Citrus Sinensis ID: 034407

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-----
MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKRAQKAEREASDLKGSMRKRMEFLDLD
ccEEEcccccccEEEEccEEEEEcccccccEEEEEEEEEcccEEEEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
cccEccHHHHHHHHHHHHEEEEEEcccccccccEEEEEEccEEEEEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
MGTLCSFDQFANAVLEGACERVIvgdlycdiplglyvirGENVVLIGEldlerdelpphlthVSVAEIKRAQKAEREASDLKGSmrkrmefldld
MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKRAQKAereasdlkgsmrkrmefldld
MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKRAQKAEREASDLKGSMRKRMEFLDLD
***LCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELP*HLTHV********************************
MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEI********************MEFLDL*
MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKR***********KGSMRKRMEFLDLD
MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKRAQKAEREASDLKGSMRKRMEFL*LD
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKRAQKAEREASDLKGSMRKRMEFLDLD
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 ?
Query95 2.2.26 [Sep-21-2011]
Q5E9Z8133 U6 snRNA-associated Sm-li yes no 0.821 0.586 0.506 6e-15
O15116133 U6 snRNA-associated Sm-li yes no 0.821 0.586 0.506 6e-15
Q8VC85133 U6 snRNA-associated Sm-li yes no 0.852 0.609 0.523 1e-14
Q54W83129 Probable U6 snRNA-associa yes no 0.747 0.550 0.464 1e-12
P87173140 U6 snRNA-associated Sm-li yes no 0.568 0.385 0.574 4e-12
P47017172 Sm-like protein LSm1 OS=S yes no 0.6 0.331 0.389 1e-07
Q5RCP396 N-alpha-acetyltransferase no no 0.568 0.562 0.454 1e-05
Q6ZWM496 N-alpha-acetyltransferase no no 0.568 0.562 0.454 1e-05
O9577796 N-alpha-acetyltransferase no no 0.568 0.562 0.454 1e-05
Q3ZCE096 N-alpha-acetyltransferase no no 0.568 0.562 0.454 1e-05
>sp|Q5E9Z8|LSM1_BOVIN U6 snRNA-associated Sm-like protein LSm1 OS=Bos taurus GN=LSM1 PE=2 SV=1 Back     alignment and function desciption
 Score = 79.3 bits (194), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 40/79 (50%), Positives = 53/79 (67%), Gaps = 1/79 (1%)

Query: 1   MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHL 60
           +G L S DQFAN VL    ER+ VG  Y DIP G++V+RGENVVL+GE+DLE++   P L
Sbjct: 29  IGFLRSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGENVVLLGEIDLEKESDTP-L 87

Query: 61  THVSVAEIKRAQKAEREAS 79
             VS+ EI   Q+ E++  
Sbjct: 88  QQVSIEEILEEQRVEQQTK 106
Plays a role in replication-dependent histone mRNA degradation. Binds specifically to the 3'-terminal U-tract of U6 snRNA.
Bos taurus (taxid: 9913)
>sp|O15116|LSM1_HUMAN U6 snRNA-associated Sm-like protein LSm1 OS=Homo sapiens GN=LSM1 PE=1 SV=1 Back     alignment and function description
>sp|Q8VC85|LSM1_MOUSE U6 snRNA-associated Sm-like protein LSm1 OS=Mus musculus GN=Lsm1 PE=2 SV=1 Back     alignment and function description
>sp|Q54W83|LSM1_DICDI Probable U6 snRNA-associated Sm-like protein LSm1 OS=Dictyostelium discoideum GN=lsm1 PE=3 SV=1 Back     alignment and function description
>sp|P87173|LSM1_SCHPO U6 snRNA-associated Sm-like protein LSm1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm1 PE=3 SV=1 Back     alignment and function description
>sp|P47017|LSM1_YEAST Sm-like protein LSm1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=LSM1 PE=1 SV=1 Back     alignment and function description
>sp|Q5RCP3|NAA38_PONAB N-alpha-acetyltransferase 38, NatC auxiliary subunit OS=Pongo abelii GN=NAA38 PE=3 SV=3 Back     alignment and function description
>sp|Q6ZWM4|NAA38_MOUSE N-alpha-acetyltransferase 38, NatC auxiliary subunit OS=Mus musculus GN=Naa38 PE=3 SV=3 Back     alignment and function description
>sp|O95777|NAA38_HUMAN N-alpha-acetyltransferase 38, NatC auxiliary subunit OS=Homo sapiens GN=NAA38 PE=1 SV=3 Back     alignment and function description
>sp|Q3ZCE0|NAA38_BOVIN N-alpha-acetyltransferase 38, NatC auxiliary subunit OS=Bos taurus GN=NAA38 PE=3 SV=3 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 ?
Query95
356560171121 PREDICTED: U6 snRNA-associated Sm-like p 1.0 0.785 0.915 2e-43
351721438128 uncharacterized protein LOC100306352 [Gl 1.0 0.742 0.915 3e-43
225442069128 PREDICTED: U6 snRNA-associated Sm-like p 1.0 0.742 0.905 4e-43
255583960128 lsm1, putative [Ricinus communis] gi|223 1.0 0.742 0.873 3e-42
224073612128 predicted protein [Populus trichocarpa] 1.0 0.742 0.894 1e-41
224119520128 predicted protein [Populus trichocarpa] 1.0 0.742 0.894 1e-41
449447922128 PREDICTED: U6 snRNA-associated Sm-like p 1.0 0.742 0.842 4e-41
323650499128 small nuclear ribonucleoprotein [Mangife 1.0 0.742 0.842 1e-40
359484235128 PREDICTED: U6 snRNA-associated Sm-like p 1.0 0.742 0.842 3e-40
18400270128 U6 snRNA-associated Sm-like protein LSm1 1.0 0.742 0.852 3e-40
>gi|356560171|ref|XP_003548368.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm1-like [Glycine max] Back     alignment and taxonomy information
 Score =  179 bits (454), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 87/95 (91%), Positives = 90/95 (94%)

