Citrus Sinensis ID: 007798

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-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------59
MMAVRAVNSCSMFRSAACPPLVSFKIQCCYYHFRSLQLRRNKSNLGFRLPACRSERQFLNRSGSQSCSVHSLVDSVMQELVAIRKRLRVFAKVKVSSGELLEDKLENQVLQKGLLLEFKKDSDRVLLAVAQRPDGKKNWMVYDQNGASCSIKPQQVTFVVPGVEKFDHKDISNFLQKAEDNLLNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLEEEAELKILSEAAALRLQWRLQQGAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVSAFAHLPEGPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVKACLRGESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALILRFIKDRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEVVR
ccccccccccccccccccccccEEEEEcccccccccccccccccccccccEEEEEEEcccccccccEEEEEEEEccccEEEEEEEEEEEEEEEEEEccccccccccccEEEccccccccccccEEEEEEEEcccccEEEEEEccccccccHHHHHHHccccccccccHHHHHHHccccccccccccccccccEEEEccccccccccEEEEEEEccccEEEEEEEcccccccccccccHHHHHHccccEEcccccccccccccccccccccccccEEEEEEEEEEcccccEEEEEEEEEEEEccccccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHcccccccccEEEEEEccccccEEEEcccccccccHHHHHHHHHHHHHcHHHHHHcccccccccccccccccccHHHHcccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEEEEEEEEccEEEEEEEEEEEEEEEEEEcccccccEEEEEEEEEcccccEEEEEEEcc
ccEEEEEcccccHccccccccEEEEEEEEEEEHHHHHHHcccccccccccccccHHHHHcccccccccHHHHHHHHHHHHHHHHHHHcEEEEEEEEcccccEccccccEEEcEEEEccccccccEEEEEccccccccccccccccHHHHHHHHccccccccHHHHHHHHcccccccccHHHHcccccHccccEEEEccccccccccEEEEEEcccccEEEEEEEEEEEEEEccccccHHHHHHccccEEccccccccccHHHccccccccccccEEEEEEEEEEcccccEEcEEEEHHHHcccHHccHHHHHHHHHccccHcHHHHHHHHHHHHHHHHHHHcccEEEcccEEEEEEcccccccEEEEEEEEccccHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEcccccHHHHHHccccHHHHHHHHHHHHHHHcccccccccccHcccHHHHHccccHHccccHHHHHHHHHHHHHcccccccHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEcEEEEEEcccEEEEEccccEEEEEEEEEEEEEcccEEEEEEEEEcccccEEEEEEEcc
mmavravnscsmfrsaacpplvsfkiQCCYYHFRSlqlrrnksnlgfrlpacrserqflnrsgsqscsvHSLVDSVMQELVAIRKRLRVFAKVKvssgelledKLENQVLQKGLLLEFKKDSDRVLLAVAqrpdgkknwmvydqngascsikpqqvtfvvpgvekfdhkDISNFLQKAEDNllnrkdlthlKVYAIDVDEADELDDALSAMRLQDGRIKVYIHvadptkyiepgslsdkdamkrgtsvflptatypmfpeklamegmslrqgevCNAVTVSVVLHsdgsiaeysvdnsiikptymLTYESATELLHLNLEEEAELKILSEAAALRLQWRLQQGAIDTATLETRikvanpedpepiinlyvedqadPAMRLVSEMMILCGEAIATYgsfnnlalpyrgqpqsnidvsafahlpegpvrsSAIVKIMRAAAidfrkpvrhgvlglpgyvqftsPIRRYMDLLAHYQVKAclrgesppfsagqleGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALILRFIKDRTAALLLVEVGLQAAAWVSVgaqigdevevkveeahprddiIYLKEVVR
mmavravnscsmfrsAACPPLVSFKIQCCYYHFRSLQLRRNKSNLGFRLPACRSERQFLNRSGSQSCSVHSLVDSVMQELVAIRKRLRVFAKVKvssgelledkleNQVLQKGLllefkkdsdRVLLAVaqrpdgkknwMVYDQNGASCSIKPQQVTFVVPGVEKFDHKDISNFLQKAEdnllnrkdlTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYihvadptkyiepgslsdkdamKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLEEEAELKILSEAAALRLQWRLQQGAIDTATLetrikvanpedpepiINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVSAFAHLPEGPVRSSAIVKIMRAAAIdfrkpvrhgvlglPGYVQFTSPIRRYMDLLAHYQVKACLRGESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEflrrqpkerQYRALILRFIKDRTAALLLVEVGLQAAAWVSVGAQIGDevevkveeahprddiiylkevvr
MMAVRAVNSCSMFRSAACPPLVSFKIQCCYYHFRSLQLRRNKSNLGFRLPACRSERQFLNRSGSQSCSVHSLVDSVMQELVAIRKRLRVFAKVKVSSGELLEDKLENQVLQKGLLLEFKKDSDRVLLAVAQRPDGKKNWMVYDQNGASCSIKPQQVTFVVPGVEKFDHKDISNFLQKAEDNLLNRKDLTHLKVYAIDVdeadelddalSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATellhlnleeeaelKILSEAAALRLQWRLQQGAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVSAFAHLPEGPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVKACLRGESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALILRFIKDRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEVVR
******VNSCSMFRSAACPPLVSFKIQCCYYHFRSLQLRRNKSNLGFRLPACRSERQFL******SCSVHSLVDSVMQELVAIRKRLRVFAKVKVSSGELLEDKLENQVLQKGLLLEFKKDSDRVLLAVAQRPDGKKNWMVYDQNGASCSIKPQQVTFVVPGVEKFDHKDISNFLQKAEDNLLNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIE*************TSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLEEEAELKILSEAAALRLQWRLQQGAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVSAFAHLPEGPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVKACLRGESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALILRFIKDRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK****
*********CSMFRSAACPPLVSFKIQCCYYHFRSLQLRR*****GFRLPA****************SVHSLVDSVMQELVAIRKRLRVFAKVKVSSGELLEDKLENQVLQKGLLLEFKKDSDRVLLAVAQRPDGKKNWMVYDQNGASCSIKPQQVTFVVPGVEKFDHK************LLNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLEEEAELKILSEAAALRLQWRLQQGAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQ**********LPEGPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVKACLRGESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALILRFIKDRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEVVR
********SCSMFRSAACPPLVSFKIQCCYYHFRSLQLRRNKSNLGFRLPACRSERQF***********HSLVDSVMQELVAIRKRLRVFAKVKVSSGELLEDKLENQVLQKGLLLEFKKDSDRVLLAVAQRPDGKKNWMVYDQNGASCSIKPQQVTFVVPGVEKFDHKDISNFLQKAEDNLLNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLEEEAELKILSEAAALRLQWRLQQGAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVSAFAHLPEGPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVKACLRGESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALILRFIKDRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEVVR
*MAVRA*NSCSMFRSAACPPLVSFKIQCCYYHFRSLQLRRNKSNLGFRLPACRSER*FLNR**SQSCSVHSLVDSVMQELVAIRKRLRVFAKVKVSSGELLEDKLENQVLQKGLLLEFKKDSDRVLLAVAQRPDGKKNWMVYDQNGASCSIKPQQVTFVVPGVEKFDHKDISNFLQKAEDNLLNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLEEEAELKILSEAAALRLQWRLQQGAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVSAFAHLPEGPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVKACLRGESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALILRFIKDRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEVVR
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MMAVRAVNSCSMFRSAACPPLVSFKIQCCYYHFRSLQLRRNKSNLGFRLPACRSERQFLNRSGSQSCSVHSLVDSVMQELVAIRKRLRVFAKVKVSSGELLEDKLENQVLQKGLLLEFKKDSDRVLLAVAQRPDGKKNWMVYDQNGASCSIKPQQVTFVVPGVEKFDHKDISNFLQKAEDNLLNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLEEEAELKILSEAAALRLQWRLQQGAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVSAFAHLPEGPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVKACLRGESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALILRFIKDRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEVVR
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 ?
Query589 2.2.26 [Sep-21-2011]
Q6NQJ6803 Ribonuclease II, chloropl yes no 0.701 0.514 0.770 0.0
P73177666 Uncharacterized ribonucle N/A no 0.675 0.597 0.397 1e-69
Q9PK00692 Ribonuclease R OS=Chlamyd yes no 0.604 0.514 0.272 7e-29
O84402694 Ribonuclease R OS=Chlamyd yes no 0.604 0.512 0.267 1e-27
O32231779 Ribonuclease R OS=Bacillu yes no 0.499 0.377 0.277 2e-27
Q9Z848676 Ribonuclease R OS=Chlamyd yes no 0.599 0.522 0.272 3e-26
Q9CH00 817 Ribonuclease R 1 OS=Lacto yes no 0.507 0.365 0.294 1e-25
O67834705 Ribonuclease R OS=Aquifex yes no 0.563 0.470 0.272 3e-25
Q9WZI1710 Ribonuclease R OS=Thermot yes no 0.531 0.440 0.285 7e-25
C3LW69678 Exoribonuclease 2 OS=Vibr yes no 0.621 0.539 0.276 3e-24
>sp|Q6NQJ6|RNR1_ARATH Ribonuclease II, chloroplastic/mitochondrial OS=Arabidopsis thaliana GN=RNR1 PE=1 SV=1 Back     alignment and function desciption
 Score =  640 bits (1651), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 319/414 (77%), Positives = 370/414 (89%), Gaps = 1/414 (0%)

