Citrus Sinensis ID: 034651

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--------
MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK
ccccccccEEEccHHHHHHHHcccccEEEEEEEcccEEEEEEEEEEccccEEEEEEEEEEEEccccEEEEcEEEEEcccEEEEEEccc
cccccEEEEEccHHHHHHHHHHcccEEEEEEEEcccEEEEEEEEccHHHHHEEHHccEEEcccccccccccEEEEccccEEEEEEccc
MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLddaeevhikkntrkplgrillkgdnITLMMNTGK
mastkvqrimtqpINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEvhikkntrkplgrillkgdnitlmmntgk
MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK
*******RIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITL******
***********QPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVH*****RKPLGRILLKGDNITLMMNT**
MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK
***TKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNT**
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooo
iiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMNTGK
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 ?
Query88 2.2.26 [Sep-21-2011]
Q7ZUG092 Small nuclear ribonucleop yes no 0.897 0.858 0.746 4e-31
A1XQR992 Small nuclear ribonucleop yes no 0.965 0.923 0.682 1e-30
P6230592 Small nuclear ribonucleop yes no 0.943 0.902 0.698 2e-30
P6230492 Small nuclear ribonucleop yes no 0.943 0.902 0.698 2e-30
P6230392 Small nuclear ribonucleop yes no 0.943 0.902 0.698 2e-30
A4FUI292 Small nuclear ribonucleop yes no 0.943 0.902 0.698 2e-30
Q9VLV594 Probable small nuclear ri yes no 0.977 0.914 0.651 2e-29
A8XDT090 Probable small nuclear ri N/A no 0.943 0.922 0.602 2e-25
Q9XTU690 Probable small nuclear ri yes no 0.943 0.922 0.590 8e-25
Q9USZ384 Small nuclear ribonucleop yes no 0.909 0.952 0.604 9e-22
>sp|Q7ZUG0|RUXE_DANRE Small nuclear ribonucleoprotein E OS=Danio rerio GN=snrpe PE=3 SV=1 Back     alignment and function desciption
 Score =  132 bits (333), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 59/79 (74%), Positives = 72/79 (91%)

Query: 5  KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
          KVQ++M QPINLIFR+LQ+++RI +WL+EQ ++RIEG IIGFDEYMNLVLDDAEEVH+K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRISVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEVHMKT 68

Query: 65 NTRKPLGRILLKGDNITLM 83
            RKPLGRI+LKGDNITL+
Sbjct: 69 KNRKPLGRIMLKGDNITLL 87
Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5.
Danio rerio (taxid: 7955)
>sp|A1XQR9|RUXE_PIG Small nuclear ribonucleoprotein E OS=Sus scrofa GN=SNRPE PE=3 SV=1 Back     alignment and function description
>sp|P62305|RUXE_MOUSE Small nuclear ribonucleoprotein E OS=Mus musculus GN=Snrpe PE=2 SV=1 Back     alignment and function description
>sp|P62304|RUXE_HUMAN Small nuclear ribonucleoprotein E OS=Homo sapiens GN=SNRPE PE=1 SV=1 Back     alignment and function description
>sp|P62303|RUXE_CHICK Small nuclear ribonucleoprotein E OS=Gallus gallus GN=SNRPE PE=3 SV=1 Back     alignment and function description
>sp|A4FUI2|RUXE_BOVIN Small nuclear ribonucleoprotein E OS=Bos taurus GN=SNRPE PE=3 SV=1 Back     alignment and function description
>sp|Q9VLV5|RUXE_DROME Probable small nuclear ribonucleoprotein E OS=Drosophila melanogaster GN=SmE PE=3 SV=1 Back     alignment and function description
>sp|A8XDT0|RUXE_CAEBR Probable small nuclear ribonucleoprotein E OS=Caenorhabditis briggsae GN=snr-6 PE=3 SV=1 Back     alignment and function description
>sp|Q9XTU6|RUXE_CAEEL Probable small nuclear ribonucleoprotein E OS=Caenorhabditis elegans GN=snr-6 PE=3 SV=1 Back     alignment and function description
>sp|Q9USZ3|RUXE_SCHPO Small nuclear ribonucleoprotein E OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=sme1 PE=1 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 ?
Query88
1522421788 putative small nuclear ribonucleoprotein 1.0 1.0 0.965 1e-41
24205160188 hypothetical protein SORBIDRAFT_03g00195 1.0 1.0 0.954 2e-41
35714504088 PREDICTED: small nuclear ribonucleoprote 1.0 1.0 0.943 4e-41
22545595688 PREDICTED: small nuclear ribonucleoprote 1.0 1.0 0.943 5e-41
31358649588 small nuclear ribonucleoprotein E [Hevea 1.0 1.0 0.954 5e-41
35714613288 PREDICTED: small nuclear ribonucleoprote 1.0 1.0 0.943 5e-41
28284821688 small nuclear ribonucleoprotein polypept 1.0 1.0 0.943 8e-41
19560689688 small nuclear ribonucleoprotein E [Zea m 1.0 1.0 0.931 8e-41
19563870888 small nuclear ribonucleoprotein E [Zea m 1.0 1.0 0.931 1e-40
35654776688 PREDICTED: small nuclear ribonucleoprote 1.0 1.0 0.943 1e-40
>gi|15224217|ref|NP_179464.1| putative small nuclear ribonucleoprotein [Arabidopsis thaliana] gi|297836770|ref|XP_002886267.1| hypothetical protein ARALYDRAFT_900374 [Arabidopsis lyrata subsp. lyrata] gi|4185140|gb|AAD08943.1| putative small nuclear ribonucleoprotein E [Arabidopsis thaliana] gi|21592486|gb|AAM64436.1| putative small nuclear ribonucleoprotein E [Arabidopsis thaliana] gi|26452632|dbj|BAC43399.1| putative small nuclear ribonucleoprotein E [Arabidopsis thaliana] gi|28973515|gb|AAO64082.1| putative small nuclear ribonucleoprotein E [Arabidopsis thaliana] gi|297332107|gb|EFH62526.1| hypothetical protein ARALYDRAFT_900374 [Arabidopsis lyrata subsp. lyrata] gi|330251706|gb|AEC06800.1| putative small nuclear ribonucleoprotein [Arabidopsis thaliana] Back     alignment and taxonomy information
 Score =  173 bits (439), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 85/88 (96%), Positives = 86/88 (97%)

