Citrus Sinensis ID: 029223

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-------
MRPPRGGGGFRGGRDGGRGGRGGGRFGGGGRGGGGRGGFGFRDEGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFLPQPKGQAQAGARGGRGGGGFRGRGGGRGGGRGRGGGGGGFRGRGGPPRGGRGGGFRGRGRF
ccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcEEEcccccEEEEEcccccccccccEEcccccccEEEEEEcccccEEEEEEEEcccccccccccccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
ccccccccccccccccccccccccccccccccccccccccccccccccHEEEcccEEccccccEEEEEEccccccccccEEEcccccccEEEEEEcccccEEEEEEccccEEEcccccccEEEEcccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
mrpprggggfrggrdggrggrgggrfggggrggggrggfgfrdegppaeVVEVSSFLhacegdavtkltnekipyfnapiylqnktqigkvdeifgpinesYFSVKMMEGIVATSYslgdkfyidpskllplarflpqpkgqaqagarggrggggfrgrgggrgggrgrggggggfrgrggpprggrgggfrgrgrf
mrpprggggfrggrdggrggrgggrfggggrggggrGGFGFRDEGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFLPQPKGQaqagarggrggggfrgrgggrgggrgrggggggfrgrggpprggrgggfrgrgrf
MRPPrggggfrggrdggrggrgggrfggggrggggrggfgfrdEGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFLPQPKGQAQAGArggrggggfrgrgggrgggrgrggggggfrgrggpprggrgggfrgrgrf
*************************************************VVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFL*************************************************************
************************************************EVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLA****************************************************************
*********FRGGRDGGRGGRGGGRFGGGGRGGGGRGGFGFRDEGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFLPQ*************GGGGFRGRGGGRGGGRGRGGGGGGFRGRGGPPRGGRGGGFRGRGRF
*******************************************EGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFLPQ***********************************************************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MRPPRGGGGFRGGRDGGRGGRGGGRFGGGGRGGGGRGGFGFRDEGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFLPQPKGQAQAGARGGRGGGGFRGRGGGRGGGRGRGGGGGGFRGRGGPPRGGRGGGFRGRGRF
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 ?
Query197 2.2.26 [Sep-21-2011]
Q8VZT0202 Putative H/ACA ribonucleo yes no 0.771 0.752 0.722 6e-51
Q9FK53189 H/ACA ribonucleoprotein c no no 0.512 0.534 0.831 3e-46
Q6CJ45219 H/ACA ribonucleoprotein c yes no 0.609 0.547 0.581 1e-34
P28007205 H/ACA ribonucleoprotein c yes no 0.573 0.551 0.557 4e-33
Q6FSB0222 H/ACA ribonucleoprotein c yes no 0.492 0.436 0.628 4e-33
Q2HH48210 H/ACA ribonucleoprotein c N/A no 0.497 0.466 0.642 2e-32
Q9CY66231 H/ACA ribonucleoprotein c yes no 0.517 0.441 0.586 1e-30
P0CN78203 H/ACA ribonucleoprotein c yes no 0.502 0.487 0.63 1e-30
P0CN79203 H/ACA ribonucleoprotein c N/A no 0.502 0.487 0.63 1e-30
Q5RJV1218 H/ACA ribonucleoprotein c yes no 0.507 0.458 0.607 2e-30
>sp|Q8VZT0|NLAL1_ARATH Putative H/ACA ribonucleoprotein complex subunit 1-like protein 1 OS=Arabidopsis thaliana GN=At3g03920 PE=2 SV=1 Back     alignment and function desciption
 Score =  200 bits (508), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 112/155 (72%), Positives = 122/155 (78%), Gaps = 3/155 (1%)

Query: 43  DEGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESY 102
           DEGPP+EVVEV++F+HACEGDAVTKL+ EKIP+FNAPIYL+NKTQIGKVDEIFGPINES 
Sbjct: 51  DEGPPSEVVEVATFVHACEGDAVTKLSQEKIPHFNAPIYLENKTQIGKVDEIFGPINESL 110

Query: 103 FSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFLPQPKGQAQAGARGGRGGGGFRGRGGG 162
           FS+KMMEGIVATSYS GDKF+IDP KLLPLARFLPQPKGQ+  G  G   G    G   G
Sbjct: 111 FSIKMMEGIVATSYSPGDKFFIDPYKLLPLARFLPQPKGQSTGGRGGAGRGR---GDSRG 167

Query: 163 RGGGRGRGGGGGGFRGRGGPPRGGRGGGFRGRGRF 197
           RG G     G G  RG   PPRGG  G FRGRGRF
Sbjct: 168 RGRGGSFSRGRGAPRGGRFPPRGGSRGSFRGRGRF 202
Required for ribosome biogenesis. Part of a complex which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Pseudouridine ("psi") residues may serve to stabilize the conformation of rRNAs.
Arabidopsis thaliana (taxid: 3702)
>sp|Q9FK53|NLAL2_ARATH H/ACA ribonucleoprotein complex subunit 1-like protein 2 OS=Arabidopsis thaliana GN=At5g18180 PE=2 SV=1 Back     alignment and function description
>sp|Q6CJ45|GAR1_KLULA H/ACA ribonucleoprotein complex subunit 1 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=GAR1 PE=3 SV=1 Back     alignment and function description
>sp|P28007|GAR1_YEAST H/ACA ribonucleoprotein complex subunit 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=GAR1 PE=1 SV=1 Back     alignment and function description
>sp|Q6FSB0|GAR1_CANGA H/ACA ribonucleoprotein complex subunit 1 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=GAR1 PE=3 SV=1 Back     alignment and function description
>sp|Q2HH48|GAR1_CHAGB H/ACA ribonucleoprotein complex subunit 1 OS=Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) GN=GAR1 PE=3 SV=1 Back     alignment and function description
>sp|Q9CY66|GAR1_MOUSE H/ACA ribonucleoprotein complex subunit 1 OS=Mus musculus GN=Gar1 PE=2 SV=1 Back     alignment and function description
>sp|P0CN78|GAR1_CRYNJ H/ACA ribonucleoprotein complex subunit 1 OS=Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) GN=GAR1 PE=3 SV=1 Back     alignment and function description
>sp|P0CN79|GAR1_CRYNB H/ACA ribonucleoprotein complex subunit 1 OS=Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) GN=GAR1 PE=3 SV=1 Back     alignment and function description
>sp|Q5RJV1|GAR1_XENTR H/ACA ribonucleoprotein complex subunit 1 OS=Xenopus tropicalis GN=gar1 PE=2 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 ?
Query197
224144798188 predicted protein [Populus trichocarpa] 0.527 0.553 0.903 5e-51
195645644191 h/ACA ribonucleoprotein complex subunit 0.517 0.534 0.901 5e-51
212724098191 uncharacterized protein LOC100193822 [Ze 0.517 0.534 0.901 6e-51
224125874204 predicted protein [Populus trichocarpa] 0.512 0.495 0.930 1e-50
195628096196 h/ACA ribonucleoprotein complex subunit 0.517 0.520 0.901 1e-50
115486013196 Os11g0579800 [Oryza sativa Japonica Grou 0.517 0.520 0.892 2e-50
125534871196 hypothetical protein OsI_36586 [Oryza sa 0.517 0.520 0.892 2e-50
255568916194 H/ACA ribonucleoprotein complex subunit, 0.517 0.525 0.911 4e-50
195610388191 h/ACA ribonucleoprotein complex subunit 0.517 0.534 0.892 6e-50
413925372190 putative H/ACA ribonucleoprotein complex 0.502 0.521 0.909 1e-49
>gi|224144798|ref|XP_002325418.1| predicted protein [Populus trichocarpa] gi|222862293|gb|EEE99799.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  206 bits (523), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 94/104 (90%), Positives = 101/104 (97%)

