Citrus Sinensis ID: 034463

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----
MLVIQIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK
cccHHHHHHHHcccHHHHHHHHHHcEEEEEEEEEEEEEEccccHHHHccEEEEEEEcccccccccccccccccccccEEEEcccEEEEEEcccc
cEEEEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHccccccccccccccccccccHHHHHEEcccEEEEEEEccc
MLVIQIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTelpktgkgkkkalpvnkdrFISKMFLRGDSVIIVLRNPK
MLVIQIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMwtelpktgkgkkkalpvnkdrfiskmflrgdsviivlrnpk
MLVIQIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK
**VIQIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKT*****KALPVNKDRFISKMFLRGDSVIIVL****
******RFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREM********************RFISKMFLRGDSVIIVLRNP*
MLVIQIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTEL*********ALPVNKDRFISKMFLRGDSVIIVLRNPK
MLVIQIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPK*********PVNKDRFISKMFLRGDSVIIVLRNP*
ooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MLVIQIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK
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 ?
Query94 2.2.26 [Sep-21-2011]
Q54NC5112 Probable small nuclear ri yes no 0.670 0.562 0.857 9e-22
Q9VI10119 Probable small nuclear ri yes no 0.670 0.529 0.888 1e-20
P62317118 Small nuclear ribonucleop no no 0.670 0.533 0.857 2e-19
P62316118 Small nuclear ribonucleop yes no 0.670 0.533 0.857 2e-19
Q3SZF8118 Small nuclear ribonucleop yes no 0.670 0.533 0.857 2e-19
Q18786118 Probable small nuclear ri yes no 0.670 0.533 0.841 6e-19
O14036115 Small nuclear ribonucleop yes no 0.659 0.539 0.682 1e-18
Q06217110 Small nuclear ribonucleop yes no 0.595 0.509 0.619 6e-16
Q9Y7M493 Probable U6 snRNA-associa no no 0.617 0.623 0.389 0.0002
>sp|Q54NC5|SMD2_DICDI Probable small nuclear ribonucleoprotein Sm D2 OS=Dictyostelium discoideum GN=snrpd2 PE=3 SV=1 Back     alignment and function desciption
 Score =  102 bits (253), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 54/63 (85%), Positives = 61/63 (96%)

Query: 31  QLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 90
           +LLGRVRAFDRHCNMVLENV+E+WTE+PKT KGKKKA P+NKDRFISKMFLRGDSVI+VL
Sbjct: 42  KLLGRVRAFDRHCNMVLENVKEIWTEVPKTAKGKKKAKPINKDRFISKMFLRGDSVILVL 101

Query: 91  RNP 93
           +NP
Sbjct: 102 KNP 104
Required for pre-mRNA splicing. Required for snRNP biogenesis.
Dictyostelium discoideum (taxid: 44689)
>sp|Q9VI10|SMD2_DROME Probable small nuclear ribonucleoprotein Sm D2 OS=Drosophila melanogaster GN=SmD2 PE=3 SV=1 Back     alignment and function description
>sp|P62317|SMD2_MOUSE Small nuclear ribonucleoprotein Sm D2 OS=Mus musculus GN=Snrpd2 PE=2 SV=1 Back     alignment and function description
>sp|P62316|SMD2_HUMAN Small nuclear ribonucleoprotein Sm D2 OS=Homo sapiens GN=SNRPD2 PE=1 SV=1 Back     alignment and function description
>sp|Q3SZF8|SMD2_BOVIN Small nuclear ribonucleoprotein Sm D2 OS=Bos taurus GN=SNRPD2 PE=3 SV=1 Back     alignment and function description
>sp|Q18786|SMD2_CAEEL Probable small nuclear ribonucleoprotein Sm D2 OS=Caenorhabditis elegans GN=snr-4 PE=1 SV=1 Back     alignment and function description
>sp|O14036|SMD2_SCHPO Small nuclear ribonucleoprotein Sm D2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=smd2 PE=1 SV=1 Back     alignment and function description
>sp|Q06217|SMD2_YEAST Small nuclear ribonucleoprotein Sm D2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SMD2 PE=1 SV=2 Back     alignment and function description
>sp|Q9Y7M4|LSM3_SCHPO Probable U6 snRNA-associated Sm-like protein LSm3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm3 PE=1 SV=2 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 ?
Query94
57900175 431 putative small nuclear ribonucleoprotein 0.680 0.148 0.937 2e-29
297604251105 Os05g0314100 [Oryza sativa Japonica Grou 0.680 0.609 0.968 2e-29
212722184105 uncharacterized protein LOC100193106 [Ze 0.680 0.609 0.968 2e-29
226506222104 LOC100280773 [Zea mays] gi|195607934|gb| 0.680 0.615 0.968 2e-29
413918936104 hypothetical protein ZEAMMB73_850141 [Ze 0.680 0.615 0.968 2e-29
212720721105 uncharacterized protein LOC100193568 [Ze 0.680 0.609 0.968 3e-29
414586344102 TPA: hypothetical protein ZEAMMB73_87910 0.680 0.627 0.968 3e-29
326493364107 predicted protein [Hordeum vulgare subsp 0.680 0.598 0.968 3e-29
192910682105 small nuclear ribonucleoprotein-like pro 0.680 0.609 0.968 3e-29
255573198103 small nuclear ribonucleoprotein sm d2, p 0.680 0.621 0.953 5e-29
>gi|57900175|dbj|BAD88260.1| putative small nuclear ribonucleoprotein [Oryza sativa Japonica Group] Back     alignment and taxonomy information
 Score =  132 bits (333), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 60/64 (93%), Positives = 63/64 (98%)