Query: 176 QKAEDNLLNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGS 235
           + ++ + + R DLTHLKVYAIDVDEADELDDALSA RLQDGRIK++IHVADP +Y+ PGS
Sbjct: 390 ESSDIDAVRRIDLTHLKVYAIDVDEADELDDALSATRLQDGRIKIWIHVADPARYVTPGS 449

Query: 236 LSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSV 295
             D++A +RGTSVFLPTATYPMFPEKLAMEGMSLRQGE CNAV+VSVVL SDG I EYSV
Sbjct: 450 KVDREARRRGTSVFLPTATYPMFPEKLAMEGMSLRQGENCNAVSVSVVLRSDGCITEYSV 509

Query: 296 DNSIIKPTYMLTYESATELLHLNLEEEAELKILSEAAALRLQWRLQQGAIDTATLETRIK 355
           DNSII+PTYMLTYESA+ELLHLNLEEEAELK+LSEAA +R QWR +QGA+DT TLETRIK
Sbjct: 510 DNSIIRPTYMLTYESASELLHLNLEEEAELKLLSEAAFIRSQWRREQGAVDTTTLETRIK 569

Query: 356 VANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDV 415
           V NPEDPEP+INLYVE+QAD AMRLV EMMILCGE +AT+GS +N+ LPYRGQPQSNIDV
Sbjct: 570 VVNPEDPEPLINLYVENQADLAMRLVFEMMILCGEVVATFGSQHNIPLPYRGQPQSNIDV 629

Query: 416 SAFAHLPEGPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQV 475
           SAFAHLPEGPVRSS+IVK+MRAA ++FR PVRHGVLG+PGYVQFTSPIRRYMDL AHYQ+
Sbjct: 630 SAFAHLPEGPVRSSSIVKVMRAAEMNFRCPVRHGVLGIPGYVQFTSPIRRYMDLTAHYQI 689

Query: 476 KACLR-GESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALI 534
           KA LR G++ PFSAG+LEG+A+ VNMQ+++ R+LSNT LRYW+IEFLRRQ K ++Y AL+
Sbjct: 690 KAFLRGGDNFPFSAGELEGIAASVNMQSKVVRKLSNTGLRYWVIEFLRRQEKGKKYTALV 749

Query: 535 LRFIKDRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEVV 588
           LRF+KDR A+LLLVEVG QA AWVS G Q+GDE+EV+VEEAHPRDD+I  KEV+
Sbjct: 750 LRFVKDRIASLLLVEVGFQATAWVSEGKQVGDEIEVRVEEAHPRDDLILFKEVI 803
3'-5' exoribonuclease that catalyzes 3' maturation of chloroplast and mitochondrion ribosomal RNAs; degrades short nucleotidic extensions to generate the mature 3'-ends. Involved in the maturation of 23S, 16S and 5S rRNAs.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 1EC: .EC: 1EC: 3EC: .EC: 1
>sp|P73177|RN2H_SYNY3 Uncharacterized ribonuclease sll1290 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=sll1290 PE=3 SV=1 Back     alignment and function description
>sp|Q9PK00|RNR_CHLMU Ribonuclease R OS=Chlamydia muridarum (strain MoPn / Nigg) GN=rnr PE=3 SV=1 Back     alignment and function description
>sp|O84402|RNR_CHLTR Ribonuclease R OS=Chlamydia trachomatis (strain D/UW-3/Cx) GN=rnr PE=3 SV=1 Back     alignment and function description
>sp|O32231|RNR_BACSU Ribonuclease R OS=Bacillus subtilis (strain 168) GN=rnr PE=3 SV=1 Back     alignment and function description
>sp|Q9Z848|RNR_CHLPN Ribonuclease R OS=Chlamydia pneumoniae GN=rnr PE=3 SV=1 Back     alignment and function description
>sp|Q9CH00|RNR1_LACLA Ribonuclease R 1 OS=Lactococcus lactis subsp. lactis (strain IL1403) GN=rnr1 PE=3 SV=1 Back     alignment and function description
>sp|O67834|RNR_AQUAE Ribonuclease R OS=Aquifex aeolicus (strain VF5) GN=rnr PE=3 SV=1 Back     alignment and function description
>sp|Q9WZI1|RNR_THEMA Ribonuclease R OS=Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) GN=rnr PE=3 SV=1 Back     alignment and function description
>sp|C3LW69|RNB_VIBCM Exoribonuclease 2 OS=Vibrio cholerae serotype O1 (strain M66-2) GN=rnb 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 ?
Query589
224090693 792 predicted protein [Populus trichocarpa] 0.713 0.530 0.828 0.0
449520221 809 PREDICTED: LOW QUALITY PROTEIN: ribonucl 0.718 0.522 0.778 0.0
449448900 809 PREDICTED: ribonuclease II, chloroplasti 0.718 0.522 0.778 0.0
297740364 720 unnamed protein product [Vitis vinifera] 0.684 0.559 0.842 0.0
225440376 792 PREDICTED: uncharacterized ribonuclease 0.679 0.505 0.842 0.0
356566110 783 PREDICTED: uncharacterized ribonuclease 0.718 0.540 0.755 0.0
42567593 803 Ribonuclease II/R family protein [Arabid 0.701 0.514 0.770 0.0
297806163 803 EMB2730 [Arabidopsis lyrata subsp. lyrat 0.701 0.514 0.768 1e-180
7406421 782 ribonuclease II-like protein [Arabidopsi 0.665 0.501 0.724 1e-165
218189347 774 hypothetical protein OsI_04386 [Oryza sa 0.684 0.520 0.717 1e-165
>gi|224090693|ref|XP_002309062.1| predicted protein [Populus trichocarpa] gi|222855038|gb|EEE92585.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  744 bits (1920), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 352/425 (82%), Positives = 392/425 (92%), Gaps = 5/425 (1%)

Query: 167 DHKDISNFLQKAEDNL---LNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIH 223
           DH D    +  AED L   +NRKDLTHLKVYAIDVDEADELDDALSA RLQDGRIKV+IH
Sbjct: 369 DHPD--EIISAAEDLLSEPINRKDLTHLKVYAIDVDEADELDDALSATRLQDGRIKVWIH 426

Query: 224 VADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVV 283
           VADP +Y++PGS  D++AM+RGTSVFLPTATYPMFPEKLAMEGMSL+QGEVCNAVTVSV+
Sbjct: 427 VADPARYVQPGSKVDREAMRRGTSVFLPTATYPMFPEKLAMEGMSLKQGEVCNAVTVSVI 486

Query: 284 LHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLEEEAELKILSEAAALRLQWRLQQG 343
           LHSDG IAEYSVDNSIIKPTYMLTYESA+ELLH+NL+EEAELK+LSE+A+LRLQWR +QG
Sbjct: 487 LHSDGCIAEYSVDNSIIKPTYMLTYESASELLHMNLDEEAELKLLSESASLRLQWRCEQG 546

Query: 344 AIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLAL 403
           A+DTATLETRIKV NPEDPEP INLYVE+QADPAMRLVSEMM+LCGE IATYGS NN+ L
Sbjct: 547 AVDTATLETRIKVPNPEDPEPSINLYVENQADPAMRLVSEMMLLCGEVIATYGSCNNIPL 606

Query: 404 PYRGQPQSNIDVSAFAHLPEGPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPI 463
           PYRGQPQSNIDVSAFAHLPEGPVRS+AIV+IMR A ID RKP+RHGVLGLPGYVQFTSPI
Sbjct: 607 PYRGQPQSNIDVSAFAHLPEGPVRSAAIVRIMRGAEIDIRKPIRHGVLGLPGYVQFTSPI 666

Query: 464 RRYMDLLAHYQVKACLRGESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRR 523
           RRY+DLLAHYQVKA LRG+SPP SAGQLEGMAS++NMQTR+ RRL ++SL+YW+IEFL+R
Sbjct: 667 RRYLDLLAHYQVKAVLRGDSPPLSAGQLEGMASLINMQTRVVRRLCSSSLQYWMIEFLKR 726

Query: 524 QPKERQYRALILRFIKDRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIY 583
           QPKE++YRALILRFIKDR AALLLVEVGLQA AWVS+G QIGDEV+V+VEEAHPRDDII 
Sbjct: 727 QPKEKKYRALILRFIKDRVAALLLVEVGLQATAWVSLGTQIGDEVQVRVEEAHPRDDIIS 786