Query: 43  DEGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESY 102
           DEGPP+EVVEVSSFLHACEGDAVTKLTNEKIPYFNAPI+LQNKTQIGKVDEIFGPINES+
Sbjct: 41  DEGPPSEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIFLQNKTQIGKVDEIFGPINESH 100

Query: 103 FSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFLPQPKGQAQAG 146
           FS+KMMEGIVATSY+ G+KFYIDP+KLLPLARFL QPKGQAQA 
Sbjct: 101 FSIKMMEGIVATSYAPGEKFYIDPNKLLPLARFLSQPKGQAQAA 144

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|195645644|gb|ACG42290.1| h/ACA ribonucleoprotein complex subunit 1-like protein 1 [Zea mays] Back     alignment and taxonomy information
>gi|212724098|ref|NP_001132376.1| uncharacterized protein LOC100193822 [Zea mays] gi|194694218|gb|ACF81193.1| unknown [Zea mays] Back     alignment and taxonomy information
>gi|224125874|ref|XP_002319696.1| predicted protein [Populus trichocarpa] gi|222858072|gb|EEE95619.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|195628096|gb|ACG35878.1| h/ACA ribonucleoprotein complex subunit 1-like protein 1 [Zea mays] Back     alignment and taxonomy information
>gi|115486013|ref|NP_001068150.1| Os11g0579800 [Oryza sativa Japonica Group] gi|77551701|gb|ABA94498.1| H/ACA ribonucleoprotein complex subunit 1-like protein 1, putative, expressed [Oryza sativa Japonica Group] gi|113645372|dbj|BAF28513.1| Os11g0579800 [Oryza sativa Japonica Group] gi|125577612|gb|EAZ18834.1| hypothetical protein OsJ_34372 [Oryza sativa Japonica Group] gi|215768512|dbj|BAH00741.1| unnamed protein product [Oryza sativa Japonica Group] Back     alignment and taxonomy information
>gi|125534871|gb|EAY81419.1| hypothetical protein OsI_36586 [Oryza sativa Indica Group] Back     alignment and taxonomy information
>gi|255568916|ref|XP_002525428.1| H/ACA ribonucleoprotein complex subunit, putative [Ricinus communis] gi|223535241|gb|EEF36918.1| H/ACA ribonucleoprotein complex subunit, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|195610388|gb|ACG27024.1| h/ACA ribonucleoprotein complex subunit 1-like protein 1 [Zea mays] Back     alignment and taxonomy information
>gi|413925372|gb|AFW65304.1| putative H/ACA ribonucleoprotein complex subunit family protein [Zea mays] 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 ?
Query197
TAIR|locus:2079349202 AT3G03920 "AT3G03920" [Arabido 0.522 0.509 0.844 3.1e-44
TAIR|locus:2172329189 AT5G18180 "AT5G18180" [Arabido 0.507 0.529 0.83 6.6e-42
SGD|S000001131205 GAR1 "Protein component of the 0.492 0.473 0.628 2.6e-31
CGD|CAL0002072186 GAR1 [Candida albicans (taxid: 0.482 0.510 0.652 3.3e-31
UNIPROTKB|Q59TT0186 GAR1 "Putative uncharacterized 0.482 0.510 0.652 3.3e-31
POMBASE|SPBC20F10.01194 gar1 "snoRNP pseudouridylase b 0.487 0.494 0.614 4.2e-31
ASPGD|ASPL0000026673197 AN10712 [Emericella nidulans ( 0.487 0.487 0.625 5.4e-31
UNIPROTKB|F1MRF7210 GAR1 "Uncharacterized protein" 0.502 0.471 0.594 9.1e-29
UNIPROTKB|I3LVQ6210 LOC100516629 "Uncharacterized 0.502 0.471 0.594 9.1e-29
RGD|1563995226 Gar1 "GAR1 ribonucleoprotein h 0.502 0.438 0.594 1.2e-28
TAIR|locus:2079349 AT3G03920 "AT3G03920" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 466 (169.1 bits), Expect = 3.1e-44, P = 3.1e-44
 Identities = 87/103 (84%), Positives = 97/103 (94%)

Query:    44 EGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYF 103
             EGPP+EVVEV++F+HACEGDAVTKL+ EKIP+FNAPIYL+NKTQIGKVDEIFGPINES F
Sbjct:    52 EGPPSEVVEVATFVHACEGDAVTKLSQEKIPHFNAPIYLENKTQIGKVDEIFGPINESLF 111

Query:   104 SVKMMEGIVATSYSLGDKFYIDPSKLLPLARFLPQPKGQAQAG 146
             S+KMMEGIVATSYS GDKF+IDP KLLPLARFLPQPKGQ+  G
Sbjct:   112 SIKMMEGIVATSYSPGDKFFIDPYKLLPLARFLPQPKGQSTGG 154
GO:0003723 "RNA binding" evidence=ISS
GO:0005634 "nucleus" evidence=ISM
GO:0009982 "pseudouridine synthase activity" evidence=IEA
GO:0030515 "snoRNA binding" evidence=IEA
GO:0031120 "snRNA pseudouridine synthesis" evidence=IEA
GO:0042254 "ribosome biogenesis" evidence=IEA
GO:0009535 "chloroplast thylakoid membrane" evidence=IDA
GO:0005730 "nucleolus" evidence=IDA
GO:0005829 "cytosol" evidence=RCA
GO:0001510 "RNA methylation" evidence=RCA
GO:0006364 "rRNA processing" evidence=RCA
GO:0009909 "regulation of flower development" evidence=RCA
GO:0034968 "histone lysine methylation" evidence=RCA
GO:0042991 "transcription factor import into nucleus" evidence=RCA
TAIR|locus:2172329 AT5G18180 "AT5G18180" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
SGD|S000001131 GAR1 "Protein component of the H/ACA snoRNP pseudouridylase complex" [Saccharomyces cerevisiae (taxid:4932)] Back     alignment and assigned GO terms
CGD|CAL0002072 GAR1 [Candida albicans (taxid:5476)] Back     alignment and assigned GO terms
UNIPROTKB|Q59TT0 GAR1 "Putative uncharacterized protein GAR1" [Candida albicans SC5314 (taxid:237561)] Back     alignment and assigned GO terms
POMBASE|SPBC20F10.01 gar1 "snoRNP pseudouridylase box H/ACA snoRNP complex protein Gar1" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
ASPGD|ASPL0000026673 AN10712 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
UNIPROTKB|F1MRF7 GAR1 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|I3LVQ6 LOC100516629 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
RGD|1563995 Gar1 "GAR1 ribonucleoprotein homolog (yeast)" [Rattus norvegicus (taxid:10116)] 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) ?
Q8VZT0NLAL1_ARATHNo assigned EC number0.72250.77150.7524yesno

