Citrus Sinensis ID: 033530

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------
MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPKKPTAGIDIISQIKLHSCVHCFCVCFFS
ccHHHHHHHccccEEEEEEccccEEEEEEcEEcccccEEEEEEEEEEcccccEEccEEEEEccEEEEEEcccccccHHHHHHcccccccccccccccHHHHHHHcccccccEEEEcc
ccHHHHHHcccccEEEEEEccccEEEEEEEEEcccccEEEEEEEEEccccccEEEEEEEEcHHHEEEEEccccccHHHHccccccccccccccccccEEEEEEEEEEEEEEEEEEcc
MKLVRFLMKLNNETVSielkngtivhgTITGVDISMNTHLKTVKLtlkgknpvnldhlsvrgnniryyilpdslnletllveetprvkpkkptagidiisQIKLhscvhcfcvcffs
MKLVRFLMKLNNETVsielkngtiVHGTITGVDISMNTHLKTVKltlkgknpvnldhlsvRGNNIRYYILPDSLNLETLLveetprvkpkkptaGIDIISQIKLHSCVHCFCVCFFS
MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPKKPTAGIDIISQIKLhscvhcfcvcffs
***VRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPKKPTAGIDIISQIKLHSCVHCFCVCFF*
MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLET***************************SCVHCFCVCFFS
MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPKKPTAGIDIISQIKLHSCVHCFCVCFFS
MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLLVEETPRV*****TAGIDIISQIKLHSCVHCFCVCFFS
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLLVEETPRVKPKKPTAGIDIISQIKLHSCVHCFCVCFFS
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 ?
Query117 2.2.26 [Sep-21-2011]
P62315119 Small nuclear ribonucleop yes no 0.803 0.789 0.744 9e-34
Q4R5F6119 Small nuclear ribonucleop N/A no 0.803 0.789 0.744 9e-34
P62314119 Small nuclear ribonucleop yes no 0.803 0.789 0.744 9e-34
Q3ZC10119 Small nuclear ribonucleop yes no 0.803 0.789 0.744 9e-34
Q9VU02124 Probable small nuclear ri yes no 0.777 0.733 0.714 3e-33
O42661117 Small nuclear ribonucleop yes no 0.777 0.777 0.736 1e-32
Q10013126 Probable small nuclear ri yes no 0.752 0.698 0.693 6e-29
Q02260146 Small nuclear ribonucleop yes no 0.709 0.568 0.445 8e-15
Q969L4123 U7 snRNA-associated Sm-li no no 0.692 0.658 0.320 4e-07
Q8QZX5122 U7 snRNA-associated Sm-li no no 0.692 0.663 0.296 9e-06
>sp|P62315|SMD1_MOUSE Small nuclear ribonucleoprotein Sm D1 OS=Mus musculus GN=Snrpd1 PE=2 SV=1 Back     alignment and function desciption
 Score =  141 bits (356), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 70/94 (74%), Positives = 82/94 (87%)

Query: 1  MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSV 60
          MKLVRFLMKL++ETV+IELKNGT VHGTITGVD+SMNTHLK VK+TLK + PV L+ LS+
Sbjct: 1  MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI 60

