Citrus Sinensis ID: 021004

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-------32
MEDEKDAFYVVRKGDVVGIYKTLSDCQLQAGFSVRDPSLTVYKGYGLSKEAEEYLASHGLKSSSYSVSASDVKSDLFGKIVPCPLQEPASSGEKVSDEVSLPKMLREVAAAGSTSISINTQKRHFNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQVEAECSSFTK
ccccccEEEEEEEccEEEEEccHHHHHHHHccccccccccEEEcccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccEEEEEEEcccccccccccEEEEEEcccccEEEEEEEEccccccHHHHHHHHHHHHHHHHHccccEEEEEEcHHHHHHHHccccccccccHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHHHHccccccEEcccccccc
cccccccEEEEEcccEEEEEEcHHHHHHHcccccccccEEEEEcccccccHHHHHHHccccccEEEEEHHHHHHHHHcccccccccccccccccccccccccccccccEcccccccccccccccccccHHHHHHHcccccccccccccccHHHHHHHcccccccccccccccccEEEEEEcccccccccccccEEEEEccccHHHHHHHHEcccccccHHHHHHHHHHHHHHHHccccEEEEEcccHHEHHHHccccccccHHHHHHHHHHHHHHHHccEEEEEEEcccccHHHHHHHHHHHccccccHHHHHHHccc
medekdafYVVRKGDVVGIYKTLSdcqlqagfsvrdpsltvykgyglskEAEEYLAshglksssysvsasdvksdlfgkivpcplqepassgekvsdevSLPKMLREVAAAgstsisintqkrhfnedncwntqsvpenyvaaagstsfsintqrshlnadsclntqsvpyncysctlefdgaskgnpgqagagAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGykhirvqgdsKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQVEAECSSFTK
medekdafyvvrkgdVVGIYKTLsdcqlqagfsvrdpsltVYKGYGLSKEAEEYLASHGLKSSSYSVSASDVKSDLFGKIVPcplqepassgekvsDEVSLPKMLREVAAAgstsisintqkrhfnEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREgvgiatnnvAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQVEAECSSFTK
MEDEKDAFYVVRKGDVVGIYKTLSDCQLQAGFSVRDPSLTVYKGYGLSKEAEEYLASHGLksssysvsasdvksdLFGKIVPCPLQEPASSGEKVSDEVSLPKMLREVAAAGSTSISINTQKRHFNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQVEAECSSFTK
******AFYVVRKGDVVGIYKTLSDCQLQAGFSVRDPSLTVYKGYGLSKEAEEYL********************LFGKIVP*****************************************HFNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGA********GAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLK*************
****KDA*YVVRKGDVVGIYKTLSDCQLQAG**********Y**YGLSKEAEEYLASHGLKSSSYSVSASDVKSDLFGKIVPCPLQ***********************A*GSTSISINTQKRHFNEDNCWNTQSVPENYVAA*****************DSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKD******C*****
MEDEKDAFYVVRKGDVVGIYKTLSDCQLQAGFSVRDPSLTVYKGYGLSKEAEEYLASH*************VKSDLFGKIVPCPLQ************VSLPKMLREVAAAGSTSISINTQKRHFNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQV*********
*****DAFYVVRKGDVVGIYKTLSDCQLQAGFSVRDPSLTVYKGYGLSKEAEEYLASHGLKSSSYSVSASDVKSDLFGKIVPCPLQEP******************************************WN****PENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANMGIYLKDGQVEAECS****
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MEDEKDAFYVVRKGDVVGIYKTLSDCQLQAGFSVRDPSLTVYKGYGLSKEAEEYLASHGLKSSSYSVSASDVKSDLFGKIVPCPLQEPASSGEKVSDEVSLPKMLREVAAAGSTSISINTQKRHFNEDNCWNTQSVPENYVAAAGSTSFSINTQRSHLNADSCLNTQSVPYNCYSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQGLWKINNQNxxxxxxxxxxxxxxxxxxxxxHILRNLNSEADAQANMGIYLKDGQVEAECSSFTK
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 ?
Query318 2.2.26 [Sep-21-2011]
P64956 364 Uncharacterized protein M yes no 0.389 0.340 0.424 4e-18
P64955 364 Uncharacterized protein R yes no 0.389 0.340 0.424 4e-18
Q9HSF6199 Ribonuclease HI OS=Haloba yes no 0.377 0.603 0.45 2e-17
P54162132 14.7 kDa ribonuclease H-l yes no 0.386 0.931 0.325 7e-09
F9VN79149 Ribonuclease HI OS=Sulfol yes no 0.339 0.724 0.359 2e-06
P0C2F6620 Putative ribonuclease H p no no 0.393 0.201 0.296 1e-05
P36921135 Cell wall enzyme EbsB OS= yes no 0.374 0.881 0.282 5e-05
Q9ZLH3143 Ribonuclease HI OS=Helico yes no 0.242 0.538 0.402 0.0002
A4SXM6154 Ribonuclease H OS=Polynuc yes no 0.371 0.766 0.330 0.0003
Q17XJ7143 Ribonuclease H OS=Helicob yes no 0.242 0.538 0.402 0.0005
>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 = 92.0 bits (227), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 53/125 (42%), Positives = 71/125 (56%), Gaps = 1/125 (0%)

