Psyllid ID: psy15899

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100----
Protein Sequence
MFHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAKDPLLSPVIEKKI
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHcccccccHHHHHHHHHHHHHHHcccEEEEEEEEcccccccHHHHHHHHHccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHHHHHHHccccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHccccEEEEEEEcccccccccHHHHHHHHHHHcccccHccc
Coil and Loop (DISEMBL)
MFHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDsmgslsaianpylscpiISQIYSAWCDLKTVGQYYVKLmwcpshcgirgneavdqaakdpllspviekki
Flexible Loop (DISEMBL)
MFHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGNeavdqaakdpllspviekki
Low Complexity Region (SEG)
MFHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAKDPLLSPVIEKKI
Disordered region (IsUnstruct)
***CSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGNEA******************
Disordered Region (DISOPRED)
MFHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAK************
Disordered Region (DISEMBL)
MFHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAKDPLLSPVIEKKI
Disordered Region (DISPRO)
MFHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAKDPLLS*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MFHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAKDPLLSPVIEKKI
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

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	104	2.2.26 [Sep-21-2011]
Q77373	1435	Gag-Pol polyprotein OS=Hu	yes	N/A	0.769	0.055	0.391	0.0004

>sp|Q77373|POL_HV1AN Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group O (isolate ANT70) GN=gag-pol PE=3 SV=3

 Score = 43.5 bits (101), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 36/92 (39%), Positives = 50/92 (54%), Gaps = 12/92 (13%)

Query: 5    SNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIAN-PYLS-CPIISQIYSAWCDL 62
            +N  AEL+AILL L+  K        +V+DS  +L  I++ P  S  PI+ QI     +L
Sbjct: 1059 TNQKAELMAILLALQDSKE----TVNIVTDSQYALGVISSQPTQSESPIVQQIIE---EL 1111

Query: 63   KTVGQYYVKLMWCPSHCGIRGNEAVDQ-AAKD 93
                Q Y  L W P+H GI GNE +D+  +KD
Sbjct: 1112 TKKEQVY--LTWVPAHKGIGGNEKIDKLVSKD 1141

Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the HIV genome, a 5 bp duplication of host DNA is produced at the ends of HIV-1 integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 1EC: .EC: 1EC: 3EC: .EC: 2

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	104
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.875	0.074	0.391	4e-08
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.865	0.179	0.385	7e-08
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.865	0.226	0.385	1e-07
443724607	397	hypothetical protein CAPTEDRAFT_208903 [	0.865	0.226	0.385	2e-07
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.865	0.344	0.385	3e-07
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.826	0.182	0.380	2e-06
443734745	252	hypothetical protein CAPTEDRAFT_216906 [	0.826	0.341	0.393	2e-06
443710566	377	hypothetical protein CAPTEDRAFT_186063 [	0.826	0.228	0.393	3e-06
443691945	354	hypothetical protein CAPTEDRAFT_224783 [	0.865	0.254	0.385	3e-06
443700898	300	hypothetical protein CAPTEDRAFT_212630,	0.826	0.286	0.393	3e-06

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

 Score = 62.0 bits (149), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 36/92 (39%), Positives = 49/92 (53%), Gaps = 1/92 (1%)

Query: 4    CSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLK 63
            CS   AEL AILL L ++K     +F++ SDS  +L A+       P++ +      DL 
Sbjct: 989  CSIFTAELHAILLALMAVKASERSKFIICSDSKSALQALGRMKTDIPLVHKSLKL-LDLI 1047

Query: 64   TVGQYYVKLMWCPSHCGIRGNEAVDQAAKDPL 95
            T  +  V  +W PSH GI GNEA D+ AK  L
Sbjct: 1048 TADRRDVTFIWVPSHVGIEGNEAADREAKRAL 1079

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|443693558|gb|ELT94903.1| hypothetical protein CAPTEDRAFT_189741, partial [Capitella teleta]

 Score = 61.2 bits (147), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 37/96 (38%), Positives = 58/96 (60%), Gaps = 6/96 (6%)

Query: 9   AELIAI---LLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTV 65
           AELIAI   L+ + ++K+    +F + SDS+ SL+A++N  ++ P +  I +   +L   
Sbjct: 119 AELIAIEQALIFIETVKDED--QFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRK 176

Query: 66  GQYYVKLMWCPSHCGIRGNEAVDQAAKDPLLSPVIE 101
           G+  V  +WCPSH GI GNE  D+ AK  L+ PV +
Sbjct: 177 GKLVV-FIWCPSHVGILGNEVADRLAKQALVMPVTK 211

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 60.8 bits (146), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 37/96 (38%), Positives = 58/96 (60%), Gaps = 6/96 (6%)

Query: 9   AELIAI---LLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTV 65
           AELIAI   L+ + ++K+    +F + SDS+ SL+A++N  ++ P +  I +   +L   
Sbjct: 168 AELIAIEQALIFIETVKDED--QFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRK 225

Query: 66  GQYYVKLMWCPSHCGIRGNEAVDQAAKDPLLSPVIE 101
           G+  V  +WCPSH GI GNE  D+ AK  L+ PV +
Sbjct: 226 GKKVV-FIWCPSHVGILGNEVADRQAKQALVMPVTK 260

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 59.7 bits (143), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/96 (38%), Positives = 58/96 (60%), Gaps = 6/96 (6%)

Query: 9   AELIAI---LLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTV 65
           AELIAI   L+ + ++K+    +F + SDS+ SL+A++N  ++ P +  I +   +L   
Sbjct: 168 AELIAIEQALIFIETMKDED--QFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRK 225

Query: 66  GQYYVKLMWCPSHCGIRGNEAVDQAAKDPLLSPVIE 101
           G+  V  +WCPSH GI GNE  D+ AK  L+ PV +
Sbjct: 226 GKLVV-FIWCPSHVGILGNEVADRLAKQALVMPVTK 260

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 59.3 bits (142), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 37/96 (38%), Positives = 58/96 (60%), Gaps = 6/96 (6%)

Query: 9   AELIAI---LLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTV 65
           AELIAI   L+ + ++K+    +F + SDS+ SL+A++N  ++ P +  I +   +L   
Sbjct: 73  AELIAIEQALIFIETVKDED--QFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRK 130

Query: 66  GQYYVKLMWCPSHCGIRGNEAVDQAAKDPLLSPVIE 101
           G+  V  +WCPSH GI GNE  D+ AK  L+ PV +
Sbjct: 131 GKLVV-FIWCPSHVGILGNEVADRLAKQALVMPVTK 165

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 56.6 bits (135), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/92 (38%), Positives = 54/92 (58%), Gaps = 6/92 (6%)

Query: 9   AELIAILLCLRSIK-NHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQ 67
           +E+IAIL  LR ++ ++   +F++ SDS+ ++ AI    +  P + Q+  A   +K++ Q
Sbjct: 58  SEIIAILSALRCVEADNEQHQFVICSDSLSAIMAIHGMDVRHPYVLQVLYA---IKSISQ 114

Query: 68  Y--YVKLMWCPSHCGIRGNEAVDQAAKDPLLS 97
               V  MWCPSH GI GNE  D  AK+ L S
Sbjct: 115 QEKIVVFMWCPSHVGIPGNEMADTLAKEALSS 146

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443734745|gb|ELU18611.1| hypothetical protein CAPTEDRAFT_216906 [Capitella teleta]

 Score = 56.2 bits (134), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 35/89 (39%), Positives = 48/89 (53%), Gaps = 3/89 (3%)

Query: 9   AELIAI--LLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVG 66
           AEL+AI  +L L     +   +FL+ +DS+ SL AI N  +  P + +I      L   G
Sbjct: 155 AELLAIYQVLTLLECSANDQQQFLIATDSLSSLQAIGNFNIKHPYVFKILEKCTLLHKKG 214

Query: 67  QYYVKLMWCPSHCGIRGNEAVDQAAKDPL 95
            Y V + WCPSH G+ GNE  D  AK+ L
Sbjct: 215 IYLV-MAWCPSHVGVMGNERADLLAKEAL 242

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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

 Score = 56.2 bits (134), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 35/89 (39%), Positives = 48/89 (53%), Gaps = 3/89 (3%)

Query: 9   AELIAI--LLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVG 66
           AEL+AI  +L L     +   +FL+ +DS+ SL AI N  +  P + +I      L   G
Sbjct: 224 AELLAIYQVLTLLECSANDQQQFLIATDSLSSLQAIGNFNIKHPYVFKILEKCTLLHKKG 283

Query: 67  QYYVKLMWCPSHCGIRGNEAVDQAAKDPL 95
            Y V + WCPSH G+ GNE  D  AK+ L
Sbjct: 284 IYLV-MAWCPSHVGVMGNERADLLAKEAL 311

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443691945|gb|ELT93673.1| hypothetical protein CAPTEDRAFT_224783 [Capitella teleta]

 Score = 56.2 bits (134), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/96 (38%), Positives = 57/96 (59%), Gaps = 6/96 (6%)

Query: 9   AELIAI---LLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTV 65
           AELIAI   L+ + ++K+    +F + S S+ SL+A++N  ++ P +  I S   +L   
Sbjct: 6   AELIAIEQALIFIETMKDED--QFNICSYSLSSLTALSNCDITHPYLLSILSKQNNLVRK 63

Query: 66  GQYYVKLMWCPSHCGIRGNEAVDQAAKDPLLSPVIE 101
           G+  V  +WCPSH GI GNE  D+ AK  L+ PV +
Sbjct: 64  GKLVV-FVWCPSHLGILGNEVADRLAKQALVMPVTK 98

