
Sbjct: 995  ---IIYTDSLSALKAL 1007

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 =  107 bits (266), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 81/282 (28%), Positives = 141/282 (50%), Gaps = 23/282 (8%)

Query: 24   TWCSAEQ-VMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQ 82
            TW S ++ +M L+  L    +D   ++   AS   LK+L+P+ +  +RL+TGAF T+P++
Sbjct: 779  TWGSDKKCLMNLYKSLIRTRLDYGAIIYQSASPTALKMLDPVHHLGIRLSTGAFRTSPVE 838

Query: 83   ALHLETNEPPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNK-------KIN 135
            +L++E+NE  L ++R  ++F Y  KV +  +HP +  +        ++N+        + 
Sbjct: 839  SLYVESNEWSLHLQRSYMSFLYYLKVNADKEHPSHSTINDLSSSTLFENRPSLRPPYSLR 898

Query: 136  TINVFLEEKFPLFKKIHTLTHPP--PPPWTLDTPDLNFQLHIFTKKITSSPI--IKSNFL 191
               +  E   PLF+  H L  P   PPPW     D +      TK    +PI  I++ FL
Sbjct: 899  VRGLAEETGLPLFE--HRLMAPAAYPPPWQWQLIDCDVSFMEVTKH---APIAHIRTYFL 953

Query: 192  AILQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEY 251
             +   Y      YTD SK   +   A V P  + +   +L P +SIF  E YAI AA++ 
Sbjct: 954  ELQHKYNCPA-FYTDASKSHTSVSYAAVGP--SFSAAGALHPNTSIFTAEAYAILAAVK- 1009

Query: 252  LHHPNNNTVENYVIISDSQAALQAISNIYTIQNQLITNIQTL 293
              H     ++  VI +DS + ++A+  +   +N ++ ++ +L
Sbjct: 1010 --HIRELKLQKAVIYTDSLSVVKALKTLKKHKNSILVSLYSL 1049

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 =  104 bits (260), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 80/282 (28%), Positives = 142/282 (50%), Gaps = 23/282 (8%)

Query: 24   TWCSAEQ-VMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRLATGAFCTTPIQ 82
            TW S ++ +M L+  L    +D   ++   AS   LK+L+P+ +  +RL+TGAF T+P++
Sbjct: 779  TWGSDKKCLMNLYKSLIRTRLDYGAIIYQSASPTALKMLDPVHHLGIRLSTGAFRTSPVE 838

Query: 83   ALHLETNEPPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKNK-------KIN 135
            +L++E+NE  L ++R  ++F Y  KV +  +HP +  +        ++N+        + 
Sbjct: 839  SLYVESNEWSLHLQRSYMSFLYYIKVNADKEHPSHSTINDLSCSTLFENRPSLKPPYSLR 898

Query: 136  TINVFLEEKFPLFKKIHTLTHPP--PPPWTLDTPDLNFQLHIFTKKITSSPI--IKSNFL 191
              ++  +   PLF+  H L  P   PPPW     D +      TK    +PI  I++ FL
Sbjct: 899  VRDLAEQTGLPLFE--HRLMAPAAYPPPWQWQLIDCDVSFMEVTKH---APIAHIRTYFL 953

Query: 192  AILQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEY 251
             +   Y      YTD SK   +   A V P  + +   +L P +SIF  E YAI AA++ 
Sbjct: 954  ELQHKYNCPA-FYTDASKSHTSVSYAAVGP--SFSAAGALHPNTSIFTAEAYAILAAVK- 1009

Query: 252  LHHPNNNTVENYVIISDSQAALQAISNIYTIQNQLITNIQTL 293
              H     ++  VI +DS + ++A+  +   +N ++ ++ +L
Sbjct: 1010 --HIRELKLQKAVIYTDSLSVVKALKTLKKHRNPVLVSLYSL 1049

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 92.0 bits (227), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 78/270 (28%), Positives = 124/270 (45%), Gaps = 22/270 (8%)

Query: 13   QINQIPRRNAYTWCSAEQ-VMELFGDLYLHTIDIIKVLNPDASENNLKILNPIQNQCLRL 71
            ++N I      +W +  Q ++++     L  +D    +   A    LKIL  I N  +RL
Sbjct: 782  RLNIIKTLGHTSWEAKSQTLLKIHEAFILSKLDYGAPIFSSAKHTKLKILETIHNSGIRL 841

Query: 72   ATGAFCTTPIQALHLETNEPPLEIRRKILTFNYAAKVTSVPQHPCYKLLMFPKYVQNYKN 131
            + GAF ++PI+++      P LE+R +  T   AA+++  PQ+  +     PK+  N+  
Sbjct: 842  SIGAFRSSPIKSILNIAGIPSLEVRWREQTHKLAARISRSPQNHIH----HPKHTFNHTF 897

Query: 132  KKINTINVFLEEKFPLFKKIHTLTHPPPPPWTLDTPDLNFQLHIFTKKITSSPIIKSNFL 191
             K +  N+   EK            P  PPW   + ++N  LH F K  T   I K+ F 
Sbjct: 898  IKYDLENIIPYEK------------PLCPPWQF-SMNINIDLHQFPKNSTCPHIFKNAFR 944

Query: 192  AILQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEY 251
             I  +      IYTD S  E   G A +  +  I   + L  K SI+  E  AI  A+E+
Sbjct: 945  DICSHTHPQTHIYTDASIIEGRVGMAIICDETTI--QWKLSDKCSIYTAETLAILKAIEF 1002

Query: 252  LHHPNNNTVENYVIISDSQAALQAISNIYT 281
                 N++  N  I SDS +AL ++ N+Y+
Sbjct: 1003 TISEINDS--NITIFSDSLSALTSLQNLYS 1030

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

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

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.26.4	LOW CONFIDENCE prediction!
3rd Layer	3.1.26	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	316
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	6e-23
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	2e-05
pfam00075	126	pfam00075, RNase_H, RNase H	3e-05
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	4e-05
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	0.001
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	0.003

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

 Score = 91.6 bits (228), Expect = 6e-23
 Identities = 35/105 (33%), Positives = 48/105 (45%), Gaps = 11/105 (10%)

Query: 202 RIYTDGSKDEENAGCAFVIPDRN-ITKMFSLDPKSSIFACELYAIYAALEYL---HHPNN 257
            IYTDGSK E   G  F I  +  I++ + L P  S+F  EL AI  AL+          
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 258 NTVENYVIISDSQAALQAISNI---YTIQNQLITNIQTLNQGGFK 299
                  I SDSQAAL+A+ +      +  ++   I+ L   G K
Sbjct: 61  ----KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVK 101

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

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 25/107 (23%), Positives = 39/107 (36%), Gaps = 11/107 (10%)

Query: 204 YTDGSKDEE--NAGCAFVIPDRNI--TKMFSLD-PKSSIFACELYAIYAALEYLHHPNNN 258
            TDGS       AG   V+ D         SL  P ++    EL A+  ALE        
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60

Query: 259 TVENYVIISDSQAALQAISN---IYTIQNQLITNIQTLNQGGFKCEI 302
            +   +I +DS+  +  I++    +   N L+ +I  L         
Sbjct: 61  KL---IIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRF 104

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 123

>gnl|CDD|215695 pfam00075, RNase_H, RNase H

 Score = 42.6 bits (101), Expect = 3e-05
 Identities = 26/99 (26%), Positives = 39/99 (39%), Gaps = 17/99 (17%)

Query: 198 ETHVRIYTDGS--KDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHP 255
              V +YTDGS   +    G  +V  D    +   L   ++  A EL A+  ALE L   
Sbjct: 1   PEAVTVYTDGSCNGNPGPGGAGYVT-DGGKQRSKPLPGTTNQRA-ELLALIEALEALSG- 57

Query: 256 NNNTVENYVIISDSQAALQAI-------SNIYTIQNQLI 287
                +   I +DSQ  +  I       S    I+N++ 
Sbjct: 58  -----QKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIW 91

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|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and more complex than their prokaryotic counterparts and unlike prokaryote, RNase H are essential in higher eukaryote

 Score = 43.0 bits (102), Expect = 4e-05
 Identities = 24/127 (18%), Positives = 46/127 (36%), Gaps = 29/127 (22%)

Query: 203 IYTDGS-----KDEENAGCAFVI---PDRNITKMFSLDPKSSIFACELYAIYAALEYLHH 254
           +YTDG+     +    AG          RN+++     P+++  A EL A+  AL  +  
Sbjct: 2   VYTDGACRGNGRSGARAGYGVYFGPGHPRNVSERLPGPPQTNQRA-ELRAVIHALRLIKE 60

Query: 255 PNNNTVENYVIISDSQAALQAI--------------SNIYTIQNQ-----LITNIQTLNQ 295
                    VI +DS+  +  +              S    + N+     L   ++ L +
Sbjct: 61  VGEGLT-KLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKDLIKELDKLLEELEE 119

Query: 296 GGFKCEI 302
            G + + 
Sbjct: 120 RGIRVKF 126

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

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

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 9/81 (11%)

Query: 203 IYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHH-PNNNTVE 261
           ++TDGS     AG A V+   ++ ++ +L   +S    EL A+  ALE     P N    
Sbjct: 2   VFTDGSSFVRKAGYA-VVTGPDVLEIATLPYGTSAQRAELIALIRALELAKGKPVN---- 56

Query: 262 NYVIISDSQAALQAISNIYTI 282
              I +DS  A   +  + TI
Sbjct: 57  ---IYTDSAYAFGILHALETI 74

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 135

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

 Score = 37.3 bits (87), Expect = 0.003
 Identities = 18/89 (20%), Positives = 30/89 (33%), Gaps = 22/89 (24%)