Query: 584 LKEVV 588
           LKEVV
Sbjct: 787 LKEVV 791

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|449520221|ref|XP_004167132.1| PREDICTED: LOW QUALITY PROTEIN: ribonuclease II, chloroplastic/mitochondrial-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449448900|ref|XP_004142203.1| PREDICTED: ribonuclease II, chloroplastic/mitochondrial-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297740364|emb|CBI30546.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|225440376|ref|XP_002266667.1| PREDICTED: uncharacterized ribonuclease sll1290-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|356566110|ref|XP_003551278.1| PREDICTED: uncharacterized ribonuclease sll1290-like [Glycine max] Back     alignment and taxonomy information
>gi|42567593|ref|NP_195845.2| Ribonuclease II/R family protein [Arabidopsis thaliana] gi|75127176|sp|Q6NQJ6.1|RNR1_ARATH RecName: Full=Ribonuclease II, chloroplastic/mitochondrial; Short=AtmtRNaseII; Short=RNase II; AltName: Full=Protein EMBRYO DEFECTIVE 2730; AltName: Full=Ribonucleotide reductase 1; Flags: Precursor gi|34222082|gb|AAQ62877.1| At5g02250 [Arabidopsis thaliana] gi|51970908|dbj|BAD44146.1| ribonuclease II-like protein [Arabidopsis thaliana] gi|332003067|gb|AED90450.1| Ribonuclease II/R family protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297806163|ref|XP_002870965.1| EMB2730 [Arabidopsis lyrata subsp. lyrata] gi|297316802|gb|EFH47224.1| EMB2730 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|7406421|emb|CAB85530.1| ribonuclease II-like protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|218189347|gb|EEC71774.1| hypothetical protein OsI_04386 [Oryza sativa Indica Group] gi|222619521|gb|EEE55653.1| hypothetical protein OsJ_04037 [Oryza sativa Japonica Group] 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 ?
Query589
TAIR|locus:2180172803 EMB2730 "EMBRYO DEFECTIVE 2730 0.702 0.515 0.716 1.3e-206
UNIPROTKB|Q9KLE1678 rnb "Exoribonuclease 2" [Vibri 0.597 0.519 0.246 6.6e-19
TIGR_CMR|VC_A0805678 VC_A0805 "exoribonuclease II" 0.597 0.519 0.246 6.6e-19
ZFIN|ZDB-GENE-080213-3950 dis3 "DIS3 mitotic control hom 0.397 0.246 0.266 1.3e-16
POMBASE|SPBC26H8.10970 dis3 "3'-5' exoribonuclease su 0.387 0.235 0.247 1.3e-16
TIGR_CMR|CHY_0289724 CHY_0289 "ribonuclease R" [Car 0.375 0.305 0.265 1.7e-16
MGI|MGI:1919912958 Dis3 "DIS3 mitotic control hom 0.397 0.244 0.254 2.2e-16
UNIPROTKB|E2RNY6958 DIS3 "Uncharacterized protein" 0.390 0.240 0.258 2.8e-16
TIGR_CMR|BA_5334 808 BA_5334 "ribonuclease R" [Baci 0.378 0.275 0.238 3.4e-16
UNIPROTKB|E1BXX6963 DIS3 "Uncharacterized protein" 0.414 0.253 0.250 5e-16
TAIR|locus:2180172 EMB2730 "EMBRYO DEFECTIVE 2730" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1543 (548.2 bits), Expect = 1.3e-206, Sum P(2) = 1.3e-206
 Identities = 298/416 (71%), Positives = 348/416 (83%)

Query:   175 LQKAED-NLLNRKDLTHLKVYAIDVXXXXXXXXXXSAMRLQDGRIKVYIHVADPTKYIEP 233
             L ++ D + + R DLTHLKVYAIDV          SA RLQDGRIK++IHVADP +Y+ P
Sbjct:   388 LSESSDIDAVRRIDLTHLKVYAIDVDEADELDDALSATRLQDGRIKIWIHVADPARYVTP 447

Query:   234 GSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEY 293
             GS  D++A +RGTSVFLPTATYPMFPEKLAMEGMSLRQGE CNAV+VSVVL SDG I EY
Sbjct:   448 GSKVDREARRRGTSVFLPTATYPMFPEKLAMEGMSLRQGENCNAVSVSVVLRSDGCITEY 507

Query:   294 SVDNSIIKPTYMLTYESATXXXXXXXXXXXXXKILSEAAALRLQWRLQQGAIDTATLETR 353
             SVDNSII+PTYMLTYESA+             K+LSEAA +R QWR +QGA+DT TLETR
Sbjct:   508 SVDNSIIRPTYMLTYESASELLHLNLEEEAELKLLSEAAFIRSQWRREQGAVDTTTLETR 567

Query:   354 IKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNI 413
             IKV NPEDPEP+INLYVE+QAD AMRLV EMMILCGE +AT+GS +N+ LPYRGQPQSNI
Sbjct:   568 IKVVNPEDPEPLINLYVENQADLAMRLVFEMMILCGEVVATFGSQHNIPLPYRGQPQSNI 627

Query:   414 DVSAFAHLPEGPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHY 473
             DVSAFAHLPEGPVRSS+IVK+MRAA ++FR PVRHGVLG+PGYVQFTSPIRRYMDL AHY
Sbjct:   628 DVSAFAHLPEGPVRSSSIVKVMRAAEMNFRCPVRHGVLGIPGYVQFTSPIRRYMDLTAHY 687

Query:   474 QVKACLRG-ESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRA 532
             Q+KA LRG ++ PFSAG+LEG+A+ VNMQ+++ R+LSNT LRYW+IEFLRRQ K ++Y A
Sbjct:   688 QIKAFLRGGDNFPFSAGELEGIAASVNMQSKVVRKLSNTGLRYWVIEFLRRQEKGKKYTA 747

Query:   533 LILRFIKDRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEVV 588
             L+LRF+KDR A+LLLVEVG QA AWVS G Q+GDE+EV+VEEAHPRDD+I  KEV+
Sbjct:   748 LVLRFVKDRIASLLLVEVGFQATAWVSEGKQVGDEIEVRVEEAHPRDDLILFKEVI 803
GO:0003723 "RNA binding" evidence=IEA;ISS
GO:0004540 "ribonuclease activity" evidence=IEA;ISS
GO:0009793 "embryo development ending in seed dormancy" evidence=NAS
GO:0000175 "3'-5'-exoribonuclease activity" evidence=IDA
GO:0005739 "mitochondrion" evidence=IDA
GO:0009507 "chloroplast" evidence=IDA
GO:0006364 "rRNA processing" evidence=RCA;IMP
GO:0009658 "chloroplast organization" evidence=RCA;IMP
GO:0006399 "tRNA metabolic process" evidence=RCA
GO:0009902 "chloroplast relocation" evidence=RCA
GO:0010027 "thylakoid membrane organization" evidence=RCA
GO:0034660 "ncRNA metabolic process" evidence=RCA
UNIPROTKB|Q9KLE1 rnb "Exoribonuclease 2" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)] Back     alignment and assigned GO terms
TIGR_CMR|VC_A0805 VC_A0805 "exoribonuclease II" [Vibrio cholerae O1 biovar El Tor (taxid:686)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-080213-3 dis3 "DIS3 mitotic control homolog (S. cerevisiae)" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
POMBASE|SPBC26H8.10 dis3 "3'-5' exoribonuclease subunit Dis3 (predicted)" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_0289 CHY_0289 "ribonuclease R" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
MGI|MGI:1919912 Dis3 "DIS3 mitotic control homolog (S. cerevisiae)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|E2RNY6 DIS3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
TIGR_CMR|BA_5334 BA_5334 "ribonuclease R" [Bacillus anthracis str. Ames (taxid:198094)] Back     alignment and assigned GO terms
UNIPROTKB|E1BXX6 DIS3 "Uncharacterized protein" [Gallus gallus (taxid:9031)] 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

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q6NQJ6RNR1_ARATH3, ., 1, ., 1, 3, ., 10.77050.70110.5143yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

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 ?
Query589
pfam00773322 pfam00773, RNB, RNB domain 8e-86
COG0557706 COG0557, VacB, Exoribonuclease R [Transcription] 3e-74
smart00955286 smart00955, RNB, This domain is the catalytic doma 4e-62
TIGR02063709 TIGR02063, RNase_R, ribonuclease R 9e-42
TIGR00358654 TIGR00358, 3_prime_RNase, VacB and RNase II family 3e-37
TIGR02062639 TIGR02062, RNase_B, exoribonuclease II 4e-26
COG4776645 COG4776, Rnb, Exoribonuclease II [Transcription] 2e-25
PRK05054644 PRK05054, PRK05054, exoribonuclease II; Provisiona 4e-23
PRK11642 813 PRK11642, PRK11642, exoribonuclease R; Provisional 8e-15
>gnl|CDD|216112 pfam00773, RNB, RNB domain Back     alignment and domain information 
 Score =  269 bits (690), Expect = 8e-86
 Identities = 107/326 (32%), Positives = 164/326 (50%), Gaps = 35/326 (10%)

Query: 185 RKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKR 244
           R+DL  L  + ID + A ++DDALS  +L DG  ++ +H+AD + Y+ PGS  DK+A KR
Sbjct: 1   RRDLRDLPFFTIDPETAKDIDDALSVEKLPDGGYRLGVHIADVSHYVPPGSPLDKEARKR 60

Query: 245 GTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTY 304
           GTSV+LP    PM PE+L+ +  SL  GE   A++V + +  DG + +Y +  S+I+   
Sbjct: 61  GTSVYLPEGVIPMLPEELSNDLCSLLPGEDRLALSVEITIDKDGEVLDYEIYPSVIRSKA 120