Query: 61 RGNNIRYYILPDSLNLETLLVEETPRVKPKKPTA 94
          RGNNIRY+ILPDSL L+TLLV+  P+VK KK  A
Sbjct: 61 RGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREA 94
May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through nonspecific electrostatic contacts with RNA.
Mus musculus (taxid: 10090)
>sp|Q4R5F6|SMD1_MACFA Small nuclear ribonucleoprotein Sm D1 OS=Macaca fascicularis GN=SNRPD1 PE=3 SV=1 Back     alignment and function description
>sp|P62314|SMD1_HUMAN Small nuclear ribonucleoprotein Sm D1 OS=Homo sapiens GN=SNRPD1 PE=1 SV=1 Back     alignment and function description
>sp|Q3ZC10|SMD1_BOVIN Small nuclear ribonucleoprotein Sm D1 OS=Bos taurus GN=SNRPD1 PE=3 SV=1 Back     alignment and function description
>sp|Q9VU02|SMD1_DROME Probable small nuclear ribonucleoprotein Sm D1 OS=Drosophila melanogaster GN=SmD1 PE=1 SV=1 Back     alignment and function description
>sp|O42661|SMD1_SCHPO Small nuclear ribonucleoprotein Sm D1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=smd1 PE=1 SV=1 Back     alignment and function description
>sp|Q10013|SMD1_CAEEL Probable small nuclear ribonucleoprotein Sm D1 OS=Caenorhabditis elegans GN=snr-3 PE=3 SV=1 Back     alignment and function description
>sp|Q02260|SMD1_YEAST Small nuclear ribonucleoprotein Sm D1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SMD1 PE=1 SV=1 Back     alignment and function description
>sp|Q969L4|LSM10_HUMAN U7 snRNA-associated Sm-like protein LSm10 OS=Homo sapiens GN=LSM10 PE=1 SV=1 Back     alignment and function description
>sp|Q8QZX5|LSM10_MOUSE U7 snRNA-associated Sm-like protein LSm10 OS=Mus musculus GN=Lsm10 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 ?
Query117
388509846116 unknown [Lotus japonicus] 0.811 0.818 0.989 4e-46
255559488114 small nuclear ribonucleoprotein sm d1, p 0.811 0.833 0.989 5e-46
225436986114 PREDICTED: small nuclear ribonucleoprote 0.811 0.833 0.978 9e-46
224066521115 predicted protein [Populus trichocarpa] 0.811 0.826 0.968 1e-45
388508844115 unknown [Medicago truncatula] 0.811 0.826 0.978 2e-45
357440765114 Small nuclear ribonucleoprotein Sm D1 [M 0.811 0.833 0.978 2e-45
296086730144 unnamed protein product [Vitis vinifera] 0.811 0.659 0.978 2e-45
225462054114 PREDICTED: small nuclear ribonucleoprote 0.811 0.833 0.957 2e-45
356499683116 PREDICTED: small nuclear ribonucleoprote 0.811 0.818 0.968 2e-45
359806624115 uncharacterized protein LOC100819089 [Gl 0.811 0.826 0.968 2e-45
>gi|388509846|gb|AFK42989.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
 Score =  188 bits (477), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 94/95 (98%), Positives = 94/95 (98%)

Query: 1  MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSV 60
          MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPV LDHLSV
Sbjct: 1  MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVTLDHLSV 60

Query: 61 RGNNIRYYILPDSLNLETLLVEETPRVKPKKPTAG 95
          RGNNIRYYILPDSLNLETLLVEETPRVKPKKPTAG
Sbjct: 61 RGNNIRYYILPDSLNLETLLVEETPRVKPKKPTAG 95