Query: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
          MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRI GFDEYMNLVLD+AEEV
Sbjct: 1  MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRITGFDEYMNLVLDEAEEV 60

Query: 61 HIKKNTRKPLGRILLKGDNITLMMNTGK 88
           IKKNTRKPLGRILLKGDNITLMMNTGK
Sbjct: 61 SIKKNTRKPLGRILLKGDNITLMMNTGK 88

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|242051601|ref|XP_002454946.1| hypothetical protein SORBIDRAFT_03g001950 [Sorghum bicolor] gi|241926921|gb|EES00066.1| hypothetical protein SORBIDRAFT_03g001950 [Sorghum bicolor] Back     alignment and taxonomy information
>gi|357145040|ref|XP_003573502.1| PREDICTED: small nuclear ribonucleoprotein E-like [Brachypodium distachyon] Back     alignment and taxonomy information
>gi|225455956|ref|XP_002278114.1| PREDICTED: small nuclear ribonucleoprotein E [Vitis vinifera] gi|297734216|emb|CBI15463.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|313586495|gb|ADR71258.1| small nuclear ribonucleoprotein E [Hevea brasiliensis] Back     alignment and taxonomy information
>gi|357146132|ref|XP_003573886.1| PREDICTED: small nuclear ribonucleoprotein E-like [Brachypodium distachyon] Back     alignment and taxonomy information
>gi|282848216|gb|ADB02889.1| small nuclear ribonucleoprotein polypeptide [Jatropha curcas] Back     alignment and taxonomy information
>gi|195606896|gb|ACG25278.1| small nuclear ribonucleoprotein E [Zea mays] gi|195611048|gb|ACG27354.1| small nuclear ribonucleoprotein E [Zea mays] gi|413947730|gb|AFW80379.1| small nuclear ribonucleoprotein E [Zea mays] Back     alignment and taxonomy information
>gi|195638708|gb|ACG38822.1| small nuclear ribonucleoprotein E [Zea mays] gi|223945527|gb|ACN26847.1| unknown [Zea mays] gi|414875728|tpg|DAA52859.1| TPA: Small nuclear ribonucleoprotein E isoform 1 [Zea mays] gi|414875729|tpg|DAA52860.1| TPA: Small nuclear ribonucleoprotein E isoform 2 [Zea mays] Back     alignment and taxonomy information
>gi|356547766|ref|XP_003542280.1| PREDICTED: small nuclear ribonucleoprotein E-like [Glycine max] gi|255627911|gb|ACU14300.1| unknown [Glycine max] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query88
TAIR|locus:205398988 AT2G18740 "AT2G18740" [Arabido 1.0 1.0 0.965 4.2e-40
TAIR|locus:211878188 AT4G30330 "AT4G30330" [Arabido 1.0 1.0 0.943 6.1e-39
ZFIN|ZDB-GENE-040426-111292 snrpe "small nuclear ribonucle 0.920 0.880 0.728 3.4e-29
UNIPROTKB|P6230392 SNRPE "Small nuclear ribonucle 0.920 0.880 0.716 1.5e-28
UNIPROTKB|A4FUI292 SNRPE "Small nuclear ribonucle 0.920 0.880 0.716 1.5e-28
UNIPROTKB|P6230492 SNRPE "Small nuclear ribonucle 0.920 0.880 0.716 1.5e-28
UNIPROTKB|A1XQR992 SNRPE "Small nuclear ribonucle 0.920 0.880 0.716 1.5e-28
UNIPROTKB|I3LDW992 SNRPE "Small nuclear ribonucle 0.920 0.880 0.716 1.5e-28
MGI|MGI:9834692 Snrpe "small nuclear ribonucle 0.920 0.880 0.716 1.5e-28
RGD|232167592 Snrpe "small nuclear ribonucle 0.920 0.880 0.716 1.5e-28
TAIR|locus:2053989 AT2G18740 "AT2G18740" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 427 (155.4 bits), Expect = 4.2e-40, P = 4.2e-40
 Identities = 85/88 (96%), Positives = 86/88 (97%)

Query:     1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEV 60
             MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRI GFDEYMNLVLD+AEEV
Sbjct:     1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRITGFDEYMNLVLDEAEEV 60

Query:    61 HIKKNTRKPLGRILLKGDNITLMMNTGK 88
              IKKNTRKPLGRILLKGDNITLMMNTGK
Sbjct:    61 SIKKNTRKPLGRILLKGDNITLMMNTGK 88
GO:0003674 "molecular_function" evidence=ND
GO:0005634 "nucleus" evidence=ISM;ISS
GO:0005732 "small nucleolar ribonucleoprotein complex" evidence=ISS
GO:0008150 "biological_process" evidence=ND
GO:0005829 "cytosol" evidence=IDA
TAIR|locus:2118781 AT4G30330 "AT4G30330" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-040426-1112 snrpe "small nuclear ribonucleoprotein polypeptide E" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|P62303 SNRPE "Small nuclear ribonucleoprotein E" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|A4FUI2 SNRPE "Small nuclear ribonucleoprotein E" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|P62304 SNRPE "Small nuclear ribonucleoprotein E" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|A1XQR9 SNRPE "Small nuclear ribonucleoprotein E" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|I3LDW9 SNRPE "Small nuclear ribonucleoprotein E" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:98346 Snrpe "small nuclear ribonucleoprotein E" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|2321675 Snrpe "small nuclear ribonucleoprotein polypeptide E" [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) ?
A4FUI2RUXE_BOVINNo assigned EC number0.69870.94310.9021yesno
Q9XTU6RUXE_CAEELNo assigned EC number0.59030.94310.9222yesno
P62305RUXE_MOUSENo assigned EC number0.69870.94310.9021yesno
P62304RUXE_HUMANNo assigned EC number0.69870.94310.9021yesno
Q12330RUXE_YEASTNo assigned EC number0.50.95450.8936yesno
Q9VLV5RUXE_DROMENo assigned EC number0.65110.97720.9148yesno
P62303RUXE_CHICKNo assigned EC number0.69870.94310.9021yesno
A8XDT0RUXE_CAEBRNo assigned EC number0.60240.94310.9222N/Ano
Q7ZUG0RUXE_DANRENo assigned EC number0.74680.89770.8586yesno
Q9USZ3RUXE_SCHPONo assigned EC number0.60490.90900.9523yesno
A1XQR9RUXE_PIGNo assigned EC number0.68230.96590.9239yesno
O26745RUXX_METTHNo assigned EC number0.36580.86360.9382yesno

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

Your Input:
AT2G18740
small nuclear ribonucleoprotein E, putative / snRNP-E, putative / Sm protein E, putative; small nuclear ribonucleoprotein E, putative / snRNP-E, putative / Sm protein E, putative; FUNCTIONS IN- molecular_function unknown; INVOLVED IN- biological_process unknown; LOCATED IN- small nucleolar ribonucleoprotein complex, nucleus; EXPRESSED IN- 22 plant structures; EXPRESSED DURING- 13 growth stages; CONTAINS InterPro DOMAIN/s- Like-Sm ribonucleoprotein, core (InterPro-IPR001163), Like-Sm ribonucleoprotein, eukaryotic and archaea-type, core (InterPro-IPR006649), Like-Sm ribonucleoprotein-rel [...] (88 aa)
(Arabidopsis thaliana)
Predicted Functional Partners:
AT2G03870
small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putative; small nucle [...] (99 aa)
   •• • 0.980
AT3G59810
small nuclear ribonucleoprotein F, putative / U6 snRNA-associated Sm-like protein, putative / S [...] (91 aa)
   •• • 0.970
RUXF
RUXF (SMALL NUCLEAR RIBONUCLEOPROTEIN F); SMALL NUCLEAR RIBONUCLEOPROTEIN F (RUXF); FUNCTIONS I [...] (88 aa)
   •• • 0.965
AT2G30000
unknown protein; LOCATED IN- cellular_component unknown; EXPRESSED IN- 24 plant structures; EXP [...] (110 aa)
   •  • 0.906
AT1G07170
unknown protein; LOCATED IN- cellular_component unknown; EXPRESSED IN- 24 plant structures; EXP [...] (110 aa)
   •  • 0.906
AT3G55220
splicing factor, putative; splicing factor, putative; FUNCTIONS IN- nucleic acid binding; INVOL [...] (1214 aa)
   •  • 0.871
AT3G55200
splicing factor, putative; splicing factor, putative; FUNCTIONS IN- nucleic acid binding; INVOL [...] (1214 aa)
   •  • 0.871
SNRNP-G
SNRNP-G (PROBABLE SMALL NUCLEAR RIBONUCLEOPROTEIN G); PROBABLE SMALL NUCLEAR RIBONUCLEOPROTEIN [...] (80 aa)
   •• • 0.870
AT3G07590
small nuclear ribonucleoprotein D1, putative / snRNP core protein D1, putative / Sm protein D1, [...] (114 aa)
   •• • 0.869
SAD1
SAD1 (SUPERSENSITIVE TO ABA AND DROUGHT 1); RNA binding; SAD1 encodes a polypeptide similar to [...] (88 aa)
  ••• ••0.847