Query: 305 MLTYESATELLHLNLEE-----EAELKILSEAAALRLQWRLQQGAID-TATLETRIKVAN 358
            LTYE   ELL     E       +L++L E A    + RL++GA++     E +I +  
Sbjct: 121 RLTYEEVDELLEGKPSEREAPVADDLELLYELAKALRKKRLKRGALELEDLPEAKIDL-- 178

Query: 359 PEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNID---- 414
            ++    +++   +   PA  LV E MIL  EA+A + S N +   YR  P+ +++    
Sbjct: 179 -DEDGEPVDIIRIEDRSPAHSLVEEFMILANEAVARFLSENGIPGIYRVHPEPDLEKLQD 237

Query: 415 ---------------------VSAFAHLPEGPVRSSAIVKIMRAAAIDFRKPVRHGVLGL 453
                                +      PE  + +  + + +  A      P  H  LGL
Sbjct: 238 LLKSALELDLDEEGLESLQKLLEELKDSPERRLLNLLLRRTLPRAEYST-TPAPHFGLGL 296

Query: 454 PGYVQFTSPIRRYMDLLAHYQVKACL 479
             Y  FTSPIRRY DL+ H Q+KA L
Sbjct: 297 EIYTHFTSPIRRYADLVVHRQLKALL 322

This domain is the catalytic domain of ribonuclease II. Length = 322
>gnl|CDD|223631 COG0557, VacB, Exoribonuclease R [Transcription] Back     alignment and domain information
>gnl|CDD|214935 smart00955, RNB, This domain is the catalytic domain of ribonuclease II Back     alignment and domain information
>gnl|CDD|233703 TIGR02063, RNase_R, ribonuclease R Back     alignment and domain information
>gnl|CDD|232937 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5' exoribonucleases Back     alignment and domain information
>gnl|CDD|131117 TIGR02062, RNase_B, exoribonuclease II Back     alignment and domain information
>gnl|CDD|227117 COG4776, Rnb, Exoribonuclease II [Transcription] Back     alignment and domain information
>gnl|CDD|179920 PRK05054, PRK05054, exoribonuclease II; Provisional Back     alignment and domain information
>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 589
TIGR00358654 3_prime_RNase VacB and RNase II family 3'-5' exori 100.0
TIGR02063709 RNase_R ribonuclease R. This family consists of an 100.0
PRK11642813 exoribonuclease R; Provisional 100.0
PRK05054644 exoribonuclease II; Provisional 100.0
TIGR02062639 RNase_B exoribonuclease II. This family consists o 100.0
COG0557706 VacB Exoribonuclease R [Transcription] 100.0
PF00773325 RNB: RNB domain CAUTION: The Prosite pattern does 100.0
COG4776645 Rnb Exoribonuclease II [Transcription] 100.0
KOG2102941 consensus Exosomal 3'-5' exoribonuclease complex, 100.0
cd0569769 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t 96.75
cd0570673 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a 96.61
cd0568568 S1_Tex S1_Tex: The C-terminal S1 domain of a trans 96.57
cd0569069 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p 96.53
cd0568972 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p 96.49
cd0447268 S1_PNPase S1_PNPase: Polynucleotide phosphorylase 96.47
cd0569870 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp 96.43
cd0568868 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p 96.43
cd0570768 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a 96.43
cd0447183 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai 96.36
PRK07252120 hypothetical protein; Provisional 96.36
cd0446183 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp 96.34
PF0057574 S1: S1 RNA binding domain; InterPro: IPR003029 Rib 96.32
cd0568673 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom 96.31
cd0570877 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a 96.24
PRK08582139 hypothetical protein; Provisional 96.1
cd0445276 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr 95.96
PRK05807136 hypothetical protein; Provisional 95.96
cd0569269 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p 95.93
cd0569173 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p 95.88
cd0569671 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t 95.73
cd0568479 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal 95.52
PRK08059123 general stress protein 13; Validated 95.35
cd0570373 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R 95.14
smart0031672 S1 Ribosomal protein S1-like RNA-binding domain. 94.95
cd0568770 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib 94.67
COG1098129 VacB Predicted RNA binding protein (contains ribos 94.55
cd0570574 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a 94.49
cd0447377 S1_RecJ_like S1_RecJ_like: The S1 domain of the ar 94.07
PLN00207891 polyribonucleotide nucleotidyltransferase; Provisi 93.53
cd0569566 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t 92.97
cd0016465 S1_like S1_like: Ribosomal protein S1-like RNA-bin 92.67
PHA0294588 interferon resistance protein; Provisional 92.6
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal 92.36
PRK07899 486 rpsA 30S ribosomal protein S1; Reviewed 92.26
cd0570472 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a 92.15
PTZ00248 319 eukaryotic translation initiation factor 2 subunit 91.86
PRK11824693 polynucleotide phosphorylase/polyadenylase; Provis 91.65
cd0446099 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. 91.63
PRK03987 262 translation initiation factor IF-2 subunit alpha; 90.99
PRK07400318 30S ribosomal protein S1; Reviewed 90.62
PRK07899 486 rpsA 30S ribosomal protein S1; Reviewed 90.03
PRK13806 491 rpsA 30S ribosomal protein S1; Provisional 89.04
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransfe 88.41
cd0578986 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. 88.28
PRK06676 390 rpsA 30S ribosomal protein S1; Reviewed 88.13
cd0569474 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp 88.09
TIGR00448179 rpoE DNA-directed RNA polymerase (rpoE), archaeal 87.99
cd0446567 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib 87.85
TIGR00717516 rpsA ribosomal protein S1. This model provides tru 87.13
cd0445482 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA- 86.74
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 85.85
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal 85.68
PRK00087647 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 85.6
PRK06299 565 rpsA 30S ribosomal protein S1; Reviewed 85.28
PRK12269863 bifunctional cytidylate kinase/ribosomal protein S 85.07
TIGR02696719 pppGpp_PNP guanosine pentaphosphate synthetase I/p 84.93
PRK1244287 translation initiation factor IF-1; Reviewed 84.92
PRK13806 491 rpsA 30S ribosomal protein S1; Provisional 83.52
PRK09202 470 nusA transcription elongation factor NusA; Validat 81.43
cd0445388 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik 81.35
cd0570270 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R 81.23
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases Back     alignment and domain information 
Probab=100.00  E-value=4.5e-94  Score=815.57  Aligned_cols=459  Identities=25%  Similarity=0.326  Sum_probs=384.4

Q ss_pred             cCCeeeEEeccCCCCCccc--eEEccCCCccccC----CCceEeecCCCCCCCHHHHHHHHHH---hc-ccccCCCCCCC
Q 007798          121 DSDRVLLAVAQRPDGKKNW--MVYDQNGASCSIK----PQQVTFVVPGVEKFDHKDISNFLQK---AE-DNLLNRKDLTH  190 (589)
Q Consensus       121 ~~~rv~~~i~~~p~~~~~~--~~~~~~g~~~~l~----p~~~~~~l~~~~~~~~~~~~~~~~~---~~-~~~~~R~Dl~~  190 (589)
                      .|++|++.|..||.....+  .++...|......    .--..|.++.  .|+++.++++..-   +. .....|+|||+
T Consensus       122 ~g~~V~v~i~~~p~~~~~~~g~i~~~lG~~~d~~~~~~~il~~~~i~~--~f~~~v~~~a~~~~~~~~~~~~~~R~Dlr~  199 (654)
T TIGR00358       122 EGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEIPF--EFPDGVEQQAAKLQFDVDEQAKKYREDLTD  199 (654)
T ss_pred             CCCEEEEEEccCCCCCCCceEEEEEEEcCCCCcccHHHHHHHHcCcCC--CCCHHHHHHHHhccccCChhHhhCcccccc
Confidence            4667777888888766544  2344444322210    0013466665  3777666544321   11 23467999999


Q ss_pred             CeeEEEeCCCCCCccceeEEEEecCCeEEEEEEEcCCccccCCCCHHHHHHHhcCceeecCCCccCCCChhhhhccCcCC
Q 007798          191 LKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLR  270 (589)
Q Consensus       191 l~~fTID~~~a~DiDDAiSie~~~dG~~~l~VHIADvs~~V~~gS~LD~eA~~RgtSvYLP~~~ipMLP~~Ls~~~~SL~  270 (589)
                      +++|||||++|+|+||||||+++++|+|+|||||||||+||++||+||+||++||||+|||++++||||+.||+++|||+
T Consensus       200 ~~~~TID~~~a~D~DDAisie~~~~g~~~l~VHIADVs~~V~~~s~LD~eA~~R~tSvYlp~~~ipMLP~~Ls~~~cSL~  279 (654)
T TIGR00358       200 LAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLN  279 (654)
T ss_pred             CcEEEECCCCCCcccceEEEEEeCCCcEEEEEEEechhheeCCCCHHHHHHHHhCcCccCCCCeecCCCHHHhcCccccC
Confidence            99999999999999999999999899999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeeeEEEEEEEECCCCeEeEEEEEEEEEecccccCHHHHHHHHhcCCC-------ChHHHHHHHHHHHHHHHHHHhCC
Q 007798          271 QGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLE-------EEAELKILSEAAALRLQWRLQQG  343 (589)
Q Consensus       271 ~g~~r~AlS~~~~ld~~G~I~~~~~~~s~I~s~~~LtY~~v~~~l~~~~~-------~~~~L~~L~~la~~l~~~R~~~G  343 (589)
                      ||++|+|+||.+++|++|+|.+++|++|+|+|.++|||++|+++|+++..       ..++|..|+++|+.|+++|.++|
T Consensus       280 p~~~R~a~s~~~~id~~G~i~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~~~~~~~L~~l~~la~~lr~~R~~~G  359 (654)
T TIGR00358       280 PNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRG  359 (654)
T ss_pred             CCCcceEEEEEEEECCCCCEeEEEEEEEEEEECcEEcHHHHHHHHcCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence            99999999999999999999999999999999999999999999987531       23579999999999999999999