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255559488|ref|XP_002520764.1| small nuclear ribonucleoprotein sm d1, putative [Ricinus communis] gi|223540149|gb|EEF41726.1| small nuclear ribonucleoprotein sm d1, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|225436986|ref|XP_002277211.1| PREDICTED: small nuclear ribonucleoprotein Sm D1-like isoform 1 [Vitis vinifera] gi|225436988|ref|XP_002277231.1| PREDICTED: small nuclear ribonucleoprotein Sm D1-like isoform 2 [Vitis vinifera] Back     alignment and taxonomy information
>gi|224066521|ref|XP_002302121.1| predicted protein [Populus trichocarpa] gi|118482633|gb|ABK93236.1| unknown [Populus trichocarpa] gi|118488779|gb|ABK96200.1| unknown [Populus trichocarpa] gi|222843847|gb|EEE81394.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|388508844|gb|AFK42488.1| unknown [Medicago truncatula] Back     alignment and taxonomy information
>gi|357440765|ref|XP_003590660.1| Small nuclear ribonucleoprotein Sm D1 [Medicago truncatula] gi|355479708|gb|AES60911.1| Small nuclear ribonucleoprotein Sm D1 [Medicago truncatula] Back     alignment and taxonomy information
>gi|296086730|emb|CBI32365.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|225462054|ref|XP_002275736.1| PREDICTED: small nuclear ribonucleoprotein Sm D1-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|356499683|ref|XP_003518666.1| PREDICTED: small nuclear ribonucleoprotein Sm D1-like isoform 1 [Glycine max] Back     alignment and taxonomy information
>gi|359806624|ref|NP_001241019.1| uncharacterized protein LOC100819089 [Glycine max] gi|255647733|gb|ACU24327.1| 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 ?
Query117
TAIR|locus:2091102114 AT3G07590 "AT3G07590" [Arabido 0.811 0.833 0.915 2.2e-43
DICTYBASE|DDB_G0278027131 snrpD1 "putative small nuclear 0.803 0.717 0.808 8e-37
FB|FBgn0261933124 SmD1 "Small ribonucleoprotein 0.811 0.766 0.694 5.2e-33
UNIPROTKB|Q3ZC10119 SNRPD1 "Small nuclear ribonucl 0.803 0.789 0.744 1.4e-32
UNIPROTKB|E2RIW7119 SNRPD1 "Uncharacterized protei 0.803 0.789 0.744 1.4e-32
UNIPROTKB|P62314119 SNRPD1 "Small nuclear ribonucl 0.803 0.789 0.744 1.4e-32
UNIPROTKB|F2Z5G9119 SNRPD1 "Uncharacterized protei 0.803 0.789 0.744 1.4e-32
MGI|MGI:98344119 Snrpd1 "small nuclear ribonucl 0.803 0.789 0.744 1.4e-32
RGD|1306345119 Snrpd1 "small nuclear ribonucl 0.803 0.789 0.744 1.4e-32
ZFIN|ZDB-GENE-020419-14119 snrpd1 "small nuclear ribonucl 0.803 0.789 0.734 3.7e-32
TAIR|locus:2091102 AT3G07590 "AT3G07590" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 458 (166.3 bits), Expect = 2.2e-43, P = 2.2e-43
 Identities = 87/95 (91%), Positives = 93/95 (97%)

Query:     1 MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSV 60
             MKLVRFLMKLNNETVSIELKNGT+VHGTITGVD+SMNTHLKTVK++LKGKNPV LDHLS+
Sbjct:     1 MKLVRFLMKLNNETVSIELKNGTVVHGTITGVDVSMNTHLKTVKMSLKGKNPVTLDHLSL 60

Query:    61 RGNNIRYYILPDSLNLETLLVEETPRVKPKKPTAG 95
             RGNNIRYYILPDSLNLETLLVE+TPRVKPKKP AG
Sbjct:    61 RGNNIRYYILPDSLNLETLLVEDTPRVKPKKPVAG 95
GO:0003674 "molecular_function" evidence=ND
GO:0005634 "nucleus" evidence=ISM;ISS
GO:0005732 "small nucleolar ribonucleoprotein complex" evidence=ISS
GO:0005774 "vacuolar membrane" evidence=IDA
GO:0005829 "cytosol" evidence=IDA
GO:0006626 "protein targeting to mitochondrion" evidence=RCA
GO:0009640 "photomorphogenesis" evidence=RCA
GO:0010388 "cullin deneddylation" evidence=RCA
DICTYBASE|DDB_G0278027 snrpD1 "putative small nuclear ribonucleoprotein D1" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
FB|FBgn0261933 SmD1 "Small ribonucleoprotein particle protein SmD1" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|Q3ZC10 SNRPD1 "Small nuclear ribonucleoprotein Sm D1" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2RIW7 SNRPD1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|P62314 SNRPD1 "Small nuclear ribonucleoprotein Sm D1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F2Z5G9 SNRPD1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:98344 Snrpd1 "small nuclear ribonucleoprotein D1" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1306345 Snrpd1 "small nuclear ribonucleoprotein D1" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-020419-14 snrpd1 "small nuclear ribonucleoprotein D1 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) ?
Q10013SMD1_CAEELNo assigned EC number0.69310.75210.6984yesno
Q4R5F6SMD1_MACFANo assigned EC number0.74460.80340.7899N/Ano
P62314SMD1_HUMANNo assigned EC number0.74460.80340.7899yesno
P62315SMD1_MOUSENo assigned EC number0.74460.80340.7899yesno
Q9VU02SMD1_DROMENo assigned EC number0.71420.77770.7338yesno
O42661SMD1_SCHPONo assigned EC number0.73620.77770.7777yesno
Q3ZC10SMD1_BOVINNo assigned EC number0.74460.80340.7899yesno

