Citrus Sinensis ID: 021120

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------

MEDEKDAFYVVRKGDVVGIYKTLSDCQLQAGFSVRDPSLTVYKGYGLSKEAEEYLASHGLKSSSYSVSASDVKSDLFGKIVPCPLQEPASSGEKVSDEVSLPKMLREVAAAGSTSISINTQKRHFNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQVEAECSSFTK

ccccccEEEEEEEccEEEEEccHHHHHHHHccccccccccEEEcccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccEEEEEEccccccccccEEEEEEEcccccEEEEEEEccccccHHHHHHHHHHHHHHHHHccccEEEEEccHHHHHHHHccccccccccHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHHHcccccccEEEccccccc

cccccccEEEEEcccEEEEEEcHHHHHHHHccccccccEEEEEcccccccHHHHHHHccccccEEEEEHHHHHHHHHccccccccccccccccccccccccccccccEEcccccccccccccccccccHHHHHHHccccccccccccccccHHHHHHcccccccccccccccccEEEEEEcccccccccccEEEEEEccccccEEEEEEEEEEccccHHHHHHHHHHHHHHHHccccEEEEEcccHHEEHHcccccccccHHHHHHHHHHHHHHHHcccEEEEEEcccccHHHHHHHHHHcccccccHHHHHHHccc

medekdafYVVRKGDVVGIYKTLSdcqlqagfsvrdpsltvykgyglskEAEEYLAshglksssysvsasdvksdlfgkivpcplqepassgekvsdevSLPKMLREVAAAgstsisintqkrhfnedncwntqsvpenyvaaagstsfsintqrshlnadsclntqsvpyncysctlefdgaskgnpgqagagavlraedgsvyrlregvgiatnNVAEYRALILGLKYALQKGykhirvqgdsKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQVEAECSSFTK

medekdafyvvrkgdVVGIYKTLsdcqlqagfsvrdpsltVYKGYGLSKEAEEYLASHGLKSSSYSVSASDVKSDLFGKIVPcplqepassgekvsDEVSLPKMLREVAAAgstsisintqkrhfnEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVYRLREgvgiatnnvAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQVEAECSSFTK

MEDEKDAFYVVRKGDVVGIYKTLSDCQLQAGFSVRDPSLTVYKGYGLSKEAEEYLASHGLksssysvsasdvksdLFGKIVPCPLQEPASSGEKVSDEVSLPKMLREVAAAGSTSISINTQKRHFNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQVEAECSSFTK

******AFYVVRKGDVVGIYKTLSDCQLQAGFSVRDPSLTVYKGYGLSKEAEEYL********************LFGKIVP*****************************************HFNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGA*********AGAVLRAEDGSVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLK*************

****KDA*YVVRKGDVVGIYKTLSDCQLQAG**********Y****LSKEAEEYLASHGLKSSSYSVSASDVKSDLFGKIVPCP*************************AAGSTSISINTQKRHFNEDNCWNTQSVPENYVA******************DSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQV***C*****

MEDEKDAFYVVRKGDVVGIYKTLSDCQLQAGFSVRDPSLTVYKGYGLSKEAEEYLASH*************VKSDLFGKIVPCPLQ************VSLPKMLREVAAAGSTSISINTQKRHFNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQV*********

****KDAFYVVRKGDVVGIYKTLSDCQLQAGFSVRDPSLTVYKGYGLSKEAEEYLASHGLKSSSYSVSASDVKSDLFGKIVPCPLQEPA**************************************DNCWN*QSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQVEAECS****

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MEDEKDAFYVVRKGDVVGIYKTLSDCQLQAGFSVRDPSLTVYKGYGLSKEAEEYLASHGLKSSSYSVSASDVKSDLFGKIVPCPLQEPASSGEKVSDEVSLPKMLREVAAAGSTSISINTQKRHFNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNxxxxxxxxxxxxxxxxxxxxxHILRNLNSEADAQANMGIYLKDGQVEAECSSFTK

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	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		317	2.2.26 [Sep-21-2011]
P64956		364	Uncharacterized protein M	yes	no	0.388	0.337	0.416	2e-17
P64955		364	Uncharacterized protein R	yes	no	0.388	0.337	0.416	2e-17
Q9HSF6		199	Ribonuclease HI OS=Haloba	yes	no	0.369	0.587	0.450	6e-16
P54162		132	14.7 kDa ribonuclease H-l	yes	no	0.388	0.931	0.336	4e-09
F9VN79		149	Ribonuclease HI OS=Sulfol	yes	no	0.347	0.738	0.352	3e-06
P36921		135	Cell wall enzyme EbsB OS=	yes	no	0.375	0.881	0.300	7e-06
P0C2F6		620	Putative ribonuclease H p	no	no	0.384	0.196	0.3	0.0001
Q9ZLH3		143	Ribonuclease HI OS=Helico	yes	no	0.242	0.538	0.407	0.0002
B8HPS9		157	Ribonuclease H OS=Cyanoth	yes	no	0.214	0.433	0.367	0.0007