Query: 200 HVRIYTDGSKDEEN--AGCAFVIPDRNITKMFSLDPKSSIFAC---------ELYAIYAA 248
            V I+TDG+        G   V+           D +  +            EL A+  A
Sbjct: 3   KVEIFTDGACLGNPGPGGWGAVL--------RYGDGEKELSGGEGRTTNNRAELRALIEA 54

Query: 249 LEYLHHPNNNTVENYVIISDSQAALQAIS 277
           LE L            + +DS+  ++ I+
Sbjct: 55  LEALKELG---ACEVTLYTDSKYVVEGIT 80

Length = 154

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	316
PRK08719	147	ribonuclease H; Reviewed	99.82
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.81
PRK06548	161	ribonuclease H; Provisional	99.81
PRK00203	150	rnhA ribonuclease H; Reviewed	99.78
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.76
PRK13907	128	rnhA ribonuclease H; Provisional	99.64
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.57
KOG3752|consensus	371		99.57
PRK07708	219	hypothetical protein; Validated	99.56
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.38
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	98.85
PF05380	159	Peptidase_A17: Pao retrotransposon peptidase ; Int	87.4

>PRK08719 ribonuclease H; Reviewed

Probab=99.82  E-value=1.6e-19  Score=149.78  Aligned_cols=110  Identities=23%  Similarity=0.319  Sum_probs=83.5

Q ss_pred             CceEEEEcCCCCC--C---CceEEEEEeCC--Ce--eEEEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcCh
Q psy17738        199 THVRIYTDGSKDE--E---NAGCAFVIPDR--NI--TKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDS  269 (316)
Q Consensus       199 ~~~~iytDGS~~~--~---~~G~a~~~~~~--~~--~~~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS  269 (316)
                      ..+.||||||+..  +   ..|+|+++...  ..  ..+.++....||++||+.|+..||+.+.+.       ..|+|||
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~-------~~i~tDS   75 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG-------DVIYSDS   75 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC-------CEEEech
Confidence            4689999999973  2   35888887543  32  234446666899999999999999998642       3799999


Q ss_pred             HHHHHHH--------hcccCCch-------HHHHHHHHHHhCC--------CCCCCcccHHHHHhhhhc
Q psy17738        270 QAALQAI--------SNIYTIQN-------QLITNIQTLNQGG--------FKCEILANTKTERLHMVL  315 (316)
Q Consensus       270 ~~ai~~i--------~~~~~~s~-------~i~~~~~~l~~~~--------~H~gi~gNe~AD~LAk~~  315 (316)
                      ++++++|        .+.|..++       ++++.+..+.+..        +|+|++|||.||+||+.+
T Consensus        76 ~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~~~~VkgH~g~~~Ne~aD~lA~~a  144 (147)
T PRK08719         76 DYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKVTAHSGIEGNEAADMLAQAA  144 (147)
T ss_pred             HHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEEEEEecCCCCChhHHHHHHHHHHH
Confidence            9999999        44554332       2556677666543        899999999999999975

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

Probab=99.81  E-value=2.5e-19  Score=147.84  Aligned_cols=112  Identities=21%  Similarity=0.204  Sum_probs=89.9

Q ss_pred             ceEEEEcCCCC--CCCceEEEEEeCCCeeE--EEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHH
Q psy17738        200 HVRIYTDGSKD--EENAGCAFVIPDRNITK--MFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQA  275 (316)
Q Consensus       200 ~~~iytDGS~~--~~~~G~a~~~~~~~~~~--~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~  275 (316)
                      .+.||||||+.  +|..|+|+|+..+...+  +.... .+||++||++|++.||+.+.+..   ...|.|+|||+++++.
T Consensus         3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~---~~~v~l~tDS~yv~~~   78 (154)
T COG0328           3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELG---ACEVTLYTDSKYVVEG   78 (154)
T ss_pred             ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcC---CceEEEEecHHHHHHH
Confidence            58999999998  68899999987544333  33344 89999999999999999998755   8999999999999999


Q ss_pred             Hhcc--------cCCc------h-HHHHHHHHHHhCC---------CCCCCcccHHHHHhhhhc
Q psy17738        276 ISNI--------YTIQ------N-QLITNIQTLNQGG---------FKCEILANTKTERLHMVL  315 (316)
Q Consensus       276 i~~~--------~~~s------~-~i~~~~~~l~~~~---------~H~gi~gNe~AD~LAk~~  315 (316)
                      |..+        |..+      + ++++.+.++.+..         ||.|.++||.||+||+.+
T Consensus        79 i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~  142 (154)
T COG0328          79 ITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREA  142 (154)
T ss_pred             HHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHH
Confidence            9944        1111      1 3677777776653         799999999999999864

>PRK06548 ribonuclease H; Provisional

Probab=99.81  E-value=2.2e-19  Score=150.53  Aligned_cols=112  Identities=18%  Similarity=0.186  Sum_probs=85.1

Q ss_pred             CCceEEEEcCCCC--CCCceEEEEEeCCCeeEEEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHH
Q psy17738        198 ETHVRIYTDGSKD--EENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQA  275 (316)
Q Consensus       198 ~~~~~iytDGS~~--~~~~G~a~~~~~~~~~~~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~  275 (316)
                      +..+.||||||+.  +|..|+|+++.+... .. .-....||+.|||+|++.||+.+...    ..+|.|+|||++++++
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~-~~-g~~~~~TNnraEl~Aii~aL~~~~~~----~~~v~I~TDS~yvi~~   76 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDENTW-DS-GGWDIATNNIAELTAVRELLIATRHT----DRPILILSDSKYVINS   76 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCCcE-Ec-cCCCCCCHHHHHHHHHHHHHHhhhcC----CceEEEEeChHHHHHH
Confidence            3458999999998  477899998854322 11 11246899999999999999866432    3579999999999999


Q ss_pred             Hhcc--------cC-Cch------HHHHHHHHHHhCC--------CCCCCcccHHHHHhhhhc
Q psy17738        276 ISNI--------YT-IQN------QLITNIQTLNQGG--------FKCEILANTKTERLHMVL  315 (316)
Q Consensus       276 i~~~--------~~-~s~------~i~~~~~~l~~~~--------~H~gi~gNe~AD~LAk~~  315 (316)
                      +..|        |. .++      ++++.|.++.+..        ||+|++|||.||+||+..
T Consensus        77 i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~v~~~wVkgHsg~~gNe~aD~LA~~a  139 (161)
T PRK06548         77 LTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSWVNAHTGHPLNEAADSLARQA  139 (161)
T ss_pred             HHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcCceEEEEEecCCCCHHHHHHHHHHHHH
Confidence            9953        32 222      3667777776653        799999999999999864

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.78  E-value=2.7e-18  Score=143.36  Aligned_cols=110  Identities=22%  Similarity=0.212  Sum_probs=82.7

Q ss_pred             ceEEEEcCCCC--CCCceEEEEEeCCCeeEEEe-CCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHHH
Q psy17738        200 HVRIYTDGSKD--EENAGCAFVIPDRNITKMFS-LDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAI  276 (316)
Q Consensus       200 ~~~iytDGS~~--~~~~G~a~~~~~~~~~~~~~-l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~i  276 (316)
                      .+.||||||+.  ++..|+|+|+..++....+. .....||++|||+|+..||+.+.+     ...+.|+|||++++++|
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~-----~~~v~I~tDS~yvi~~i   77 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE-----PCEVTLYTDSQYVRQGI   77 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC-----CCeEEEEECHHHHHHHH
Confidence            48999999998  46688888875443322222 234789999999999999998854     36799999999999999


Q ss_pred             hcc--------cCC-ch------HHHHHHHHHHhCC--------CCCCCcccHHHHHhhhh
Q psy17738        277 SNI--------YTI-QN------QLITNIQTLNQGG--------FKCEILANTKTERLHMV  314 (316)
Q Consensus       277 ~~~--------~~~-s~------~i~~~~~~l~~~~--------~H~gi~gNe~AD~LAk~  314 (316)
                      ..+        |.. ++      ++++.+.++.+..        +|+|++|||.||+||+.
T Consensus        78 ~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~wV~~H~~~~~N~~AD~lA~~  138 (150)
T PRK00203         78 TEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELARA  138 (150)
T ss_pred             HHHHHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEEEEecCCCCCHHHHHHHHHHHH
Confidence            963        322 22      2556666654432        79999999999999986

>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=99.76  E-value=1.9e-18  Score=140.42  Aligned_cols=109  Identities=28%  Similarity=0.303  Sum_probs=81.7

Q ss_pred             CceEEEEcCCCC--CCCceEEEEEeCCCeeEEEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHHH
Q psy17738        199 THVRIYTDGSKD--EENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAI  276 (316)
Q Consensus       199 ~~~~iytDGS~~--~~~~G~a~~~~~~~~~~~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~i  276 (316)
                      +.+.||||||+.  ++..|+|+++..+ ....+.++ ..|++.||++||..||+.+ .     ..++.|+|||+++++.|
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~-~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~-----~~~v~I~tDS~~v~~~l   73 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGG-RNFSFRLG-GQSNNRAELQAIIEALKAL-E-----HRKVTIYTDSQYVLNAL   73 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETT-EEEEEEEE-SECHHHHHHHHHHHHHHTH-S-----TSEEEEEES-HHHHHHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECC-eEEEeccc-ccchhhhheehHHHHHHHh-h-----cccccccccHHHHHHHH
Confidence            468999999987  4556888876555 34555566 8999999999999999954 3     38899999999999988


Q ss_pred             hc-----ccCCc--h-HHHHHHHHHHhCC---------CCCCC-cccHHHHHhhhhc
Q psy17738        277 SN-----IYTIQ--N-QLITNIQTLNQGG---------FKCEI-LANTKTERLHMVL  315 (316)
Q Consensus       277 ~~-----~~~~s--~-~i~~~~~~l~~~~---------~H~gi-~gNe~AD~LAk~~  315 (316)
                      ..     .+...  + .+...+.++...+         +|+|+ .|||.||+|||..
T Consensus        74 ~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a  130 (132)
T PF00075_consen   74 NKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEA  130 (132)
T ss_dssp             HTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHH
T ss_pred             HHhccccccccccccccchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHh
Confidence            88     34222  2 3555554443332         79999 6999999999964

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 ....

