Citrus Sinensis ID: 032108

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------
MSWAGPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKRVSALFFSLLFLSLHKRCCLLTMRYEIMGRSITIQFFLLHIINIF
cccccccccccHHHHHHHcccEEEEEEccccEEEEEEEEEcccccEEEEccEEEEEcccccccccccEEEEEcccEEEEEEccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccc
cccccccHHHHHHHHHHHHccEEEEEEccccEEEEEEEcHHHHHHHHHHHHEEEEEEccccccEccEEEEEEccEEEEEEEEcccHccccccccEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHcc
mswagpddvyLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIvgdlycdiplglyvirGENVVLIGEldlerdelpphlthVSVAEIKRVSALFFSLLFLSLHKRCCLLTMRYEIMGRSITIQFFLLHIINIF
mswagpddVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKRVSALFFSLLFLSLHKRCCLLTMRYEIMGRSITIQFFLLHIINIF
MSWAGPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKRVsalffsllflslHKRCCLLTMRYEIMGRSITIQFFLLHIINIF
*******DVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKRVSALFFSLLFLSLHKRCCLLTMRYEIMGRSITIQFFLLHIINI*
*************SLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVI******DIPLGLYVIRGENVVLIGELDLERDELPPH**HVSV*******************************MGRSITIQFFLLHIINIF
********VYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKRVSALFFSLLFLSLHKRCCLLTMRYEIMGRSITIQFFLLHIINIF
****GPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKRVSALFFSLLFLSLHKRCCLLTMRYEIMGRSITIQFFLLHIINIF
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSWAGPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKRVSALFFSLLFLSLHKRCCLLTMRYEIMGRSITIQFFLLHIINIF
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 ?
Query147 2.2.26 [Sep-21-2011]
Q54W83129 Probable U6 snRNA-associa yes no 0.659 0.751 0.484 3e-21
Q5E9Z8133 U6 snRNA-associated Sm-li yes no 0.605 0.669 0.577 7e-21
Q8VC85133 U6 snRNA-associated Sm-li yes no 0.605 0.669 0.577 7e-21
O15116133 U6 snRNA-associated Sm-li yes no 0.605 0.669 0.577 8e-21
P87173140 U6 snRNA-associated Sm-li yes no 0.598 0.628 0.494 3e-20
P47017172 Sm-like protein LSm1 OS=S yes no 0.585 0.5 0.4 2e-14
Q1ZXD594 N-alpha-acetyltransferase no no 0.503 0.787 0.486 5e-11
Q5RCP396 N-alpha-acetyltransferase yes no 0.523 0.802 0.397 6e-11
Q6ZWM496 N-alpha-acetyltransferase no no 0.523 0.802 0.397 6e-11
O9577796 N-alpha-acetyltransferase no no 0.523 0.802 0.397 6e-11
>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 desciption
 Score =  100 bits (249), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 47/97 (48%), Positives = 68/97 (70%)

Query: 11  LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYV 70
           +S+ L   +DKKL+V+LRDGRK +G + +FDQFAN VL+   ER+ VGD Y D  LGL+ 
Sbjct: 1   MSSGLGDEVDKKLIVVLRDGRKFIGIMRTFDQFANIVLQDTIERIYVGDCYSDKNLGLFF 60

Query: 71  IRGENVVLIGELDLERDELPPHLTHVSVAEIKRVSAL 107
           IRG+NVV++GE+D +++     L  +S  EI + +AL
Sbjct: 61  IRGDNVVILGEIDPDKEVQEKKLKKISWDEITKAAAL 97
Binds specifically to the 3'-terminal U-tract of U6 snRNA.
Dictyostelium discoideum (taxid: 44689)
>sp|Q5E9Z8|LSM1_BOVIN U6 snRNA-associated Sm-like protein LSm1 OS=Bos taurus GN=LSM1 PE=2 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|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|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|Q1ZXD5|NAA38_DICDI N-alpha-acetyltransferase 38, NatC auxiliary subunit OS=Dictyostelium discoideum GN=lsm8 PE=3 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