>sp\|P64956\|Y2253_MYCBO Uncharacterized protein Mb2253c OS=Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) GN=Mb2253c PE=4 SV=1	Back alignment and function desciption

 Score = 90.1 bits (222), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 52/125 (41%), Positives = 71/125 (56%), Gaps = 2/125 (1%)

Query: 176 CTLEFDGASKGNPGQAGAGAVLRAEDGS--VYRLREGVGIATNNVAEYRALILGLKYALQ 233
             +E DG S+GNPG AG GAV+   D S  +   ++ +G ATNNVAEYR LI GL  A++
Sbjct: 3   VVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVK 62

Query: 234 KGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEA 293
            G     V  DSKLV  Q+ G WK+ + +L  L  +A+ L  +F+      + R  N+ A
Sbjct: 63  LGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYA 122

Query: 294 DAQAN 298
           D  AN
Sbjct: 123 DRLAN 127

Mycobacterium bovis (taxid: 1765)

>sp\|P64955\|Y2228_MYCTU Uncharacterized protein Rv2228c/MT2287 OS=Mycobacterium tuberculosis GN=Rv2228c PE=1 SV=1	Back alignment and function description

>sp\|Q9HSF6\|RNH_HALSA Ribonuclease HI OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) GN=rnhA PE=1 SV=1	Back alignment and function description

>sp\|P54162\|RNHL_BACSU 14.7 kDa ribonuclease H-like protein OS=Bacillus subtilis (strain 168) GN=rnhA PE=1 SV=1	Back alignment and function description

>sp\|F9VN79\|RNH_SULTO Ribonuclease HI OS=Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) GN=rnhA PE=1 SV=1	Back alignment and function description

>sp\|P36921\|EBSB_ENTFA Cell wall enzyme EbsB OS=Enterococcus faecalis (strain ATCC 700802 / V583) GN=ebsB PE=3 SV=2	Back alignment and function description

>sp\|P0C2F6\|RNHX1_ARATH Putative ribonuclease H protein At1g65750 OS=Arabidopsis thaliana GN=At1g65750 PE=3 SV=1	Back alignment and function description

>sp\|Q9ZLH3\|RNH_HELPJ Ribonuclease HI OS=Helicobacter pylori (strain J99) GN=rnhA PE=3 SV=1	Back alignment and function description

>sp\|B8HPS9\|RNH_CYAP4 Ribonuclease H OS=Cyanothece sp. (strain PCC 7425 / ATCC 29141) GN=rnhA PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		317
359488729		287	PREDICTED: uncharacterized protein LOC10	0.892	0.986	0.576	7e-97
255552696		255	nuclease, putative [Ricinus communis] gi	0.794	0.988	0.557	2e-90
365222890		288	Hop-interacting protein THI034 [Solanum	0.902	0.993	0.544	2e-89
224108115		282	predicted protein [Populus trichocarpa]	0.880	0.989	0.532	7e-87
224077608		257	predicted protein [Populus trichocarpa]	0.794	0.980	0.544	3e-86
356565894		345	PREDICTED: uncharacterized protein LOC10	0.858	0.788	0.533	4e-85
296086505		445	unnamed protein product [Vitis vinifera]	0.883	0.629	0.533	8e-85
356526860		356	PREDICTED: uncharacterized protein LOC10	0.876	0.780	0.533	2e-84
356550140		283	PREDICTED: uncharacterized protein LOC10	0.880	0.985	0.552	9e-83
255588182		262	nuclease, putative [Ricinus communis] gi	0.810	0.980	0.514	2e-82

>gi\|359488729\|ref\|XP_002280233.2\| PREDICTED: uncharacterized protein LOC100242330 [Vitis vinifera] gi\|296087711\|emb\|CBI34967.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  359 bits (922), Expect = 7e-97,   Method: Compositional matrix adjust.
 Identities = 180/312 (57%), Positives = 225/312 (72%), Gaps = 29/312 (9%)

Query: 1   MEDEKDAFYVVRKGDVVGIYKTLSDCQLQAGFSVRDPSLTVYKGYGLSKEAEEYLASHGL 60
           ME+EKDAFYVVRKGD+VG+YK+ S+CQ QAGFSV DPS++VYKGY L K+AE +LASHGL
Sbjct: 1   MEEEKDAFYVVRKGDIVGLYKSFSECQAQAGFSVCDPSVSVYKGYCLPKDAEVFLASHGL 60