Query: 1   MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHL 60
           MGTL SFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLER+ELP H+
Sbjct: 27  MGTLRSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLEREELPEHM 86

Query: 61  THVSVAEIKRAQKAEREASDLKGSMRKRMEFLDLD 95
           T VS AEIKRAQKAEREASDLKG+MRKRMEFLD D
Sbjct: 87  TRVSTAEIKRAQKAEREASDLKGTMRKRMEFLDFD 121

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|351721438|ref|NP_001237465.1| uncharacterized protein LOC100306352 [Glycine max] gi|255628281|gb|ACU14485.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|225442069|ref|XP_002271476.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm1 [Vitis vinifera] gi|147803430|emb|CAN62239.1| hypothetical protein VITISV_033727 [Vitis vinifera] gi|297742980|emb|CBI35847.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|255583960|ref|XP_002532727.1| lsm1, putative [Ricinus communis] gi|223527535|gb|EEF29658.1| lsm1, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|224073612|ref|XP_002304120.1| predicted protein [Populus trichocarpa] gi|222841552|gb|EEE79099.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224119520|ref|XP_002331181.1| predicted protein [Populus trichocarpa] gi|118489961|gb|ABK96777.1| unknown [Populus trichocarpa x Populus deltoides] gi|222873302|gb|EEF10433.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449447922|ref|XP_004141715.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm1-like [Cucumis sativus] gi|449480489|ref|XP_004155908.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|323650499|gb|ADX97330.1| small nuclear ribonucleoprotein [Mangifera indica] Back     alignment and taxonomy information
>gi|359484235|ref|XP_003633086.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm1-like [Vitis vinifera] gi|297738539|emb|CBI27784.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|18400270|ref|NP_566476.1| U6 snRNA-associated Sm-like protein LSm1 [Arabidopsis thaliana] gi|30682974|ref|NP_850580.1| U6 snRNA-associated Sm-like protein LSm1 [Arabidopsis thaliana] gi|21536995|gb|AAM61336.1| Sm protein, putative [Arabidopsis thaliana] gi|27754337|gb|AAO22620.1| putative Sm protein [Arabidopsis thaliana] gi|28393853|gb|AAO42334.1| putative Sm protein [Arabidopsis thaliana] gi|332641944|gb|AEE75465.1| U6 snRNA-associated Sm-like protein LSm1 [Arabidopsis thaliana] gi|332641945|gb|AEE75466.1| U6 snRNA-associated Sm-like protein LSm1 [Arabidopsis thaliana] 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 ?
Query95
TAIR|locus:2087522128 LSM1B "SM-like 1B" [Arabidopsi 1.0 0.742 0.852 7.8e-39
TAIR|locus:2011246128 LSM1A "SM-like 1A" [Arabidopsi 1.0 0.742 0.8 6.5e-35
UNIPROTKB|I3LCU8133 LSM1 "Uncharacterized protein" 0.810 0.578 0.525 2e-15
FB|FBgn0261067137 LSm1 [Drosophila melanogaster 0.8 0.554 0.532 4.2e-15
UNIPROTKB|Q5E9Z8133 LSM1 "U6 snRNA-associated Sm-l 0.8 0.571 0.519 5.4e-15
UNIPROTKB|E2R7S6133 LSM1 "Uncharacterized protein" 0.8 0.571 0.519 5.4e-15
UNIPROTKB|O15116133 LSM1 "U6 snRNA-associated Sm-l 0.8 0.571 0.519 5.4e-15
RGD|1304967133 Lsm1 "LSM1 homolog, U6 small n 0.810 0.578 0.512 5.4e-15
MGI|MGI:1914457133 Lsm1 "LSM1 homolog, U6 small n 0.852 0.609 0.523 8.8e-15
ZFIN|ZDB-GENE-040801-68133 lsm1 "LSM1 homolog, U6 small n 0.810 0.578 0.5 3.8e-14
TAIR|locus:2087522 LSM1B "SM-like 1B" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 81/95 (85%), Positives = 87/95 (91%)

