Citrus Sinensis ID: 027994

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-----

MLREVAAAGSTSISINTQKRHFNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQVEAECSSFTK

cHHHHHHccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccEEEEEcccccccccccEEEEEEEcccccEEEEEEEcccccccHHHHHHHHHHHHHHHHHccccEEEEEEcHHHHHHHHccccccccccHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHHHHcccccccccccccccc

cHHHHHHHcccHEEEccccccccccHHHHccccccHHEEccccccccHHHHHHHHHHHHccccccccccccEEEEEEcccccccccccccEEEEEcccccHEEEEEEEcccccccHHHHHHHHHHHHHHHHccccEEEEEcccHHEEHHEccccccccHHHHHHHHHHHHHHHHcccEEEEEEcccccHHHHHHHHHHcccccccEEHHHHHccc

MLREVaaagstsisintqkrhfnedncwntqsvpenyvaaagstsfsintqrshlnadsclntqsvpyncysctlefdgaskgnpgqagagAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGykhirvqgdsKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQVEAECSSFTK

mlrevaaagstsisintqkrhfnedNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREgvgiatnnvAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQVEAECSSFTK

*********************FNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGA********GAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLK*************

*******************************SVPEN***********************CLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKD************

***********SISINTQKRHFNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQV*********

*LREVAAAGSTSISINTQKRHFNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQVEAECS*F**

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

MLREVAAAGSTSISINTQKRHFNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNxxxxxxxxxxxxxxxxxxxxxHILRNLNSEADAQANMGIYLKDGQVEAECSSFTK

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		215	2.2.26 [Sep-21-2011]
P64956		364	Uncharacterized protein M	yes	no	0.576	0.340	0.424	2e-18
P64955		364	Uncharacterized protein R	yes	no	0.576	0.340	0.424	2e-18
Q9HSF6		199	Ribonuclease HI OS=Haloba	yes	no	0.558	0.603	0.45	9e-18
P54162		132	14.7 kDa ribonuclease H-l	yes	no	0.572	0.931	0.325	3e-09
F9VN79		149	Ribonuclease HI OS=Sulfol	yes	no	0.502	0.724	0.359	8e-07
P0C2F6		620	Putative ribonuclease H p	no	no	0.581	0.201	0.296	6e-06
P36921		135	Cell wall enzyme EbsB OS=	yes	no	0.553	0.881	0.282	2e-05
Q9ZLH3		143	Ribonuclease HI OS=Helico	yes	no	0.358	0.538	0.402	9e-05
A4SXM6		154	Ribonuclease H OS=Polynuc	yes	no	0.548	0.766	0.330	0.0002
Q17XJ7		143	Ribonuclease H OS=Helicob	yes	no	0.358	0.538	0.402	0.0002

>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 = 92.4 bits (228), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 53/125 (42%), Positives = 71/125 (56%), Gaps = 1/125 (0%)

Query: 73  CTLEFDGASKGNPGQAGAGAVLRAEDGSVVY-RLREGVGIATNNVAEYRALILGLKYALQ 131
             +E DG S+GNPG AG GAV+   D S V    ++ +G ATNNVAEYR LI GL  A++
Sbjct: 3   VVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVK 62

Query: 132 KGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEA 191
            G     V  DSKLV  Q+ G WK+ + +L  L  +A+ L  +F+      + R  N+ A
Sbjct: 63  LGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYA 122

Query: 192 DAQAN 196
           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\|P0C2F6\|RNHX1_ARATH Putative ribonuclease H protein At1g65750 OS=Arabidopsis thaliana GN=At1g65750 PE=3 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\|Q9ZLH3\|RNH_HELPJ Ribonuclease HI OS=Helicobacter pylori (strain J99) GN=rnhA PE=3 SV=1	Back alignment and function description

>sp\|A4SXM6\|RNH_POLSQ Ribonuclease H OS=Polynucleobacter necessarius subsp. asymbioticus (strain DSM 18221 / CIP 109841 / QLW-P1DMWA-1) GN=rnhA PE=3 SV=1	Back alignment and function description