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 ?
Query88
cd0171879 cd01718, Sm_E, Sm protein E 2e-53
PTZ0013889 PTZ00138, PTZ00138, small nuclear ribonucleoprotei 6e-44
pfam0142366 pfam01423, LSM, LSM domain 4e-16
smart0065167 smart00651, Sm, snRNP Sm proteins 5e-15
cd0173169 cd01731, archaeal_Sm1, archaeal Sm protein 1 2e-11
COG195879 COG1958, LSM1, Small nuclear ribonucleoprotein (sn 2e-10
cd0060063 cd00600, Sm_like, Sm and related proteins 2e-10
PRK0073772 PRK00737, PRK00737, small nuclear ribonucleoprotei 2e-09
cd0173276 cd01732, LSm5, Like-Sm protein 5 3e-09
cd0171970 cd01719, Sm_G, Sm protein G 1e-07
cd0172668 cd01726, LSm6, Like-Sm protein 6 2e-07
cd1167869 cd11678, archaeal_LSm, archaeal Like-Sm protein 1e-06
cd0171780 cd01717, Sm_B, Sm protein B 3e-06
cd0173963 cd01739, LSm11_M, Like-Sm protein 11, middle domai 4e-06
cd0172269 cd01722, Sm_F, Sm protein F 3e-05
cd0172791 cd01727, LSm8, Like-Sm protein 8 8e-05
cd0173082 cd01730, LSm3, Like-Sm protein 3 8e-04
cd0172989 cd01729, LSm7, Like-Sm protein 7 0.002
cd0172874 cd01728, LSm1, Like-Sm protein 1 0.003
>gnl|CDD|212465 cd01718, Sm_E, Sm protein E Back     alignment and domain information 
 Score =  160 bits (406), Expect = 2e-53
 Identities = 64/79 (81%), Positives = 75/79 (94%)

Query: 7  QRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNT 66
          Q++M QPINLIFR+LQ+K+R+QIWL+EQ D+RIEG+IIGFDEYMNLVLDDAEEVH+K NT
Sbjct: 1  QKVMVQPINLIFRYLQNKSRVQIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNT 60

Query: 67 RKPLGRILLKGDNITLMMN 85
          RKPLGRILLKGDNITL+ N
Sbjct: 61 RKPLGRILLKGDNITLIQN 79

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Length = 79
>gnl|CDD|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>gnl|CDD|201787 pfam01423, LSM, LSM domain Back     alignment and domain information
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins Back     alignment and domain information
>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1 Back     alignment and domain information
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] Back     alignment and domain information
>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins Back     alignment and domain information
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>gnl|CDD|212479 cd01732, LSm5, Like-Sm protein 5 Back     alignment and domain information
>gnl|CDD|212466 cd01719, Sm_G, Sm protein G Back     alignment and domain information
>gnl|CDD|212473 cd01726, LSm6, Like-Sm protein 6 Back     alignment and domain information
>gnl|CDD|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein Back     alignment and domain information
>gnl|CDD|212464 cd01717, Sm_B, Sm protein B Back     alignment and domain information
>gnl|CDD|212485 cd01739, LSm11_M, Like-Sm protein 11, middle domain Back     alignment and domain information
>gnl|CDD|212469 cd01722, Sm_F, Sm protein F Back     alignment and domain information
>gnl|CDD|212474 cd01727, LSm8, Like-Sm protein 8 Back     alignment and domain information
>gnl|CDD|212477 cd01730, LSm3, Like-Sm protein 3 Back     alignment and domain information
>gnl|CDD|212476 cd01729, LSm7, Like-Sm protein 7 Back     alignment and domain information
>gnl|CDD|212475 cd01728, LSm1, Like-Sm protein 1 Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 88
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.96
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 99.96
KOG177488 consensus Small nuclear ribonucleoprotein E [RNA p 99.94
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.92
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.91
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.91
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.9
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.9
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.9
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.89
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.88
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.88
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.88
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.87
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.87
cd0172874 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins 99.85
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.84
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.84
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.84
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.84
cd0171779 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins 99.83
KOG178077 consensus Small Nuclear ribonucleoprotein G [RNA p 99.81
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.81
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.81
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.78
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.76
KOG346091 consensus Small nuclear ribonucleoprotein (snRNP) 99.73
KOG348279 consensus Small nuclear ribonucleoprotein (snRNP) 99.69
KOG177584 consensus U6 snRNA-associated Sm-like protein [RNA 99.68
KOG3293134 consensus Small nuclear ribonucleoprotein (snRNP) 99.61
KOG178377 consensus Small nuclear ribonucleoprotein F [RNA p 99.6
KOG1781108 consensus Small Nuclear ribonucleoprotein splicing 99.58
KOG178496 consensus Small Nuclear ribonucleoprotein splicing 99.42
KOG3172119 consensus Small nuclear ribonucleoprotein Sm D3 [R 99.35
KOG344896 consensus Predicted snRNP core protein [RNA proces 99.3
KOG1782129 consensus Small Nuclear ribonucleoprotein splicing 99.2
KOG3459114 consensus Small nuclear ribonucleoprotein (snRNP) 99.18
KOG3168177 consensus U1 snRNP component [Transcription] 99.18
KOG3428109 consensus Small nuclear ribonucleoprotein SMD1 and 99.02
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 98.91
cd0171661 Hfq Hfq, an abundant, ubiquitous RNA-binding prote 97.43
TIGR0238361 Hfq RNA chaperone Hfq. This model represents the R 97.41
PRK0039579 hfq RNA-binding protein Hfq; Provisional 97.21
COG192377 Hfq Uncharacterized host factor I protein [General 96.92
PF1443877 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1. 96.55
PF1270196 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC 96.3
PRK14091165 RNA-binding protein Hfq; Provisional 96.18
PRK14091165 RNA-binding protein Hfq; Provisional 96.16
cd0173674 LSm14_N LSm14 (also known as RAP55) belongs to a f 94.29
PF0223748 BPL_C: Biotin protein ligase C terminal domain; In 93.86
PRK14633150 hypothetical protein; Provisional 90.43
cd0173483 YlxS_C YxlS is a Bacillus subtilis gene of unknown 90.24
PRK14634155 hypothetical protein; Provisional 88.87
PRK14640152 hypothetical protein; Provisional 88.77
PRK14636176 hypothetical protein; Provisional 87.67
cd0173561 LSm12_N LSm12 belongs to a family of Sm-like prote 86.39
PRK14638150 hypothetical protein; Provisional 86.36
PRK14643164 hypothetical protein; Provisional 86.16
COG0779153 Uncharacterized protein conserved in bacteria [Fun 85.85
PRK14646155 hypothetical protein; Provisional 85.6
PRK14632172 hypothetical protein; Provisional 84.79
PRK02001152 hypothetical protein; Validated 84.74
PRK14639140 hypothetical protein; Provisional 84.3
PRK00092154 ribosome maturation protein RimP; Reviewed 84.25
PRK14631174 hypothetical protein; Provisional 84.19
PF1456342 DUF4444: Domain of unknown function (DUF4444); PDB 83.96
PRK14647159 hypothetical protein; Provisional 83.69
PRK14644136 hypothetical protein; Provisional 80.46
PRK14645154 hypothetical protein; Provisional 80.31
PF1109580 Gemin7: Gem-associated protein 7 (Gemin7); InterPr 80.25
>PTZ00138 small nuclear ribonucleoprotein; Provisional Back     alignment and domain information 
Probab=99.96  E-value=4.7e-29  Score=156.47  Aligned_cols=87  Identities=70%  Similarity=1.135  Sum_probs=80.2