Query: 61  KSSSYSVSASDVKSDLFGKIVPCPLQEPASSGEKVSDEVSLPKMLREVAAAGSTSISINT 120
           K++SY ++A+DVK D+FGK+  CP Q+P SS                    G++S  +  
Sbjct: 61  KNASYVINAADVKGDIFGKLQACPFQQPGSS-------------------KGTSSQDLPQ 101

Query: 121 QKRHFNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEF 180
           ++ H         +++      A G  S S N QR H   ++C+  Q++  NC+S  L+F
Sbjct: 102 KRLH---------EAIESINFGAVGPKSISTNCQRKHSRLENCIEAQAMSSNCHSWLLQF 152

Query: 181 DGASKGNPGQAGAGAVLRAEDGS-VYRLREGVGIATNNVAEYRALILGLKYALQKGYKHI 239
           DGASKGNPGQAGAGAVLRA+DGS V  LREGVGIATNNVAEYRALILG+KYAL+KG K I
Sbjct: 153 DGASKGNPGQAGAGAVLRADDGSAVIHLREGVGIATNNVAEYRALILGMKYALKKGIKRI 212

Query: 240 RVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANM 299
           R +GDS+LVCMQ QGLWK  NQN+A LC+EAKEL +KF SFQI H+LR  NSEADAQAN+
Sbjct: 213 RARGDSQLVCMQFQGLWKTKNQNMADLCEEAKELGKKFLSFQIEHVLREFNSEADAQANL 272

Query: 300 GIYLKDGQVEAE 311
            + L +GQV+ E
Sbjct: 273 AVNLTNGQVQEE 284

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255552696\|ref\|XP_002517391.1\| nuclease, putative [Ricinus communis] gi\|223543402\|gb\|EEF44933.1\| nuclease, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|365222890\|gb\|AEW69797.1\| Hop-interacting protein THI034 [Solanum lycopersicum]	Back alignment and taxonomy information

>gi\|224108115\|ref\|XP_002314727.1\| predicted protein [Populus trichocarpa] gi\|222863767\|gb\|EEF00898.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|224077608\|ref\|XP_002305325.1\| predicted protein [Populus trichocarpa] gi\|222848289\|gb\|EEE85836.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356565894\|ref\|XP_003551171.1\| PREDICTED: uncharacterized protein LOC100809644 [Glycine max]	Back alignment and taxonomy information

>gi\|296086505\|emb\|CBI32094.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356526860\|ref\|XP_003532034.1\| PREDICTED: uncharacterized protein LOC100779114 [Glycine max]	Back alignment and taxonomy information

>gi\|356550140\|ref\|XP_003543447.1\| PREDICTED: uncharacterized protein LOC100796237 [Glycine max]	Back alignment and taxonomy information

>gi\|255588182\|ref\|XP_002534525.1\| nuclease, putative [Ricinus communis] gi\|223525106\|gb\|EEF27855.1\| nuclease, putative [Ricinus communis]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		317
TAIR\|locus:2096692		294	AT3G01410 [Arabidopsis thalian	0.425	0.459	0.676	5.9e-74
TAIR\|locus:2176152		322	AT5G51080 [Arabidopsis thalian	0.425	0.419	0.610	1.3e-63
UNIPROTKB\|P64955		364	MT2287 "Uncharacterized protei	0.381	0.332	0.422	2.1e-17
TIGR_CMR\|CHY_0852		148	CHY_0852 "ribonuclease HI" [Ca	0.422	0.905	0.335	3.1e-13
TIGR_CMR\|BA_1623		128	BA_1623 "RNase H" [Bacillus an	0.375	0.929	0.355	7.3e-12
TAIR\|locus:2029841		213	AT1G27870 [Arabidopsis thalian	0.539	0.802	0.259	6.8e-05
TIGR_CMR\|SPO_3212		155	SPO_3212 "ribonuclease HI" [Ru	0.318	0.651	0.380	0.00023
TAIR\|locus:2090215		343	AT3G25270 [Arabidopsis thalian	0.365	0.338	0.266	0.00051

TAIR\|locus:2096692 AT3G01410 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 475 (172.3 bits), Expect = 5.9e-74, Sum P(2) = 5.9e-74
 Identities = 92/136 (67%), Positives = 108/136 (79%)

Query:   175 SCTLEFDGASKGNPGQAGAGAVLRAEDGSV-YRLREGVGIATNNVAEYRALILGLKYALQ 233
             SCT+EFDGASKGNPG+AGAGAVLRA D SV + LREGVG ATNNVAEYRAL+LGL+ AL 
Sbjct:   154 SCTIEFDGASKGNPGKAGAGAVLRASDNSVLFYLREGVGNATNNVAEYRALLLGLRSALD 213