Query: 31  QLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 90
           +LLGRVRAFD HCNMVLENVREMWTE+PKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL
Sbjct: 368 KLLGRVRAFDSHCNMVLENVREMWTEVPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 427

Query: 91  RNPK 94
           +NPK
Sbjct: 428 KNPK 431

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|297604251|ref|NP_001055168.2| Os05g0314100 [Oryza sativa Japonica Group] gi|54291778|gb|AAV32147.1| putative small nuclear ribonucleoprotein D2 [Oryza sativa Japonica Group] gi|215768148|dbj|BAH00377.1| unnamed protein product [Oryza sativa Japonica Group] gi|215768714|dbj|BAH00943.1| unnamed protein product [Oryza sativa Japonica Group] gi|218196532|gb|EEC78959.1| hypothetical protein OsI_19425 [Oryza sativa Indica Group] gi|222631079|gb|EEE63211.1| hypothetical protein OsJ_18021 [Oryza sativa Japonica Group] gi|255676234|dbj|BAF17082.2| Os05g0314100 [Oryza sativa Japonica Group] Back     alignment and taxonomy information
>gi|212722184|ref|NP_001131740.1| uncharacterized protein LOC100193106 [Zea mays] gi|194692396|gb|ACF80282.1| unknown [Zea mays] gi|195629728|gb|ACG36505.1| small nuclear ribonucleoprotein Sm D2 [Zea mays] gi|413918934|gb|AFW58866.1| Small nuclear ribonucleoprotein Sm D2 isoform 1 [Zea mays] gi|413918935|gb|AFW58867.1| Small nuclear ribonucleoprotein Sm D2 isoform 2 [Zea mays] Back     alignment and taxonomy information
>gi|226506222|ref|NP_001147167.1| LOC100280773 [Zea mays] gi|195607934|gb|ACG25797.1| small nuclear ribonucleoprotein Sm D2 [Zea mays] gi|195622778|gb|ACG33219.1| small nuclear ribonucleoprotein Sm D2 [Zea mays] gi|238013460|gb|ACR37765.1| unknown [Zea mays] gi|413942324|gb|AFW74973.1| Small nuclear ribonucleoprotein Sm D2 isoform 1 [Zea mays] gi|413942325|gb|AFW74974.1| Small nuclear ribonucleoprotein Sm D2 isoform 2 [Zea mays] gi|413942326|gb|AFW74975.1| Small nuclear ribonucleoprotein Sm D2 isoform 3 [Zea mays] Back     alignment and taxonomy information
>gi|413918936|gb|AFW58868.1| hypothetical protein ZEAMMB73_850141 [Zea mays] Back     alignment and taxonomy information
>gi|212720721|ref|NP_001132149.1| uncharacterized protein LOC100193568 [Zea mays] gi|194693576|gb|ACF80872.1| unknown [Zea mays] gi|414586342|tpg|DAA36913.1| TPA: hypothetical protein ZEAMMB73_879106 [Zea mays] gi|414586343|tpg|DAA36914.1| TPA: hypothetical protein ZEAMMB73_879106 [Zea mays] Back     alignment and taxonomy information
>gi|414586344|tpg|DAA36915.1| TPA: hypothetical protein ZEAMMB73_879106 [Zea mays] Back     alignment and taxonomy information
>gi|326493364|dbj|BAJ85143.1| predicted protein [Hordeum vulgare subsp. vulgare] Back     alignment and taxonomy information
>gi|192910682|gb|ACF06449.1| small nuclear ribonucleoprotein-like protein [Elaeis guineensis] Back     alignment and taxonomy information
>gi|255573198|ref|XP_002527528.1| small nuclear ribonucleoprotein sm d2, putative [Ricinus communis] gi|223533078|gb|EEF34837.1| small nuclear ribonucleoprotein sm d2, putative [Ricinus communis] 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 ?
Query94
TAIR|locus:2043323109 AT2G47640 "AT2G47640" [Arabido 0.680 0.587 0.953 4.4e-29
TAIR|locus:2081685109 AT3G62840 "AT3G62840" [Arabido 0.680 0.587 0.953 4.4e-29
FB|FBgn0261789119 SmD2 "Small ribonucleoprotein 0.670 0.529 0.888 5.7e-27
UNIPROTKB|G3X6Z3117 SNRPD2 "Small nuclear ribonucl 0.670 0.538 0.857 1.9e-26
UNIPROTKB|Q3SZF8118 SNRPD2 "Small nuclear ribonucl 0.670 0.533 0.857 1.9e-26
UNIPROTKB|F1PSI7118 SNRPD2 "Uncharacterized protei 0.670 0.533 0.857 1.9e-26
UNIPROTKB|P62316118 SNRPD2 "Small nuclear ribonucl 0.670 0.533 0.857 1.9e-26
MGI|MGI:98345118 Snrpd2 "small nuclear ribonucl 0.670 0.533 0.857 1.9e-26
RGD|1593018118 Snrpd2 "small nuclear ribonucl 0.670 0.533 0.857 1.9e-26
ZFIN|ZDB-GENE-040914-10118 snrpd2 "small nuclear ribonucl 0.670 0.533 0.857 1.9e-26
TAIR|locus:2043323 AT2G47640 "AT2G47640" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 323 (118.8 bits), Expect = 4.4e-29, P = 4.4e-29
 Identities = 61/64 (95%), Positives = 64/64 (100%)