Query: 176 CTLEFDGASKGNPGQAGAGAVLRAEDGSVVY-RLREGVGIATNNVAEYRALILGLKYALQ 234
             +E DG S+GNPG AG GAV+   D S V    ++ +G ATNNVAEYR LI GL  A++
Sbjct: 3   VVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVK 62

Query: 235 KGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEA 294
            G     V  DSKLV  Q+ G WK+ + +L  L  +A+ L  +F+      + R  N+ A
Sbjct: 63  LGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYA 122

Query: 295 DAQAN 299
           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 ?
Query318
359488729287 PREDICTED: uncharacterized protein LOC10 0.893 0.989 0.576 3e-98
255552696255 nuclease, putative [Ricinus communis] gi 0.795 0.992 0.557 5e-92
365222890288 Hop-interacting protein THI034 [Solanum 0.902 0.996 0.544 8e-91
224108115282 predicted protein [Populus trichocarpa] 0.880 0.992 0.532 1e-88
224077608257 predicted protein [Populus trichocarpa] 0.795 0.984 0.544 7e-88
356565894345 PREDICTED: uncharacterized protein LOC10 0.858 0.791 0.533 1e-86
296086505 445 unnamed protein product [Vitis vinifera] 0.883 0.631 0.533 3e-86
356526860356 PREDICTED: uncharacterized protein LOC10 0.877 0.783 0.533 5e-86
255588182262 nuclease, putative [Ricinus communis] gi 0.811 0.984 0.514 7e-84
356550140283 PREDICTED: uncharacterized protein LOC10 0.880 0.989 0.552 7e-84
>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 =  364 bits (934), Expect = 3e-98,   Method: Compositional matrix adjust.
 Identities = 180/312 (57%), Positives = 225/312 (72%), Gaps = 28/312 (8%)

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 DGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHI 240
           DGASKGNPGQAGAGAVLRA+DGS V  LREGVGIATNNVAEYRALILG+KYAL+KG K I
Sbjct: 153 DGASKGNPGQAGAGAVLRADDGSAVIHLREGVGIATNNVAEYRALILGMKYALKKGIKRI 212

Query: 241 RVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEADAQANM 300
           R +GDS+LVCMQ QGLWK  NQN+A LC+EAKEL +KF SFQI H+LR  NSEADAQAN+
Sbjct: 213 RARGDSQLVCMQFQGLWKTKNQNMADLCEEAKELGKKFLSFQIEHVLREFNSEADAQANL 272

Query: 301 GIYLKDGQVEAE 312
            + 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|255588182|ref|XP_002534525.1| nuclease, putative [Ricinus communis] gi|223525106|gb|EEF27855.1| nuclease, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|356550140|ref|XP_003543447.1| PREDICTED: uncharacterized protein LOC100796237 [Glycine max] 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 ?
Query318
TAIR|locus:2096692294 AT3G01410 [Arabidopsis thalian 0.427 0.462 0.676 5.2e-75
TAIR|locus:2176152322 AT5G51080 [Arabidopsis thalian 0.427 0.422 0.610 1.1e-64
UNIPROTKB|P64955 364 MT2287 "Uncharacterized protei 0.383 0.335 0.422 1.1e-18
TIGR_CMR|CHY_0852148 CHY_0852 "ribonuclease HI" [Ca 0.424 0.912 0.335 2.2e-14
TIGR_CMR|BA_1623128 BA_1623 "RNase H" [Bacillus an 0.374 0.929 0.352 1.3e-11
TIGR_CMR|SPO_3212155 SPO_3212 "ribonuclease HI" [Ru 0.320 0.658 0.380 2.7e-06
TAIR|locus:2029841213 AT1G27870 [Arabidopsis thalian 0.534 0.798 0.267 0.00028
TAIR|locus:2096692 AT3G01410 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 485 (175.8 bits), Expect = 5.2e-75, Sum P(2) = 5.2e-75
 Identities = 92/136 (67%), Positives = 109/136 (80%)