Query:   234 KGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEA 293
             KG+K++ V GDS LVCMQ+QG WK N+  +A LCK+AKEL   F++F I HI R  NSEA
Sbjct:   214 KGFKNVHVLGDSMLVCMQVQGAWKTNHPKMAELCKQAKELMNSFKTFDIKHIAREKNSEA 273

Query:   294 DAQANMGIYLKDGQVE 309
             D QAN  I+L DGQ +
Sbjct:   274 DKQANSAIFLADGQTQ 289

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=ISS

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0006310 "DNA recombination" evidence=RCA

GO:0007059 "chromosome segregation" evidence=RCA

GO:0007062 "sister chromatid cohesion" evidence=RCA

GO:0007126 "meiosis" evidence=RCA

GO:0007129 "synapsis" evidence=RCA

GO:0007131 "reciprocal meiotic recombination" evidence=RCA

GO:0010332 "response to gamma radiation" evidence=RCA

GO:0031048 "chromatin silencing by small RNA" evidence=RCA

GO:0032204 "regulation of telomere maintenance" evidence=RCA

GO:0032504 "multicellular organism reproduction" evidence=RCA

GO:0042138 "meiotic DNA double-strand break formation" evidence=RCA

GO:0043247 "telomere maintenance in response to DNA damage" evidence=RCA

GO:0045132 "meiotic chromosome segregation" evidence=RCA

GO:0048451 "petal formation" evidence=RCA

GO:0048453 "sepal formation" evidence=RCA

TAIR\|locus:2176152 AT5G51080 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|P64955 MT2287 "Uncharacterized protein Rv2228c/MT2287" [Mycobacterium tuberculosis (taxid:1773)]	Back alignment and assigned GO terms

TIGR_CMR\|CHY_0852 CHY_0852 "ribonuclease HI" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]	Back alignment and assigned GO terms

TIGR_CMR\|BA_1623 BA_1623 "RNase H" [Bacillus anthracis str. Ames (taxid:198094)]	Back alignment and assigned GO terms

TAIR\|locus:2029841 AT1G27870 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TIGR_CMR\|SPO_3212 SPO_3212 "ribonuclease HI" [Ruegeria pomeroyi DSS-3 (taxid:246200)]	Back alignment and assigned GO terms

TAIR\|locus:2090215 AT3G25270 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by 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	0.691
3rd Layer	3.1.26.4	LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		317
cd09279		128	cd09279, RNase_HI_archaeal_like, RNAse HI family t	3e-52
PRK07238		372	PRK07238, PRK07238, bifunctional RNase H/acid phos	8e-30
COG0328		154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	1e-25
cd06222		123	cd06222, RNase_H, RNase H is an endonuclease that	4e-25
pfam13456		88	pfam13456, RVT_3, Reverse transcriptase-like	2e-24
PRK13907		128	PRK13907, rnhA, ribonuclease H; Provisional	2e-14
cd09278		139	cd09278, RNase_HI_prokaryote_like, RNase HI family	4e-10
PRK07708		219	PRK07708, PRK07708, hypothetical protein; Validate	7e-09
pfam00075		126	pfam00075, RNase_H, RNase H	1e-07
cd09280		150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	2e-06
PRK00203		150	PRK00203, rnhA, ribonuclease H; Reviewed	1e-05
pfam01693		43	pfam01693, Cauli_VI, Caulimovirus viroplasmin	0.001

>gnl\|CDD\|187703 cd09279, RNase_HI_archaeal_like, RNAse HI family that includes Archaeal RNase HI	Back alignment and domain information

 Score =  167 bits (426), Expect = 3e-52
 Identities = 64/127 (50%), Positives = 84/127 (66%), Gaps = 1/127 (0%)

Query: 176 CTLEFDGASKGNPGQAGAGAVLRAEDGSVYRLREGVGI-ATNNVAEYRALILGLKYALQK 234
            TL FDGAS+GNPG AGAG V+++ DG V      +G  ATNN AEY ALI GL+ AL+ 
Sbjct: 1   WTLYFDGASRGNPGPAGAGIVIKSPDGEVLEQSIPLGFPATNNEAEYEALIAGLELALEL 60

Query: 235 GYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEAD 294
           G K + + GDS+LV  QIQG +++ N+ LA   +EA+EL +KF+  +I  I R  N EAD
Sbjct: 61  GIKKLEIYGDSQLVVNQIQGEYEVKNERLAPYLEEARELLKKFEEVEIKWIPREENKEAD 120

Query: 295 AQANMGI 301
           A AN  +
Sbjct: 121 ALANQAL 127

Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties. Length = 128

>gnl\|CDD\|180903 PRK07238, PRK07238, bifunctional RNase H/acid phosphatase; Provisional	Back alignment and domain information