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443700898|gb|ELT99633.1| hypothetical protein CAPTEDRAFT_212630, partial [Capitella teleta]

 Score = 55.8 bits (133), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 35/89 (39%), Positives = 48/89 (53%), Gaps = 3/89 (3%)

Query: 9   AELIAI--LLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVG 66
           AEL+AI  +L L     +   +FL+ +DS+ SL AI N  +  P + +I      L   G
Sbjct: 155 AELLAIYQVLTLLECSANDQQQFLIATDSLSSLQAIGNFNIKHPYVFKILQKCTLLHKKG 214

Query: 67  QYYVKLMWCPSHCGIRGNEAVDQAAKDPL 95
            Y V + WCPSH G+ GNE  D  AK+ L
Sbjct: 215 IYLV-MAWCPSHVGVMGNERADLLAKEAL 242

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	104
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.817	0.174	0.318	0.00025

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

 Score = 99 (39.9 bits), Expect = 0.00025, P = 0.00025
 Identities = 28/88 (31%), Positives = 41/88 (46%)

Query:     8 IAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCP--IISQIYSAWCDLKTV 65
             +AEL  ILL L  I        ++ +D+  +L A+ NP       I+  I  A    +  
Sbjct:   223 VAELQGILLALVIILQRQMQHAVIFTDNQATLQALRNPGSQSGQYILEAIIMALNKGRKA 282

Query:    66 GQYYVKLMWCPSHCGIRGNEAVDQAAKD 93
             G   V   W P+H G+ GNE  D+ AK+
Sbjct:   283 G-LNVHFRWIPAHRGVEGNEQADRRAKE 309


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.325   0.137   0.441    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      104       104   0.00091  102 3  11 22  0.36    30
                                                     29  0.50    31


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  593 (63 KB)
  Total size of DFA:  124 KB (2078 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  9.91u 0.17s 10.08t   Elapsed:  00:00:01
  Total cpu time:  9.91u 0.17s 10.08t   Elapsed:  00:00:01
  Start:  Thu Aug 15 17:18:23 2013   End:  Thu Aug 15 17:18:24 2013

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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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	104
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	1e-21
pfam00075	126	pfam00075, RNase_H, RNase H	5e-11
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	1e-06
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	0.001

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

 Score = 81.9 bits (203), Expect = 1e-21
 Identities = 35/92 (38%), Positives = 49/92 (53%), Gaps = 3/92 (3%)

Query: 3   HCSNGIAELIAILLCLRSIKN--HPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWC 60
           +CS   AEL+AIL  L+        A +  + SDS  +L A+ +P  S P++ +I  A  
Sbjct: 34  YCSVFDAELLAILEALQLALREGRRARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIR 93

Query: 61  DLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAK 92
           +L   G   V+L W P H GI GNE  D+ AK
Sbjct: 94  ELANHGVK-VRLHWVPGHSGIEGNERADRLAK 124

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 128

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

 Score = 54.6 bits (132), Expect = 5e-11
 Identities = 27/95 (28%), Positives = 43/95 (45%), Gaps = 12/95 (12%)

Query: 3   HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPY----LSCPIISQIYSA 58
             +N  AEL+A++  L ++         + +DS   +  I N +     S PI ++I+  
Sbjct: 37  GTTNQRAELLALIEALEALSGQK---VNIYTDSQYVIGGITNGWPTKSESKPIKNEIW-- 91

Query: 59  WCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAKD 93
             +L       V + W P H GI GNE  D+ AK 
Sbjct: 92  --ELLQKKHK-VYIQWVPGHSGIPGNELADKLAKQ 123

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

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

 Score = 43.1 bits (102), Expect = 1e-06
 Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 5/93 (5%)

Query: 3   HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDL 62
             +N  AEL+A+L  L    +    + ++ +DS   +  I +        + +      L
Sbjct: 36  AATNNEAELLALLEALELALDLGLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLL 95

Query: 63  KTVGQYYVKLMWCPSHCGIRGNEAVDQAAKDPL 95
            +     ++    P      GNE  D+ AK+  
Sbjct: 96  LS-KFIDIRFEHVPRE----GNEVADRLAKEAA 123

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

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

 Score = 35.4 bits (82), Expect = 0.001
 Identities = 23/101 (22%), Positives = 36/101 (35%), Gaps = 11/101 (10%)

Query: 3   HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIA---------NPYLSCPIIS 53
             +N  AEL A++  L ++K   A    L +DS   +  I              +     
Sbjct: 40  RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPV 99

Query: 54  QIYSAWCDLKTVGQ--YYVKLMWCPSHCGIRGNEAVDQAAK 92
           +    W +L  + +    V   W   H G   NE  DQ A+
Sbjct: 100 KNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140

Length = 154

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	104
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.93
PRK06548	161	ribonuclease H; Provisional	99.92
PRK08719	147	ribonuclease H; Reviewed	99.91
PRK00203	150	rnhA ribonuclease H; Reviewed	99.9
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.9
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.83
PRK13907	128	rnhA ribonuclease H; Provisional	99.76
KOG3752|consensus	371		99.73
PRK07708	219	hypothetical protein; Validated	99.71
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.7
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.61
KOG1812|consensus	384		92.39
COG0296	628	GlgB 1,4-alpha-glucan branching enzyme [Carbohydra	89.92

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

Probab=99.93  E-value=2.8e-26  Score=154.14  Aligned_cols=95  Identities=24%  Similarity=0.268  Sum_probs=83.1

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCC---CC--------Ch-HHHHHHHHHHHHHHhCCcce
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPY---LS--------CP-IISQIYSAWCDLKTVGQYYV   70 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~---~~--------~~-~~~~i~~~~~~l~~~~~~~v   70 (104)
                      .+||++||++|++.||+.+.+.+.+.|.|+|||+|++++|+.|.   ..        .| ..+++++.+.++..+ ...|
T Consensus        40 ~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~-~~~v  118 (154)
T COG0328          40 RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKR-HELV  118 (154)
T ss_pred             cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhh-CCeE
Confidence            58999999999999999999889999999999999999999541   11        12 346888888888887 6799


Q ss_pred             EEEeecCCCCCchhHHHHHHHccccCCC
Q psy15899         71 KLMWCPSHCGIRGNEAVDQAAKDPLLSP   98 (104)
Q Consensus        71 ~~~WVpgH~g~~gNe~AD~lAk~a~~~~   98 (104)
                      .++|||||+|.++||+||+||+.+++.+
T Consensus       119 ~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328         119 FWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             EEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999998765

>PRK06548 ribonuclease H; Provisional

Probab=99.92  E-value=9.5e-25  Score=148.08  Aligned_cols=92  Identities=23%  Similarity=0.253  Sum_probs=76.1

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcC---------CCCCCh--H-HHHHHHHHHHHHHhCCcce
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIAN---------PYLSCP--I-ISQIYSAWCDLKTVGQYYV   70 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~---------~~~~~~--~-~~~i~~~~~~l~~~~~~~v   70 (104)
                      ..||++|||+|++.||+.+.. +...|.|+|||+|++++++.         |...++  + .+++++.+.++.++  ..|
T Consensus        39 ~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~--~~v  115 (161)
T PRK06548         39 IATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN--RNI  115 (161)
T ss_pred             CCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc--Cce
Confidence            479999999999999986643 45689999999999999994         323333  3 47888888788764  479


Q ss_pred             EEEeecCCCCCchhHHHHHHHccccCC
Q psy15899         71 KLMWCPSHCGIRGNEAVDQAAKDPLLS   97 (104)
Q Consensus        71 ~~~WVpgH~g~~gNe~AD~lAk~a~~~   97 (104)
                      .|.|||||+|++|||.||+||++|+..
T Consensus       116 ~~~wVkgHsg~~gNe~aD~LA~~aa~~  142 (161)
T PRK06548        116 RMSWVNAHTGHPLNEAADSLARQAANN  142 (161)
T ss_pred             EEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence            999999999999999999999998853

>PRK08719 ribonuclease H; Reviewed

Probab=99.91  E-value=5.9e-24  Score=142.35  Aligned_cols=88  Identities=24%  Similarity=0.306  Sum_probs=72.0

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhc--------CCCC-CCh--H-HHHHHHHHHHHHHhCCcce
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIA--------NPYL-SCP--I-ISQIYSAWCDLKTVGQYYV   70 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~--------~~~~-~~~--~-~~~i~~~~~~l~~~~~~~v   70 (104)
                      ..||++|||.|++.||+.+.+.    .+|+|||+|++++++        +.+. ..+  + ..++++.+.++..  ...|
T Consensus        47 ~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~--~~~i  120 (147)
T PRK08719         47 YTDNAELELLALIEALEYARDG----DVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA--RKYV  120 (147)
T ss_pred             CccHHHHHHHHHHHHHHHcCCC----CEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC--CCcE
Confidence            4799999999999999999653    389999999999984        3333 222  2 3677777766765  5679


Q ss_pred             EEEeecCCCCCchhHHHHHHHccccC
Q psy15899         71 KLMWCPSHCGIRGNEAVDQAAKDPLL   96 (104)
Q Consensus        71 ~~~WVpgH~g~~gNe~AD~lAk~a~~   96 (104)
                      .|.|||||+|++|||.||+||++|++
T Consensus       121 ~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719        121 EVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             EEEEecCCCCChhHHHHHHHHHHHhh
Confidence            99999999999999999999999875

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.90  E-value=8.5e-24  Score=141.60  Aligned_cols=95  Identities=21%  Similarity=0.277  Sum_probs=76.7