Query:   175 SCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQ 234
             SCT+EFDGASKGNPG+AGAGAVLRA D SV++ LREGVG ATNNVAEYRAL+LGL+ AL 
Sbjct:   154 SCTIEFDGASKGNPGKAGAGAVLRASDNSVLFYLREGVGNATNNVAEYRALLLGLRSALD 213

Query:   235 KGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEA 294
             KG+K++ V GDS LVCMQ+QG WK N+  +A LCK+AKEL   F++F I HI R  NSEA
Sbjct:   214 KGFKNVHVLGDSMLVCMQVQGAWKTNHPKMAELCKQAKELMNSFKTFDIKHIAREKNSEA 273

Query:   295 DAQANMGIYLKDGQVE 310
             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

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 LevelEC numberConfidence of Prediction
3rd Layer3.1.260.691
3rd Layer3.1.26.4LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00020795001
SubName- Full=Chromosome chr14 scaffold_21, whole genome shotgun sequence; (308 aa)
(Vitis vinifera)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

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 ?
Query318
cd09279128 cd09279, RNase_HI_archaeal_like, RNAse HI family t 3e-51
PRK07238 372 PRK07238, PRK07238, bifunctional RNase H/acid phos 3e-31
cd06222123 cd06222, RNase_H, RNase H is an endonuclease that 2e-26
COG0328154 COG0328, RnhA, Ribonuclease HI [DNA replication, r 9e-26
pfam1345688 pfam13456, RVT_3, Reverse transcriptase-like 2e-24
PRK13907128 PRK13907, rnhA, ribonuclease H; Provisional 3e-14
cd09278139 cd09278, RNase_HI_prokaryote_like, RNase HI family 6e-10
PRK07708219 PRK07708, PRK07708, hypothetical protein; Validate 6e-10
pfam00075126 pfam00075, RNase_H, RNase H 2e-07
PRK00203150 PRK00203, rnhA, ribonuclease H; Reviewed 5e-06
cd09280150 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase 5e-06
pfam0169343 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 =  165 bits (420), Expect = 3e-51
 Identities = 64/128 (50%), Positives = 84/128 (65%), Gaps = 2/128 (1%)

Query: 176 CTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGI-ATNNVAEYRALILGLKYALQ 234
            TL FDGAS+GNPG AGAG V+++ DG  V      +G  ATNN AEY ALI GL+ AL+
Sbjct: 1   WTLYFDGASRGNPGPAGAGIVIKSPDG-EVLEQSIPLGFPATNNEAEYEALIAGLELALE 59

Query: 235 KGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEA 294
            G K + + GDS+LV  QIQG +++ N+ LA   +EA+EL +KF+  +I  I R  N EA
Sbjct: 60  LGIKKLEIYGDSQLVVNQIQGEYEVKNERLAPYLEEARELLKKFEEVEIKWIPREENKEA 119

Query: 295 DAQANMGI 302
           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|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|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
>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 318
KOG3752371 consensus Ribonuclease H [Replication, recombinati 99.96
PRK13907128 rnhA ribonuclease H; Provisional 99.93
COG0328154 RnhA Ribonuclease HI [DNA replication, recombinati 99.93
PRK07708219 hypothetical protein; Validated 99.91
PRK07238 372 bifunctional RNase H/acid phosphatase; Provisional 99.9
PRK06548161 ribonuclease H; Provisional 99.89
PRK08719147 ribonuclease H; Reviewed 99.88
PRK00203150 rnhA ribonuclease H; Reviewed 99.87
cd06222130 RnaseH RNase H (RNase HI) is an endonuclease that 99.82
COG3341225 Predicted double-stranded RNA/RNA-DNA hybrid bindi 99.8
PF00075132 RNase_H: RNase H; InterPro: IPR002156 The RNase H 99.79
PF0169344 Cauli_VI: Caulimovirus viroplasmin; InterPro: IPR0 99.73
PF1345687 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH 99.64
KOG1812 384 consensus Predicted E3 ubiquitin ligase [Posttrans 96.54
PF05380159 Peptidase_A17: Pao retrotransposon peptidase ; Int 84.49
>KOG3752 consensus Ribonuclease H [Replication, recombination and repair] Back     alignment and domain information 
Probab=99.96  E-value=5.1e-29  Score=231.97  Aligned_cols=128  Identities=29%  Similarity=0.259  Sum_probs=98.4