>gnl\|CDD\|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and repair]	Back alignment and domain information

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

>gnl\|CDD\|205634 pfam13456, RVT_3, Reverse transcriptase-like	Back alignment and domain information

>gnl\|CDD\|139967 PRK13907, rnhA, ribonuclease H; Provisional	Back alignment and domain information

>gnl\|CDD\|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in prokaryotes	Back alignment and domain information

>gnl\|CDD\|181088 PRK07708, PRK07708, hypothetical protein; Validated	Back alignment and domain information

>gnl\|CDD\|215695 pfam00075, RNase_H, RNase H	Back alignment and domain information

>gnl\|CDD\|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and more complex than their prokaryotic counterparts and unlike prokaryote, RNase H are essential in higher eukaryote	Back alignment and domain information

>gnl\|CDD\|178927 PRK00203, rnhA, ribonuclease H; Reviewed	Back alignment and domain information

>gnl\|CDD\|201924 pfam01693, Cauli_VI, Caulimovirus viroplasmin	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		317
KOG3752		371	consensus Ribonuclease H [Replication, recombinati	99.97
PRK13907		128	rnhA ribonuclease H; Provisional	99.94
COG0328		154	RnhA Ribonuclease HI [DNA replication, recombinati	99.93
PRK07708		219	hypothetical protein; Validated	99.91
PRK07238		372	bifunctional RNase H/acid phosphatase; Provisional	99.9
PRK06548		161	ribonuclease H; Provisional	99.89
PRK00203		150	rnhA ribonuclease H; Reviewed	99.88
PRK08719		147	ribonuclease H; Reviewed	99.87
COG3341		225	Predicted double-stranded RNA/RNA-DNA hybrid bindi	99.85
cd06222		130	RnaseH RNase H (RNase HI) is an endonuclease that	99.81
PF00075		132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.8
PF01693		44	Cauli_VI: Caulimovirus viroplasmin; InterPro: IPR0	99.77
PF13456		87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.65
KOG1812		384	consensus Predicted E3 ubiquitin ligase [Posttrans	95.57

>KOG3752 consensus Ribonuclease H [Replication, recombination and repair]	Back alignment and domain information

Probab=99.97  E-value=1.9e-30  Score=240.47  Aligned_cols=129  Identities=29%  Similarity=0.265  Sum_probs=98.2

Q ss_pred             ceEEEEEeCcccCCCC---ceEEEEEEEcCCCCEEEEeecc--ccccchHHHHHHHHHHHHHHHHcCCcEEEEEeChHHH
Q 021120          174 YSCTLEFDGASKGNPG---QAGAGAVLRAEDGSVYRLREGV--GIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLV  248 (317)
Q Consensus       174 ~~~~iytDGS~~~n~~---~aG~Gvvi~~~~g~~~~~s~~~--~~~tnn~AEl~All~AL~~a~~~g~~~i~I~tDS~~v  248 (317)
                      +.++|||||||..|+.   .+|||+++.++.  ..+.++++  +.+|||+|||.|+++||+.|++.++.+|+|.|||+++
T Consensus       211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~--e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~  288 (371)
T KOG3752|consen  211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGH--ELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYF  288 (371)
T ss_pred             cceEEEecCccccCCCCCCcceeEEeeCCCC--cccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHH
Confidence            4589999999998764   489999997543  33445554  6899999999999999999999998899999999999


Q ss_pred             HHHHhc--------ccccCC--------hhHHHHHHHHHHHhhcC--CcEEE----EEeCCCccHHHHHHHHHhhcCC
Q 021120          249 CMQIQG--------LWKINN--------QNLAGLCKEAKELKEKF--QSFQI----NHILRNLNSEADAQANMGIYLK  304 (317)
Q Consensus       249 i~~v~~--------~w~~~~--------~~~~~l~~~i~~l~~~f--~~v~~----~Hv~~~~Ne~AD~LAk~A~~~~  304 (317)
                      |++++-        +|+..+        ..+.+++.++.+|....  ..|.+    +|.+..+|++||.||+.+..+.
T Consensus       289 i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~~  366 (371)
T KOG3752|consen  289 INSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGSTLA  366 (371)
T ss_pred             HHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhhh
Confidence            999983        333322        13456666666665552  33433    6667899999999999986543

>PRK13907 rnhA ribonuclease H; Provisional	Back alignment and domain information

>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK07708 hypothetical protein; Validated	Back alignment and domain information

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional	Back alignment and domain information

>PRK06548 ribonuclease H; Provisional	Back alignment and domain information

>PRK00203 rnhA ribonuclease H; Reviewed	Back alignment and domain information

>PRK08719 ribonuclease H; Reviewed	Back alignment and domain information

>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]	Back alignment and domain information