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCC--------C-CCC--hH-HHHHHHHHHHHHHhCCcce
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANP--------Y-LSC--PI-ISQIYSAWCDLKTVGQYYV   70 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~--------~-~~~--~~-~~~i~~~~~~l~~~~~~~v   70 (104)
                      ..|+++|||.|++.||+.+.+  ...|.|+|||++++++|+.|        + ..+  ++ ..++++.+.++..  ...|
T Consensus        40 ~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~--~~~v  115 (150)
T PRK00203         40 LTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALK--RHQI  115 (150)
T ss_pred             CCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhc--cCce
Confidence            468999999999999998864  46899999999999999862        1 122  22 2556666666664  5789


Q ss_pred             EEEeecCCCCCchhHHHHHHHccccCCCccc
Q psy15899         71 KLMWCPSHCGIRGNEAVDQAAKDPLLSPVIE  101 (104)
Q Consensus        71 ~~~WVpgH~g~~gNe~AD~lAk~a~~~~~~~  101 (104)
                      .|.|||||+|++||+.||+||++|+..+..+
T Consensus       116 ~~~wV~~H~~~~~N~~AD~lA~~a~~~~~~~  146 (150)
T PRK00203        116 KWHWVKGHAGHPENERCDELARAGAEEATLE  146 (150)
T ss_pred             EEEEecCCCCCHHHHHHHHHHHHHHHHhhhc
Confidence            9999999999999999999999998766544

>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site

Probab=99.90  E-value=9.4e-24  Score=136.88  Aligned_cols=85  Identities=32%  Similarity=0.495  Sum_probs=68.1

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcC-----CCCCC----hHHHHHHHHHHHHHHhCCcceEEE
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIAN-----PYLSC----PIISQIYSAWCDLKTVGQYYVKLM   73 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~-----~~~~~----~~~~~i~~~~~~l~~~~~~~v~~~   73 (104)
                      ..|+++|||.|+..||+ +..  .+.++|||||+++++.+..     .+...    ++..+|+    ++..+ +..|.|.
T Consensus        37 ~~s~~~aEl~Ai~~AL~-~~~--~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~----~~~~~-~~~v~~~  108 (132)
T PF00075_consen   37 GQSNNRAELQAIIEALK-ALE--HRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIW----ELLSR-GIKVRFR  108 (132)
T ss_dssp             SECHHHHHHHHHHHHHH-THS--TSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHH----HHHHH-SSEEEEE
T ss_pred             ccchhhhheehHHHHHH-Hhh--cccccccccHHHHHHHHHHhccccccccccccccchhhee----ecccc-ceEEeee
Confidence            46899999999999999 543  3999999999999998877     33222    2445555    44455 8899999


Q ss_pred             eecCCCCC-chhHHHHHHHcccc
Q psy15899         74 WCPSHCGI-RGNEAVDQAAKDPL   95 (104)
Q Consensus        74 WVpgH~g~-~gNe~AD~lAk~a~   95 (104)
                      |||||+|+ .||+.||+|||+|+
T Consensus       109 ~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen  109 WVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             ESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             eccCcCCCchhHHHHHHHHHHhc
Confidence            99999999 69999999999986

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

>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=99.83  E-value=1.3e-19  Score=113.91  Aligned_cols=92  Identities=25%  Similarity=0.324  Sum_probs=77.2

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCC-CChHHHHHHHHHHHHHHhCCcceEEEeecCCCCC
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYL-SCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGI   81 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~   81 (104)
                      ..|++.+|+.|++.||+++...+..++.|+|||+.+++.++++.. .......++..+.++..+ +..+.|.|||+|+|.
T Consensus        38 ~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~i~~v~~h~~~  116 (130)
T cd06222          38 NTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKR-FHKVRFEWVPGHSGI  116 (130)
T ss_pred             CCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHHhC-CCeEEEEEcCCCCCC
Confidence            578999999999999999998899999999999999999998764 222334444444455555 889999999999999


Q ss_pred             chhHHHHHHHcccc
Q psy15899         82 RGNEAVDQAAKDPL   95 (104)
Q Consensus        82 ~gNe~AD~lAk~a~   95 (104)
                      ++|+.||.|||++.
T Consensus       117 ~~n~~ad~la~~~~  130 (130)
T cd06222         117 EGNERADALAKEAA  130 (130)
T ss_pred             cchHHHHHHHHhhC
Confidence            99999999999874

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

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.76  E-value=3.4e-18  Score=111.27  Aligned_cols=89  Identities=21%  Similarity=0.230  Sum_probs=76.5

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCChHHHHHHHHHHHHHHhCCcceEEEeecCCCCCc
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIR   82 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~   82 (104)
                      .+|++.||+.|++.||+.+.+.+..+|.|+|||+++++.+++.+..++-...+++.+..+..+ +..+.|.|||+    +
T Consensus        38 ~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~-f~~~~~~~v~r----~  112 (128)
T PRK13907         38 TMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIKS-FDLFFIKWIPS----S  112 (128)
T ss_pred             ccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHhc-CCceEEEEcCc----h
Confidence            479999999999999999999888999999999999999998765544456666666677776 77888999995    7


Q ss_pred             hhHHHHHHHccccC
Q psy15899         83 GNEAVDQAAKDPLL   96 (104)
Q Consensus        83 gNe~AD~lAk~a~~   96 (104)
                      +|+.||.||+.|..
T Consensus       113 ~N~~Ad~LA~~a~~  126 (128)
T PRK13907        113 QNKVADELARKAIL  126 (128)
T ss_pred             hchhHHHHHHHHHh
Confidence            99999999999875

>KOG3752|consensus

Probab=99.73  E-value=1e-17  Score=124.91  Aligned_cols=94  Identities=20%  Similarity=0.227  Sum_probs=74.4

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCC---CC--------h----H--HHHHHHHHHHHHHh
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYL---SC--------P----I--ISQIYSAWCDLKTV   65 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~---~~--------~----~--~~~i~~~~~~l~~~   65 (104)
                      -.|+|+|||.|+..||+.+.+.+..+|+|.|||+++++.|+.|..   +.        +    +  ..+....+.+|.+.
T Consensus       253 ~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~  332 (371)
T KOG3752|consen  253 RQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQE  332 (371)
T ss_pred             cccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhh
Confidence            468999999999999999998888899999999999999986421   11        1    1  12333344455543


Q ss_pred             -CCcceEEEeecCCCCCchhHHHHHHHccccC
Q psy15899         66 -GQYYVKLMWCPSHCGIRGNEAVDQAAKDPLL   96 (104)
Q Consensus        66 -~~~~v~~~WVpgH~g~~gNe~AD~lAk~a~~   96 (104)
                       ....|.+.|||||.|+.||++||.||++++.
T Consensus       333 ~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~  364 (371)
T KOG3752|consen  333 ISNKKVQQEYVGGHSGILGNEMADALARKGST  364 (371)
T ss_pred             hccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence             1589999999999999999999999999854

>PRK07708 hypothetical protein; Validated

Probab=99.71  E-value=1e-16  Score=113.52  Aligned_cols=97  Identities=16%  Similarity=0.089  Sum_probs=79.9

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCe--EEEEeccHHHHHHhcCCCC-CChHHHHHHHHHHHHHHhCCcceEEEeecCCC
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMR--FLLVSDSMGSLSAIANPYL-SCPIISQIYSAWCDLKTVGQYYVKLMWCPSHC   79 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~--v~I~tDS~~~l~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~   79 (104)
                      .+|++.||+.|++.||+.+.+.+.++  |.|++||+++++.+++.+. .++....+.+.+.++.+++...+.|.|||   
T Consensus       115 ~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp---  191 (219)
T PRK07708        115 IYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS---  191 (219)
T ss_pred             cccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC---
Confidence            47999999999999999999887655  8999999999999997654 45555566666666666645568889998   


Q ss_pred             CCchhHHHHHHHccccCCCccccc
Q psy15899         80 GIRGNEAVDQAAKDPLLSPVIEKK  103 (104)
Q Consensus        80 g~~gNe~AD~lAk~a~~~~~~~~~  103 (104)
                       ++.|+.||+||++|++....+++
T Consensus       192 -R~~N~~AD~LAk~Al~~~~~~~~  214 (219)
T PRK07708        192 -RKQNKEADQLATQALEGTVIESH  214 (219)
T ss_pred             -chhhhHHHHHHHHHHhcCCCCch
Confidence             68999999999999988777665

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

Probab=99.70  E-value=1.4e-16  Score=96.17  Aligned_cols=85  Identities=22%  Similarity=0.130  Sum_probs=66.5

Q ss_pred             hhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCChHHHHHHHHHHHHHHhCCcceEEEeecCCCCCchhH
Q psy15899          6 NGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGNE   85 (104)
Q Consensus         6 ~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~gNe   85 (104)
                      |..||+.|+..||+++.+.+.++|.|+|||+.+++.+++..........+.+.+..+.+. +..+.|.|||    +++|.
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~-~~~~~~~~i~----r~~N~   75 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDR-FWNVSVSHIP----REQNK   75 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCC-CSCEEEEE------GGGSH
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhcc-ccceEEEEEC----hHHhH
Confidence            578999999999999999999999999999999999998743322334444445467776 8899999999    79999


Q ss_pred             HHHHHHcccc
Q psy15899         86 AVDQAAKDPL   95 (104)
Q Consensus        86 ~AD~lAk~a~   95 (104)
                      .||.|||.|.
T Consensus        76 ~A~~LA~~a~   85 (87)
T PF13456_consen   76 VADALAKFAL   85 (87)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999999875