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 ?
Query197
pfam04410154 pfam04410, Gar1, Gar1/Naf1 RNA binding region 1e-35
COG327798 COG3277, GAR1, RNA-binding protein involved in rRN 1e-22
PTZ00146 293 PTZ00146, PTZ00146, fibrillarin; Provisional 3e-08
PTZ00146 293 PTZ00146, PTZ00146, fibrillarin; Provisional 2e-07
PTZ00146 293 PTZ00146, PTZ00146, fibrillarin; Provisional 1e-06
PTZ00146 293 PTZ00146, PTZ00146, fibrillarin; Provisional 4e-06
PTZ00146 293 PTZ00146, PTZ00146, fibrillarin; Provisional 7e-06
pfam05918543 pfam05918, API5, Apoptosis inhibitory protein 5 (A 9e-06
PTZ00146293 PTZ00146, PTZ00146, fibrillarin; Provisional 2e-05
PRK1314973 PRK13149, PRK13149, H/ACA RNA-protein complex comp 2e-05
pfam05918543 pfam05918, API5, Apoptosis inhibitory protein 5 (A 7e-05
PTZ00146293 PTZ00146, PTZ00146, fibrillarin; Provisional 1e-04
PTZ00146 293 PTZ00146, PTZ00146, fibrillarin; Provisional 3e-04
PTZ00146 293 PTZ00146, PTZ00146, fibrillarin; Provisional 4e-04
pfam05918543 pfam05918, API5, Apoptosis inhibitory protein 5 (A 4e-04
PRK11634629 PRK11634, PRK11634, ATP-dependent RNA helicase Dea 4e-04
PTZ00146293 PTZ00146, PTZ00146, fibrillarin; Provisional 5e-04
PRK10590456 PRK10590, PRK10590, ATP-dependent RNA helicase Rhl 5e-04
PTZ00146293 PTZ00146, PTZ00146, fibrillarin; Provisional 6e-04
PTZ00146293 PTZ00146, PTZ00146, fibrillarin; Provisional 6e-04
PTZ00146293 PTZ00146, PTZ00146, fibrillarin; Provisional 8e-04
PTZ00146 293 PTZ00146, PTZ00146, fibrillarin; Provisional 8e-04
pfam05918543 pfam05918, API5, Apoptosis inhibitory protein 5 (A 9e-04
PRK10590456 PRK10590, PRK10590, ATP-dependent RNA helicase Rhl 0.001
PTZ00146293 PTZ00146, PTZ00146, fibrillarin; Provisional 0.002
pfam05918543 pfam05918, API5, Apoptosis inhibitory protein 5 (A 0.002
pfam05091 517 pfam05091, eIF-3_zeta, Eukaryotic translation init 0.002
COG4371 334 COG4371, COG4371, Predicted membrane protein [Func 0.002
>gnl|CDD|190975 pfam04410, Gar1, Gar1/Naf1 RNA binding region Back     alignment and domain information 
 Score =  122 bits (308), Expect = 1e-35
 Identities = 57/157 (36%), Positives = 72/157 (45%), Gaps = 6/157 (3%)

Query: 27  GGGGRGGGGRGGFGFRDEGPPAEVVEVSSFLHACEGDAVTKLTN-EKIPYFNAPIYLQNK 85
             GG   G  GG      GPP E+ E+ +     E   V K TN EK+  F + + L++K
Sbjct: 1   NEGGGEEGPPGGPPDYTIGPPTEIEELGTISSVVENQVVIKSTNSEKVLDFGSILCLEDK 60

Query: 86  TQIGKVDEIFGPINESYFSVK-MMEGIVATSYSLGDKFYIDPSKLLPLARFLPQPKGQAQ 144
           T IGKVDEIFGP+N  ++SVK   EGI A S  +GDK Y  P    P  RFL QP  Q +
Sbjct: 61  TVIGKVDEIFGPVNNPFYSVKFSSEGIQAKSLKVGDKVYYVPD---PAQRFLTQPLKQQK 117

Query: 145 AG-ARGGRGGGGFRGRGGGRGGGRGRGGGGGGFRGRG 180
              A  G          G             G +G+ 
Sbjct: 118 GTDASNGHDEELPEEERGEFSDDEAEAEAKRGRKGKK 154