>sp\|Q17XJ7\|RNH_HELAH Ribonuclease H OS=Helicobacter acinonychis (strain Sheeba) 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		215
359488729		287	PREDICTED: uncharacterized protein LOC10	0.790	0.592	0.676	3e-61
365222890		288	Hop-interacting protein THI034 [Solanum	0.8	0.597	0.621	4e-58
255552696		255	nuclease, putative [Ricinus communis] gi	0.804	0.678	0.642	1e-57
224077608		257	predicted protein [Populus trichocarpa]	0.665	0.556	0.727	3e-56
449452100		373	PREDICTED: uncharacterized protein LOC10	0.809	0.466	0.617	3e-56
255588182		262	nuclease, putative [Ricinus communis] gi	0.827	0.679	0.601	4e-56
224108115		282	predicted protein [Populus trichocarpa]	0.767	0.585	0.633	6e-55
356565894		345	PREDICTED: uncharacterized protein LOC10	0.646	0.402	0.719	1e-54
356550140		283	PREDICTED: uncharacterized protein LOC10	0.762	0.579	0.664	2e-54
296086505		445	unnamed protein product [Vitis vinifera]	0.786	0.379	0.6	5e-54

>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 =  240 bits (612), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 115/170 (67%), Positives = 135/170 (79%)

Query: 40  AAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDG 99
           A G  S S N QR H   ++C+  Q++  NC+S  L+FDGASKGNPGQAGAGAVLRA+DG
Sbjct: 115 AVGPKSISTNCQRKHSRLENCIEAQAMSSNCHSWLLQFDGASKGNPGQAGAGAVLRADDG 174

Query: 100 SVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQ 159
           S V  LREGVGIATNNVAEYRALILG+KYAL+KG K IR +GDS+LVCMQ QGLWK  NQ
Sbjct: 175 SAVIHLREGVGIATNNVAEYRALILGMKYALKKGIKRIRARGDSQLVCMQFQGLWKTKNQ 234

Query: 160 NLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQVEAE 209
           N+A LC+EAKEL +KF SFQI H+LR  NSEADAQAN+ + L +GQV+ E
Sbjct: 235 NMADLCEEAKELGKKFLSFQIEHVLREFNSEADAQANLAVNLTNGQVQEE 284

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

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

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

>gi\|449452100\|ref\|XP_004143798.1\| PREDICTED: uncharacterized protein LOC101210930 [Cucumis sativus]	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

>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\|356565894\|ref\|XP_003551171.1\| PREDICTED: uncharacterized protein LOC100809644 [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\|296086505\|emb\|CBI32094.3\| unnamed protein product [Vitis vinifera]	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		215
TAIR\|locus:2096692		294	AT3G01410 [Arabidopsis thalian	0.632	0.462	0.676	3e-46
TAIR\|locus:2176152		322	AT5G51080 [Arabidopsis thalian	0.632	0.422	0.610	2.2e-43
UNIPROTKB\|P64955		364	MT2287 "Uncharacterized protei	0.567	0.335	0.422	1.1e-18
TIGR_CMR\|CHY_0852		148	CHY_0852 "ribonuclease HI" [Ca	0.627	0.912	0.335	1.4e-14
TIGR_CMR\|BA_1623		128	BA_1623 "RNase H" [Bacillus an	0.553	0.929	0.352	5e-12
TIGR_CMR\|SPO_3212		155	SPO_3212 "ribonuclease HI" [Ru	0.474	0.658	0.380	1.1e-06
TAIR\|locus:2029841		213	AT1G27870 [Arabidopsis thalian	0.790	0.798	0.267	0.00012
TAIR\|locus:2090215		343	AT3G25270 [Arabidopsis thalian	0.539	0.338	0.272	0.00047

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

 Score = 485 (175.8 bits), Expect = 3.0e-46, P = 3.0e-46
 Identities = 92/136 (67%), Positives = 109/136 (80%)

Query:    72 SCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQ 131
             SCT+EFDGASKGNPG+AGAGAVLRA D SV++ LREGVG ATNNVAEYRAL+LGL+ AL 
Sbjct:   154 SCTIEFDGASKGNPGKAGAGAVLRASDNSVLFYLREGVGNATNNVAEYRALLLGLRSALD 213