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

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

>PF01693 Cauli_VI: Caulimovirus viroplasmin; InterPro: IPR011320 This entry represents the N-terminal domain of RNase HI, which has a 3-layer alpha/beta/alpha structure []	Back alignment and domain information

>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B	Back alignment and domain information

>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		317
3hst_B		141	N-Terminal Rnase H Domain Of Rv2228c From Mycobacte		2e-18
3u3g_D		140	Structure Of Lc11-Rnase H1 Isolated From Compost By		5e-12
2ehg_A		149	Crystal Structure Of Hyperthermophilic Archaeal Rna		2e-07
3aly_A		143	Crystal Structure Of Rnase Hi From Sulfolobus Tokod		2e-07

>pdb|3HST|B Chain B, N-Terminal Rnase H Domain Of Rv2228c From Mycobacterium Tuberculosis As A Fusion Protein With Maltose Binding Protein Length = 141

Back alignment and structure

Iteration: 1

Score = 89.7 bits (221), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 52/125 (41%), Positives = 71/125 (56%), Gaps = 2/125 (1%) Query: 176 CTLEFDGASKGNPGQAGAGAVLRAEDGS--VYRLREGVGIATNNVAEYRALILGLKYALQ 233 +E DG S+GNPG AG GAV+ D S + ++ +G ATNNVAEYR LI GL A++ Sbjct: 4 VVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVK 63 Query: 234 KGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEA 293 G V DSKLV Q+ G WK+ + +L L +A+ L +F+ + R N+ A Sbjct: 64 LGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYA 123 Query: 294 DAQAN 298 D AN Sbjct: 124 DRLAN 128

PyMOL of 3hst

>pdb|3U3G|D Chain D, Structure Of Lc11-Rnase H1 Isolated From Compost By Metagenomic Approach: Insight Into The Structural Bases For Unusual Enzymatic Properties Of Sto-Rnase H1 Length = 140

Back alignment and structure

>pdb|2EHG|A Chain A, Crystal Structure Of Hyperthermophilic Archaeal Rnase Hi Length = 149

Back alignment and structure

>pdb|3ALY|A Chain A, Crystal Structure Of Rnase Hi From Sulfolobus Tokodaii With C-Terminal Deletion Length = 143

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		317
3hst_B		141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	6e-55
3u3g_D		140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	5e-50
2ehg_A		149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	2e-48
1zbf_A		142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	5e-22
2kq2_A		147	Ribonuclease H-related protein; PSI, NESG, protein	9e-13
2qkb_A		154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	4e-10
3qio_A		150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	2e-08
3bsu_A		53	Ribonuclease H1, RNAse H1; RNAse H, RNA/DNA hybrid	9e-08
3p1g_A		165	Xenotropic murine leukemia virus-related virus (X	1e-07
1qhk_A		47	RNAse HI, protein (ribonuclease HI); ribonuclease	1e-07
3h08_A		146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	6e-07
2e4l_A		158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	8e-07
1ril_A		166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	1e-06
1jl1_A		155	Ribonuclease HI; RNAse HI, protein stability, ther	1e-06

>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain, fusion protein, maltose binding protein, HYDR; HET: MLR TAR; 2.25A {Mycobacterium tuberculosis} Length = 141	Back alignment and structure

 Score =  174 bits (444), Expect = 6e-55
 Identities = 52/128 (40%), Positives = 72/128 (56%), Gaps = 2/128 (1%)

Query: 176 CTLEFDGASKGNPGQAGAGAVLRAEDGS--VYRLREGVGIATNNVAEYRALILGLKYALQ 233
             +E DG S+GNPG AG GAV+   D S  +   ++ +G ATNNVAEYR LI GL  A++
Sbjct: 4   VVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVK 63

Query: 234 KGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEA 293
            G     V  DSKLV  Q+ G WK+ + +L  L  +A+ L  +F+      + R  N+ A
Sbjct: 64  LGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYA 123

Query: 294 DAQANMGI 301
           D  AN  +
Sbjct: 124 DRLANDAM 131

PyMOL of 3hst

>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism} Length = 140	Back alignment and structure

>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A Length = 149	Back alignment and structure

>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE motif, hydrolase; 1.50A {Bacillus halodurans} SCOP: c.55.3.1 PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A 2g8f_A 2g8v_A 2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A* 2r7y_A* Length = 142	Back alignment and structure

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

>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A* Length = 154	Back alignment and structure

>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A Length = 150	Back alignment and structure

>3bsu_A Ribonuclease H1, RNAse H1; RNAse H, RNA/DNA hybrid; HET: DNA 5IU; 2.10A {Homo sapiens} Length = 53	Back alignment and structure