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.64  E-value=2.1e-15  Score=122.45  Aligned_cols=111  Identities=20%  Similarity=0.194  Sum_probs=87.5

Q ss_pred             eEEEEcCCCC--CCCceEEEEEeCCCee--EEEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHHH
Q psy17738        201 VRIYTDGSKD--EENAGCAFVIPDRNIT--KMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAI  276 (316)
Q Consensus       201 ~~iytDGS~~--~~~~G~a~~~~~~~~~--~~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~i  276 (316)
                      +.||||||+.  +|..|+|+|+.+....  ..+.. ...|++.||+.|++.||+.+.+..   ..++.|++||+.+++.+
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~-~~~tn~~AE~~All~aL~~a~~~g---~~~v~i~sDS~~vi~~~   77 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPL-GTMSNHEAEYHALLAALKYCTEHN---YNIVSFRTDSQLVERAV   77 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecc-cccCCcHHHHHHHHHHHHHHHhCC---CCEEEEEechHHHHHHH
Confidence            6899999998  4789999998664332  22223 467999999999999999998865   57899999999999999


Q ss_pred             hcccCCch---HHHHHHHHHHhCC-----CCCCCcccHHHHHhhhhc
Q psy17738        277 SNIYTIQN---QLITNIQTLNQGG-----FKCEILANTKTERLHMVL  315 (316)
Q Consensus       277 ~~~~~~s~---~i~~~~~~l~~~~-----~H~gi~gNe~AD~LAk~~  315 (316)
                      .+.+....   .+++.+..+.+..     -|+-.+.|+.||.||+..
T Consensus        78 ~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~~a  124 (128)
T PRK13907         78 EKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKA  124 (128)
T ss_pred             hHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCchhchhHHHHHHHH
Confidence            99775322   3566666666553     388889999999999864

>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=99.57  E-value=4.2e-14  Score=112.11  Aligned_cols=111  Identities=26%  Similarity=0.251  Sum_probs=85.2

Q ss_pred             EEEEcCCCCC--CCceEEEEEeCCCeeEEEe---CCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHHH
Q psy17738        202 RIYTDGSKDE--ENAGCAFVIPDRNITKMFS---LDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAI  276 (316)
Q Consensus       202 ~iytDGS~~~--~~~G~a~~~~~~~~~~~~~---l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~i  276 (316)
                      .+|||||...  +++|+|+++.+......+.   .....+++.+|+.|+..||+.+....   ..++.|++||+.+++.+
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~---~~~i~i~~Ds~~~~~~~   77 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELG---GKKVNIYTDSQYVINAL   77 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCC---CceEEEEECHHHHHHHh
Confidence            4899999984  5899999886643222221   22578999999999999999987654   78999999999999999


Q ss_pred             hcccCCc----hHHHHHHHHHHhCC---------CCCCCcccHHHHHhhhhc
Q psy17738        277 SNIYTIQ----NQLITNIQTLNQGG---------FKCEILANTKTERLHMVL  315 (316)
Q Consensus       277 ~~~~~~s----~~i~~~~~~l~~~~---------~H~gi~gNe~AD~LAk~~  315 (316)
                      .+.....    ..++..+.++.+.+         +|+|+.+|+.||.|||..
T Consensus        78 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~  129 (130)
T cd06222          78 TGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEA  129 (130)
T ss_pred             hccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhh
Confidence            9876422    23556666655332         699999999999999864

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

>KOG3752|consensus

Probab=99.57  E-value=1.6e-14  Score=132.98  Aligned_cols=114  Identities=22%  Similarity=0.226  Sum_probs=88.1

Q ss_pred             CCceEEEEcCCCCC-----CCceEEEEEeCCCe-eEEEeCC-CCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChH
Q psy17738        198 ETHVRIYTDGSKDE-----ENAGCAFVIPDRNI-TKMFSLD-PKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQ  270 (316)
Q Consensus       198 ~~~~~iytDGS~~~-----~~~G~a~~~~~~~~-~~~~~l~-~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~  270 (316)
                      .+...+|||||+..     ..+|+|||+.++.. ..+.++. ...|||+|||.|+..||+-+.+..   ..+++|.|||.
T Consensus       210 ~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~---~~kv~I~TDS~  286 (371)
T KOG3752|consen  210 IEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKN---INKVVIRTDSE  286 (371)
T ss_pred             ccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcC---CCcEEEEechH
Confidence            44589999999983     45999999977643 5666764 789999999999999999997754   56999999999


Q ss_pred             HHHHHHhccc---C-----Cc-h-H----------HHHHHHHHHhC-----------CCCCCCcccHHHHHhhhh
Q psy17738        271 AALQAISNIY---T-----IQ-N-Q----------LITNIQTLNQG-----------GFKCEILANTKTERLHMV  314 (316)
Q Consensus       271 ~ai~~i~~~~---~-----~s-~-~----------i~~~~~~l~~~-----------~~H~gi~gNe~AD~LAk~  314 (316)
                      ++++.|+.|-   .     .+ + +          .+..+.+|.+.           +||.|+.|||.||.||+.
T Consensus       287 ~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARk  361 (371)
T KOG3752|consen  287 YFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARK  361 (371)
T ss_pred             HHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhh
Confidence            9999999762   1     11 1 1          12334444333           389999999999999984

>PRK07708 hypothetical protein; Validated

Probab=99.56  E-value=3.3e-14  Score=125.34  Aligned_cols=119  Identities=18%  Similarity=0.147  Sum_probs=90.4

Q ss_pred             hcCCceEEEEcCCCC--CCCceEEEEEeC--CCeeE----EEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEc
Q psy17738        196 NYETHVRIYTDGSKD--EENAGCAFVIPD--RNITK----MFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIIS  267 (316)
Q Consensus       196 ~~~~~~~iytDGS~~--~~~~G~a~~~~~--~~~~~----~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~s  267 (316)
                      ..++.+.+|+|||..  ++++|+|+|+..  +....    ...++...||+.||+.|++.||+.+.+.+ .....|.|++
T Consensus        69 ~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g-~~~~~V~I~~  147 (219)
T PRK07708         69 EEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELG-VKHEPVTFRG  147 (219)
T ss_pred             cCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcC-CCcceEEEEe
Confidence            556789999999996  578999988854  33222    12355568999999999999999998764 2233589999


Q ss_pred             ChHHHHHHHhcccCCchH----HHHHHHHHHhCC------CCCCCcccHHHHHhhhhc
Q psy17738        268 DSQAALQAISNIYTIQNQ----LITNIQTLNQGG------FKCEILANTKTERLHMVL  315 (316)
Q Consensus       268 DS~~ai~~i~~~~~~s~~----i~~~~~~l~~~~------~H~gi~gNe~AD~LAk~~  315 (316)
                      ||+.+++.+.+.|...+.    +.+.+.++.+..      -|.....|+.||+||+.+
T Consensus       148 DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~A  205 (219)
T PRK07708        148 DSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQA  205 (219)
T ss_pred             ccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHHH
Confidence            999999999998865553    345555554432      288999999999999975

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.38  E-value=2.9e-12  Score=122.37  Aligned_cols=111  Identities=17%  Similarity=0.178  Sum_probs=87.4

Q ss_pred             ceEEEEcCCCC--CCCceEEEEEeCC--C-eeE--EEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHH
Q psy17738        200 HVRIYTDGSKD--EENAGCAFVIPDR--N-ITK--MFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAA  272 (316)
Q Consensus       200 ~~~iytDGS~~--~~~~G~a~~~~~~--~-~~~--~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~a  272 (316)
                      .+.||||||+.  +|..|+|+++.+.  . ...  ...++ .+||+.||+.|++.||+.+.+..   ..++.|++||+.+
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g---~~~v~i~~DS~lv   77 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELG---ATEVEVRMDSKLV   77 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCC---CCeEEEEeCcHHH
Confidence            37899999998  4678999988653  2 212  23344 78999999999999999998866   6789999999999


Q ss_pred             HHHHhcccCCchH----HHHHHHHHHhCC-----CCCCCcccHHHHHhhhh
Q psy17738        273 LQAISNIYTIQNQ----LITNIQTLNQGG-----FKCEILANTKTERLHMV  314 (316)
Q Consensus       273 i~~i~~~~~~s~~----i~~~~~~l~~~~-----~H~gi~gNe~AD~LAk~  314 (316)
                      ++.+.+.|...++    ++..+..+.+..     -|.-.++|+.||.||+.
T Consensus        78 i~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~  128 (372)
T PRK07238         78 VEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANE  128 (372)
T ss_pred             HHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHH
Confidence            9999988865542    445666666653     37778999999999986

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

Probab=98.85  E-value=7.9e-09  Score=77.22  Aligned_cols=76  Identities=21%  Similarity=0.206  Sum_probs=60.3