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 ?
Query147
351721438128 uncharacterized protein LOC100306352 [Gl 0.714 0.820 0.904 9e-49
255583960128 lsm1, putative [Ricinus communis] gi|223 0.714 0.820 0.876 5e-48
225442069128 PREDICTED: U6 snRNA-associated Sm-like p 0.714 0.820 0.876 2e-47
224073612128 predicted protein [Populus trichocarpa] 0.714 0.820 0.885 4e-47
224119520128 predicted protein [Populus trichocarpa] 0.714 0.820 0.876 1e-46
18400270128 U6 snRNA-associated Sm-like protein LSm1 0.727 0.835 0.841 1e-46
357514091131 U6 snRNA-associated Sm-like protein LSm1 0.700 0.786 0.864 2e-46
297829970128 hypothetical protein ARALYDRAFT_478821 [ 0.727 0.835 0.841 2e-46
323650499128 small nuclear ribonucleoprotein [Mangife 0.714 0.820 0.819 9e-45
449447922128 PREDICTED: U6 snRNA-associated Sm-like p 0.714 0.820 0.819 1e-44
>gi|351721438|ref|NP_001237465.1| uncharacterized protein LOC100306352 [Glycine max] gi|255628281|gb|ACU14485.1| unknown [Glycine max] Back     alignment and taxonomy information
 Score =  197 bits (502), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 95/105 (90%), Positives = 99/105 (94%)

Query: 1   MSWAGPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDL 60
           MSWAGP+D+YLSTSLASYLDKKLLVLLRDGRKLMGTL SFDQFANAVLEGACERVIVGDL
Sbjct: 1   MSWAGPEDIYLSTSLASYLDKKLLVLLRDGRKLMGTLRSFDQFANAVLEGACERVIVGDL 60

Query: 61  YCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKRVS 105
           YCDIPLGLYVIRGENVVLIGELDLER+ELP H+T VS AEIKR  
Sbjct: 61  YCDIPLGLYVIRGENVVLIGELDLEREELPEHMTRVSTAEIKRAQ 105

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>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|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|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|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
>gi|357514091|ref|XP_003627334.1| U6 snRNA-associated Sm-like protein LSm1 [Medicago truncatula] gi|355521356|gb|AET01810.1| U6 snRNA-associated Sm-like protein LSm1 [Medicago truncatula] Back     alignment and taxonomy information
>gi|297829970|ref|XP_002882867.1| hypothetical protein ARALYDRAFT_478821 [Arabidopsis lyrata subsp. lyrata] gi|297328707|gb|EFH59126.1| hypothetical protein ARALYDRAFT_478821 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|323650499|gb|ADX97330.1| small nuclear ribonucleoprotein [Mangifera indica] 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

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 ?
Query147
TAIR|locus:2087522128 LSM1B "SM-like 1B" [Arabidopsi 0.700 0.804 0.873 3.1e-44
TAIR|locus:2011246128 LSM1A "SM-like 1A" [Arabidopsi 0.700 0.804 0.815 1.6e-40
UNIPROTKB|Q5E9Z8133 LSM1 "U6 snRNA-associated Sm-l 0.605 0.669 0.577 3.5e-20
UNIPROTKB|E2R7S6133 LSM1 "Uncharacterized protein" 0.605 0.669 0.577 3.5e-20
UNIPROTKB|O15116133 LSM1 "U6 snRNA-associated Sm-l 0.605 0.669 0.577 3.5e-20
UNIPROTKB|I3LCU8133 LSM1 "Uncharacterized protein" 0.605 0.669 0.577 3.5e-20
MGI|MGI:1914457133 Lsm1 "LSM1 homolog, U6 small n 0.605 0.669 0.577 3.5e-20
POMBASE|SPBC3D6.08c140 lsm1 "mRNA decapping complex s 0.517 0.542 0.578 4.4e-20
RGD|1304967133 Lsm1 "LSM1 homolog, U6 small n 0.605 0.669 0.577 4.4e-20
FB|FBgn0261067137 LSm1 [Drosophila melanogaster 0.585 0.627 0.574 9.2e-20
TAIR|locus:2087522 LSM1B "SM-like 1B" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 466 (169.1 bits), Expect = 3.1e-44, P = 3.1e-44
 Identities = 90/103 (87%), Positives = 97/103 (94%)