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:
BRADI3G47250.1
annotation not avaliable (172 aa)
(Brachypodium distachyon)
Predicted Functional Partners:
BRADI3G02620.1
Small nuclear ribonucleoprotein E (88 aa)
   •••• 0.537
BRADI3G16900.1
annotation not avaliable (93 aa)
   •••••0.495
BRADI2G56060.2
annotation not avaliable (98 aa)
   •• • 0.473
BRADI2G26720.1
annotation not avaliable (89 aa)
   •• • 0.450

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 ?
Query117
cd0172492 cd01724, Sm_D1, Sm protein D1 2e-60
pfam0142366 pfam01423, LSM, LSM domain 6e-17
smart0065167 smart00651, Sm, snRNP Sm proteins 2e-16
COG195879 COG1958, LSM1, Small nuclear ribonucleoprotein (sn 7e-13
cd0172170 cd01721, Sm_D3, Sm protein D3 3e-12
cd0060063 cd00600, Sm_like, Sm and related proteins 7e-11
cd0173378 cd01733, LSm10, Like-Sm protein 10 3e-09
cd0172376 cd01723, LSm4, Like-Sm protein 4 4e-08
cd0172589 cd01725, LSm2, Like-Sm protein 2 3e-05
cd0172269 cd01722, Sm_F, Sm protein F 6e-04
cd0173169 cd01731, archaeal_Sm1, archaeal Sm protein 1 0.002
cd0172668 cd01726, LSm6, Like-Sm protein 6 0.003
>gnl|CDD|212471 cd01724, Sm_D1, Sm protein D1 Back     alignment and domain information 
 Score =  179 bits (457), Expect = 2e-60
 Identities = 75/92 (81%), Positives = 85/92 (92%)

Query: 2  KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVR 61
          KLVRFLMKL+NETV+IELKNGT+VHGTITGVD+SMNTHLK VKLTLKGKNPV+LD LS+R
Sbjct: 1  KLVRFLMKLSNETVTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLKGKNPVSLDTLSIR 60

Query: 62 GNNIRYYILPDSLNLETLLVEETPRVKPKKPT 93
          GNNIRY ILPDSLNL+TLLV++TP+ K KK  
Sbjct: 61 GNNIRYIILPDSLNLDTLLVDDTPKAKAKKRA 92