Q ss_pred             ceEEEEEcCcccCCCC---ceEEEEEEEeCCCcEEEEeeccc--CCCcchHHHHHHHHHHHHHHHHcCCeeEEEEcCcHH
Q 021004          174 YSCTLEFDGASKGNPG---QAGAGAVLRAEDGSVVYRLREGV--GIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKL  248 (318)
Q Consensus       174 ~~~~iytDGS~~~~~~---~~G~Gvvi~~~~g~~~~~~~~~~--~~~Tnn~AEl~Ail~AL~~a~~~g~~~v~I~tDS~~  248 (318)
                      +.++|||||||..|+.   .+||||++.+++...   .++++  +.+|||+|||.|+++||+.|++.++.+|+|.|||++
T Consensus       211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N---~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~  287 (371)
T KOG3752|consen  211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELN---VSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEY  287 (371)
T ss_pred             cceEEEecCccccCCCCCCcceeEEeeCCCCccc---ccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHH
Confidence            4689999999998764   499999998765432   23333  579999999999999999999998889999999999


Q ss_pred             HHHHHcc--------cccccc--------hhHHHHHHHHHHHHhcC--CcEEE----EEeCCcccHHHHHHHHHHhcC
Q 021004          249 VCMQIQG--------LWKINN--------QNLAGLCKEAKELKEKF--QSFQI----NHILRNLNSEADAQANMGIYL  304 (318)
Q Consensus       249 vi~~l~~--------~w~~~~--------~~~~~l~~~i~~l~~~f--~~v~~----~Hv~r~~Ne~AD~LAk~A~~~  304 (318)
                      +|++|+-        +|+..+        ..+.+.+..+.+|.+..  ..|++    +|.+..+|++||.||+++..+
T Consensus       288 ~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~  365 (371)
T KOG3752|consen  288 FINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL  365 (371)
T ss_pred             HHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence            9999983        344332        13456777777766652  33433    666789999999999998544

>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
>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
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only] 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
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family 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 ?
Query318
3hst_B141 N-Terminal Rnase H Domain Of Rv2228c From Mycobacte 5e-19
3u3g_D140 Structure Of Lc11-Rnase H1 Isolated From Compost By 3e-13
2ehg_A149 Crystal Structure Of Hyperthermophilic Archaeal Rna 2e-07
3aly_A143 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 = 91.7 bits (226), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 53/125 (42%), Positives = 71/125 (56%), Gaps = 1/125 (0%)
Query: 176 CTLEFDGASKGNPGQAGAGAVLRAEDGSVVY-RLREGVGIATNNVAEYRALILGLKYALQ 234
             +E DG S+GNPG AG GAV+   D S V    ++ +G ATNNVAEYR LI GL  A++
Sbjct: 4   VVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVK 63
Query: 235 KGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEA 294
            G     V  DSKLV  Q+ G WK+ + +L  L  +A+ L  +F+      + R  N+ A
Sbjct: 64  LGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYA 123
Query: 295 DAQAN 299
           D  AN
Sbjct: 124 DRLAN 128
>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 ?
Query318
3hst_B141 Protein RV2228C/MT2287; ribonuclease H1, RV2228C N 1e-55
3u3g_D140 Ribonuclease H, RNAse H1; hydrolase, cleave the RN 4e-52
2ehg_A149 Ribonuclease HI; RNAse HI, hyperthermophilic archa 7e-49
1zbf_A142 Ribonuclease H-related protein; RNAse H, RNA/DNA h 3e-21
2kq2_A147 Ribonuclease H-related protein; PSI, NESG, protein 2e-11
2qkb_A154 Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy 2e-10
3qio_A150 GAG-POL polyprotein; RNAse H, inhibitor, nuclease, 3e-08
3bsu_A53 Ribonuclease H1, RNAse H1; RNAse H, RNA/DNA hybrid 9e-08
1qhk_A47 RNAse HI, protein (ribonuclease HI); ribonuclease 1e-07
3p1g_A165 Xenotropic murine leukemia virus-related virus (X 1e-07
3h08_A146 RNH (ribonuclease H); RNAse H, 3D-structure, endon 1e-06
2e4l_A158 Ribonuclease HI, RNAse HI; hydrolase, endoribonucl 2e-06
1ril_A166 Ribonuclease H; hydrolase(endoribonuclease); 2.80A 2e-06
1jl1_A155 Ribonuclease HI; RNAse HI, protein stability, ther 2e-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 =  176 bits (448), Expect = 1e-55
 Identities = 53/128 (41%), Positives = 73/128 (57%), Gaps = 1/128 (0%)