Q ss_pred             CCccccceeeecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcE
Q 034651            1 MASTKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNI   80 (88)
Q Consensus         1 ~~~~~~~~~~~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I   80 (88)
                      |++++.||.|..|+..+.+++.++.+|.||++++++++++|+|.|||+|||++|+||+|+..+++..+.+|.++||||||
T Consensus         3 ~~~~~~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV   82 (89)
T PTZ00138          3 MTKRKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNI   82 (89)
T ss_pred             CcccccceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEE
Confidence            67778899999999999999999999999999988999999999999999999999999864455678999999999999


Q ss_pred             EEEEecC
Q 034651           81 TLMMNTG   87 (88)
Q Consensus        81 ~~I~~~~   87 (88)
                      ++|++.+
T Consensus        83 ~~I~~~~   89 (89)
T PTZ00138         83 TLIMAAK   89 (89)
T ss_pred             EEEEcCC
Confidence            9998753

>cd01718 Sm_E 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
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification] Back     alignment and domain information
>PRK00737 small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>cd01732 LSm5 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
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences Back     alignment and domain information
>cd01726 LSm6 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
>cd01720 Sm_D2 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
>cd01730 LSm3 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
>cd01722 Sm_F 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
>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
>cd01719 Sm_G 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
>cd01729 LSm7 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
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] Back     alignment and domain information
>cd01728 LSm1 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
>smart00651 Sm snRNP Sm proteins 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
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins Back     alignment and domain information
>cd01727 LSm8 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
>cd01717 Sm_B 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
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification] 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
>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
>cd00600 Sm_like 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
>cd06168 LSm9 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
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification] Back     alignment and domain information
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification] Back     alignment and domain information
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification] Back     alignment and domain information
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification] Back     alignment and domain information
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification] Back     alignment and domain information
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification] Back     alignment and domain information
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification] Back     alignment and domain information
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification] Back     alignment and domain information
>KOG3168 consensus U1 snRNP component [Transcription] Back     alignment and domain information
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification] Back     alignment and domain information
>cd01739 LSm11_C 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
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others Back     alignment and domain information
>TIGR02383 Hfq RNA chaperone Hfq Back     alignment and domain information
>PRK00395 hfq RNA-binding protein Hfq; Provisional Back     alignment and domain information
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only] Back     alignment and domain information
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1 Back     alignment and domain information
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A Back     alignment and domain information
>PRK14091 RNA-binding protein Hfq; Provisional Back     alignment and domain information
>PRK14091 RNA-binding protein Hfq; Provisional Back     alignment and domain information
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that 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
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown Back     alignment and domain information
>PRK14633 hypothetical protein; Provisional Back     alignment and domain information
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold Back     alignment and domain information
>PRK14634 hypothetical protein; Provisional Back     alignment and domain information
>PRK14640 hypothetical protein; Provisional Back     alignment and domain information
>PRK14636 hypothetical protein; Provisional Back     alignment and domain information
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that 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
>PRK14638 hypothetical protein; Provisional Back     alignment and domain information
>PRK14643 hypothetical protein; Provisional Back     alignment and domain information
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK14646 hypothetical protein; Provisional Back     alignment and domain information
>PRK14632 hypothetical protein; Provisional Back     alignment and domain information
>PRK02001 hypothetical protein; Validated Back     alignment and domain information
>PRK14639 hypothetical protein; Provisional Back     alignment and domain information
>PRK00092 ribosome maturation protein RimP; Reviewed Back     alignment and domain information
>PRK14631 hypothetical protein; Provisional Back     alignment and domain information
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A Back     alignment and domain information
>PRK14647 hypothetical protein; Provisional Back     alignment and domain information
>PRK14644 hypothetical protein; Provisional Back     alignment and domain information
>PRK14645 hypothetical protein; Provisional Back     alignment and domain information
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins 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 ?
Query88
3cw1_E92 Crystal Structure Of Human Spliceosomal U1 Snrnp Le 2e-31
1loj_A87 Crystal Structure Of A Methanobacterial Sm-Like Arc 2e-05
1jbm_A86 Heptameric Crystal Structure Of Mth649, An Sm-Like 2e-05
1jri_A85 The Crystal Structure Of An Sm-Like Archaeal Protei 2e-05
1i81_A83 Crystal Structure Of A Heptameric Lsm Protein From 3e-05
3swn_A82 Structure Of The Lsm657 Complex: An Assembly Interm 1e-04
1m8v_A77 Structure Of Pyrococcus Abyssii Sm Protein In Compl 2e-04
1h64_175 Crystal Structure Of The Sm-Related Protein Of P. A 2e-04
1th7_A81 Crystal Structure Of An Archaeal Sm Protein From Su 2e-04
4emk_A94 Crystal Structure Of Splsm567 Length = 94 5e-04
2fwk_A121 Crystal Structure Of Cryptosporidium Parvum U6 Snrn 7e-04
>pdb|3CW1|E Chain E, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 92 Back     alignment and structure 
Iteration: 1