Query:     1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHL 60
             MGTL SFDQFANAVLEGACERVIVG+ YCDIPLGLYVIRGENVVLIGELD ER+ELPPH+
Sbjct:    34 MGTLRSFDQFANAVLEGACERVIVGEQYCDIPLGLYVIRGENVVLIGELDTEREELPPHM 93

Query:    61 THVSVAEIKRAQKAEREASDLKGSMRKRMEFLDLD 95
               VS AEIKRAQK EREAS+L+G+MRKRMEFLD D
Sbjct:    94 IRVSEAEIKRAQKVEREASELRGTMRKRMEFLDFD 128
GO:0005634 "nucleus" evidence=ISM;ISS
GO:0005732 "small nucleolar ribonucleoprotein complex" evidence=ISS
GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA
GO:0000932 "cytoplasmic mRNA processing body" evidence=IDA
GO:0005515 "protein binding" evidence=IPI
GO:0016070 "RNA metabolic process" evidence=IGI
TAIR|locus:2011246 LSM1A "SM-like 1A" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|I3LCU8 LSM1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
FB|FBgn0261067 LSm1 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|Q5E9Z8 LSM1 "U6 snRNA-associated Sm-like protein LSm1" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2R7S6 LSM1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|O15116 LSM1 "U6 snRNA-associated Sm-like protein LSm1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
RGD|1304967 Lsm1 "LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
MGI|MGI:1914457 Lsm1 "LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-040801-68 lsm1 "LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [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) ?
Q8VC85LSM1_MOUSENo assigned EC number0.52320.85260.6090yesno

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:
GSVIVG00034053001
SubName- Full=Putative uncharacterized protein (Chromosome chr9 scaffold_7, whole genome shotgun sequence); (128 aa)
(Vitis vinifera)
Predicted Functional Partners:
GSVIVG00020489001
SubName- Full=Chromosome chr5 scaffold_2, whole genome shotgun sequence; (87 aa)
   •••• 0.874
GSVIVG00023663001
SubName- Full=Chromosome chr7 scaffold_31, whole genome shotgun sequence; (97 aa)
   •••• 0.845
GSVIVG00008837001
SubName- Full=Chromosome chr13 scaffold_210, whole genome shotgun sequence; (113 aa)
   •••• 0.830
GSVIVG00031776001
hypothetical protein LOC100253870 (172 aa)
   •••• 0.816
GSVIVG00017697001
SubName- Full=Chromosome chr17 scaffold_16, whole genome shotgun sequence; (86 aa)
   •  • 0.449
GSVIVG00033465001
SubName- Full=Chromosome chr19 scaffold_66, whole genome shotgun sequence; (107 aa)
   •• • 0.403

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 ?
Query95
cd0172874 cd01728, LSm1, Like-Sm protein 1 1e-23
cd0172791 cd01727, LSm8, Like-Sm protein 8 2e-12
smart0065167 smart00651, Sm, snRNP Sm proteins 1e-10
pfam0142366 pfam01423, LSM, LSM domain 1e-09
COG195879 COG1958, LSM1, Small nuclear ribonucleoprotein (sn 3e-06
cd0173169 cd01731, archaeal_Sm1, archaeal Sm protein 1 5e-04
cd0171970 cd01719, Sm_G, Sm protein G 6e-04
>gnl|CDD|212475 cd01728, LSm1, Like-Sm protein 1 Back     alignment and domain information 
 Score = 85.3 bits (212), Expect = 1e-23
 Identities = 33/49 (67%), Positives = 40/49 (81%)