Query: 176 CTLEFDGASKGNPGQAGAGAVLRAEDGS-VVYRLREGVGIATNNVAEYRALILGLKYALQ 234
             +E DG S+GNPG AG GAV+   D S V+   ++ +G ATNNVAEYR LI GL  A++
Sbjct: 4   VVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVK 63

Query: 235 KGYKHIRVQGDSKLVCMQIQGLWKINNQNLAGLCKEAKELKEKFQSFQINHILRNLNSEA 294
            G     V  DSKLV  Q+ G WK+ + +L  L  +A+ L  +F+      + R  N+ A
Sbjct: 64  LGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVPRARNTYA 123

Query: 295 DAQANMGI 302
           D  AN  +
Sbjct: 124 DRLANDAM 131
>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
>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
>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
>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 ?
Query318
3u3g_D140 Ribonuclease H, RNAse H1; hydrolase, cleave the RN 99.96
3hst_B141 Protein RV2228C/MT2287; ribonuclease H1, RV2228C N 99.96
2ehg_A149 Ribonuclease HI; RNAse HI, hyperthermophilic archa 99.95
2qkb_A154 Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy 99.91
3h08_A146 RNH (ribonuclease H); RNAse H, 3D-structure, endon 99.91
2lsn_A165 Reverse transcriptase; RNAse H, viral protein; NMR 99.9
1jl1_A155 Ribonuclease HI; RNAse HI, protein stability, ther 99.9
2e4l_A158 Ribonuclease HI, RNAse HI; hydrolase, endoribonucl 99.9
3qio_A150 GAG-POL polyprotein; RNAse H, inhibitor, nuclease, 99.9
1ril_A166 Ribonuclease H; hydrolase(endoribonuclease); 2.80A 99.9
2kq2_A147 Ribonuclease H-related protein; PSI, NESG, protein 99.88
3p1g_A165 Xenotropic murine leukemia virus-related virus (X 99.87
3bsu_A53 Ribonuclease H1, RNAse H1; RNAse H, RNA/DNA hybrid 99.85
1qhk_A47 RNAse HI, protein (ribonuclease HI); ribonuclease 99.85
1zbf_A142 Ribonuclease H-related protein; RNAse H, RNA/DNA h 99.8
4htu_A134 Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine, 99.77
1mu2_A555 HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym 99.76
2zd1_A557 Reverse transcriptase/ribonuclease H; P51/P66, het 99.71
1rw3_A455 POL polyprotein; RNA and DNA dependent DNA polymer 80.23
>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism} Back     alignment and structure
Probab=99.96  E-value=6e-29  Score=205.15  Aligned_cols=132  Identities=33%  Similarity=0.469  Sum_probs=121.6

Q ss_pred             ceEEEEEcCcccCCCCceEEEEEEEeCCCcEEEEeecccCCCcchHHHHHHHHHHHHHHHHcCCe----eEEEEcCcHHH
Q 021004          174 YSCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYK----HIRVQGDSKLV  249 (318)
Q Consensus       174 ~~~~iytDGS~~~~~~~~G~Gvvi~~~~g~~~~~~~~~~~~~Tnn~AEl~Ail~AL~~a~~~g~~----~v~I~tDS~~v  249 (318)
                      ..++|||||||+++++.+|+|+++++.+|+.+...+...+..|||+||++|+++||+++.+.+.+    +|+|+|||++|
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            36899999999999999999999999888877677766667899999999999999999998888    99999999999