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

>1qhk_A RNAse HI, protein (ribonuclease HI); ribonuclease HI N-terminal domain, hydrolase; NMR {Saccharomyces cerevisiae} SCOP: d.100.1.2 Length = 47	Back alignment and structure

>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum} Length = 146	Back alignment and structure

>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A Length = 158	Back alignment and structure

>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A Length = 166	Back alignment and structure

>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ... Length = 155	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		317
3hst_B		141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.96
3u3g_D		140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.96
2ehg_A		149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.95
3h08_A		146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.92
2qkb_A		154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.91
2lsn_A		165	Reverse transcriptase; RNAse H, viral protein; NMR	99.91
2e4l_A		158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.91
1jl1_A		155	Ribonuclease HI; RNAse HI, protein stability, ther	99.91
1ril_A		166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.9
3qio_A		150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.9
2kq2_A		147	Ribonuclease H-related protein; PSI, NESG, protein	99.9
3bsu_A		53	Ribonuclease H1, RNAse H1; RNAse H, RNA/DNA hybrid	99.88
3p1g_A		165	Xenotropic murine leukemia virus-related virus (X	99.88
1qhk_A		47	RNAse HI, protein (ribonuclease HI); ribonuclease	99.88
1zbf_A		142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.83
4htu_A		134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.79
1mu2_A		555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.77
2zd1_A		557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.71
3ugs_B		225	Undecaprenyl pyrophosphate synthase; niaid, csgid,	82.8

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

Probab=99.96  E-value=1.1e-28  Score=203.74  Aligned_cols=130  Identities=40%  Similarity=0.577  Sum_probs=119.4

Q ss_pred             eEEEEEeCcccCCCCceEEEEEEEcCC-CCE-EEEeeccccccchHHHHHHHHHHHHHHHHcCCcEEEEEeChHHHHHHH
Q 021120          175 SCTLEFDGASKGNPGQAGAGAVLRAED-GSV-YRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQI  252 (317)
Q Consensus       175 ~~~iytDGS~~~n~~~aG~Gvvi~~~~-g~~-~~~s~~~~~~tnn~AEl~All~AL~~a~~~g~~~i~I~tDS~~vi~~v  252 (317)
                      .++|||||||+++++.+|+|+++++++ +.. ..++...+..|||+||++|+++||+++.+.+.++|.|+|||++|++++
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~i   82 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQM   82 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCCCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHHH
Confidence            589999999999999999999999875 554 456666678999999999999999999999999999999999999999


Q ss_pred             hcccccCChhHHHHHHHHHHHhhcCCcEEEEEeCCCccHHHHHHHHHhhcCC
Q 021120          253 QGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLK  304 (317)
Q Consensus       253 ~~~w~~~~~~~~~l~~~i~~l~~~f~~v~~~Hv~~~~Ne~AD~LAk~A~~~~  304 (317)
                      ++.|+.+++.+..++++++.++.+|..|.+.||++++|+.||+||+.|++..
T Consensus        83 ~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~~~N~~AD~LA~~a~~~~  134 (141)
T 3hst_B           83 SGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYADRLANDAMDAA  134 (141)
T ss_dssp             TTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECCGGGCHHHHHHHHHHHHHH
T ss_pred             hCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcCCcccHHHHHHHHHHHHHh
Confidence            9999999988999999999999999999999999999999999999998753

PyMOL of 3hst

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

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

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

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

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

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

>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ...	Back alignment and structure

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

>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} SCOP: c.55.3.1 PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A	Back alignment and structure

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

>3bsu_A Ribonuclease H1, RNAse H1; RNAse H, RNA/DNA hybrid; HET: DNA 5IU; 2.10A {Homo sapiens}	Back alignment and structure

>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A 4e89_A	Back alignment and structure

>1qhk_A RNAse HI, protein (ribonuclease HI); ribonuclease HI N-terminal domain, hydrolase; NMR {Saccharomyces cerevisiae} SCOP: d.100.1.2	Back alignment and structure

>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE motif, hydrolase; 1.50A {Bacillus halodurans} SCOP: c.55.3.1 PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A 2g8f_A 2g8v_A 2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A* 2r7y_A*	Back alignment and structure

>4htu_A Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine, W-C base PAIR, wobble base PAIR, D helix; HET: DNA UCL; 1.49A {Bacillus halodurans} PDB: 3d0p_A* 4hue_A* 4huf_A* 4hug_A* 1zbf_A 1zbi_A 2g8u_A 3uld_A* 3ey1_A* 3twh_A* 2g8f_A 2g8v_A 2g8w_A 2g8i_A 2g8h_A 2g8k_A 3i8d_A* 2r7y_A* 1zbl_A	Back alignment and structure