Query:   132 KGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEA 191
             KG+K++ V GDS LVCMQ+QG WK N+  +A LCK+AKEL   F++F I HI R  NSEA
Sbjct:   214 KGFKNVHVLGDSMLVCMQVQGAWKTNHPKMAELCKQAKELMNSFKTFDIKHIAREKNSEA 273

Query:   192 DAQANMGIYLKDGQVE 207
             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

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

TAIR\|locus:2029841 AT1G27870 [Arabidopsis thaliana (taxid:3702)]	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		215
cd09279		128	cd09279, RNase_HI_archaeal_like, RNAse HI family t	1e-51
PRK07238		372	PRK07238, PRK07238, bifunctional RNase H/acid phos	1e-32
cd06222		123	cd06222, RNase_H, RNase H is an endonuclease that	2e-26
COG0328		154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	1e-25
pfam13456		88	pfam13456, RVT_3, Reverse transcriptase-like	2e-24
PRK13907		128	PRK13907, rnhA, ribonuclease H; Provisional	5e-15
PRK07708		219	PRK07708, PRK07708, hypothetical protein; Validate	2e-10
cd09278		139	cd09278, RNase_HI_prokaryote_like, RNase HI family	1e-09
pfam00075		126	pfam00075, RNase_H, RNase H	4e-07
PRK00203		150	PRK00203, rnhA, ribonuclease H; Reviewed	7e-06
cd09280		150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	2e-05

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

 Score =  162 bits (412), Expect = 1e-51
 Identities = 64/128 (50%), Positives = 84/128 (65%), Gaps = 2/128 (1%)

Query: 73  CTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGI-ATNNVAEYRALILGLKYALQ 131
            TL FDGAS+GNPG AGAG V+++ DG  V      +G  ATNN AEY ALI GL+ AL+
Sbjct: 1   WTLYFDGASRGNPGPAGAGIVIKSPDG-EVLEQSIPLGFPATNNEAEYEALIAGLELALE 59

Query: 132 KGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEA 191
            G K + + GDS+LV  QIQG +++ N+ LA   +EA+EL +KF+  +I  I R  N EA
Sbjct: 60  LGIKKLEIYGDSQLVVNQIQGEYEVKNERLAPYLEEARELLKKFEEVEIKWIPREENKEA 119

Query: 192 DAQANMGI 199
           DA AN  +
Sbjct: 120 DALANQAL 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\|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\|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and repair]	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\|181088 PRK07708, PRK07708, hypothetical protein; Validated	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\|215695 pfam00075, RNase_H, RNase H	Back alignment and domain information

>gnl\|CDD\|178927 PRK00203, rnhA, ribonuclease H; Reviewed	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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		215
PRK07708		219	hypothetical protein; Validated	99.97
PRK13907		128	rnhA ribonuclease H; Provisional	99.96
COG0328		154	RnhA Ribonuclease HI [DNA replication, recombinati	99.95
PRK07238		372	bifunctional RNase H/acid phosphatase; Provisional	99.93
PRK06548		161	ribonuclease H; Provisional	99.9
PRK08719		147	ribonuclease H; Reviewed	99.9
PRK00203		150	rnhA ribonuclease H; Reviewed	99.89
cd06222		130	RnaseH RNase H (RNase HI) is an endonuclease that	99.88
PF00075		132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.84
PF13456		87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.76
KOG3752		371	consensus Ribonuclease H [Replication, recombinati	99.66
KOG1812		384	consensus Predicted E3 ubiquitin ligase [Posttrans	96.58
PF05380		159	Peptidase_A17: Pao retrotransposon peptidase ; Int	86.5
COG3341		225	Predicted double-stranded RNA/RNA-DNA hybrid bindi	82.93

>PRK07708 hypothetical protein; Validated	Back alignment and domain information

Probab=99.97  E-value=2.1e-29  Score=202.64  Aligned_cols=161  Identities=24%  Similarity=0.289  Sum_probs=138.2