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 D1 heterodimerizes with subunit D2 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 DB, D3, E, F, and G subunits. Length = 92
>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|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] Back     alignment and domain information
>gnl|CDD|212468 cd01721, Sm_D3, Sm protein D3 Back     alignment and domain information
>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins Back     alignment and domain information
>gnl|CDD|212480 cd01733, LSm10, Like-Sm protein 10 Back     alignment and domain information
>gnl|CDD|212470 cd01723, LSm4, Like-Sm protein 4 Back     alignment and domain information
>gnl|CDD|212472 cd01725, LSm2, Like-Sm protein 2 Back     alignment and domain information
>gnl|CDD|212469 cd01722, Sm_F, Sm protein F Back     alignment and domain information
>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1 Back     alignment and domain information
>gnl|CDD|212473 cd01726, LSm6, Like-Sm protein 6 Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 117
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.96
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.93
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.93
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.91
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.91
KOG3172119 consensus Small nuclear ribonucleoprotein Sm D3 [R 99.89
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.88
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.87
KOG3428109 consensus Small nuclear ribonucleoprotein SMD1 and 99.86
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.85
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.85
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.84
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.84
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.84
KOG3293134 consensus Small nuclear ribonucleoprotein (snRNP) 99.82
KOG344896 consensus Predicted snRNP core protein [RNA proces 99.82
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.82
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.81
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.8
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.77
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.75
KOG348279 consensus Small nuclear ribonucleoprotein (snRNP) 99.75
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.73
cd0171779 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins 99.72
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 99.7
cd0172874 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins 99.7
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.68
KOG178377 consensus Small nuclear ribonucleoprotein F [RNA p 99.67
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.65
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.62
KOG178077 consensus Small Nuclear ribonucleoprotein G [RNA p 99.59
KOG346091 consensus Small nuclear ribonucleoprotein (snRNP) 99.29
KOG177584 consensus U6 snRNA-associated Sm-like protein [RNA 99.28
KOG177488 consensus Small nuclear ribonucleoprotein E [RNA p 99.25
KOG1781108 consensus Small Nuclear ribonucleoprotein splicing 98.89
KOG178496 consensus Small Nuclear ribonucleoprotein splicing 98.56
KOG3168177 consensus U1 snRNP component [Transcription] 98.52
KOG1782129 consensus Small Nuclear ribonucleoprotein splicing 98.38
PF1443877 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1. 98.32
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 97.62
PF1270196 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC 97.5
KOG3459114 consensus Small nuclear ribonucleoprotein (snRNP) 97.27
PF1109580 Gemin7: Gem-associated protein 7 (Gemin7); InterPr 96.86
cd0173674 LSm14_N LSm14 (also known as RAP55) belongs to a f 96.53
PF1084266 DUF2642: Protein of unknown function (DUF2642); In 96.27
cd0171661 Hfq Hfq, an abundant, ubiquitous RNA-binding prote 95.47
TIGR0238361 Hfq RNA chaperone Hfq. This model represents the R 95.46
PF0223748 BPL_C: Biotin protein ligase C terminal domain; In 95.29
PRK0039579 hfq RNA-binding protein Hfq; Provisional 94.97
cd0173561 LSm12_N LSm12 belongs to a family of Sm-like prote 94.49
PF06372166 Gemin6: Gemin6 protein; InterPro: IPR009422 This f 94.2
KOG1073 361 consensus Uncharacterized mRNA-associated protein 93.72
COG192377 Hfq Uncharacterized host factor I protein [General 93.48
PRK14638150 hypothetical protein; Provisional 92.13
PRK14642197 hypothetical protein; Provisional 91.69
PRK14639140 hypothetical protein; Provisional 91.37
PRK02001152 hypothetical protein; Validated 90.69
PRK14091165 RNA-binding protein Hfq; Provisional 89.31
cd0173483 YlxS_C YxlS is a Bacillus subtilis gene of unknown 88.46
PRK14091165 RNA-binding protein Hfq; Provisional 88.12
PRK14644136 hypothetical protein; Provisional 88.03
COG0779153 Uncharacterized protein conserved in bacteria [Fun 87.54
PRK00092154 ribosome maturation protein RimP; Reviewed 87.09
PRK14640152 hypothetical protein; Provisional 86.49
PRK14633150 hypothetical protein; Provisional 85.17
PRK14632172 hypothetical protein; Provisional 84.23
PRK14636176 hypothetical protein; Provisional 83.93
PRK14645154 hypothetical protein; Provisional 83.22
PRK14634155 hypothetical protein; Provisional 82.72
PRK14643164 hypothetical protein; Provisional 82.34
PF02576141 DUF150: Uncharacterised BCR, YhbC family COG0779; 81.64
PRK14646155 hypothetical protein; Provisional 81.25
PRK14647159 hypothetical protein; Provisional 80.46
>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 
Probab=99.96  E-value=2.4e-29  Score=171.05  Aligned_cols=87  Identities=84%  Similarity=1.217  Sum_probs=82.6

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEEcCCCCcchhhhh
Q 033530            2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLLV   81 (117)
Q Consensus         2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lpd~id~~~~l~   81 (117)
                      +|+.||+++.|++|+||||||.+|+|+|.++|+|||++|+||+++.++++...++.++|||++|+||++||++|+.++|.
T Consensus         1 ~~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~~~~~l~   80 (90)
T cd01724           1 KLVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLNLDTLLV   80 (90)
T ss_pred             CHhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCCcchhhh
Confidence            58899999999999999999999999999999999999999999988888899999999999999999999999999999


Q ss_pred             hcCcccC
Q 033530           82 EETPRVK   88 (117)
Q Consensus        82 ~~~~~~~   88 (117)
                      +.+++.+
T Consensus        81 ~~~~~~~   87 (90)
T cd01724          81 DSTPKPK   87 (90)
T ss_pred             hcCCccc
Confidence            9975544