Q ss_pred             CcccCCcceEEEecCCCCCCCeEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhcCCCcccccCCCCCCChh-hhh---
Q 007798          344 AIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVS-AFA---  419 (589)
Q Consensus       344 ai~~~~pe~~i~l~~~~d~~~~v~i~~~~~~~~a~~LVeE~MIlAN~~~A~~l~~~~ip~lyR~q~~p~~~~~-~l~---  419 (589)
                      +++|+.||.+|.+++  + +.++.+...+ +++||.|||||||+||++||+|+.++++|++||+|+.|+..+. ++.   
T Consensus       360 ai~~~~~e~~~~~d~--~-g~~~~i~~~~-~~~a~~lIeE~MilAN~~vA~~~~~~~~p~iyR~h~~p~~~~~~~l~~~~  435 (654)
T TIGR00358       360 LIDFEHPETKFIVDE--E-GRVIDIVAEV-RRIAEKIIEEAMIVANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFL  435 (654)
T ss_pred             CcccCCCceeEEECC--C-CCeeEEEecc-CcHHHHHHHHHHHHHHHHHHHHHHHcCCCeEEecCCCCCHHHHHHHHHHH
Confidence            999999999999986  2 3457887777 8999999999999999999999999999999999999976543 111   


Q ss_pred             -----cCCC---C---c-----------------chHHHHHHhhhcCccccCCCCCccccCCCCcccccccccchhhHHH
Q 007798          420 -----HLPE---G---P-----------------VRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLA  471 (589)
Q Consensus       420 -----~l~~---~---~-----------------~~~~~l~r~m~~a~ys~~~p~~HfgLgl~~YthfTSPIRRY~DLiv  471 (589)
                           .++.   +   +                 +....++|+|++|.|++ +|.+|||||++.|||||||||||+||+|
T Consensus       436 ~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~llr~m~~A~y~~-~~~~HfgL~~~~YthfTSPIRRY~DLiv  514 (654)
T TIGR00358       436 AELGLTLPGGNAENVTTLDGACWLREVKDRPEYEILVTRLLRSLSQAEYSP-EPLGHFGLGLEHYAHFTSPIRRYPDLTN  514 (654)
T ss_pred             HHcCCCccCCCcCCCChHHHHHHHHHhhCCCHHHHHHHHHHHhhcccccCC-CCCCccccccccccccCCccccchHHHH
Confidence                 1111   0   0                 12346789999999999 9999999999999999999999999999


Q ss_pred             HHHHHHHHcCCCC----CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcEEEEEEEEEeeC-------
Q 007798          472 HYQVKACLRGESP----PFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALILRFIKD-------  540 (589)
Q Consensus       472 HrqL~a~L~g~~~----~~~~~~L~~i~~~~~~~~r~a~~aer~~~~~~~~~~L~~~~~g~~~~a~V~~~~~~-------  540 (589)
                      ||||+++|.|+..    +++.++|..++.+||.+++.++++||++.+||.++||+++. |++|+|+|+++...       
T Consensus       515 Hr~L~a~l~~~~~~~~~~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~i-G~~~~g~I~~v~~~GifV~L~  593 (654)
T TIGR00358       515 HRLIKAVLAKEQTDTERYQPQDELLQIAEHCSDTERRARDAERDVADWLKCRYLLDKV-GTEFSGEISSVTRFGMFVRLD  593 (654)
T ss_pred             HHHHHHHHcCCCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhCC-CcEEEEEEEeEEcCcEEEEec
Confidence            9999999987632    25677899999999999999999999999999999999999 79999999995332       


Q ss_pred             ---eeEEEEeeccceeE----------EE-EeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798          541 ---RTAALLLVEVGLQA----------AA-WVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV  587 (589)
Q Consensus       541 ---~~~~V~l~~lg~~~----------~~-~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v  587 (589)
                         .+|+|++++++-+.          .. +.+..|++||+|+|+|.+||+.+++|+|+.+
T Consensus       594 ~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I~f~l~  654 (654)
T TIGR00358       594 DNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSIIFELV  654 (654)
T ss_pred             CCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeEEEEEC
Confidence               35667777664332          11 2235699999999999999999999999853

This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
>TIGR02063 RNase_R ribonuclease R Back     alignment and domain information
>PRK11642 exoribonuclease R; Provisional Back     alignment and domain information
>PRK05054 exoribonuclease II; Provisional Back     alignment and domain information
>TIGR02062 RNase_B exoribonuclease II Back     alignment and domain information
>COG0557 VacB Exoribonuclease R [Transcription] Back     alignment and domain information
>PF00773 RNB: RNB domain CAUTION: The Prosite pattern does not correspond to this Pfam Back     alignment and domain information
>COG4776 Rnb Exoribonuclease II [Transcription] Back     alignment and domain information
>KOG2102 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp44/Dis3 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa Back     alignment and domain information
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain Back     alignment and domain information
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain Back     alignment and domain information
>PRK07252 hypothetical protein; Provisional Back     alignment and domain information
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains Back     alignment and domain information
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain Back     alignment and domain information
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>PRK08582 hypothetical protein; Provisional Back     alignment and domain information
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain Back     alignment and domain information
>PRK05807 hypothetical protein; Provisional Back     alignment and domain information
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide Back     alignment and domain information
>PRK08059 general stress protein 13; Validated Back     alignment and domain information
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease Back     alignment and domain information
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional Back     alignment and domain information
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>PHA02945 interferon resistance protein; Provisional Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional Back     alignment and domain information
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional Back     alignment and domain information
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain Back     alignment and domain information
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated Back     alignment and domain information
>PRK07400 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain Back     alignment and domain information
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form Back     alignment and domain information
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>TIGR00717 rpsA ribosomal protein S1 Back     alignment and domain information
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain Back     alignment and domain information
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase Back     alignment and domain information
>PRK12442 translation initiation factor IF-1; Reviewed Back     alignment and domain information
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>PRK09202 nusA transcription elongation factor NusA; Validated Back     alignment and domain information
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain Back     alignment and domain information
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits 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 ?
Query589
2r7d_A469 Crystal Structure Of Ribonuclease Ii Family Protein 4e-18
4ifd_J1003 Crystal Structure Of An 11-subunit Eukaryotic Exoso 7e-16
2wp8_J977 Yeast Rrp44 Nuclease Length = 977 9e-16
2vnu_D760 Crystal Structure Of Sc Rrp44 Length = 760 3e-13
2ix1_A664 Rnase Ii D209n Mutant Length = 664 5e-10
2ix1_A664 Rnase Ii D209n Mutant Length = 664 4e-04
2ix0_A663 Rnase Ii Length = 663 5e-10
2ix0_A663 Rnase Ii Length = 663 4e-04
2id0_A644 Escherichia Coli Rnase Ii Length = 644 3e-09
2id0_A644 Escherichia Coli Rnase Ii Length = 644 9e-04
>pdb|2R7D|A Chain A, Crystal Structure Of Ribonuclease Ii Family Protein From Deinococcus Radiodurans, Triclinic Crystal Form. Northeast Structural Genomics Target Drr63 Length = 469 Back     alignment and structure 
Iteration: 1