Q ss_pred             HHHHcccccccchhHHHHHHHHHHH-HhcCCcEEEEEeCCcccHHHHHHHHHHhcCC
Q 021004          250 CMQIQGLWKINNQNLAGLCKEAKEL-KEKFQSFQINHILRNLNSEADAQANMGIYLK  305 (318)
Q Consensus       250 i~~l~~~w~~~~~~~~~l~~~i~~l-~~~f~~v~~~Hv~r~~Ne~AD~LAk~A~~~~  305 (318)
                      ++++++.|+.++..+..+++++..+ ..+|..|.+.||++++|+.||+||++|+...
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            9999999998888899999999999 9999999999999999999999999998653
>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
>2lsn_A Reverse transcriptase; RNAse H, viral protein; NMR {Simian foamy virus} 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
>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
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_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
>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
>3bsu_A Ribonuclease H1, RNAse H1; RNAse H, RNA/DNA hybrid; HET: DNA 5IU; 2.10A {Homo sapiens} 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
>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 318
d1zbfa1132 c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Ba 5e-17
d1s1ta1110 c.55.3.1 (A:430-539) HIV RNase H (Domain of revers 1e-14
d1mu2a1126 c.55.3.1 (A:430-555) HIV RNase H (Domain of revers 2e-12
d1jl1a_152 c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli 8e-10
d1rila_147 c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph 5e-09
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 = 74.2 bits (182), Expect = 5e-17
 Identities = 26/118 (22%), Positives = 44/118 (37%), Gaps = 13/118 (11%)

Query: 177 TLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKG 236
           +L  D  S+GNPG      V       +    RE + I TNN+ E+ A++ GL+Y  ++ 
Sbjct: 6   SLSVDVGSQGNPGIVEYKGVDTKTGEVLFE--REPIPIGTNNMGEFLAIVHGLRYLKERN 63

Query: 237 YKHIRVQGDSKLVCMQIQGLWKIN--------NQNLAGLCKEA-KELKEKFQSFQINH 285
                +  +S+     ++   K             +  L  EA + L        I  
Sbjct: 64  -SRKPIYSNSQTAIKWVKD-KKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILK 119
>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 ?
Query318
d1rila_147 RNase H (RNase HI) {Thermus thermophilus [TaxId: 2 99.86
d1mu2a1126 HIV RNase H (Domain of reverse transcriptase) {Hum 99.86
d1jl1a_152 RNase H (RNase HI) {Escherichia coli [TaxId: 562]} 99.85
d1qhka_47 N-terminal domain of RNase HI {Baker's yeast (Sacc 99.82
d1zbfa1132 BH0863-like Ribonuclease H {Bacillus halodurans [T 99.79
d1s1ta1110 HIV RNase H (Domain of reverse transcriptase) {Hum 99.76
>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=99.86  E-value=5.5e-23  Score=169.78  Aligned_cols=128  Identities=25%  Similarity=0.238  Sum_probs=97.5

Q ss_pred             eEEEEEcCcccCCCCceEEEEEEEeCCCcEEEEeecccCCCcchHHHHHHHHHHHHHHHHcCCeeEEEEcCcHHHHHHHc
Q 021004          175 SCTLEFDGASKGNPGQAGAGAVLRAEDGSVVYRLREGVGIATNNVAEYRALILGLKYALQKGYKHIRVQGDSKLVCMQIQ  254 (318)
Q Consensus       175 ~~~iytDGS~~~~~~~~G~Gvvi~~~~g~~~~~~~~~~~~~Tnn~AEl~Ail~AL~~a~~~g~~~v~I~tDS~~vi~~l~  254 (318)
                      .++|||||||++|++.+|||+++...+...  .+.+.....|||+|||+|+++||+++..  ...+.|++||+++++.++
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~~~~~~--~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~--~~~i~i~tds~~~~~~~~   78 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRFHAHEK--LLSGGEACTTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYLKKAFT   78 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCC--EECCEEEEECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHHHHHHH
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEECCcce--EEecccccccHHHHHHHHHHHHhhhccC--CceEEEecchhhhhcccc
Confidence            478999999999999999999987655432  2333445679999999999999986533  357999999999999887


Q ss_pred             cc----ccccc--------hhHHHHHHHHHHHHhcCC---cEEEEEeCCcccHHHHHHHHHHhcCCC
Q 021004          255 GL----WKINN--------QNLAGLCKEAKELKEKFQ---SFQINHILRNLNSEADAQANMGIYLKD  306 (318)
Q Consensus       255 ~~----w~~~~--------~~~~~l~~~i~~l~~~f~---~v~~~Hv~r~~Ne~AD~LAk~A~~~~~  306 (318)
                      ..    |..+.        -.+.+||+++..+...+.   .|+.+|+++++|+.||+||++|+....
T Consensus        79 ~~~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~~  145 (147)
T d1rila_          79 EGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQA  145 (147)
T ss_dssp             SSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             ccchhhhhhccccccccccchhHHHHHHHHHHhhhcccceEEccCCCCCcchHHHHHHHHHHHHHhc
Confidence            52    22111        146789999988776531   222467789999999999999998754
>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