Query:    31 QLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 90
             +LLGRVRAFDRHCNMVLENVREMWTE+PKTGKGKKKALPVN+DRFISKMFLRGDSVIIVL
Sbjct:    46 KLLGRVRAFDRHCNMVLENVREMWTEVPKTGKGKKKALPVNRDRFISKMFLRGDSVIIVL 105

Query:    91 RNPK 94
             RNPK
Sbjct:   106 RNPK 109
GO:0003674 "molecular_function" evidence=ND
GO:0005634 "nucleus" evidence=ISM;ISS
GO:0005732 "small nucleolar ribonucleoprotein complex" evidence=ISS
GO:0005730 "nucleolus" evidence=IDA
GO:0005829 "cytosol" evidence=IDA
GO:0001510 "RNA methylation" evidence=RCA
TAIR|locus:2081685 AT3G62840 "AT3G62840" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
FB|FBgn0261789 SmD2 "Small ribonucleoprotein particle protein SmD2" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|G3X6Z3 SNRPD2 "Small nuclear ribonucleoprotein Sm D2" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|Q3SZF8 SNRPD2 "Small nuclear ribonucleoprotein Sm D2" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|F1PSI7 SNRPD2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|P62316 SNRPD2 "Small nuclear ribonucleoprotein Sm D2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:98345 Snrpd2 "small nuclear ribonucleoprotein D2" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1593018 Snrpd2 "small nuclear ribonucleoprotein D2 polypeptide" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-040914-10 snrpd2 "small nuclear ribonucleoprotein D2 polypeptide" [Danio rerio (taxid:7955)] 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) ?
P62316SMD2_HUMANNo assigned EC number0.85710.67020.5338yesno
Q18786SMD2_CAEELNo assigned EC number0.84120.67020.5338yesno
Q9VI10SMD2_DROMENo assigned EC number0.88880.67020.5294yesno
Q3SZF8SMD2_BOVINNo assigned EC number0.85710.67020.5338yesno
Q54NC5SMD2_DICDINo assigned EC number0.85710.67020.5625yesno