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.61  E-value=6.2e-15  Score=110.78  Aligned_cols=91  Identities=16%  Similarity=0.194  Sum_probs=76.8

Q ss_pred             CcchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCC-CChHHHHHHHHHHHHHHhCCcceEEEeecCCCC
Q psy15899          2 FHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYL-SCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCG   80 (104)
Q Consensus         2 ~~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g   80 (104)
                      ..+||+.||+.|++.||+.+.+.+.++|.|++||+++++.+++.+. +++-...+.+.+.++.++ +..+.|.|||+   
T Consensus        41 ~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~-f~~~~i~~v~r---  116 (372)
T PRK07238         41 GRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQ-FGRVTYTWIPR---  116 (372)
T ss_pred             CCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhc-CCceEEEECCc---
Confidence            3589999999999999999999899999999999999999997654 455445555556677776 78999999994   


Q ss_pred             CchhHHHHHHHccccCC
Q psy15899         81 IRGNEAVDQAAKDPLLS   97 (104)
Q Consensus        81 ~~gNe~AD~lAk~a~~~   97 (104)
                       ++|+.||.||+.|...
T Consensus       117 -~~N~~AD~LA~~a~~~  132 (372)
T PRK07238        117 -ARNAHADRLANEAMDA  132 (372)
T ss_pred             -hhhhHHHHHHHHHHHh
Confidence             8999999999998643

>KOG1812|consensus

Probab=92.39  E-value=0.67  Score=35.63  Aligned_cols=90  Identities=12%  Similarity=0.024  Sum_probs=54.8

Q ss_pred             chhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCCh--HHHHHHHHHHHHHHhCCcceEEEeecCCCCC
Q psy15899          4 CSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCP--IISQIYSAWCDLKTVGQYYVKLMWCPSHCGI   81 (104)
Q Consensus         4 ~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~~~--~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~   81 (104)
                      .+...+|++|+..+|..+.+.+...+++++|+....+.+.....+..  .+..+.+.+..++.+ .....-.-+|.   .
T Consensus        47 ~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~~~~~~~~~~~~l~~~v~~~r~~-l~~~~~i~~~~---~  122 (384)
T KOG1812|consen   47 ITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGREKPEQHRKIVLLVELVQRIREQ-LTSSEPILVPK---N  122 (384)
T ss_pred             cchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH-hhcccceeccc---c
Confidence            46788999999999999999999999999997766665544332221  233344444444443 22122222221   1


Q ss_pred             chhHHHHHHHccccCC
Q psy15899         82 RGNEAVDQAAKDPLLS   97 (104)
Q Consensus        82 ~gNe~AD~lAk~a~~~   97 (104)
                      .....|=.||+++..+
T Consensus       123 ~d~~~~~~lA~e~i~s  138 (384)
T KOG1812|consen  123 ADIKFAYKLAREAIVS  138 (384)
T ss_pred             hhhHHHHHHHHHhhcc
Confidence            1223466788877654

>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]

Probab=89.92  E-value=0.49  Score=38.65  Aligned_cols=72  Identities=14%  Similarity=0.009  Sum_probs=45.2

Q ss_pred             HHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCC--------CCC--hHHHHHHHHHHHHHHhCCcceEEEeecCCCCCc
Q psy15899         13 AILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPY--------LSC--PIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIR   82 (104)
Q Consensus        13 Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~--------~~~--~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~   82 (104)
                      ++..=|.++++.|.+.|.+.-=++..-.  .+|.        +.+  |--.++...++++.+. |..|-+-|||+|.+..
T Consensus       166 ~a~~llpYl~elG~T~IELMPv~e~p~~--~sWGYq~~g~yAp~sryGtPedfk~fVD~aH~~-GIgViLD~V~~HF~~d  242 (628)
T COG0296         166 LAIELLPYLKELGITHIELMPVAEHPGD--RSWGYQGTGYYAPTSRYGTPEDFKALVDAAHQA-GIGVILDWVPNHFPPD  242 (628)
T ss_pred             HHHHHhHHHHHhCCCEEEEcccccCCCC--CCCCCCcceeccccccCCCHHHHHHHHHHHHHc-CCEEEEEecCCcCCCC
Confidence            3444566666777777776542221111  0110        011  1335677777778877 9999999999999999


Q ss_pred             hhHHH
Q psy15899         83 GNEAV   87 (104)
Q Consensus        83 gNe~A   87 (104)
                      ||-.+
T Consensus       243 ~~~L~  247 (628)
T COG0296         243 GNYLA  247 (628)
T ss_pred             cchhh
Confidence            98765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	104
3k2p_A	136	Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain		8e-04
1hrh_A	136	Crystal Structure Of The Ribonuclease H Domain Of H		8e-04
3lp3_A	138	P15 Hiv Rnaseh Domain With Inhibitor Mk3 Length = 1		8e-04

>pdb|3K2P|A Chain A, Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain With The Inhibitor Beta-Thujaplicinol Bound At The Active Site Length = 136

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 29/91 (31%), Positives = 45/91 (49%), Gaps = 11/91 (12%)
Query: 1   MFHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAI-ANPYLS-CPIISQIYSA 58
           + + +N   EL AI L L+       +   +V+DS  +L  I A P  S   +++QI   
Sbjct: 45  LTNTTNQKTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIE- 99
Query: 59  WCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQ 89
               + + +  V L W P+H GI GNE VD+
Sbjct: 100 ----QLIKKEKVYLAWVPAHKGIGGNEQVDK 126

>pdb|1HRH|A Chain A, Crystal Structure Of The Ribonuclease H Domain Of Hiv-1 Reverse Transcriptase Length = 136

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 29/91 (31%), Positives = 45/91 (49%), Gaps = 11/91 (12%)
Query: 1   MFHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAI-ANPYLS-CPIISQIYSA 58
           + + +N   EL AI L L+       +   +V+DS  +L  I A P  S   +++QI   
Sbjct: 43  LTNTTNQKTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIE- 97
Query: 59  WCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQ 89
               + + +  V L W P+H GI GNE VD+
Sbjct: 98  ----QLIKKEKVYLAWVPAHKGIGGNEQVDK 124

>pdb|3LP3|A Chain A, P15 Hiv Rnaseh Domain With Inhibitor Mk3 Length = 138

Iteration: 1
 Score = 38.5 bits (88), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 29/91 (31%), Positives = 45/91 (49%), Gaps = 11/91 (12%)
Query: 1   MFHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAI-ANPYLS-CPIISQIYSA 58
           + + +N   EL AI L L+       +   +V+DS  +L  I A P  S   +++QI   
Sbjct: 45  LTNTTNQKTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIE- 99
Query: 59  WCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQ 89
               + + +  V L W P+H GI GNE VD+
Sbjct: 100 ----QLIKKEKVYLAWVPAHKGIGGNEQVDK 126

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	104
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	3e-07
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	3e-06
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	7e-06
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	7e-05

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

 Score = 45.9 bits (109), Expect = 3e-07
 Identities = 29/87 (33%), Positives = 43/87 (49%), Gaps = 11/87 (12%)

Query: 5   SNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAI-ANPYLS-CPIISQIYSAWCDL 62
           +N   EL AI L L+       +   +V+DS  +L  I A P  S   +++QI       
Sbjct: 475 TNQKTELQAIYLALQ----DSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIE----- 525

Query: 63  KTVGQYYVKLMWCPSHCGIRGNEAVDQ 89
           + + +  V L W P+H GI GNE VD+
Sbjct: 526 QLIKKEKVYLAWVPAHKGIGGNEQVDK 552

>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B Length = 555

 Score = 42.8 bits (101), Expect = 3e-06
 Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 11/87 (12%)

Query: 5   SNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAI-ANPYLS-CPIISQIYSAWCDL 62
           +N  AEL A  + L      P +   ++ DS   +  + + P  S   I++QI       
Sbjct: 472 TNQQAELEAFAMALTDSG--PKVN--IIVDSQYVMGIVASQPTESESKIVNQIIE----- 522

Query: 63  KTVGQYYVKLMWCPSHCGIRGNEAVDQ 89
           + + +  + + W P+H GI GN+ VD 
Sbjct: 523 EMIKKEAIYVAWVPAHKGIGGNQEVDH 549

>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A Length = 165

 Score = 41.4 bits (97), Expect = 7e-06
 Identities = 23/108 (21%), Positives = 41/108 (37%), Gaps = 26/108 (24%)

Query: 9   AELIAILLCLRSIKNHPAMRFLLVSDSM---------GSLSAIANPYLSCPIISQIYSAW 59
           AELIA+   L+  +        + +DS               I N      I++ + + +
Sbjct: 66  AELIALTQALKMAEGKK---LNVYTDSRYAFATAHVHSEGREIKNKNE---ILALLKALF 119

Query: 60  CDLKTVGQYYVKLMWCPSHCG-----IRGNEAVDQAAKDPLLSPVIEK 102
              +      + ++ CP H        RGN   DQAA++  +  V+E 
Sbjct: 120 LPKR------LSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLET 161

>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 = 7e-05
 Identities = 16/93 (17%), Positives = 28/93 (30%), Gaps = 14/93 (15%)

Query: 6   NGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAI-----ANPYLSCPIISQIYSAWC 60
           N   E+ A L  ++       ++  ++ D  G          A    +         A+ 
Sbjct: 50  NVAGEIAAALYAVKKASQLG-VKIRILHDYAGIAFWATGEWKAKNEFT--------QAYA 100