Query:     1 MSWAGPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDL 60
             MSWAGP+++YLSTSLASYLD+KLLVLLRDGRKLMGTL SFDQFANAVLEGACERVIVG+ 
Sbjct:     1 MSWAGPEEIYLSTSLASYLDRKLLVLLRDGRKLMGTLRSFDQFANAVLEGACERVIVGEQ 60

Query:    61 YCDIPLGLYVIRGENVVLIGELDLERDELPPHLTHVSVAEIKR 103
             YCDIPLGLYVIRGENVVLIGELD ER+ELPPH+  VS AEIKR
Sbjct:    61 YCDIPLGLYVIRGENVVLIGELDTEREELPPHMIRVSEAEIKR 103
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|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
UNIPROTKB|I3LCU8 LSM1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] 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
POMBASE|SPBC3D6.08c lsm1 "mRNA decapping complex subunit (predicted)" [Schizosaccharomyces pombe (taxid:4896)] 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
FB|FBgn0261067 LSm1 [Drosophila melanogaster (taxid:7227)] 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) ?
O15116LSM1_HUMANNo assigned EC number0.57770.60540.6691yesno
Q8VC85LSM1_MOUSENo assigned EC number0.57770.60540.6691yesno
Q5E9Z8LSM1_BOVINNo assigned EC number0.57770.60540.6691yesno

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 ?
Query147
cd0172874 cd01728, LSm1, Like-Sm protein 1 2e-36
cd0172791 cd01727, LSm8, Like-Sm protein 8 1e-19
smart0065167 smart00651, Sm, snRNP Sm proteins 2e-17
pfam0142366 pfam01423, LSM, LSM domain 1e-16
COG195879 COG1958, LSM1, Small nuclear ribonucleoprotein (sn 9e-13
cd0171970 cd01719, Sm_G, Sm protein G 7e-11
cd0173169 cd01731, archaeal_Sm1, archaeal Sm protein 1 6e-10
cd0060063 cd00600, Sm_like, Sm and related proteins 1e-07
cd0171780 cd01717, Sm_B, Sm protein B 6e-07
cd0172989 cd01729, LSm7, Like-Sm protein 7 8e-07
PRK0073772 PRK00737, PRK00737, small nuclear ribonucleoprotei 1e-06
cd0172668 cd01726, LSm6, Like-Sm protein 6 1e-04
cd0616873 cd06168, LSMD1, LSM domain containing 1 1e-04
cd1167869 cd11678, archaeal_LSm, archaeal Like-Sm protein 0.001
>gnl|CDD|212475 cd01728, LSm1, Like-Sm protein 1 Back     alignment and domain information 
 Score =  119 bits (301), Expect = 2e-36
 Identities = 48/71 (67%), Positives = 58/71 (81%)

Query: 12 STSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVI 71
          + SL   LDKK+LV+LRDGRKL+G L SFDQFAN VLE   ER+IVG+ Y DIP GL++I
Sbjct: 4  TASLEEELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQYGDIPRGLFII 63