 Score = 89.7 bits (221), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 102/361 (28%), Positives = 150/361 (41%), Gaps = 29/361 (8%)
Query: 180 DNLLNRKDLTHLKVYAIDVXXXXXXXXXXSAMRLQDGRIKVYIHVADPTKYIEPGSLSDK 239
           D    R DLTHL  +AID               L  G  ++++HVAD    + P S  D 
Sbjct: 76  DPAEERLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPLDL 135
Query: 240 DAMKRGTSVFLPTATYPMFPEKL-AMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNS 298
           +A  RG +++LP  T    P++L A  G+ L   EV  A+++ + L  DG+     V  +
Sbjct: 136 EARARGATLYLPDRTIGXLPDELVAKAGLGLH--EVSPALSICLDLDPDGNAEAVDVLLT 193
Query: 299 IIKPTYMLTYESATXXXXXXXXXXXXXKILSEAAALRLQWRLQQGAIDTATLETRIKVAN 358
            +K    L Y+ A                L+ A+    +    +GA+     E R+K   
Sbjct: 194 RVK-VQRLAYQEAQARLEAGEEPFVTLARLARASRRLRE---GEGALSIDLPEVRVKADE 249
Query: 359 PEDPEPIINLYVEDQADPAMR-LVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVSA 417
                      V     P  R +V E   L G   A +   N + LP+  Q     +V+ 
Sbjct: 250 -------TGASVFPLPKPEXRTVVQECXTLAGWGTAIFADDNEIPLPFATQDYPTREVAG 302
Query: 418 FAHLPEGPVRSSAIVKIMRAAAIDFR-KPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVK 476
              LP    R   + +        F+  P  H   GL  Y Q TSP RRY+DL+ H Q++
Sbjct: 303 DT-LPAXWARRKTLARTR------FQPSPGPHHGXGLDLYAQATSPXRRYLDLVVHQQLR 355
Query: 477 ACLRGESPPFSAGQLEGMA-SIVNMQ-TRIARRLSNTSLRYWIIEFLRRQPKERQYRALI 534
           A L G  P  S      +A S  N   TR A RLS    R+  + F+  QP ER + A++
Sbjct: 356 AFLAGRDPLSSKVXAAHIAESQXNADATRQAERLSR---RHHTLRFIAAQP-ERVWDAVV 411
Query: 535 L 535
           +
Sbjct: 412 V 412
>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome Complex Bound To Rna Length = 1003 Back     alignment and structure
>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease Length = 977 Back     alignment and structure
>pdb|2VNU|D Chain D, Crystal Structure Of Sc Rrp44 Length = 760 Back     alignment and structure
>pdb|2IX1|A Chain A, Rnase Ii D209n Mutant Length = 664 Back     alignment and structure
>pdb|2IX1|A Chain A, Rnase Ii D209n Mutant Length = 664 Back     alignment and structure
>pdb|2IX0|A Chain A, Rnase Ii Length = 663 Back     alignment and structure
>pdb|2IX0|A Chain A, Rnase Ii Length = 663 Back     alignment and structure
>pdb|2ID0|A Chain A, Escherichia Coli Rnase Ii Length = 644 Back     alignment and structure
>pdb|2ID0|A Chain A, Escherichia Coli Rnase Ii Length = 644 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 ?
Query589
2r7d_A469 Ribonuclease II family protein; structural genomic 1e-115
2wp8_J977 Exosome complex exonuclease DIS3; nucleus, hydrola 1e-51
2vnu_D760 Exosome complex exonuclease RRP44; hydrolase-RNA c 2e-50
2id0_A644 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, 3e-46
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-08
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-05
>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2, structure initiative, northeast structural genomics consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP: b.40.4.5 b.40.4.16 PDB: 2r7f_A Length = 469 Back     alignment and structure
 Score =  349 bits (898), Expect = e-115
 Identities = 104/410 (25%), Positives = 170/410 (41%), Gaps = 22/410 (5%)

Query: 179 EDNLLNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSD 238
            D    R DLTHL  +AID +   + DDA+    L  G  ++++HVAD    + P S  D
Sbjct: 75  FDPAEERLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPLD 134

Query: 239 KDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNS 298
            +A  RG +++LP  T  M P++L      L   EV  A+++ + L  DG+     V  +
Sbjct: 135 LEARARGATLYLPDRTIGMLPDELV-AKAGLGLHEVSPALSICLDLDPDGNAEAVDVLLT 193

Query: 299 IIKPTYMLTYESATELLHLNLEEEAELKILSEAAALRLQWRLQQGAIDTATLETRIKVAN 358
            +K    L Y+ A   L      E     L+  A    + R  +GA+     E R+K   
Sbjct: 194 RVK-VQRLAYQEAQARLE---AGEEPFVTLARLARASRRLREGEGALSIDLPEVRVKAD- 248

Query: 359 PEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVSAF 418
            E    +              +V E M L G   A +   N + LP+  Q     +V   
Sbjct: 249 -ETGASV----FPLPKPEMRTVVQECMTLAGWGTAIFADDNEIPLPFATQDYPTREV--- 300

Query: 419 AHLPEGPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVKAC 478
               +      A  K +         P  H  +GL  Y Q TSP+RRY+DL+ H Q++A 
Sbjct: 301 --AGDTLPAMWARRKTLARTRFQ-PSPGPHHGMGLDLYAQATSPMRRYLDLVVHQQLRAF 357

Query: 479 LRGESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALILRFI 538
           L G   P S+  +    +   M     R+    S R+  + F+  QP+   + A+++   
Sbjct: 358 LAGR-DPLSSKVMAAHIAESQMNADATRQAERLSRRHHTLRFIAAQPER-VWDAVVVD-R 414

Query: 539 KDRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEVV 588
           +   A LL+ ++       V+  A  G  ++V+  +       +  + V+
Sbjct: 415 RGAQATLLIPDLAFDVQ--VNTPAAPGTALQVQFADIDLPQMRVRARSVL 462
>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} Length = 977 Back     alignment and structure
>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 Length = 760 Back     alignment and structure
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A Length = 644 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query589
2r7d_A469 Ribonuclease II family protein; structural genomic 100.0
2id0_A644 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, 100.0
2vnu_D760 Exosome complex exonuclease RRP44; hydrolase-RNA c 100.0
2wp8_J977 Exosome complex exonuclease DIS3; nucleus, hydrola 100.0
1kl9_A182 Eukaryotic translation initiation factor 2 subuni; 97.1
2a19_A175 EIF-2- alpha, eukaryotic translation initiation fa 97.09
2k52_A80 Uncharacterized protein MJ1198; metal-binding, zin 96.86
3bzc_A785 TEX; helix-turn-helix, helix-hairpin-helix, S1 dom 96.84
2k4k_A130 GSP13, general stress protein 13; cytoplasm, stres 96.76
1luz_A88 Protein K3, protein K2; stranded anti-parallel bet 96.76
2khi_A115 30S ribosomal protein S1; acetylation, phosphoprot 96.5
2khj_A109 30S ribosomal protein S1; OB fold, acetylation, ph 96.01
2cqo_A119 Nucleolar protein of 40 kDa; S1 domain, OB-fold, s 95.78
2eqs_A103 ATP-dependent RNA helicase DHX8; S1 domain, OB-fol 95.64
1q8k_A 308 Eukaryotic translation initiation factor 2 subunit 95.35
3aev_A 275 Translation initiation factor 2 subunit alpha; pro 95.31
1wi5_A119 RRP5 protein homolog; S1 domain, OB-fold, structur 94.57
1go3_E187 DNA-directed RNA polymerase subunit E; transferase 94.25
4ayb_E180 DNA-directed RNA polymerase; transferase, multi-su 94.05
2ckz_B218 C25, DNA-directed RNA polymerase III 25 KD polypep 93.93
2c35_B172 Human RPB7, DNA-directed RNA polymerase II 19 kDa 93.84
3ayh_B203 DNA-directed RNA polymerase III subunit RPC8; tran 93.39
1y14_B171 B16, RPB7, DNA-directed RNA polymerase II 19 kDa p 93.2
2b8k_G215 B16, DNA-directed RNA polymerase II 19 kDa polypep 93.1
1e3p_A757 Guanosine pentaphosphate synthetase; polyribonucle 93.09
3cw2_C 266 Translation initiation factor 2 subunit alpha; AIF 92.25
3h0g_G172 DNA-directed RNA polymerase II subunit RPB7; trans 91.96
4aid_A726 Polyribonucleotide nucleotidyltransferase; transfe 91.89
3psi_A 1219 Transcription elongation factor SPT6; nucleus; 3.3 90.3
3cdi_A723 Polynucleotide phosphorylase; mRNA turnover, RNAse 89.97
3go5_A285 Multidomain protein with S1 RNA-binding domains; s 87.64
3psf_A1030 Transcription elongation factor SPT6; nucleus; 2.5 86.04
>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2, structure initiative, northeast structural genomics consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP: b.40.4.5 b.40.4.16 PDB: 2r7f_A Back     alignment and structure
Probab=100.00  E-value=5.5e-98  Score=816.53  Aligned_cols=384  Identities=27%  Similarity=0.390  Sum_probs=364.4