Gar1 is a small nucleolar RNP that is required for pre-mRNA processing and pseudouridylation. It is co-immunoprecipitated with the H/ACA families of snoRNAs. This family represents the conserved central region of Gar1. This region is necessary and sufficient for normal cell growth, and specifically binds two snoRNAs snR10 and snR30. This region is also necessary for nucleolar targeting, and it is thought that the protein is co-transported to the nucleolus as part of a nucleoprotein complex. In humans, Gar1 is also component of telomerase in vivo. Naf1 is an essentail protein that plays a role in ribosome biogenesis, modification of spliceosomal small nuclear RNAs and telomere synthesis, and is homologous to Gar1. Length = 154
>gnl|CDD|225816 COG3277, GAR1, RNA-binding protein involved in rRNA processing [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional Back     alignment and domain information
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional Back     alignment and domain information
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional Back     alignment and domain information
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional Back     alignment and domain information
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional Back     alignment and domain information
>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5) Back     alignment and domain information
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional Back     alignment and domain information
>gnl|CDD|183872 PRK13149, PRK13149, H/ACA RNA-protein complex component Gar1; Reviewed Back     alignment and domain information
>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5) Back     alignment and domain information
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional Back     alignment and domain information
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional Back     alignment and domain information
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional Back     alignment and domain information
>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5) Back     alignment and domain information
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional Back     alignment and domain information
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional Back     alignment and domain information
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional Back     alignment and domain information
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional Back     alignment and domain information
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional Back     alignment and domain information
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional Back     alignment and domain information
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional Back     alignment and domain information
>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5) Back     alignment and domain information
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional Back     alignment and domain information
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional Back     alignment and domain information
>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5) Back     alignment and domain information
>gnl|CDD|218425 pfam05091, eIF-3_zeta, Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) Back     alignment and domain information
>gnl|CDD|226808 COG4371, COG4371, Predicted membrane protein [Function unknown] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 197
KOG3262215 consensus H/ACA small nucleolar RNP component GAR1 100.0
COG327798 GAR1 RNA-binding protein involved in rRNA processi 99.9
PRK1314973 H/ACA RNA-protein complex component Gar1; Reviewed 99.89
PF04410154 Gar1: Gar1/Naf1 RNA binding region; InterPro: IPR0 99.86
KOG3262215 consensus H/ACA small nucleolar RNP component GAR1 98.81
KOG3428109 consensus Small nuclear ribonucleoprotein SMD1 and 98.5
KOG2236 483 consensus Uncharacterized conserved protein [Funct 98.3
PLN03134144 glycine-rich RNA-binding protein 4; Provisional 96.38
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 94.09
TIGR01661352 ELAV_HUD_SF ELAV/HuD family splicing factor. These 94.03
TIGR01648 578 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein 92.66
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 91.42
TIGR01659346 sex-lethal sex-lethal family splicing factor. This 91.34
TIGR01659346 sex-lethal sex-lethal family splicing factor. This 90.72
KOG3172119 consensus Small nuclear ribonucleoprotein Sm D3 [R 90.09
KOG3293134 consensus Small nuclear ribonucleoprotein (snRNP) 90.04
KOG0116419 consensus RasGAP SH3 binding protein rasputin, con 89.76
KOG0121153 consensus Nuclear cap-binding protein complex, sub 89.05
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 88.14
TIGR01649 481 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor 86.47
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 83.79
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 83.58
KOG0415479 consensus Predicted peptidyl prolyl cis-trans isom 83.37
TIGR01661 352 ELAV_HUD_SF ELAV/HuD family splicing factor. These 82.37
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information 
Probab=100.00  E-value=3.2e-53  Score=353.81  Aligned_cols=195  Identities=65%  Similarity=1.116  Sum_probs=139.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCC-CCCCCCCCCCcceEEeeceeeeccCceEecccccccCcc
Q 029223            1 MRPPRGGGGFRGGRDGGRGGRGG---GRFGGGGRGGGGRG-GFGFRDEGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYF   76 (197)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~gg~~gg~gg~-~~g~~~~gPPs~vl~lG~~sh~ce~dlV~K~~~~~VP~~   76 (197)
                      |+|||++++++++++ =+++.++   +.|.++..-+|+++ ++.++|+.||++|++|++|+|+||+|||||+++++||||
T Consensus         1 ~~~~rgggg~~g~~g-fRgg~ggg~~gg~rgg~g~grgg~~~~~~~d~gpp~evvelg~flh~Cegd~Vck~~~~kIPyf   79 (215)
T KOG3262|consen    1 GGGPRGGGGGGGGGG-FRGGGGGGRGGGFRGGNGFGRGGRGGRGFQDQGPPEEVVELGKFLHMCEGDLVCKLTNKKIPYF   79 (215)
T ss_pred             CCCCcCCCCCCCCCC-cccCCCCCCCCCcccCcccccCCcccCCcccCCCchhhhhhhhhhhhcCCceEEeeccccCCCC
Confidence            788998766655532 1221111   12222221123321 455789999999999999999999999999999999999


Q ss_pred             cceEEccCCeeeeeeeEEecccCCceeEEeecCCccccccccCcEEEEcCCCCCcCCccCCCCCCCCCC----------C
Q 029223           77 NAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYIDPSKLLPLARFLPQPKGQAQA----------G  146 (197)
Q Consensus        77 na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~d~v~a~s~~~GdklyIdp~klLPLdrflPkpk~~~g~----------g  146 (197)
                      ||||||||++|||||||||+|||++|+||||+|.|+|+||+++||||||++|||||++|||+|....+.          +
T Consensus        80 NAPIylenk~qIGKVDEIfG~i~d~~fsIK~~dgv~assfk~g~k~fi~p~KllPl~RFLP~p~~~kk~~~~~~~~~~~g  159 (215)
T KOG3262|consen   80 NAPIYLENKEQIGKVDEIFGPINDVHFSIKPSDGVQASSFKPGDKLFIDPDKLLPLDRFLPQPVGPKKPKGADRIKPGPG  159 (215)
T ss_pred             CCceeecchhhhcchhhhcccccccEEEEecCCCceeecccCCCeEEecccccCcHhhcCCCCCCCCCcccccccCCCCC
Confidence            999999999999999999999999999999999999999999999999999999999999987533211          2


Q ss_pred             CCCCCCC---CCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 029223          147 ARGGRGG---GGFRGRGG-GRGGGRGRGGGGGGFRGRGGPPRGGRGGGFRGRGRF  197 (197)
Q Consensus       147 grGggrg---~~~ggrgg-~~g~~~g~f~~~g~~~~~~~~~~g~~~~~~~~~~~~  197 (197)
                      +++++++   .++++.++ +|++.+++|++.++.++++-+ |++.+++|++++|.
T Consensus       160 g~gg~rGgRg~~rGg~~grGrgg~~Gg~rgggg~rGG~~~-Rgg~ggg~rgrgR~  213 (215)
T KOG3262|consen  160 GRGGGRGGRGGGRGGFGGRGRGGGGGGFRGGGGSRGGFRG-RGGHGGGFRGRGRG  213 (215)
T ss_pred             CCCcCcCCCCCCcCCCCCCCCCCCCCcccCCCCCCCCccc-cCCCCCCCCCCCCC
Confidence            2222222   11222111 122233455555444444333 78888888887763

>COG3277 GAR1 RNA-binding protein involved in rRNA processing [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed Back     alignment and domain information
>PF04410 Gar1: Gar1/Naf1 RNA binding region; InterPro: IPR007504 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs Back     alignment and domain information
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification] Back     alignment and domain information
>KOG2236 consensus Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>PLN03134 glycine-rich RNA-binding protein 4; Provisional Back     alignment and domain information
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor Back     alignment and domain information
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family Back     alignment and domain information
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>TIGR01659 sex-lethal sex-lethal family splicing factor Back     alignment and domain information
>TIGR01659 sex-lethal sex-lethal family splicing factor Back     alignment and domain information
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification] Back     alignment and domain information
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification] Back     alignment and domain information
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms] Back     alignment and domain information
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification] Back     alignment and domain information
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family Back     alignment and domain information
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor 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 ?
Query197
3u28_C114 Crystal Structure Of A Cbf5-Nop10-Gar1 Complex From 2e-31
>pdb|3U28|C Chain C, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex From Saccharomyces Cerevisiae Length = 114 Back     alignment and structure 
Iteration: 1

 Score =  131 bits (329), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 59/93 (63%), Positives = 73/93 (78%)
Query: 45  GPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFS 104
           GPP  V+E+ +FLH CEGD V +  N KIPYFNAPIYL+NKTQ+GKVDEI GP+NE +F+
Sbjct: 22  GPPDTVLEMGAFLHPCEGDIVCRSINTKIPYFNAPIYLENKTQVGKVDEILGPLNEVFFT 81
Query: 105 VKMMEGIVATSYSLGDKFYIDPSKLLPLARFLP 137
           +K  +G+ ATS+  GDKFYI   KLLP+ RFLP
Sbjct: 82  IKCGDGVQATSFKEGDKFYIAADKLLPIERFLP 114