 Score =  130 bits (328), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 58/83 (69%), Positives = 73/83 (87%)
Query: 5  KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
          KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68
Query: 65 NTRKPLGRILLKGDNITLMMNTG 87
           +RK LGRI+LKGDNITL+ +  
Sbjct: 69 KSRKQLGRIMLKGDNITLLQSVS 91
>pdb|1LOJ|A Chain A, Crystal Structure Of A Methanobacterial Sm-Like Archaeal Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump) Length = 87 Back     alignment and structure
>pdb|1JBM|A Chain A, Heptameric Crystal Structure Of Mth649, An Sm-Like Archaeal Protein From Methanobacterium Thermautotrophicum Length = 86 Back     alignment and structure
>pdb|1JRI|A Chain A, The Crystal Structure Of An Sm-Like Archaeal Protein With Two Heptamers In The Asymmetric Unit. Length = 85 Back     alignment and structure
>pdb|1I81|A Chain A, Crystal Structure Of A Heptameric Lsm Protein From Methanobacterium Thermoautotrophicum Length = 83 Back     alignment and structure
>pdb|3SWN|A Chain A, Structure Of The Lsm657 Complex: An Assembly Intermediate Of The Lsm1 7 And Lsm2 8 Rings Length = 82 Back     alignment and structure
>pdb|1M8V|A Chain A, Structure Of Pyrococcus Abyssii Sm Protein In Complex With A Uridine Heptamer Length = 77 Back     alignment and structure
>pdb|1H64|1 Chain 1, Crystal Structure Of The Sm-Related Protein Of P. Abyssi The Biological Unit Is A Heptamer Length = 75 Back     alignment and structure
>pdb|1TH7|A Chain A, Crystal Structure Of An Archaeal Sm Protein From Sulfolobus Solfataricus Length = 81 Back     alignment and structure
>pdb|4EMK|A Chain A, Crystal Structure Of Splsm567 Length = 94 Back     alignment and structure
>pdb|2FWK|A Chain A, Crystal Structure Of Cryptosporidium Parvum U6 Snrna- Associated Sm-Like Protein Lsm5 Length = 121 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query88
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 7e-37
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 3e-27
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 4e-20
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 2e-18
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 5e-15
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 4e-13
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 8e-12
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 9e-12
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 5e-11
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 6e-10
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 3e-09
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 4e-09
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 1e-08
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 2e-08
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 5e-08
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 8e-08
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 2e-07
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 3e-07
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 3e-07
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 9e-07
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 2e-04
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 2e-04
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 2e-04
>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E Length = 92 Back     alignment and structure
 Score =  118 bits (297), Expect = 7e-37
 Identities = 58/81 (71%), Positives = 73/81 (90%)

Query: 5  KVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK 64
          KVQ++M QPINLIFR+LQ+++RIQ+WL+EQ ++RIEG IIGFDEYMNLVLDDAEE+H K 
Sbjct: 9  KVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKT 68