Query: 72 RGENVVLIGEL 82
          RGENVVL+GE+
Sbjct: 64 RGENVVLLGEI 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|212466 cd01719, Sm_G, Sm protein G Back     alignment and domain information
>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1 Back     alignment and domain information
>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins Back     alignment and domain information
>gnl|CDD|212464 cd01717, Sm_B, Sm protein B Back     alignment and domain information
>gnl|CDD|212476 cd01729, LSm7, Like-Sm protein 7 Back     alignment and domain information
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>gnl|CDD|212473 cd01726, LSm6, Like-Sm protein 6 Back     alignment and domain information
>gnl|CDD|212486 cd06168, LSMD1, LSM domain containing 1 Back     alignment and domain information
>gnl|CDD|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 147
KOG1782129 consensus Small Nuclear ribonucleoprotein splicing 99.97
cd0172874 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins 99.89
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.87
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.86
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.85
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.85
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.84
cd0171779 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins 99.83
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.83
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.82
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.79
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.79
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.79
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.78
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 99.78
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.77
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.77
KOG178077 consensus Small Nuclear ribonucleoprotein G [RNA p 99.77
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.76
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.73
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.72
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.71
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.71
KOG178496 consensus Small Nuclear ribonucleoprotein splicing 99.67
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.67
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.63
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.63
KOG348279 consensus Small nuclear ribonucleoprotein (snRNP) 99.61
KOG1781108 consensus Small Nuclear ribonucleoprotein splicing 99.61
KOG346091 consensus Small nuclear ribonucleoprotein (snRNP) 99.43
KOG178377 consensus Small nuclear ribonucleoprotein F [RNA p 99.4
KOG3168177 consensus U1 snRNP component [Transcription] 99.34
KOG177584 consensus U6 snRNA-associated Sm-like protein [RNA 99.3
KOG177488 consensus Small nuclear ribonucleoprotein E [RNA p 99.18
KOG3293134 consensus Small nuclear ribonucleoprotein (snRNP) 98.96
KOG344896 consensus Predicted snRNP core protein [RNA proces 98.88
KOG3172119 consensus Small nuclear ribonucleoprotein Sm D3 [R 98.64
KOG3428109 consensus Small nuclear ribonucleoprotein SMD1 and 98.12
KOG3459114 consensus Small nuclear ribonucleoprotein (snRNP) 97.86
PF1443877 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1. 97.71
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 97.67
PF0223748 BPL_C: Biotin protein ligase C terminal domain; In 96.32
PF1270196 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC 95.69
cd0171661 Hfq Hfq, an abundant, ubiquitous RNA-binding prote 94.77
PF06372166 Gemin6: Gemin6 protein; InterPro: IPR009422 This f 94.66
TIGR0238361 Hfq RNA chaperone Hfq. This model represents the R 94.49
PRK0039579 hfq RNA-binding protein Hfq; Provisional 93.71
PF1109580 Gemin7: Gem-associated protein 7 (Gemin7); InterPr 93.54
cd0173674 LSm14_N LSm14 (also known as RAP55) belongs to a f 93.06
PRK14638150 hypothetical protein; Provisional 92.98
PRK14639140 hypothetical protein; Provisional 92.18
COG192377 Hfq Uncharacterized host factor I protein [General 91.16
PRK02001152 hypothetical protein; Validated 90.95
cd0173483 YlxS_C YxlS is a Bacillus subtilis gene of unknown 90.41
PRK14644136 hypothetical protein; Provisional 89.9
cd0173561 LSm12_N LSm12 belongs to a family of Sm-like prote 89.66
PRK14640152 hypothetical protein; Provisional 88.46
PF1084266 DUF2642: Protein of unknown function (DUF2642); In 87.77
PRK14636176 hypothetical protein; Provisional 86.07
PRK14091165 RNA-binding protein Hfq; Provisional 85.14
PRK14633150 hypothetical protein; Provisional 85.06
PF02576141 DUF150: Uncharacterised BCR, YhbC family COG0779; 84.99
PRK14645154 hypothetical protein; Provisional 84.88
PRK14091165 RNA-binding protein Hfq; Provisional 84.76
PRK14632172 hypothetical protein; Provisional 83.94
COG0779153 Uncharacterized protein conserved in bacteria [Fun 83.76
PRK14642197 hypothetical protein; Provisional 83.75
PRK14634155 hypothetical protein; Provisional 83.53
PRK14647159 hypothetical protein; Provisional 81.48
PRK00092154 ribosome maturation protein RimP; Reviewed 81.24
PRK14646155 hypothetical protein; Provisional 80.2
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information 
Probab=99.97  E-value=3.9e-32  Score=202.49  Aligned_cols=122  Identities=49%  Similarity=0.738  Sum_probs=114.4

Q ss_pred             CCchhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEeccCCccc
Q 032108            8 DVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELDLERD   87 (147)
Q Consensus         8 ~~~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD~~~e   87 (147)
                      ++|.+.+|.++++|++.|.|+|||++.|+|+|||||+|+||++|+||++.++.|++++.|.++|||+||+++|++|.++|
T Consensus         7 ~~~~t~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE   86 (129)
T KOG1782|consen    7 DLPFTTSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKE   86 (129)
T ss_pred             CCCchhHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchh
Confidence            57888889999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCCCccCHHHHHHHHHHhhhhhhhhhhHhhhhhhhccccccc
Q 032108           88 ELPPHLTHVSVAEIKRVSALFFSLLFLSLHKRCCLLTMRYEIMGR  132 (147)
Q Consensus        88 ~~~~~~~~v~~~ei~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (147)
                        ..+++++|++|++..++.++++|++.++.|- .|+.|++.++.
T Consensus        87 --~~~l~~i~~~e~~~~~~~~q~~k~e~~~lkg-~m~~rg~~~D~  128 (129)
T KOG1782|consen   87 --EEPLEQISFEEALNEIKREQEAKKEEERLKG-TMAERGEFLDF  128 (129)
T ss_pred             --hccceeCCHHHHHHHHHHHHHHhhhHHHHHH-HHHHhcccccC
Confidence              4799999999999888888888888777777 89999998764