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:
4324004
LSM domain containing protein (456 aa)
(Oryza sativa Japonica)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query94
cd0172089 cd01720, Sm_D2, Sm protein D2 6e-38
cd0173082 cd01730, LSm3, Like-Sm protein 3 5e-12
smart0065167 smart00651, Sm, snRNP Sm proteins 4e-09
pfam0142366 pfam01423, LSM, LSM domain 7e-08
COG195879 COG1958, LSM1, Small nuclear ribonucleoprotein (sn 1e-06
cd0173169 cd01731, archaeal_Sm1, archaeal Sm protein 1 2e-05
cd0060063 cd00600, Sm_like, Sm and related proteins 1e-04
cd0173963 cd01739, LSm11_M, Like-Sm protein 11, middle domai 0.004
>gnl|CDD|212467 cd01720, Sm_D2, Sm protein D2 Back     alignment and domain information 
 Score =  121 bits (306), Expect = 6e-38
 Identities = 54/62 (87%), Positives = 58/62 (93%), Gaps = 1/62 (1%)

Query: 32 LLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLR 91
          LL RV+AFDRHCNMVLENV+EMWTE+PKTGKGKK   PVNKDRFISKMFLRGDSVI+VLR
Sbjct: 29 LLARVKAFDRHCNMVLENVKEMWTEVPKTGKGKKSK-PVNKDRFISKMFLRGDSVILVLR 87

Query: 92 NP 93
          NP
Sbjct: 88 NP 89

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 D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Length = 89
>gnl|CDD|212477 cd01730, LSm3, Like-Sm protein 3 Back     alignment and domain information
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins Back     alignment and domain information
>gnl|CDD|201787 pfam01423, LSM, LSM domain Back     alignment and domain information
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] Back     alignment and domain information
>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1 Back     alignment and domain information
>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins Back     alignment and domain information
>gnl|CDD|212485 cd01739, LSm11_M, Like-Sm protein 11, middle domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 94
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 99.91
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.9
KOG177488 consensus Small nuclear ribonucleoprotein E [RNA p 99.89
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.88
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.85
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.84
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.81
cd0171779 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins 99.8
KOG346091 consensus Small nuclear ribonucleoprotein (snRNP) 99.78
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.78
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.78
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.78
cd0172874 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins 99.77
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.76
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.71
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.71
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.69
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.68
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.66
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.64
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.6
KOG178077 consensus Small Nuclear ribonucleoprotein G [RNA p 99.57
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.52
KOG1781108 consensus Small Nuclear ribonucleoprotein splicing 99.51
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.5
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.43
KOG177584 consensus U6 snRNA-associated Sm-like protein [RNA 99.42
KOG3168177 consensus U1 snRNP component [Transcription] 99.42
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.39
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.37
KOG3459114 consensus Small nuclear ribonucleoprotein (snRNP) 99.32
KOG1782129 consensus Small Nuclear ribonucleoprotein splicing 99.21
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 99.21
KOG178496 consensus Small Nuclear ribonucleoprotein splicing 99.09
KOG348279 consensus Small nuclear ribonucleoprotein (snRNP) 98.8
KOG178377 consensus Small nuclear ribonucleoprotein F [RNA p 98.63
KOG344896 consensus Predicted snRNP core protein [RNA proces 97.75
KOG3172119 consensus Small nuclear ribonucleoprotein Sm D3 [R 96.87
KOG3293134 consensus Small nuclear ribonucleoprotein (snRNP) 96.54
cd0171661 Hfq Hfq, an abundant, ubiquitous RNA-binding prote 95.81
TIGR0238361 Hfq RNA chaperone Hfq. This model represents the R 95.62
KOG3428109 consensus Small nuclear ribonucleoprotein SMD1 and 95.41
PRK0039579 hfq RNA-binding protein Hfq; Provisional 95.28
COG192377 Hfq Uncharacterized host factor I protein [General 95.14
PRK14091165 RNA-binding protein Hfq; Provisional 92.11
PRK14091165 RNA-binding protein Hfq; Provisional 91.67
PF1443877 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1. 86.21
>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 
Probab=99.91  E-value=8.4e-25  Score=140.52  Aligned_cols=72  Identities=25%  Similarity=0.529  Sum_probs=64.5