Q ss_pred             chHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHHHhcccCCc---hHHHHHHHHHHhCC-----CCCCCcccHHH
Q psy17738        237 IFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAISNIYTIQ---NQLITNIQTLNQGG-----FKCEILANTKT  308 (316)
Q Consensus       237 v~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~i~~~~~~s---~~i~~~~~~l~~~~-----~H~gi~gNe~A  308 (316)
                      +..||+.|+..||+++.+.+   ..+|.|.|||+.+++.|++.....   ..++..++.+.+..     -|.-.++|..|
T Consensus         1 ~~~aE~~al~~al~~a~~~g---~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~A   77 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELG---IRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPREQNKVA   77 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT----SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GGGSHHH
T ss_pred             CcHHHHHHHHHHHHHHHHCC---CCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChHHhHHH
Confidence            46899999999999999877   899999999999999999875322   24778888888775     39999999999


Q ss_pred             HHhhhhc
Q psy17738        309 ERLHMVL  315 (316)
Q Consensus       309 D~LAk~~  315 (316)
                      |.|||..
T Consensus        78 ~~LA~~a   84 (87)
T PF13456_consen   78 DALAKFA   84 (87)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999964

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

Probab=87.40  E-value=1.8  Score=36.19  Aligned_cols=67  Identities=13%  Similarity=0.234  Sum_probs=41.0

Q ss_pred             CceEEEEcCCCCCCCceEEEEEeC---CCeeEE--E---eC-C-CCCCchHHHHHHHHHHHHHhcCCC---CCCCCcEEE
Q psy17738        199 THVRIYTDGSKDEENAGCAFVIPD---RNITKM--F---SL-D-PKSSIFACELYAIYAALEYLHHPN---NNTVENYVI  265 (316)
Q Consensus       199 ~~~~iytDGS~~~~~~G~a~~~~~---~~~~~~--~---~l-~-~~~tv~~AEl~Ai~~Al~~~~~~~---~~~~~~i~I  265 (316)
                      ..+++|+|+|.  ...|+.+|...   +.....  +   +. + ...|+=+-||+|+..|.+++....   +....++.+
T Consensus        80 ~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~~~~l~~~~~~~~~  157 (159)
T PF05380_consen   80 VELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTVKKELDIEISQVVF  157 (159)
T ss_pred             eeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHHHHHcCCCcceeEE
Confidence            35899999994  45666666543   221111  1   11 1 245999999999999999874421   233556666


Q ss_pred             Ec
Q psy17738        266 IS  267 (316)
Q Consensus       266 ~s  267 (316)
                      +|
T Consensus       158 wt  159 (159)
T PF05380_consen  158 WT  159 (159)
T ss_pred             eC
Confidence            54

---

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	316
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	1e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	8e-04

>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 = 44.1 bits (104), Expect = 1e-05
 Identities = 19/72 (26%), Positives = 29/72 (40%), Gaps = 11/72 (15%)

Query: 203 IYTDGSKDEEN----AGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNN 258
            YTDGS   +     AG A V  +  +    +L   +S    EL A+  AL+       N
Sbjct: 26  WYTDGSSFLQEGQRRAGAA-VTTETEVIWARALPAGTSAQRAELIALTQALKMAEGKKLN 84

Query: 259 TVENYVIISDSQ 270
                 + +DS+
Sbjct: 85  ------VYTDSR 90

>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 = 42.9 bits (100), Expect = 1e-04
 Identities = 36/277 (12%), Positives = 78/277 (28%), Gaps = 75/277 (27%)

Query: 1   MRSAIDYTSMYRQINQIPRRNAYTWC----SAEQVMELFGDLYL--HTIDI-IKVL---- 49
             +  D    ++ +N                  +  ++F  L +   +  I   +L    
Sbjct: 340 GLATWDN---WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIW 396

Query: 50  NPDASENNLKILNPIQNQCLRLATGAFCTTPIQALHLETNEPPLE---IRRKILTFNYAA 106
                 + + ++N +    L        T  I +++LE          + R I+  +Y  
Sbjct: 397 FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVD-HYNI 455

Query: 107 KVTSVPQHPCYKLLMFPKYVQNY---------KNKKINTINVFLEEKFPLFKKI------ 151
             T           + P Y+  Y         KN +         E+  LF+ +      
Sbjct: 456 PKTFDSDD------LIPPYLDQYFYSHIGHHLKNIE-------HPERMTLFRMVFLDFRF 502

Query: 152 ------HTLTHPPPPPWTLDT-PDLNF-QLHIFTKKITSSPIIKS--NFLAILQNYETHV 201
                 H  T        L+T   L F + +I         ++ +  +F   L   E ++
Sbjct: 503 LEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDF---LPKIEENL 559

Query: 202 RIYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIF 238
                                 ++ ++  +    +IF
Sbjct: 560 ICS----------------KYTDLLRIALMAEDEAIF 580

>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 = 38.5 bits (90), Expect = 8e-04
 Identities = 15/82 (18%), Positives = 24/82 (29%), Gaps = 11/82 (13%)

Query: 196 NYETHVRIYTDGSKDEEN--AGCAFVIPDRNITKMFSLDP-----KSSIFACELYAIYAA 248
           +  T   +YTDGS          AFV   +   +   +            A E+ A   A
Sbjct: 2   DDRTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYA 61

Query: 249 LEYLHHPNNNTVENYVIISDSQ 270
           ++              I+ D  
Sbjct: 62  VKKASQLG----VKIRILHDYA 79

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	316
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.83
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.82
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.81
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.8
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.8
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.8
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.78
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.77
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.75
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.74
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.71
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.69
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.66
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.65
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.41
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.29

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

Probab=99.83  E-value=1.2e-20  Score=155.64  Aligned_cols=111  Identities=22%  Similarity=0.221  Sum_probs=85.1

Q ss_pred             CceEEEEcCCCCC--CCceEEEEEeCCCeeEE--EeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHH
Q psy17738        199 THVRIYTDGSKDE--ENAGCAFVIPDRNITKM--FSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQ  274 (316)
Q Consensus       199 ~~~~iytDGS~~~--~~~G~a~~~~~~~~~~~--~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~  274 (316)
                      ..+.||||||+..  |..|+|+|+..++....  ..+ ..+||+.||+.|++.||+.+.+     ..+|.|+|||+++++
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~-----~~~v~I~tDS~~vi~   76 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALKE-----PARVQLYSDSAYLVN   76 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS-----CCEEEEEESCHHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcCc-----cCcEEEEeChHHHHH
Confidence            4689999999983  56899998876543322  223 3689999999999999999865     578999999999999


Q ss_pred             HHhccc---------C------Cch-HHHHHHHHHHhCC--------CCCCCcccHHHHHhhhhc
Q psy17738        275 AISNIY---------T------IQN-QLITNIQTLNQGG--------FKCEILANTKTERLHMVL  315 (316)
Q Consensus       275 ~i~~~~---------~------~s~-~i~~~~~~l~~~~--------~H~gi~gNe~AD~LAk~~  315 (316)
                      .|.+.|         .      ..+ ++++.+.++.+..        ||+|++|||.||+|||..
T Consensus        77 ~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~~~v~~~~V~gH~g~~~N~~AD~LA~~a  141 (146)
T 3h08_A           77 AMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLHRVTFHKVKGHSDNPYNSRADELARLA  141 (146)
T ss_dssp             HHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHHSEEEEEECCC-CCSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhhCceEEEEcCCcCCcHhHHHHHHHHHHH
Confidence            999821         1      112 3666666665542        899999999999999964

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

Probab=99.82  E-value=2.3e-20  Score=155.27  Aligned_cols=115  Identities=21%  Similarity=0.250  Sum_probs=90.1

Q ss_pred             CCceEEEEcCCCCC-C----CceEEEEEeCCCe-eEEEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHH
Q psy17738        198 ETHVRIYTDGSKDE-E----NAGCAFVIPDRNI-TKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQA  271 (316)
Q Consensus       198 ~~~~~iytDGS~~~-~----~~G~a~~~~~~~~-~~~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~  271 (316)
                      .+.+.||||||+.. +    ..|+|+|+.++.. ..+..++..+||+.||+.|++.||+.+.+..   ..+|.|+|||++
T Consensus         5 ~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~---~~~v~i~tDS~~   81 (154)
T 2qkb_A            5 GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQN---INKLVLYTNSMF   81 (154)
T ss_dssp             TTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTT---CCEEEEEESCHH
T ss_pred             CCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCC---CceEEEEECcHH
Confidence            46799999999983 2    2799998865432 3455665578999999999999999997754   689999999999


Q ss_pred             HHHHHhcc--------cCC------ch-HHHHHHHHHHhCC--------CCCCCcccHHHHHhhhhc
Q psy17738        272 ALQAISNI--------YTI------QN-QLITNIQTLNQGG--------FKCEILANTKTERLHMVL  315 (316)
Q Consensus       272 ai~~i~~~--------~~~------s~-~i~~~~~~l~~~~--------~H~gi~gNe~AD~LAk~~  315 (316)
                      +++.|.++        |..      .+ ++++.+.++.+..        +|+|++|||.||+|||..
T Consensus        82 vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~~~v~~~~V~~H~g~~~N~~AD~LA~~a  148 (154)
T 2qkb_A           82 TINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLAREG  148 (154)
T ss_dssp             HHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTTCEEEEEECCTTSSCHHHHHHHHHHHHH
T ss_pred             HHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcCCceEEEEccCCCCCHhHHHHHHHHHHH
Confidence            99999974        221      12 3677777766542        799999999999999864

>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=99.81  E-value=1.4e-19  Score=149.79  Aligned_cols=109  Identities=25%  Similarity=0.273  Sum_probs=82.2