Q ss_pred             cCCCCCCCCeeEEEeCCCCCCccceeEEEEecCCeEEEEEEEcCCccccCCCCHHHHHHHhcCceeecCCCccCCCChhh
Q 007798          183 LNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKL  262 (589)
Q Consensus       183 ~~R~Dl~~l~~fTID~~~a~DiDDAiSie~~~dG~~~l~VHIADvs~~V~~gS~LD~eA~~RgtSvYLP~~~ipMLP~~L  262 (589)
                      ++|+|||++++|||||++|+|+|||||+++++||+|+|||||||||+||+|||+||+||++||||||||++++||||+.|
T Consensus        79 ~~R~Dlr~l~~~TID~~~a~D~DDAvsve~~~~g~~~l~VHIADVs~~V~~gs~LD~eA~~RgtSvYlp~~~ipMLP~~L  158 (469)
T 2r7d_A           79 EERLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPLDLEARARGATLYLPDRTIGMLPDEL  158 (469)
T ss_dssp             SCCEECTTSCEEEEECTTCCCCCEEEEEEECSTTCEEEEEEEECGGGTCCTTSHHHHHHHHHCBCEECSSCEECSSCHHH
T ss_pred             cCceecccCCEEEEcCCCCCCccceEEEEEeCCCCEEEEEEeccHhheeCCCCHHHHHHHHhCceEecCCceEcCCChHH
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccCcCCCCCeeeEEEEEEEECCCCeEeEEEEEEEEEecccccCHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHhC
Q 007798          263 AMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLEEEAELKILSEAAALRLQWRLQQ  342 (589)
Q Consensus       263 s~~~~SL~~g~~r~AlS~~~~ld~~G~I~~~~~~~s~I~s~~~LtY~~v~~~l~~~~~~~~~L~~L~~la~~l~~~R~~~  342 (589)
                       +++|||+||++|+||||.|++|++|+|.+++|++|+|+|+ +|||++|+++|+++   .++|..|+++|+.|+++|.++
T Consensus       159 -~~~cSL~pg~dr~als~~~~id~~G~i~~~~~~~svI~s~-rltY~~v~~~l~~~---~~~L~~L~~la~~lr~~R~~~  233 (469)
T 2r7d_A          159 -VAKAGLGLHEVSPALSICLDLDPDGNAEAVDVLLTRVKVQ-RLAYQEAQARLEAG---EEPFVTLARLARASRRLREGE  233 (469)
T ss_dssp             -HHHHSTTSSSSEEEEEEEEEECTTSCEEEEEEEEEEECEE-EEEHHHHHHHHHTT---CTTHHHHHHHHHHHHHHHHHT
T ss_pred             -hcccCCCCCCceEEEEEEEEEcCCCCEeeeEEEEEEEEec-cccHHHHHHHHhCC---cHHHHHHHHHHHHHHHHHHhC
Confidence             8999999999999999999999999999999999999999 99999999999875   478999999999999999999


Q ss_pred             CCcccCCcceEEEecCCCCCCCeEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhcCCCcccccCCCCCCChhhhhcCC
Q 007798          343 GAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVSAFAHLP  422 (589)
Q Consensus       343 Gai~~~~pe~~i~l~~~~d~~~~v~i~~~~~~~~a~~LVeE~MIlAN~~~A~~l~~~~ip~lyR~q~~p~~~~~~l~~l~  422 (589)
                      |+++|+.||.+|.+++   +  .+.+.+.+ ++++++|||||||+||++||+|+.++++|++||+|+.|+.++     ++
T Consensus       234 Gai~~~~pe~~i~~d~---~--~~~i~~~~-~~~a~~lIeE~MilAN~~vA~~l~~~~ip~~yR~h~~p~~~~-----~~  302 (469)
T 2r7d_A          234 GALSIDLPEVRVKADE---T--GASVFPLP-KPEMRTVVQECMTLAGWGTAIFADDNEIPLPFATQDYPTREV-----AG  302 (469)
T ss_dssp             TCCCCCCCCEEEEEET---T--EEEEEECC-CCHHHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEECCCSSCC-----CC
T ss_pred             CCcccCCCceEEEECC---C--cceEEecC-CCcHHHHHHHHHHHHHHHHHHHHHHcCCCeeEeeCCCCCccc-----Cc
Confidence            9999999999999986   2  58888887 999999999999999999999999999999999999997653     37


Q ss_pred             CCcchHHHHHHhhhcCccccCCCCCccccCCCCcccccccccchhhHHHHHHHHHHHcCCCCCCChhhHHHHHHHHHHHH
Q 007798          423 EGPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVKACLRGESPPFSAGQLEGMASIVNMQT  502 (589)
Q Consensus       423 ~~~~~~~~l~r~m~~a~ys~~~p~~HfgLgl~~YthfTSPIRRY~DLivHrqL~a~L~g~~~~~~~~~L~~i~~~~~~~~  502 (589)
                      ++.+.+..++|+|++|.|++ +|.+|||||++.|||||||||||+||+|||||+++|.|+ ++|+.++|+.++.+||.++
T Consensus       303 ~~~~~~~~l~r~m~~a~y~~-~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~a~l~~~-~~~~~~~l~~~~~~~~~~e  380 (469)
T 2r7d_A          303 DTLPAMWARRKTLARTRFQP-SPGPHHGMGLDLYAQATSPMRRYLDLVVHQQLRAFLAGR-DPLSSKVMAAHIAESQMNA  380 (469)
T ss_dssp             CSHHHHHHHHHHCCCEEEES-SCCCBTTTTBSCCCCCSCTTTBHHHHHHHHHHHHHHTTC-CCCCHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHhcccccccC-CCCCchhhCccceeeECCcccccHHHHHHHHHHHHHcCC-CCCCHHHHHHHHHHHHHHH
Confidence            77788889999999999999 999999999999999999999999999999999999887 5789999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCCcEEEEEEEEEeeCeeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeE
Q 007798          503 RIARRLSNTSLRYWIIEFLRRQPKERQYRALILRFIKDRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDII  582 (589)
Q Consensus       503 r~a~~aer~~~~~~~~~~L~~~~~g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i  582 (589)
                      +.++++||++.+||+++||++++ |++|+|+|++. ++++|+|+++++|++  .+.+..|++||+|+|+|.+||+.+++|
T Consensus       381 r~a~~aer~~~~~~~~~~l~~~~-g~~f~g~vv~l-~~~~glV~v~~l~~d--~~~~~~~~lGd~V~V~v~~vd~~~~~i  456 (469)
T 2r7d_A          381 DATRQAERLSRRHHTLRFIAAQP-ERVWDAVVVDR-RGAQATLLIPDLAFD--VQVNTPAAPGTALQVQFADIDLPQMRV  456 (469)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCT-TCCEEEEEEEE-ETTEEEEEEGGGTEE--EEEECCCCTTCEEEEEEEEEETTTTEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCC-CCEEEEEEEEE-eCcEEEEEECCCCeE--EecCCcCCCCCEEEEEEEEEccCCCEE
Confidence            99999999999999999999999 69999999984 467899999999988  566678999999999999999999999


Q ss_pred             EEEEec
Q 007798          583 YLKEVV  588 (589)
Q Consensus       583 ~~~~v~  588 (589)
                      +|+.+.
T Consensus       457 ~f~~~~  462 (469)
T 2r7d_A          457 RARSVL  462 (469)
T ss_dssp             EEEECC
T ss_pred             EEEEEh
Confidence            999864
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A Back     alignment and structure
>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 Back     alignment and structure
>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} Back     alignment and structure
>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 Back     alignment and structure
>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A Back     alignment and structure
>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Back     alignment and structure
>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A Back     alignment and structure
>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Back     alignment and structure
>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5 Back     alignment and structure
>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Back     alignment and structure
>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Back     alignment and structure
>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1 Back     alignment and structure
>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A Back     alignment and structure
>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5 Back     alignment and structure
>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1 Back     alignment and structure
>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E Back     alignment and structure
>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae} Back     alignment and structure
>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1 Back     alignment and structure
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe} Back     alignment and structure
>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ... Back     alignment and structure
>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 Back     alignment and structure
>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A Back     alignment and structure
>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B* Back     alignment and structure
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Back     alignment and structure
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Back     alignment and structure
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Back     alignment and structure
>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae} Back     alignment and structure
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} 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 589
d2ix0a4385 b.40.4.16 (A:173-557) Exoribonuclease 2, RNB {Esch 2e-56
d2vnud4416 b.40.4.16 (D:495-910) Exosome complex exonuclease 6e-56
d2r7da2401 b.40.4.16 (A:3-403) Ribonuclease II family protein 1e-52
>d2ix0a4 b.40.4.16 (A:173-557) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Length = 385 Back     information, alignment and structure

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: RNB domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

 Score =  192 bits (489), Expect = 2e-56
 Identities = 87/384 (22%), Positives = 147/384 (38%), Gaps = 45/384 (11%)

Query: 176 QKAEDNLLNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGS 235
            +  D  L R+DLT L    ID    +++DDAL A  L D ++++ + +ADPT +I  GS
Sbjct: 8   TEMLDEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGS 67

Query: 236 LSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSV 295
             DK A  R  + +LP    PM P +L+ +  SLR  EV   +   + L +DG+I +   
Sbjct: 68  KLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIE 127

Query: 296 D-NSIIKPTYMLTYESATELLHLNLEEEA-------ELKILSEAAALRLQWRLQQGAIDT 347
              + I+    L Y+  ++ L    + +        ++++L++    R +WR     +  
Sbjct: 128 FFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFK 187

Query: 348 ATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYR- 406
              + R  +    +   I    V +    A R+V E MI      A           Y  
Sbjct: 188 DRPDYRFILGEKGEVLDI----VAEPRRIANRIVEEAMIAANICAARVLRDKLGFGIYNV 243

Query: 407 ----------------------------GQPQSNIDVSAFAHLPEGPVRSSAIVKIMRAA 438
                                               +             S I +    A
Sbjct: 244 HMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFA 303