Q ss_pred             chhhhccCCCccChHHHHhhc-cCCCCCCCCCCCCCCCeEEEEEcccccCCCCceEEEEEEEeCCCcEEEEe--eeccC-
Q 027994           35 ENYVAAAGSTSFSINTQRSHL-NADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRL--REGVG-  110 (215)
Q Consensus        35 ~~~~~~~~~~~w~~~~~~~~~-~~~~~~~~~~~~~~~~~~~i~tDGS~~~~~~~~G~G~v~~~~~g~~~~~~--~~~~~-  110 (215)
                      +-.|...-...|++++++++. +++++|+         .+++|||||++++++.+|+|+|++++.|......  ...++ 
T Consensus        44 ~~~~~d~~~~~~~~k~~~~~~~~~~~ep~---------~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~  114 (219)
T PRK07708         44 ELEFYDEMDTEWSLKELKKLSKEVEEEPH---------EILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEG  114 (219)
T ss_pred             eEEEecCCCCEeeHHHHhhhhhhhccCCC---------cEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccc
Confidence            334555566789999999999 6666665         6999999999999999999999998877544322  23443 


Q ss_pred             cccchHHhHHHHHHHHHHHHHcCCee--EEEEeChHHHHHHHhcccccCChhHHHHHHHHHHHHhcCCc-eEEEEeCCCC
Q 027994          111 IATNNVAEYRALILGLKYALQKGYKH--IRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQS-FQINHILRNL  187 (215)
Q Consensus       111 ~~tn~~AEl~Ai~~aL~~a~~~g~~~--v~I~tDS~~vi~~i~~~~~~~~~~~~~l~~~i~~l~~~~~~-~~~~hv~r~~  187 (215)
                      ..|||.||+.|++.||+.|.++|+++  |.|++||++|++++++.|+++++.+..+++.+..+..+|.. +.+.||+|.+
T Consensus       115 ~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~  194 (219)
T PRK07708        115 IYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQ  194 (219)
T ss_pred             cccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchh
Confidence            58999999999999999999999876  89999999999999999999999999999999999888764 7889999999


Q ss_pred             CHHHHHHHHHhhcccCC
Q 027994          188 NSEADAQANMGIYLKDG  204 (215)
Q Consensus       188 N~~AD~LAk~a~~~~~~  204 (215)
                      |+.||.||++|++..+.
T Consensus       195 N~~AD~LAk~Al~~~~~  211 (219)
T PRK07708        195 NKEADQLATQALEGTVI  211 (219)
T ss_pred             hhHHHHHHHHHHhcCCC
Confidence            99999999999986543

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

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

>PRK08719 ribonuclease H; Reviewed	Back alignment and domain information

>PRK00203 rnhA ribonuclease H; Reviewed	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

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

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

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

>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family	Back alignment and domain information

>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]	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		215
3hst_B		141	N-Terminal Rnase H Domain Of Rv2228c From Mycobacte		2e-19
3u3g_D		140	Structure Of Lc11-Rnase H1 Isolated From Compost By		1e-13
2ehg_A		149	Crystal Structure Of Hyperthermophilic Archaeal Rna		6e-08
3aly_A		143	Crystal Structure Of Rnase Hi From Sulfolobus Tokod		7e-08

>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 = 92.0 bits (227), Expect = 2e-19, Method: Compositional matrix adjust. Identities = 53/125 (42%), Positives = 72/125 (57%), Gaps = 1/125 (0%) Query: 73 CTLEFDGASKGNPGQAGAGAVLRAEDGS-VVYRLREGVGIATNNVAEYRALILGLKYALQ 131 +E DG S+GNPG AG GAV+ D S V+ ++ +G ATNNVAEYR LI GL A++ Sbjct: 4 VVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVK 63 Query: 132 KGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEA 191 G V DSKLV Q+ G WK+ + +L L +A+ L +F+ + R N+ A Sbjct: 64 LGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYA 123 Query: 192 DAQAN 196 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		215
3hst_B		141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	4e-56
3u3g_D		140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	5e-52
2ehg_A		149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	3e-49
1zbf_A		142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	3e-21
2kq2_A		147	Ribonuclease H-related protein; PSI, NESG, protein	4e-11
2qkb_A		154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	3e-10
3qio_A		150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	3e-08
3p1g_A		165	Xenotropic murine leukemia virus-related virus (X	1e-07
2e4l_A		158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	2e-06
3h08_A		146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	2e-06
1ril_A		166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	3e-06
1jl1_A		155	Ribonuclease HI; RNAse HI, protein stability, ther	4e-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 (442), Expect = 4e-56
 Identities = 53/128 (41%), Positives = 73/128 (57%), Gaps = 1/128 (0%)