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

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

>3ugs_B Undecaprenyl pyrophosphate synthase; niaid, csgid, structural genomics, center for structural GEN infectious diseases; HET: FFT; 2.46A {Campylobacter jejuni} SCOP: c.101.1.0	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		317
d1zbfa1		132	c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Ba	3e-17
d1s1ta1		110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	5e-15
d1mu2a1		126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	8e-13
d1jl1a_		152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	6e-10
d1rila_		147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	1e-08
d1qhka_		47	d.100.1.2 (A:) N-terminal domain of RNase HI {Bake	5e-08

>d1zbfa1 c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Bacillus halodurans [TaxId: 86665]} Length = 132	Back information, alignment and structure


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

 Score = 74.5 bits (183), Expect = 3e-17
 Identities = 26/117 (22%), Positives = 45/117 (38%), Gaps = 12/117 (10%)

Query: 177 TLEFDGASKGNPGQAGAGAVLRAEDGSVYRLREGVGIATNNVAEYRALILGLKYALQKGY 236
           +L  D  S+GNPG      V       ++  RE + I TNN+ E+ A++ GL+Y  ++  
Sbjct: 6   SLSVDVGSQGNPGIVEYKGVDTKTGEVLF-EREPIPIGTNNMGEFLAIVHGLRYLKERN- 63

Query: 237 KHIRVQGDSKLVCMQIQGLWKIN--------NQNLAGLCKEA-KELKEKFQSFQINH 284
               +  +S+     ++   K             +  L  EA + L        I  
Sbjct: 64  SRKPIYSNSQTAIKWVKD-KKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILK 119

PyMOL of d1zbfa1

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

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

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]} Length = 152	Back information, alignment and structure

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]} Length = 147	Back information, alignment and structure

>d1qhka_ d.100.1.2 (A:) N-terminal domain of RNase HI {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 47	Back information, alignment and structure

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		317
d1rila_		147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.88
d1mu2a1		126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.87
d1jl1a_		152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.86
d1qhka_		47	N-terminal domain of RNase HI {Baker's yeast (Sacc	99.85
d1zbfa1		132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.81
d1s1ta1		110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.78

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

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

Probab=99.88  E-value=2e-23  Score=172.01  Aligned_cols=127  Identities=24%  Similarity=0.220  Sum_probs=98.0

Q ss_pred             eEEEEEeCcccCCCCceEEEEEEEcCCCCEEEEeeccccccchHHHHHHHHHHHHHHHHcCCcEEEEEeChHHHHHHHhc
Q 021120          175 SCTLEFDGASKGNPGQAGAGAVLRAEDGSVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQG  254 (317)
Q Consensus       175 ~~~iytDGS~~~n~~~aG~Gvvi~~~~g~~~~~s~~~~~~tnn~AEl~All~AL~~a~~~g~~~i~I~tDS~~vi~~v~~  254 (317)
                      .++|||||||.+|++.+|||+++...+... .+.+.....|||+|||+|+++||+++..  ...+.|++||+++++.++.
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~~~~~~-~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~--~~~i~i~tds~~~~~~~~~   79 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRFHAHEK-LLSGGEACTTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYLKKAFTE   79 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCC-EECCEEEEECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHHHHHHHS
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEECCcce-EEecccccccHHHHHHHHHHHHhhhccC--CceEEEecchhhhhccccc
Confidence            368999999999999999999987654333 4455556789999999999999987543  3579999999999998875


Q ss_pred             cc----ccC-----C---hhHHHHHHHHHHHhhcC----CcEEEEEeCCCccHHHHHHHHHhhcCCC
Q 021120          255 LW----KIN-----N---QNLAGLCKEAKELKEKF----QSFQINHILRNLNSEADAQANMGIYLKD  305 (317)
Q Consensus       255 ~w----~~~-----~---~~~~~l~~~i~~l~~~f----~~v~~~Hv~~~~Ne~AD~LAk~A~~~~~  305 (317)
                      .|    ..+     .   -.+.+||+++..+...+    .+| .+|+++++|+.||+||++|++...
T Consensus        80 ~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~~~~v~~~wV-kgHsg~~gNe~AD~LAk~aa~~~~  145 (147)
T d1rila_          80 GWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFV-KGHTGHPENERVDREARRQAQSQA  145 (147)
T ss_dssp             SHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCC-CGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             cchhhhhhccccccccccchhHHHHHHHHHHhhhcccceEEc-cCCCCCcchHHHHHHHHHHHHHhc
Confidence            32    211     1   14578999988876553    333 378889999999999999998754

PyMOL of d1rila_

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]}	Back information, alignment and structure

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1qhka_ d.100.1.2 (A:) N-terminal domain of RNase HI {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

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

>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]}	Back information, alignment and structure