Query: 1  MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGEL 49
          +G L SFDQFAN VLE   ER+IVG+ Y DIP GL++IRGENVVL+GE+
Sbjct: 26 IGILRSFDQFANLVLEDTVERIIVGNQYGDIPRGLFIIRGENVVLLGEI 74

The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. Accumulation of uridylated RNAs in an lsm1 mutant suggests an involvement of the LSm1-7 complex in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm1-7, together with Pat1, are also called the decapping activator. 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. Length = 74
>gnl|CDD|212474 cd01727, LSm8, Like-Sm protein 8 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|212466 cd01719, Sm_G, Sm protein G Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 95
KOG1782129 consensus Small Nuclear ribonucleoprotein splicing 99.88
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.71
cd0172874 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins 99.71
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.7
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.67
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 99.67
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.63
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.62
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.62
KOG178496 consensus Small Nuclear ribonucleoprotein splicing 99.59
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.57
cd0171779 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins 99.56
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.54
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.53
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.45
KOG178077 consensus Small Nuclear ribonucleoprotein G [RNA p 99.44
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.44
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.43
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.43
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.41
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.37
KOG177488 consensus Small nuclear ribonucleoprotein E [RNA p 99.34
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.27
KOG1781108 consensus Small Nuclear ribonucleoprotein splicing 99.25
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.24
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.24
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.17
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.06
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.03
KOG346091 consensus Small nuclear ribonucleoprotein (snRNP) 98.9
KOG348279 consensus Small nuclear ribonucleoprotein (snRNP) 98.83
KOG177584 consensus U6 snRNA-associated Sm-like protein [RNA 98.71
KOG178377 consensus Small nuclear ribonucleoprotein F [RNA p 98.7
KOG3168177 consensus U1 snRNP component [Transcription] 98.52
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 97.1
KOG344896 consensus Predicted snRNP core protein [RNA proces 97.07
KOG3459114 consensus Small nuclear ribonucleoprotein (snRNP) 96.86
KOG3293134 consensus Small nuclear ribonucleoprotein (snRNP) 95.75
KOG3172119 consensus Small nuclear ribonucleoprotein Sm D3 [R 94.6
KOG3428109 consensus Small nuclear ribonucleoprotein SMD1 and 92.03
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information 
Probab=99.88  E-value=1.4e-23  Score=146.34  Aligned_cols=93  Identities=55%  Similarity=0.935  Sum_probs=80.5

Q ss_pred             CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeeeCCcccCCCCCCceecHHHHHHHHHHHH----
Q 034407            1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKRAQKAER----   76 (95)
Q Consensus         1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~d~~~e~~~~~~~~v~~~ei~~~~~~~~----   76 (95)
                      +|+|+|||||.|+||++|+||++.++.|...+.|.++|||+||+++|++|.++|  ..++.++|+++++..++.++    
T Consensus        33 ~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE--~~~l~~i~~~e~~~~~~~~q~~k~  110 (129)
T KOG1782|consen   33 IGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKE--EEPLEQISFEEALNEIKREQEAKK  110 (129)
T ss_pred             hhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchh--hccceeCCHHHHHHHHHHHHHHhh
Confidence            599999999999999999999999999999999999999999999999999998  47999999998865444444    


Q ss_pred             HHhhhhhhhhhhcccccCC
Q 034407           77 EASDLKGSMRKRMEFLDLD   95 (95)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~   95 (95)
                      +++..+..++.+++|+|.+
T Consensus       111 e~~~lkg~m~~rg~~~D~~  129 (129)
T KOG1782|consen  111 EEERLKGTMAERGEFLDFD  129 (129)
T ss_pred             hHHHHHHHHHHhcccccCC
Confidence            4444455677889999875

>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
>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
>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
>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
>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
>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
>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
>PTZ00138 small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] 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
>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
>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
>PRK00737 small nuclear ribonucleoprotein; Provisional 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
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification] Back     alignment and domain information
>smart00651 Sm snRNP Sm 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
>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
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] 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
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification] 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
>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
>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
>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
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification] Back     alignment and domain information
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification] Back     alignment and domain information
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification] Back     alignment and domain information
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification] Back     alignment and domain information
>KOG3168 consensus U1 snRNP component [Transcription] 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
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification] Back     alignment and domain information
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification] Back     alignment and domain information
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [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
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query95
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 3e-13
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 4e-13
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 2e-12
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 5e-12
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 3e-10
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 3e-10
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 5e-07
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 1e-06
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 1e-06
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 4e-06
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 5e-06
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 8e-06
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 1e-05
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 1e-05
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 1e-05
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 2e-05
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 6e-04
>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
 Score = 58.6 bits (142), Expect = 3e-13
 Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 4/57 (7%)