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 D1 heterodimerizes with subunit D2 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 DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
>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
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>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
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification] 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
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification] 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
>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
>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
>smart00651 Sm snRNP Sm proteins Back     alignment and domain information
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification] Back     alignment and domain information
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification] 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
>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
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] 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
>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
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [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
>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
>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
>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
>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
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification] 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
>PTZ00138 small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification] Back     alignment and domain information
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [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
>KOG1774 consensus Small nuclear ribonucleoprotein E [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
>KOG3168 consensus U1 snRNP component [Transcription] Back     alignment and domain information
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1 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
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A Back     alignment and domain information
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification] 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
>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
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function 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
>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
>PRK00395 hfq RNA-binding protein Hfq; 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
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins Back     alignment and domain information
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only] Back     alignment and domain information
>PRK14638 hypothetical protein; Provisional Back     alignment and domain information
>PRK14642 hypothetical protein; Provisional Back     alignment and domain information
>PRK14639 hypothetical protein; Provisional Back     alignment and domain information
>PRK02001 hypothetical protein; Validated Back     alignment and domain information
>PRK14091 RNA-binding protein Hfq; 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
>PRK14091 RNA-binding protein Hfq; Provisional Back     alignment and domain information
>PRK14644 hypothetical protein; Provisional Back     alignment and domain information
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK00092 ribosome maturation protein RimP; Reviewed Back     alignment and domain information
>PRK14640 hypothetical protein; Provisional Back     alignment and domain information
>PRK14633 hypothetical protein; Provisional Back     alignment and domain information
>PRK14632 hypothetical protein; Provisional Back     alignment and domain information
>PRK14636 hypothetical protein; Provisional Back     alignment and domain information
>PRK14645 hypothetical protein; Provisional Back     alignment and domain information
>PRK14634 hypothetical protein; Provisional Back     alignment and domain information
>PRK14643 hypothetical protein; Provisional Back     alignment and domain information
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [] Back     alignment and domain information
>PRK14646 hypothetical protein; Provisional Back     alignment and domain information
>PRK14647 hypothetical protein; Provisional 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 ?
Query117
1b34_A119 Crystal Structure Of The D1d2 Sub-Complex From The 1e-34
3pgw_Z126 Crystal Structure Of Human U1 Snrnp Length = 126 2e-04
3cw1_D126 Crystal Structure Of Human Spliceosomal U1 Snrnp Le 3e-04
1d3b_A75 Crystal Structure Of The D3b Subcomplex Of The Huma 6e-04
>pdb|1B34|A Chain A, Crystal Structure Of The D1d2 Sub-Complex From The Human Snrnp Core Domain Length = 119 Back     alignment and structure 
Iteration: 1

 Score =  141 bits (355), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 70/94 (74%), Positives = 82/94 (87%)
Query: 1  MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSV 60
          MKLVRFLMKL++ETV+IELKNGT VHGTITGVD+SMNTHLK VK+TLK + PV L+ LS+
Sbjct: 1  MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI 60
Query: 61 RGNNIRYYILPDSLNLETLLVEETPRVKPKKPTA 94
          RGNNIRY+ILPDSL L+TLLV+  P+VK KK  A
Sbjct: 61 RGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREA 94
>pdb|3PGW|Z Chain Z, Crystal Structure Of Human U1 Snrnp Length = 126 Back     alignment and structure
>pdb|3CW1|D Chain D, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 126 Back     alignment and structure
>pdb|1D3B|A Chain A, Crystal Structure Of The D3b Subcomplex Of The Human Core Snrnp Domain At 2.0a Resolution Length = 75 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 ?
Query117
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 1e-37
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 2e-28
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 1e-25
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 1e-24
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 6e-16
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 2e-12
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 1e-10
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 7e-10
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 6e-09
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 7e-09
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 1e-07
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 1e-07
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 8e-07
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 1e-05
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 8e-04
>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
 Score =  122 bits (307), Expect = 1e-37
 Identities = 70/95 (73%), Positives = 82/95 (86%)

Query: 1  MKLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSV 60
          MKLVRFLMKL++ETV+IELKNGT VHGTITGVD+SMNTHLK VK+TLK + PV L+ LS+
Sbjct: 1  MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI 60