Query: 65 NTRKPLGRILLKGDNITLMMN 85
           +RK LGRI+LKGDNITL+ +
Sbjct: 69 KSRKQLGRIMLKGDNITLLQS 89
>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A Length = 94 Back     alignment and structure
>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Length = 77 Back     alignment and structure
>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Length = 121 Back     alignment and structure
>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A* Length = 75 Back     alignment and structure
>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Length = 81 Back     alignment and structure
>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A* Length = 77 Back     alignment and structure
>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A Length = 83 Back     alignment and structure
>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F Length = 86 Back     alignment and structure
>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Length = 81 Back     alignment and structure
>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G Length = 76 Back     alignment and structure
>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae} Length = 96 Back     alignment and structure
>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B Length = 75 Back     alignment and structure
>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe} Length = 93 Back     alignment and structure
>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Length = 93 Back     alignment and structure
>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C Length = 113 Back     alignment and structure
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231 Back     alignment and structure
>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B Length = 118 Back     alignment and structure
>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe} Length = 105 Back     alignment and structure
>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A Length = 91 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 Length = 119 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 Length = 126 Back     alignment and structure
>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 Length = 75 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query88
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.96
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.94
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.93
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.93
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.92
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.92
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.91
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.91
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.91
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.91
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.91
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.91
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.9
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.9
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.9
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.89
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.89
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.89
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.88
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 99.88
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.86
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 99.86
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.82
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.78
1y96_A86 Gemin6, SIP2, GEM-associated protein 6; SM fold, p 98.28
2qtx_A71 Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi 97.69
1u1s_A82 HFQ protein; SM-like bacterial protein, riken stru 97.5
3ahu_A78 Protein HFQ; SM-like motif, protein-RNA complex, t 97.45
3sb2_A79 Protein HFQ; SM-like, RNA chaperone, chaperone; 2. 97.36
1kq1_A77 HFQ, HOST factor for Q beta; hexamer, RNA binding 97.32
2ylb_A74 Protein HFQ; RNA-binding protein, LSM protein, RNA 97.3
2y90_A104 Protein HFQ; RNA-binding protein, SM-like, RNA cha 97.28
3hfo_A70 SSR3341 protein; HFQ, SM, RNA-binding protein, sRN 95.81
3hfn_A72 ASL2047 protein; HFQ, SM, RNA-binding protein, sRN 95.4
1ycy_A71 Conserved hypothetical protein; structural genomic 94.63
2vxe_A88 CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA 94.21
2fb7_A95 SM-like protein, LSM-14_N (RAP55); DR.13312, BC055 93.48
2vc8_A84 Enhancer of mRNA-decapping protein 3; P-BODY compo 86.4
>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E Back     alignment and structure
Probab=99.96  E-value=2.8e-30  Score=161.92  Aligned_cols=84  Identities=69%  Similarity=1.160  Sum_probs=73.0

Q ss_pred             cccceeeecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEE
Q 034651            4 TKVQRIMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLM   83 (88)
Q Consensus         4 ~~~~~~~~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I   83 (88)
                      ++.||.|..|+++|+++++++++|.+|++..+|++|+|+|.|||+|||++|+||+|++.++++.+.+|.++|||+||++|
T Consensus         8 ~~~~~~m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~iRG~nV~~i   87 (92)
T 3s6n_E            8 QKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLL   87 (92)
T ss_dssp             ------CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCCEEEEEEEEECGGGEEEE
T ss_pred             CccceeccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCceeEcCeEEEeCCEEEEE
Confidence            35689999999999999999999999998888999999999999999999999999965666789999999999999999


Q ss_pred             EecC
Q 034651           84 MNTG   87 (88)
Q Consensus        84 ~~~~   87 (88)
                      ++.+
T Consensus        88 ~~~~   91 (92)
T 3s6n_E           88 QSVS   91 (92)
T ss_dssp             EEC-
T ss_pred             EeCC
Confidence            9976
>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Back     alignment and structure
>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A Back     alignment and structure
>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A Back     alignment and structure
>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Back     alignment and structure
>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F Back     alignment and structure
>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A* Back     alignment and structure
>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Back     alignment and structure
>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A* Back     alignment and structure
>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Back     alignment and structure
>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 Back     alignment and structure
>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B Back     alignment and structure
>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae} Back     alignment and structure
>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Back     alignment and structure
>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe} Back     alignment and structure
>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe} Back     alignment and structure
>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B Back     alignment and structure
>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G Back     alignment and structure
>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C 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
>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_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
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Back     alignment and structure
>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like P; OB-like fold, B-sheet toroid, 14-MER, cadmium-binding site, translation; 2.00A {Pyrobaculum aerophilum} SCOP: b.38.1.1 Back     alignment and structure
>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} Back     alignment and structure
>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii} Back     alignment and structure
>1u1s_A HFQ protein; SM-like bacterial protein, riken structural genomics/proteomics initiative, RSGI, structural genomics, RNA binding protein; 1.60A {Pseudomonas aeruginosa} SCOP: b.38.1.2 PDB: 1u1t_A 3qui_A* 3m4g_A 3inz_A Back     alignment and structure
>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A Back     alignment and structure
>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2 Back     alignment and structure
>1kq1_A HFQ, HOST factor for Q beta; hexamer, RNA binding protein, translational regulator, SM motif; 1.55A {Staphylococcus aureus} SCOP: b.38.1.2 PDB: 1kq2_A Back     alignment and structure
>2ylb_A Protein HFQ; RNA-binding protein, LSM protein, RNA chaperone; 1.15A {Salmonella enterica subsp} PDB: 2yht_A 1hk9_A 2ylc_A* 3gib_A* 3rer_A* 3qo3_A* 3res_A* Back     alignment and structure
>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A {Escherichia coli} PDB: 3qhs_A Back     alignment and structure
>3hfo_A SSR3341 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 1.30A {Synechocystis SP} Back     alignment and structure
>3hfn_A ASL2047 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 2.31A {Nostoc SP} Back     alignment and structure
>1ycy_A Conserved hypothetical protein; structural genomics, southeast collaboratory for structural genomics, secsg, protein structure initiative; 2.80A {Pyrococcus furiosus} SCOP: b.38.1.4 Back     alignment and structure
>2vxe_A CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA decay, LSM proteins, translational repression, transcription; NMR {Drosophila melanogaster} Back     alignment and structure
>2fb7_A SM-like protein, LSM-14_N (RAP55); DR.13312, BC055387, AAH55387, stronGly BENT five-stranded antiparallel beta- sheet, structural genomics, PSI; NMR {Danio rerio} SCOP: b.38.1.5 PDB: 2vxf_A Back     alignment and structure
>2vc8_A Enhancer of mRNA-decapping protein 3; P-BODY component, cytoplasm, SM-like protein, protein-binding; 1.31A {Homo sapiens} 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 88
d1b34b_93 b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s 4e-15
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 3e-14
d2fwka192 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr 2e-12
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 4e-12
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 1e-11
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 5e-11
d1d3bb_81 b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa 2e-10
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 7e-10
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 2e-09
d1n9ra_68 b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S 3e-09
d1d3ba_72 b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s 3e-08
d1b34a_80 b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s 4e-05
d1m5q1_127 b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch 6e-05
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93 Back     information, alignment and structure