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query197
3u28_C114 H/ACA ribonucleoprotein complex subunit 1; pseudou 100.0
2ey4_C82 Small nucleolar RNP similar to GAR1; trimeric comp 99.92
2hvy_B104 GAR1, small nucleolar RNP similar to GAR1; H/ACA R 99.91
2eqn_A103 Hypothetical protein LOC92345; NAF1 domain, hypoth 99.85
2v3m_A131 NAF1; ribosomal protein, GAR1, snoRNP, phosphoryla 99.81
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 97.48
1wez_A102 HnRNP H', FTP-3, heterogeneous nuclear ribonucleop 96.57
1h2v_Z156 20 kDa nuclear CAP binding protein; CAP-binding-co 96.23
3pgw_S 437 U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM 96.18
2dh8_A105 DAZ-associated protein 1; RRM domain, structural g 96.18
2lcw_A116 RNA-binding protein FUS; RRM, nucleic acid binding 95.14
1x4c_A108 Splicing factor, arginine/serine-rich 1; structura 96.03
2cqd_A116 RNA-binding region containing protein 1; RNA recog 95.83
2cq3_A103 RNA-binding protein 9; RRM domain, structural geno 95.76
1why_A97 Hypothetical protein riken cDNA 1810017N16; RNA re 95.74
2dnz_A95 Probable RNA-binding protein 23; RNA recognition m 95.7
3ex7_B126 RNA-binding protein 8A; protein-RNA complex, mRNA 95.64
1u6f_A139 Tcubp1, RNA-binding protein UBP1; trypanosome, mRN 95.63
1x4a_A109 Splicing factor, arginine/serine-rich 1 (splicing 95.59
2hgn_A139 Heterogeneous nuclear ribonucleoprotein F; RNA rec 95.53
2cq0_A103 Eukaryotic translation initiation factor 3 subunit 95.43
2dgv_A92 HnRNP M, heterogeneous nuclear ribonucleoprotein M 95.34
2dgw_A91 Probable RNA-binding protein 19; RRM domain, struc 95.31
1x5t_A96 Splicing factor 3B subunit 4; structure genomics, 95.3
2cq1_A101 PTB-like protein L; RRM domain, structural genomic 95.27
1wf0_A88 TDP-43, TAR DNA-binding protein-43; structural gen 95.27
2cqb_A102 Peptidyl-prolyl CIS-trans isomerase E; RNA recogni 95.21
1wex_A104 Hypothetical protein (riken cDNA 2810036L13); stru 95.17
2cpf_A98 RNA binding motif protein 19; RNA recognition moti 94.98
1sjq_A105 Polypyrimidine tract-binding protein 1; babbab mot 94.95
3r27_A100 HnRNP L, heterogeneous nuclear ribonucleoprotein L 94.95
2dgu_A103 Heterogeneous nuclear ribonucleoprotein Q; RRM dom 94.95
2d9p_A103 Polyadenylate-binding protein 3; RRM domain, struc 94.95
1x5s_A102 Cold-inducible RNA-binding protein; structure geno 94.91
2dgs_A99 DAZ-associated protein 1; RRM domain, structural g 94.89
2cpz_A115 CUG triplet repeat RNA-binding protein 1; RRM doma 94.88
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 94.73
2lxi_A91 RNA-binding protein 10; NMR {Homo sapiens} 94.72
2dnm_A103 SRP46 splicing factor; RRM domain, RBD, structural 94.67
2dng_A103 Eukaryotic translation initiation factor 4H; RRM d 94.66
4f25_A115 Polyadenylate-binding protein 1; RRM fold, transla 94.62
1whw_A99 Hypothetical protein riken cDNA 1200009A02; RNA re 94.61
2dhg_A104 TRNA selenocysteine associated protein (SECP43); R 94.55
2fc8_A102 NCL protein; structure genomics, RRM_1 domain, str 94.47
1x4b_A116 Heterogeneous nuclear ribonucleoproteins A2/B1; st 94.45
2do0_A114 HnRNP M, heterogeneous nuclear ribonucleoprotein M 94.41
2hgl_A136 HNRPF protein, heterogeneous nuclear ribonucleopro 94.41
2cpy_A114 RNA-binding protein 12; RRM domain, structural gen 94.4
2ad9_A119 Polypyrimidine tract-binding protein 1; RBD, RRM, 94.37
2dgt_A92 RNA-binding protein 30; RRM domain, structural gen 94.37
2div_A99 TRNA selenocysteine associated protein; structural 94.32
1x4h_A111 RNA-binding protein 28; structural genomics, RRM d 94.31
3bs9_A87 Nucleolysin TIA-1 isoform P40; RNA recognition mot 94.22
1x4d_A102 Matrin 3; structural genomics, RRM domain, NPPSFA, 94.22
2cqi_A103 Nucleolysin TIAR; RNA recognition motif, RRM, RNA 94.14
2cqg_A103 TDP-43, TAR DNA-binding protein-43; RNA recognitio 94.1
2dnq_A90 RNA-binding protein 4B; RRM domain,RBD, structural 94.1
2cpj_A99 Non-POU domain-containing octamer-binding protein; 93.98
2fc9_A101 NCL protein; structure genomics, RRM_1 domain, str 93.97
2do4_A100 Squamous cell carcinoma antigen recognized by T- c 93.91
2cpx_A115 Hypothetical protein FLJ11016; RRM domain, structu 93.9
1x4f_A112 Matrin 3; structural genomics, RRM domain, NPPSFA, 93.88
1wi8_A104 EIF-4B, eukaryotic translation initiation factor 4 93.83
2cqp_A98 RNA-binding protein 12; RNA recognition motif, RRM 93.8
2dnh_A105 Bruno-like 5, RNA binding protein; RRM domain, RBD 93.78
1wel_A124 RNA-binding protein 12; structural genomics, NPPSF 93.74
2dgo_A115 Cytotoxic granule-associated RNA binding protein 1 93.67
2cph_A107 RNA binding motif protein 19; RNA recognition moti 93.53
2kxn_B129 Transformer-2 protein homolog beta; SR protein, RR 93.33
2cpi_A111 CCR4-NOT transcription complex subunit 4; RNA reco 93.28
3d2w_A89 TAR DNA-binding protein 43; DP-43 proteinopathy, T 93.26
1x5u_A105 Splicing factor 3B subunit 4 (spliceosome associat 93.22
2err_A109 Ataxin-2-binding protein 1; protein-RNA complex, R 93.19
2dnp_A90 RNA-binding protein 14; RRM domain, RBD, structura 93.19
3s8s_A110 Histone-lysine N-methyltransferase SETD1A; chromat 93.06
2rs2_A109 Musashi-1, RNA-binding protein musashi homolog 1; 93.03
2cpe_A113 RNA-binding protein EWS; RNA recognition motif, RR 92.97
2ek1_A95 RNA-binding protein 12; RNA recognition motif, dim 92.94
1x4g_A109 Nucleolysin TIAR; structural genomics, RRM domain, 92.89
1p27_B106 RNA-binding protein 8A; nuclear protein, mRNA spli 92.84
2dgx_A96 KIAA0430 protein; RRM domain, structural genomics, 92.79
2db1_A118 Heterogeneous nuclear ribonucleoprotein F; RRM dom 92.59
1wg5_A104 Heterogeneous nuclear ribonucleoprotein H; structu 92.17