Query: 2  GTLCSFDQFANAVLEGACERVIVGD----LYCDIPLGLYVIRGENVVLIGELDLERD 54
          GTL +FD   N VL  A E +   +       +    +  IRG+ V LI     + D
Sbjct: 35 GTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTPSEDDD 91
>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_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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query95
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.67
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.67
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.63
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.6
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.6
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.59
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.59
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.58
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.57
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.57
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.56
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.56
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.55
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.55
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.54
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.53
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.52
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.5
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.48
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 99.46
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.45
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.42
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.32
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 99.27
>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
Probab=99.67  E-value=3.8e-17  Score=111.10  Aligned_cols=55  Identities=35%  Similarity=0.443  Sum_probs=42.0

Q ss_pred             CeeEEEeccccceEecceEEEEecCc----ccceeccceEEEecCcEEEEeeeCCcccC
Q 034407            1 MGTLCSFDQFANAVLEGACERVIVGD----LYCDIPLGLYVIRGENVVLIGELDLERDE   55 (95)
Q Consensus         1 iG~L~gfDq~mNLVL~d~~Eri~~~~----~~~~~~lG~~lIRGdnIv~I~~~d~~~e~   55 (95)
                      +|+|+|||+||||||++|+|++..++    ....+.+|+++|||+||++|+++|.+++-
T Consensus        47 ~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~ee~  105 (113)
T 4emk_C           47 TGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPMDGSEEI  105 (113)
T ss_dssp             EEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEECC-----
T ss_pred             EEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEecCccccc
Confidence            49999999999999999999875432    13478999999999999999999988863
>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
>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
>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Back     alignment and structure
>3s6n_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
>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_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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe} Back     alignment and structure
>1b34_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
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Back     alignment and structure
>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like P; OB-like fold, B-sheet toroid, 14-MER, cadmium-binding site, translation; 2.00A {Pyrobaculum aerophilum} SCOP: b.38.1.1 Back     alignment and structure
>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

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 95
d1d3bb_81 b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa 2e-11
d1m5q1_127 b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch 3e-11
d1n9ra_68 b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S 7e-11
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 3e-09
d2fwka192 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr 4e-09
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 4e-09
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 7e-09
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 9e-09
d1b34b_93 b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s 1e-08
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 2e-08
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 3e-08
d1d3ba_72 b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s 0.004
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 81 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: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.5 bits (126), Expect = 2e-11
 Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 12/64 (18%)

Query: 2  GTLCSFDQFANAVLEGACERVIVGDLYCDIP-------LGLYVIRGENVVLIGELDLERD 54
          GT  +FD+  N +L    E   +               LGL ++RGEN+V +       +
Sbjct: 23 GTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSM-----TVE 77

Query: 55 ELPP 58
            PP
Sbjct: 78 GPPP 81
>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
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 71 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
>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
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Length = 71 Back     information, alignment and structure
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93 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
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 74 Back     information, alignment and structure
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query95
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.59
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.57
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.56
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.56
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.54
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.54
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.54
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.51
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.51
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.48
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.29
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.07
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 98.91
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.59  E-value=5.5e-16  Score=95.36  Aligned_cols=47  Identities=40%  Similarity=0.359  Sum_probs=40.7

Q ss_pred             CeeEEEeccccceEecceEEEEecCcccceeccceEEEecCcEEEEeeeC
Q 034407            1 MGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD   50 (95)
Q Consensus         1 iG~L~gfDq~mNLVL~d~~Eri~~~~~~~~~~lG~~lIRGdnIv~I~~~d   50 (95)
                      .|+|+|||+|||++|++|+|++..+   ....+|.++|||+||.+|++++
T Consensus        21 ~G~L~~~D~~mNlvL~~~~e~~~~~---~~~~lg~~~IRG~nI~~I~~~p   67 (68)
T d1n9ra_          21 RGTLVSTDNYFNLQLNEAEEFVAGV---SHGTLGEIFIRCNNVLYIRELP   67 (68)
T ss_dssp             EEEEEECCTTTCEEEEEEEEEETTE---EEEECCSEEECGGGEEEEEECC
T ss_pred             EEEEEEECCcCceEEeeEEEEecCC---cccCcCeEEEECCEEEEEEeCC
Confidence            3999999999999999999975322   3668999999999999999765
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} 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
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} 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
>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} 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
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} 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
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} 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