>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
>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
>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
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences Back     alignment and domain information
>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
>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
>PRK00737 small nuclear ribonucleoprotein; Provisional 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
>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
>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
>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
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] Back     alignment and domain information
>smart00651 Sm snRNP Sm proteins Back     alignment and domain information
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification] 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
>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
>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
>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
>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
>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
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [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
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [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
>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
>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
>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
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [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
>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
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A 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
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins Back     alignment and domain information
>TIGR02383 Hfq RNA chaperone Hfq Back     alignment and domain information
>PRK00395 hfq RNA-binding protein Hfq; Provisional Back     alignment and domain information
>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
>PRK14638 hypothetical protein; Provisional Back     alignment and domain information
>PRK14639 hypothetical protein; Provisional Back     alignment and domain information
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only] Back     alignment and domain information
>PRK02001 hypothetical protein; Validated 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
>PRK14644 hypothetical protein; Provisional Back     alignment and domain information
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>PRK14640 hypothetical protein; Provisional 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
>PRK14636 hypothetical protein; Provisional Back     alignment and domain information
>PRK14091 RNA-binding protein Hfq; Provisional Back     alignment and domain information
>PRK14633 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
>PRK14645 hypothetical protein; Provisional Back     alignment and domain information
>PRK14091 RNA-binding protein Hfq; Provisional Back     alignment and domain information
>PRK14632 hypothetical protein; Provisional Back     alignment and domain information
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK14642 hypothetical protein; Provisional Back     alignment and domain information
>PRK14634 hypothetical protein; Provisional Back     alignment and domain information
>PRK14647 hypothetical protein; Provisional Back     alignment and domain information
>PRK00092 ribosome maturation protein RimP; Reviewed Back     alignment and domain information
>PRK14646 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 ?
Query147
1i8f_A81 The Crystal Structure Of A Heptameric Archaeal Sm P 7e-07
3cw1_G76 Crystal Structure Of Human Spliceosomal U1 Snrnp Le 7e-05
3swn_C117 Structure Of The Lsm657 Complex: An Assembly Interm 2e-04
4emk_C113 Crystal Structure Of Splsm567 Length = 113 4e-04
>pdb|1I8F|A Chain A, The Crystal Structure Of A Heptameric Archaeal Sm Protein: Implications For The Eukaryotic Snrnp Core Length = 81 Back     alignment and structure 
Iteration: 1

 Score = 49.7 bits (117), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 30/69 (43%), Positives = 42/69 (60%), Gaps = 4/69 (5%)
Query: 11 LSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYV 70
          L  +L   + K++LV LRD  ++ G L SFDQ  N +LE A E +I G++Y     G  V
Sbjct: 12 LGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDA-EEIIDGNVY---KRGTMV 67
Query: 71 IRGENVVLI 79
          +RGENV+ I
Sbjct: 68 VRGENVLFI 76
>pdb|3CW1|G Chain G, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 76 Back     alignment and structure
>pdb|3SWN|C Chain C, Structure Of The Lsm657 Complex: An Assembly Intermediate Of The Lsm1 7 And Lsm2 8 Rings Length = 117 Back     alignment and structure
>pdb|4EMK|C Chain C, Crystal Structure Of Splsm567 Length = 113 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 ?
Query147
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 1e-24
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 9e-24
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 1e-23
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 2e-22
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 4e-21
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 7e-19
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 2e-15
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 1e-13
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 2e-13
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 2e-13
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 2e-13
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 2e-13
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 3e-13
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 9e-12
3pgw_B231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 2e-10
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 2e-09
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 6e-08
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 1e-07
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 4e-07
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 4e-05
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 7e-04
>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
 Score = 88.9 bits (221), Expect = 1e-24
 Identities = 27/83 (32%), Positives = 42/83 (50%), Gaps = 9/83 (10%)