Query: 61 RGNNIRYYILPDSLNLETLLVEETPRVKPKKPTAG 95
          RGNNIRY+ILPDSL L+TLLV+  P+VK KK  A 
Sbjct: 61 RGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREAV 95
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query117
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 99.96
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 99.95
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.93
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.92
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.9
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.89
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.89
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.87
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.87
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.87
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.86
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.86
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.86
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.85
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.84
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.83
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.81
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.8
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.79
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.77
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.77
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.75
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.75
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.71
1y96_A86 Gemin6, SIP2, GEM-associated protein 6; SM fold, p 98.94
2vxe_A88 CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA 97.03
4a53_A125 EDC3; RNA binding protein; NMR {Schizosaccharomyce 96.63
2fb7_A95 SM-like protein, LSM-14_N (RAP55); DR.13312, BC055 96.61
1y96_B85 Gemin7, SIP3, GEM-associated protein 7; SM fold, p 96.6
2vc8_A84 Enhancer of mRNA-decapping protein 3; P-BODY compo 96.55
1u1s_A82 HFQ protein; SM-like bacterial protein, riken stru 96.4
1kq1_A77 HFQ, HOST factor for Q beta; hexamer, RNA binding 96.35
3ahu_A78 Protein HFQ; SM-like motif, protein-RNA complex, t 96.32
2ylb_A74 Protein HFQ; RNA-binding protein, LSM protein, RNA 96.28
2qtx_A71 Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi 95.87
2y90_A104 Protein HFQ; RNA-binding protein, SM-like, RNA cha 95.83
3sb2_A79 Protein HFQ; SM-like, RNA chaperone, chaperone; 2. 95.34
1ycy_A71 Conserved hypothetical protein; structural genomic 94.25
2rm4_A103 CG6311-PB, DM EDC3; enhancer of mRNA decapping, P- 92.72
3hfo_A70 SSR3341 protein; HFQ, SM, RNA-binding protein, sRN 89.3
3hfn_A72 ASL2047 protein; HFQ, SM, RNA-binding protein, sRN 83.73
3rux_A270 BIRA bifunctional protein; biotin-protein ligase, 83.63
1ib8_A164 Conserved protein SP14.3; nucleic acid binding pro 82.66
>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
Probab=99.96  E-value=2.5e-29  Score=179.13  Aligned_cols=98  Identities=21%  Similarity=0.400  Sum_probs=83.9

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEEcCCCCcchhhhh
Q 033530            2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLLV   81 (117)
Q Consensus         2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lpd~id~~~~l~   81 (117)
                      ..++||++++|++|+|+||||++|+|+|.+||+|||++|+||+++.++++..+++.+||||++|+||++||+++.+|+|+
T Consensus         5 ~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~IRGnnI~~I~lpd~l~~~~~l~   84 (126)
T 2y9a_D            5 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDMLKNAPMLK   84 (126)
T ss_dssp             CSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCSSCSSSSHHH
T ss_pred             cHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEEEeCCEEEEEEccccccchHHhh
Confidence            45899999999999999999999999999999999999999999988888899999999999999999999999999999


Q ss_pred             hcCcccCCCCCCCCccee
Q 033530           82 EETPRVKPKKPTAGIDII   99 (117)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~   99 (117)
                      ++.+|.+.+++++|+..+
T Consensus        85 ~~~~k~~~~~~~~g~~~~  102 (126)
T 2y9a_D           85 SMKNKNQGSGAGRGKAAI  102 (126)
T ss_dssp             HHHHHHC-----------
T ss_pred             hhhhcccccccCcCchhh
Confidence            999888777666666543
>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_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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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_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
>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
>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} 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
>4a53_A EDC3; RNA binding protein; NMR {Schizosaccharomyces pombe} PDB: 4a54_A 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
>1y96_B Gemin7, SIP3, GEM-associated protein 7; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} 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
>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
>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
>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_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
>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii} 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
>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2 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
>2rm4_A CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-BODY component, SM-like protein,, protein binding; NMR {Drosophila melanogaster} 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
>3rux_A BIRA bifunctional protein; biotin-protein ligase, ligase-ligase inhibitor complex; HET: BS5; 1.70A {Mycobacterium tuberculosis} PDB: 3l1a_A 3l2z_A 2cgh_A Back     alignment and structure
>1ib8_A Conserved protein SP14.3; nucleic acid binding protein, ribosomal protein, essential gene, structural genomics; NMR {Streptococcus pneumoniae} SCOP: b.38.2.1 d.52.4.1 Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 117
d1b34a_80 b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s 1e-31
d1d3ba_72 b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s 2e-18
d1m5q1_127 b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch 2e-16
d1n9ra_68 b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S 2e-14
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 4e-14
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 6e-14
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 9e-14
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 2e-13
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 1e-12
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 3e-12
d1d3bb_81 b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa 0.001
d2fwka192 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr 0.002
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80 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: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  104 bits (262), Expect = 1e-31
 Identities = 63/80 (78%), Positives = 73/80 (91%)