Query: 61  DLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAKD 93
            L    +         +H G   N+ VD  AK 
Sbjct: 101 KLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAKS 133

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	104
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.93
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.93
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.92
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.92
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.92
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.91
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.91
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.91
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.88
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.86
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.86
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.85
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.84
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.83
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.35
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.1
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	83.18
1ea9_C	583	Cyclomaltodextrinase; hydrolase, glycosidase; 3.2A	81.05

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

Probab=99.93  E-value=5.6e-26  Score=151.24  Aligned_cols=94  Identities=24%  Similarity=0.311  Sum_probs=78.8

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCC--------C-CCCh---HHHHHHHHHHHHHHhCCcce
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANP--------Y-LSCP---IISQIYSAWCDLKTVGQYYV   70 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~--------~-~~~~---~~~~i~~~~~~l~~~~~~~v   70 (104)
                      .+|+++|||.|++.||+.+.+.+.++|.|+|||++++++|++|        + ...+   ...++++.+.++..  +..|
T Consensus        47 ~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~--~~~v  124 (154)
T 2qkb_A           47 RQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ--GMDI  124 (154)
T ss_dssp             SCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT--TCEE
T ss_pred             CCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc--CCce
Confidence            5799999999999999999988889999999999999999874        1 1221   23556666656665  5679


Q ss_pred             EEEeecCCCCCchhHHHHHHHccccCCC
Q psy15899         71 KLMWCPSHCGIRGNEAVDQAAKDPLLSP   98 (104)
Q Consensus        71 ~~~WVpgH~g~~gNe~AD~lAk~a~~~~   98 (104)
                      .|.|||||+|++||+.||+||++|+..+
T Consensus       125 ~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A          125 QWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             EEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             EEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            9999999999999999999999998765

>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=99.93  E-value=1.5e-25  Score=149.30  Aligned_cols=91  Identities=26%  Similarity=0.316  Sum_probs=73.1

Q ss_pred             CcchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCC---C------CCh--H-HHHHHHHHHHHHHhCCcc
Q psy15899          2 FHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPY---L------SCP--I-ISQIYSAWCDLKTVGQYY   69 (104)
Q Consensus         2 ~~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~---~------~~~--~-~~~i~~~~~~l~~~~~~~   69 (104)
                      ..+||++|||.|++.||+.+    .++|.|+|||++++++|++|.   .      ..+  + ..++++.+.+++.+ +..
T Consensus        45 ~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~-~~~  119 (150)
T 3qio_A           45 TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIK-KEK  119 (150)
T ss_dssp             SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHTT-CSE
T ss_pred             CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhh-cCc
Confidence            35799999999999999986    489999999999999998751   1      111  1 24555554454455 889


Q ss_pred             eEEEeecCCCCCchhHHHHHHHccccCC
Q psy15899         70 VKLMWCPSHCGIRGNEAVDQAAKDPLLS   97 (104)
Q Consensus        70 v~~~WVpgH~g~~gNe~AD~lAk~a~~~   97 (104)
                      |.|.|||||+|++|||+||+||++|+..
T Consensus       120 v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A          120 VYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             EEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             eEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            9999999999999999999999999875

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

Probab=99.92  E-value=1.2e-25  Score=148.37  Aligned_cols=91  Identities=22%  Similarity=0.220  Sum_probs=72.8

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcC-C--------C-CCC--h-HHHHHHHHHHHHHHhCCcc
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIAN-P--------Y-LSC--P-IISQIYSAWCDLKTVGQYY   69 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~-~--------~-~~~--~-~~~~i~~~~~~l~~~~~~~   69 (104)
                      .+|+++|||.|++.||+.+.+  .++|.|+|||++++++|++ |        + ...  + ..+++++.+.++..+  ..
T Consensus        41 ~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~--~~  116 (146)
T 3h08_A           41 ATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTL--HR  116 (146)
T ss_dssp             EECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHHSSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHH--SE
T ss_pred             CCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHHHHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhh--Cc
Confidence            468999999999999999976  6899999999999999987 2        1 111  1 235566666566664  47


Q ss_pred             eEEEeecCCCCCchhHHHHHHHccccCC
Q psy15899         70 VKLMWCPSHCGIRGNEAVDQAAKDPLLS   97 (104)
Q Consensus        70 v~~~WVpgH~g~~gNe~AD~lAk~a~~~   97 (104)
                      |.|.|||||+|+++|+.||+|||+|+..
T Consensus       117 v~~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A          117 VTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             EEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             eEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence            9999999999999999999999999864

>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=99.92  E-value=3.2e-25  Score=148.01  Aligned_cols=94  Identities=22%  Similarity=0.356  Sum_probs=77.2

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCC--------C-CCC--hH-HHHHHHHHHHHHHhCCcce
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANP--------Y-LSC--PI-ISQIYSAWCDLKTVGQYYV   70 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~--------~-~~~--~~-~~~i~~~~~~l~~~~~~~v   70 (104)
                      .+|+++|||.|++.||+.+.+  ..+|.|+|||++++++|++|        + ..+  ++ ..++++.+.++.+  ...|
T Consensus        41 ~~tn~~aEl~A~~~aL~~~~~--~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~--~~~v  116 (155)
T 1jl1_A           41 RTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI  116 (155)
T ss_dssp             EECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT--TCEE
T ss_pred             CCcHHHHHHHHHHHHHHHhCc--CCcEEEEeCHHHHHHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHHc--cCce
Confidence            478999999999999999976  38999999999999999973        2 111  21 2456666656665  5689


Q ss_pred             EEEeecCCCCCchhHHHHHHHccccCCCcc
Q psy15899         71 KLMWCPSHCGIRGNEAVDQAAKDPLLSPVI  100 (104)
Q Consensus        71 ~~~WVpgH~g~~gNe~AD~lAk~a~~~~~~  100 (104)
                      .|.|||||+|++||+.||+||++|+..+.+
T Consensus       117 ~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  146 (155)
T 1jl1_A          117 KWEWVKGHAGHPENERADELARAAAMNPTL  146 (155)
T ss_dssp             EEEECCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             EEEEcCCCCCCHHHHHHHHHHHHHHhccch
Confidence            999999999999999999999999987654

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

Probab=99.92  E-value=6.9e-25  Score=146.85  Aligned_cols=91  Identities=23%  Similarity=0.320  Sum_probs=74.9

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcC--------CCC-CC--h-HHHHHHHHHHHHHHhCCcce
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIAN--------PYL-SC--P-IISQIYSAWCDLKTVGQYYV   70 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~--------~~~-~~--~-~~~~i~~~~~~l~~~~~~~v   70 (104)
                      .+|+++|||.|++.||+.+.+  .++|.|+|||++++++|++        .+. ..  + ...++++.+.++..  ...|
T Consensus        43 ~~tn~~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~--~~~v  118 (158)
T 2e4l_A           43 LTTNNRMELLAPIVALEALKE--PCKIILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQ--LHQI  118 (158)
T ss_dssp             EECHHHHHHHHHHHHHHTCSS--CCEEEEEECCHHHHHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHT--TSEE
T ss_pred             CCccHHHHHHHHHHHHHHhcc--CCeEEEEeCHHHHHHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHc--cCcE
Confidence            478999999999999999865  3899999999999999998        222 11  1 12456666656665  5689


Q ss_pred             EEEeecCCCCCchhHHHHHHHccccCC
Q psy15899         71 KLMWCPSHCGIRGNEAVDQAAKDPLLS   97 (104)
Q Consensus        71 ~~~WVpgH~g~~gNe~AD~lAk~a~~~   97 (104)
                      .|.|||||+|++||+.||+||++|+..
T Consensus       119 ~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A          119 DWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             EEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             EEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            999999999999999999999999976

>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=99.91  E-value=3.7e-25  Score=149.61  Aligned_cols=96  Identities=24%  Similarity=0.258  Sum_probs=73.0

Q ss_pred             CcchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCChH-HHHHHHHHHHHHHhCCcceEEEeecCCCC
Q psy15899          2 FHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPI-ISQIYSAWCDLKTVGQYYVKLMWCPSHCG   80 (104)
Q Consensus         2 ~~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~~~~-~~~i~~~~~~l~~~~~~~v~~~WVpgH~g   80 (104)
                      ..+||++||+.|++.||+++   ..++|.|||||+|+++++-......++ ..+++..+...+.+ +..|.|.|||||+|
T Consensus        59 ~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~iw~~~~g~~v~n~dl~~~l~~~l~~-~~~v~~~wVkgH~g  134 (165)
T 3p1g_A           59 AGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFL-PKRLSIIHCPGHQK  134 (165)
T ss_dssp             TTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHHHSCCCSCCCSSHHHHHHHHHHTTS-BSEEEEEECCSSCC
T ss_pred             CCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhhhcccCCCcccCHHHHHHHHHHHhc-CCceEEEEecCCCC
Confidence            35799999999999999998   368999999999999998211111221 23444333232334 78999999999999


Q ss_pred             -----CchhHHHHHHHccccCCCccc
Q psy15899         81 -----IRGNEAVDQAAKDPLLSPVIE  101 (104)
Q Consensus        81 -----~~gNe~AD~lAk~a~~~~~~~  101 (104)
                           ++|||+||+|||+|+..+.++
T Consensus       135 ~~~~~~~gNe~AD~LA~~aa~~~~~~  160 (165)
T 3p1g_A          135 GNSAEARGNRMADQAAREAAMKAVLE  160 (165)
T ss_dssp             SCSHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCcCcchHHHHHHHHHHHHHhcCCCc
Confidence                 999999999999998765443