2dis_A109 Unnamed protein product; structural genomics, RRM 92.16
2j76_E100 EIF-4B, EIF4B, eukaryotic translation initiation f 92.14
2dgp_A106 Bruno-like 4, RNA binding protein; RRM domain, str 92.1
2m2b_A131 RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio 92.06
2kvi_A96 Nuclear polyadenylated RNA-binding protein 3; RNA- 92.03
2hgm_A126 HNRPF protein, heterogeneous nuclear ribonucleopro 91.97
1fjc_A96 Nucleolin RBD2, protein C23; RNP, RRM, RNA binding 91.94
2xs2_A102 Deleted in azoospermia-like; RNA binding protein-R 91.85
2x1f_A96 MRNA 3'-END-processing protein RNA15; transcriptio 91.82
3beg_B115 Splicing factor, arginine/serine-rich 1; kinase, S 91.76
1wf1_A110 RNA-binding protein RALY; structural genomics, RRM 91.71
2cpd_A99 Apobec-1 stimulating protein; RNA recognition moti 91.69
2lkz_A95 RNA-binding protein 5; RRM; NMR {Homo sapiens} 91.68
2e5i_A124 Heterogeneous nuclear ribonucleoprotein L-like; RR 91.63
1rk8_A165 CG8781-PA, CG8781-PA protein; mRNA processing, RRM 91.41
2cqh_A93 IGF-II mRNA-binding protein 2 isoform A; RNA recog 91.22
2f3j_A177 RNA and export factor binding protein 2; RRM domai 91.2
2e5g_A94 U6 snRNA-specific terminal uridylyltransferase 1; 91.15
2jrs_A108 RNA-binding protein 39; RNA binding motif of RBM39 90.91
2e5h_A94 Zinc finger CCHC-type and RNA-binding motif- conta 90.88
2la4_A101 Nuclear and cytoplasmic polyadenylated RNA-bindin 90.85
1oo0_B110 CG8781-PA, drosophila Y14; RNA recognition motif, 90.77
3s7r_A87 Heterogeneous nuclear ribonucleoprotein A/B; ferre 90.69
2dha_A123 FLJ20171 protein; RRM domain, structural genomics, 90.43
1l3k_A196 Heterogeneous nuclear ribonucleoprotein A1; nuclea 90.32
2lea_A135 Serine/arginine-rich splicing factor 2; SR protein 90.08
2jvo_A108 Nucleolar protein 3; nucleus, phosphorylation, rib 89.93
2e44_A96 Insulin-like growth factor 2 mRNA binding protein 89.92
2fy1_A116 RNA-binding motif protein, Y chromosome, family 1 89.87
2ytc_A85 PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s 89.83
1fj7_A101 Nucleolin RBD1, protein C23; RNP, RRM, RNA binding 89.63
3zzy_A130 Polypyrimidine tract-binding protein 1; protein bi 89.61
2e5j_A97 Methenyltetrahydrofolate synthetase domain contain 89.48
1x5p_A97 Negative elongation factor E; structure genomics, 89.14
2ku7_A140 MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio 89.05
4a8x_A88 RNA-binding protein with serine-rich domain 1; tra 89.01
2khc_A118 Testis-specific RNP-type RNA binding protein; RRM, 88.87
3md1_A83 Nuclear and cytoplasmic polyadenylated RNA-bindin 88.85
2i2y_A150 Fusion protein consists of immunoglobin G- binding 88.85
1l3k_A196 Heterogeneous nuclear ribonucleoprotein A1; nuclea 88.54
2lmi_A107 GRSF-1, G-rich sequence factor 1; G-rich RNA seque 88.44
3q2s_C229 Cleavage and polyadenylation specificity factor S; 88.39
2cqc_A95 Arginine/serine-rich splicing factor 10; RNA recog 88.32
2yh0_A198 Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli 88.17
3ucg_A89 Polyadenylate-binding protein 2; ferredoxin-like, 87.98
2ywk_A95 Putative RNA-binding protein 11; RRM-domain, struc 87.98
3egn_A143 RNA-binding protein 40; RNA recognition motif (RRM 87.96
2qfj_A216 FBP-interacting repressor; protein-DNA complex; HE 87.63
2cq2_A114 Hypothetical protein LOC91801; RRM domain, structu 87.47
3p5t_L90 Cleavage and polyadenylation specificity factor S; 87.19
2hzc_A87 Splicing factor U2AF 65 kDa subunit; RNA splicing, 87.15
4f02_A213 Polyadenylate-binding protein 1; mRNA, eukaryotic 87.13
2jwn_A124 Embryonic polyadenylate-binding protein 2-B; epabp 87.07
1x4e_A85 RNA binding motif, single-stranded interacting pro 87.0
2diu_A96 KIAA0430 protein; structural genomics, RRM domain, 86.93
1nu4_A97 U1A RNA binding domain; RNA recognition motif, U1 86.9
2xnq_A97 Nuclear polyadenylated RNA-binding protein 3; tran 86.76
3tyt_A205 Heterogeneous nuclear ribonucleoprotein L; ferredo 86.76
2cjk_A167 Nuclear polyadenylated RNA-binding protein 4; HRP1 86.72
1x5o_A114 RNA binding motif, single-stranded interacting pro 85.17
2kt5_A124 RNA and export factor-binding protein 2; chaperone 84.49
2jvr_A111 Nucleolar protein 3; RNA recognition motif, nucleu 84.39
2hvz_A101 Splicing factor, arginine/serine-rich 7; RRM, RNA 84.34
1sjr_A164 Polypyrimidine tract-binding protein 1; extended b 84.3
1p1t_A104 Cleavage stimulation factor, 64 kDa subunit; RNA r 84.08
2la6_A99 RNA-binding protein FUS; structural genomics, nort 83.97
2dnn_A109 RNA-binding protein 12; RRM domain, RBD, structura 83.89
2kn4_A158 Immunoglobulin G-binding protein G, splicing FACT 83.83
4fxv_A99 ELAV-like protein 1; RNA recognition motif, putati 83.72
2nlw_A105 Eukaryotic translation initiation factor 3 subunit 83.58
4f02_A213 Polyadenylate-binding protein 1; mRNA, eukaryotic 83.41
3pgw_A282 U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c 83.23
2dit_A112 HIV TAT specific factor 1 variant; structural geno 83.17
2ki2_A90 SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA 83.06
1fje_B175 Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin 82.94
2yh0_A198 Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli 82.38
3n9u_C156 Cleavage and polyadenylation specificity factor S; 82.21
3lqv_A115 PRE-mRNA branch site protein P14; cysless mutant, 81.52
1uaw_A77 Mouse-musashi-1; RNP-type structure, RNA binding p 80.78
>3u28_C H/ACA ribonucleoprotein complex subunit 1; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_C Back     alignment and structure
Probab=100.00  E-value=1.2e-40  Score=258.47  Aligned_cols=97  Identities=61%  Similarity=1.090  Sum_probs=91.0