Query: 439 AIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVKACLRGESPPFSAGQLEGMASIV 498
            I   +P  H  LGL  Y  +TSPIR+Y D++ H  +KA ++GE+        + +   +
Sbjct: 304 EI-STEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRP---QDEITVQM 359

Query: 499 NMQTRIARRLSNTSLRYWIIEFLR 522
             + R+ R        +    FL+
Sbjct: 360 AERRRLNRMAERDVGDWLYARFLK 383
>d2vnud4 b.40.4.16 (D:495-910) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]} Length = 416 Back     information, alignment and structure
>d2r7da2 b.40.4.16 (A:3-403) Ribonuclease II family protein DR0020 {Deinococcus radiodurans [TaxId: 1299]} Length = 401 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 ?
Query589
d2r7da2401 Ribonuclease II family protein DR0020 {Deinococcus 100.0
d2ix0a4385 Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5 100.0
d2vnud4416 Exosome complex exonuclease RRP44 {Saccharomyces c 100.0
d2ix0a387 Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5 97.47
d1go3e1106 C-terminal domain of RNA polymerase II subunit RBP 97.08
d1kl9a286 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 96.72
d2ahob284 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 96.22
d1y14b191 C-terminal domain of RNA polymerase II subunit RBP 96.09
d3bzka494 Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287] 95.94
d2c35b194 C-terminal domain of RNA polymerase II subunit RBP 94.98
d1sroa_76 S1 RNA-binding domain of polyribonucleotide phosph 94.89
d2ba0a183 S1-domain of exosome complex RNA-binding protein 1 92.51
d2r7da158 Ribonuclease II family protein DR0020 {Deinococcus 92.07
d2z0sa188 S1-domain of exosome complex RNA-binding protein 1 90.91
d2je6i187 S1-domain of exosome complex RNA-binding protein 1 89.65
d1wi5a_119 S1-domain of RRP5 protein homolog (PDCD11, KIAA018 88.52
d2nn6h195 S1-domain of Ribosomal RNA-processing protein 4, R 87.85
d1luza_85 Viral structural mimic of eIF2alpha {Vaccinia viru 82.88
>d2r7da2 b.40.4.16 (A:3-403) Ribonuclease II family protein DR0020 {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: RNB domain-like
domain: Ribonuclease II family protein DR0020
species: Deinococcus radiodurans [TaxId: 1299]

Probab=100.00  E-value=5.2e-82  Score=676.91  Aligned_cols=326  Identities=29%  Similarity=0.405  Sum_probs=300.0

Q ss_pred             ccCCCCCCCCeeEEEeCCCCCCccceeEEEEecCCeEEEEEEEcCCccccCCCCHHHHHHHhcCceeecCCCccCCCChh
Q 007798          182 LLNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEK  261 (589)
Q Consensus       182 ~~~R~Dl~~l~~fTID~~~a~DiDDAiSie~~~dG~~~l~VHIADvs~~V~~gS~LD~eA~~RgtSvYLP~~~ipMLP~~  261 (589)
                      .++|+|||++++|||||++|+|+||||||+++++|.|+|||||||||+||++||+||++|++||||+|||++++||||+.
T Consensus        76 ~~~R~Dlr~l~~~tID~~~a~D~DDAisie~~~~g~~~l~VHIADVs~~v~~~s~Ld~eA~~R~tSvYlp~~~~pMLP~~  155 (401)
T d2r7da2          76 AEERLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPLDLEARARGATLYLPDRTIGMLPDE  155 (401)
T ss_dssp             TSCCEECTTSCEEEEECTTCCCCCEEEEEEECSTTCEEEEEEEECGGGTCCTTSHHHHHHHHHCBCEECSSCEECSSCHH
T ss_pred             cccccccccCcEEEECCCCCcccccceeEEEcCCCcEEEEEeecchhhhccCCChHHHHHHHhCccccCCCCeeecCcHH
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhccCcCCCCCeeeEEEEEEEECCCCeEeEEEEEEEEEecccccCHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHh
Q 007798          262 LAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLEEEAELKILSEAAALRLQWRLQ  341 (589)
Q Consensus       262 Ls~~~~SL~~g~~r~AlS~~~~ld~~G~I~~~~~~~s~I~s~~~LtY~~v~~~l~~~~~~~~~L~~L~~la~~l~~~R~~  341 (589)
                      |++. |||.||++|+|+|+.+++|.+|+|.+++|.+++|++ ++|||++|+++++++   ++.|..|..+++.++++|.+
T Consensus       156 ls~~-~SL~~~~~r~als~~~~ld~~g~i~~~~~~~s~I~~-~~ltY~~v~~~~~~~---~~~l~~l~~~~~~l~~~R~~  230 (401)
T d2r7da2         156 LVAK-AGLGLHEVSPALSICLDLDPDGNAEAVDVLLTRVKV-QRLAYQEAQARLEAG---EEPFVTLARLARASRRLREG  230 (401)
T ss_dssp             HHHH-HSTTSSSSEEEEEEEEEECTTSCEEEEEEEEEEECE-EEEEHHHHHHHHHTT---CTTHHHHHHHHHHHHHHHHH
T ss_pred             Hhcc-cccccCccccccceEEEEccCCCcccceEEEEEEEE-eeccHHHHHHHhhcc---chhHHHHHHHHHHHHHHHHh
Confidence            9975 999999999999999999999999999999999999 589999999999875   35688999999999999999


Q ss_pred             CCCcccCCcceEEEecCCCCCCCeEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhcCCCcccccCCCCCCChhhhhcC
Q 007798          342 QGAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVSAFAHL  421 (589)
Q Consensus       342 ~Gai~~~~pe~~i~l~~~~d~~~~v~i~~~~~~~~a~~LVeE~MIlAN~~~A~~l~~~~ip~lyR~q~~p~~~~~~l~~l  421 (589)
                      +|+++++.|+.++.+++.   +  ..+...+ ...++.||+||||+||.++|+|+.++++|++||+|+.|+...     .
T Consensus       231 ~gal~~~~~~~~~~~d~~---~--~~~~~~~-~~~s~~lVeE~MilAN~~~A~~l~~~~~p~iyR~~~~p~~~~-----~  299 (401)
T d2r7da2         231 EGALSIDLPEVRVKADET---G--ASVFPLP-KPEMRTVVQECMTLAGWGTAIFADDNEIPLPFATQDYPTREV-----A  299 (401)
T ss_dssp             TTCCCCCCCCEEEEEETT---E--EEEEECC-CCHHHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEECCCSSCC-----C
T ss_pred             cCCcccccccceeeeccC---C--cccceee-ccchhhhhHhHhhhcchhHHHHHhhccCCccccccCCCchhh-----h
Confidence            999999999999999762   2  4455555 789999999999999999999999999999999999885432     1


Q ss_pred             CCCcchHHHHHHhhhcCccccCCCCCccccCCCCcccccccccchhhHHHHHHHHHHHcCCCCCCChhhHHHHHHHHHHH
Q 007798          422 PEGPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVKACLRGESPPFSAGQLEGMASIVNMQ  501 (589)
Q Consensus       422 ~~~~~~~~~l~r~m~~a~ys~~~p~~HfgLgl~~YthfTSPIRRY~DLivHrqL~a~L~g~~~~~~~~~L~~i~~~~~~~  501 (589)
                      .+.......++++|++|.|++ +|.+|||||++.|||||||||||+||+|||||+++|.|++ +++.+++..++.+++.+
T Consensus       300 ~~~l~~~~~~~~~~~~a~ys~-~~~~H~gLgl~~YthfTSPIRRY~DLivhrqL~a~L~~~~-~~~~~~l~~~~~~~~~~  377 (401)
T d2r7da2         300 GDTLPAMWARRKTLARTRFQP-SPGPHHGMGLDLYAQATSPMRRYLDLVVHQQLRAFLAGRD-PLSSKVMAAHIAESQMN  377 (401)
T ss_dssp             CCSHHHHHHHHHHCCCEEEES-SCCCBTTTTBSCCCCCSCTTTBHHHHHHHHHHHHHHTTCC-CCCHHHHHHHHHHHHHH
T ss_pred             hccHHHHHHhhhhcceeeEcC-CCCcChhccCCceeeeCChhhhhHHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHHHHH
Confidence            111223456678999999999 9999999999999999999999999999999999999885 78899999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCC
Q 007798          502 TRIARRLSNTSLRYWIIEFLRRQP  525 (589)
Q Consensus       502 ~r~a~~aer~~~~~~~~~~L~~~~  525 (589)
                      ++.++++||++.+||+++||++++
T Consensus       378 ~~~~~~~er~~~~~~~~~yl~~~p  401 (401)
T d2r7da2         378 ADATRQAERLSRRHHTLRFIAAQP  401 (401)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTCT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCc
Confidence            999999999999999999999875
>d2ix0a4 b.40.4.16 (A:173-557) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2vnud4 b.40.4.16 (D:495-910) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]} Back     information, alignment and structure
>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d2r7da1 b.40.4.5 (A:404-461) Ribonuclease II family protein DR0020 {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1luza_ b.40.4.5 (A:) Viral structural mimic of eIF2alpha {Vaccinia virus [TaxId: 10245]} Back     information, alignment and structure