Query: 2  KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVR 61
          KLVRFLMKL++ETV+IELKNGT VHGTITGVD+SMNTHLK VK+TLK + PV L+ LS+R
Sbjct: 1  KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIR 60

Query: 62 GNNIRYYILPDSLNLETLLV 81
          GNNIRY+ILPDSL L+TLLV
Sbjct: 61 GNNIRYFILPDSLPLDTLLV 80
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72 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
>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
>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
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Length = 71 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
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 71 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
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query117
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.96
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.93
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.88
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.88
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.87
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.87
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.87
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.86
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.86
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 99.84
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.74
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.7
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.67
d2vxfa180 LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) 97.12
d1kq1a_60 Pleiotropic translational regulator Hfq {Staphyloc 95.14
d1u1sa166 Pleiotropic translational regulator Hfq {Pseudomon 94.53
d1ycya166 Hypothetical protein PF1955 {Pyrococcus furiosus [ 94.09
d1biaa247 Biotin repressor/biotin holoenzyme synthetase, C-t 93.63
d1ib8a174 Hypothetical protein SP14.3 (SP0552) {Streptococcu 89.94
>d1b34a_ b.38.1.1 (A:) D1 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: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=1.2e-29  Score=166.40  Aligned_cols=79  Identities=78%  Similarity=1.179  Sum_probs=77.1

Q ss_pred             chhHHHhhcCCCEEEEEEcCCcEEEEEEEEeccccceEEccEEEEeCCCCceeeceEEEecCeEEEEEcCCCCcchhhh
Q 033530            2 KLVRFLMKLNNETVSIELKNGTIVHGTITGVDISMNTHLKTVKLTLKGKNPVNLDHLSVRGNNIRYYILPDSLNLETLL   80 (117)
Q Consensus         2 ~l~~~L~~l~gk~V~VeLkng~~~~G~L~~~D~~MNl~L~da~~~~~~~~~~~~~~v~IRG~~I~~I~lpd~id~~~~l   80 (117)
                      +|++||++++|++|+||||||.+|+|+|.++|+|||++|+||+++.+++++.+++.+||||++|+||++||++|+.++|
T Consensus         1 ~lv~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~~Ir~i~lPd~l~~~~~L   79 (80)
T d1b34a_           1 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLL   79 (80)
T ss_dssp             CHHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTTCCHHHHT
T ss_pred             CHHHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEEEcccEEEcCCEEEEEECCCCccccccc
Confidence            6899999999999999999999999999999999999999999999999999999999999999999999999999987
>d1d3ba_ b.38.1.1 (A:) D3 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
>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
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} 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
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} 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
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} 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
>d2vxfa1 b.38.1.5 (A:6-85) LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) [TaxId: 7955]} Back     information, alignment and structure
>d1kq1a_ b.38.1.2 (A:) Pleiotropic translational regulator Hfq {Staphylococcus aureus [TaxId: 1280]} 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
>d1ycya1 b.38.1.4 (A:5-70) Hypothetical protein PF1955 {Pyrococcus furiosus [TaxId: 2261]} 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
>d1ib8a1 b.38.2.1 (A:91-164) Hypothetical protein SP14.3 (SP0552) {Streptococcus pneumoniae [TaxId: 1313]} Back     information, alignment and structure