Q ss_pred             CCCCCCCcceEEeeceeeeccCceEecccccccCcccceEEccCCeeeeeeeEEecccCCceeEEeecCCccccccccCc
Q 029223           41 FRDEGPPAEVVEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGD  120 (197)
Q Consensus        41 ~~~~gPPs~vl~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~d~v~a~s~~~Gd  120 (197)
                      ++|++||++|++||+|+|+|+++||||+++++||||||+||+||+++||||+|||||||++|+|||++++++|+||+++|
T Consensus        18 ~~~~gpp~~v~elG~f~H~ceg~lV~k~~~~~VP~fNapVy~enK~~IGKVdEIFGPin~~YfsVK~~~gv~a~Sfk~gd   97 (114)
T 3u28_C           18 GSHMGPPDTVLEMGAFLHPCEGDIVCRSINTKIPYFNAPIYLENKTQVGKVDEILGPLNEVFFTIKCGDGVQATSFKEGD   97 (114)
T ss_dssp             -----CCSCEEEEEEEEEEETTEEEEEECSSSEECTTCEEECTTCCEEEEEEEEESBTTSCEEEEEECTTCCGGGCCTTC
T ss_pred             CCCCCCCHHHheeeeEEEEeCCeEEEEeCCCCCCCCCCEeEccCCccceeEeEEeCCCCccEEEEEecCCCcccccccCC
Confidence            56999999999999999999999999999889999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCCCcCCccCC
Q 029223          121 KFYIDPSKLLPLARFLP  137 (197)
Q Consensus       121 klyIdp~klLPLdrflP  137 (197)
                      ++||+++|||||+||||
T Consensus        98 k~YId~~kllPl~rFlp  114 (114)
T 3u28_C           98 KFYIAADKLLPIERFLP  114 (114)
T ss_dssp             EEEEEGGGEECGGGGCC
T ss_pred             EEEECccccCcHHhcCC
Confidence            99999999999999997
>2ey4_C Small nucleolar RNP similar to GAR1; trimeric complex, structural genomics, PSI, protein structur initiative; 2.11A {Pyrococcus furiosus} SCOP: b.43.3.5 PDB: 3mqk_C 2rfk_C Back     alignment and structure
>2hvy_B GAR1, small nucleolar RNP similar to GAR1; H/ACA RNA, RNP, pseudouridine synthase, guide RNA, isomerase biosynthetic protein-RNA complex; HET: ATP; 2.30A {Pyrococcus furiosus} SCOP: b.43.3.5 PDB: 3hay_B* Back     alignment and structure
>2eqn_A Hypothetical protein LOC92345; NAF1 domain, hypothetical protein BC008207 [HOMO sapiens], structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2v3m_A NAF1; ribosomal protein, GAR1, snoRNP, phosphorylation, hypothetical protein; 2.74A {Saccharomyces cerevisiae} Back     alignment and structure
>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A Back     alignment and structure
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Back     alignment and structure
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Back     alignment and structure
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Back     alignment and structure
>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Back     alignment and structure
>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Back     alignment and structure
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Back     alignment and structure
>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Back     alignment and structure
>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Back     alignment and structure
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Back     alignment and structure
>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Back     alignment and structure
>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D Back     alignment and structure
>2lxi_A RNA-binding protein 10; NMR {Homo sapiens} Back     alignment and structure
>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Back     alignment and structure
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Back     alignment and structure
>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Back     alignment and structure
>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Back     alignment and structure
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Back     alignment and structure
>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Back     alignment and structure
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Back     alignment and structure
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Back     alignment and structure
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Back     alignment and structure
>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Back     alignment and structure
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Back     alignment and structure
>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Back     alignment and structure
>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Back     alignment and structure
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Back     alignment and structure
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Back     alignment and structure
>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens} Back     alignment and structure
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Back     alignment and structure
>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Back     alignment and structure
>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Back     alignment and structure
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Back     alignment and structure
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Back     alignment and structure
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Back     alignment and structure
>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Back     alignment and structure
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Back     alignment and structure
>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Back     alignment and structure
>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Back     alignment and structure
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Back     alignment and structure
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Back     alignment and structure
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Back     alignment and structure
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Back     alignment and structure
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Back     alignment and structure
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Back     alignment and structure
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Back     alignment and structure
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Back     alignment and structure
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Back     alignment and structure
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Back     alignment and structure
>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Back     alignment and structure
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Back     alignment and structure
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0 Back     alignment and structure
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Back     alignment and structure
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Back     alignment and structure
>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Back     alignment and structure
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Back     alignment and structure
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Back     alignment and structure
>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Back     alignment and structure
>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Back     alignment and structure
>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Back     alignment and structure
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Back     alignment and structure
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Back     alignment and structure
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Back     alignment and structure
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Back     alignment and structure
>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Back     alignment and structure
>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Back     alignment and structure
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Back     alignment and structure
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Back     alignment and structure
>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Back     alignment and structure
>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Back     alignment and structure
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Back     alignment and structure
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Back     alignment and structure
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Back     alignment and structure
>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Back     alignment and structure
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Back     alignment and structure
>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens} Back     alignment and structure
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Back     alignment and structure
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Back     alignment and structure
>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Back     alignment and structure
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Back     alignment and structure
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Back     alignment and structure
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Back     alignment and structure
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Back     alignment and structure
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Back     alignment and structure
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B Back     alignment and structure
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 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 197
d2ey4c173 b.43.3.5 (C:1-73) Gar1 homolog PF1791 {Archaeon Py 1e-21
>d2ey4c1 b.43.3.5 (C:1-73) Gar1 homolog PF1791 {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 73 Back     information, alignment and structure