Query: 1  MSWAGPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDL 60
          MS A P +      L  ++DKKL + L  GR + G L  FD F N V++   E    G  
Sbjct: 1  MSKAHPPE------LKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQ- 53

Query: 61 YCDIPLGLYVIRGENVVLIGELD 83
               +G+ VIRG +++++  L+
Sbjct: 54 --QNNIGMVVIRGNSIIMLEALE 74
>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
>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
>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
>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
>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Length = 121 Back     alignment and structure
>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A* Length = 75 Back     alignment and structure
>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_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
>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
>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
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231 Back     alignment and structure
>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Length = 77 Back     alignment and structure
>3s6n_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
>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
>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B Length = 118 Back     alignment and structure
>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe} Length = 105 Back     alignment and structure
>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 Length = 130 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query147
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.88
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.88
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.88
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.86
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.86
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.86
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.85
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.85
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.85
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.85
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.85
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.85
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.84
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.83
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.83
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.82
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.82
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.82
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.81
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 99.79
3pgw_B231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.78
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.78
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 99.73
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.72
1y96_A86 Gemin6, SIP2, GEM-associated protein 6; SM fold, p 98.65
2vxe_A88 CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA 95.23
2qtx_A71 Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi 95.13
2fb7_A95 SM-like protein, LSM-14_N (RAP55); DR.13312, BC055 95.01
3ahu_A78 Protein HFQ; SM-like motif, protein-RNA complex, t 94.9
2ylb_A74 Protein HFQ; RNA-binding protein, LSM protein, RNA 94.73
1u1s_A82 HFQ protein; SM-like bacterial protein, riken stru 94.6
1kq1_A77 HFQ, HOST factor for Q beta; hexamer, RNA binding 94.55
3sb2_A79 Protein HFQ; SM-like, RNA chaperone, chaperone; 2. 93.72
4a53_A125 EDC3; RNA binding protein; NMR {Schizosaccharomyce 92.59
2y90_A104 Protein HFQ; RNA-binding protein, SM-like, RNA cha 92.52
1y96_B85 Gemin7, SIP3, GEM-associated protein 7; SM fold, p 92.4
3hfo_A70 SSR3341 protein; HFQ, SM, RNA-binding protein, sRN 92.02
3hfn_A72 ASL2047 protein; HFQ, SM, RNA-binding protein, sRN 89.83
2vc8_A84 Enhancer of mRNA-decapping protein 3; P-BODY compo 88.77
3rux_A270 BIRA bifunctional protein; biotin-protein ligase, 87.87
1ycy_A71 Conserved hypothetical protein; structural genomic 83.88
1ib8_A164 Conserved protein SP14.3; nucleic acid binding pro 83.48
>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
Probab=99.88  E-value=3.1e-23  Score=142.03  Aligned_cols=75  Identities=36%  Similarity=0.635  Sum_probs=53.1

Q ss_pred             CCCCCCCCCchhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEe
Q 032108            1 MSWAGPDDVYLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIG   80 (147)
Q Consensus         1 Ms~~~~~~~~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~   80 (147)
                      ||++++      +.|.+++|++|+|.|+|||+|.|+|.|||+|||++|+||.|+...++   .+.+|.++|||+||++++
T Consensus         1 ms~~~~------~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~---~~~lg~v~iRG~~I~~i~   71 (76)
T 3s6n_G            1 MSKAHP------PELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQ---QNNIGMVVIRGNSIIMLE   71 (76)
T ss_dssp             -------------------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC-------CBSSEEECSSSEEEEE
T ss_pred             CCCcch------HHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCc---EeEcCEEEECCCeEEEEE
Confidence            787544      56999999999999999999999999999999999999999875433   578999999999999999