Query: 73  CTLEFDGASKGNPGQAGAGAVLRAEDGS-VVYRLREGVGIATNNVAEYRALILGLKYALQ 131
             +E DG S+GNPG AG GAV+   D S V+   ++ +G ATNNVAEYR LI GL  A++
Sbjct: 4   VVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVK 63

Query: 132 KGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEA 191
            G     V  DSKLV  Q+ G WK+ + +L  L  +A+ L  +F+      + R  N+ A
Sbjct: 64  LGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYA 123

Query: 192 DAQANMGI 199
           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

>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

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

>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		215
3u3g_D		140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.97
3hst_B		141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.97
2ehg_A		149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.96
2qkb_A		154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.93
3h08_A		146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.93
3qio_A		150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.93
2lsn_A		165	Reverse transcriptase; RNAse H, viral protein; NMR	99.92
1ril_A		166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.92
1jl1_A		155	Ribonuclease HI; RNAse HI, protein stability, ther	99.92
2e4l_A		158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.92
3p1g_A		165	Xenotropic murine leukemia virus-related virus (X	99.91
2kq2_A		147	Ribonuclease H-related protein; PSI, NESG, protein	99.9
1zbf_A		142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.83
1mu2_A		555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.82
4htu_A		134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.81
2zd1_A		557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.79
2zd1_B		428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	90.13
1rw3_A		455	POL polyprotein; RNA and DNA dependent DNA polymer	87.45

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

Probab=99.97  E-value=2e-31  Score=199.48  Aligned_cols=132  Identities=33%  Similarity=0.469  Sum_probs=123.2

Q ss_pred             CeEEEEEcccccCCCCceEEEEEEEeCCCcEEEEeeeccCcccchHHhHHHHHHHHHHHHHcCCe----eEEEEeChHHH
Q 027994           71 YSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYK----HIRVQGDSKLV  146 (215)
Q Consensus        71 ~~~~i~tDGS~~~~~~~~G~G~v~~~~~g~~~~~~~~~~~~~tn~~AEl~Ai~~aL~~a~~~g~~----~v~I~tDS~~v  146 (215)
                      ..++||||||+.++++.+|+|+++++++|..+...+...+..||++||+.|++.||+++.+.+.+    +|.|+|||++|
T Consensus         2 ~~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~v   81 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELI   81 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEEEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHH
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCCCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHH
Confidence            36899999999999999999999999999887777777778899999999999999999999988    99999999999


Q ss_pred             HHHHhcccccCChhHHHHHHHHHHH-HhcCCceEEEEeCCCCCHHHHHHHHHhhccc
Q 027994          147 CMQIQGLWKINNQNLAGLCKEAKEL-KEKFQSFQINHILRNLNSEADAQANMGIYLK  202 (215)
Q Consensus       147 i~~i~~~~~~~~~~~~~l~~~i~~l-~~~~~~~~~~hv~r~~N~~AD~LAk~a~~~~  202 (215)
                      ++++++.|+.++..+..+++++..+ ..+|..+.|.||+|++|+.||.||++|+...
T Consensus        82 i~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~~~~N~~AD~LA~~a~~~~  138 (140)
T 3u3g_D           82 VRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEAIDKA  138 (140)
T ss_dssp             HHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECCGGGGHHHHHHHHHHHHHH
T ss_pred             HHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcCchhhHHHHHHHHHHHHhc
Confidence            9999999998888999999999999 8998899999999999999999999998754

PyMOL of 3u3g

>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

>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

>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

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

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

>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

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

>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

>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

>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

>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

>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

>2zd1_B P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} SCOP: e.8.1.2 PDB: 2ykm_B* 2ykn_B* 2ze2_B* 3bgr_B* 3ig1_B* 3irx_B* 3is9_B* 3qo9_B* 3v4i_B* 3v6d_B* 3v81_B* 3klf_B* 3kk1_B* 3kjv_B* 3kk2_B* 3kk3_B* 2be2_B* 1n5y_B* 1bqm_B* 1n6q_B* ...	Back alignment and structure