>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=99.91  E-value=1.1e-25  Score=149.22  Aligned_cols=94  Identities=16%  Similarity=0.118  Sum_probs=77.6

Q ss_pred             chhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHhCCcceEEEeecCCCCCc
Q psy15899          4 CSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLS-CPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIR   82 (104)
Q Consensus         4 ~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~-~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~   82 (104)
                      +||++|||.|++.||+++.+.+. +|.|+|||+.+.+.+.+.+.. .+....+.+.+.++.   . .|.|.|||||+|++
T Consensus        48 ~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i~~w~~~~w~~~~~~~~~~~~l~~~l~---~-~v~~~wV~gH~g~~  122 (147)
T 2kq2_A           48 MRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMNQYR---G-IYSFEKVKAHSGNE  122 (147)
T ss_dssp             TCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTHHHHTTSSSSCCHHHHHHHHCGGGGGS---T-TCCBCCCCCCCCCH
T ss_pred             ccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHHHHHHhCCCccCCcchHHHHHHHHHhc---C-CeeEEEecCcCCCc
Confidence            58999999999999999887777 999999999998888765544 344455555544442   2 79999999999999


Q ss_pred             hhHHHHHHHccccCCCcccc
Q psy15899         83 GNEAVDQAAKDPLLSPVIEK  102 (104)
Q Consensus        83 gNe~AD~lAk~a~~~~~~~~  102 (104)
                      |||+||+|||+|+..+..|-
T Consensus       123 ~Ne~AD~LA~~a~~~~~~~~  142 (147)
T 2kq2_A          123 FNDYVDMKAKSALGIRDLEH  142 (147)
T ss_dssp             HHHHHHHHHHHHHTCCCTTC
T ss_pred             chHHHHHHHHHHHhcccccc
Confidence            99999999999999887764

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

Probab=99.91  E-value=1.2e-24  Score=146.89  Aligned_cols=93  Identities=22%  Similarity=0.171  Sum_probs=75.9

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcC----------CCCCCh--H-HHHHHHHHHHHHHhCCcc
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIAN----------PYLSCP--I-ISQIYSAWCDLKTVGQYY   69 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~----------~~~~~~--~-~~~i~~~~~~l~~~~~~~   69 (104)
                      .+|+++|||.|++.||+.+.+.  .+|.|+|||++++++|++          |...++  + ..++++.+.++..  ...
T Consensus        45 ~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~--~~~  120 (166)
T 1ril_A           45 CTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA--PHR  120 (166)
T ss_dssp             EECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT--TSE
T ss_pred             CCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHHh--cCe
Confidence            4689999999999999998763  599999999999999998          222222  1 2456666666665  458


Q ss_pred             eEEEeecCCCCCchhHHHHHHHccccCCCc
Q psy15899         70 VKLMWCPSHCGIRGNEAVDQAAKDPLLSPV   99 (104)
Q Consensus        70 v~~~WVpgH~g~~gNe~AD~lAk~a~~~~~   99 (104)
                      |.|.|||||+|+++|+.||+||++|+....
T Consensus       121 v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~  150 (166)
T 1ril_A          121 VRFHFVKGHTGHPENERVDREARRQAQSQA  150 (166)
T ss_dssp             EECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             EEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence            999999999999999999999999987654

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

Probab=99.88  E-value=1.4e-22  Score=137.03  Aligned_cols=91  Identities=13%  Similarity=0.141  Sum_probs=70.1

Q ss_pred             chhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCC---------CCC--ChH-HHHHHHHHHHHHHhCCcceE
Q psy15899          4 CSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANP---------YLS--CPI-ISQIYSAWCDLKTVGQYYVK   71 (104)
Q Consensus         4 ~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~---------~~~--~~~-~~~i~~~~~~l~~~~~~~v~   71 (104)
                      .+++.||+.|+..||+.+++. ..+|.|+|||+|++++|+.|         ...  .|+ ..++++.+.+++.. ...|.
T Consensus        54 ~te~~Aei~Al~~al~~al~~-~~~v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~-~~~v~  131 (165)
T 2lsn_A           54 HTAQMAEIAAVEFACKKALKI-PGPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSM-KPDIT  131 (165)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHS-SSCEEEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHH-CTTCE
T ss_pred             HHHHHHHHHHHHHHHHHHhcC-CCeEEEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhC-CCCEE
Confidence            456777888888777777654 46899999999999999863         111  122 35666666676666 77899


Q ss_pred             EEeecCCCCC------chhHHHHHHHccccC
Q psy15899         72 LMWCPSHCGI------RGNEAVDQAAKDPLL   96 (104)
Q Consensus        72 ~~WVpgH~g~------~gNe~AD~lAk~a~~   96 (104)
                      |.|||||+|.      +|||+||+||++|+.
T Consensus       132 ~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~  162 (165)
T 2lsn_A          132 IQHEKGHQPTNTSIHTEGNALADKLATQGSY  162 (165)
T ss_dssp             EEECCSSSCSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEeCCCCccCCCCChHHHHHHHHHHHhhh
Confidence            9999999994      689999999999974

>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=99.86  E-value=2.9e-21  Score=125.62  Aligned_cols=91  Identities=18%  Similarity=0.248  Sum_probs=78.3

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCC-CCChHHHHHHHHHHHHHHhCCcceEEEeecCCCCC
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPY-LSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGI   81 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~-~~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~   81 (104)
                      .+|+++||+.|++.||+++.+.+.++|.|+|||+++++.+++.+ .+++.+..+++.+.++..+ +..|.|.|||    .
T Consensus        43 ~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~-~~~v~~~~V~----~  117 (141)
T 3hst_B           43 RATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQ-FRRINYEWVP----R  117 (141)
T ss_dssp             EECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHHHTTSSCCCSHHHHHHHHHHHHHHTT-SSEEEEEECC----G
T ss_pred             CCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHHHhCCcccCCHHHHHHHHHHHHHHhc-CCeEEEEEcC----C
Confidence            47999999999999999999888999999999999999999854 4555556666666677776 7899999999    4


Q ss_pred             chhHHHHHHHccccCCC
Q psy15899         82 RGNEAVDQAAKDPLLSP   98 (104)
Q Consensus        82 ~gNe~AD~lAk~a~~~~   98 (104)
                      ++|+.||+||++|+...
T Consensus       118 ~~N~~AD~LA~~a~~~~  134 (141)
T 3hst_B          118 ARNTYADRLANDAMDAA  134 (141)
T ss_dssp             GGCHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHh
Confidence            99999999999997643

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

Probab=99.86  E-value=2.3e-21  Score=125.48  Aligned_cols=90  Identities=13%  Similarity=0.176  Sum_probs=75.8

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCC----eEEEEeccHHHHHHhcCCCC-CChHHHHHHHHHHHH-HHhCCcceEEEeec
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAM----RFLLVSDSMGSLSAIANPYL-SCPIISQIYSAWCDL-KTVGQYYVKLMWCP   76 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~----~v~I~tDS~~~l~~l~~~~~-~~~~~~~i~~~~~~l-~~~~~~~v~~~WVp   76 (104)
                      .+|+++||+.|++.||+.+.+.+.+    +|.|+|||+++++.+++++. +++.+..+++.+.++ .++ +..|.|.|||
T Consensus        42 ~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~-~~~v~~~~V~  120 (140)
T 3u3g_D           42 ETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMER-VPNLVFVHIP  120 (140)
T ss_dssp             EECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHH-CTTCEEEECC
T ss_pred             CCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcC-CCcEEEEEcC
Confidence            4799999999999999999987777    99999999999999998764 455445555556576 666 6799999999


Q ss_pred             CCCCCchhHHHHHHHccccCC
Q psy15899         77 SHCGIRGNEAVDQAAKDPLLS   97 (104)
Q Consensus        77 gH~g~~gNe~AD~lAk~a~~~   97 (104)
                          .++|+.||+|||+|+..
T Consensus       121 ----~~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D          121 ----REKNARADELVNEAIDK  137 (140)
T ss_dssp             ----GGGGHHHHHHHHHHHHH
T ss_pred             ----chhhHHHHHHHHHHHHh
Confidence                59999999999998753

>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=99.85  E-value=3.1e-21  Score=149.81  Aligned_cols=85  Identities=25%  Similarity=0.360  Sum_probs=71.3

Q ss_pred             CcchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC--ChHHHHHHHHHHHHHHhCCcceEEEeecCCC
Q psy15899          2 FHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLS--CPIISQIYSAWCDLKTVGQYYVKLMWCPSHC   79 (104)
Q Consensus         2 ~~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~--~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~   79 (104)
                      ..+||++||+.|++.||+.    +.+++.|+|||+++++++++|...  .++.+++.    ++..+ +..|.|.|||||+
T Consensus       469 ~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~~~~~~~~~l~~~~~----~~~~~-~~~v~~~wV~~H~  539 (555)
T 1mu2_A          469 EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQPTESESKIVNQII----EEMIK-KEAIYVAWVPAHK  539 (555)
T ss_dssp             SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTCCSEESCHHHHHHH----HHHHH-CSEEEEEECCSSS
T ss_pred             CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhcccccccHHHHHHHH----HHhcc-CCcEEEEEEECCC
Confidence            3579999999999999998    578999999999999999997643  23444444    44344 7889999999999


Q ss_pred             CCchhHHHHHHHcccc
Q psy15899         80 GIRGNEAVDQAAKDPL   95 (104)
Q Consensus        80 g~~gNe~AD~lAk~a~   95 (104)
                      |++|||.||+||++|+
T Consensus       540 g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          540 GIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             CCTTHHHHHHHHHTTC
T ss_pred             CChhHHHHHHHHHhhC
Confidence            9999999999999985