Q ss_pred             ccCC
Q 032108           81 ELDL   84 (147)
Q Consensus        81 ~iD~   84 (147)
                      ++|.
T Consensus        72 ~~d~   75 (76)
T 3s6n_G           72 ALER   75 (76)
T ss_dssp             C---
T ss_pred             eccC
Confidence            8874
>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
>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
>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
>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_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
>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
>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
>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
>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A Back     alignment and structure
>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Back     alignment and structure
>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
>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
>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
>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Back     alignment and structure
>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe} Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like P; OB-like fold, B-sheet toroid, 14-MER, cadmium-binding site, translation; 2.00A {Pyrobaculum aerophilum} SCOP: b.38.1.1 Back     alignment and structure
>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} Back     alignment and structure
>2vxe_A CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA decay, LSM proteins, translational repression, transcription; NMR {Drosophila melanogaster} 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
>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
>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
>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
>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2 Back     alignment and structure
>4a53_A EDC3; RNA binding protein; NMR {Schizosaccharomyces pombe} PDB: 4a54_A Back     alignment and structure
>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A {Escherichia coli} PDB: 3qhs_A Back     alignment and structure
>1y96_B Gemin7, SIP3, GEM-associated protein 7; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} Back     alignment and structure
>3hfo_A SSR3341 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 1.30A {Synechocystis SP} Back     alignment and structure
>3hfn_A ASL2047 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 2.31A {Nostoc SP} Back     alignment and structure
>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
>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
>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
>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 147
d1d3bb_81 b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa 4e-22
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 2e-18
d2fwka192 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr 2e-17
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 8e-17
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 4e-16
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 4e-16
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 1e-15
d1n9ra_68 b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S 6e-15
d1m5q1_127 b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch 2e-13
d1b34b_93 b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s 2e-13
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 8e-13
d1d3ba_72 b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s 1e-06
d1b34a_80 b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s 8e-05
>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 = 81.8 bits (202), Expect = 4e-22
 Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 12/86 (13%)

Query: 13 TSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIP------- 65
          + +  ++D ++  +L+DGR  +GT  +FD+  N +L    E   +               
Sbjct: 1  SKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRV 60

Query: 66 LGLYVIRGENVVLIGELDLERDELPP 91
          LGL ++RGEN+V +       +  PP
Sbjct: 61 LGLVLLRGENLVSM-----TVEGPPP 81
>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
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 74 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
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 127 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
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72 Back     information, alignment and structure
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query147
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.86
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.84
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.83
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.82
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.82
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.82
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.81
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.81
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.8
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.8
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.75
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.65
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 99.61
d1biaa247 Biotin repressor/biotin holoenzyme synthetase, C-t 95.96
d2vxfa180 LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) 95.59
d1kq1a_60 Pleiotropic translational regulator Hfq {Staphyloc 93.91
d1u1sa166 Pleiotropic translational regulator Hfq {Pseudomon 92.99
d1ib8a174 Hypothetical protein SP14.3 (SP0552) {Streptococcu 91.75
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Back     information, alignment and structure
class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.86  E-value=3.9e-22  Score=133.88  Aligned_cols=70  Identities=40%  Similarity=0.571  Sum_probs=63.2

Q ss_pred             chhHHHhhccCCeEEEEEcCCeEEEEEEEEecCccceEecceEEEeeeCceeeeeecceEEEeeccEEEEeccC
Q 032108           10 YLSTSLASYLDKKLLVLLRDGRKLMGTLCSFDQFANAVLEGACERVIVGDLYCDIPLGLYVIRGENVVLIGELD   83 (147)
Q Consensus        10 ~~~~~L~~~ldKkV~V~L~dGR~l~G~L~sfDq~mNLVL~da~E~i~~~~~~~~~~~G~vlIRG~nVv~I~~iD   83 (147)
                      +..+.|.+++||+|.|.|+||+.|.|+|.|||+|||++|++|.|+.. ++   .+.+|.++|||+||++|++++
T Consensus         2 t~~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~-~~---~~~~g~v~iRG~~I~~I~~~P   71 (71)
T d1i8fa_           2 TLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIID-GN---VYKRGTMVVRGENVLFISPVP   71 (71)
T ss_dssp             CHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEET-TE---EEEEEEEEECGGGEEEEEECC
T ss_pred             cHhHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEEC-CC---EEEcceEEEeCCeEEEEeCCC
Confidence            46789999999999999999999999999999999999999999853 32   478999999999999999763
>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
>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
>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} 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
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} 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
>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
>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
>d1ib8a1 b.38.2.1 (A:91-164) Hypothetical protein SP14.3 (SP0552) {Streptococcus pneumoniae [TaxId: 1313]} Back     information, alignment and structure