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D2 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.2 bits (151), Expect = 4e-15
 Identities = 15/85 (17%), Positives = 45/85 (52%), Gaps = 15/85 (17%)

Query: 11 TQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKK------ 64
          T P++++ + +++  ++ I    + + ++ GR+  FD + N+VL++ +E+  +       
Sbjct: 1  TGPLSVLTQSVKNNTQVLINC--RNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKG 58

Query: 65 -------NTRKPLGRILLKGDNITL 82
                 N  + + ++ L+GD++ +
Sbjct: 59 KKKSKPVNKDRYISKMFLRGDSVIV 83
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Length = 75 Back     information, alignment and structure
>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} Length = 92 Back     information, alignment and structure
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Length = 71 Back     information, alignment and structure
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Length = 72 Back     information, alignment and structure
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 74 Back     information, alignment and structure
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 81 Back     information, alignment and structure
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 71 Back     information, alignment and structure
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Length = 76 Back     information, alignment and structure
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 68 Back     information, alignment and structure
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72 Back     information, alignment and structure
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80 Back     information, alignment and structure
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 127 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query88
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.93
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.92
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.92
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.91
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.91
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.9
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.9
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.9
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.89
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.89
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.82
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.82
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 99.7
d1u1sa166 Pleiotropic translational regulator Hfq {Pseudomon 97.37
d1kq1a_60 Pleiotropic translational regulator Hfq {Staphyloc 97.27
d2vxfa180 LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) 95.95
d1biaa247 Biotin repressor/biotin holoenzyme synthetase, C-t 95.27
d1ycya166 Hypothetical protein PF1955 {Pyrococcus furiosus [ 93.31
d1ib8a174 Hypothetical protein SP14.3 (SP0552) {Streptococcu 90.34
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Back     information, alignment and structure
class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

Probab=99.93  E-value=3.5e-26  Score=136.95  Aligned_cols=73  Identities=27%  Similarity=0.516  Sum_probs=66.7

Q ss_pred             eeecchHHHHHhhcCcceEEEEEEeCCCeEEEEEEEEeccccceEEeceEEEEecCCeeeecCeEEEeCCcEEEEEe
Q 034651            9 IMTQPINLIFRFLQSKARIQIWLFEQKDLRIEGRIIGFDEYMNLVLDDAEEVHIKKNTRKPLGRILLKGDNITLMMN   85 (88)
Q Consensus         9 ~~~~Pl~~L~~~l~k~~~V~V~lk~~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~g~v~iRG~~I~~I~~   85 (88)
                      .|..|+.+|+++++++  |+|++++ +++.|.|+|.|||+|||++|+||+|+ .++++.+.++.++|||+||.+|.|
T Consensus         2 ~~~~P~~~L~~~~~~~--V~V~lk~-~~~~~~G~L~~~D~~mNlvL~~~~e~-~~~~~~~~~g~~~IRG~~I~~I~p   74 (75)
T d1ljoa_           2 AMVLPNQMVKSMVGKI--IRVEMKG-EENQLVGKLEGVDDYMNLYLTNAMEC-KGEEKVRSLGEIVLRGNNVVLIQP   74 (75)
T ss_dssp             CCCCHHHHHHHTTTSE--EEEEETT-CSSEEEEEEEEECTTCCEEEEEEEEE-ETTEEEEEEEEEEECGGGEEEEEE
T ss_pred             CccccHHHHHHhcCCE--EEEEEEC-CCEEEEEEEEEEcCCCcEEEeEEEEE-cCCCcEeEcceEEEeCCEEEEEEC
Confidence            3889999999999996  9999986 35899999999999999999999998 466788999999999999999987
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Back     information, alignment and structure
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Back     information, alignment and structure
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} Back     information, alignment and structure
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Back     information, alignment and structure
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} 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
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Back     information, alignment and structure
>d1u1sa1 b.38.1.2 (A:6-71) Pleiotropic translational regulator Hfq {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1kq1a_ b.38.1.2 (A:) Pleiotropic translational regulator Hfq {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d2vxfa1 b.38.1.5 (A:6-85) LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) [TaxId: 7955]} Back     information, alignment and structure
>d1biaa2 b.34.1.1 (A:271-317) Biotin repressor/biotin holoenzyme synthetase, C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ycya1 b.38.1.4 (A:5-70) Hypothetical protein PF1955 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1ib8a1 b.38.2.1 (A:91-164) Hypothetical protein SP14.3 (SP0552) {Streptococcus pneumoniae [TaxId: 1313]} Back     information, alignment and structure