Q ss_pred             CCceEEEEcCCCC--CCCceEEEEEeCCCeeEEEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHH
Q psy17738        198 ETHVRIYTDGSKD--EENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQA  275 (316)
Q Consensus       198 ~~~~~iytDGS~~--~~~~G~a~~~~~~~~~~~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~  275 (316)
                      .+.+.||||||+.  +|..|+|+++.++.. ....+ ..+||+.||++|+..||+.+       ..++.|+|||++++++
T Consensus        10 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~-~~~~~-~~~Tnn~aEl~A~i~AL~~~-------~~~v~i~tDS~~v~~~   80 (150)
T 3qio_A           10 VGAETFYVDGAANRETKLGKAGYVTNRGRQ-KVVTL-TDTTNQKTELQAIYLALQDS-------GLEVNIVTDSQYALGI   80 (150)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCE-EEEEE-SSCCHHHHHHHHHHHHHHHS-------CSEEEEEESCHHHHHH
T ss_pred             CCCEEEEEccCCCCCCCCeEEEEEEEcCCE-EEEeC-CCCCHHHHHHHHHHHHHHhC-------CCcEEEEeCcHHHHHH
Confidence            4579999999997  466888888866543 23344 47899999999999999985       4789999999999999


Q ss_pred             Hhcc--------cCC------ch-HHHHHHHH-HHhCC--------CCCCCcccHHHHHhhhhc
Q psy17738        276 ISNI--------YTI------QN-QLITNIQT-LNQGG--------FKCEILANTKTERLHMVL  315 (316)
Q Consensus       276 i~~~--------~~~------s~-~i~~~~~~-l~~~~--------~H~gi~gNe~AD~LAk~~  315 (316)
                      |.++        |..      .+ ++++.+.+ +.+..        +|+|++|||+||+||++.
T Consensus        81 i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a  144 (150)
T 3qio_A           81 ITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAG  144 (150)
T ss_dssp             HHHHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHH
Confidence            9986        111      12 24555443 33321        799999999999999974

>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=99.80  E-value=1e-19  Score=151.50  Aligned_cols=110  Identities=22%  Similarity=0.226  Sum_probs=85.6

Q ss_pred             ceEEEEcCCCC--CCCceEEEEEeCCCeeE--EEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHH
Q psy17738        200 HVRIYTDGSKD--EENAGCAFVIPDRNITK--MFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQA  275 (316)
Q Consensus       200 ~~~iytDGS~~--~~~~G~a~~~~~~~~~~--~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~  275 (316)
                      .+.||||||+.  ++..|+|+|+...+...  +..+ ..+||+.||+.|+..||+.+.+     ..++.|+|||+++++.
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~-----~~~v~I~tDS~~vi~~   77 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE-----HAEVILSTDSQYVRQG   77 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS-----CCEEEEEECCHHHHHH
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc-----CCcEEEEeCHHHHHHH
Confidence            58999999998  35689999886544322  2223 3679999999999999999865     3789999999999999


Q ss_pred             Hhcc--------cCC------ch-HHHHHHHHHHhCC--------CCCCCcccHHHHHhhhhc
Q psy17738        276 ISNI--------YTI------QN-QLITNIQTLNQGG--------FKCEILANTKTERLHMVL  315 (316)
Q Consensus       276 i~~~--------~~~------s~-~i~~~~~~l~~~~--------~H~gi~gNe~AD~LAk~~  315 (316)
                      |.+|        |..      .+ ++++.+.++.+..        ||+|++|||.||+||+..
T Consensus        78 i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a  140 (155)
T 1jl1_A           78 ITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAA  140 (155)
T ss_dssp             HHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcccccccCCccCCHHHHHHHHHHHccCceEEEEcCCCCCCHHHHHHHHHHHHH
Confidence            9972        321      12 4667777776542        899999999999999864

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

Probab=99.80  E-value=1.2e-19  Score=151.55  Aligned_cols=111  Identities=24%  Similarity=0.203  Sum_probs=86.0

Q ss_pred             CceEEEEcCCCC--CCCceEEEEEeCCCeeE--EEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHH
Q psy17738        199 THVRIYTDGSKD--EENAGCAFVIPDRNITK--MFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQ  274 (316)
Q Consensus       199 ~~~~iytDGS~~--~~~~G~a~~~~~~~~~~--~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~  274 (316)
                      ..+.||||||+.  ++..|+|+|+.+++...  +..+ ..+||+.||+.|+..||+.+.+     ..+|.|+|||+++++
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~-----~~~v~I~tDS~~vi~   78 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKE-----PCKIILTSDSQYMRQ   78 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS-----CCEEEEEECCHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhcc-----CCeEEEEeCHHHHHH
Confidence            458999999998  46689999886544322  2223 3579999999999999998854     378999999999999


Q ss_pred             HHhc--------ccCC------ch-HHHHHHHHHHhCC--------CCCCCcccHHHHHhhhhc
Q psy17738        275 AISN--------IYTI------QN-QLITNIQTLNQGG--------FKCEILANTKTERLHMVL  315 (316)
Q Consensus       275 ~i~~--------~~~~------s~-~i~~~~~~l~~~~--------~H~gi~gNe~AD~LAk~~  315 (316)
                      .|.+        .|..      .+ ++++.+.++.+..        ||+|++|||.||+||+..
T Consensus        79 ~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LAk~a  142 (158)
T 2e4l_A           79 GIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQLHQIDWRWVKGHAGHAENERCDQLARAA  142 (158)
T ss_dssp             HHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTTSEEEEEECCTTCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHccCcEEEEEccCCCCchhHHHHHHHHHHH
Confidence            9998        3321      12 4667777776542        899999999999999864

>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=99.80  E-value=4e-20  Score=152.68  Aligned_cols=114  Identities=14%  Similarity=0.022  Sum_probs=86.0

Q ss_pred             CCceEEEEcCCCCCCCceEEEEEeCCCee--EEE-eC--CC--CCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChH
Q psy17738        198 ETHVRIYTDGSKDEENAGCAFVIPDRNIT--KMF-SL--DP--KSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQ  270 (316)
Q Consensus       198 ~~~~~iytDGS~~~~~~G~a~~~~~~~~~--~~~-~l--~~--~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~  270 (316)
                      ++.+.||||||+..|..|+|+|+.+++..  .+. +.  +.  .+||+.||++|++.||+.+.+..   . +|.|+|||+
T Consensus         4 ~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~---~-~v~I~tDS~   79 (147)
T 2kq2_A            4 RTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLG---V-KIRILHDYA   79 (147)
T ss_dssp             TSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHT---C-CCCBSSCCS
T ss_pred             CCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCC---C-eEEEEECcH
Confidence            46789999999999889999998654432  223 22  22  36999999999999999876643   3 899999999


Q ss_pred             HHHHHHhcccCCchH-HH---HHHHHHHhC------CCCCCCcccHHHHHhhhhc
Q psy17738        271 AALQAISNIYTIQNQ-LI---TNIQTLNQG------GFKCEILANTKTERLHMVL  315 (316)
Q Consensus       271 ~ai~~i~~~~~~s~~-i~---~~~~~l~~~------~~H~gi~gNe~AD~LAk~~  315 (316)
                      .+.+.+.+.|..+.. ..   +.+++|.+.      .+|+|++|||+||+|||+.
T Consensus        80 ~i~~w~~~~w~~~~~~~~~~~~l~~~l~~~v~~~wV~gH~g~~~Ne~AD~LA~~a  134 (147)
T 2kq2_A           80 GIAFWATGEWKAKNEFTQAYAKLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAKSA  134 (147)
T ss_dssp             THHHHTTSSSSCCHHHHHHHHCGGGGGSTTCCBCCCCCCCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCccCCcchHHHHHHHHHhcCCeeEEEecCcCCCcchHHHHHHHHHH
Confidence            988888887866553 22   333343322      2799999999999999864

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

Probab=99.78  E-value=2.2e-19  Score=151.18  Aligned_cols=112  Identities=18%  Similarity=0.121  Sum_probs=85.0

Q ss_pred             CceEEEEcCCCC--CCCceEEEEEeCCCeeEEEeC-CCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHH
Q psy17738        199 THVRIYTDGSKD--EENAGCAFVIPDRNITKMFSL-DPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQA  275 (316)
Q Consensus       199 ~~~~iytDGS~~--~~~~G~a~~~~~~~~~~~~~l-~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~  275 (316)
                      ..+.||||||+.  ++..|+|+|+.+++....+.. ...+||+.||+.|++.||+.+.+     ..+|.|+|||+++++.
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~-----~~~v~I~tDS~~vi~~   81 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE-----PCEVDLYTDSHYLKKA   81 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS-----CCEEEEECCCHHHHHH
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHhcc-----CCeEEEEeChHHHHHH
Confidence            468999999998  356899999865432222221 13679999999999999998865     3589999999999999


Q ss_pred             Hhc-c--------cCC------ch-HHHHHHHHHHhCC--------CCCCCcccHHHHHhhhhc
Q psy17738        276 ISN-I--------YTI------QN-QLITNIQTLNQGG--------FKCEILANTKTERLHMVL  315 (316)
Q Consensus       276 i~~-~--------~~~------s~-~i~~~~~~l~~~~--------~H~gi~gNe~AD~LAk~~  315 (316)
                      |.+ |        |..      .+ ++++.+.++.+..        ||+|++|||.||+|||+.
T Consensus        82 i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LAk~a  145 (166)
T 1ril_A           82 FTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQ  145 (166)
T ss_dssp             HHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCCCGGGSCTHHHHHHHHHHHH
T ss_pred             HhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHhcCeEEEEEeeCCCCchhHHHHHHHHHHH
Confidence            998 2        321      12 3677777766542        799999999999999864