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Gar1-like SnoRNP
domain: Gar1 homolog PF1791
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 82.1 bits (203), Expect = 1e-21
 Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 3/74 (4%)

Query: 52  EVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGI 111
            +   LH  +   +   TN  +P  N  +  +    +G V ++FGP+   Y ++K     
Sbjct: 3   RLGKVLHYAKQGFLIVRTN-WVPSLNDRVVDKRLQFVGIVKDVFGPVKMPYVAIKPKVSN 61

Query: 112 VATSYSLGDKFYID 125
                 +G+  Y+D
Sbjct: 62  PEI--YVGEVLYVD 73

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query197
d2ey4c173 Gar1 homolog PF1791 {Archaeon Pyrococcus furiosus 99.74
d1weza_102 Heterogeneous nuclear ribonucleoprotein H' {Human 96.63
d2adca288 Polypyrimidine tract-binding protein {Human (Homo 96.33
d1wf0a_88 TAR DNA-binding protein 43, TDP-43 {Human (Homo sa 96.33
d2cpza1102 CUG triplet repeat RNA-binding protein 1 {Human (H 95.93
d2cq3a193 RNA-binding protein 9 {Human (Homo sapiens) [TaxId 95.83
d1wg5a_104 Heterogeneous nuclear ribonucleoprotein H' {Human 95.68
d2b0ga183 Splicesomal U1A protein {Drosophila melanogaster [ 95.48
d1whya_97 Putative RNA-binding protein 15B, Rbm15b {Mouse (M 95.35
d2cqia190 Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960 95.35
d1cvja289 Poly(A)-binding protein {Human (Homo sapiens) [Tax 94.87
d2cq1a188 Polypyrimidine tract-binding protein 2, PTBP2 {Hum 94.73
d1wexa_104 Heterogeneous nuclear ribonucleoprotein L-like {Mo 94.69
d1u6fa1139 RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId 94.52
d1whwa_99 Probable RNA-binding protein 19, Rbm19 {Mouse (Mus 94.46
d2cqca183 Arginine/serine-rich splicing factor 10 {Human (Ho 94.43
d1x4ha198 RNA-binding protein 28 {Mouse (Mus musculus) [TaxI 94.3
d2cqba189 Peptidyl-prolyl cis-trans isomerase E, N-terminal 94.08
d1wi8a_104 Eukaryotic translation initiation factor 4B {Human 94.03
d1fjca_96 Nucleolin {Golden hamster (Mesocricetus auratus) [ 93.95
d1x5ua193 Splicing factor 3B subunit 4 {Human (Homo sapiens) 93.79
d2cpxa1102 RNA-binding protein 41, RBM41 {Human (Homo sapiens 93.78
d1x4ga196 Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960 93.72
d1h2vz_93 CBP20, 20KDa nuclear cap-binding protein {Human (H 93.62
d1rk8a_88 RNA-binding protein 8 {Fruit fly (Drosophila melan 93.6
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 93.54
d2cqda1103 RNA-binding region containing protein 1 {Human (Ho 93.52
d2adba1108 Polypyrimidine tract-binding protein {Human (Homo 93.2
d2cqga190 TAR DNA-binding protein 43, TDP-43 {Human (Homo sa 92.88
d1x4fa199 Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} 92.12
d1u2fa_90 Splicing factor U2AF 65 KDa subunit {Human (Homo s 92.04
d2cq0a190 Eukaryotic translation initiation factor 3 subunit 91.91
d1x4ba1103 Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu 91.7
d2cpea1101 RNA-binding protein EWS {Human (Homo sapiens) [Tax 91.65
d1wf2a_98 Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu 91.48
d2u2fa_85 Splicing factor U2AF 65 KDa subunit {Human (Homo s 91.44
d2cpda186 APOBEC1 stimulating protein {Human (Homo sapiens) 91.32
d2ghpa275 U4/U6 snRNA-associated-splicing factor PRP24 {Bake 91.18
d2cpja186 Non-POU domain-containing octamer-binding protein, 90.46
d2ghpa386 U4/U6 snRNA-associated-splicing factor PRP24 {Bake 90.35
d2cpya1103 RNA-binding protein 12 {Human (Homo sapiens) [TaxI 90.31
d1x4aa195 Splicing factor, arginine/serine-rich 1, SFRS1 {Hu 89.87
d1wela1112 RNA-binding protein 12 {Human (Homo sapiens) [TaxI 89.86
d1b7fa182 Sex-lethal protein {Drosophila melanogaster [TaxId 89.23
d2cpha194 Probable RNA-binding protein 19, Rbm19 {Mouse (Mus 89.07
d1fxla182 Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9 89.01
d2cqpa186 RNA-binding protein 12 {Mouse (Mus musculus) [TaxI 88.69
d2cpfa185 Probable RNA-binding protein 19, Rbm19 {Mouse (Mus 88.49
d1x5ta183 Splicing factor 3B subunit 4 {Human (Homo sapiens) 88.47
d1l3ka184 Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human 87.86
d1nu4a_91 Splicesomal U1A protein {Human (Homo sapiens) [Tax 87.38
d1l3ka279 Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human 87.28
d2ghpa181 U4/U6 snRNA-associated-splicing factor PRP24 {Bake 87.15
d1x4da189 Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} 86.62
d1cvja180 Poly(A)-binding protein {Human (Homo sapiens) [Tax 86.51
d1u1qa_183 Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human 86.35
d1x5sa190 Cold-inducible RNA-binding protein {Human (Homo sa 85.38
d1x5oa1101 RNA-binding motif, single-stranded-interacting pro 85.28
d1uawa_77 Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} 85.0
d2cq4a1101 RNA binding protein 23 {Human (Homo sapiens) [TaxI 84.92
d1wg4a_98 Splicing factor, arginine/serine-rich 9 (SFRS9) {M 84.5
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 83.93
d2f9da1114 Pre-mRNA branch site protein p14 {Human (Homo sapi 83.16
d2msta_75 Neural RNA-binding protein Musashi-1 {Mouse (Mus m 83.06
d1p1ta_104 Cleavage stimulation factor, 64 kda subunit {Human 82.87
d1fjeb191 Nucleolin {Golden hamster (Mesocricetus auratus) [ 82.68
d2cqha180 IGF-II mRNA-binding protein 2 isoform A {Human (Ho 81.17
d2f1la175 16S rRNA processing protein RimM, C-terminal domai 81.05
d1hd0a_75 Heterogeneous nuclear ribonucleoprotein d0 {Human 80.97
>d2ey4c1 b.43.3.5 (C:1-73) Gar1 homolog PF1791 {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Gar1-like SnoRNP
domain: Gar1 homolog PF1791
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=99.74  E-value=1.5e-18  Score=123.56  Aligned_cols=72  Identities=21%  Similarity=0.389  Sum_probs=63.5

Q ss_pred             EEeeceeeeccCceEecccccccCcccceEEccCCeeeeeeeEEecccCCceeEEeecCCccccccccCcEEEEc
Q 029223           51 VEVSSFLHACEGDAVTKLTNEKIPYFNAPIYLQNKTQIGKVDEIFGPINESYFSVKMMEGIVATSYSLGDKFYID  125 (197)
Q Consensus        51 l~lG~~sh~ce~dlV~K~~~~~VP~~na~V~~knkt~IGkV~EIFGpIn~~Y~sVK~~d~v~a~s~~~GdklyId  125 (197)
                      ..||+++|.|++.+|+... +++|++|+.|++++++.||+|+|||||+++||++||+.+...+.  ++++++|||
T Consensus         2 k~lG~i~hi~~~~~vI~~~-~~~p~~~~~v~~~~~~~iG~v~evfGpv~~P~~~v~~~~~~~~~--~vG~kvYvd   73 (73)
T d2ey4c1           2 KRLGKVLHYAKQGFLIVRT-NWVPSLNDRVVDKRLQFVGIVKDVFGPVKMPYVAIKPKVSNPEI--YVGEVLYVD   73 (73)
T ss_dssp             BCCCCEEEEETTTEEEEEC-SSCCCTTCEEECTTCCCCEEEEEEEEESSSCEEEEEECSSSCST--TBTCCCEEC
T ss_pred             cEeEEEEEEcCCceEEEEC-CCCCCCCCEeECcCCcEEEEEEEEECCCCCcEEEEEECCCChhH--hCCCeEEeC
Confidence            4689999999998777654 57999999999999999999999999999999999997765543  469999997
>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Back     information, alignment and structure
>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Back     information, alignment and structure
>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Back     information, alignment and structure
>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2f1la1 b.41.1.4 (A:101-175) 16S rRNA processing protein RimM, C-terminal domain {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure