Citrus Sinensis ID: 027718

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------22
Protein Sequence
MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFGGLF
Secondary Structure (PSIPRED)
ccccccccccccccEEEEEccccccccccccEEEEEEEccccccccccccccccccccHHHHHHHHHHHHHcccEEEEEEEEcHHHHHHHHHccccccHHHHHHHHHHHHHHHHHcccccccEEEEcccccHHHHHHHHHcccccccEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccEEEEEEEEcccccEccEEEEEEEEEHHHHHHHHHccHHHcccccHHHHHHHHHHHcccccccEEEEEEcHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHccccEEEEEEEccccHHHHHHHHHHHccccEEEEEccHHHHcHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHccccccccc
Coil and Loop (DISEMBL)
mgseaalpkwasnpcimgideagrgpvlgpmvygclycpcsyqqtlatlnfadsktlKEEKREELFEDlkvndsvgwavdiidpRELSAKMLNKNKinlneishdsAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLsqrfpsikfvvskkadslypvvsgASIVAKVtrdrtlrgwIFEETAENmhrnfgsgypggarCLKLSIVCNNfqsfgglf
Flexible Loop (DISEMBL)
mgseaalpkwasnpCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELfedlkvndsvgwavDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAklsqrfpsIKFVvskkadslypvvsgasivakvtrdrTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFGGLF
Low Complexity Region (SEG)
MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFGGLF
Disordered region (IsUnstruct)
*********WASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKT*******ELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFG***
Disordered Region (DISOPRED)
***EAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFGGLF
Disordered Region (DISEMBL)
********KWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFGGLF
Disordered Region (DISPRO)
**********ASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFGGLF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFGGLF
Positional Conservation
no confident homologs detected

---

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	219	2.2.26 [Sep-21-2011]
Q9SEZ6	296	Ribonuclease H2 subunit A	yes	no	0.981	0.726	0.726	9e-91
Q5U209	301	Ribonuclease H2 subunit A	yes	no	0.863	0.627	0.515	5e-54
Q9VPP5	347	Ribonuclease H2 subunit A	yes	no	0.844	0.533	0.544	1e-53
O75792	299	Ribonuclease H2 subunit A	yes	no	0.863	0.632	0.513	2e-53
Q9CWY8	301	Ribonuclease H2 subunit A	yes	no	0.858	0.624	0.513	1e-52
Q2TBT5	299	Ribonuclease H2 subunit A	yes	no	0.863	0.632	0.5	3e-52
Q54D13	289	Ribonuclease H2 subunit A	yes	no	0.931	0.705	0.5	3e-48
Q9U6P6	297	Ribonuclease H2 subunit A	yes	no	0.885	0.653	0.465	1e-43
Q10236	326	Ribonuclease H2 subunit A	yes	no	0.835	0.561	0.502	2e-41
Q9P5X8	317	Ribonuclease H2 subunit A	N/A	no	0.853	0.589	0.415	4e-34

>sp|Q9SEZ6|RNH2A_ARATH Ribonuclease H2 subunit A OS=Arabidopsis thaliana GN=At2g25100 PE=2 SV=2

 Score =  332 bits (852), Expect = 9e-91,   Method: Compositional matrix adjust.
 Identities = 157/216 (72%), Positives = 185/216 (85%), Gaps = 1/216 (0%)

Query: 1   MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEE 60
           M SE   P+WAS PC+MGIDEAGRGPVLGPMVYGC+YCP SYQ +LA+L+FADSKTLKEE
Sbjct: 1   MESECLTPEWASQPCLMGIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEE 60

Query: 61  KREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGIL 120
           KREEL+E LK++ S+GWAVD+IDPRELSAKML KNK NLNEISH+SA+GLI RVL++G+L
Sbjct: 61  KREELYESLKLDKSLGWAVDVIDPRELSAKMLAKNKTNLNEISHNSAMGLIKRVLDMGVL 120

Query: 121 LTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 180
           LTE YLDTVGD +KY+ KLS+RFPSIKFVVSKKADSL+P+VSGASIVAKVTRDR L+ W+
Sbjct: 121 LTEAYLDTVGDPDKYRIKLSERFPSIKFVVSKKADSLFPIVSGASIVAKVTRDRALKEWL 180

Query: 181 FEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFG 216
            EET E+++RNFGSGYPG     K  +V +    FG
Sbjct: 181 VEETGEDINRNFGSGYPGDPET-KAWLVQHKHSVFG 215

Catalytic subunit of RNase HII, an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. Participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication. Mediates the excision of single ribonucleotides from DNA:RNA duplexes.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 1EC: .EC: 2EC: 6EC: .EC: 4

>sp|Q5U209|RNH2A_RAT Ribonuclease H2 subunit A OS=Rattus norvegicus GN=Rnaseh2a PE=2 SV=1

 Score =  210 bits (535), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 98/190 (51%), Positives = 131/190 (68%), Gaps = 1/190 (0%)

Query: 13  NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN 72
            PC++G+DEAGRGPVLGPMVY   YCP S    L  L  ADSKTL E +RE LF  ++ +
Sbjct: 27  EPCVLGVDEAGRGPVLGPMVYAICYCPLSRLADLEALKVADSKTLTENERERLFAKMEED 86

Query: 73  -DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGD 131
            D VGWA+DI+ P  +S  ML + K NLN +SHD+A GLI   ++  + +T+V++DTVG 
Sbjct: 87  GDFVGWALDILSPNLISTSMLGRVKYNLNSMSHDTAAGLIQHAMDQNVKVTQVFVDTVGM 146

Query: 132 AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN 191
            E YQA+L QRFP I+  V  KADSL+PVVS ASI+AKV RD+ ++ W F E+ + +  +
Sbjct: 147 PETYQARLQQRFPGIEVTVKAKADSLFPVVSAASIIAKVARDQAVKNWQFVESLQGLDSD 206

Query: 192 FGSGYPGGAR 201
           +GSGYP   +
Sbjct: 207 YGSGYPNDPK 216

Catalytic subunit of RNase HII, an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. Participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication. Mediates the excision of single ribonucleotides from DNA:RNA duplexes.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: 4

>sp|Q9VPP5|RNH2A_DROME Ribonuclease H2 subunit A OS=Drosophila melanogaster GN=CG13690 PE=2 SV=1

 Score =  209 bits (531), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 103/189 (54%), Positives = 128/189 (67%), Gaps = 4/189 (2%)

Query: 14  PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVND 73
           PC++G+DEAGRGPVLGPMVYG  YCP    + L  L  ADSK L E KR+ +F D+   +
Sbjct: 70  PCMLGVDEAGRGPVLGPMVYGISYCPLESNKALEDLGCADSKQLTEGKRDIIFNDINTKE 129

Query: 74  ----SVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTV 129
                VGWAV+II P  +S  M  ++K +LNE+S DSA+GLI + ++ G+ + EVY+DTV
Sbjct: 130 YATSCVGWAVEIISPNTISTSMYRRSKCSLNEVSMDSAMGLIQQAIDAGVNIAEVYVDTV 189

Query: 130 GDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMH 189
           G  EKYQ KL +RFPS K  V+KKADS YP+VS ASI AKVTRD  L+ W F E      
Sbjct: 190 GPPEKYQEKLLKRFPSFKITVAKKADSTYPIVSAASICAKVTRDHALKVWSFPEGLVIKD 249

Query: 190 RNFGSGYPG 198
             FGSGYPG
Sbjct: 250 NEFGSGYPG 258

Catalytic subunit of RNase HII, an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. Participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication. Mediates the excision of single ribonucleotides from DNA:RNA duplexes.

Drosophila melanogaster (taxid: 7227)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: 4

>sp|O75792|RNH2A_HUMAN Ribonuclease H2 subunit A OS=Homo sapiens GN=RNASEH2A PE=1 SV=2

 Score =  209 bits (531), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 97/189 (51%), Positives = 128/189 (67%)

Query: 13  NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN 72
            PC++G+DEAGRGPVLGPMVY   YCP      L  L  ADSKTL E +RE LF  ++  
Sbjct: 27  EPCVLGVDEAGRGPVLGPMVYAICYCPLPRLADLEALKVADSKTLLESERERLFAKMEDT 86

Query: 73  DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDA 132
           D VGWA+D++ P  +S  ML + K NLN +SHD+A GLI   L+ G+ +T+V++DTVG  
Sbjct: 87  DFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDTVGMP 146

Query: 133 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
           E YQA+L Q FP I+  V  KAD+LYPVVS ASI AKV RD+ ++ W F E  +++  ++
Sbjct: 147 ETYQARLQQSFPGIEVTVKAKADALYPVVSAASICAKVARDQAVKKWQFVEKLQDLDTDY 206

Query: 193 GSGYPGGAR 201
           GSGYP   +
Sbjct: 207 GSGYPNDPK 215

Catalytic subunit of RNase HII, an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. Participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication. Mediates the excision of single ribonucleotides from DNA:RNA duplexes.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: 4

>sp|Q9CWY8|RNH2A_MOUSE Ribonuclease H2 subunit A OS=Mus musculus GN=Rnaseh2a PE=1 SV=2

 Score =  206 bits (524), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 97/189 (51%), Positives = 129/189 (68%), Gaps = 1/189 (0%)

Query: 14  PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN- 72
           PC++G+DEAGRGPVLGPMVY   YCP S    L  L  ADSKTL E +RE LF  ++ + 
Sbjct: 28  PCVLGVDEAGRGPVLGPMVYAICYCPLSRLADLEALKVADSKTLTENERERLFAKMEEDG 87

Query: 73  DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDA 132
           D VGWA+D++ P  +S  ML + K NLN +SHD+A GLI   L+  + +T+V++DTVG  
Sbjct: 88  DFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFVDTVGMP 147

Query: 133 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
           E YQA+L Q FP I+  V  KADSL+PVVS ASI AKV RD+ ++ W F E  +++  ++
Sbjct: 148 ETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQFVENLQDLDSDY 207

Query: 193 GSGYPGGAR 201
           GSGYP   +
Sbjct: 208 GSGYPNDPK 216

Catalytic subunit of RNase HII, an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. Participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication. Mediates the excision of single ribonucleotides from DNA:RNA duplexes.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: 4

>sp|Q2TBT5|RNH2A_BOVIN Ribonuclease H2 subunit A OS=Bos taurus GN=RNASEH2A PE=1 SV=1

 Score =  204 bits (519), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 95/190 (50%), Positives = 130/190 (68%), Gaps = 1/190 (0%)

Query: 13  NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN 72
            PC++G+DEAGRGPVLGPMVY   YCP S  + L  L  ADSKTL E +R+ LF  ++ +
Sbjct: 27  EPCVLGVDEAGRGPVLGPMVYAICYCPLSRLEDLEALKVADSKTLSESERDRLFAKMEED 86

Query: 73  -DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGD 131
            D VGWA+D++ P  +S  ML + K NLN +SHD+A GL+   L+ G+ + +V++DTVG 
Sbjct: 87  GDFVGWALDVLSPNLISTSMLGRVKYNLNALSHDTATGLVQFALDQGVNVAQVFVDTVGL 146

Query: 132 AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN 191
            E YQ +L QRFP I+  V  KAD+LYPVVS ASI AKV RD+ ++ W F E  +++  +
Sbjct: 147 PETYQERLQQRFPGIEVTVKAKADALYPVVSAASICAKVARDQAVKNWKFVEKLQDLDTD 206

Query: 192 FGSGYPGGAR 201
           +GSGYP   +
Sbjct: 207 YGSGYPNDPK 216

Catalytic subunit of RNase HII, an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. Participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication. Mediates the excision of single ribonucleotides from DNA:RNA duplexes.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: 4

>sp|Q54D13|RNH2A_DICDI Ribonuclease H2 subunit A OS=Dictyostelium discoideum GN=rnaseh2A PE=3 SV=1

 Score =  191 bits (486), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 106/212 (50%), Positives = 136/212 (64%), Gaps = 8/212 (3%)

Query: 12  SNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDL-K 70
           S P +MGIDEAGRGPV+GPMVYGC Y P S   TL ++ F DSK L E++R++LF+ + +
Sbjct: 18  SEPFVMGIDEAGRGPVMGPMVYGCCYAPISKSTTLKSMKFNDSKKLTEQQRDQLFDKMGE 77

Query: 71  VNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG 130
            N  + +  D+I    LS KML K  I+LN ISH+SAIGLI  VL  G+ + E+YLDTVG
Sbjct: 78  SNKILAYETDVITAEILSEKMLYKKPISLNVISHESAIGLIRSVLKKGVNVQELYLDTVG 137

Query: 131 DAEKYQAKLSQRFPSI-KFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFE-----ET 184
             +KYQ  L + FP I K +VSKKADSLYP+VS ASI AKV RD  +    F+     + 
Sbjct: 138 PPDKYQLMLKKLFPEIGKIIVSKKADSLYPIVSAASIAAKVVRDFEITNKNFDYLNIYDQ 197

Query: 185 AENMHRNFGSGYPGGARCLKLSIVCNNFQSFG 216
            E +  +FGSGYP      K  +V N  + FG
Sbjct: 198 DEQLSTDFGSGYPSDPLSKKW-LVKNRDKVFG 228

Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Participates in DNA replication.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: 4

>sp|Q9U6P6|RNH2A_CAEEL Ribonuclease H2 subunit A OS=Caenorhabditis elegans GN=rnh-2 PE=2 SV=1

 Score =  176 bits (446), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 94/202 (46%), Positives = 122/202 (60%), Gaps = 8/202 (3%)

Query: 14  PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELF----EDL 69
           PC++GIDEAGRGPVLGPMVY     P      L  L   DSK L E KREE+F    ED 
Sbjct: 21  PCVLGIDEAGRGPVLGPMVYAAAISPLDQNVELKNLGVDDSKALNEAKREEIFNKMNEDE 80

Query: 70  KVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTV 129
            +   + +A+  + P  +S  ML + K +LNE+SH++AI LI   L   + + E+ +DTV
Sbjct: 81  DIQQIIAYALRCLSPELISCSMLKRQKYSLNEVSHEAAITLIRDALACNVNVVEIKVDTV 140

Query: 130 GDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENM- 188
           G    YQAKL + FP I   V++KADSL+P+VS ASI AKVTRD  LR W F E    + 
Sbjct: 141 GPKATYQAKLEKLFPGISICVTEKADSLFPIVSAASIAAKVTRDSRLRNWQFREKNIKVP 200

Query: 189 HRNFGSGYPGGA---RCLKLSI 207
              +GSGYPG     + L+LS+
Sbjct: 201 DAGYGSGYPGDPNTKKFLQLSV 222

Catalytic subunit of RNase HII, an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. Participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication. Mediates the excision of single ribonucleotides from DNA:RNA duplexes.

Caenorhabditis elegans (taxid: 6239)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: 4

>sp|Q10236|RNH2A_SCHPO Ribonuclease H2 subunit A OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rnh201 PE=3 SV=1

 Score =  169 bits (427), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 100/199 (50%), Positives = 121/199 (60%), Gaps = 16/199 (8%)

Query: 12  SNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDL-- 69
           S P  +G+DEAGRGPVLGPMVY   YCP  +   L    FADSKTL   KREEL + +  
Sbjct: 61  SQPYRLGVDEAGRGPVLGPMVYAVAYCPVDFD--LTNYGFADSKTLASLKREELLKLICN 118

Query: 70  ---KVNDSVGWAVDIIDPRELSAKMLN-KNKINLNEISHDSAIGLITRVLNIGILLTEVY 125
              ++  +VGW+   I  REL+A ML  +NK NLN  +HD+ I LI +V   GI +TE+Y
Sbjct: 119 KSNELGKNVGWSTMSISARELAAGMLRYRNKYNLNLQAHDTTIDLIKKVYESGINVTEIY 178

Query: 126 LDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETA 185
           +DTVG    YQ KL   FP  K  V+KKADSL+P+VS ASI AKVTRD  L      E A
Sbjct: 179 VDTVGPPISYQEKLQAHFPQAKVTVTKKADSLFPIVSLASICAKVTRDIQL------ECA 232

Query: 186 ENMHR--NFGSGYPGGARC 202
               R  N+GSGY   AR 
Sbjct: 233 RESIRTENWGSGYSSDART 251

Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Participates in DNA replication.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: 4

>sp|Q9P5X8|RNH2A_NEUCR Ribonuclease H2 subunit A OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=rnh-201 PE=3 SV=1

 Score =  144 bits (363), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 84/202 (41%), Positives = 120/202 (59%), Gaps = 15/202 (7%)

Query: 12  SNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTL--ATLNFADSKTLKEEKREELFEDL 69
           + PC +G+DEAGRGPVLGPMVY   Y P +    L     +F DSK L    R  L ++L
Sbjct: 41  NTPCCLGVDEAGRGPVLGPMVYSAFYLPLTLSDPLLKQKHSFDDSKVLTPAVRLSLMKEL 100

Query: 70  -----KVNDSVGWAVDIIDPRELSAKMLNKNK---INLNEISHDSAIGLITRVLNIGILL 121
                +++D+ G+A   + P  +S+ ML  +K    NLN+ + D+ I LI  +   G+ +
Sbjct: 101 CTKDTELHDNCGYATSSLSPLSISSGMLKASKAQIYNLNQQAMDATIALIKGIYERGVNV 160

Query: 122 TEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIF 181
           T++++DT+G    YQ KL + FP+ K  V+KKADSLYPVVS AS+VAKVTRD  L     
Sbjct: 161 TDIFIDTIGQPAAYQKKLERVFPTAKITVAKKADSLYPVVSAASVVAKVTRDIAL----- 215

Query: 182 EETAENMHRNFGSGYPGGARCL 203
           E    +    +GSGYP  ++C+
Sbjct: 216 EVLWADRTMAWGSGYPSDSKCV 237

Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Participates in DNA replication.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: 4

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	219
225464178	297	PREDICTED: ribonuclease H2 subunit A iso	0.904	0.666	0.848	4e-97
255549406	299	ribonuclease hi large subunit, putative	0.981	0.719	0.784	1e-94
449468774	297	PREDICTED: ribonuclease H2 subunit A-lik	0.904	0.666	0.808	2e-93
224097610	297	predicted protein [Populus trichocarpa]	0.904	0.666	0.818	1e-92
356536350	297	PREDICTED: ribonuclease H2 subunit A-lik	0.899	0.663	0.818	1e-90
255640332	219	unknown [Glycine max]	0.899	0.899	0.813	4e-90
297825539	296	predicted protein [Arabidopsis lyrata su	0.981	0.726	0.726	3e-89
18400719	296	Ribonuclease H2 subunit A [Arabidopsis t	0.981	0.726	0.726	5e-89
294464821	293	unknown [Picea sitchensis]	0.899	0.672	0.777	4e-86
125533439	298	hypothetical protein OsI_35154 [Oryza sa	0.885	0.651	0.738	3e-83

>gi|225464178|ref|XP_002269817.1| PREDICTED: ribonuclease H2 subunit A isoform 1 [Vitis vinifera] gi|296086584|emb|CBI32219.3| unnamed protein product [Vitis vinifera]

 Score =  359 bits (922), Expect = 4e-97,   Method: Compositional matrix adjust.
 Identities = 168/198 (84%), Positives = 184/198 (92%)

Query: 1   MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEE 60
           MGSE ALPKWAS PC+MGIDEAGRGPVLGPMVYGCLYC  SY  TL+TLNFADSKTLKEE
Sbjct: 1   MGSETALPKWASEPCMMGIDEAGRGPVLGPMVYGCLYCARSYHNTLSTLNFADSKTLKEE 60

Query: 61  KREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGIL 120
           KREELFE+LK ++S+GWAVD+IDP ELSAKML KNKINLNEISHDSAIGLITRVLN+G+L
Sbjct: 61  KREELFENLKADESIGWAVDVIDPWELSAKMLKKNKINLNEISHDSAIGLITRVLNMGVL 120

Query: 121 LTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 180
           LTEVY+DTVGDAEKY+ KLS+RFP++KFVV+KKADSLYPVVSGASIVAKVTRDR LR W+
Sbjct: 121 LTEVYVDTVGDAEKYRIKLSERFPAVKFVVAKKADSLYPVVSGASIVAKVTRDRALRDWV 180

Query: 181 FEETAENMHRNFGSGYPG 198
             ETAENMHRNFGSGYPG
Sbjct: 181 LVETAENMHRNFGSGYPG 198

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255549406|ref|XP_002515756.1| ribonuclease hi large subunit, putative [Ricinus communis] gi|223545084|gb|EEF46595.1| ribonuclease hi large subunit, putative [Ricinus communis]

 Score =  351 bits (901), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 171/218 (78%), Positives = 191/218 (87%), Gaps = 3/218 (1%)

Query: 1   MGSE--AALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLK 58
           MGSE  + LPKWAS PCIMGIDEAGRGPVLGPMVYGCLYC  SY++TL+TL+FADSKTLK
Sbjct: 1   MGSETQSTLPKWASKPCIMGIDEAGRGPVLGPMVYGCLYCARSYERTLSTLSFADSKTLK 60

Query: 59  EEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIG 118
           E+KREELFE+LK N+S+GWAVD+IDPRELSAKML KNKINLNEISH+SAIGLITRVLN G
Sbjct: 61  EDKREELFENLKANESIGWAVDVIDPRELSAKMLQKNKINLNEISHESAIGLITRVLNEG 120

Query: 119 ILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRG 178
           +LLT+VYLDTVGDAEKY+ KLS+RFPSIKFVV+KKADSLYPVVSGASIVAKVTRDR LR 
Sbjct: 121 VLLTQVYLDTVGDAEKYRIKLSERFPSIKFVVAKKADSLYPVVSGASIVAKVTRDRALRN 180

Query: 179 WIFEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFG 216
           W+ EETAE + RNFGSGYPG     K  +  +  Q FG
Sbjct: 181 WVLEETAEGISRNFGSGYPGDPET-KAWLKQHKHQVFG 217

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449468774|ref|XP_004152096.1| PREDICTED: ribonuclease H2 subunit A-like [Cucumis sativus] gi|449529756|ref|XP_004171864.1| PREDICTED: ribonuclease H2 subunit A-like [Cucumis sativus]

 Score =  347 bits (890), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 160/198 (80%), Positives = 182/198 (91%)

Query: 1   MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEE 60
           M S+ +LPKW S PC+MGIDEAGRGPVLGPMVYGCLYC  SY + L++LNFADSKTLKEE
Sbjct: 1   MSSQDSLPKWTSKPCVMGIDEAGRGPVLGPMVYGCLYCASSYLKQLSSLNFADSKTLKEE 60

Query: 61  KREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGIL 120
           KREELFEDLK N+S+GWAVD+IDPRELS+KMLNK KINLNEISHDSA+GL+T+VL++G+L
Sbjct: 61  KREELFEDLKANESIGWAVDVIDPRELSSKMLNKVKINLNEISHDSAMGLVTKVLSMGVL 120

Query: 121 LTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 180
           LTEVY+DTVGD EKY+ KLS++FP+IKFVV+KKADSLYPVVSGASIVAKVTRDR LR W 
Sbjct: 121 LTEVYVDTVGDPEKYRIKLSEKFPNIKFVVAKKADSLYPVVSGASIVAKVTRDRALREWA 180

Query: 181 FEETAENMHRNFGSGYPG 198
            EETAENMHRNFGSGYPG
Sbjct: 181 LEETAENMHRNFGSGYPG 198

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224097610|ref|XP_002311009.1| predicted protein [Populus trichocarpa] gi|222850829|gb|EEE88376.1| predicted protein [Populus trichocarpa]

 Score =  344 bits (882), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 162/198 (81%), Positives = 179/198 (90%)

Query: 1   MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEE 60
           M SE+ LP WAS PCIMGIDEAGRGPVLGPMVYGCLYC  SY++TL+TL FADSKTLKEE
Sbjct: 1   MESESILPDWASKPCIMGIDEAGRGPVLGPMVYGCLYCARSYEKTLSTLKFADSKTLKEE 60

Query: 61  KREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGIL 120
           KREELFE LK N+ +GWAVD+IDPRELSAKML K KINLNEISHDSA GL+TRVLN+G+L
Sbjct: 61  KREELFEKLKANELIGWAVDVIDPRELSAKMLKKIKINLNEISHDSASGLVTRVLNMGVL 120

Query: 121 LTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 180
           LT+VY+DTVGD EKY+ KLS+RFPSIKFVV+KKADSLYPVVSGASIVAKVTRDR LR W+
Sbjct: 121 LTDVYVDTVGDPEKYRIKLSERFPSIKFVVAKKADSLYPVVSGASIVAKVTRDRALRDWV 180

Query: 181 FEETAENMHRNFGSGYPG 198
            +ETAENM RNFGSGYPG
Sbjct: 181 LDETAENMTRNFGSGYPG 198

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356536350|ref|XP_003536702.1| PREDICTED: ribonuclease H2 subunit A-like isoform 1 [Glycine max]

 Score =  338 bits (866), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 162/198 (81%), Positives = 178/198 (89%), Gaps = 1/198 (0%)

Query: 1   MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEE 60
           MGS+  LPKWAS PC+MGIDEAGRGPVLGPMVYGCLYC  SY +TL+TL+FADSKTLKEE
Sbjct: 1   MGSKI-LPKWASKPCVMGIDEAGRGPVLGPMVYGCLYCSQSYLKTLSTLSFADSKTLKEE 59

Query: 61  KREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGIL 120
           KREELFE LK+NDS+GW VD+IDPRELSAKML KNKINLNEISH SA+GLI RVL +G+L
Sbjct: 60  KREELFETLKLNDSIGWDVDVIDPRELSAKMLKKNKINLNEISHSSAMGLIDRVLKMGVL 119

Query: 121 LTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 180
           LTEVY+DTVGDA KY+ KLS  FPSIKFVV+KKADSLYPVVSGASIVAKVTRDR LR W+
Sbjct: 120 LTEVYIDTVGDAGKYEMKLSNSFPSIKFVVAKKADSLYPVVSGASIVAKVTRDRALREWV 179

Query: 181 FEETAENMHRNFGSGYPG 198
            +ETAENM RNFGSGYPG
Sbjct: 180 LDETAENMQRNFGSGYPG 197

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255640332|gb|ACU20454.1| unknown [Glycine max]

 Score =  336 bits (861), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 161/198 (81%), Positives = 177/198 (89%), Gaps = 1/198 (0%)

Query: 1   MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEE 60
           MGS+  LPKWAS PC+MGIDEAGRGPVLGPMVYGCLYC  SY +TL+TL+FADSKTLKEE
Sbjct: 1   MGSKI-LPKWASKPCVMGIDEAGRGPVLGPMVYGCLYCSQSYLKTLSTLSFADSKTLKEE 59

Query: 61  KREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGIL 120
           KREELFE LK+NDS+GW VD+IDPRELSAKML KNKINLNEISH SA+GLI RVL +G+L
Sbjct: 60  KREELFETLKLNDSIGWDVDVIDPRELSAKMLKKNKINLNEISHSSAMGLIDRVLKMGVL 119

Query: 121 LTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 180
           LTEVY+DTVGDA KY+ KLS  FPSIKFVV+KKADSLYPVVSGASIVAKVTRDR  R W+
Sbjct: 120 LTEVYIDTVGDAGKYEMKLSNSFPSIKFVVAKKADSLYPVVSGASIVAKVTRDRASREWV 179

Query: 181 FEETAENMHRNFGSGYPG 198
            +ETAENM RNFGSGYPG
Sbjct: 180 LDETAENMQRNFGSGYPG 197

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297825539|ref|XP_002880652.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297326491|gb|EFH56911.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  333 bits (854), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 157/216 (72%), Positives = 186/216 (86%), Gaps = 1/216 (0%)

Query: 1   MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEE 60
           M S+   P+W+S PC+MGIDEAGRGPVLGPMVYGC+YCP SYQ +LA+L+FADSKTLKEE
Sbjct: 1   MESDCLTPEWSSQPCLMGIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEE 60

Query: 61  KREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGIL 120
           KREEL+E+LK++ S+GWAVD+IDPRELSAKML KNK NLNEISH+SA+GLI RVL++G+L
Sbjct: 61  KREELYENLKLDKSLGWAVDVIDPRELSAKMLAKNKTNLNEISHNSAMGLIKRVLDMGVL 120

Query: 121 LTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 180
           LTE YLDTVGD EKY+ KLS+RFPSIKFVVSKKADSL+P+VSGASIVAKVTRDR LR W+
Sbjct: 121 LTEAYLDTVGDPEKYRIKLSERFPSIKFVVSKKADSLFPIVSGASIVAKVTRDRALREWL 180

Query: 181 FEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFG 216
            EET E+++RNFGSGYPG     K  +V +    FG
Sbjct: 181 VEETGEDINRNFGSGYPGDPET-KAWLVQHKHSVFG 215

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18400719|ref|NP_565584.1| Ribonuclease H2 subunit A [Arabidopsis thaliana] gi|49066054|sp|Q9SEZ6.2|RNH2A_ARATH RecName: Full=Ribonuclease H2 subunit A; Short=RNase H2 subunit A; AltName: Full=Ribonuclease HI large subunit; Short=RNase HI large subunit; AltName: Full=Ribonuclease HI subunit A gi|26450346|dbj|BAC42289.1| putative ribonuclease large subunit [Arabidopsis thaliana] gi|28973385|gb|AAO64017.1| putative ribonuclease large subunit [Arabidopsis thaliana] gi|330252563|gb|AEC07657.1| Ribonuclease H2 subunit A [Arabidopsis thaliana]

 Score =  332 bits (852), Expect = 5e-89,   Method: Compositional matrix adjust.
 Identities = 157/216 (72%), Positives = 185/216 (85%), Gaps = 1/216 (0%)

Query: 1   MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEE 60
           M SE   P+WAS PC+MGIDEAGRGPVLGPMVYGC+YCP SYQ +LA+L+FADSKTLKEE
Sbjct: 1   MESECLTPEWASQPCLMGIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEE 60

Query: 61  KREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGIL 120
           KREEL+E LK++ S+GWAVD+IDPRELSAKML KNK NLNEISH+SA+GLI RVL++G+L
Sbjct: 61  KREELYESLKLDKSLGWAVDVIDPRELSAKMLAKNKTNLNEISHNSAMGLIKRVLDMGVL 120

Query: 121 LTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 180
           LTE YLDTVGD +KY+ KLS+RFPSIKFVVSKKADSL+P+VSGASIVAKVTRDR L+ W+
Sbjct: 121 LTEAYLDTVGDPDKYRIKLSERFPSIKFVVSKKADSLFPIVSGASIVAKVTRDRALKEWL 180

Query: 181 FEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFG 216
            EET E+++RNFGSGYPG     K  +V +    FG
Sbjct: 181 VEETGEDINRNFGSGYPGDPET-KAWLVQHKHSVFG 215

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|294464821|gb|ADE77916.1| unknown [Picea sitchensis]

 Score =  323 bits (827), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 154/198 (77%), Positives = 173/198 (87%), Gaps = 1/198 (0%)

Query: 1   MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEE 60
           MGS   LP WAS PCIMGIDEAGRGPVLGPMVYGCLYC  SYQ+TLATL FADSKTLKEE
Sbjct: 1   MGSNP-LPDWASEPCIMGIDEAGRGPVLGPMVYGCLYCSASYQETLATLKFADSKTLKEE 59

Query: 61  KREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGIL 120
           KREELFE LK + S+GWAVDIIDPRELSAKML + K+NLN ISHD+A+GL+  VL+ GIL
Sbjct: 60  KREELFESLKADASLGWAVDIIDPRELSAKMLQRIKVNLNTISHDAAMGLVNTVLSKGIL 119

Query: 121 LTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 180
           L+EVY+DTVGDA+KY+ KL ++FP IKFVVSKKADSLYP+VSGASIVAKVTRD  LRGW+
Sbjct: 120 LSEVYVDTVGDADKYRIKLEEKFPGIKFVVSKKADSLYPIVSGASIVAKVTRDNALRGWV 179

Query: 181 FEETAENMHRNFGSGYPG 198
            +ETAE + RNFGSGYPG
Sbjct: 180 LDETAEGISRNFGSGYPG 197

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125533439|gb|EAY79987.1| hypothetical protein OsI_35154 [Oryza sativa Indica Group]

 Score =  313 bits (802), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 144/195 (73%), Positives = 172/195 (88%), Gaps = 1/195 (0%)

Query: 5   AALPKWASN-PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKRE 63
           A  P+WA+  PC+MGIDEAGRGPVLGPMVYGC+YC  SYQ TLATL FADSKTLKEE+RE
Sbjct: 4   AVAPEWATKEPCLMGIDEAGRGPVLGPMVYGCMYCARSYQDTLATLKFADSKTLKEEQRE 63

Query: 64  ELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTE 123
           ELFE LK N S+GW VD+I P+ELSAKML ++K+NLNEISH+SA+GL+ R L++G+LL E
Sbjct: 64  ELFESLKDNSSIGWEVDVICPKELSAKMLKRSKVNLNEISHNSAMGLVKRALDMGVLLAE 123

Query: 124 VYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEE 183
           VY+DTVGDAEKY+ KL+++FP IKFVV+KKADSL+PVVSGASIV+KVTRDR LR W+F+E
Sbjct: 124 VYIDTVGDAEKYRIKLTEKFPGIKFVVAKKADSLFPVVSGASIVSKVTRDRALRNWVFDE 183

Query: 184 TAENMHRNFGSGYPG 198
           TA+NMH N GSGYPG
Sbjct: 184 TAQNMHMNTGSGYPG 198

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	219
TAIR|locus:2040189	296	AT2G25100 [Arabidopsis thalian	0.981	0.726	0.726	1.3e-82
FB|FBgn0031252	347	CG13690 [Drosophila melanogast	0.844	0.533	0.544	8.3e-51
ZFIN|ZDB-GENE-040426-976	307	rnaseh2a "ribonuclease H2, sub	0.835	0.596	0.548	3.6e-50
RGD|1307248	301	Rnaseh2a "ribonuclease H2, sub	0.840	0.611	0.529	4.6e-50
UNIPROTKB|Q5U209	301	Rnaseh2a "Ribonuclease H2 subu	0.840	0.611	0.529	4.6e-50
UNIPROTKB|O75792	299	RNASEH2A "Ribonuclease H2 subu	0.840	0.615	0.527	2e-49
UNIPROTKB|F1SDX8	301	RNASEH2A "Ribonuclease" [Sus s	0.840	0.611	0.518	4.1e-49
MGI|MGI:1916974	301	Rnaseh2a "ribonuclease H2, lar	0.840	0.611	0.524	4.1e-49
GENEDB_PFALCIPARUM|PFF1150w	288	PFF1150w "ribonuclease H1 larg	0.894	0.680	0.534	5.2e-49
UNIPROTKB|Q2TBT5	299	RNASEH2A "Ribonuclease H2 subu	0.867	0.635	0.502	5.2e-49

TAIR|locus:2040189 AT2G25100 [Arabidopsis thaliana (taxid:3702)]

 Score = 828 (296.5 bits), Expect = 1.3e-82, P = 1.3e-82
 Identities = 157/216 (72%), Positives = 185/216 (85%)

Query:     1 MGSEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEE 60
             M SE   P+WAS PC+MGIDEAGRGPVLGPMVYGC+YCP SYQ +LA+L+FADSKTLKEE
Sbjct:     1 MESECLTPEWASQPCLMGIDEAGRGPVLGPMVYGCMYCPISYQSSLASLHFADSKTLKEE 60

Query:    61 KREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGIL 120
             KREEL+E LK++ S+GWAVD+IDPRELSAKML KNK NLNEISH+SA+GLI RVL++G+L
Sbjct:    61 KREELYESLKLDKSLGWAVDVIDPRELSAKMLAKNKTNLNEISHNSAMGLIKRVLDMGVL 120

Query:   121 LTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 180
             LTE YLDTVGD +KY+ KLS+RFPSIKFVVSKKADSL+P+VSGASIVAKVTRDR L+ W+
Sbjct:   121 LTEAYLDTVGDPDKYRIKLSERFPSIKFVVSKKADSLFPIVSGASIVAKVTRDRALKEWL 180

Query:   181 FEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFG 216
              EET E+++RNFGSGYPG     K  +V +    FG
Sbjct:   181 VEETGEDINRNFGSGYPGDPET-KAWLVQHKHSVFG 215

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=ISS

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0005737 "cytoplasm" evidence=ISM

GO:0016070 "RNA metabolic process" evidence=IEA

FB|FBgn0031252 CG13690 [Drosophila melanogaster (taxid:7227)]

 Score = 528 (190.9 bits), Expect = 8.3e-51, P = 8.3e-51
 Identities = 103/189 (54%), Positives = 128/189 (67%)

Query:    14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVND 73
             PC++G+DEAGRGPVLGPMVYG  YCP    + L  L  ADSK L E KR+ +F D+   +
Sbjct:    70 PCMLGVDEAGRGPVLGPMVYGISYCPLESNKALEDLGCADSKQLTEGKRDIIFNDINTKE 129

Query:    74 ----SVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTV 129
                  VGWAV+II P  +S  M  ++K +LNE+S DSA+GLI + ++ G+ + EVY+DTV
Sbjct:   130 YATSCVGWAVEIISPNTISTSMYRRSKCSLNEVSMDSAMGLIQQAIDAGVNIAEVYVDTV 189

Query:   130 GDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMH 189
             G  EKYQ KL +RFPS K  V+KKADS YP+VS ASI AKVTRD  L+ W F E      
Sbjct:   190 GPPEKYQEKLLKRFPSFKITVAKKADSTYPIVSAASICAKVTRDHALKVWSFPEGLVIKD 249

Query:   190 RNFGSGYPG 198
               FGSGYPG
Sbjct:   250 NEFGSGYPG 258

GO:0004523 "ribonuclease H activity" evidence=ISS;NAS

GO:0003723 "RNA binding" evidence=IEA

GO:0016070 "RNA metabolic process" evidence=IEA

ZFIN|ZDB-GENE-040426-976 rnaseh2a "ribonuclease H2, subunit A" [Danio rerio (taxid:7955)]

 Score = 522 (188.8 bits), Expect = 3.6e-50, P = 3.6e-50
 Identities = 101/184 (54%), Positives = 128/184 (69%)

Query:    15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDL-KVND 73
             C +GIDEAGRGPVLGPMVYG  +CP S ++ L  L  ADSKTL E +RE LF  L +   
Sbjct:    29 CCLGIDEAGRGPVLGPMVYGICFCPVSRKEDLKNLKVADSKTLTEAERENLFVKLDEAKS 88

Query:    74 SVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAE 133
              VGWA+ I+ P  +S  ML + K NLN +SHD+AIGL+   L+ G+ L EV++DTVG AE
Sbjct:    89 FVGWALQILSPNMISTSMLQRAKYNLNALSHDAAIGLVQYALDSGVQLKEVFVDTVGPAE 148

Query:   134 KYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG 193
             KYQ KLSQRFP ++  V  KADSL+P+VS ASI AKV RD  ++ W F E   ++  ++G
Sbjct:   149 KYQDKLSQRFPGVEVTVRPKADSLFPIVSAASICAKVARDHAVKSWKFAEDLGDVDTDYG 208

Query:   194 SGYP 197
             SGYP
Sbjct:   209 SGYP 212

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0016070 "RNA metabolic process" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

RGD|1307248 Rnaseh2a "ribonuclease H2, subunit A" [Rattus norvegicus (taxid:10116)]

 Score = 521 (188.5 bits), Expect = 4.6e-50, P = 4.6e-50
 Identities = 98/185 (52%), Positives = 130/185 (70%)

Query:    14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN- 72
             PC++G+DEAGRGPVLGPMVY   YCP S    L  L  ADSKTL E +RE LF  ++ + 
Sbjct:    28 PCVLGVDEAGRGPVLGPMVYAICYCPLSRLADLEALKVADSKTLTENERERLFAKMEEDG 87

Query:    73 DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDA 132
             D VGWA+DI+ P  +S  ML + K NLN +SHD+A GLI   ++  + +T+V++DTVG  
Sbjct:    88 DFVGWALDILSPNLISTSMLGRVKYNLNSMSHDTAAGLIQHAMDQNVKVTQVFVDTVGMP 147

Query:   133 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
             E YQA+L QRFP I+  V  KADSL+PVVS ASI+AKV RD+ ++ W F E+ + +  ++
Sbjct:   148 ETYQARLQQRFPGIEVTVKAKADSLFPVVSAASIIAKVARDQAVKNWQFVESLQGLDSDY 207

Query:   193 GSGYP 197
             GSGYP
Sbjct:   208 GSGYP 212

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA;ISO;ISS

GO:0005634 "nucleus" evidence=IEA

GO:0006401 "RNA catabolic process" evidence=ISO;ISS

GO:0016070 "RNA metabolic process" evidence=IEA

GO:0032299 "ribonuclease H2 complex" evidence=ISO;ISS

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|Q5U209 Rnaseh2a "Ribonuclease H2 subunit A" [Rattus norvegicus (taxid:10116)]

 Score = 521 (188.5 bits), Expect = 4.6e-50, P = 4.6e-50
 Identities = 98/185 (52%), Positives = 130/185 (70%)

Query:    14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN- 72
             PC++G+DEAGRGPVLGPMVY   YCP S    L  L  ADSKTL E +RE LF  ++ + 
Sbjct:    28 PCVLGVDEAGRGPVLGPMVYAICYCPLSRLADLEALKVADSKTLTENERERLFAKMEEDG 87

Query:    73 DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDA 132
             D VGWA+DI+ P  +S  ML + K NLN +SHD+A GLI   ++  + +T+V++DTVG  
Sbjct:    88 DFVGWALDILSPNLISTSMLGRVKYNLNSMSHDTAAGLIQHAMDQNVKVTQVFVDTVGMP 147

Query:   133 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
             E YQA+L QRFP I+  V  KADSL+PVVS ASI+AKV RD+ ++ W F E+ + +  ++
Sbjct:   148 ETYQARLQQRFPGIEVTVKAKADSLFPVVSAASIIAKVARDQAVKNWQFVESLQGLDSDY 207

Query:   193 GSGYP 197
             GSGYP
Sbjct:   208 GSGYP 212

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|O75792 RNASEH2A "Ribonuclease H2 subunit A" [Homo sapiens (taxid:9606)]

 Score = 515 (186.3 bits), Expect = 2.0e-49, P = 2.0e-49
 Identities = 97/184 (52%), Positives = 127/184 (69%)

Query:    14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVND 73
             PC++G+DEAGRGPVLGPMVY   YCP      L  L  ADSKTL E +RE LF  ++  D
Sbjct:    28 PCVLGVDEAGRGPVLGPMVYAICYCPLPRLADLEALKVADSKTLLESERERLFAKMEDTD 87

Query:    74 SVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAE 133
              VGWA+D++ P  +S  ML + K NLN +SHD+A GLI   L+ G+ +T+V++DTVG  E
Sbjct:    88 FVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDTVGMPE 147

Query:   134 KYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG 193
              YQA+L Q FP I+  V  KAD+LYPVVS ASI AKV RD+ ++ W F E  +++  ++G
Sbjct:   148 TYQARLQQSFPGIEVTVKAKADALYPVVSAASICAKVARDQAVKKWQFVEKLQDLDTDYG 207

Query:   194 SGYP 197
             SGYP
Sbjct:   208 SGYP 211

GO:0003723 "RNA binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0032299 "ribonuclease H2 complex" evidence=IDA

GO:0004523 "ribonuclease H activity" evidence=IDA

GO:0006260 "DNA replication" evidence=TAS

GO:0006401 "RNA catabolic process" evidence=IDA

GO:0004540 "ribonuclease activity" evidence=TAS

UNIPROTKB|F1SDX8 RNASEH2A "Ribonuclease" [Sus scrofa (taxid:9823)]

 Score = 512 (185.3 bits), Expect = 4.1e-49, P = 4.1e-49
 Identities = 96/185 (51%), Positives = 128/185 (69%)

Query:    14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN- 72
             PC++G+DEAGRGPVLGPMVY   YCP S    L  L  ADSKTL E +R+ LF  ++ + 
Sbjct:    28 PCVLGVDEAGRGPVLGPMVYAICYCPLSRLADLEALKVADSKTLSESERDRLFAKMEEDG 87

Query:    73 DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDA 132
             D VGWA+D++ P  +S  ML + K NLN +SHD+A GL+   L+ G+ + +V++DTVG  
Sbjct:    88 DFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLVQYALDQGVKVAQVFVDTVGLP 147

Query:   133 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
             E YQ +L QRFP I+  V  KAD+LYPVVS ASI AKV RD+ +R W F E  +++  ++
Sbjct:   148 ETYQERLQQRFPDIEVTVKAKADALYPVVSAASICAKVARDQAVRNWQFVEKLQDLDTDY 207

Query:   193 GSGYP 197
             GSGYP
Sbjct:   208 GSGYP 212

GO:0032299 "ribonuclease H2 complex" evidence=IEA

GO:0006401 "RNA catabolic process" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

MGI|MGI:1916974 Rnaseh2a "ribonuclease H2, large subunit" [Mus musculus (taxid:10090)]

 Score = 512 (185.3 bits), Expect = 4.1e-49, P = 4.1e-49
 Identities = 97/185 (52%), Positives = 128/185 (69%)

Query:    14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN- 72
             PC++G+DEAGRGPVLGPMVY   YCP S    L  L  ADSKTL E +RE LF  ++ + 
Sbjct:    28 PCVLGVDEAGRGPVLGPMVYAICYCPLSRLADLEALKVADSKTLTENERERLFAKMEEDG 87

Query:    73 DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDA 132
             D VGWA+D++ P  +S  ML + K NLN +SHD+A GLI   L+  + +T+V++DTVG  
Sbjct:    88 DFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFVDTVGMP 147

Query:   133 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
             E YQA+L Q FP I+  V  KADSL+PVVS ASI AKV RD+ ++ W F E  +++  ++
Sbjct:   148 ETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQFVENLQDLDSDY 207

Query:   193 GSGYP 197
             GSGYP
Sbjct:   208 GSGYP 212

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0006401 "RNA catabolic process" evidence=ISO

GO:0016070 "RNA metabolic process" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0032299 "ribonuclease H2 complex" evidence=ISO;IDA

GO:0046872 "metal ion binding" evidence=IEA

GENEDB_PFALCIPARUM|PFF1150w PFF1150w "ribonuclease H1 large subunit, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 511 (184.9 bits), Expect = 5.2e-49, P = 5.2e-49
 Identities = 109/204 (53%), Positives = 138/204 (67%)

Query:    17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDS-- 74
             +GIDEAGRGPVLGPMVY   YC   +++ L  +   DSK + E  RE++F  +K+N+S  
Sbjct:    19 LGIDEAGRGPVLGPMVYSGFYCNKEHEKLLKEMKIDDSKKITEADREKMF--VKLNNSKL 76

Query:    75 -VGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAE 133
               GW V I+ P+++SAKML K K NLNEISHD+AI +I  V+N G  LTEV++DTVG A 
Sbjct:    77 PFGWRVHILLPQDISAKMLKKQKYNLNEISHDTAISIIEHVINRGCNLTEVFVDTVGKAS 136

Query:   134 KYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG 193
              Y+ KL + FP IK  V +KADSLYPVVS ASI AKVTRD  L+ W +EE   N+   FG
Sbjct:   137 VYEEKLQKMFPHIKCTVKEKADSLYPVVSAASICAKVTRDFLLKKWKYEEPIINIDNGFG 196

Query:   194 SGYPGGARCLKLSIVCNNFQS-FG 216
             SGYPG    +  + + NNF S FG
Sbjct:   197 SGYPGDP--VTKNFLKNNFDSVFG 218

GO:0006401 "RNA catabolic process" evidence=ISS

UNIPROTKB|Q2TBT5 RNASEH2A "Ribonuclease H2 subunit A" [Bos taurus (taxid:9913)]

 Score = 511 (184.9 bits), Expect = 5.2e-49, P = 5.2e-49
 Identities = 96/191 (50%), Positives = 130/191 (68%)

Query:     8 PKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFE 67
             P     PC++G+DEAGRGPVLGPMVY   YCP S  + L  L  ADSKTL E +R+ LF 
Sbjct:    22 PVCLKEPCVLGVDEAGRGPVLGPMVYAICYCPLSRLEDLEALKVADSKTLSESERDRLFA 81

Query:    68 DLKVN-DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYL 126
              ++ + D VGWA+D++ P  +S  ML + K NLN +SHD+A GL+   L+ G+ + +V++
Sbjct:    82 KMEEDGDFVGWALDVLSPNLISTSMLGRVKYNLNALSHDTATGLVQFALDQGVNVAQVFV 141

Query:   127 DTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAE 186
             DTVG  E YQ +L QRFP I+  V  KAD+LYPVVS ASI AKV RD+ ++ W F E  +
Sbjct:   142 DTVGLPETYQERLQQRFPGIEVTVKAKADALYPVVSAASICAKVARDQAVKNWKFVEKLQ 201

Query:   187 NMHRNFGSGYP 197
             ++  ++GSGYP
Sbjct:   202 DLDTDYGSGYP 212

GO:0032299 "ribonuclease H2 complex" evidence=ISS

GO:0004523 "ribonuclease H activity" evidence=ISS

GO:0006401 "RNA catabolic process" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O74035	RNH2_PYRKO	3, ., 1, ., 2, 6, ., 4	0.3431	0.8356	0.8026	yes	no
A1RYM0	RNH2_THEPD	3, ., 1, ., 2, 6, ., 4	0.3232	0.8127	0.8356	yes	no
Q9CWY8	RNH2A_MOUSE	3, ., 1, ., 2, 6, ., 4	0.5132	0.8584	0.6245	yes	no
Q9SEZ6	RNH2A_ARATH	3, ., 1, ., 2, 6, ., 4	0.7268	0.9817	0.7263	yes	no
Q2NEI6	RNH2_METST	3, ., 1, ., 2, 6, ., 4	0.3232	0.8264	0.8537	yes	no
Q5U209	RNH2A_RAT	3, ., 1, ., 2, 6, ., 4	0.5157	0.8630	0.6279	yes	no
O75792	RNH2A_HUMAN	3, ., 1, ., 2, 6, ., 4	0.5132	0.8630	0.6321	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.26	0.963
3rd Layer	3.1.26.4	0.946

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	fgenesh4_pg.C_LG_VIII000164	hypothetical protein; Endonuclease that specifically degrades the RNA of RNA- DNA hybrids (By similarity) (297 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.XIII.413.1	annotation not avaliable (325 aa)				•	•		•		0.795
	gw1.IX.5004.1	hypothetical protein (664 aa)	•			•			•		0.719
	gw1.V.2541.1	hypothetical protein (1081 aa)				•			•		0.659
	eugene3.00660007	hypothetical protein (2222 aa)				•	•		•		0.645
	estExt_Genewise1_v1.C_LG_I1046	proliferating cell nuclear antigen (PCNA); This protein is an auxiliary protein of DNA polymera [...] (268 aa)				•	•		•		0.578
	estExt_Genewise1_v1.C_LG_IX3930	proliferating cell nuclear antigen (PCNA); This protein is an auxiliary protein of DNA polymera [...] (265 aa)				•	•		•		0.569
	eugene3.00120511	hypothetical protein (944 aa)				•	•		•		0.567
	gw1.I.2892.1	thymidylate kinase (EC-2.7.4.9) (210 aa)				•			•		0.525
	estExt_fgenesh4_pg.C_LG_III1005	replication factor C subunit (331 aa)				•			•		0.491
	estExt_fgenesh4_pm.C_LG_XVIII0380	hypothetical protein (311 aa)	•			•	•		•		0.476

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	219
cd07181	221	cd07181, RNase_HII_eukaryota_like, Mammalian RNase	1e-110
cd06266	210	cd06266, RNase_HII, Ribonuclease H (RNase H) type	1e-105
pfam01351	199	pfam01351, RNase_HII, Ribonuclease HII	3e-48
TIGR00729	206	TIGR00729, TIGR00729, ribonuclease H, mammalian HI	1e-44
cd07180	204	cd07180, RNase_HII_Archaea_like, Archaeal ribonucl	8e-41
COG0164	199	COG0164, RnhB, Ribonuclease HII [DNA replication,	1e-37
PRK00015	197	PRK00015, rnhB, ribonuclease HII; Validated	2e-27
cd07182	179	cd07182, RNase_HII_bacteria_HII_like, bacterial Ri	6e-22
PRK14551	212	PRK14551, rnhB, ribonuclease HII; Provisional	9e-20
cd06590	207	cd06590, RNase_HII_bacteria_HIII_like, bacterial R	8e-16
PRK13926	207	PRK13926, PRK13926, ribonuclease HII; Provisional	3e-12
COG1039	297	COG1039, RnhC, Ribonuclease HIII [DNA replication,	1e-08
TIGR00716	284	TIGR00716, rnhC, ribonuclease HIII	3e-08
PRK13925	198	PRK13925, rnhB, ribonuclease HII; Provisional	3e-08
PRK14550	204	PRK14550, rnhB, ribonuclease HII; Provisional	8e-07
PRK00996	304	PRK00996, PRK00996, ribonuclease HIII; Provisional	8e-06

>gnl|CDD|187694 cd07181, RNase_HII_eukaryota_like, Mammalian RNase HII is functional when it forms a complex with two other accessory protein

 Score =  315 bits (810), Expect = e-110
 Identities = 120/187 (64%), Positives = 143/187 (76%), Gaps = 1/187 (0%)

Query: 17  MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKV-NDSV 75
           +GIDEAGRGPVLGPMVYG  YCP SY++ L  L FADSKTL EEKREELF+ LK  +D++
Sbjct: 1   LGIDEAGRGPVLGPMVYGAAYCPISYKEELKKLGFADSKTLTEEKREELFKKLKEKDDAL 60

Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
           GWA  I+ P+ +S KML + K NLNEISHD+AIGLI  VL+ G+ +TEVY+DTVG  EKY
Sbjct: 61  GWATRILSPQYISTKMLARTKYNLNEISHDAAIGLIREVLDKGVNVTEVYVDTVGPPEKY 120

Query: 136 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSG 195
           QAKL ++FP IKF V KKADSLYP+VS ASIVAKVTRDR L+ W F+ET      + GSG
Sbjct: 121 QAKLQKKFPGIKFTVEKKADSLYPIVSAASIVAKVTRDRALKNWQFDETLIKDSGDLGSG 180

Query: 196 YPGGARC 202
           YP   + 
Sbjct: 181 YPSDPKT 187

Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with two other accessory proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause neurological disorder. Length = 221

>gnl|CDD|187691 cd06266, RNase_HII, Ribonuclease H (RNase H) type II family (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII)

 Score =  300 bits (771), Expect = e-105
 Identities = 117/186 (62%), Positives = 141/186 (75%), Gaps = 2/186 (1%)

Query: 17  MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVG 76
           +GIDEAGRGPVLGPMVY   YCP SY + L +L FADSK L EEKREELF+++K + +VG
Sbjct: 1   LGIDEAGRGPVLGPMVYAAAYCPISYLEKLESLGFADSKQLTEEKREELFDEIKEDKAVG 60

Query: 77  WAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQ 136
           WAV I+ P  +S KML ++K NLNEISHD+AIGLI  +L+ G+ +TEVY+DTVG  EKYQ
Sbjct: 61  WAVRILSPEYISRKMLARSKYNLNEISHDAAIGLIRNLLDKGVKVTEVYVDTVGPPEKYQ 120

Query: 137 AKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGY 196
           AKL +RFP IKF V KKADS YP+VS ASIVAKVTRDR L  W F+E  ++    FGSGY
Sbjct: 121 AKLLKRFPGIKFTVEKKADSKYPIVSAASIVAKVTRDRALEQWKFDEGLDSGD--FGSGY 178

Query: 197 PGGARC 202
           P   + 
Sbjct: 179 PSDPKT 184

Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes, but no prokaryotic genome contains the combination of only RNase HI and HIII. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli. Length = 210

>gnl|CDD|216451 pfam01351, RNase_HII, Ribonuclease HII

 Score =  156 bits (397), Expect = 3e-48
 Identities = 66/192 (34%), Positives = 87/192 (45%), Gaps = 16/192 (8%)

Query: 17  MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVG 76
            GIDE GRGP+ GP+V   +Y P      L  L   DSK L ++KREEL E +K      
Sbjct: 1   AGIDEVGRGPLAGPLVVAAVYLPPERLDELRKLGVKDSKKLSDKKREELAELIK------ 54

Query: 77  WAVDIIDPRELSAKMLNK---NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAE 133
                I+ R+L A  +     N+INLN I H   + +I  V  +G+   E+ +D     +
Sbjct: 55  ---KRIETRKLVAGNIKYAEANEINLNNILHALHLAMIRAVQKLGVKPDEILVDGFRPPK 111

Query: 134 KYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG 193
               K    F         KADS Y  V+ ASI+AKVTRD  L      +       + G
Sbjct: 112 SLPMKQEAIFKIKV-TAEHKADSKYLSVAAASIIAKVTRDEMLE---LLKRFPGYGLDKG 167

Query: 194 SGYPGGARCLKL 205
           SGYP       L
Sbjct: 168 SGYPSDPHTEAL 179

Length = 199

>gnl|CDD|129812 TIGR00729, TIGR00729, ribonuclease H, mammalian HI/archaeal HII subfamily

 Score =  147 bits (373), Expect = 1e-44
 Identities = 70/187 (37%), Positives = 100/187 (53%), Gaps = 21/187 (11%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQT-LATLNFADSKTLKEEKREELFEDLKVNDS 74
           + GIDEAGRGPV+GP+V   ++     ++  L  L   DSK L   +REELF  ++ N  
Sbjct: 1   VAGIDEAGRGPVIGPLVV-GVFAIEEKREEELRKLGVKDSKKLTPGRREELFSKIR-NKL 58

Query: 75  VGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGIL-LTEVYLDTVGDAE 133
             + V  I P E+  +      INLNE   +      ++   I I   +EVY+D+V    
Sbjct: 59  GRYEVLKITPEEIDRER----NINLNENEIEK----FSKAAIILIEKPSEVYVDSVDVNP 110

Query: 134 K---YQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHR 190
           K    + K+ +R   IK +   KAD+ YPVVS ASI+AKV RDR +      E+ +  + 
Sbjct: 111 KRFKREIKIKERIEGIKVIAEHKADAKYPVVSAASIIAKVERDREI------ESLKRKYG 164

Query: 191 NFGSGYP 197
           +FGSGYP
Sbjct: 165 DFGSGYP 171

This enzyme cleaves RNA from DNA-RNA hybrids. Archaeal members of this subfamily of RNase H are designated RNase HII and one has been shown to be active as a monomer. A member from Homo sapiens was characterized as RNase HI, large subunit [DNA metabolism, DNA replication, recombination, and repair]. Length = 206

>gnl|CDD|187693 cd07180, RNase_HII_Archaea_like, Archaeal ribonuclease HII

 Score =  137 bits (348), Expect = 8e-41
 Identities = 72/186 (38%), Positives = 104/186 (55%), Gaps = 21/186 (11%)

Query: 17  MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVG 76
            GIDEAGRGPV+GPMV   +       + L  L   DSK L  +KREELF ++     V 
Sbjct: 1   CGIDEAGRGPVIGPMVVAGVAIDEEDLKKLEELGVKDSKKLTPKKREELFNEIL---KVA 57

Query: 77  WAVDIIDPRELSAKMLNK--NKINLNEISHDSAIGLITRV-LNIGILLTEVYLDTVG-DA 132
             V I+    +S + +++   + NLNE+  ++   LI R+ L   I    VY+D    + 
Sbjct: 58  DDVVIV---VVSPEEIDERRERGNLNELEVEAFAELINRLKLKPEI----VYVDACDVNE 110

Query: 133 EKYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN 191
           E++  +L +R  +   V+++ KAD+ YPVVS ASI+AKVTRDR       EE  +  + +
Sbjct: 111 ERFAERLRERLNTGVEVIAEHKADAKYPVVSAASIIAKVTRDR-----EIEELKK-EYGD 164

Query: 192 FGSGYP 197
           FGSGYP
Sbjct: 165 FGSGYP 170

Ribonuclease (RNase) H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, archaeal RNase HII and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication or repair. Some archaeal RNase HII show broad divalent cation specificity. It is proposed that three of the four acidic residues at the active site are involved in metal binding and the fourth one involved in the catalytic process in archaea. Most archaeal genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli. Length = 204

>gnl|CDD|223242 COG0164, RnhB, Ribonuclease HII [DNA replication, recombination, and repair]

 Score =  129 bits (326), Expect = 1e-37
 Identities = 59/186 (31%), Positives = 86/186 (46%), Gaps = 32/186 (17%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           + G+DEAGRGP+ GP+V   +  P         L   DSK L  +KREELFE++K    +
Sbjct: 2   VAGVDEAGRGPLAGPVVAAAVILPPDRLPKKLGLK--DSKKLSPKKREELFEEIKEKA-L 58

Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
            W V II   E+       +++N+ E +      +   V  +      V +D        
Sbjct: 59  AWGVGIIPAEEI-------DELNILEATKL---AMRRAVAGLSSQPDLVLVDGND----L 104

Query: 136 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHR----N 191
              L Q   +I      K D+  P ++ ASI+AKVTRDR     + EE A+  +     +
Sbjct: 105 PLGLPQPAVAI-----IKGDAKSPSIAAASILAKVTRDR-----LMEELAK-EYPEYGFD 153

Query: 192 FGSGYP 197
            GSGYP
Sbjct: 154 KGSGYP 159

Length = 199

>gnl|CDD|234574 PRK00015, rnhB, ribonuclease HII; Validated

 Score =  102 bits (258), Expect = 2e-27
 Identities = 48/160 (30%), Positives = 82/160 (51%), Gaps = 26/160 (16%)

Query: 15  CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDS 74
            I G+DEAGRGP+ GP+V   +       + +  LN  DSK L E+KREEL+E++K   +
Sbjct: 19  LIAGVDEAGRGPLAGPVVAAAVILDPD--RPIEGLN--DSKKLSEKKREELYEEIK-EKA 73

Query: 75  VGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEK 134
           + ++V I  P E+       +++N+ E +  +    +  ++    +L         D   
Sbjct: 74  LAYSVGIASPEEI-------DELNILEATLLAMRRAVEGLVKPDYVLV--------DG-- 116

Query: 135 YQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174
              ++ +     + +V  K D+  P ++ ASI+AKVTRDR
Sbjct: 117 --NRVPKLPIPQEAIV--KGDAKSPSIAAASILAKVTRDR 152

Length = 197

>gnl|CDD|187695 cd07182, RNase_HII_bacteria_HII_like, bacterial Ribonuclease HII-like

 Score = 88.2 bits (220), Expect = 6e-22
 Identities = 49/160 (30%), Positives = 76/160 (47%), Gaps = 31/160 (19%)

Query: 18  GIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGW 77
           G+DEAGRGP+ GP+V   +  P      +  LN  DSK L E+KREEL+E++K   ++ W
Sbjct: 2   GVDEAGRGPLAGPVVAAAVILP--PDFEIEGLN--DSKKLSEKKREELYEEIK-EKALAW 56

Query: 78  AVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLD---TVGDAEK 134
            + I    E+       ++IN   I   + + +   V  + +    V +D          
Sbjct: 57  GIGIASVEEI-------DRIN---ILQATLLAMKRAVEGLKVKPDLVLVDGNRLPPLPIP 106

Query: 135 YQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174
            +A           +V  K D+    ++ ASI+AKVTRDR
Sbjct: 107 QEA-----------IV--KGDAKSASIAAASILAKVTRDR 133

Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. Bacterial RNase HII has a role in primer removal based on its involvement in ribonucleotide-specific catalytic activity in the presence of RNA/DNA hybrid substrates. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII and HIII; double deletion of these leads to cellular lethality. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype. Length = 179

>gnl|CDD|237752 PRK14551, rnhB, ribonuclease HII; Provisional

 Score = 83.3 bits (206), Expect = 9e-20
 Identities = 55/187 (29%), Positives = 80/187 (42%), Gaps = 22/187 (11%)

Query: 15  CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDS 74
              G+DEAG+GPVLG M    +                DSK L  E+REEL  +L+ +D+
Sbjct: 1   MRFGVDEAGKGPVLGSMFAAAVRAD----PAALPDGIDDSKRLSPERREELAAELREDDA 56

Query: 75  VGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGD--A 132
           +   V  I P  +     + N + +   +H  A+     V   GI       D  GD  A
Sbjct: 57  IAVGVAEIPPARIDDPETDMNTLTVA--AHAEALS---GVATDGI---TGLCDA-GDVDA 107

Query: 133 EKYQAKLSQRF-PSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN 191
            ++  +++ R    +       AD   P+V  ASIVAKV RD  +        A   + +
Sbjct: 108 GRFARRVADRVALDVSVSAEHGADEEDPLVGAASIVAKVARDAHV-----AALAAE-YGD 161

Query: 192 FGSGYPG 198
            GSGYP 
Sbjct: 162 VGSGYPS 168

Length = 212

>gnl|CDD|187692 cd06590, RNase_HII_bacteria_HIII_like, bacterial Ribonuclease HIII-like

 Score = 72.6 bits (179), Expect = 8e-16
 Identities = 49/187 (26%), Positives = 77/187 (41%), Gaps = 20/187 (10%)

Query: 18  GIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGW 77
           G DE G+G   GP+V   +Y      + L  L   DSK L +EK  +L   +K    +  
Sbjct: 2   GSDEVGKGDYFGPLVVAAVYVDKENIEKLKELGVKDSKKLTDEKIIQLAPKIK--KKIPH 59

Query: 78  AVDIIDPRELSAKMLNKNKINLNEI---SHDSAIGLITRVLNIGILLTEVYLDTVGDAEK 134
           +V  + P + +   L K   NLN+I    H+ A   I  +L        + +D     + 
Sbjct: 60  SVLSLGPEKYNE--LIKKGNNLNKIKALLHNKA---INNLLQKPKKPEAILIDQFASEKV 114

Query: 135 YQAKL-SQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG 193
           Y   L  ++          KA+S +  V+ ASI+A   R        F E  + + + +G
Sbjct: 115 YFNYLKKEKIVKEPLYFRTKAESKHLAVAAASIIA---RYA------FLEKMDKLSKQYG 165

Query: 194 SGYPGGA 200
              P GA
Sbjct: 166 VKLPKGA 172

Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII and HIII. RNases HIII are distinguished by having a large (70-90 residues) N-terminal extension of unknown function. In addition, the active site of RNase HIII differs from that of other RNases H; replacing the fourth residue (aspartate) of the acidic "DEDD" motif with a glutamate. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes, however, no prokaryotic genomes contain the combination of both RNase HI and HIII. This mutual exclusive gene inheritance might be the result of functional redundancy of RNase HI and HIII in prokaryotes. Length = 207

>gnl|CDD|184400 PRK13926, PRK13926, ribonuclease HII; Provisional

 Score = 63.0 bits (153), Expect = 3e-12
 Identities = 50/164 (30%), Positives = 80/164 (48%), Gaps = 32/164 (19%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCP-CSYQQTLATLNFADSKTLKEEKREELFEDLKVNDS 74
           + G+DEAGRG   GP+V   +  P   Y        F DSKTL    RE L E+++   +
Sbjct: 24  VAGVDEAGRGAWAGPVVVAAVILPPGEYP-------FRDSKTLSPAAREALAEEVR-RVA 75

Query: 75  VGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRV-LNIGILLTEVYLDTVGDAE 133
           + WAV   +  E+       +++N+ + +H +A   + R+ +    L+T+ YL       
Sbjct: 76  LAWAVGHAEAAEI-------DRLNVLKATHLAAARALARLAVAPEALVTD-YL------- 120

Query: 134 KYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLR 177
               +L    P    +   KAD+L P V+ AS++AK  RDR +R
Sbjct: 121 ----RLPTPLP---LLAPPKADALSPTVAAASLLAKTERDRLMR 157

Length = 207

>gnl|CDD|223969 COG1039, RnhC, Ribonuclease HIII [DNA replication, recombination, and repair]

 Score = 53.9 bits (130), Expect = 1e-08
 Identities = 41/161 (25%), Positives = 69/161 (42%), Gaps = 13/161 (8%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           ++G DE G+G   GP+V   +Y        L  L   DSK L ++K ++L   +K    +
Sbjct: 85  LIGSDEVGKGDYFGPLVVCAVYVSKENLPKLKELGVKDSKKLSDKKIQQLAPIIK--PLI 142

Query: 76  GWAVDIIDPR---ELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLD---TV 129
             +V  +DP+   EL  K  N N +      H+ AI  +            + +D   + 
Sbjct: 143 PHSVLTLDPKKYNELYKKFNNANSMKT--FLHNQAIQNLLPQKGAQ--PEFIVIDQFASS 198

Query: 130 GDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKV 170
            + + Y  K + +F         KA+S    V+ ASI+A+ 
Sbjct: 199 ENYKNYLQKETNKFSEPVL-FLTKAESKSLAVAVASIIARY 238

Length = 297

>gnl|CDD|129799 TIGR00716, rnhC, ribonuclease HIII

 Score = 52.6 bits (126), Expect = 3e-08
 Identities = 42/155 (27%), Positives = 73/155 (47%), Gaps = 6/155 (3%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           ++G DE+G+G + GP+V  C+Y P      +++LN  DSK L +++ E L  +LK    V
Sbjct: 83  VIGCDESGKGDIFGPLVLCCVYIPEENYLKVSSLNPRDSKRLSDKRIERLALNLK--PLV 140

Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
                 + P + +   L +   NLN++       LI R+L     ++EV +D    +  +
Sbjct: 141 KAYCYELKPEKYNK--LYRKFRNLNKMMAHFHKLLIERLLKEECGVSEVVVDQFAPSNPF 198

Query: 136 QAKLSQRFPS-IKFVVSKKADSLYPVVSGASIVAK 169
              L  R       +   +A+     V+ ASI A+
Sbjct: 199 FNHLKGRDIVGEDVIFETEAER-NLAVAAASIFAR 232

This enzyme cleaves RNA from DNA-RNA hybrids. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other. The only RNase H homolog in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This model describes bacterial RNase III [DNA metabolism, DNA replication, recombination, and repair]. Length = 284

>gnl|CDD|184399 PRK13925, rnhB, ribonuclease HII; Provisional

 Score = 51.5 bits (124), Expect = 3e-08
 Identities = 37/162 (22%), Positives = 64/162 (39%), Gaps = 20/162 (12%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           I G+DE GRG + GP+    +      +  L      DSK L  ++R +L   +    + 
Sbjct: 10  IAGVDEVGRGALFGPVFAAAVILSEKAEPQLLQAGLTDSKKLSPKRRAQLVPLILTL-AS 68

Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
            W +     RE          I+   I   + + ++  +  +    +   +D  G+    
Sbjct: 69  DWGIGQASARE----------IDRLGIRQATELAMLRALKKLKSPPSLCLVD--GNLPLR 116

Query: 136 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLR 177
                QR      +V  K DS    ++ ASI+AKV RD  ++
Sbjct: 117 LWPGPQR-----TIV--KGDSKSAAIAAASILAKVWRDDLIK 151

Length = 198

>gnl|CDD|173015 PRK14550, rnhB, ribonuclease HII; Provisional

 Score = 47.6 bits (113), Expect = 8e-07
 Identities = 45/167 (26%), Positives = 76/167 (45%), Gaps = 27/167 (16%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
            +GIDEAGRG + G +    + C          +   DSK L  +KR  L + +K +  V
Sbjct: 2   TLGIDEAGRGCLAGSLFVAGVACNEKTALEFLKMGLKDSKKLSPKKRFFLEDKIKTHGEV 61

Query: 76  GWAV-----DIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG 130
           G+ V     + ID   L A +    K+ + EI           + N   L  E+ +D  G
Sbjct: 62  GFFVVKKSANEIDSLGLGACL----KLAIQEI-----------LENGCSLANEIKID--G 104

Query: 131 DAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLR 177
           +       L++R+P+I+ ++  K D     ++ AS++AK  +DR + 
Sbjct: 105 NT---AFGLNKRYPNIQTII--KGDETIAQIAMASVLAKAFKDREML 146

Length = 204

>gnl|CDD|234886 PRK00996, PRK00996, ribonuclease HIII; Provisional

 Score = 45.3 bits (108), Expect = 8e-06
 Identities = 46/167 (27%), Positives = 70/167 (41%), Gaps = 25/167 (14%)

Query: 14  PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVND 73
             I G DE G+G   GP+    +Y        L  L   DSK L + K  ++   L+  +
Sbjct: 88  SLI-GSDEVGKGDYFGPLTVAAVYVDKEQIPFLKKLGVKDSKKLTDTKIRQIAPQLR--E 144

Query: 74  SVGWAVDIIDPR---ELSAKMLNKNKINLNEISHDSAIGLITRVLN----IGILL----- 121
            +  +V ++ P    EL AK  N+NK  L    H+ AI  + + +       I++     
Sbjct: 145 KIPHSVLLLSPEKYNELQAKGYNQNK--LKAWLHNQAIDNLLQKIAGIQPEKIVIDQFAS 202

Query: 122 TEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVA 168
            EVY        KY  K   +F         KA+S +  V+ ASI+A
Sbjct: 203 PEVYQ-------KYLKKEKNKFRD-NVTFETKAESKHLAVAAASIIA 241

Length = 304

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	219
cd07181	216	RNaseH_typeII_eukaryota_like Eukaryotic Ribonuclea	100.0
KOG2299	301	consensus Ribonuclease HI [Replication, recombinat	100.0
cd07180	204	RNaseH_typeII_Archaea_like Archaeal ribonuclease H	100.0
cd06266	193	RNaseH_typeII Ribonuclease H type II. Ribonuclease	100.0
PRK14551	212	rnhB ribonuclease HII; Provisional	100.0
TIGR00729	206	ribonuclease H, mammalian HI/archaeal HII subfamil	100.0
COG0164	199	RnhB Ribonuclease HII [DNA replication, recombinat	100.0
cd06590	208	RNaseH_typeII_bacteria_HIII_like bacterial Ribonuc	100.0
PRK13925	198	rnhB ribonuclease HII; Provisional	100.0
PRK00015	197	rnhB ribonuclease HII; Validated	100.0
cd07182	179	RNaseH_typeII_bacteria_HII_like bacterial Ribonucl	100.0
PRK14550	204	rnhB ribonuclease HII; Provisional	100.0
PRK00996	304	ribonuclease HIII; Provisional	100.0
PF01351	198	RNase_HII: Ribonuclease HII; InterPro: IPR024567 R	100.0
PRK13926	207	ribonuclease HII; Provisional	100.0
TIGR00716	284	rnhC ribonuclease HIII. Two types of ribonuclease	100.0
COG1039	297	RnhC Ribonuclease HIII [DNA replication, recombina	100.0

>cd07181 RNaseH_typeII_eukaryota_like Eukaryotic Ribonuclease HII; putative role in Okazaki fragment removal during replication

Probab=100.00  E-value=4.7e-60  Score=403.49  Aligned_cols=191  Identities=63%  Similarity=1.014  Sum_probs=173.7

Q ss_pred             eeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcC-cccEEEEEEChhhHhHHhhhhh
Q 027718           17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVND-SVGWAVDIIDPRELSAKMLNKN   95 (219)
Q Consensus        17 iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~-~~~~~v~~i~p~~id~~~~~~~   95 (219)
                      +|||||||||+|||||||||+++.+..+.|..+||+|||+||+++|++|+++|++.. ++.|.+.+++|++||+.|...+
T Consensus         1 iGiDEaGRG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~L~~~I~~~~~~~~~~i~~i~~~~id~~~~~~~   80 (216)
T cd07181           1 LGIDEAGRGPVLGPMVYGIAYCPISYEEDLKKLGFADSKTLTEEKREELFKKIKEKSEALGWATRILSPQYISAKMLART   80 (216)
T ss_pred             CCCcCCCCCCChhhhEEEEEEEchHhhhhhhhcCCCcCCcCCHHHHHHHHHHHHhccccceEEEEEECHHHHCHHhhhcc
Confidence            699999999999999999999998876778778999999999999999999999742 5789999999999998765434


Q ss_pred             hchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHHHH
Q 027718           96 KINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRT  175 (219)
Q Consensus        96 ~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~~  175 (219)
                      ..|||+++++++.+++++++..+..++.++||+++++++|.++|+..+|+.++++++|||++|++||||||||||+||++
T Consensus        81 ~~nln~~~~~~~~~~i~~~~~~~~~~~~vliD~~~~~~~~~~~L~~~~~~~~~~~~~kaD~~~~~VAAASIvAKV~RD~~  160 (216)
T cd07181          81 KYNLNEISHDAAIGLIKSVLDKGVNVTEVYVDTVGPPEKYQAKLKKLFPGIKFTVEKKADSLYPIVSAASIVAKVTRDRA  160 (216)
T ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCCCEEEECCCCChhHHHHhhhhcCCCCceEEeeCcccccHHHHHHHHHHHHHHHHH
Confidence            57999999999999998877655567899999999888999999876677778889999999999999999999999999


Q ss_pred             HHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718          176 LRGWIFEETAENMHRNFGSGYPGGARCLKLSI  207 (219)
Q Consensus       176 m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~  207 (219)
                      |++|++.||.|+|.+++|||||||+||++|..
T Consensus       161 m~~l~~~~~~~~~~~~~gsGYpsd~~t~~~l~  192 (216)
T cd07181         161 LKNWQFDEYLIDPDGDFGSGYPSDPKTKKWLK  192 (216)
T ss_pred             HHHHHhhCccccccCCCceECCCHHHHHHHHH
Confidence            99999999999999999999999999999994

Ribonuclease (RNase) HII endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is a type II RNase H that is active during replication and is believed to play a role in removal

>KOG2299 consensus Ribonuclease HI [Replication, recombination and repair]

Probab=100.00  E-value=1.1e-55  Score=376.77  Aligned_cols=203  Identities=59%  Similarity=0.978  Sum_probs=190.1

Q ss_pred             CCCCCCcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhc----CcccEEEEEECh
Q 027718            9 KWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN----DSVGWAVDIIDP   84 (219)
Q Consensus         9 ~~~~~~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~----~~~~~~v~~i~p   84 (219)
                      +|++.++++|||||||||++||||+|+++||.+....|..+|+.|||+|++.+|++|+++|+++    ..++|++.+++|
T Consensus        23 ~~~~~PcvlGIDEAGRGPVLGPMVYa~~ycP~~~~~~l~~lgfaDSK~L~e~kRe~lf~~i~~d~~~~~~vgwA~~~isP  102 (301)
T KOG2299|consen   23 EQKSEPCVLGIDEAGRGPVLGPMVYAAAYCPLDYLEDLENLGFADSKTLTEAKREELFNKIKEDEELTSNVGWATDCISP  102 (301)
T ss_pred             cccCCceEeeccccCCCCcccceeeEEEeccchhhhhhhhcCccchhhccHHHHHHHHHHHhhhhhhhhceeeEeeecCH
Confidence            5666799999999999999999999999999998888999999999999999999999999763    237899999999


Q ss_pred             hhHhHHhhhhhhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHH
Q 027718           85 RELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGA  164 (219)
Q Consensus        85 ~~id~~~~~~~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAA  164 (219)
                      .+|...|++++.+|||..+|++++.+|+.+++.++....|++|+.|+|.+|...|++.||++++++..|||+.|+.||||
T Consensus       103 ~~IS~~Ml~r~kynLNevshdsam~LI~~v~~~gvnvteiyVDTVGpp~~Yq~kLek~FP~~k~tV~kKADSlfpiVS~A  182 (301)
T KOG2299|consen  103 REISASMLRRNKYNLNEVSHDSAMGLIDEVLDQGVNVTEIYVDTVGPPAKYQEKLEKRFPGIKFTVTKKADSLFPIVSAA  182 (301)
T ss_pred             HHHHHHHHHHhcCCchhhhhHHHHHHHHHHHHhCCceEEEEEecCCChHHHHHHHHhhCCCeEEEEeecccccccchhhh
Confidence            99999999888999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHhHHHHHHHHHHhhHhcccccccCCCccccCCchhhhhhhhhhhh
Q 027718          165 SIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVCNN  211 (219)
Q Consensus       165 SIlAKv~RD~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~~~~~  211 (219)
                      ||+|||+||+.+++|+..+.....+.++|||||+||.|++|++.+.+
T Consensus       183 SI~AKVtRD~alk~w~~~E~~~~~d~~~GSGYP~DP~T~~wLk~~v~  229 (301)
T KOG2299|consen  183 SIVAKVTRDRALKEWQFEEKLSDPDEDLGSGYPSDPETKAWLKENVD  229 (301)
T ss_pred             hhhhhhhhccccceeeeeeecccCCccccCCCCCChhHHHHHHhccc
Confidence            99999999999999987777777788999999999999999986543

>cd07180 RNaseH_typeII_Archaea_like Archaeal ribonuclease HII

Probab=100.00  E-value=6.1e-54  Score=362.97  Aligned_cols=186  Identities=37%  Similarity=0.590  Sum_probs=162.9

Q ss_pred             eeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhh
Q 027718           17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK   96 (219)
Q Consensus        17 iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~~   96 (219)
                      ||||||||||+|||||||||+++.+....|..+||+|||+||+++|++|+++|++. .+.|++.+++|++||+++   ..
T Consensus         1 iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~-~~~~~i~~i~~~~id~~~---~~   76 (204)
T cd07180           1 CGIDEAGRGPVIGPMVVAGVAIDEESLKKLKSLGVKDSKKLTPKKREELYNEILKV-ADDVVIVIVSPEEIDERR---EA   76 (204)
T ss_pred             CCCCCCCCCCcccceEEEEEEECHHHhhhHhhcCCCcCCCCCHHHHHHHHHHHHhc-CCeEEEEEECHHHhChhh---hh
Confidence            69999999999999999999999987778888999999999999999999999984 678999999999999876   36


Q ss_pred             chHHHHHHHHHHHHHHHHHhcCCCCCEEEECCC-CChHHHHHHhhccC-CCcceEEeecCccchhhHHHHhHHhHHHHHH
Q 027718           97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTV-GDAEKYQAKLSQRF-PSIKFVVSKKADSLYPVVSGASIVAKVTRDR  174 (219)
Q Consensus        97 ~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~-~~~~~~~~~L~~~~-~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~  174 (219)
                      .|||.++.++|.++++++.   .++..++||++ +++++|.++|++.+ ++.++++++|||+++++||||||||||+||+
T Consensus        77 ~nln~~~~~~~~~~i~~l~---~~~~~iliD~~~~~~~~~~~~l~~~~~~~~~~~~~~KgD~~~~~VAaASIlAKv~Rd~  153 (204)
T cd07180          77 HNLNELEAEAFAELINRLS---DKPDIVYVDACDVNEERFAEELRERLNSGVEVIAEHKADAKYPVVSAASIIAKVERDR  153 (204)
T ss_pred             cCHHHHHHHHHHHHHHHhh---cCCCEEEEeCCCCCHHHHHHHHHHhcCCCCcEEEEeCCcccCchhhHHHHHHHHHHHH
Confidence            7999999999999998875   24678999999 46778888887654 3567788999999999999999999999999


Q ss_pred             HHHHhhHhcccccccCCCccccCCchhhhhhhhhhhhhccccC
Q 027718          175 TLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFGG  217 (219)
Q Consensus       175 ~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~~~~~~~~~~~  217 (219)
                      +|++|++.||      ++|+|||+|+.|++|.+  +++..|||
T Consensus       154 ~m~~l~~~~~------~~g~Gy~sd~~t~~~l~--~~~~~~g~  188 (204)
T cd07180         154 EIEELKEEYG------DFGSGYPSDPRTIKFLR--NYYREHGE  188 (204)
T ss_pred             HHHHHHHhcc------cCCCcCCCCHHHHHHHH--HHHHhhCC
Confidence            9999998885      56799999999999985  33444444

Ribonuclease (RNase) H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, archaeal RNase HII and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication or repair. Some archaeal RNase HII show broad divalent cation specificity. It is proposed that three of the four acidic residues at the active site are involved in metal binding and the fourth one involved in the catalytic process in archaea. Most archaeal genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears tha

>cd06266 RNaseH_typeII Ribonuclease H type II

Probab=100.00  E-value=2.4e-53  Score=356.16  Aligned_cols=178  Identities=37%  Similarity=0.522  Sum_probs=161.2

Q ss_pred             eeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhh
Q 027718           17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK   96 (219)
Q Consensus        17 iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~~   96 (219)
                      +|||||||||+|||||||||+++.+..+.|..+||+|||+||+++|++|+++|++ ..+.|.+.+++|++||+       
T Consensus         1 iGiDEaGrG~~~GPlvva~v~~~~~~~~~l~~~gv~DSK~Lt~~~r~~l~~~I~~-~~~~~~v~~~~p~~id~-------   72 (193)
T cd06266           1 AGIDEAGRGPLAGPVVAAAVILPKENIEILKILGVKDSKKLSEKKREELFEEIKE-EALAYAIGIISPEEIDE-------   72 (193)
T ss_pred             CCCcccCcCCcchheEEEEEEEchhhcccccccCCCCcccCCHHHHHHHHHHHHh-hCCeEEEEEECHHHHCH-------
Confidence            6999999999999999999999999888888999999999999999999999998 36899999999999974       


Q ss_pred             chHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHHHHH
Q 027718           97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTL  176 (219)
Q Consensus        97 ~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~~m  176 (219)
                      .|||.++..+|.+++.++.   .++..++||++++++.|.. +....++.++++++|||++|++||||||||||+||+.|
T Consensus        73 ~nl~~~~~~~~~~~i~~l~---~~~~~i~iD~~~~~~~~~~-~~~~~~~~~~~~~~kaD~~~~~VaAASIiAKv~rd~~m  148 (193)
T cd06266          73 LNILQATALAMARAILNLG---VKPDEVLVDGNGVPEKYFA-LEKKFLPIPVTAIVKGDSKSPSVAAASILAKVTRDRLM  148 (193)
T ss_pred             HHHHHHHHHHHHHHHHhcC---CCCCEEEECCCCChhhhhh-hcccCCCCCeEEEeccccccHhHHHHHHHHHHHHHHHH
Confidence            5999999999998888764   3568999999999988876 44445678889999999999999999999999999999


Q ss_pred             HHhhHhcccccccCCCccccCCchhhhhhhhh
Q 027718          177 RGWIFEETAENMHRNFGSGYPGGARCLKLSIV  208 (219)
Q Consensus       177 ~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~~  208 (219)
                      +.|+..||.|+|  ++|+|||+|+||++|.+-
T Consensus       149 ~~l~~~~~~~~~--~~gsGy~s~~~~~~~~~~  178 (193)
T cd06266         149 EELDEEYPGYGF--AKGKGYPTDPHTEAILKY  178 (193)
T ss_pred             HHHHHHCCCCCC--cCCcCcCcHHHHHHHHHh
Confidence            999999999887  577999999999999764

Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes, however, no prokaryotic genome contained the combination of only RNase HI and HIII. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escheri

>PRK14551 rnhB ribonuclease HII; Provisional

Probab=100.00  E-value=2e-52  Score=355.54  Aligned_cols=174  Identities=29%  Similarity=0.426  Sum_probs=151.6

Q ss_pred             EeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhh
Q 027718           16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKN   95 (219)
Q Consensus        16 ~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~   95 (219)
                      ++|||||||||+|||||||||+++.+.   + ..||+|||+||+++|++|+++|++...+.|++.+++|++||+     .
T Consensus         2 ~iGiDEaGRG~v~GPlVvaav~~~~~~---~-~~gv~DSK~Ls~~~R~~l~~~I~~~~~~~~~i~~isp~~Id~-----~   72 (212)
T PRK14551          2 RFGVDEAGKGPVLGSMFAAAVRADPAA---L-PDGIDDSKRLSPERREELAAELREDDAIAVGVAEIPPARIDD-----P   72 (212)
T ss_pred             eeCccCCCCCCccccceEEEEEECccc---C-cCCCcCcccCCHHHHHHHHHHHHhccCceEEEEEeCHHHHCc-----c
Confidence            799999999999999999999999763   2 359999999999999999999997423689999999999985     2


Q ss_pred             hchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCC-ChHHHHHHhhccC-CCcceEEeecCccchhhHHHHhHHhHHHHH
Q 027718           96 KINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEKYQAKLSQRF-PSIKFVVSKKADSLYPVVSGASIVAKVTRD  173 (219)
Q Consensus        96 ~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~-~~~~~~~~L~~~~-~~~~~~~~~KaD~~~~sVAAASIlAKv~RD  173 (219)
                      ..|||.++..+|.+++++++.   ++..++||++. ++++|..++++.+ ++.++++++|||++|++||||||||||+||
T Consensus        73 ~~nln~~~~~a~~~ai~~l~~---~~~~v~iD~~~~~~~~~~~~l~~~~~~~~~~~~~~KaD~~~~~VAAASIlAKv~RD  149 (212)
T PRK14551         73 ETDMNTLTVAAHAEALSGVAT---DGITGLCDAGDVDAGRFARRVADRVALDVSVSAEHGADEEDPLVGAASIVAKVARD  149 (212)
T ss_pred             ccCHHHHHHHHHHHHHHhhcc---CCCEEEECCCCCchHHHHHhhhhccCCCCceEEEecccchhHHHHHHHHHHHHHHH
Confidence            479999999999999987642   35789999984 6677887887664 356778899999999999999999999999


Q ss_pred             HHHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718          174 RTLRGWIFEETAENMHRNFGSGYPGGARCLKLSI  207 (219)
Q Consensus       174 ~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~  207 (219)
                      +.|++|++.||      ++|||||||++|++|.+
T Consensus       150 ~~m~~l~~~y~------~~GsGYpsd~~t~~~l~  177 (212)
T PRK14551        150 AHVAALAAEYG------DVGSGYPSDPTTREFLR  177 (212)
T ss_pred             HHHHHHHHHCC------CCCCcCCCcHHHHHHHH
Confidence            99999998886      56799999999999964

>TIGR00729 ribonuclease H, mammalian HI/archaeal HII subfamily

Probab=100.00  E-value=2.8e-52  Score=353.32  Aligned_cols=179  Identities=37%  Similarity=0.568  Sum_probs=153.3

Q ss_pred             EeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhh
Q 027718           16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKN   95 (219)
Q Consensus        16 ~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~   95 (219)
                      ++|||||||||+|||||||||+++.+....|..+||+|||+||+++|++|+++|++. .+.|++..++|++||+.+    
T Consensus         1 iiGiDEaGrG~~~GPlvva~v~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~-~~~~~i~~i~p~~id~~~----   75 (206)
T TIGR00729         1 VAGIDEAGRGPVIGPLVVGVFAIEEKREEELRKLGVKDSKKLTPGRREELFSKIRNK-LGRYEVLKITPEEIDRER----   75 (206)
T ss_pred             CcCccCCCCCCccCceEEEEEEechhhhhhHhhcCCccCCcCCHHHHHHHHHHHHhh-cCcEEEEEEcHHHHChHH----
Confidence            589999999999999999888877765667778899999999999999999999974 578999999999999754    


Q ss_pred             hchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHH-HHHHhh--ccCCCcceEEeecCccchhhHHHHhHHhHHHH
Q 027718           96 KINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEK-YQAKLS--QRFPSIKFVVSKKADSLYPVVSGASIVAKVTR  172 (219)
Q Consensus        96 ~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~-~~~~L~--~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~R  172 (219)
                      ..|||.++..++.++++++..   ++..++||+++.++. |...+.  ..+|+.++++++|||+++++||||||||||+|
T Consensus        76 ~~nln~~~~~a~~~~i~~l~~---~~~~v~iD~~~~~~~~~~~~~~~~~~~~~~~~~~~~KaD~~~~~VAAASIlAKv~R  152 (206)
T TIGR00729        76 NINLNENEIEKFSKAAIILIE---KPSEVYVDSVDVNPKRFKREIKIKERIEGIKVIAEHKADAKYPVVSAASIIAKVER  152 (206)
T ss_pred             HhhHHHHHHHHHHHHHHHHhc---CCcEEEEcCCCCcHHHHHHHHHHhccCCCCcEEEEeccccccchhhHHHHHHHHHH
Confidence            479999999999999887642   357899999986654 332222  23566788899999999999999999999999


Q ss_pred             HHHHHHhhHhcccccccCCCccccCCchhhhhhhhh
Q 027718          173 DRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIV  208 (219)
Q Consensus       173 D~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~~  208 (219)
                      |++|++|++.||.      +|+|||||++|++|.+.
T Consensus       153 D~~m~~l~~~~~~------~GsGY~sd~~t~~~l~~  182 (206)
T TIGR00729       153 DREIESLKRKYGD------FGSGYPSDPRTREWLEE  182 (206)
T ss_pred             HHHHHHHHHhcCC------CCCcCCCCHHHHHHHHH
Confidence            9999999988865      57999999999999864

Archaeal members of this subfamily of RNase H are designated RNase HII and one has been shown to be active as a monomer. A member from Homo sapiens was characterized as RNase HI, large subunit.

>COG0164 RnhB Ribonuclease HII [DNA replication, recombination, and repair]

Probab=100.00  E-value=1.5e-52  Score=350.41  Aligned_cols=177  Identities=32%  Similarity=0.450  Sum_probs=149.3

Q ss_pred             cEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhh
Q 027718           15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNK   94 (219)
Q Consensus        15 ~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~   94 (219)
                      .++|||||||||++||||+|||++|.+...  ..+|++|||+||+++|++|+++|++ .++.|.+.++++++||      
T Consensus         1 ~vaGIDEAGRGpl~GPvV~Aavil~~~~~~--~~~Gl~DSKkLs~~kRe~L~~~I~~-~a~~~~v~~~~~~~Id------   71 (199)
T COG0164           1 LVAGVDEAGRGPLAGPVVAAAVILPPDRLP--KKLGLKDSKKLSPKKREELFEEIKE-KALAWGVGIIPAEEID------   71 (199)
T ss_pred             CcCcccCCCcCCcccceeEEEEEECccccc--cccCccccccCCHHHHHHHHHHHHh-hccEEEEEEcCHHHHh------
Confidence            378999999999999999999999997543  5589999999999999999999995 4789999999999995      


Q ss_pred             hhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHHH
Q 027718           95 NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDR  174 (219)
Q Consensus        95 ~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~  174 (219)
                       +.||+++++.++.+++..+.   .+++.++||+++.+.        .++.. .++++|||+++++||||||||||+||+
T Consensus        72 -~~ni~~a~~~am~~av~~l~---~~~~~vlvD~~~~~~--------~l~~~-~~a~~KgDa~~~~IaAASIvAKV~RDr  138 (199)
T COG0164          72 -ELNILEATKLAMRRAVAGLS---SQPDLVLVDGNDLPL--------GLPQP-AVAIIKGDAKSPSIAAASILAKVTRDR  138 (199)
T ss_pred             -hhhHHHHHHHHHHHHHHhcc---ccCCEEEEeCCCccc--------cCCCC-cceeeccchhhHHHHHHHHHHHHHHHH
Confidence             58999999988887777653   234889999886221        11111 277899999999999999999999999


Q ss_pred             HHHHhhHhcccccccCCCccccCCchhhhhhhh---hh-hhhccc
Q 027718          175 TLRGWIFEETAENMHRNFGSGYPGGARCLKLSI---VC-NNFQSF  215 (219)
Q Consensus       175 ~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~---~~-~~~~~~  215 (219)
                      +|++|++.||+|+|+.|  ||||||+||.+|.+   +. .|+++|
T Consensus       139 ~m~~l~~~yp~Y~~~~~--~GY~T~~h~~a~~~~~~~~~~hR~Sf  181 (199)
T COG0164         139 LMEELAKEYPEYGFDKG--SGYPTDPHTEALLKKGGTPGIHRRSF  181 (199)
T ss_pred             HHHHHHhhCcCcCcccC--CCCCChHHHHHHHHhCCCCceeeccc
Confidence            99999999999999655  99999999999983   22 455555

>cd06590 RNaseH_typeII_bacteria_HIII_like bacterial Ribonuclease HIII-like

Probab=100.00  E-value=7.1e-52  Score=351.23  Aligned_cols=184  Identities=21%  Similarity=0.248  Sum_probs=165.7

Q ss_pred             eeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhh
Q 027718           17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK   96 (219)
Q Consensus        17 iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~~   96 (219)
                      +|||||||||+|||||||||+++.+....|..+||+|||+||+++|++|++.|++  .+.|++..++|++||.++.  +.
T Consensus         1 iGiDEaGRG~~~GPlVvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~--~~~~~v~~i~~~~in~~~~--~~   76 (208)
T cd06590           1 IGSDEVGKGDYFGPLVVAAVYVDKENISKLKKLGVKDSKKLTDKKIIRLAPKIKK--KIPYSVLSLGPEKYNELYK--KG   76 (208)
T ss_pred             CCCCCCCCCCCcCccEEEEEEEcHHHHHHHHHCCCCcCCcCCHHHHHHHHHHHHh--cCCEEEEecCHHHHHHHHH--cc
Confidence            6999999999999999999999987777788899999999999999999999998  3789999999999998752  36


Q ss_pred             chHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccC--CCcceEEeecCccchhhHHHHhHHhHHHHHH
Q 027718           97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRF--PSIKFVVSKKADSLYPVVSGASIVAKVTRDR  174 (219)
Q Consensus        97 ~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~--~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~  174 (219)
                      .|+|.++.++|.+++++++..+..++.+++|+++.+++|..+|++.+  +++++++++|||++|++||||||||||+||+
T Consensus        77 ~nln~l~~~~~~~ai~~l~~~~~~~~~v~vD~~~~~~~~~~~l~~~~~~~~~~~~~~~kaD~~~~~VaAASIlAKv~Rd~  156 (208)
T cd06590          77 KNLNKLKALLHNKAINNLLEKPKKPVAILIDQFASEKVYKRYLKKEKKIVKEPLIFRTKAESKHLAVAAASILARYAFLE  156 (208)
T ss_pred             CCHHHHHHHHHHHHHHHHHHhcCCCCEEEecCCCCHHHHHHHHHhhccCCCCceEEEecCcccchHHHHHHHHHHHHHHH
Confidence            79999999999999998875445678899999999889988888765  5678889999999999999999999999999


Q ss_pred             HHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718          175 TLRGWIFEETAENMHRNFGSGYPGGARCLKLSI  207 (219)
Q Consensus       175 ~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~  207 (219)
                      .|++|++.   |+|..++|+|||+|+.|++|.+
T Consensus       157 ~m~~l~~~---yg~~~~~G~g~~~~~~~~~~l~  186 (208)
T cd06590         157 KMEKLSKQ---YGMKLPKGASSKVDEQAAEIIK  186 (208)
T ss_pred             HHHHHHHH---hCCCCCCCCCcHHHHHHHHHHH
Confidence            99998655   6899999999999999999876

Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII and HIII. RNases HIII are distinguished by having a large (70-90 residues) N-terminal extension of unknown function. In addition, the active site of RNase HIII differs from that of other RNases H; replacing the fourth residue (aspartate) of the acidic "DEDD" motif with a glutamate. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes, however, no prokaryotic genomes contain the combination of both RNase HI and HIII. This mutual exclusive gen

>PRK13925 rnhB ribonuclease HII; Provisional

Probab=100.00  E-value=1.2e-51  Score=347.21  Aligned_cols=181  Identities=21%  Similarity=0.313  Sum_probs=153.4

Q ss_pred             CCcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhh
Q 027718           13 NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKML   92 (219)
Q Consensus        13 ~~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~   92 (219)
                      .+.++|||||||||+|||||||||+++.+....|..+||+|||+||+++|++|+++|++. ...|++.+++|++||    
T Consensus         7 ~~~iiGiDEAGRGpv~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~~Re~l~~~I~~~-~~~~~i~~i~~~eId----   81 (198)
T PRK13925          7 SELIAGVDEVGRGALFGPVFAAAVILSEKAEPQLLQAGLTDSKKLSPKRRAQLVPLILTL-ASDWGIGQASAREID----   81 (198)
T ss_pred             CCeEEeecCCCCCCChHHhEEEEEEEchHhhhhhhhcCCCCcccCCHHHHHHHHHHHHhh-CCcEEEEEECHHHhC----
Confidence            468999999999999999999999999887777888999999999999999999999874 567999999999996    


Q ss_pred             hhhhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHH
Q 027718           93 NKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTR  172 (219)
Q Consensus        93 ~~~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~R  172 (219)
                         ..|||.++..++.++++++   ..+++.|++|+++...        .+++.. ..++|||++|++||||||||||+|
T Consensus        82 ---~~ni~~~~~~a~~~~i~~l---~~~~~~v~iD~~~~~~--------~~~~~~-~~v~kaD~~~~~VaAASIiAKV~R  146 (198)
T PRK13925         82 ---RLGIRQATELAMLRALKKL---KSPPSLCLVDGNLPLR--------LWPGPQ-RTIVKGDSKSAAIAAASILAKVWR  146 (198)
T ss_pred             ---HhhHHHHHHHHHHHHHHhc---CCCCCEEEECCccccC--------cCCCCc-eeecccccccHHHHHHHHHHHHHH
Confidence               4689999988888777654   2346789999986321        122222 345799999999999999999999


Q ss_pred             HHHHHHhhHhcccccccCCCccccCCchhhhh---hhhhhhhhccc
Q 027718          173 DRTLRGWIFEETAENMHRNFGSGYPGGARCLK---LSIVCNNFQSF  215 (219)
Q Consensus       173 D~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~---~~~~~~~~~~~  215 (219)
                      |++|+.|++.||+|+|+.|  +||||++|+..   +.....|+++|
T Consensus       147 D~~m~~l~~~yp~y~f~~~--kGY~t~~h~~~i~~~G~~p~hR~sf  190 (198)
T PRK13925        147 DDLIKRLAKKYPGYGLEKN--KGYGTAQHRQALLKLGPTPLHRKSF  190 (198)
T ss_pred             HHHHHHHHHHCCCCCcccC--CCCCcHHHHHHHHHhCcCHHHcCCC
Confidence            9999999999999999877  89999999865   45566777766

>PRK00015 rnhB ribonuclease HII; Validated

Probab=100.00  E-value=4.8e-51  Score=343.55  Aligned_cols=166  Identities=30%  Similarity=0.411  Sum_probs=145.6

Q ss_pred             CcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhh
Q 027718           14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN   93 (219)
Q Consensus        14 ~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~   93 (219)
                      ..++|||||||||+|||||||||+++.+..  +  +||+|||+||+++|++|+++|++. .+.|++.+++|++||+    
T Consensus        18 ~~viGiDEaGrG~v~GPlvvaav~~~~~~~--l--~gv~DSK~Ls~~~R~~l~~~I~~~-~~~~~i~~isp~~id~----   88 (197)
T PRK00015         18 GLIAGVDEAGRGPLAGPVVAAAVILDPDRP--I--EGLNDSKKLSEKKREELYEEIKEK-ALAYSVGIASPEEIDE----   88 (197)
T ss_pred             cEEEeecCcCCCCcccceeEEEEEECcccc--c--CCCCCcccCCHHHHHHHHHHHHHh-CceEEEEEcCHHHHHH----
Confidence            579999999999999999999999987632  2  699999999999999999999984 5789999999999974    


Q ss_pred             hhhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHH
Q 027718           94 KNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRD  173 (219)
Q Consensus        94 ~~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD  173 (219)
                         .|+|+++..++.++++++    ..+..++||+++.++.          ..++++++|||++|++||||||||||+||
T Consensus        89 ---~nln~~~~~a~~~~i~~l----~~~~~i~vD~~~~~~~----------~~~~~~~~kaD~~~~~VaAASIvAKv~RD  151 (197)
T PRK00015         89 ---LNILEATLLAMRRAVEGL----VKPDYVLVDGNRVPKL----------PIPQEAIVKGDAKSPSIAAASILAKVTRD  151 (197)
T ss_pred             ---hhHHHHHHHHHHHHHHhc----CCCCEEEECCCCCCCC----------CCCeEEEEcCCcccHHHHHHHHHHHHHHH
Confidence               699999999988888765    2457899999986521          12356678999999999999999999999


Q ss_pred             HHHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718          174 RTLRGWIFEETAENMHRNFGSGYPGGARCLKLSI  207 (219)
Q Consensus       174 ~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~  207 (219)
                      ++|+.|+++||.|+|..+  ||||||+||++|.+
T Consensus       152 ~~m~~l~~~~~~yg~~~~--sGY~s~~~~~a~~~  183 (197)
T PRK00015        152 RLMEELDKEYPGYGFAKH--KGYGTKEHLEALAK  183 (197)
T ss_pred             HHHHHHHHhCcCCCCcCC--CcCCCHHHHHHHHH
Confidence            999999999999998766  89999999999875

>cd07182 RNaseH_typeII_bacteria_HII_like bacterial Ribonuclease HII-like

Probab=100.00  E-value=2e-50  Score=335.36  Aligned_cols=162  Identities=30%  Similarity=0.429  Sum_probs=141.5

Q ss_pred             eeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhh
Q 027718           17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK   96 (219)
Q Consensus        17 iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~~   96 (219)
                      +|||||||||+|||||||||+++.+...    +||+|||+||+++|++|+++|++. .+.|++.+++|++||+       
T Consensus         1 ~GiDEaGRG~~~GPlvvaav~~~~~~~~----~gv~DSK~Ls~~~R~~l~~~I~~~-~~~~~v~~~~~~~Id~-------   68 (179)
T cd07182           1 AGVDEAGRGPLAGPVVAAAVILPPDFEI----EGLNDSKKLSEKKREELYEEIKEK-ALAWGIGIASPEEIDR-------   68 (179)
T ss_pred             CCCcCccCCCcccceEEEEEEECcccCc----CCCCCcccCCHHHHHHHHHHHHHh-cccEEEEEECHHHHCH-------
Confidence            6999999999999999999999886422    799999999999999999999984 6789999999999964       


Q ss_pred             chHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHHHHH
Q 027718           97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTL  176 (219)
Q Consensus        97 ~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~~m  176 (219)
                      .|||+++..++.++++++   ...++.+++|++..++.          ..++++++|||+++++||||||||||+||++|
T Consensus        69 ~nl~~~~~~a~~~ai~~l---~~~~~~v~iD~~~~~~~----------~~~~~~~~KaD~~~~~VaAASIvAKv~RD~~m  135 (179)
T cd07182          69 INILQATLLAMRRAVEGL---PVKPDYVLVDGNRLPPL----------PIPQEAIVKGDAKSASIAAASILAKVTRDRLM  135 (179)
T ss_pred             hhHHHHHHHHHHHHHHhC---CCCCCEEEECCcCCCCC----------CCCeEEEeccccccHHHHHHHHHHHHHHHHHH
Confidence            699999999988888765   23567899999875432          23567789999999999999999999999999


Q ss_pred             HHhhHhcccccccCCCccccCCchhhhhh
Q 027718          177 RGWIFEETAENMHRNFGSGYPGGARCLKL  205 (219)
Q Consensus       177 ~~l~~~~p~y~~~~~~GsGYpsd~~t~~~  205 (219)
                      ++|+++||+|+|+.|  +||||++|+..+
T Consensus       136 ~~l~~~~~~yg~~~~--~GY~s~~h~~~i  162 (179)
T cd07182         136 IELDKKYPGYGFAKH--KGYGTKEHLEAL  162 (179)
T ss_pred             HHHHHHCcCCCCcCC--CCCCcHHHHHHH
Confidence            999999999999666  899999998653

Bacterial ribonuclease (RNase) HII has a role in primer removal based on its involvement in ribonucleotide-specific catalytic activity in the presence of RNA/DNA hybrid substrates. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII and HIII- double deletion of these leads to cellular lethality. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli.

>PRK14550 rnhB ribonuclease HII; Provisional

Probab=100.00  E-value=3.3e-50  Score=339.68  Aligned_cols=182  Identities=23%  Similarity=0.271  Sum_probs=148.0

Q ss_pred             cEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhh
Q 027718           15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNK   94 (219)
Q Consensus        15 ~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~   94 (219)
                      .++|||||||||+|||||||||+++.+....+..+||+|||+||+++|++|+++|++...+.|.+..++|++||      
T Consensus         1 ~~~GiDEAGRGpl~GPvVvaav~~~~~~~~~l~~~gv~DSKkLs~~~Re~L~~~I~~~~~~~~~i~~~~~~eID------   74 (204)
T PRK14550          1 MTLGIDEAGRGCLAGSLFVAGVACNEKTALEFLKMGLKDSKKLSPKKRFFLEDKIKTHGEVGFFVVKKSANEID------   74 (204)
T ss_pred             CeeCccCcCCCCccchheEEEEEEChhhccchhhcCccChhhCCHHHHHHHHHHHHhccCcEEEEEEECHHHHH------
Confidence            37999999999999999999999998765566678999999999999999999999753368999999999996      


Q ss_pred             hhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHHH
Q 027718           95 NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDR  174 (219)
Q Consensus        95 ~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~  174 (219)
                       ..|||.++..++.++++++   ...++.+++|++..+..+     ..++  ++.+++|||++|++||||||||||+||+
T Consensus        75 -~~ni~~a~~~am~~al~~l---~~~~~~vliDg~~~~~~~-----~~~~--~~~~~~KgD~~~~~VAAASIiAKV~RD~  143 (204)
T PRK14550         75 -SLGLGACLKLAIQEILENG---CSLANEIKIDGNTAFGLN-----KRYP--NIQTIIKGDETIAQIAMASVLAKAFKDR  143 (204)
T ss_pred             -HHHHHHHHHHHHHHHHHhC---CCCCCEEEECCccCcccc-----ccCc--ceeEEEcccccchhHHHHHHHHHHHHHH
Confidence             4689988876666666543   234578999987533211     1112  3457799999999999999999999999


Q ss_pred             HHHHhhHhcccccccCCCccccCCchhhhhh---hhhhhhhccc
Q 027718          175 TLRGWIFEETAENMHRNFGSGYPGGARCLKL---SIVCNNFQSF  215 (219)
Q Consensus       175 ~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~---~~~~~~~~~~  215 (219)
                      +|++|+++||+|+|+.|  |||||.+|..++   ...-.|+++|
T Consensus       144 ~M~~l~~~~p~Ygf~~~--kGY~T~~h~~ai~~~G~~p~hR~Sf  185 (204)
T PRK14550        144 EMLELHALFKEYGWDKN--CGYGTKQHIEAIIKLGATPFHRHSF  185 (204)
T ss_pred             HHHHHHHhCCCCCCcCC--CCCCCHHHHHHHHHhCcCHHHcCCc
Confidence            99999999999999755  899999998654   3445566666

>PRK00996 ribonuclease HIII; Provisional

Probab=100.00  E-value=3.7e-49  Score=351.39  Aligned_cols=187  Identities=22%  Similarity=0.260  Sum_probs=166.0

Q ss_pred             CcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhh
Q 027718           14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN   93 (219)
Q Consensus        14 ~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~   93 (219)
                      ..+||||||||||+|||||||||+++.+....|..+||+|||+||+++|++|+++|++.  +.|++.+++|++||+++. 
T Consensus        87 ~~viGiDEaGrG~~fGPlvvaav~v~~~~~~~l~~lgv~DSK~Ls~~kr~~La~~I~~~--~~~~v~~~~p~~~n~l~~-  163 (304)
T PRK00996         87 LSLIGSDEVGKGDYFGPLTVAAVYVDKEQIPFLKKLGVKDSKKLTDTKIRQIAPQLREK--IPHSVLLLSPEKYNELQA-  163 (304)
T ss_pred             ceEEeecCCCCCCcccceEEEEEEEchhhcchhhhcCCCccccCCHHHHHHHHHHHHHh--cCEEEEEeCHHHhhhHHH-
Confidence            45899999999999999999999999888888889999999999999999999999984  689999999999998763 


Q ss_pred             hhhchHHHHHHHHHHHHHHHHHhc--CCCCCEEEECCCCChHHHHHHhhcc--CCCcceEEeecCccchhhHHHHhHHhH
Q 027718           94 KNKINLNEISHDSAIGLITRVLNI--GILLTEVYLDTVGDAEKYQAKLSQR--FPSIKFVVSKKADSLYPVVSGASIVAK  169 (219)
Q Consensus        94 ~~~~Nin~~~~~~~~~li~~~l~~--~~~~~~i~iD~~~~~~~~~~~L~~~--~~~~~~~~~~KaD~~~~sVAAASIlAK  169 (219)
                       ...|+|.++.+.|.+++.++++.  +..++.|+||+|+.+++|.++|...  .+..++++++|||++|++|||||||| 
T Consensus       164 -~~~nln~l~a~~h~~ai~~l~~k~~~~~p~~iliD~f~~~~~y~~~l~~e~~~~~~~~~~~~KaD~~~~~VAAASIiA-  241 (304)
T PRK00996        164 -KGYNQNKLKAWLHNQAIDNLLQKIAGIQPEKIVIDQFASPEVYQKYLKKEKNKFRDNVTFETKAESKHLAVAAASIIA-  241 (304)
T ss_pred             -hhhhHHHHHHHHHHHHHHHHHhhccCCCCCEEEECCCCCchHHHHHhhhhccCCCCceEEEeccchhhHHHHHHHHHH-
Confidence             35799999888888888887653  4456799999999999999999753  23456788999999999999999999 


Q ss_pred             HHHHHHHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718          170 VTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSI  207 (219)
Q Consensus       170 v~RD~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~  207 (219)
                        ||++|++|++++|+|+|..++|+|||+|+.+++|.+
T Consensus       242 --R~~~l~~~~~l~~~yg~~~~kGag~~~d~~a~~~i~  277 (304)
T PRK00996        242 --RYAFLENMDKLSKEAGMTLPKGAGAKVDKVAAQILK  277 (304)
T ss_pred             --HHHHHHHHHHhCcCCCCCCCCCCCCHHHHHHHHHHH
Confidence              999999999999999999999999999999877654

>PF01351 RNase_HII: Ribonuclease HII; InterPro: IPR024567 Ribonuclease HII and HIII are endonucleases that specifically degrade the RNA of RNA-DNA hybrids

Probab=100.00  E-value=3.8e-49  Score=331.83  Aligned_cols=181  Identities=39%  Similarity=0.585  Sum_probs=148.6

Q ss_pred             eeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhh
Q 027718           17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNK   96 (219)
Q Consensus        17 iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~~   96 (219)
                      +|||||||||+|||||||||+++.+..+.|..+||+|||+||+++|++|+++|+.   +.+..  +.+..++..  ..+.
T Consensus         1 iG~DEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~---i~~~~--~~~~~~~~~--~~~~   73 (198)
T PF01351_consen    1 IGIDEAGRGDVFGPLVVAAVYLPEEDIEKLKELGVKDSKKLSDKKREELAEKIKK---ISYSE--VSPYPIGYI--SPKE   73 (198)
T ss_dssp             EEEEEESSS-SBS-EEEEEEEEEGGGHHHHHHTTGCCGTTS-HHHHHHHHHHHHE---EEEEE--EECHHHHHH--HTTT
T ss_pred             CCCCCCCCCCcccchheEEEEeccccHHHHHhhccCccccCCHHHHHHHHHHHHh---hchhh--hhhcccccc--chHH
Confidence            7999999999999999999999999999999999999999999999999999992   33443  344444321  1256


Q ss_pred             chHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHHHHH
Q 027718           97 INLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTL  176 (219)
Q Consensus        97 ~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~~m  176 (219)
                      +|+|.+++..+..+++.+.+.+..++.++||+|+.++++...+++.++ .++++++|||++|++|||||||||++||+.|
T Consensus        74 in~n~i~~~~~~~~~~~l~~~~~~~~~v~iD~~~~~~~~~~~~~~~~~-~~~~~~~Kad~~~~~VAAASIvAK~~rd~~~  152 (198)
T PF01351_consen   74 INLNNILAALHNAMIRALLKLGVQPDEVLIDQFGSPEKYYNKLEKIFK-IKVVFEPKADSKYPSVAAASIVAKVTRDEMI  152 (198)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHTTSEESEEEEEESSSHHHHHHHHHHHST-SEEEEETTHHHCSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccCCceeecchhhcchhcccchheecC-cceeeecccchhhHHHHHHHHHHHHHHHHHH
Confidence            888888888888888887776667789999999999888888888777 7889999999999999999999999999555


Q ss_pred             HHhhHhcccccccCCCccccCCchhhhhhhhh
Q 027718          177 RGWIFEETAENMHRNFGSGYPGGARCLKLSIV  208 (219)
Q Consensus       177 ~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~~  208 (219)
                      +. .+.+|.|+|  ++|+|||+|+||++|.+.
T Consensus       153 ~~-~~~~~~~~~--~~gsGy~s~~~~~~~~~~  181 (198)
T PF01351_consen  153 EL-LSKYPGYGF--PKGSGYPSDPHTRAILKK  181 (198)
T ss_dssp             HH-HHHHHTS-H--CCTSSSTTSHHHHHHHHH
T ss_pred             HH-HHhCcCCCC--ccCCCCChHHHHHHHHHh
Confidence            55 445666665  678999999999999764

Proteins which belong to this family have been found in bacteria, archaea, and eukaryota. The domain represented by this entry is found in ribonucleases HII aand HIII.; PDB: 2ETJ_A 3O3H_A 3O3G_A 3O3F_A 3KIO_A 3P5J_A 1UAX_B 2DFF_A 1IO2_A 2DFH_A ....

>PRK13926 ribonuclease HII; Provisional

Probab=100.00  E-value=1.8e-47  Score=323.71  Aligned_cols=163  Identities=30%  Similarity=0.448  Sum_probs=138.2

Q ss_pred             CcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhh
Q 027718           14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN   93 (219)
Q Consensus        14 ~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~   93 (219)
                      ..++|||||||||+|||||||||+++...      ++++|||+||+++|++|+++|++. ...|++.+++|++||+    
T Consensus        22 ~~i~GiDEAGRG~~~GPlVvaav~~~~~~------~~~~DSK~Ls~~~R~~L~~~I~~~-~~~~~i~~isp~~Id~----   90 (207)
T PRK13926         22 LRVAGVDEAGRGAWAGPVVVAAVILPPGE------YPFRDSKTLSPAAREALAEEVRRV-ALAWAVGHAEAAEIDR----   90 (207)
T ss_pred             cEEEeecCcCCCCccccceEEEEEECccC------CCccccccCCHHHHHHHHHHHHHh-CceEEEEEeCHHHHhH----
Confidence            57999999999999999999999998753      479999999999999999999975 5689999999999964    


Q ss_pred             hhhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHH
Q 027718           94 KNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRD  173 (219)
Q Consensus        94 ~~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD  173 (219)
                         .|||.++++++.++++++   ...++.+++|...        +.   ...++++++|||++|++||||||||||+||
T Consensus        91 ---~ni~~a~~~a~~~~l~~l---~~~~~~v~~D~~~--------~~---~~~~~~~~~KgD~~~~~VaAASIvAKv~RD  153 (207)
T PRK13926         91 ---LNVLKATHLAAARALARL---AVAPEALVTDYLR--------LP---TPLPLLAPPKADALSPTVAAASLLAKTERD  153 (207)
T ss_pred             ---HHHHHHHHHHHHHHHHhc---CCCCCEEEECccc--------CC---CCCCeEEEecCccccHHHHHHHHHHHHHHH
Confidence               689999999988888654   2346789999531        11   124577889999999999999999999999


Q ss_pred             HHHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718          174 RTLRGWIFEETAENMHRNFGSGYPGGARCLKLSI  207 (219)
Q Consensus       174 ~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~  207 (219)
                      ++|++|+++||+|+|..|  +|||+..| ++|.+
T Consensus       154 ~~m~~l~~~~~~yg~~~~--kGY~t~~h-~~~l~  184 (207)
T PRK13926        154 RLMRELDARYPGYGFARH--KGYGTPAH-REALA  184 (207)
T ss_pred             HHHHHHHHhCccCCCcCC--CCCCCHHH-HHHHH
Confidence            999999999999999777  89995554 55543

>TIGR00716 rnhC ribonuclease HIII

Probab=100.00  E-value=1.4e-45  Score=325.66  Aligned_cols=179  Identities=25%  Similarity=0.312  Sum_probs=152.7

Q ss_pred             CcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhh
Q 027718           14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN   93 (219)
Q Consensus        14 ~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~   93 (219)
                      ..+||||||||||+|||||||||+++.+....|+.+||+|||+||+++|++|+++|++.  +.|++.+++|++||.++. 
T Consensus        81 ~~viGiDEaGrG~~fGPlvvaav~v~~~~~~~L~~lGv~DSK~Ls~~kr~~la~~I~~~--~~~~i~~l~p~~~n~~~~-  157 (284)
T TIGR00716        81 RSVIGCDESGKGDIFGPLVLCCVYIPEENYLKVSSLNPRDSKRLSDKRIERLALNLKPL--VKAYCYELKPEKYNKLYR-  157 (284)
T ss_pred             ceEEeecCCCCCCcccceEEEEEEEChhhhhhhhhcCCCCcccCCHHHHHHHHHHHHHh--CCEEEEEeCHHHhcHHHH-
Confidence            34999999999999999999999999887788889999999999999999999999984  579999999999997653 


Q ss_pred             hhhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhcc-CCCcceEEeecCccchhhHHHHhHHhHHHH
Q 027718           94 KNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQR-FPSIKFVVSKKADSLYPVVSGASIVAKVTR  172 (219)
Q Consensus        94 ~~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~-~~~~~~~~~~KaD~~~~sVAAASIlAKv~R  172 (219)
                       ...|+|.++.+.|.++|.+++......+.|+||+|+.++.|.+++... ++..++++++|||+ |++||||||||   |
T Consensus       158 -~~~nln~l~a~~h~~aI~~l~~~~~~~~~i~ID~f~~~~~y~~~l~~~~~~~~~~~~~~KaE~-~~aVAAASIiA---R  232 (284)
T TIGR00716       158 -KFRNLNKMMAHFHKLLIERLLKEECGVSEVVVDQFAPSNPFFNHLKGRDIVGEDVIFETEAER-NLAVAAASIFA---R  232 (284)
T ss_pred             -HHHHHHHHHHHHHHHHHHHHhhCcCCCcEEEECCCCCchHhhhhcccccccCCceeeeccccc-chhhhHHHHHH---H
Confidence             357999999999999998886533233579999999888777666542 34567888999998 99999999999   9


Q ss_pred             HHHHHHhhHhcccccccCCCccccCCchhh
Q 027718          173 DRTLRGWIFEETAENMHRNFGSGYPGGARC  202 (219)
Q Consensus       173 D~~m~~l~~~~p~y~~~~~~GsGYpsd~~t  202 (219)
                      |++|++|++++|+|+|..++  ||++..+.
T Consensus       233 ~~~l~~l~~l~~~yg~~~pk--Ga~~~v~~  260 (284)
T TIGR00716       233 YKFLQSLKELERELGIKLPK--GASKEVKE  260 (284)
T ss_pred             HHHHHHHHHhCcccCCcCCC--CCChHHHH
Confidence            99999999999999999885  55544433

Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other. The only RNase H homolog in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This model describes bacterial RNase III.

>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]

Probab=100.00  E-value=8.7e-42  Score=296.92  Aligned_cols=185  Identities=23%  Similarity=0.251  Sum_probs=169.1

Q ss_pred             CcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhh
Q 027718           14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLN   93 (219)
Q Consensus        14 ~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~   93 (219)
                      ..+||+||+|+||+||||+||||++++++++.|.++||+|||+|||.++.+|++.|++  .+.+.+..++|++||+++. 
T Consensus        83 ~~~IGsDEvG~GDyFGpl~v~av~v~~e~~~~L~~lgV~DSKkL~D~kI~~la~~ik~--~i~~~~l~l~p~kYNel~~-  159 (297)
T COG1039          83 KNLIGSDEVGKGDYFGPLVVCAVYVSKENLPKLKELGVKDSKKLSDKKIQQLAPIIKP--LIPHSVLTLDPKKYNELYK-  159 (297)
T ss_pred             ccccCCCCCCCCCccCCceEEEEEcCHHHHHHHHhcCCcccccCCHHHHHHHHHHHHH--hcCceEEEEChHHHHHHHH-
Confidence            5799999999999999999999999999999999999999999999999999999998  4899999999999999885 


Q ss_pred             hhhchHHHHHHHHHHHHHHHHHh-cCCCCCEEEECCCCChHHHHHHhhcc--CCCcceEEeecCccchhhHHHHhHHhHH
Q 027718           94 KNKINLNEISHDSAIGLITRVLN-IGILLTEVYLDTVGDAEKYQAKLSQR--FPSIKFVVSKKADSLYPVVSGASIVAKV  170 (219)
Q Consensus        94 ~~~~Nin~~~~~~~~~li~~~l~-~~~~~~~i~iD~~~~~~~~~~~L~~~--~~~~~~~~~~KaD~~~~sVAAASIlAKv  170 (219)
                       +..|.|.+..+.|.++|++++. .+.+++.|+||+|.+.+.|.+||++.  .+..++.+.+|||++|++||||||+|  
T Consensus       160 -k~~N~n~mkt~lH~~ai~~ll~~~~~~~~~ivIDqFa~~~~~~~yl~k~~~~~~~p~~f~~kaEs~~laVAvASIiA--  236 (297)
T COG1039         160 -KFNNANSMKTFLHNQAIQNLLPQKGAQPEFIVIDQFASSENYKNYLQKETNKFSEPVLFLTKAESKSLAVAVASIIA--  236 (297)
T ss_pred             -hhhhHHHHHHHHHHHHHHHHHHhccCCCeEEEeccccchhHHHHHHHhhccCCCCceeeeecccccchhHHHHHHHH--
Confidence             5689999988889999999885 66778999999999999999999876  23556778999999999999999999  


Q ss_pred             HHHHHHHHhhHhcccccccCCCccccCCchhhhhh
Q 027718          171 TRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKL  205 (219)
Q Consensus       171 ~RD~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~  205 (219)
                       ||.|+..|+++..+|++..++|+|-.+|.-.+++
T Consensus       237 -R~~Fl~~~~~l~~~~gv~LPkGAg~~V~~~a~~i  270 (297)
T COG1039         237 -RYAFLQSLKQLSRQYGVQLPKGAGPAVDQAAAEI  270 (297)
T ss_pred             -HHHHHHHHHHHHHHhCCcCCCCCchhHHHHHHHH
Confidence             9999999999999999999999997777766554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	219
3puf_A	302	Crystal Structure Of Human Rnase H2 Complex Length		1e-54
3p5j_A	301	The Structure Of The Human Rnase H2 Complex Defines		9e-54
3p56_A	299	The Structure Of The Human Rnase H2 Complex Defines		7e-53
3kio_A	301	Mouse Rnase H2 Complex Length = 301		5e-52
1io2_A	213	Crystal Structure Of Type 2 Ribonuclease H From Hyp		8e-19
1x1p_A	212	Crystal Structure Of Tk-Rnase Hii(1-197)-A(28-42) L		9e-19
2dfe_A	209	Crystal Structure Of Tk-Rnase Hii(1-200)-C Length =		1e-18
2dfh_A	221	Crystal Structure Of Tk-Rnase Hii(1-212)-C Length =		1e-18
2dff_A	213	Crystal Structure Of Tk-Rnase Hii(1-204)-C Length =		1e-18
1eke_A	230	Crystal Structure Of Class Ii Ribonuclease H (Rnase		5e-18
1uax_A	220	Crystal Structure Of The Ribonuclease H2 From Pyroc		9e-17
3p83_D	217	Structure Of The Pcna:rnase Hii Complex From Archae		9e-15
1i39_A	225	Rnase Hii From Archaeoglobus Fulgidus Length = 225		1e-14
3o3g_A	222	T. Maritima Rnase H2 In Complex With Nucleic Acid S		3e-04
2d0a_A	310	Crystal Structure Of Bst-Rnase Hiii Length = 310		6e-04
3asm_A	310	Crystal Structure Of Q54a Mutant Protein Of Bst-Rna		6e-04
3o3f_A	222	T. Maritima Rnase H2 D107n In Complex With Nucleic		9e-04

>pdb|3PUF|A Chain A, Crystal Structure Of Human Rnase H2 Complex Length = 302

Iteration: 1
 Score =  209 bits (531), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 97/189 (51%), Positives = 128/189 (67%)
Query: 13  NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN 72
            PC++G+DEAGRGPVLGPMVY   YCP      L  L  ADSKTL E +RE LF  ++  
Sbjct: 30  EPCVLGVDEAGRGPVLGPMVYAICYCPLPRLADLEALKVADSKTLLESERERLFAKMEDT 89
Query: 73  DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDA 132
           D VGWA+D++ P  +S  ML + K NLN +SHD+A GLI   L+ G+ +T+V++DTVG  
Sbjct: 90  DFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDTVGMP 149
Query: 133 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
           E YQA+L Q FP I+  V  KAD+LYPVVS ASI AKV RD+ ++ W F E  +++  ++
Sbjct: 150 ETYQARLQQSFPGIEVTVKAKADALYPVVSAASICAKVARDQAVKKWQFVEKLQDLDTDY 209
Query: 193 GSGYPGGAR 201
           GSGYP   +
Sbjct: 210 GSGYPNDPK 218

>pdb|3P5J|A Chain A, The Structure Of The Human Rnase H2 Complex Defines Key Interaction Interfaces Relevant To Enzyme Function And Human Disease Length = 301

Iteration: 1
 Score =  206 bits (524), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 97/189 (51%), Positives = 129/189 (68%), Gaps = 1/189 (0%)
Query: 14  PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN- 72
           PC++G+DEAGRGPVLGPMVY   YCP S    L  L  ADSKTL E +RE LF  ++ + 
Sbjct: 28  PCVLGVDEAGRGPVLGPMVYAICYCPLSRLADLEALKVADSKTLTENERERLFAKMEEDG 87
Query: 73  DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDA 132
           D VGWA+D++ P  +S  ML + K NLN +SHD+A GLI   L+  + +T+V++DTVG  
Sbjct: 88  DFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFVDTVGMP 147
Query: 133 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
           E YQA+L Q FP I+  V  KADSL+PVVS ASI AKV RD+ ++ W F E  +++  ++
Sbjct: 148 ETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQFVENLQDLDSDY 207
Query: 193 GSGYPGGAR 201
           GSGYP   +
Sbjct: 208 GSGYPNDPK 216

>pdb|3P56|A Chain A, The Structure Of The Human Rnase H2 Complex Defines Key Interaction Interfaces Relevant To Enzyme Function And Human Disease Length = 299

Iteration: 1
 Score =  203 bits (516), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 95/189 (50%), Positives = 126/189 (66%)
Query: 13  NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN 72
            PC++G+ EAGRGPVLGPMVY   YCP      L  L  ADSKTL E +RE LF  ++  
Sbjct: 27  EPCVLGVAEAGRGPVLGPMVYAICYCPLPRLADLEALKVADSKTLLESERERLFAKMEDT 86
Query: 73  DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDA 132
           D VGWA+D++ P  +S  ML + K NLN +SHD+A GLI   L+ G+ +T+V++DTVG  
Sbjct: 87  DFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDTVGMP 146
Query: 133 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
           E YQA+L Q FP I+  V  KA +LYPVVS ASI AKV RD+ ++ W F E  +++  ++
Sbjct: 147 ETYQARLQQSFPGIEVTVKAKAAALYPVVSAASICAKVARDQAVKKWQFVEKLQDLDTDY 206
Query: 193 GSGYPGGAR 201
           GSGYP   +
Sbjct: 207 GSGYPNDPK 215

>pdb|3KIO|A Chain A, Mouse Rnase H2 Complex Length = 301

Iteration: 1
 Score =  200 bits (509), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 95/189 (50%), Positives = 126/189 (66%), Gaps = 1/189 (0%)
Query: 14  PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN- 72
           PC++G+DEAGRGPVLGP VY   YCP S    L  L  ADSKTL E +RE LF   + + 
Sbjct: 28  PCVLGVDEAGRGPVLGPXVYAICYCPLSRLADLEALKVADSKTLTENERERLFAKXEEDG 87
Query: 73  DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDA 132
           D VGWA+D++ P  +S   L + K NLN +SHD+A GLI   L+  + +T+V++DTVG  
Sbjct: 88  DFVGWALDVLSPNLISTSXLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFVDTVGXP 147
Query: 133 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
           E YQA+L Q FP I+  V  KADSL+PVVS ASI AKV RD+ ++ W F E  +++  ++
Sbjct: 148 ETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQFVENLQDLDSDY 207
Query: 193 GSGYPGGAR 201
           GSGYP   +
Sbjct: 208 GSGYPNDPK 216

>pdb|1IO2|A Chain A, Crystal Structure Of Type 2 Ribonuclease H From Hyperthermophilic Archaeon, Thermococcus Kodakaraensis Kod1 Length = 213

Iteration: 1
 Score = 90.1 bits (222), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 70/204 (34%), Positives = 103/204 (50%), Gaps = 21/204 (10%)
Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           I GIDEAGRGPV+GPMV   +    +    L  L   DSK L  ++RE+LF     N+ +
Sbjct: 3   IAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLF-----NEIL 57
Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLN-IGILLTEVYLDTVG-DAE 133
           G   D +   EL   ++   +  LNE   ++      + LN + +    +Y D    D E
Sbjct: 58  GVLDDYV-ILELPPDVIGSREGTLNEFEVEN----FAKALNSLKVKPDVIYADAADVDEE 112
Query: 134 KYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
           ++  +L +R      VV+K KAD ++PVVS ASI+AKVTRDR +      E  +  +   
Sbjct: 113 RFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV------EKLKEEYGEI 166
Query: 193 GSGYPGGARCLKLSIVCNNFQSFG 216
           GSGYP   R    + + N ++  G
Sbjct: 167 GSGYPSDPRT--RAFLENYYREHG 188

>pdb|1X1P|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-197)-A(28-42) Length = 212

Iteration: 1
 Score = 90.1 bits (222), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 68/190 (35%), Positives = 97/190 (51%), Gaps = 19/190 (10%)
Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           I GIDEAGRGPV+GPMV   +    +    L  L   DSK L  ++RE+LF     N+ +
Sbjct: 3   IAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLF-----NEIL 57
Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLN-IGILLTEVYLDTVG-DAE 133
           G   D +   EL   ++   +  LNE   ++      + LN + +    +Y D    D E
Sbjct: 58  GVLDDYV-ILELPPDVIGSREGTLNEFEVEN----FAKALNSLKVKPDVIYADAADVDEE 112
Query: 134 KYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
           ++  +L +R      VV+K KAD ++PVVS ASI+AKVTRDR +      E  +  +   
Sbjct: 113 RFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV------EKLKEEYGEI 166
Query: 193 GSGYPGGARC 202
           GSGYP   R 
Sbjct: 167 GSGYPSDPRT 176

>pdb|2DFE|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-200)-C Length = 209

Iteration: 1
 Score = 89.7 bits (221), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 68/190 (35%), Positives = 97/190 (51%), Gaps = 19/190 (10%)
Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           I GIDEAGRGPV+GPMV   +    +    L  L   DSK L  ++RE+LF     N+ +
Sbjct: 3   IAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLF-----NEIL 57
Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLN-IGILLTEVYLDTVG-DAE 133
           G   D +   EL   ++   +  LNE   ++      + LN + +    +Y D    D E
Sbjct: 58  GVLDDYV-ILELPPDVIGSREGTLNEFEVEN----FAKALNSLKVKPDVIYADAADVDEE 112
Query: 134 KYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
           ++  +L +R      VV+K KAD ++PVVS ASI+AKVTRDR +      E  +  +   
Sbjct: 113 RFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV------EKLKEEYGEI 166
Query: 193 GSGYPGGARC 202
           GSGYP   R 
Sbjct: 167 GSGYPSDPRT 176

>pdb|2DFH|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-212)-C Length = 221

Iteration: 1
 Score = 89.7 bits (221), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 68/190 (35%), Positives = 97/190 (51%), Gaps = 19/190 (10%)
Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           I GIDEAGRGPV+GPMV   +    +    L  L   DSK L  ++RE+LF     N+ +
Sbjct: 3   IAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLF-----NEIL 57
Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLN-IGILLTEVYLDTVG-DAE 133
           G   D +   EL   ++   +  LNE   ++      + LN + +    +Y D    D E
Sbjct: 58  GVLDDYV-ILELPPDVIGSREGTLNEFEVEN----FAKALNSLKVKPDVIYADAADVDEE 112
Query: 134 KYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
           ++  +L +R      VV+K KAD ++PVVS ASI+AKVTRDR +      E  +  +   
Sbjct: 113 RFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV------EKLKEEYGEI 166
Query: 193 GSGYPGGARC 202
           GSGYP   R 
Sbjct: 167 GSGYPSDPRT 176

>pdb|2DFF|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-204)-C Length = 213

Iteration: 1
 Score = 89.7 bits (221), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 68/190 (35%), Positives = 97/190 (51%), Gaps = 19/190 (10%)
Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           I GIDEAGRGPV+GPMV   +    +    L  L   DSK L  ++RE+LF     N+ +
Sbjct: 3   IAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLF-----NEIL 57
Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLN-IGILLTEVYLDTVG-DAE 133
           G   D +   EL   ++   +  LNE   ++      + LN + +    +Y D    D E
Sbjct: 58  GVLDDYV-ILELPPDVIGSREGTLNEFEVEN----FAKALNSLKVKPDVIYADAADVDEE 112
Query: 134 KYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
           ++  +L +R      VV+K KAD ++PVVS ASI+AKVTRDR +      E  +  +   
Sbjct: 113 RFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV------EKLKEEYGEI 166
Query: 193 GSGYPGGARC 202
           GSGYP   R 
Sbjct: 167 GSGYPSDPRT 176

>pdb|1EKE|A Chain A, Crystal Structure Of Class Ii Ribonuclease H (Rnase Hii) With Mes Ligand Length = 230

Iteration: 1
 Score = 87.4 bits (215), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 70/205 (34%), Positives = 106/205 (51%), Gaps = 29/205 (14%)
Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           I+GIDEAGRGPVLGP V          ++ L  L   DSK L + KR  L    K+ +++
Sbjct: 3   IIGIDEAGRGPVLGPXVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYL---KKLLENL 59
Query: 76  GWAVDIIDPRELSAKMLNK--NKINLNEISHDS----AIGLITRVLNIGILLTEVYLDTV 129
           G+    ++ R L A+ +N+  N INLN+I  ++    A  LI + LNI     E+Y+D  
Sbjct: 60  GY----VEKRILEAEEINQLXNSINLNDIEINAFSKVAKNLIEK-LNIRDDEIEIYIDAC 114
Query: 130 GD---------AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 180
                       +K +  + +R  +IK +   KAD+ YPVVS ASI+AK  RD  +  + 
Sbjct: 115 STNTKKFEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYY- 173
Query: 181 FEETAENMHRNFGSGYPGGARCLKL 205
                + ++ + GSGYP   + +K 
Sbjct: 174 -----KKIYGDIGSGYPSDPKTIKF 193

>pdb|1UAX|A Chain A, Crystal Structure Of The Ribonuclease H2 From Pyrococcus Horikoshii Ot3 Length = 220

Iteration: 1
 Score = 83.2 bits (204), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 59/191 (30%), Positives = 96/191 (50%), Gaps = 21/191 (10%)
Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           + G+DEAGRGPV+GP+V G         + L  +   DSK L   +RE+LF  L ++   
Sbjct: 3   VAGVDEAGRGPVIGPLVIGVAVIDEKNIERLRDIGVKDSKQLTPGQREKLFSKL-IDILD 61
Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
            + V ++ P+E+  +  + N++         A   +  + ++ I   ++Y+D+     K 
Sbjct: 62  DYYVLLVTPKEIDERHHSMNELE--------AEKFVVALNSLRIKPQKIYVDSADVDPKR 113
Query: 136 QAKLSQRFPSIKF----VVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN 191
            A L +    +K+    +   KAD+ Y +VS ASI+AKVTRDR +      E  +  +  
Sbjct: 114 FASLIK--AGLKYEATVIAEHKADAKYEIVSAASIIAKVTRDREI------EKLKQKYGE 165
Query: 192 FGSGYPGGARC 202
           FGSGYP   R 
Sbjct: 166 FGSGYPSDPRT 176

>pdb|3P83|D Chain D, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus Fulgidus. Length = 217

Iteration: 1
 Score = 76.6 bits (187), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 61/195 (31%), Positives = 94/195 (48%), Gaps = 20/195 (10%)
Query: 8   PKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFE 67
           P++       GIDEAG+G V+GP+V   + C  S +  L  L   DSK L + +REEL E
Sbjct: 6   PEFPGRLMKAGIDEAGKGCVIGPLVVAGVAC--SDEDRLRKLGVKDSKKLSQGRREELAE 63
Query: 68  DLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEV-YL 126
           +++        V  + P  L  +M  K    +NEI  +    +I R      L  E+ Y+
Sbjct: 64  EIR--KICRTEVLKVSPENLDERMAAKT---INEILKECYAEIILR------LKPEIAYV 112
Query: 127 DTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAE 186
           D+     +  ++  +    ++ V   KAD  YP+V+ ASI+AKV R+R +      E  +
Sbjct: 113 DSPDVIPERLSRELEEITGLRVVAEHKADEKYPLVAAASIIAKVEREREI------ERLK 166
Query: 187 NMHRNFGSGYPGGAR 201
               +FGSGY    R
Sbjct: 167 EKFGDFGSGYASDPR 181

>pdb|1I39|A Chain A, Rnase Hii From Archaeoglobus Fulgidus Length = 225

Iteration: 1
 Score = 76.6 bits (187), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 60/185 (32%), Positives = 91/185 (49%), Gaps = 20/185 (10%)
Query: 18  GIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGW 77
           GIDEAG+G V+GP+V   +   CS +  L  L   DSK L + +REEL E+++       
Sbjct: 24  GIDEAGKGCVIGPLVVAGV--ACSDEDRLRKLGVKDSKKLSQGRREELAEEIR--KICRT 79
Query: 78  AVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEV-YLDTVGDAEKYQ 136
            V  + P  L  +M  K    +NEI  +    +I R      L  E+ Y+D+     +  
Sbjct: 80  EVLKVSPENLDERMAAKT---INEILKECYAEIILR------LKPEIAYVDSPDVIPERL 130
Query: 137 AKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGY 196
           ++  +    ++ V   KAD  YP+V+ ASI+AKV R+R +      E  +    +FGSGY
Sbjct: 131 SRELEEITGLRVVAEHKADEKYPLVAAASIIAKVEREREI------ERLKEKFGDFGSGY 184
Query: 197 PGGAR 201
               R
Sbjct: 185 ASDPR 189

>pdb|3O3G|A Chain A, T. Maritima Rnase H2 In Complex With Nucleic Acid Substrate And Calcium Ions Length = 222

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 46/182 (25%), Positives = 82/182 (45%), Gaps = 31/182 (17%)
Query: 15  CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDS 74
            + G+DEAGRG + GP+V          ++ +  +N  DSK L   KRE L +++    +
Sbjct: 12  IVAGVDEAGRGCLAGPVV----AAAVVLEKEIEGIN--DSKQLSPAKRERLLDEIMEKAA 65
Query: 75  VGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEK 134
           VG  + I  P E          I+L  I + + + +   + N+ +  + V +D  G    
Sbjct: 66  VG--IGIASPEE----------IDLYNIFNATKLAMNRALENLSVKPSFVLVDGKG---- 109
Query: 135 YQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGW--IFEETAENMHRNF 192
               +    P    V   K D    ++  ASIVAKV RDR +  +  ++ + + + H+ +
Sbjct: 110 ----IELSVPGTCLV---KGDQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKHKGY 162
Query: 193 GS 194
            +
Sbjct: 163 AT 164

>pdb|2D0A|A Chain A, Crystal Structure Of Bst-Rnase Hiii Length = 310

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 48/188 (25%), Positives = 80/188 (42%), Gaps = 17/188 (9%)
Query: 17  MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVG 76
           +G DE G G   GP+V    Y    +   +A L   DSK L +E  + +     + ++V 
Sbjct: 94  IGSDEVGTGDYFGPIVVAAAYVDRPHIAKIAALGVKDSKQLNDEAIKRIAP--AIMETVP 151
Query: 77  WAVDIID-PRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTE-VYLDTVGDAEK 134
            AV ++D P+    +     +  +  + H+    L+  V  I     E + +D     + 
Sbjct: 152 HAVTVLDNPQYNRWQRSGMPQTKMKALLHNRT--LVKLVDAIAPAEPEAIIIDEFLKRDS 209
Query: 135 YQAKLSQRFPSIKFVVS--KKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
           Y   LS     I+  V    KA+S++  V+ ASI+A+         ++F E  E + R  
Sbjct: 210 YFRYLSDEDRIIRERVHCLPKAESVHVSVAAASIIAR---------YVFLEEMEQLSRAV 260
Query: 193 GSGYPGGA 200
           G   P GA
Sbjct: 261 GLLLPKGA 268

>pdb|3ASM|A Chain A, Crystal Structure Of Q54a Mutant Protein Of Bst-Rnase Hiii Length = 310

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 48/188 (25%), Positives = 80/188 (42%), Gaps = 17/188 (9%)
Query: 17  MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVG 76
           +G DE G G   GP+V    Y    +   +A L   DSK L +E  + +     + ++V 
Sbjct: 94  IGSDEVGTGDYFGPIVVAAAYVDRPHIAKIAALGVKDSKQLNDEAIKRIAP--AIMETVP 151
Query: 77  WAVDIID-PRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTE-VYLDTVGDAEK 134
            AV ++D P+    +     +  +  + H+    L+  V  I     E + +D     + 
Sbjct: 152 HAVTVLDNPQYNRWQRSGMPQTKMKALLHNRT--LVKLVDAIAPAEPEAIIIDEFLKRDS 209
Query: 135 YQAKLSQRFPSIKFVVS--KKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
           Y   LS     I+  V    KA+S++  V+ ASI+A+         ++F E  E + R  
Sbjct: 210 YFRYLSDEDRIIRERVHCLPKAESVHVSVAAASIIAR---------YVFLEEMEQLSRAV 260
Query: 193 GSGYPGGA 200
           G   P GA
Sbjct: 261 GLLLPKGA 268

>pdb|3O3F|A Chain A, T. Maritima Rnase H2 D107n In Complex With Nucleic Acid Substrate And Magnesium Ions Length = 222

Iteration: 1
 Score = 40.0 bits (92), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 45/182 (24%), Positives = 82/182 (45%), Gaps = 31/182 (17%)
Query: 15  CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDS 74
            + G+DEAGRG + GP+V          ++ +  +N  DSK L   KRE L +++    +
Sbjct: 12  IVAGVDEAGRGCLAGPVVA----AAVVLEKEIEGIN--DSKQLSPAKRERLLDEIMEKAA 65
Query: 75  VGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEK 134
           VG  + I  P E          I+L  I + + + +   + N+ +  + V ++  G    
Sbjct: 66  VG--IGIASPEE----------IDLYNIFNATKLAMNRALENLSVKPSFVLVNGKG---- 109
Query: 135 YQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGW--IFEETAENMHRNF 192
               +    P    V   K D    ++  ASIVAKV RDR +  +  ++ + + + H+ +
Sbjct: 110 ----IELSVPGTCLV---KGDQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKHKGY 162
Query: 193 GS 194
            +
Sbjct: 163 AT 164

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	219
3kio_A	301	Ribonuclease H2 subunit A; aicardi-goutieres syndr	1e-86
1eke_A	230	Ribonuclease HII; endonuclease, structural genomic	4e-66
1i39_A	225	Ribonuclease HII, RNAse HII; mixed beta sheet, hel	2e-62
1io2_A	213	Ribonuclease HII; endonuclease, hydrolase; 2.00A {	7e-62
1uax_A	220	Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid	2e-61
2d0b_A	310	RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hyd	4e-50
2etj_A	250	Ribonuclease HII, RNAse HII; TM0915, ribonuclease	2e-16

>3kio_A Ribonuclease H2 subunit A; aicardi-goutieres syndrome, RNAse H2, protein complex, autoimmune disease, endonuclease, hydrolase, metal-binding; 2.90A {Mus musculus} PDB: 3p5j_A 3puf_A 3p56_A Length = 301

 Score =  257 bits (657), Expect = 1e-86
 Identities = 97/199 (48%), Positives = 129/199 (64%), Gaps = 1/199 (0%)

Query: 8   PKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFE 67
                 PC++G+DEAGRGPVLGPMVY   YCP S    L  L  ADSKTL E +RE LF 
Sbjct: 22  AVCLKEPCVLGVDEAGRGPVLGPMVYAICYCPLSRLADLEALKVADSKTLTENERERLFA 81

Query: 68  DLKVN-DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYL 126
            ++ + D VGWA+D++ P  +S  ML + K NLN +SHD+A GLI   L+  + +T+V++
Sbjct: 82  KMEEDGDFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFV 141

Query: 127 DTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAE 186
           DTVG  E YQA+L Q FP I+  V  KADSL+PVVS ASI AKV RD+ ++ W F E  +
Sbjct: 142 DTVGMPETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQFVENLQ 201

Query: 187 NMHRNFGSGYPGGARCLKL 205
           ++  ++GSGYP   +    
Sbjct: 202 DLDSDYGSGYPNDPKTKAW 220

>1eke_A Ribonuclease HII; endonuclease, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: MES; 2.00A {Methanocaldococcus jannaschii} SCOP: c.55.3.1 Length = 230

 Score =  202 bits (516), Expect = 4e-66
 Identities = 66/202 (32%), Positives = 100/202 (49%), Gaps = 23/202 (11%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           I+GIDEAGRGPVLGPMV          ++ L  L   DSK L + KR  L + L+  +  
Sbjct: 3   IIGIDEAGRGPVLGPMVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYLKKLLE--NLG 60

Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRV---LNIGILLTEVYLDTVGD- 131
                I++  E++  M   N INLN+I  ++   +   +   LNI     E+Y+D     
Sbjct: 61  YVEKRILEAEEINQLM---NSINLNDIEINAFSKVAKNLIEKLNIRDDEIEIYIDACSTN 117

Query: 132 --------AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEE 183
                    +K +  + +R  +IK +   KAD+ YPVVS ASI+AK  RD  +  +    
Sbjct: 118 TKKFEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYY---- 173

Query: 184 TAENMHRNFGSGYPGGARCLKL 205
             + ++ + GSGYP   + +K 
Sbjct: 174 --KKIYGDIGSGYPSDPKTIKF 193

>1i39_A Ribonuclease HII, RNAse HII; mixed beta sheet, helix-loop-helix, hydrolase; 1.95A {Archaeoglobus fulgidus} SCOP: c.55.3.1 PDB: 1i3a_A 3p83_D* Length = 225

 Score =  193 bits (492), Expect = 2e-62
 Identities = 55/191 (28%), Positives = 86/191 (45%), Gaps = 19/191 (9%)

Query: 10  WASN-PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFED 68
                    GIDEAG+G V+GP+V   + C    +  L  L   DSK L + +REEL E+
Sbjct: 15  VPRGSHMKAGIDEAGKGCVIGPLVVAGVACS--DEDRLRKLGVKDSKKLSQGRREELAEE 72

Query: 69  LKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDT 128
           ++        V  + P  L  +M  K    +NEI  +    +I R+          Y+D+
Sbjct: 73  IR--KICRTEVLKVSPENLDERMAAKT---INEILKECYAEIILRLK-----PEIAYVDS 122

Query: 129 VGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENM 188
                +  ++  +    ++ V   KAD  YP+V+ ASI+AKV R+R +         +  
Sbjct: 123 PDVIPERLSRELEEITGLRVVAEHKADEKYPLVAAASIIAKVEREREIERL------KEK 176

Query: 189 HRNFGSGYPGG 199
             +FGSGY   
Sbjct: 177 FGDFGSGYASD 187

>1io2_A Ribonuclease HII; endonuclease, hydrolase; 2.00A {Thermococcus kodakarensis} SCOP: c.55.3.1 PDB: 2dfh_A 2dff_A 2dfe_A 1x1p_A Length = 213

 Score =  191 bits (487), Expect = 7e-62
 Identities = 58/187 (31%), Positives = 89/187 (47%), Gaps = 17/187 (9%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           I GIDEAGRGPV+GPMV   +    +    L  L   DSK L  ++RE+LF ++      
Sbjct: 3   IAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEIL-GVLD 61

Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEK 134
            + +  + P  + ++        LNE   +        + ++ +    +Y D    D E+
Sbjct: 62  DYVILELPPDVIGSRE-----GTLNEFEVE---NFAKALNSLKVKPDVIYADAADVDEER 113

Query: 135 YQAKLSQRFP-SIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG 193
           +  +L +R     + V   KAD ++PVVS ASI+AKVTRDR +         +  +   G
Sbjct: 114 FARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAVEKL------KEEYGEIG 167

Query: 194 SGYPGGA 200
           SGYP   
Sbjct: 168 SGYPSDP 174

>1uax_A Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid ribonucleotidohydrolase, hydrolase; 2.00A {Pyrococcus horikoshii} SCOP: c.55.3.1 Length = 220

 Score =  190 bits (485), Expect = 2e-61
 Identities = 56/186 (30%), Positives = 91/186 (48%), Gaps = 17/186 (9%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           + G+DEAGRGPV+GP+V G         + L  +   DSK L   +RE+LF  L  +   
Sbjct: 3   VAGVDEAGRGPVIGPLVIGVAVIDEKNIERLRDIGVKDSKQLTPGQREKLFSKLI-DILD 61

Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
            + V ++ P+E+  +       ++NE+  +     +  + ++ I   ++Y+D+     K 
Sbjct: 62  DYYVLLVTPKEIDERH-----HSMNELEAE---KFVVALNSLRIKPQKIYVDSADVDPKR 113

Query: 136 QAKLSQRFP--SIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG 193
            A L +         +   KAD+ Y +VS ASI+AKVTRDR +         +  +  FG
Sbjct: 114 FASLIKAGLKYEATVIAEHKADAKYEIVSAASIIAKVTRDREIEKL------KQKYGEFG 167

Query: 194 SGYPGG 199
           SGYP  
Sbjct: 168 SGYPSD 173

>2d0b_A RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolase; 2.10A {Geobacillus stearothermophilus} PDB: 2d0a_A 2d0c_A 3asm_A Length = 310

 Score =  164 bits (416), Expect = 4e-50
 Identities = 38/198 (19%), Positives = 73/198 (36%), Gaps = 9/198 (4%)

Query: 3   SEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKR 62
             A       +   +G DE G G   GP+V    Y    +   +A L   DSK L +E  
Sbjct: 80  PSALAAHQLGSLSAIGSDEVGTGDYFGPIVVAAAYVDRPHIAKIAALGVKDSKQLNDEAI 139

Query: 63  EELFEDLKVNDSVGWAVDIIDPRELSAKM-LNKNKINLNEISHDSAIGLITRVLNIGILL 121
           + +   +   ++V  AV ++D  + +        +  +  + H+  +  +   +      
Sbjct: 140 KRIAPAIM--ETVPHAVTVLDNPQYNRWQRSGMPQTKMKALLHNRTLVKLVDAIA-PAEP 196

Query: 122 TEVYLDTVGDAEKYQAKLSQ--RFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGW 179
             + +D     + Y   LS   R    +     KA+S++  V+ ASI+A+      +   
Sbjct: 197 EAIIIDEFLKRDSYFRYLSDEDRIIRERVHCLPKAESVHVSVAAASIIARYVFLEEMEQL 256

Query: 180 IFEETAENMHRNFGSGYP 197
                A  +    G+G  
Sbjct: 257 ---SRAVGLLLPKGAGAI 271

>2etj_A Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII (EC 3.1.26.4) (RNAse HII), structur genomics, joint center for structural genomics; 1.74A {Thermotoga maritima} SCOP: c.55.3.1 PDB: 3o3g_A* 3o3f_A* 3o3h_A* Length = 250

 Score = 74.6 bits (184), Expect = 2e-16
 Identities = 40/159 (25%), Positives = 64/159 (40%), Gaps = 29/159 (18%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           + G+DEAGRG + GP+V   +                DSK L   KRE L +++    + 
Sbjct: 26  VAGVDEAGRGCLAGPVVAAAVVLEKEI------EGINDSKQLSPAKRERLLDEIMEKAA- 78

Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
              + I  P E+       +  N   I + + + +   + N+ +  + V +D        
Sbjct: 79  -VGIGIASPEEI-------DLYN---IFNATKLAMNRALENLSVKPSFVLVDGK------ 121

Query: 136 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174
              +    P    V   K D    ++  ASIVAKV RDR
Sbjct: 122 --GIELSVPGTCLV---KGDQKSKLIGAASIVAKVFRDR 155

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	219
3kio_A	301	Ribonuclease H2 subunit A; aicardi-goutieres syndr	100.0
1eke_A	230	Ribonuclease HII; endonuclease, structural genomic	100.0
1io2_A	213	Ribonuclease HII; endonuclease, hydrolase; 2.00A {	100.0
1i39_A	225	Ribonuclease HII, RNAse HII; mixed beta sheet, hel	100.0
1uax_A	220	Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid	100.0
2d0b_A	310	RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hyd	100.0
2etj_A	250	Ribonuclease HII, RNAse HII; TM0915, ribonuclease	100.0
3vn5_A	257	RNAse HIII, ribonuclease HIII; hydrolase; 1.98A {A	100.0

>3kio_A Ribonuclease H2 subunit A; aicardi-goutieres syndrome, RNAse H2, protein complex, autoimmune disease, endonuclease, hydrolase, metal-binding; 2.90A {Mus musculus} PDB: 3p5j_A 3puf_A 3p56_A

Probab=100.00  E-value=6.1e-58  Score=404.56  Aligned_cols=204  Identities=48%  Similarity=0.849  Sum_probs=180.9

Q ss_pred             CcCCCCC-CCcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhc-CcccEEEEEEC
Q 027718            6 ALPKWAS-NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN-DSVGWAVDIID   83 (219)
Q Consensus         6 ~~~~~~~-~~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~-~~~~~~v~~i~   83 (219)
                      .+|.++. .++++|||||||||+|||||+|||++|.+....|..+||+|||+||+++|++|+++|++. .++.|++.+++
T Consensus        19 ~~p~~~~~~~~v~GvDEaGRGplaGPvV~aavil~~~~~~~l~~~gl~DSKkLs~~kRe~L~~~I~~~~~a~~~~v~~~s   98 (301)
T 3kio_A           19 PVPAVCLKEPCVLGVDEAGRGPVLGPMVYAICYCPLSRLADLEALKVADSKTLTENERERLFAKMEEDGDFVGWALDVLS   98 (301)
T ss_dssp             CCCTHHHHSCEEEEEEEECSSCSBSCEEEEEEEEEGGGGGGCCCCCSCC--CCCHHHHHHHHHHHHHTTTTCEEEEEEEC
T ss_pred             CCchhhcCCceEEeeeCCCCCCccccceEEEEEEchhhhhhHhhcCCCccccCCHHHHHHHHHHHHhhcccceEEEEecC
Confidence            4788888 479999999999999999999999999987777888999999999999999999999973 26789999999


Q ss_pred             hhhHhHHhhhhhhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHH
Q 027718           84 PRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSG  163 (219)
Q Consensus        84 p~~id~~~~~~~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAA  163 (219)
                      |++||+.|++....|||.++|.+++.++++++..+..++.++||+++.+++|.++|+..+|++++++++|||++|++|||
T Consensus        99 ~~eId~~m~~~~~~nlN~l~~~~~~~~i~~~~~l~~~p~~vlVD~~~~p~~y~~~L~~~~p~~~~~~~~KgDs~~~sVAA  178 (301)
T 3kio_A           99 PNLISTSMLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFVDTVGMPETYQARLQQHFPGIEVTVKAKADSLFPVVSA  178 (301)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHHHHHHTTCCEEEEEEECSSCCHHHHHHHHHSSTTSEEEEETTGGGTSHHHHH
T ss_pred             HHHHHHHhhhcccccHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHHhhcCCCCceEEEeccchhhhHHHH
Confidence            99999988766678999999999999999988777788899999999999999999888899999999999999999999


Q ss_pred             HhHHhHHHHHHHHHHhhHhcccccccCCCccccCCchhhhhhhhhh
Q 027718          164 ASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVC  209 (219)
Q Consensus       164 ASIlAKv~RD~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~~~  209 (219)
                      |||||||+||++|++|+..........++||||||||+|++|++..
T Consensus       179 ASIlAKV~RD~~M~~~~f~e~l~~~~~~~GsGYPSDp~T~~~L~~~  224 (301)
T 3kio_A          179 ASIFAKVARDKAVKNWQFVENLQDLDSDYGSGYPNDPKTKAWLRKH  224 (301)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCCCCCCSSSTTSHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHhhhhhhHHhhCCCCCCcCCCCHHHHHHHHHc
Confidence            9999999999999988644333334568999999999999999875

>1eke_A Ribonuclease HII; endonuclease, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: MES; 2.00A {Methanocaldococcus jannaschii} SCOP: c.55.3.1

Probab=100.00  E-value=8.7e-56  Score=379.24  Aligned_cols=182  Identities=34%  Similarity=0.492  Sum_probs=159.9

Q ss_pred             cEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhh
Q 027718           15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNK   94 (219)
Q Consensus        15 ~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~   94 (219)
                      .++|||||||||+|||||+|||+++.+....|..+||+|||+||+++|++|+++|++. + .|++.+++|++||+.|.  
T Consensus         2 ~i~GvDEaGRGplaGPvv~aavil~~~~~~~l~~~gv~DSK~Ls~~~Re~L~~~I~~~-~-~~~v~~~~~~eId~~~~--   77 (230)
T 1eke_A            2 IIIGIDEAGRGPVLGPMVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYLKKLLENL-G-YVEKRILEAEEINQLMN--   77 (230)
T ss_dssp             EEEEEEEECSSCSBSCEEEEEEEEEGGGHHHHHTTTCC---CCCHHHHHHHHHHHHHH-S-EEEEEEECHHHHHHHTT--
T ss_pred             CEecccCCCCCCchhhheEEEEEEchhhhhhhhhcCCCCcccCCHHHHHHHHHHHHHh-C-CEEEEEeCHHHHhcccc--
Confidence            3799999999999999999999999987777888999999999999999999999985 5 89999999999999874  


Q ss_pred             hhchHHHHHHHHHHHHHHHHHhc---CCCCCEEEECCCC-ChHHHHHHhhccC--------CCcceEEeecCccchhhHH
Q 027718           95 NKINLNEISHDSAIGLITRVLNI---GILLTEVYLDTVG-DAEKYQAKLSQRF--------PSIKFVVSKKADSLYPVVS  162 (219)
Q Consensus        95 ~~~Nin~~~~~~~~~li~~~l~~---~~~~~~i~iD~~~-~~~~~~~~L~~~~--------~~~~~~~~~KaD~~~~sVA  162 (219)
                       ..|||++++.+|.++++++...   +..++.++||+++ ++++|.++|+..+        |..++++++|||++|++||
T Consensus        78 -~~Ni~~a~~~a~~~ai~~l~~~~~~~~~~~~vliD~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~KgD~~~~~VA  156 (230)
T 1eke_A           78 -SINLNDIEINAFSKVAKNLIEKLNIRDDEIEIYIDACSTNTKKFEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVS  156 (230)
T ss_dssp             -TSCHHHHHHHHHHHHHHHHHHHTTCCSSEEEEEEECCSSCHHHHHHHHHHHHHHHHTTTTCEEEEEEETTGGGTCHHHH
T ss_pred             -ccCHHHHHHHHHHHHHHHHhhhhccCCCCCEEEECCCCCChHHHHHHHhhhhcccccccCCCCceEEEECcccccHHHH
Confidence             6799999999999999988764   4457899999998 6778877776533        3467889999999999999


Q ss_pred             HHhHHhHHHHHHHHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718          163 GASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSI  207 (219)
Q Consensus       163 AASIlAKv~RD~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~  207 (219)
                      ||||||||+||++|++|++.||      ++|+|||||++|++|.+
T Consensus       157 AASIlAKv~RD~~m~~l~~~yp------~~gkGY~td~~t~~~l~  195 (230)
T 1eke_A          157 AASIIAKAERDEIIDYYKKIYG------DIGSGYPSDPKTIKFLE  195 (230)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTS------CCTTSSTTSHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHcC------CCCCcCCchHHHHHHHH
Confidence            9999999999999999999987      45699999999999987

>1io2_A Ribonuclease HII; endonuclease, hydrolase; 2.00A {Thermococcus kodakarensis} SCOP: c.55.3.1 PDB: 2dfh_A 2dff_A 2dfe_A 1x1p_A

Probab=100.00  E-value=8.3e-55  Score=369.26  Aligned_cols=178  Identities=34%  Similarity=0.512  Sum_probs=159.7

Q ss_pred             cEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhh
Q 027718           15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNK   94 (219)
Q Consensus        15 ~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~   94 (219)
                      .++|||||||||+|||||+|||+++.+....|..+|++|||+||+++|++|+++|++. ++.|++.+++|++||+.    
T Consensus         2 ~i~GvDEaGRGplaGPvv~aavil~~~~~~~l~~~gv~DSK~Ls~~~Re~L~~~I~~~-a~~~~v~~~~~~eId~~----   76 (213)
T 1io2_A            2 KIAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEILGV-LDDYVILELPPDVIGSR----   76 (213)
T ss_dssp             EEEEEEEECSSCSBSCEEEEEEEEEGGGHHHHHHTTGGGCTTCCHHHHHHHHHHHHTT-CSEEEEEEECHHHHHTC----
T ss_pred             CEeccCCCCCCCccchheEEEEEEChhhhhhhhhcCCCCcccCCHHHHHHHHHHHHHh-CceEEEEEECHHHHcch----
Confidence            3799999999999999999999999987777788999999999999999999999985 67899999999999853    


Q ss_pred             hhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCC-ChHHHHHHhhccCC-CcceEEeecCccchhhHHHHhHHhHHHH
Q 027718           95 NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEKYQAKLSQRFP-SIKFVVSKKADSLYPVVSGASIVAKVTR  172 (219)
Q Consensus        95 ~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~-~~~~~~~~L~~~~~-~~~~~~~~KaD~~~~sVAAASIlAKv~R  172 (219)
                       ..|||++++.+|.++++++..   .++.++||+++ ++++|.++|+..++ ..++++++|||++|++||||||||||+|
T Consensus        77 -~~Ni~~a~~~a~~~ai~~l~~---~p~~vlvD~~~~~~~~~~~~l~~~~~~~~~~~~~~KgD~~~~~VAAASIlAKv~R  152 (213)
T 1io2_A           77 -EGTLNEFEVENFAKALNSLKV---KPDVIYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTR  152 (213)
T ss_dssp             -SSCHHHHHHHHHHHHHHHCSS---CCSEEEEECCSSCHHHHHHHHHHTCSSCCEEEEETTHHHHCHHHHHHHHHHHHHH
T ss_pred             -hhHHHHHHHHHHHHHHHhccc---cCCEEEECCCCCCHHHHHHHHhhccCCCCceEEEeCcccccHHHHHHHHHHHHHH
Confidence             259999999999988887633   46799999998 67889888887654 5788899999999999999999999999


Q ss_pred             HHHHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718          173 DRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSI  207 (219)
Q Consensus       173 D~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~  207 (219)
                      |++|++|++.||      ++|+|||||++|++|.+
T Consensus       153 D~~m~~l~~~y~------~~g~GY~td~~t~~~l~  181 (213)
T 1io2_A          153 DRAVEKLKEEYG------EIGSGYPSDPRTRAFLE  181 (213)
T ss_dssp             HHHHHHHHHHHS------CCCSSCTTSHHHHHHHH
T ss_pred             HHHHHHHHHHcC------CCCCcCCchHHHHHHHH
Confidence            999999999997      45699999999999987

>1i39_A Ribonuclease HII, RNAse HII; mixed beta sheet, helix-loop-helix, hydrolase; 1.95A {Archaeoglobus fulgidus} SCOP: c.55.3.1 PDB: 1i3a_A 3p83_D*

Probab=100.00  E-value=4.4e-54  Score=367.21  Aligned_cols=177  Identities=32%  Similarity=0.473  Sum_probs=156.6

Q ss_pred             CCcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhh
Q 027718           13 NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKML   92 (219)
Q Consensus        13 ~~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~   92 (219)
                      ..+++|||||||||+|||||+|||++|.+.  .|..+||+|||+||+++|++|+++|++. +. |++.+++|++||+.| 
T Consensus        19 ~~~i~GvDEaGRGplaGPvV~aavil~~~~--~l~~~gv~DSKkLs~~kRe~L~~~I~~~-a~-~~v~~~s~~eID~~~-   93 (225)
T 1i39_A           19 SHMKAGIDEAGKGCVIGPLVVAGVACSDED--RLRKLGVKDSKKLSQGRREELAEEIRKI-CR-TEVLKVSPENLDERM-   93 (225)
T ss_dssp             --CEEEEEEECTTCSBSCEEEEEEEESCHH--HHHHTTCTTCTTCCHHHHHHHHHHHHHH-EE-EEEEEECHHHHHHHT-
T ss_pred             CeEEEEecCCCCcCchhhhEEEEEEEcchh--hcccCCCCcCCcCCHHHHHHHHHHHHHh-CC-EEEEEECHHHHhhhc-
Confidence            367999999999999999999999999864  5567899999999999999999999985 45 999999999999987 


Q ss_pred             hhhhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCC-ChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHH
Q 027718           93 NKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVT  171 (219)
Q Consensus        93 ~~~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~-~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~  171 (219)
                        ...|||++++.+|.++++++.     ++.++||+++ ++++|.++|+..++ .++++++|||+++++||||||||||+
T Consensus        94 --~~~Ni~~a~~~am~~ai~~l~-----~~~vlvD~~~~~~~~~~~~l~~~~~-~~~~~~~KgD~~~~~VAAASIlAKv~  165 (225)
T 1i39_A           94 --AAKTINEILKECYAEIILRLK-----PEIAYVDSPDVIPERLSRELEEITG-LRVVAEHKADEKYPLVAAASIIAKVE  165 (225)
T ss_dssp             --TTSCHHHHHHHHHHHHHHHHC-----CSEEEEEESSSCCHHHHHHHHHHHC-SEEEEEETGGGTCHHHHHHHHHHHHH
T ss_pred             --ccccHHHHHHHHHHHHHHhCC-----CCEEEECCCCCChHHHHHHhhhcCC-CceEEEecccccchHHHHHHHHHHHH
Confidence              467999999999999988763     3789999998 67888888865444 67889999999999999999999999


Q ss_pred             HHHHHHHhhHhcccccccCCCccccCCchhhhhhhhh
Q 027718          172 RDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIV  208 (219)
Q Consensus       172 RD~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~~  208 (219)
                      ||++|++|++.||      ++|+|||||++|++|.+.
T Consensus       166 RD~~m~~l~~~yp------~~gkGY~tD~~t~~hl~~  196 (225)
T 1i39_A          166 REREIERLKEKFG------DFGSGYASDPRTREVLKE  196 (225)
T ss_dssp             HHHHHHHHHHHHC------CCCSSSTTSHHHHHHHHH
T ss_pred             HHHHHHHHHHHCC------CCCCcCCChHHHHHHHHH
Confidence            9999999999997      456999999999999884

>1uax_A Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid ribonucleotidohydrolase, hydrolase; 2.00A {Pyrococcus horikoshii} SCOP: c.55.3.1

Probab=100.00  E-value=6.3e-54  Score=365.37  Aligned_cols=177  Identities=31%  Similarity=0.527  Sum_probs=158.0

Q ss_pred             EeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhh
Q 027718           16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKN   95 (219)
Q Consensus        16 ~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~   95 (219)
                      ++|||||||||+|||||+|||++|.+....|..+|++|||+||+++|++|+++|++. +..|++.+++|++||+.     
T Consensus         3 i~GvDEaGRGplaGPvv~aavil~~~~~~~l~~~gl~DSK~Ls~~~Re~L~~~I~~~-a~~~~v~~~~~~eId~~-----   76 (220)
T 1uax_A            3 VAGVDEAGRGPVIGPLVIGVAVIDEKNIERLRDIGVKDSKQLTPGQREKLFSKLIDI-LDDYYVLLVTPKEIDER-----   76 (220)
T ss_dssp             EEEEEEECSSCSBSCEEEEEEEEEGGGHHHHHHHTGGGSTTSCHHHHHHHHHHHHHH-SSEEEEEEECHHHHHTC-----
T ss_pred             EEeecCCCCCCchhhhEEEEEEEchhhhhhhhhcCCCCcccCCHHHHHHHHHHHHHh-CceEEEEEECHHHHcCh-----
Confidence            789999999999999999999999987777778899999999999999999999985 67899999999999853     


Q ss_pred             hchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCC-ChHHHHHHhhccCC-CcceEEeecCccchhhHHHHhHHhHHHHH
Q 027718           96 KINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEKYQAKLSQRFP-SIKFVVSKKADSLYPVVSGASIVAKVTRD  173 (219)
Q Consensus        96 ~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~-~~~~~~~~L~~~~~-~~~~~~~~KaD~~~~sVAAASIlAKv~RD  173 (219)
                      ..|||++++.+|.++++++.   ..++.++||+++ ++++|.++|+..++ ..++++++|||++|++||||||||||+||
T Consensus        77 ~~Ni~~a~~~am~~ai~~l~---~~~~~vlvD~~~~~~~~~~~~l~~~~~~~~~~~~~~KgD~~~~~VAAASIlAKv~RD  153 (220)
T 1uax_A           77 HHSMNELEAEKFVVALNSLR---IKPQKIYVDSADVDPKRFASLIKAGLKYEATVIAEHKADAKYEIVSAASIIAKVTRD  153 (220)
T ss_dssp             SSCHHHHHHHHHHHHHHTCS---SCCSEEEEECTTSCHHHHHHHHHHHCSSCCEEEEETTHHHHCHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHhcC---CCCCEEEECCCCCChHHHHHHhhhccCCCCceEEEeccchhhHHHHHHHHHHHHHHH
Confidence            25999999999988887652   346789999998 67888888876553 57888999999999999999999999999


Q ss_pred             HHHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718          174 RTLRGWIFEETAENMHRNFGSGYPGGARCLKLSI  207 (219)
Q Consensus       174 ~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~  207 (219)
                      ++|++|++.||      ++|+|||||++|++|.+
T Consensus       154 ~~m~~l~~~yp------~~gkGY~td~~t~~~l~  181 (220)
T 1uax_A          154 REIEKLKQKYG------EFGSGYPSDPRTKEWLE  181 (220)
T ss_dssp             HHHHHHHHHHC------CCTTSCTTCHHHHHHHH
T ss_pred             HHHHHHHHHcC------CCCCcCCchHHHHHHHH
Confidence            99999999997      45699999999999987

>2d0b_A RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolase; 2.10A {Geobacillus stearothermophilus} PDB: 2d0a_A 2d0c_A 3asm_A

Probab=100.00  E-value=1.3e-49  Score=354.15  Aligned_cols=188  Identities=21%  Similarity=0.250  Sum_probs=160.8

Q ss_pred             CCcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhh
Q 027718           13 NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKML   92 (219)
Q Consensus        13 ~~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~   92 (219)
                      ...++|||||||||+|||||+|||++|.+..+.|..+||+|||+||+++|++|+++|++.  +.|++.+++|++||+++.
T Consensus        90 ~~~i~GvDEaGRGplaGPvV~aavil~~~~~~~l~~~gl~DSKkLs~~kRe~L~~~I~~~--~~~~v~~~s~~eId~l~a  167 (310)
T 2d0b_A           90 SLSAIGSDEVGTGDYFGPIVVAAAYVDRPHIAKIAALGVKDSKQLNDEAIKRIAPAIMET--VPHAVTVLDNPQYNRWQR  167 (310)
T ss_dssp             TSCEEEEEEECTTCSBSCEEEEEEEECGGGHHHHHHTCCTTGGGCCHHHHHHHHHHHHHH--SCEEEEEECHHHHHHHHH
T ss_pred             CceEEeecCCCCCCchhhhEEEEEEEchhhhhhhhhcCCCcCCcCCHHHHHHHHHHHHHh--cCeEEEEECHHHHhHHHh
Confidence            356899999999999999999999999987766778899999999999999999999985  489999999999998743


Q ss_pred             h-hhhchHHHHHHHHHH-HHHHHHHhcCCCCCEEEECCCCChHHHHHHhhc--cCCCcceEEeecCccchhhHHHHhHHh
Q 027718           93 N-KNKINLNEISHDSAI-GLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQ--RFPSIKFVVSKKADSLYPVVSGASIVA  168 (219)
Q Consensus        93 ~-~~~~Nin~~~~~~~~-~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~--~~~~~~~~~~~KaD~~~~sVAAASIlA  168 (219)
                      . .+..||+.++|+.++ ++++.+ . +..++.++||+++.+++|.++|+.  .++..++++++|||++|++||||||||
T Consensus       168 ~~i~~~~l~~~~~~~ai~~~i~~L-~-~~~p~~vliD~~~~~~~~~~~L~~~~~~~~~~~~~~~KgD~~~~~VAAASIlA  245 (310)
T 2d0b_A          168 SGMPQTKMKALLHNRTLVKLVDAI-A-PAEPEAIIIDEFLKRDSYFRYLSDEDRIIRERVHCLPKAESVHVSVAAASIIA  245 (310)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHHHH-T-TCCCSEEEEECSSCHHHHHHHTTTCSSCCCTTEEEETTGGGTCHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHHHHHHHHhc-c-cCCCCEEEECCCCChHHHHHHHhhccccCCCceEEEeccccccHHHHHHHHHH
Confidence            1 234466776766554 333433 2 357889999999999999988874  345678889999999999999999999


Q ss_pred             HHHHHHHHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718          169 KVTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSI  207 (219)
Q Consensus       169 Kv~RD~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~  207 (219)
                         ||++|++|+++||+|+|+.|+|+|||+|..+++|.+
T Consensus       246 ---RD~~m~~l~~~~p~Yg~~~~kGygt~~h~~a~~~L~  281 (310)
T 2d0b_A          246 ---RYVFLEEMEQLSRAVGLLLPKGAGAIVDEAAARIIR  281 (310)
T ss_dssp             ---HHHHHHHHHHHHHHHTSCCCSSSSHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHhCcccCCCCCcCCCCHHHHHHHHHHH
Confidence               999999999999999999999999999999877765

>2etj_A Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII (EC 3.1.26.4) (RNAse HII), structur genomics, joint center for structural genomics; 1.74A {Thermotoga maritima} SCOP: c.55.3.1 PDB: 3o3g_A* 3o3f_A* 3o3h_A*

Probab=100.00  E-value=7.9e-50  Score=343.83  Aligned_cols=174  Identities=25%  Similarity=0.341  Sum_probs=135.5

Q ss_pred             CCCC-CcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHh
Q 027718           10 WASN-PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELS   88 (219)
Q Consensus        10 ~~~~-~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id   88 (219)
                      |..+ .+++|||||||||+|||||+|||++|.+      .+|++|||+||+++|++|+++|++. ++. ++.+++|++||
T Consensus        19 ~~~g~~~i~GvDEAGRGplaGPvV~AAVil~~~------~~Gl~DSKkLs~~kRe~L~~~I~~~-a~~-~v~~~sp~eID   90 (250)
T 2etj_A           19 YKKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKE------IEGINDSKQLSPAKRERLLDEIMEK-AAV-GIGIASPEEID   90 (250)
T ss_dssp             GTTTSSSEEEEEEECTTCSBSCEEEEEEEECSC------CC----------CHHHHHHHHHHHH-EEE-EEEEECHHHHH
T ss_pred             HhCCCceEEEecCCCCCCchhhheEEEEEEcCC------ccCCCccccCCHHHHHHHHHHHHHh-hCC-eEEEECHHHHC
Confidence            4443 6799999999999999999999999986      4799999999999999999999985 566 99999999997


Q ss_pred             HHhhhhhhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHh
Q 027718           89 AKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVA  168 (219)
Q Consensus        89 ~~~~~~~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlA  168 (219)
                      +       .|||+++..++.+++..+   +.+++.++||+++.+  +         .++.++++|||++|++||||||||
T Consensus        91 ~-------~NI~~at~~Am~rAi~~L---~~~p~~vlVDg~~~~--l---------~~~~~~ivKgD~~~~sVAAASIlA  149 (250)
T 2etj_A           91 L-------YNIFNATKLAMNRALENL---SVKPSFVLVDGKGIE--L---------SVPGTCLVKGDQKSKLIGAASIVA  149 (250)
T ss_dssp             H-------HCHHHHHHHHHHHHHHHS---SSCCSEEEEESSSCC--C---------SSCEEEETTHHHHCHHHHHHHHHH
T ss_pred             H-------HhHHHHHHHHHHHHHHhc---CCCCCEEEECCCCCC--C---------CCceEEEecccccchhHHHHHHHH
Confidence            4       699999888877666543   456789999998754  1         245677899999999999999999


Q ss_pred             HHHHHHHHHHhhHhcccccccCCCccccCCchhhhhh----hhhhhhhccc
Q 027718          169 KVTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKL----SIVCNNFQSF  215 (219)
Q Consensus       169 Kv~RD~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~----~~~~~~~~~~  215 (219)
                      ||+||++|++|++.||+|+|+.|  +||||..| ++|    .++..++++|
T Consensus       150 KV~RD~~M~~l~~~yp~Ygf~~~--kGY~T~~h-~~al~~~G~~~~HR~Sf  197 (250)
T 2etj_A          150 KVFRDRLMSEFHRMYPQFSFHKH--KGYATKEH-LNEIRKNGVLPIHRLSF  197 (250)
T ss_dssp             HHHHHHHHHHHHHHCTTSCHHHH--TTCCCHHH-HHHHHHHCCCTTBCTTS
T ss_pred             HHHHHHHHHHHHHHCcccCCcCC--CcCCcHHH-HHHHHHcCcCCeEECCc
Confidence            99999999999999999999776  89999554 444    3444555555

>3vn5_A RNAse HIII, ribonuclease HIII; hydrolase; 1.98A {Aquifex aeolicus}

Probab=100.00  E-value=3e-46  Score=324.14  Aligned_cols=167  Identities=26%  Similarity=0.289  Sum_probs=145.5

Q ss_pred             eeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhhhc
Q 027718           18 GIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKI   97 (219)
Q Consensus        18 GiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~~~   97 (219)
                      |||||||||+|||||+|||++|.+....|..+||+|||+||+++|++|+++|++.  +.|++.+++|++||++|.  +..
T Consensus        75 GvDEaGRGplaGPvv~aavil~~~~~~~L~~~gv~DSKkLs~~kRe~L~~~I~~~--~~~~v~~~s~~eID~~~~--~~~  150 (257)
T 3vn5_A           75 GCDESGKGDIFGSLVLCCVCIPEENYLKVSSLNPRDTKRLSDKRVERLYLALKPL--VKAYCYEIKPEEYNKLYR--KFR  150 (257)
T ss_dssp             EEEEESTTCSBSCEEEEEEECCGGGHHHHHHTCTTCCTTTCHHHHHHHHHHHGGG--SEEEEEEECHHHHHHHHH--HHS
T ss_pred             CccCCCCCCcccccEEEEEEEchhhhhhHhhcCCCccccCCHHHHHHHHHHHHHh--cCEEEEEECHHHHhhhcc--ccc
Confidence            9999999999999999999999987777778999999999999999999999984  789999999999998763  347