>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=99.77  E-value=8.7e-19  Score=147.17  Aligned_cols=110  Identities=19%  Similarity=0.136  Sum_probs=81.6

Q ss_pred             ceEEEEcCCCC--CCCceEEEEEeCCC-eeEEEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHHH
Q psy17738        200 HVRIYTDGSKD--EENAGCAFVIPDRN-ITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAI  276 (316)
Q Consensus       200 ~~~iytDGS~~--~~~~G~a~~~~~~~-~~~~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~i  276 (316)
                      .+.||||||+.  +|..|+|+++..++ ......+...+||++||++|+..||+.+ .     ..++.|+|||++++++|
T Consensus        23 ~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~-~-----~~~v~I~tDS~~vi~~i   96 (165)
T 3p1g_A           23 DYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA-E-----GKKLNVYTDSRYAFATA   96 (165)
T ss_dssp             SEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT-B-----TSEEEEEECCHHHHHHH
T ss_pred             CEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc-c-----CceEEEEEchHHHHhhh
Confidence            58999999998  67788888775543 3223345668899999999999999998 2     57899999999999999


Q ss_pred             hcc---cCCch-HHHHHH-HHHHhCC--------CCCC-----CcccHHHHHhhhhc
Q psy17738        277 SNI---YTIQN-QLITNI-QTLNQGG--------FKCE-----ILANTKTERLHMVL  315 (316)
Q Consensus       277 ~~~---~~~s~-~i~~~~-~~l~~~~--------~H~g-----i~gNe~AD~LAk~~  315 (316)
                      -..   .+..+ ++++.+ +++.+..        ||+|     ++|||.||+|||+.
T Consensus        97 w~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~a  153 (165)
T 3p1g_A           97 HVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREA  153 (165)
T ss_dssp             HSCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHH
T ss_pred             hcccCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHH
Confidence            211   11222 344444 4443321        8999     99999999999864

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

Probab=99.75  E-value=1.3e-18  Score=141.42  Aligned_cols=112  Identities=21%  Similarity=0.252  Sum_probs=86.9

Q ss_pred             ceEEEEcCCCC--CCCceEEEEEeC--CCee--EEEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCC----cEEEEcCh
Q psy17738        200 HVRIYTDGSKD--EENAGCAFVIPD--RNIT--KMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVE----NYVIISDS  269 (316)
Q Consensus       200 ~~~iytDGS~~--~~~~G~a~~~~~--~~~~--~~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~----~i~I~sDS  269 (316)
                      .+.||||||+.  +|..|+|+++.+  +...  .+..++ .+||+.||+.|+..||+.+.+..   ..    ++.|+|||
T Consensus         3 ~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~---~~~~~~~v~i~tDS   78 (140)
T 3u3g_D            3 KIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIG-ETTNNVAEYEALIRALEDLQMFG---DKLVDMEVEVRMDS   78 (140)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEE-EECHHHHHHHHHHHHHHHHGGGG---GGGTTCEEEEEESC
T ss_pred             eEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCC-CCchHHHHHHHHHHHHHHHHHcC---CCCCCceEEEEeCh
Confidence            58999999998  467899999865  3332  222233 57999999999999999997754   44    99999999


Q ss_pred             HHHHHHHhcccCCch----HHHHHHHHH-HhCC-----CCCCCcccHHHHHhhhhc
Q psy17738        270 QAALQAISNIYTIQN----QLITNIQTL-NQGG-----FKCEILANTKTERLHMVL  315 (316)
Q Consensus       270 ~~ai~~i~~~~~~s~----~i~~~~~~l-~~~~-----~H~gi~gNe~AD~LAk~~  315 (316)
                      +++++.+.++|+..+    ++++.+.++ .+..     .|+-.+|||.||+|||..
T Consensus        79 ~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~~~N~~AD~LA~~a  134 (140)
T 3u3g_D           79 ELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEA  134 (140)
T ss_dssp             HHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCGGGGHHHHHHHHHH
T ss_pred             HHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCchhhHHHHHHHHHH
Confidence            999999999886444    245566666 4442     488899999999999863

>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=99.74  E-value=2.5e-18  Score=140.20  Aligned_cols=112  Identities=18%  Similarity=0.173  Sum_probs=87.6

Q ss_pred             ceEEEEcCCCC--CCCceEEEEEeCC---Cee--EEEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHH
Q psy17738        200 HVRIYTDGSKD--EENAGCAFVIPDR---NIT--KMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAA  272 (316)
Q Consensus       200 ~~~iytDGS~~--~~~~G~a~~~~~~---~~~--~~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~a  272 (316)
                      .++||||||+.  +|..|+|+++.+.   ...  ....++ .+||+.||+.|++.||+.+.+..   ..++.|+|||+++
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~---~~~v~i~tDS~~v   78 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIG-RATNNVAEYRGLIAGLDDAVKLG---ATEAAVLMDSKLV   78 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEE-EECHHHHHHHHHHHHHHHHHHHT---CSEEEEEESCHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCC-CCchHHHHHHHHHHHHHHHHHCC---CceEEEEeChHHH
Confidence            48999999998  4678999988653   222  222233 78999999999999999998755   6889999999999


Q ss_pred             HHHHhcccCCchH----HHHHHHHHHhCC-----CCCCCcccHHHHHhhhhc
Q psy17738        273 LQAISNIYTIQNQ----LITNIQTLNQGG-----FKCEILANTKTERLHMVL  315 (316)
Q Consensus       273 i~~i~~~~~~s~~----i~~~~~~l~~~~-----~H~gi~gNe~AD~LAk~~  315 (316)
                      ++.+.+.|...+.    +++.++++.+.+     .|+-.+|||.||+||+..
T Consensus        79 v~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~~~N~~AD~LA~~a  130 (141)
T 3hst_B           79 VEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLANDA  130 (141)
T ss_dssp             HHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCGGGCHHHHHHHHHH
T ss_pred             HHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCCcccHHHHHHHHHH
Confidence            9999998755543    345566666553     488889999999999863

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

Probab=99.71  E-value=2.2e-17  Score=138.51  Aligned_cols=112  Identities=16%  Similarity=0.110  Sum_probs=79.9

Q ss_pred             CceEEEEcCCCC--CCC-----ceEEEEEeCCC----eeEEEeCC-CCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEE
Q psy17738        199 THVRIYTDGSKD--EEN-----AGCAFVIPDRN----ITKMFSLD-PKSSIFACELYAIYAALEYLHHPNNNTVENYVII  266 (316)
Q Consensus       199 ~~~~iytDGS~~--~~~-----~G~a~~~~~~~----~~~~~~l~-~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~  266 (316)
                      ..+.|||||||.  +|+     .|+|+|+..++    ....+..+ ...+++.||+.|+..||+.+...    +.+|.|+
T Consensus         6 ~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~----~~~v~I~   81 (165)
T 2lsn_A            6 YEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKI----PGPVLVI   81 (165)
T ss_dssp             CSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHS----SSCEEEE
T ss_pred             ceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcC----CCeEEEE
Confidence            458999999998  344     79999885432    23333332 45778889999998888876553    4679999


Q ss_pred             cChHHHHHHHhcc--------cCC------ch-HHHHHHHHHH-hC--------CCCCCC------cccHHHHHhhhh
Q psy17738        267 SDSQAALQAISNI--------YTI------QN-QLITNIQTLN-QG--------GFKCEI------LANTKTERLHMV  314 (316)
Q Consensus       267 sDS~~ai~~i~~~--------~~~------s~-~i~~~~~~l~-~~--------~~H~gi------~gNe~AD~LAk~  314 (316)
                      |||++++++|..|        |..      .+ ++++.+.++. ..        .||.|+      +|||+||+||++
T Consensus        82 TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~  159 (165)
T 2lsn_A           82 TDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQ  159 (165)
T ss_dssp             ESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHH
T ss_pred             eChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHH
Confidence            9999999999864        221      12 4666666543 33        179984      689999999986

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

Probab=99.69  E-value=4.3e-17  Score=134.51  Aligned_cols=112  Identities=18%  Similarity=0.189  Sum_probs=85.3

Q ss_pred             eEEEEcCCCC---CCCceE-EEEEeCC-CeeEEEe--CC---CCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChH
Q psy17738        201 VRIYTDGSKD---EENAGC-AFVIPDR-NITKMFS--LD---PKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQ  270 (316)
Q Consensus       201 ~~iytDGS~~---~~~~G~-a~~~~~~-~~~~~~~--l~---~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~  270 (316)
                      +.||||||+.   +|+.|+ |+++.++ .....+.  ++   ..+||+.||+.|+..||+.+.+..   ..++.|+|||+
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g---~~~v~i~tDS~   78 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLG---ISSPIIKGDSQ   78 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHT---CCSCEEEESCH
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcC---CCEEEEEeChH
Confidence            6899999997   377886 9888653 3323232  33   378999999999999999998754   57899999999


Q ss_pred             HHHHHHhcccCCch----HHHHHHHHHHhCC----CCCCCcccHHHHHhhhhc
Q psy17738        271 AALQAISNIYTIQN----QLITNIQTLNQGG----FKCEILANTKTERLHMVL  315 (316)
Q Consensus       271 ~ai~~i~~~~~~s~----~i~~~~~~l~~~~----~H~gi~gNe~AD~LAk~~  315 (316)
                      ++++.+.++|..++    .+++.+..+.+..    .|+-.++||.||+||+..
T Consensus        79 ~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~~v~~~~V~~~~N~~AD~LA~~a  131 (149)
T 2ehg_A           79 LVIKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPREENKEADRLSRVA  131 (149)
T ss_dssp             HHHHHHTTSSCCCCTTHHHHHHHHHHHHHHHTCEEEECCGGGCHHHHHHHHHH
T ss_pred             HHHHHHhCccccCCHHHHHHHHHHHHHHhcCCEEEEEcCCcccHHHHHHHHHH
Confidence            99999999876443    3555555554432    377779999999999864