Q ss_pred             EEEEeeeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeC
Q 034463            4 IQIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRG   83 (94)
Q Consensus         4 ~~~~~~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRG   83 (94)
                      ++.+|+||+++.++   ++|+.++.+++++|+|+|||+||||+|+||+|+...   .          ++++.+|.+++||
T Consensus         8 ~~~l~~~l~~~~~V---~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~---~----------~~~~~lG~iliRG   71 (79)
T cd01718           8 INLIFRFLQSKQRV---QIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLK---T----------KTRKPLGRILLKG   71 (79)
T ss_pred             HHHHHHHHccCcEE---EEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecC---C----------ceEeEcCcEEEeC
Confidence            56789999999999   999999999999999999999999999999998642   0          1356899999999


Q ss_pred             CeEEEEEe
Q 034463           84 DSVIIVLR   91 (94)
Q Consensus        84 dnVv~I~~   91 (94)
                      |||++|+|
T Consensus        72 nnV~~I~p   79 (79)
T cd01718          72 DNITLIQN   79 (79)
T ss_pred             CEEEEEcC
Confidence            99999996

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. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
>PTZ00138 small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification] 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
>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
>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
>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
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification] 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
>PRK00737 small nuclear ribonucleoprotein; Provisional 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
>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
>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
>smart00651 Sm snRNP Sm proteins 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
>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
>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
>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
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] 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
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification] 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
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] 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
>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
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification] Back     alignment and domain information
>KOG3168 consensus U1 snRNP component [Transcription] 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
>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
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm 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
>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
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [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
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification] Back     alignment and domain information
>KOG3448 consensus Predicted snRNP core protein [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
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification] 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
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification] 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
>PRK14091 RNA-binding protein Hfq; Provisional Back     alignment and domain information
>PRK14091 RNA-binding protein Hfq; Provisional Back     alignment and domain information
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1 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 ?
Query94
1b34_B118 Crystal Structure Of The D1d2 Sub-Complex From The 1e-20
4emg_A93 Crystal Structure Of Splsm3 Length = 93 5e-05
>pdb|1B34|B Chain B, Crystal Structure Of The D1d2 Sub-Complex From The Human Snrnp Core Domain Length = 118 Back     alignment and structure 
Iteration: 1

 Score = 94.4 bits (233), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 54/63 (85%), Positives = 62/63 (98%)
Query: 31  QLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 90
           +LLGRV+AFDRHCNMVLENV+EMWTE+PK+GKGKKK+ PVNKDR+ISKMFLRGDSVI+VL
Sbjct: 51  KLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVL 110
Query: 91  RNP 93
           RNP
Sbjct: 111 RNP 113
>pdb|4EMG|A Chain A, Crystal Structure Of Splsm3 Length = 93 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 ?
Query94
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 3e-26
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 7e-18
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 1e-15
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 1e-13
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 2e-06
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 2e-06
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 2e-06
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 6e-06
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 7e-06
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 9e-06
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 1e-05
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 2e-05
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 9e-05
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 1e-04
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 1e-04
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 2e-04
>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
 Score = 92.7 bits (230), Expect = 3e-26
 Identities = 54/63 (85%), Positives = 62/63 (98%)

Query: 31  QLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 90
           +LLGRV+AFDRHCNMVLENV+EMWTE+PK+GKGKKK+ PVNKDR+ISKMFLRGDSVI+VL
Sbjct: 51  KLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVL 110

Query: 91  RNP 93
           RNP
Sbjct: 111 RNP 113
>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
>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
>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_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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query94
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.9
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.87
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.84
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.81
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.81
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.79
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.79
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.78
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.78
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.78
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.78
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.78
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.77
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.77
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.76
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.76
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.76
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.73
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.73
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 99.72
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.72
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.68
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.61
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 99.53
3sb2_A79 Protein HFQ; SM-like, RNA chaperone, chaperone; 2. 95.79
1u1s_A82 HFQ protein; SM-like bacterial protein, riken stru 95.76
2qtx_A71 Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi 95.67
2ylb_A74 Protein HFQ; RNA-binding protein, LSM protein, RNA 95.63
2y90_A104 Protein HFQ; RNA-binding protein, SM-like, RNA cha 95.25
3ahu_A78 Protein HFQ; SM-like motif, protein-RNA complex, t 95.06
1kq1_A77 HFQ, HOST factor for Q beta; hexamer, RNA binding 94.97
1y96_A86 Gemin6, SIP2, GEM-associated protein 6; SM fold, p 92.36
3hfo_A70 SSR3341 protein; HFQ, SM, RNA-binding protein, sRN 86.79
3hfn_A72 ASL2047 protein; HFQ, SM, RNA-binding protein, sRN 83.15
>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=99.90  E-value=1e-24  Score=142.17  Aligned_cols=74  Identities=20%  Similarity=0.526  Sum_probs=66.0