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHHHHHH
Q 027718           98 NLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLR  177 (219)
Q Consensus        98 Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~~m~  177 (219)
                      |||.++..+|.+++..+... ..++.++||+++.+.    +|     ..++++++|||+ +++||||||||   ||++|+
T Consensus       151 Nin~~~~~am~~Ai~~L~~~-~~~~~vlvD~~~~~~----~l-----~~~~~~~~KgD~-~~sVAAASIlA---Rd~~m~  216 (257)
T 3vn5_A          151 NLNKMMTHFYKLLIERVKEE-CGVSEVVVDKYQPSN----PF-----GEDVIFETEAER-NLAVAVASIFA---RYKFLQ  216 (257)
T ss_dssp             SHHHHHHHHHHHHHHHHHHH-HTCSCEEECCCSSSC----CS-----CTTEEECBTTBC-CHHHHHHHHHH---HHHHHH
T ss_pred             cHHHHHHHHHHHHHHHhhcc-CCCCEEEECCCCCcc----cC-----CCCeEEEEccch-hHHHHHHHHHH---HHHHHH
Confidence            99999999999998887543 125789999997543    12     246788999999 99999999999   999999


Q ss_pred             HhhHhcccccccCCCccccCCchhhhh
Q 027718          178 GWIFEETAENMHRNFGSGYPGGARCLK  204 (219)
Q Consensus       178 ~l~~~~p~y~~~~~~GsGYpsd~~t~~  204 (219)
                      +|+++||+|+|+.|  +|||+..|..+
T Consensus       217 ~l~~~~p~Ygf~~~--kGYgT~~H~~A  241 (257)
T 3vn5_A          217 SLKEVERELGIKIP--KGTSKEVKELA  241 (257)
T ss_dssp             HHHHHHHHHCSCCC--CSCCHHHHHHH
T ss_pred             HHHHhCccCCCcCC--CCCCcHHHHHH
Confidence            99999999999877  78888887754

---

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	219
d1ekea_	225	c.55.3.1 (A:) Class II ribonuclease H (RNase HII)	4e-23
d1io2a_	213	c.55.3.1 (A:) Class II ribonuclease H (RNase HII)	9e-23
d1uaxa_	211	c.55.3.1 (A:) Class II ribonuclease H (RNase HII)	2e-20
d1i39a_	200	c.55.3.1 (A:) Class II ribonuclease H (RNase HII)	2e-15
d2etja1	221	c.55.3.1 (A:1-221) Class II ribonuclease H (RNase	5e-15

>d1ekea_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 225

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: Class II ribonuclease H (RNase HII)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 90.7 bits (224), Expect = 4e-23
 Identities = 62/199 (31%), Positives = 92/199 (46%), Gaps = 17/199 (8%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           I+GIDEAGRGPVLGPMV          ++ L  L   DSK L + KR  L + L+    V
Sbjct: 3   IIGIDEAGRGPVLGPMVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYLKKLLENLGYV 62

Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGD---- 131
              +   +        +N N I +N  +       +   LNI     E+Y+D        
Sbjct: 63  EKRILEAEEINQLMNSINLNDIEIN--AFSKVAKNLIEKLNIRDDEIEIYIDACSTNTKK 120

Query: 132 -----AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAE 186
                 +K +  + +R  +IK +   KAD+ YPVVS ASI+AK  RD  +  +      +
Sbjct: 121 FEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYY------K 174

Query: 187 NMHRNFGSGYPGGARCLKL 205
            ++ + GSGYP   + +K 
Sbjct: 175 KIYGDIGSGYPSDPKTIKF 193

>d1io2a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Thermococcus kodakaraensis [TaxId: 311400]} Length = 213

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: Class II ribonuclease H (RNase HII)
species: Archaeon Thermococcus kodakaraensis [TaxId: 311400]

 Score = 89.4 bits (221), Expect = 9e-23
 Identities = 61/205 (29%), Positives = 95/205 (46%), Gaps = 19/205 (9%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           I GIDEAGRGPV+GPMV   +    +    L  L   DSK L  ++RE+LF ++      
Sbjct: 3   IAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEIL-GVLD 61

Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEK 134
            + +  + P  + ++           ++          + ++ +    +Y D    D E+
Sbjct: 62  DYVILELPPDVIGSRE--------GTLNEFEVENFAKALNSLKVKPDVIYADAADVDEER 113

Query: 135 YQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG 193
           +  +L +R      VV+K KAD ++PVVS ASI+AKVTRDR +     E      +   G
Sbjct: 114 FARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAVEKLKEE------YGEIG 167

Query: 194 SGYPGGARCLKLSIVCNNFQSFGGL 218
           SGYP   R      + N ++  G  
Sbjct: 168 SGYPSDPRTRA--FLENYYREHGEF 190

>d1uaxa_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Length = 211

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: Class II ribonuclease H (RNase HII)
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

 Score = 83.0 bits (204), Expect = 2e-20
 Identities = 54/189 (28%), Positives = 89/189 (47%), Gaps = 17/189 (8%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           + G+DEAGRGPV+GP+V G         + L  +   DSK L   +RE+      ++   
Sbjct: 3   VAGVDEAGRGPVIGPLVIGVAVIDEKNIERLRDIGVKDSKQLTPGQREK-LFSKLIDILD 61

Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
            + V ++ P+E+  +  + N++   +            + ++ I   ++Y+D+     K 
Sbjct: 62  DYYVLLVTPKEIDERHHSMNELEAEKFVV--------ALNSLRIKPQKIYVDSADVDPKR 113

Query: 136 QAKLSQRFPSIKFVVS--KKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG 193
            A L +     +  V    KAD+ Y +VS ASI+AKVTRDR +         +  +  FG
Sbjct: 114 FASLIKAGLKYEATVIAEHKADAKYEIVSAASIIAKVTRDREIEKL------KQKYGEFG 167

Query: 194 SGYPGGARC 202
           SGYP   R 
Sbjct: 168 SGYPSDPRT 176

>d1i39a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 200

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: Class II ribonuclease H (RNase HII)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 69.9 bits (170), Expect = 2e-15
 Identities = 51/182 (28%), Positives = 82/182 (45%), Gaps = 18/182 (9%)

Query: 18  GIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGW 77
           GIDEAG+G V+GP+V   + C    +  L  L   DSK L + +REEL E+++       
Sbjct: 4   GIDEAGKGCVIGPLVVAGVACS--DEDRLRKLGVKDSKKLSQGRREELAEEIRKICR--T 59

Query: 78  AVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQA 137
            V  + P  L  +M  K    + +  +   I  +             Y+D+     +  +
Sbjct: 60  EVLKVSPENLDERMAAKTINEILKECYAEIILRLKP--------EIAYVDSPDVIPERLS 111

Query: 138 KLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYP 197
           +  +    ++ V   KAD  YP+V+ ASI+AKV R+R +         +    +FGSGY 
Sbjct: 112 RELEEITGLRVVAEHKADEKYPLVAAASIIAKVEREREIERL------KEKFGDFGSGYA 165

Query: 198 GG 199
             
Sbjct: 166 SD 167

>d2etja1 c.55.3.1 (A:1-221) Class II ribonuclease H (RNase HII) {Thermotoga maritima [TaxId: 2336]} Length = 221

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: Class II ribonuclease H (RNase HII)
species: Thermotoga maritima [TaxId: 2336]

 Score = 68.9 bits (168), Expect = 5e-15
 Identities = 42/182 (23%), Positives = 72/182 (39%), Gaps = 31/182 (17%)

Query: 16  IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
           + G+DEAGRG + GP+V   +      +         DSK L   KRE L +++    +V
Sbjct: 14  VAGVDEAGRGCLAGPVVAAAVVLEKEIE------GINDSKQLSPAKRERLLDEIMEKAAV 67

Query: 76  GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
           G  +   +  +             N I + + + +   + N+ +  + V +D  G     
Sbjct: 68  GIGIASPEEID-----------LYN-IFNATKLAMNRALENLSVKPSFVLVDGKGI---- 111

Query: 136 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSG 195
                    S+      K D    ++  ASIVAKV RDR +  +       + H++   G
Sbjct: 112 -------ELSVPGTCLVKGDQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKH--KG 162

Query: 196 YP 197
           Y 
Sbjct: 163 YA 164

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	219
d1io2a_	213	Class II ribonuclease H (RNase HII) {Archaeon Ther	100.0
d1ekea_	225	Class II ribonuclease H (RNase HII) {Archaeon Meth	100.0
d1i39a_	200	Class II ribonuclease H (RNase HII) {Archaeon Arch	100.0
d1uaxa_	211	Class II ribonuclease H (RNase HII) {Archaeon Pyro	100.0
d2etja1	221	Class II ribonuclease H (RNase HII) {Thermotoga ma	100.0

>d1io2a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Thermococcus kodakaraensis [TaxId: 311400]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: Class II ribonuclease H (RNase HII)
species: Archaeon Thermococcus kodakaraensis [TaxId: 311400]

Probab=100.00  E-value=5.5e-51  Score=342.85  Aligned_cols=187  Identities=33%  Similarity=0.516  Sum_probs=158.5

Q ss_pred             cEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhh
Q 027718           15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNK   94 (219)
Q Consensus        15 ~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~   94 (219)
                      .|+|||||||||+|||||||||+++.+....+..+||+|||+||+++|++|+++|++. ...|.+..++|++++.     
T Consensus         2 ~i~GvDEaGRG~l~GPvvvaav~~~~~~~~~l~~~gv~DSK~Ls~~kR~~l~~~I~~~-~~~~~i~~~~~~~~~~-----   75 (213)
T d1io2a_           2 KIAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEILGV-LDDYVILELPPDVIGS-----   75 (213)
T ss_dssp             EEEEEEEECSSCSBSCEEEEEEEEEGGGHHHHHHTTGGGCTTCCHHHHHHHHHHHHTT-CSEEEEEEECHHHHHT-----
T ss_pred             cEEeecCcCccccccceEEEEEEEchhhcchhhhcCcchhhhCcHHHHHHHHHHHHHH-HHHhhhhcccHHHHhh-----
Confidence            3799999999999999999999999998888889999999999999999999999985 6789999999999875     


Q ss_pred             hhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCC-ChHHHHHHhhccCC-CcceEEeecCccchhhHHHHhHHhHHHH
Q 027718           95 NKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEKYQAKLSQRFP-SIKFVVSKKADSLYPVVSGASIVAKVTR  172 (219)
Q Consensus        95 ~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~-~~~~~~~~L~~~~~-~~~~~~~~KaD~~~~sVAAASIlAKv~R  172 (219)
                      +..|+|.+...++.++++.+   ...++.+++|++. ++..|...+.+..+ ..++++++|||++|++||||||||||+|
T Consensus        76 ~~~~~~~~~~~~~~~ai~~l---~~~~~~v~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~KgD~~~~~VAAASIlAKv~R  152 (213)
T d1io2a_          76 REGTLNEFEVENFAKALNSL---KVKPDVIYADAADVDEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTR  152 (213)
T ss_dssp             CSSCHHHHHHHHHHHHHHHC---SSCCSEEEEECCSSCHHHHHHHHHHTCSSCCEEEEETTHHHHCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHhc---CCCCCEEEECcccccchhhhhhhcccccccceeEEeecccccchhhhHHHHHHHHHH
Confidence            45789998888877776653   3457889999987 55666666655443 4467778899999999999999999999


Q ss_pred             HHHHHHhhHhcccccccCCCccccCCchhhhhhhhhhhhhccccCC
Q 027718          173 DRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFGGL  218 (219)
Q Consensus       173 D~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~~~~~~~~~~~~  218 (219)
                      |++|++|++.||+|      |+|||+|+||++|.+  ++++.+||+
T Consensus       153 D~~m~~l~~~y~~~------g~GY~s~~h~~a~l~--~~~~~~~~~  190 (213)
T d1io2a_         153 DRAVEKLKEEYGEI------GSGYPSDPRTRAFLE--NYYREHGEF  190 (213)
T ss_dssp             HHHHHHHHHHHSCC------CSSCTTSHHHHHHHH--HHHHHHSSC
T ss_pred             HHHHHHHHHhCCcC------CCCCCCHHHHHHHHH--hcccccCCC
Confidence            99999999999855      689999999999975  345555553

>d1ekea_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: Class II ribonuclease H (RNase HII)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=100.00  E-value=6e-49  Score=330.53  Aligned_cols=191  Identities=35%  Similarity=0.487  Sum_probs=152.9

Q ss_pred             cEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhh
Q 027718           15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNK   94 (219)
Q Consensus        15 ~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~   94 (219)
                      .+||+|||||||+|||||||||+++.+..+.|..+||+|||+||+++|++|++.|++.  ..+.+.+++|.+||+.+   
T Consensus         2 iviGvDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~kr~~l~~~i~~~--~~~~~~~~~~~~~~~~~---   76 (225)
T d1ekea_           2 IIIGIDEAGRGPVLGPMVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYLKKLLENL--GYVEKRILEAEEINQLM---   76 (225)
T ss_dssp             EEEEEEEECSSCSBSCEEEEEEEEEGGGHHHHHTTTCC---CCCHHHHHHHHHHHHHH--SEEEEEEECHHHHHHHT---
T ss_pred             EEEEecCCCCcccccceeEEEEEEchhhchhhhccCCCchhcCCHHHHHHHHHHHHHh--ccceeEeeechhhhhhh---
Confidence            4799999999999999999999999999999999999999999999999999999984  57899999999999887   


Q ss_pred             hhchHHHHHHHHHHHHHHHHHh-c--CCCCCEEEECCCCChHH-HH----HHhhc----cCCCcceEEeecCccchhhHH
Q 027718           95 NKINLNEISHDSAIGLITRVLN-I--GILLTEVYLDTVGDAEK-YQ----AKLSQ----RFPSIKFVVSKKADSLYPVVS  162 (219)
Q Consensus        95 ~~~Nin~~~~~~~~~li~~~l~-~--~~~~~~i~iD~~~~~~~-~~----~~L~~----~~~~~~~~~~~KaD~~~~sVA  162 (219)
                      ...|+|.+...++..++..++. .  ......+++|++..+.+ +.    ..+..    ..+++++++++|||++|++||
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~KaD~~~~~VA  156 (225)
T d1ekea_          77 NSINLNDIEINAFSKVAKNLIEKLNIRDDEIEIYIDACSTNTKKFEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVS  156 (225)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHTTCCSSEEEEEEECCSSCHHHHHHHHHHHHHHHHTTTTCEEEEEEETTGGGTCHHHH
T ss_pred             hHHHHHHHHHHHHhhhhhhhHhhccccCCceEEEeeccccccccchhhhhhhhcccccCCCCCcCEEEEecCcccchhHH
Confidence            5678888877777776666543 2  22334689999975543 22    22222    234567889999999999999


Q ss_pred             HHhHHhHHHHHHHHHHhhHhcccccccCCCccccCCchhhhhhhhhhhhhccccCC
Q 027718          163 GASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFGGL  218 (219)
Q Consensus       163 AASIlAKv~RD~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~~~~~~~~~~~~  218 (219)
                      ||||||||+||++|++|++.||.|      |+|||+|++|++|.+  +++..+||+
T Consensus       157 AASIlAKv~RD~~m~~l~~~~~~~------G~Gy~~d~~~~~~~~--~~~~~~~g~  204 (225)
T d1ekea_         157 AASIIAKAERDEIIDYYKKIYGDI------GSGYPSDPKTIKFLE--DYFKKHKKL  204 (225)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSCC------TTSSTTSHHHHHHHH--HHHHHHSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCC------CCCCCchHHHHHHHH--HHHhhhcCC
Confidence            999999999999999999999854      689999999999976  334444443

>d1i39a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: Class II ribonuclease H (RNase HII)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=100.00  E-value=6.4e-49  Score=326.74  Aligned_cols=173  Identities=32%  Similarity=0.485  Sum_probs=147.0

Q ss_pred             EeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhh
Q 027718           16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKN   95 (219)
Q Consensus        16 ~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~   95 (219)
                      -+|||||||||+|||||||||+++.+  +.+..+||+|||+||+++|++|++.|++.  +.|.+..++|++||+.+   .
T Consensus         2 ~aGiDEaGrG~~~GPvvvaav~~~~~--~~~~~~gv~DSK~Ls~~kr~~l~~~I~~~--~~~~i~~~~~~~id~~~---~   74 (200)
T d1i39a_           2 KAGIDEAGKGCVIGPLVVAGVACSDE--DRLRKLGVKDSKKLSQGRREELAEEIRKI--CRTEVLKVSPENLDERM---A   74 (200)
T ss_dssp             EEEEEEECTTCSBSCEEEEEEEESCH--HHHHHTTCTTCTTCCHHHHHHHHHHHHHH--EEEEEEEECHHHHHHHT---T
T ss_pred             ccCCcCcCCCCcccceEEEEEEECch--hccccccchhhhcCCHHHHHHHHHHHhhc--chhheeeechhhhhHHH---H
Confidence            58999999999999999999999976  35678899999999999999999999984  67999999999999877   4


Q ss_pred             hchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCC-ChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHHhHHHHHH
Q 027718           96 KINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDR  174 (219)
Q Consensus        96 ~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~-~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIlAKv~RD~  174 (219)
                      ..|+|.++..++..++..+     ..+.+++|... .++.+...+. .++++++++++|||++|++||||||||||+||+
T Consensus        75 ~~~~~~~~~~~~~~~~~~~-----~~~~~~i~~~~~~~~~~~~~~~-~~~~~~i~~~~KgD~~~~~VAAASIiAKv~RD~  148 (200)
T d1i39a_          75 AKTINEILKECYAEIILRL-----KPEIAYVDSPDVIPERLSRELE-EITGLRVVAEHKADEKYPLVAAASIIAKVERER  148 (200)
T ss_dssp             TSCHHHHHHHHHHHHHHHH-----CCSEEEEEESSSCCHHHHHHHH-HHHCSEEEEEETGGGTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhcc-----cccceeeccccchhhhhccccc-cccceeEEEEeccccccccccHHHHHHHHHHHH
Confidence            5688888888877776654     23567777654 4555544443 346788999999999999999999999999999


Q ss_pred             HHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718          175 TLRGWIFEETAENMHRNFGSGYPGGARCLKLSI  207 (219)
Q Consensus       175 ~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~  207 (219)
                      +|++|++.||+|      |+|||+|++|++|.+
T Consensus       149 ~m~~l~~~~p~y------G~gy~s~~~t~~~l~  175 (200)
T d1i39a_         149 EIERLKEKFGDF------GSGYASDPRTREVLK  175 (200)
T ss_dssp             HHHHHHHHHCCC------CSSSTTSHHHHHHHH
T ss_pred             HHHHHHHHCCcC------CCcCCCcHHHHHHHH
Confidence            999999999854      689999999999975

>d1uaxa_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: Class II ribonuclease H (RNase HII)
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=100.00  E-value=6.6e-49  Score=329.85  Aligned_cols=186  Identities=30%  Similarity=0.514  Sum_probs=150.1

Q ss_pred             EeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhHhHHhhhhh
Q 027718           16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELSAKMLNKN   95 (219)
Q Consensus        16 ~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~id~~~~~~~   95 (219)
                      |+|||||||||+|||||||||+++.+..+.|..+||+|||+||+++|++|++.|++. ...|++..++|++||+.+    
T Consensus         3 I~GvDEaGRG~l~GPvvvaav~~~~~~~~~l~~~gv~DSK~Ls~~kR~~l~~~i~~~-~~~~~i~~~s~~eId~~~----   77 (211)
T d1uaxa_           3 VAGVDEAGRGPVIGPLVIGVAVIDEKNIERLRDIGVKDSKQLTPGQREKLFSKLIDI-LDDYYVLLVTPKEIDERH----   77 (211)
T ss_dssp             EEEEEEECSSCSBSCEEEEEEEEEGGGHHHHHHHTGGGSTTSCHHHHHHHHHHHHHH-SSEEEEEEECHHHHHTCS----
T ss_pred             EEeecCCCcccchhhhEEEEEEEChhhhhhhhhcCCccchhCCHHHHHHHHHHHhhc-ccceEEeehhhHHHhhcc----
Confidence            799999999999999999999999998888889999999999999999999999885 578999999999999743    


Q ss_pred             hchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCC-ChHHHHHHhhccCC-CcceEEeecCccchhhHHHHhHHhHHHHH
Q 027718           96 KINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEKYQAKLSQRFP-SIKFVVSKKADSLYPVVSGASIVAKVTRD  173 (219)
Q Consensus        96 ~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~-~~~~~~~~L~~~~~-~~~~~~~~KaD~~~~sVAAASIlAKv~RD  173 (219)
                       .|+|.+....+...+.   .....++.+++|.+. ++..+...+...++ ...+++++|||+++++||||||||||+||
T Consensus        78 -~~~n~l~a~~~~~~~~---~l~~~~~~i~vd~~~~~~~~~~~~~~~~~~~~~~~~~~~KgD~~~~~VAAASIiAKv~RD  153 (211)
T d1uaxa_          78 -HSMNELEAEKFVVALN---SLRIKPQKIYVDSADVDPKRFASLIKAGLKYEATVIAEHKADAKYEIVSAASIIAKVTRD  153 (211)
T ss_dssp             -SCHHHHHHHHHHHHHH---TCSSCCSEEEEECTTSCHHHHHHHHHHHCSSCCEEEEETTHHHHCHHHHHHHHHHHHHHH
T ss_pred             -cchhHHHHHHHHHHHH---hcCCCcceeeeecccccccccchhhccCCCCCceEEEeeccccccccchHHHHHHHHHHH
Confidence             4666665444433322   334557789998875 55555555544443 45677889999999999999999999999


Q ss_pred             HHHHHhhHhcccccccCCCccccCCchhhhhhhhhhhhhccccCC
Q 027718          174 RTLRGWIFEETAENMHRNFGSGYPGGARCLKLSIVCNNFQSFGGL  218 (219)
Q Consensus       174 ~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~~~~~~~~~~~~  218 (219)
                      ++|++|++.||+|      |+|||+|+.|++|...  +++.|||+
T Consensus       154 ~~m~~l~~~~p~y------g~~~~~gy~Tk~hl~~--~~~~~g~~  190 (211)
T d1uaxa_         154 REIEKLKQKYGEF------GSGYPSDPRTKEWLEE--YYKQYGDF  190 (211)
T ss_dssp             HHHHHHHHHHCCC------TTSCTTCHHHHHHHHH--HHHHHSSC
T ss_pred             HHHHHHHHHCCCC------CCCCCCchhHHHHHHH--HHHHhCCC
Confidence            9999999999865      4588888899888643  34456653

>d2etja1 c.55.3.1 (A:1-221) Class II ribonuclease H (RNase HII) {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: Class II ribonuclease H (RNase HII)
species: Thermotoga maritima [TaxId: 2336]

Probab=100.00  E-value=2.5e-47  Score=322.95  Aligned_cols=168  Identities=24%  Similarity=0.323  Sum_probs=135.0

Q ss_pred             CCCCC-CcEeeeecCCcCCcccceeeEEEEcccccchhhhccCcCCCCCCCHHHHHHHHHHhhhcCcccEEEEEEChhhH
Q 027718            9 KWASN-PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPREL   87 (219)
Q Consensus         9 ~~~~~-~~~iGiDEaGrG~~~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~l~~~I~~~~~~~~~v~~i~p~~i   87 (219)
                      .|+++ .+++|||||||||++||||+|||++|.+.      .||+|||+||+++|+++++.|+..  ..|++..++|++|
T Consensus         6 l~~~~~~~iiGiDEAGRGpv~GPmVvaav~~~~~~------~gv~DSK~Lt~~kR~~l~~~i~~~--~~~~i~~~~~~ei   77 (221)
T d2etja1           6 LYKKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKEI------EGINDSKQLSPAKRERLLDEIMEK--AAVGIGIASPEEI   77 (221)
T ss_dssp             GGTTTSSSEEEEEEECTTCSBSCEEEEEEEECSCC------C----------CHHHHHHHHHHHH--EEEEEEEECHHHH
T ss_pred             HHHcCCCEEEEecCCCCCCcccceeEEEEEECCCc------chhhhhccCCHHHHHHHhhhhhhc--cceEEEecchhHH
Confidence            45665 68999999999999999999999999752      489999999999999999999984  5799999999999


Q ss_pred             hHHhhhhhhchHHHHHHHHHHHHHHHHHhcCCCCCEEEECCCCChHHHHHHhhccCCCcceEEeecCccchhhHHHHhHH
Q 027718           88 SAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIV  167 (219)
Q Consensus        88 d~~~~~~~~~Nin~~~~~~~~~li~~~l~~~~~~~~i~iD~~~~~~~~~~~L~~~~~~~~~~~~~KaD~~~~sVAAASIl  167 (219)
                      |       ..||+.++..++.+++.++   ...+..+++|+...+           +..+.++++|||++|++|||||||
T Consensus        78 d-------~~ni~~a~~~a~~~ai~~l---~~~~~~~~~D~~~~~-----------~~~~~~~~~KaD~~~~~VaAASIi  136 (221)
T d2etja1          78 D-------LYNIFNATKLAMNRALENL---SVKPSFVLVDGKGIE-----------LSVPGTCLVKGDQKSKLIGAASIV  136 (221)
T ss_dssp             H-------HHCHHHHHHHHHHHHHHHS---SSCCSEEEEESSSCC-----------CSSCEEEETTHHHHCHHHHHHHHH
T ss_pred             H-------hcChHHHHHHHHHHHHHHh---hhhhccccccccCCC-----------CCCCceeEEcCCccchhhhHHHHH
Confidence            6       4789999888887776654   445688999986422           345667889999999999999999


Q ss_pred             hHHHHHHHHHHhhHhcccccccCCCccccCCchhhhhhhh
Q 027718          168 AKVTRDRTLRGWIFEETAENMHRNFGSGYPGGARCLKLSI  207 (219)
Q Consensus       168 AKv~RD~~m~~l~~~~p~y~~~~~~GsGYpsd~~t~~~~~  207 (219)
                      |||+||++|+++++.||+|+|+.|  |||||++|+..|.+
T Consensus       137 AKv~RD~~m~~l~~~~p~yg~~~~--sGY~T~~h~~ai~~  174 (221)
T d2etja1         137 AKVFRDRLMSEFHRMYPQFSFHKH--KGYATKEHLNEIRK  174 (221)
T ss_dssp             HHHHHHHHHHHHHHHCTTSCHHHH--TTCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCCCccC--cCCCcHHHHHHHHH
Confidence            999999999999999999999765  99999999988743