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

Probab=99.84  E-value=7.4e-21  Score=125.40  Aligned_cols=90  Identities=17%  Similarity=0.266  Sum_probs=77.1

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCC-CChHHHHHHHHHHHHHHhCCcceEEEeecCCCCC
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYL-SCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGI   81 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~   81 (104)
                      .+||++||+.|++.||+.+.+.+.++|.|+|||+++++.+++++. +++....+++.+.++.++ . .|.|.||||    
T Consensus        45 ~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~-~-~v~~~~V~~----  118 (149)
T 2ehg_A           45 NSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKK-L-NATLIWVPR----  118 (149)
T ss_dssp             TCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHH-H-TCEEEECCG----
T ss_pred             CccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHHHHHhCccccCCHHHHHHHHHHHHHHhc-C-CEEEEEcCC----
Confidence            689999999999999999998888999999999999999998764 344556666666677776 4 699999997    


Q ss_pred             chhHHHHHHHccccCCC
Q psy15899         82 RGNEAVDQAAKDPLLSP   98 (104)
Q Consensus        82 ~gNe~AD~lAk~a~~~~   98 (104)
                      ++|+.||+||++|+..+
T Consensus       119 ~~N~~AD~LA~~a~~~~  135 (149)
T 2ehg_A          119 EENKEADRLSRVAYELV  135 (149)
T ss_dssp             GGCHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhh
Confidence            69999999999998543

>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=99.83  E-value=4.7e-21  Score=148.87  Aligned_cols=84  Identities=31%  Similarity=0.389  Sum_probs=68.3

Q ss_pred             CcchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCC--hHHHHHHHHHHHHHHhCCcceEEEeecCCC
Q psy15899          2 FHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSC--PIISQIYSAWCDLKTVGQYYVKLMWCPSHC   79 (104)
Q Consensus         2 ~~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~~--~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~   79 (104)
                      ..+||++||+.|++.||+.+    .+++.|+|||+++++++++|...+  ++..++.+    ...+ ...|.|.|||||+
T Consensus       472 ~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~~~~~~~~~l~~~~~~----~l~~-~~~v~~~wV~~H~  542 (557)
T 2zd1_A          472 TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQPDKSESELVNQIIE----QLIK-KEKVYLAWVPAHK  542 (557)
T ss_dssp             CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTTCCSEESSHHHHHHHH----HHHH-CSEEEEEECCSSS
T ss_pred             CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhcCCccCCHHHHHHHHH----HHhc-CCCEEEEEcCCCC
Confidence            35899999999999999998    689999999999999999987652  34444443    2334 6689999999999


Q ss_pred             CCchhHHHHHHHccc
Q psy15899         80 GIRGNEAVDQAAKDP   94 (104)
Q Consensus        80 g~~gNe~AD~lAk~a   94 (104)
                      |++|||.||+||++|
T Consensus       543 g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          543 GIGGNEQVDKLVSAG  557 (557)
T ss_dssp             CCTTCCGGGGCC---
T ss_pred             CChhHHHHHHHHhcC
Confidence            999999999999986

>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=99.35  E-value=9.7e-14  Score=91.55  Aligned_cols=84  Identities=15%  Similarity=0.098  Sum_probs=63.6

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC-C---h-HHHHHHHHHHHH---HHhCCcceEEEe
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLS-C---P-IISQIYSAWCDL---KTVGQYYVKLMW   74 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~-~---~-~~~~i~~~~~~l---~~~~~~~v~~~W   74 (104)
                      .+||++||++|++.||+.+.+.+. +|.|+|||+++++.+.+.+.+ .   + ...++++++.++   +.  ...+....
T Consensus        48 ~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~--~~~~~~~~  124 (142)
T 1zbf_A           48 IGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLN--THTYETPI  124 (142)
T ss_dssp             EECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHH--HCCCCCCE
T ss_pred             CcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHHHcCCccCCCCCCcccHHHHHHHHHHHHHHh--hCCCceeE
Confidence            479999999999999999998776 999999999999999976522 1   1 234455444333   33  44567777


Q ss_pred             ecCCCCCchhHHHHH
Q psy15899         75 CPSHCGIRGNEAVDQ   89 (104)
Q Consensus        75 VpgH~g~~gNe~AD~   89 (104)
                      |+-|++..||..||.
T Consensus       125 ~kw~~~~~ge~pad~  139 (142)
T 1zbf_A          125 LKWQTDKWGEIKADY  139 (142)
T ss_dssp             EECCHHHHCSCTTCC
T ss_pred             EEeccCccCcCcccc
Confidence            888888899988883

>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=99.10  E-value=1.1e-10  Score=76.17  Aligned_cols=42  Identities=21%  Similarity=0.282  Sum_probs=37.5

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCC
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANP   45 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~   45 (104)
                      .+||++||++|++.||+.+.+.+.. +.|+|||+++++.+.++
T Consensus        42 ~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi~~~   83 (134)
T 4htu_A           42 IGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWVKDK   83 (134)
T ss_dssp             EECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHHHHT
T ss_pred             CCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHHHcC
Confidence            5799999999999999999886544 89999999999999864

>1rw3_A POL polyprotein; RNA and DNA dependent DNA polymerase, reverse transcriptase, transferase, replication; 3.00A {Moloney murine leukemia virus} SCOP: e.8.1.2

Probab=83.18  E-value=0.39  Score=35.99  Aligned_cols=41  Identities=7%  Similarity=0.082  Sum_probs=31.7

Q ss_pred             chhhHHHHHHHHHHHHHhhhC-CCCeEEEEeccHHHHHHhcCC
Q psy15899          4 CSNGIAELIAILLCLRSIKNH-PAMRFLLVSDSMGSLSAIANP   45 (104)
Q Consensus         4 ~s~~~aEl~Ai~~aL~~~~~~-~~~~v~I~tDS~~~l~~l~~~   45 (104)
                      .+++.-|++|+..|++..... ...+++|+||+. ++..+.+.
T Consensus       387 ys~~ekEllAi~~a~~~~~~yl~g~~~~v~tDh~-~~~~l~~~  428 (455)
T 1rw3_A          387 WPPCLRMVAAIAVLTKDAGKLTMGQPLVIKAPHA-VEALVKQP  428 (455)
T ss_dssp             SCCSSHHHHHHHHHHHHHHGGGCSSCEEEECSSC-TTTTSSST
T ss_pred             cchHHHHHHHHHHHHHHHHHHcCCCcEEEEecCh-HHHHhCCC
Confidence            356789999999999988643 457999999997 66655543

>1ea9_C Cyclomaltodextrinase; hydrolase, glycosidase; 3.2A {Bacillus SP} SCOP: b.1.18.2 b.71.1.1 c.1.8.1

Probab=81.05  E-value=1.1  Score=34.56  Aligned_cols=73  Identities=8%  Similarity=-0.091  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHHhhhCCCCeEEEE--eccHHHHHH--hcCCCCCC---hHHHHHHHHHHHHHHhCCcceEEEeecCCCCCc
Q psy15899         10 ELIAILLCLRSIKNHPAMRFLLV--SDSMGSLSA--IANPYLSC---PIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIR   82 (104)
Q Consensus        10 El~Ai~~aL~~~~~~~~~~v~I~--tDS~~~l~~--l~~~~~~~---~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g~~   82 (104)
                      -+.+|..-|.++++.|.+.|.+.  .++.+- ..  ........   |...++.+.+.++.++ |+.|-+-||+.|++..
T Consensus       170 d~~gi~~~LdyLk~LGvt~I~L~Pi~~~~~~-~GYd~~dy~~idp~~Gt~~df~~lv~~~H~~-Gi~VilD~V~NH~~~~  247 (583)
T 1ea9_C          170 DLQGVIDHLDHLSKLGVNAVYFTPLFKATTN-HKYDTEDYFQIDPQFGDKDTLKKLVDLCHER-GIRVLLDAVFNHSGRT  247 (583)
T ss_dssp             CHHHHHHTHHHHHHHTCSEEEECCCSSCSSS-STTSCSCTTCCCTTTCCHHHHHHHHHHHTTT-TCEEEEECCCSBCCTT
T ss_pred             CHHHHHHhhHHHHHcCCCEEEECCCccCCCC-CCcCcccccccCcccCCHHHHHHHHHHHHHC-CCEEEEEEccccCCCc
Confidence            46788888999998888887754  122110 00  00001111   2456778888888888 9999999999999975


Q ss_pred             hh
Q psy15899         83 GN   84 (104)
Q Consensus        83 gN   84 (104)
                      ..
T Consensus       248 ~~  249 (583)
T 1ea9_C          248 FP  249 (583)
T ss_dssp             TH
T ss_pred             cH
Confidence            44

---

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	104
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	9e-05
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	0.001
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	0.003

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

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

 Score = 36.8 bits (84), Expect = 9e-05
 Identities = 17/90 (18%), Positives = 32/90 (35%), Gaps = 7/90 (7%)

Query: 3   HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDL 62
             +N  AEL A  +           +  ++ DS   +  +A+                  
Sbjct: 41  QTTNQQAELEAFAMA----LTDSGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIE--- 93

Query: 63  KTVGQYYVKLMWCPSHCGIRGNEAVDQAAK 92
           + + +  + + W P+H GI GN+ VD    
Sbjct: 94  EMIKKEAIYVAWVPAHKGIGGNQEVDHLVS 123