Q ss_pred             EEEEeeeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeC
Q 034463            4 IQIRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRG   83 (94)
Q Consensus         4 ~~~~~~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRG   83 (94)
                      ++++++|++++.+|   ++|+.+++||+++|+|+|||+||||+|+||+|++..   .          .+++++|.++|||
T Consensus        18 l~lL~~~l~~~v~V---~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~---~----------~~~~~lg~v~iRG   81 (92)
T 3s6n_E           18 INLIFRYLQNRSRI---QVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSK---T----------KSRKQLGRIMLKG   81 (92)
T ss_dssp             HHHHHHHHHHTCEE---EEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSS---S----------CCEEEEEEEEECG
T ss_pred             HHHHHHHhCCCEEE---EEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecC---C----------CceeEcCeEEEeC
Confidence            56789999999999   999999999999999999999999999999998642   1          1367899999999


Q ss_pred             CeEEEEEeCC
Q 034463           84 DSVIIVLRNP   93 (94)
Q Consensus        84 dnVv~I~~~~   93 (94)
                      +||++|+|.+
T Consensus        82 ~nV~~i~~~~   91 (92)
T 3s6n_E           82 DNITLLQSVS   91 (92)
T ss_dssp             GGEEEEEEC-
T ss_pred             CEEEEEEeCC
Confidence            9999999986
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2 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
>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii} 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
>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A 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
>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} 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

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 94
d1b34b_93 b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s 7e-24
d2fwka192 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr 6e-13
d1d3bb_81 b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa 7e-11
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 4e-07
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 2e-06
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 3e-06
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 5e-06
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 7e-06
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 4e-05
d1n9ra_68 b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S 7e-04
>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 = 84.6 bits (209), Expect = 7e-24
 Identities = 54/64 (84%), Positives = 62/64 (96%)

Query: 31 QLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVL 90
          +LLGRV+AFDRHCNMVLENV+EMWTE+PK+GKGKKK+ PVNKDR+ISKMFLRGDSVI+VL
Sbjct: 26 KLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVL 85

Query: 91 RNPK 94
          RNP 
Sbjct: 86 RNPL 89
>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
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 81 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
>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
>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
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Length = 75 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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query94
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.93
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.84
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.84
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.8
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.76
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.76
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.74
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.74
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.74
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.73
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.55
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.39
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 99.23
d1u1sa166 Pleiotropic translational regulator Hfq {Pseudomon 95.4
d1kq1a_60 Pleiotropic translational regulator Hfq {Staphyloc 95.35
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} 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]

Probab=99.93  E-value=3.3e-27  Score=152.56  Aligned_cols=84  Identities=65%  Similarity=1.006  Sum_probs=59.8

Q ss_pred             EEeeeeeCcceEEEEEEEEEecCCEEEEEEEeeecCeeceEeeceEEeeeecCCCCCCccccccceeeEeeCeEEEeCCe
Q 034463            6 IRFSFRNSQTTLMLFCFWALEFIVLQLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS   85 (94)
Q Consensus         6 ~~~~~~~~~~~i~~l~~~l~~~~~r~~~G~L~gfD~hmNLVL~d~~E~~~~~~~~~~~~~~~k~~~~~r~lG~v~iRGdn   85 (94)
                      +++++++++.+|   .+++  +++|++.|+|+|||+||||||+||+|++...++..+..+..+...++|++|++++||||
T Consensus         6 ~l~~~~~~~~rV---~V~l--r~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdn   80 (93)
T d1b34b_           6 VLTQSVKNNTQV---LINC--RNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDS   80 (93)
T ss_dssp             HHHHHHHHTCEE---EEEE--TTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGG
T ss_pred             HHHHHHhCCcEE---EEEE--CCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCE
Confidence            456777788899   8888  88999999999999999999999999988655433222222334467899999999999


Q ss_pred             EEEEEeCCC
Q 034463           86 VIIVLRNPK   94 (94)
Q Consensus        86 Vv~I~~~~~   94 (94)
                      |++|.++|.
T Consensus        81 Vv~I~~~p~   89 (93)
T d1b34b_          81 VIVVLRNPL   89 (93)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEcChh
Confidence            999999984
>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} 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
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Back     information, alignment and structure
>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
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} 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
>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