>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=99.66  E-value=2.1e-16  Score=156.75  Aligned_cols=109  Identities=20%  Similarity=0.179  Sum_probs=84.2

Q ss_pred             CCceEEEEcCCCC--CCCceEEEEEeCCCeeEEEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHH
Q psy17738        198 ETHVRIYTDGSKD--EENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQA  275 (316)
Q Consensus       198 ~~~~~iytDGS~~--~~~~G~a~~~~~~~~~~~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~  275 (316)
                      .+.+.||||||+.  +|..|+|+++..++.. ...++ .+||+.||+.|++.||+.    .   ..++.|+|||+++++.
T Consensus       434 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~-~~~~~-~~TNn~aEl~A~i~aL~~----~---~~~v~I~tDS~~v~~~  504 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDK-VKKLE-QTTNQQAELEAFAMALTD----S---GPKVNIIVDSQYVMGI  504 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEE-EEEES-SCCHHHHHHHHHHHHHHT----S---CSEEEEEESCHHHHHH
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCCEe-eccCC-CCCHHHHHHHHHHHHHHc----C---CCeEEEEEehHHHHHH
Confidence            3569999999998  3457888888665432 33343 689999999999999997    2   5789999999999999


Q ss_pred             HhcccCCch-HHHHHHH-HHHhCC--------CCCCCcccHHHHHhhhhc
Q psy17738        276 ISNIYTIQN-QLITNIQ-TLNQGG--------FKCEILANTKTERLHMVL  315 (316)
Q Consensus       276 i~~~~~~s~-~i~~~~~-~l~~~~--------~H~gi~gNe~AD~LAk~~  315 (316)
                      |.++...++ .+++.+. .+.+..        +|+|++|||+||+||++.
T Consensus       505 i~~~~~~~~~~l~~~~~~~~~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  554 (555)
T 1mu2_A          505 VASQPTESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQG  554 (555)
T ss_dssp             HHTCCSEESCHHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHHTT
T ss_pred             HhcccccccHHHHHHHHHHhccCCcEEEEEEECCCCChhHHHHHHHHHhh
Confidence            999765455 3554443 334432        799999999999999974

>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=99.65  E-value=1.7e-16  Score=157.61  Aligned_cols=109  Identities=24%  Similarity=0.239  Sum_probs=83.4

Q ss_pred             CCceEEEEcCCCC--CCCceEEEEEeCCCeeEEEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHH
Q psy17738        198 ETHVRIYTDGSKD--EENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQA  275 (316)
Q Consensus       198 ~~~~~iytDGS~~--~~~~G~a~~~~~~~~~~~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~  275 (316)
                      .+.+.||||||+.  +|..|+|+++.++.. ..+.. ..+||+.||+.|++.||+.+       ..++.|+|||++|++.
T Consensus       437 ~~~~~iytDGs~~~n~g~~g~g~v~~~~~~-~~~~~-~~~TNn~aEl~Ai~~aL~~~-------~~~v~I~tDS~~vi~~  507 (557)
T 2zd1_A          437 VGAETFYVDGAANRETKLGKAGYVTNKGRQ-KVVPL-TNTTNQKTELQAIYLALQDS-------GLEVNIVTDSQYALGI  507 (557)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEETTSCE-EEEEE-CSCCHHHHHHHHHHHHHHHS-------CSEEEEEECCHHHHHH
T ss_pred             CCCEEEEEccCCCCCCCceEEEEEEECCcE-EEecC-CCCCHHHHHHHHHHHHHHhC-------CCcEEEEeChHHHHHH
Confidence            3468999999997  355788888865543 23343 37899999999999999998       3789999999999999


Q ss_pred             HhcccCCch-HHHHH-HHHHHhCC--------CCCCCcccHHHHHhhhhc
Q psy17738        276 ISNIYTIQN-QLITN-IQTLNQGG--------FKCEILANTKTERLHMVL  315 (316)
Q Consensus       276 i~~~~~~s~-~i~~~-~~~l~~~~--------~H~gi~gNe~AD~LAk~~  315 (316)
                      |.++...++ ++++. ++.+.+..        +|+|++|||+||+||++.
T Consensus       508 i~~~~~~~~~~l~~~~~~~l~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          508 IQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             HTTCCSEESSHHHHHHHHHHHHCSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             HhcCCccCCHHHHHHHHHHHhcCCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            999876544 45544 34555542        799999999999999863

>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=99.41  E-value=4.4e-14  Score=115.40  Aligned_cols=108  Identities=16%  Similarity=0.101  Sum_probs=79.1

Q ss_pred             CCceEEEEcCCCC--CCCceEEEEEeCCCeeEEEeCC-CCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHH
Q psy17738        198 ETHVRIYTDGSKD--EENAGCAFVIPDRNITKMFSLD-PKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQ  274 (316)
Q Consensus       198 ~~~~~iytDGS~~--~~~~G~a~~~~~~~~~~~~~l~-~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~  274 (316)
                      .+.+.||||||+.  +|..|+|+|+..+......+.+ ..+||+.||++|++.||+.+.+..   . ++.|+|||+++++
T Consensus         9 ~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~~~TNN~aEl~A~i~aL~~~~~~~---~-~v~i~tDS~~vi~   84 (142)
T 1zbf_A            9 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN---S-RKPIYSNSQTAIK   84 (142)
T ss_dssp             CCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTT---C-CCCEEESCHHHHH
T ss_pred             CCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccCCcCcHHHHHHHHHHHHHHHHhCC---C-eEEEEEehHHHHH
Confidence            4568999999997  5778999998643332222211 257999999999999999998754   3 8999999999999


Q ss_pred             HHhcccC-C------ch-HHHHHHHHH----HhCC-------CCCCCcccHHHH
Q psy17738        275 AISNIYT-I------QN-QLITNIQTL----NQGG-------FKCEILANTKTE  309 (316)
Q Consensus       275 ~i~~~~~-~------s~-~i~~~~~~l----~~~~-------~H~gi~gNe~AD  309 (316)
                      .+.+.+. .      .+ ++.+.++++    ....       +|.+.-||.-||
T Consensus        85 w~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~~~~~~~~~kw~~~~~ge~pad  138 (142)
T 1zbf_A           85 WVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  138 (142)
T ss_dssp             HHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             HHHcCCccCCCCCCcccHHHHHHHHHHHHHHhhCCCceeEEEeccCccCcCccc
Confidence            9998762 1      12 355554443    3332       788888998888

>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=99.29  E-value=1.9e-12  Score=104.04  Aligned_cols=77  Identities=18%  Similarity=0.085  Sum_probs=59.5

Q ss_pred             CCceEEEEcCCCC--CCCceEEEEEeCCCe-e-EEEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHH
Q psy17738        198 ETHVRIYTDGSKD--EENAGCAFVIPDRNI-T-KMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAAL  273 (316)
Q Consensus       198 ~~~~~iytDGS~~--~~~~G~a~~~~~~~~-~-~~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai  273 (316)
                      +....||||||+.  +|..|+|+|+.+... . ....++ .+||+.||++|++.||+.+.+..    .++.|+|||++++
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~~-~tTNN~aEl~A~i~aL~~l~~~~----~~v~i~tDSqyVi   77 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKERN----SRKPIYSNSQTAI   77 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEEE-EECHHHHHHHHHHHHHHHHHHTT----CCCCEEESCHHHH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCCC-CCchHHHHHHHHHHHHHHHHhCC----CCEEEEcchHHHH
Confidence            4567899999998  577888666654332 2 222233 78999999999999999997743    3489999999999


Q ss_pred             HHHhcc
Q psy17738        274 QAISNI  279 (316)
Q Consensus       274 ~~i~~~  279 (316)
                      +.|.++
T Consensus        78 ~wi~~~   83 (134)
T 4htu_A           78 KWVKDK   83 (134)
T ss_dssp             HHHHHT
T ss_pred             HHHHcC
Confidence            999875

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	316
d1s1ta1	110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	0.002

>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]} Length = 110

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]

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 18/80 (22%), Positives = 26/80 (32%), Gaps = 7/80 (8%)

Query: 203 IYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVEN 262
            Y DG+ + E              +       ++    EL AIY AL+            
Sbjct: 11  FYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLE------- 63

Query: 263 YVIISDSQAALQAISNIYTI 282
             I++DSQ AL  I      
Sbjct: 64  VNIVTDSQYALGIIQAQPDQ 83

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	316
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.85
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.78
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.77
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.54
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.51

>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=99.85  E-value=2.2e-21  Score=154.21  Aligned_cols=108  Identities=21%  Similarity=0.165  Sum_probs=82.5