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]} Length = 152

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Escherichia coli [TaxId: 562]

 Score = 33.8 bits (76), Expect = 0.001
 Identities = 11/35 (31%), Positives = 18/35 (51%)

Query: 67  QYYVKLMWCPSHCGIRGNEAVDQAAKDPLLSPVIE 101
           Q+ +K  W   H G   NE  D+ A+   ++P +E
Sbjct: 111 QHQIKWEWVKGHAGHPENERADELARAAAMNPTLE 145

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]} Length = 147

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

 Score = 32.6 bits (73), Expect = 0.003
 Identities = 9/34 (26%), Positives = 15/34 (44%)

Query: 59  WCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAK 92
              L  +  + V+  +   H G   NE VD+ A+
Sbjct: 105 EALLLAMAPHRVRFHFVKGHTGHPENERVDREAR 138

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	104
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.93
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.9
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.89
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.72
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.53

>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=99.93  E-value=1.2e-25  Score=143.88  Aligned_cols=84  Identities=24%  Similarity=0.357  Sum_probs=68.2

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCC--hHHHHHHHHHHHHHHhCCcceEEEeecCCCC
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSC--PIISQIYSAWCDLKTVGQYYVKLMWCPSHCG   80 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~~--~~~~~i~~~~~~l~~~~~~~v~~~WVpgH~g   80 (104)
                      ..||++|||.|++.||+..    ..++.|||||+++++.+++++..+  .....   .+..+. + ...|.|.|||||+|
T Consensus        41 ~~tnn~AEl~Ai~~al~~~----~~~i~I~tDS~~v~~~~~~~~~~~~~~~~~~---~~~~~~-~-~~~v~~~wV~gH~g  111 (126)
T d1mu2a1          41 QTTNQQAELEAFAMALTDS----GPKVNIIVDSQYVMGIVASQPTESESKIVNQ---IIEEMI-K-KEAIYVAWVPAHKG  111 (126)
T ss_dssp             SCCHHHHHHHHHHHHHHTS----CSEEEEEESCHHHHHHHHTCCSEESCHHHHH---HHHHHH-H-CSEEEEEECCSSSC
T ss_pred             CCcchHHHHHHHHHHhccC----CcceEEEechHHHHHHHhcCCccccchHHHH---HHHHhh-h-cceeEEEEEeCCCC
Confidence            5799999999999999864    678999999999999999876532  22222   222333 3 67899999999999


Q ss_pred             CchhHHHHHHHcccc
Q psy15899         81 IRGNEAVDQAAKDPL   95 (104)
Q Consensus        81 ~~gNe~AD~lAk~a~   95 (104)
                      ++|||+||+||++|.
T Consensus       112 ~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1         112 IGGNQEVDHLVSQGI  126 (126)
T ss_dssp             CTTHHHHHHHHHTTC
T ss_pred             CcchHHHHHHHHhhC
Confidence            999999999999984

>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=99.90  E-value=1.2e-24  Score=141.98  Aligned_cols=91  Identities=24%  Similarity=0.271  Sum_probs=73.0

Q ss_pred             chhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCC----------CC--hH-HHHHHHHHHHHHHhCCcce
Q psy15899          4 CSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYL----------SC--PI-ISQIYSAWCDLKTVGQYYV   70 (104)
Q Consensus         4 ~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~----------~~--~~-~~~i~~~~~~l~~~~~~~v   70 (104)
                      .|+++||+.|++.||+++..  ...+.|+|||+++++++..++.          ..  ++ ..++++.+..+..  ...|
T Consensus        41 ~Tnn~aEl~Ai~~AL~~~~~--~~~i~i~tds~~~~~~~~~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~--~~~v  116 (147)
T d1rila_          41 TTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA--PHRV  116 (147)
T ss_dssp             ECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT--TSEE
T ss_pred             ccHHHHHHHHHHHHhhhccC--CceEEEecchhhhhccccccchhhhhhccccccccccchhHHHHHHHHHHhh--hccc
Confidence            58999999999999998753  6789999999999998876421          11  12 2455655556554  6789


Q ss_pred             EEEeecCCCCCchhHHHHHHHccccCCC
Q psy15899         71 KLMWCPSHCGIRGNEAVDQAAKDPLLSP   98 (104)
Q Consensus        71 ~~~WVpgH~g~~gNe~AD~lAk~a~~~~   98 (104)
                      .|.|||||+|++|||.||+|||+|+...
T Consensus       117 ~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_         117 RFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             ECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             ceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence            9999999999999999999999998765

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Escherichia coli [TaxId: 562]

Probab=99.89  E-value=1.5e-23  Score=136.55  Aligned_cols=95  Identities=22%  Similarity=0.299  Sum_probs=74.9

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCC---------CCh---HHHHHHHHHHHHHHhCCcce
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYL---------SCP---IISQIYSAWCDLKTVGQYYV   70 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~---------~~~---~~~~i~~~~~~l~~~~~~~v   70 (104)
                      ..|+++||++|++.||+++..  ...+.++|||++++..++.+..         ..+   ...+++..+..+..  ...|
T Consensus        39 ~~tnn~aE~~Ai~~Al~~~~~--~~~i~i~tds~~~i~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~--~~~V  114 (152)
T d1jl1a_          39 RTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI  114 (152)
T ss_dssp             EECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT--TCEE
T ss_pred             cccHHHHHHhhhhhhhhhhcc--cceEEEeecceeeEEcccchhhHhHhccchhcccCeeecHHHHHHHHHHhh--ccee
Confidence            468999999999999998753  6789999999999998876421         111   12344444445544  6789


Q ss_pred             EEEeecCCCCCchhHHHHHHHccccCCCccc
Q psy15899         71 KLMWCPSHCGIRGNEAVDQAAKDPLLSPVIE  101 (104)
Q Consensus        71 ~~~WVpgH~g~~gNe~AD~lAk~a~~~~~~~  101 (104)
                      .|+|||||+|++|||+||+|||+|+..|.++
T Consensus       115 ~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~  145 (152)
T d1jl1a_         115 KWEWVKGHAGHPENERADELARAAAMNPTLE  145 (152)
T ss_dssp             EEEECCSSTTCHHHHHHHHHHHHHHHSCCBC
T ss_pred             EEEEecccCCCccHHHHHHHHHHHHhCCCCC
Confidence            9999999999999999999999999988765

>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=99.72  E-value=9.3e-18  Score=105.02  Aligned_cols=67  Identities=28%  Similarity=0.369  Sum_probs=53.9

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC--ChHHHHHHHHHHHHHHhCCcceEEEeecCC
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLS--CPIISQIYSAWCDLKTVGQYYVKLMWCPSH   78 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~--~~~~~~i~~~~~~l~~~~~~~v~~~WVpgH   78 (104)
                      ..||++|||.|++.||+.    ..+++.|||||+|+++++++++..  .++.+++.+    ++.+ ...|.|.|||||
T Consensus        42 ~~TNn~aEl~Avi~aL~~----~~~~v~I~TDS~yvi~~i~~~~~~~~~~l~~~il~----~l~~-~~~v~i~WVpgH  110 (110)
T d1s1ta1          42 DTTNQKTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIE----QLIK-KEKVYLAWVPAH  110 (110)
T ss_dssp             SCCHHHHHHHHHHHHHHH----SCSEEEEEECCHHHHHHHHHCCSEESCHHHHHHHH----HHHH-CSEEEEEECCSS
T ss_pred             cCcHHHHHHHHHHHHHHh----CCCeEEEEEehHHHHHHHhcCccccchHHHHHHHH----HHhc-CCceEEEEeCCC
Confidence            579999999999999985    367899999999999999987653  335555543    3334 678999999999

>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=99.53  E-value=4.2e-16  Score=100.14  Aligned_cols=83  Identities=16%  Similarity=0.100  Sum_probs=64.4

Q ss_pred             cchhhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCC----h-HHHHHHHHHHH---HHHhCCcceEEEe
Q psy15899          3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSC----P-IISQIYSAWCD---LKTVGQYYVKLMW   74 (104)
Q Consensus         3 ~~s~~~aEl~Ai~~aL~~~~~~~~~~v~I~tDS~~~l~~l~~~~~~~----~-~~~~i~~~~~~---l~~~~~~~v~~~W   74 (104)
                      ..||++|||+|++.||+.+.+.+ .++.|||||+|+++.+.++..+.    + ..+++++++.+   ++.  ...+.+.|
T Consensus        41 ~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~~kt~~~~~vkN~~l~~~i~~a~~~lk--~h~~~~~~  117 (132)
T d1zbfa1          41 IGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKKAKSTLVRNEETALIWKLVDEAEEWLN--THTYETPI  117 (132)
T ss_dssp             EECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTCCCCCCCCSTTTHHHHHHHHHHHHHHH--HCCCCCCE
T ss_pred             ccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCceecCcCCCcccHHHHHHHHHHHHHHH--hCCcCcee
Confidence            57999999999999999998755 67999999999999998654221    1 23455544433   333  56799999


Q ss_pred             ecCCCCCchhHHHH
Q psy15899         75 CPSHCGIRGNEAVD   88 (104)
Q Consensus        75 VpgH~g~~gNe~AD   88 (104)
                      |+.|+..-||..||
T Consensus       118 ~KW~~~~wG~i~AD  131 (132)
T d1zbfa1         118 LKWQTDKWGEIKAD  131 (132)
T ss_dssp             EECCHHHHCSCTTC
T ss_pred             EEecCcccccCCCC
Confidence            99999999998887