>1rw3_A POL polyprotein; RNA and DNA dependent DNA polymerase, reverse transcriptase, transferase, replication; 3.00A {Moloney murine leukemia virus} SCOP: e.8.1.2	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		215
d1zbfa1		132	c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Ba	1e-16
d1s1ta1		110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	9e-15
d1mu2a1		126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	4e-12
d1jl1a_		152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	2e-09
d1rila_		147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	2e-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 = 71.5 bits (175), Expect = 1e-16
 Identities = 26/118 (22%), Positives = 44/118 (37%), Gaps = 13/118 (11%)

Query: 74  TLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKG 133
           +L  D  S+GNPG      V       +    RE + I TNN+ E+ A++ GL+Y  ++ 
Sbjct: 6   SLSVDVGSQGNPGIVEYKGVDTKTGEVLFE--REPIPIGTNNMGEFLAIVHGLRYLKERN 63

Query: 134 YKHIRVQGDSKLVCMQIQGLWKIN--------NQNLAGLCKEA-KELKEKFQSFQINH 182
                +  +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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		215
d1mu2a1		126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.87
d1rila_		147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.87
d1jl1a_		152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.86
d1zbfa1		132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.81
d1s1ta1		110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.8

>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

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

Probab=99.87  E-value=3.8e-22  Score=145.29  Aligned_cols=117  Identities=19%  Similarity=0.160  Sum_probs=88.6

Q ss_pred             CeEEEEEcccccCCCCceEEEEEEEeCCCcEEEEeeeccCcccchHHhHHHHHHHHHHHHHcCCeeEEEEeChHHHHHHH
Q 027994           71 YSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQI  150 (215)
Q Consensus        71 ~~~~i~tDGS~~~~~~~~G~G~v~~~~~g~~~~~~~~~~~~~tn~~AEl~Ai~~aL~~a~~~g~~~v~I~tDS~~vi~~i  150 (215)
                      +..++||||||.++++.+|+|+++.....     .....+..||+.|||.|++.||+    ...+++.|+|||++|++++
T Consensus         6 ~~~t~YTDGS~~~n~~~~~~g~~~~~~~~-----~~~~~~~~tnn~AEl~Ai~~al~----~~~~~i~I~tDS~~v~~~~   76 (126)
T d1mu2a1           6 GAETFYTDGSCNRQSKEGKAGYVTDRGKD-----KVKKLEQTTNQQAELEAFAMALT----DSGPKVNIIVDSQYVMGIV   76 (126)
T ss_dssp             TCEEEEEEEEECTTTCCEEEEEEETTSCE-----EEEEESSCCHHHHHHHHHHHHHH----TSCSEEEEEESCHHHHHHH
T ss_pred             CCcEEEEcCCCCCCCCcEEEEEEecCCCE-----EEEecCCCcchHHHHHHHHHHhc----cCCcceEEEechHHHHHHH
Confidence            45799999999999888999987754332     12344568999999999999986    3457999999999999999


Q ss_pred             hcccccCChhHHHHHHHHHHHHhcCCceEEEEeC----CCCCHHHHHHHHHhh
Q 027994          151 QGLWKINNQNLAGLCKEAKELKEKFQSFQINHIL----RNLNSEADAQANMGI  199 (215)
Q Consensus       151 ~~~~~~~~~~~~~l~~~i~~l~~~~~~~~~~hv~----r~~N~~AD~LAk~a~  199 (215)
                      ++.|+....  ..+.+.+..+... ..+.|.||+    +++|+.||+||++|+
T Consensus        77 ~~~~~~~~~--~~~~~~~~~~~~~-~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          77 ASQPTESES--KIVNQIIEEMIKK-EAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             HTCCSEESC--HHHHHHHHHHHHC-SEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             hcCCccccc--hHHHHHHHHhhhc-ceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            986654432  2344445555444 467777665    788999999999885

PyMOL of d1mu2a1

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

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