Q ss_pred             CceEEEEcCCCC-C-CCceEEEEEeCCCeeEEEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHHH
Q psy17738        199 THVRIYTDGSKD-E-ENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAI  276 (316)
Q Consensus       199 ~~~~iytDGS~~-~-~~~G~a~~~~~~~~~~~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~i  276 (316)
                      +...||||||+. + +..|+|++++.+.. ....++ ..||++||+.||.+||+..       ..++.|+|||+++++.+
T Consensus         6 ~~~t~YTDGS~~~n~~~~~~g~~~~~~~~-~~~~~~-~~tnn~AEl~Ai~~al~~~-------~~~i~I~tDS~~v~~~~   76 (126)
T d1mu2a1           6 GAETFYTDGSCNRQSKEGKAGYVTDRGKD-KVKKLE-QTTNQQAELEAFAMALTDS-------GPKVNIIVDSQYVMGIV   76 (126)
T ss_dssp             TCEEEEEEEEECTTTCCEEEEEEETTSCE-EEEEES-SCCHHHHHHHHHHHHHHTS-------CSEEEEEESCHHHHHHH
T ss_pred             CCcEEEEcCCCCCCCCcEEEEEEecCCCE-EEEecC-CCcchHHHHHHHHHHhccC-------CcceEEEechHHHHHHH
Confidence            457899999987 3 44566666655543 334454 6799999999999999853       57899999999999999


Q ss_pred             hcccCCch-H-HHHHHHHHHhCC--------CCCCCcccHHHHHhhhhc
Q psy17738        277 SNIYTIQN-Q-LITNIQTLNQGG--------FKCEILANTKTERLHMVL  315 (316)
Q Consensus       277 ~~~~~~s~-~-i~~~~~~l~~~~--------~H~gi~gNe~AD~LAk~~  315 (316)
                      .+++..+. + ..+.++.+.+..        +|+|++|||+||+||++.
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~v~~~wV~gH~g~~gNe~AD~LA~~a  125 (126)
T d1mu2a1          77 ASQPTESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQG  125 (126)
T ss_dssp             HTCCSEESCHHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHHTT
T ss_pred             hcCCccccchHHHHHHHHhhhcceeEEEEEeCCCCCcchHHHHHHHHhh
Confidence            99875443 3 445566665552        899999999999999973

>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=99.78  E-value=7.1e-20  Score=149.03  Aligned_cols=111  Identities=17%  Similarity=0.086  Sum_probs=81.7

Q ss_pred             ceEEEEcCCCCC--CCceEEEEEeCCCe-eEEEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHHH
Q psy17738        200 HVRIYTDGSKDE--ENAGCAFVIPDRNI-TKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAI  276 (316)
Q Consensus       200 ~~~iytDGS~~~--~~~G~a~~~~~~~~-~~~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~i  276 (316)
                      .+.||||||+..  |..|+|+|+..... .........+||++||+.|+..||+++..     ...+.|++||+++++++
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~-----~~~i~i~tds~~~~~~~   77 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE-----PCEVDLYTDSHYLKKAF   77 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS-----CCEEEEECCCHHHHHHH
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhccC-----CceEEEecchhhhhccc
Confidence            589999999984  45788888754432 22222223579999999999999997644     56899999999999998


Q ss_pred             hccc----------CCc-----h-HHHHHHHHHHhCC--------CCCCCcccHHHHHhhhhc
Q psy17738        277 SNIY----------TIQ-----N-QLITNIQTLNQGG--------FKCEILANTKTERLHMVL  315 (316)
Q Consensus       277 ~~~~----------~~s-----~-~i~~~~~~l~~~~--------~H~gi~gNe~AD~LAk~~  315 (316)
                      ...+          ...     + ++++.+..+.+..        ||+|++|||.||+|||..
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~~~~v~~~wVkgHsg~~gNe~AD~LAk~a  140 (147)
T d1rila_          78 TEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQ  140 (147)
T ss_dssp             HSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCCCGGGSCTHHHHHHHHHHHH
T ss_pred             cccchhhhhhccccccccccchhHHHHHHHHHHhhhcccceEEccCCCCCcchHHHHHHHHHH
Confidence            7642          111     1 3556666655542        799999999999999963

>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=99.77  E-value=3.2e-19  Score=145.54  Aligned_cols=111  Identities=23%  Similarity=0.222  Sum_probs=83.1

Q ss_pred             ceEEEEcCCCCC--CCceEEEEEeCCCeeEEEeC-CCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHHH
Q psy17738        200 HVRIYTDGSKDE--ENAGCAFVIPDRNITKMFSL-DPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAI  276 (316)
Q Consensus       200 ~~~iytDGS~~~--~~~G~a~~~~~~~~~~~~~l-~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~i  276 (316)
                      .+.||||||+..  |..|+|+|+..++....+.. .+..|++.||++|+..|++++..     ...+.|++||++++..+
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~~-----~~~i~i~tds~~~i~~~   76 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKE-----HAEVILSTDSQYVRQGI   76 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCS-----CCEEEEEECCHHHHHHH
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhcc-----cceEEEeecceeeEEcc
Confidence            489999999983  56899998866544333332 24679999999999999998754     56789999999999999


Q ss_pred             hccc--------C-Cch------HHHHHHHHHHhC--------CCCCCCcccHHHHHhhhhc
Q psy17738        277 SNIY--------T-IQN------QLITNIQTLNQG--------GFKCEILANTKTERLHMVL  315 (316)
Q Consensus       277 ~~~~--------~-~s~------~i~~~~~~l~~~--------~~H~gi~gNe~AD~LAk~~  315 (316)
                      ..+.        . ..+      ++++.+..+.+.        .||+|++|||.||+|||+.
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~~~~V~~~wV~gH~g~~gNe~AD~LAk~a  138 (152)
T d1jl1a_          77 TQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAA  138 (152)
T ss_dssp             HTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTCHHHHHHHHHHHHH
T ss_pred             cchhhHhHhccchhcccCeeecHHHHHHHHHHhhcceeEEEEecccCCCccHHHHHHHHHHH
Confidence            7652        1 111      245556565543        2899999999999999974

>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=99.54  E-value=1.4e-14  Score=111.38  Aligned_cols=90  Identities=27%  Similarity=0.280  Sum_probs=64.9

Q ss_pred             CCceEEEEcCCCC-C-CCceEEEEEeCCCeeEEEeCCCCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHH
Q psy17738        198 ETHVRIYTDGSKD-E-ENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQA  275 (316)
Q Consensus       198 ~~~~~iytDGS~~-~-~~~G~a~~~~~~~~~~~~~l~~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~  275 (316)
                      .+...+|||||+. + +..|+|++..++.. ....++ .+||++||+.|++.||+..       ..++.|+|||++++++
T Consensus         6 ~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~-~~~~~~-~~TNn~aEl~Avi~aL~~~-------~~~v~I~TDS~yvi~~   76 (110)
T d1s1ta1           6 VGAETFYVDGAANRETKLGKAGYVTNRGRQ-KVVTLT-DTTNQKTELQAIYLALQDS-------GLEVNIVTDSQYALGI   76 (110)
T ss_dssp             TTSEEEEEEEEEETTTTEEEEEEEETTSCE-EEEEES-SCCHHHHHHHHHHHHHHHS-------CSEEEEEECCHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCCCcEEEEEEecCCe-EEEecc-cCcHHHHHHHHHHHHHHhC-------CCeEEEEEehHHHHHH
Confidence            3457899999987 3 44556666655433 344454 6799999999999999853       4679999999999999


Q ss_pred             HhcccCCchH-HH-HHHHHHHhC
Q psy17738        276 ISNIYTIQNQ-LI-TNIQTLNQG  296 (316)
Q Consensus       276 i~~~~~~s~~-i~-~~~~~l~~~  296 (316)
                      +.+++....+ ++ +.++.+.+.
T Consensus        77 i~~~~~~~~~~l~~~il~~l~~~   99 (110)
T d1s1ta1          77 IQAQPDQSESELVNQIIEQLIKK   99 (110)
T ss_dssp             HHHCCSEESCHHHHHHHHHHHHC
T ss_pred             HhcCccccchHHHHHHHHHHhcC
Confidence            9998865543 44 444555543

>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=99.51  E-value=2.6e-15  Score=118.21  Aligned_cols=104  Identities=16%  Similarity=0.120  Sum_probs=75.8

Q ss_pred             EEEEcCCCC--CCCceEEEEEeCCCeeEEEeCC-CCCCchHHHHHHHHHHHHHhcCCCCCCCCcEEEEcChHHHHHHHhc
Q psy17738        202 RIYTDGSKD--EENAGCAFVIPDRNITKMFSLD-PKSSIFACELYAIYAALEYLHHPNNNTVENYVIISDSQAALQAISN  278 (316)
Q Consensus       202 ~iytDGS~~--~~~~G~a~~~~~~~~~~~~~l~-~~~tv~~AEl~Ai~~Al~~~~~~~~~~~~~i~I~sDS~~ai~~i~~  278 (316)
                      .||||||+.  +|..|+|+|+...+....++-+ +.+||++||++|+..||+.+.+.    ..++.|+|||+++++.+.+
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~----~~~i~I~tDS~yvi~wv~~   81 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKER----NSRKPIYSNSQTAIKWVKD   81 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHT----TCCCCEEESCHHHHHHHHH
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcC----CceEEEEeccHHHHHHHHh
Confidence            489999999  6889999888665443333321 46899999999999999999764    3578999999999999987


Q ss_pred             cc-C------Cch-HHHHHHHH----HHhCC-------CCCCCcccHHHH
Q psy17738        279 IY-T------IQN-QLITNIQT----LNQGG-------FKCEILANTKTE  309 (316)
Q Consensus       279 ~~-~------~s~-~i~~~~~~----l~~~~-------~H~gi~gNe~AD  309 (316)
                      +. .      ..+ ++.+.+++    |..+.       ||..--||..||
T Consensus        82 ~~~kt~~~~~vkN~~l~~~i~~a~~~lk~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          82 KKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             TCCCCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             CceecCcCCCcccHHHHHHHHHHHHHHHhCCcCceeEEecCcccccCCCC
Confidence            64 1      112 35444443    33332       687778888887