Psyllid ID: psy10177

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------
MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDKEKEHCPQLQQVSVEDILNAQRKEQEVKQERSRMLAKRLKERGLSFVPDLINDDLF
cEEEccccEEEEEEEEEcccccEEEEcEEEEEEccccccEEEEEEEEEEcccEEEEEccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccc
cEEEccccEEEEEEEcHHHHHHHHHHHHHEEEEEcccccccccEEEEEEccEEEEEEEEccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccc
MVLLRDGRTLIGYLRSVDQFANLVLHKTIErihvgnqygdiprgifiiRGENVVLMGevdkekehcpqlqqVSVEDILNAQRKEQEVKQERSRMLAKRLKErglsfvpdlinddlf
MVLLRDGRTLIGYLRSVDQFANLVLHKTIERihvgnqygdiprgiFIIRGENVVLMGEVDKEKEHCPQLQQVSVEDILNAQRKEQEVKQERSRMLAkrlkerglsfvpdlinddlf
MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDKEKEHCPQLQQVSVEDILNAQRKEQEVKQERSRMLAKRLKERGLSFVPDLINDDLF
***LRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD********************************************************
MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDKE*E*******VSVED*************************RGLSFVPD**N**LF
MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDKEKEHCPQLQQVSVEDILNAQ************MLAKRLKERGLSFVPDLINDDLF
MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDKEKEHCPQLQQVSVEDILNAQRKEQEVKQERSRMLAKR***RGLSFVPDLI*****
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDKEKEHCPQLQQVSVEDILNAQRKEQEVKQERSRMLAKRLKERGLSFVPDLINDDLF
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 ?
Query116 2.2.26 [Sep-21-2011]
O15116133 U6 snRNA-associated Sm-li yes N/A 0.913 0.796 0.679 2e-36
Q5E9Z8133 U6 snRNA-associated Sm-li yes N/A 0.913 0.796 0.679 2e-36
Q8VC85133 U6 snRNA-associated Sm-li yes N/A 0.913 0.796 0.660 1e-35
P87173140 U6 snRNA-associated Sm-li yes N/A 0.982 0.814 0.483 9e-22
Q54W83129 Probable U6 snRNA-associa yes N/A 0.991 0.891 0.435 7e-18
P47017172 Sm-like protein LSm1 OS=S yes N/A 0.982 0.662 0.391 9e-17
Q1ZXD594 N-alpha-acetyltransferase no N/A 0.646 0.797 0.4 8e-09
Q5RCP396 N-alpha-acetyltransferase no N/A 0.637 0.770 0.346 3e-07
Q6ZWM496 N-alpha-acetyltransferase no N/A 0.637 0.770 0.346 3e-07
O9577796 N-alpha-acetyltransferase no N/A 0.637 0.770 0.346 3e-07
>sp|O15116|LSM1_HUMAN U6 snRNA-associated Sm-like protein LSm1 OS=Homo sapiens GN=LSM1 PE=1 SV=1 Back     alignment and function desciption
 Score =  150 bits (380), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 72/106 (67%), Positives = 89/106 (83%)

Query: 1   MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60
           +VLLRDGRTLIG+LRS+DQFANLVLH+T+ERIHVG +YGDIPRGIF++RGENVVL+GE+D
Sbjct: 19  LVLLRDGRTLIGFLRSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGENVVLLGEID 78

Query: 61  KEKEHCPQLQQVSVEDILNAQRKEQEVKQERSRMLAKRLKERGLSF 106
            EKE    LQQVS+E+IL  QR EQ+ K E  ++  + LK+RGLS 
Sbjct: 79  LEKESDTPLQQVSIEEILEEQRVEQQTKLEAEKLKVQALKDRGLSI 124
Plays a role in replication-dependent histone mRNA degradation. Binds specifically to the 3'-terminal U-tract of U6 snRNA.
Homo sapiens (taxid: 9606)
>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|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|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|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 ?
Query116
156553084134 PREDICTED: U6 snRNA-associated Sm-like p 1.0 0.865 0.732 1e-43
66529526134 PREDICTED: u6 snRNA-associated Sm-like p 1.0 0.865 0.724 1e-43
383861132134 PREDICTED: U6 snRNA-associated Sm-like p 1.0 0.865 0.724 1e-43
307212313134 U6 snRNA-associated Sm-like protein LSm1 1.0 0.865 0.741 2e-43
357609556138 LSM1-like protein [Danaus plexippus] 1.0 0.840 0.724 3e-42
389609539138 Sm protein G, putative [Papilio xuthus] 1.0 0.840 0.724 1e-41
157136994160 Sm protein G, putative [Aedes aegypti] g 0.991 0.718 0.713 4e-41
307172327138 U6 snRNA-associated Sm-like protein LSm1 1.0 0.840 0.689 5e-41
148298867138 LSM1-like protein [Bombyx mori] gi|95102 1.0 0.840 0.706 6e-41
242021605139 lsm1, putative [Pediculus humanus corpor 1.0 0.834 0.706 8e-41
>gi|156553084|ref|XP_001600131.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm1-like [Nasonia vitripennis] Back     alignment and taxonomy information
 Score =  180 bits (456), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 85/116 (73%), Positives = 105/116 (90%)

Query: 1   MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60
           MVLLRDGRTLIGYLRSVDQFANLVLH+TIERIHVG +YGDIPRG+FI+RGENVVL+GE+D
Sbjct: 19  MVLLRDGRTLIGYLRSVDQFANLVLHRTIERIHVGKEYGDIPRGVFIVRGENVVLLGEID 78

Query: 61  KEKEHCPQLQQVSVEDILNAQRKEQEVKQERSRMLAKRLKERGLSFVPDLINDDLF 116
           K+KE    L +VSV+DIL+AQR+EQE+KQ++ R + K LK+RGLS++PDL +DD+F
Sbjct: 79  KDKEKNLPLSEVSVDDILDAQRREQELKQDQERRMNKALKDRGLSYIPDLGHDDMF 134

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|66529526|ref|XP_624639.1| PREDICTED: u6 snRNA-associated Sm-like protein LSm1-like [Apis mellifera] gi|340709308|ref|XP_003393252.1| PREDICTED: u6 snRNA-associated Sm-like protein LSm1-like [Bombus terrestris] gi|350425090|ref|XP_003494008.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm1-like [Bombus impatiens] gi|380023316|ref|XP_003695469.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm1-like [Apis florea] Back     alignment and taxonomy information
>gi|383861132|ref|XP_003706040.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm1-like [Megachile rotundata] Back     alignment and taxonomy information
>gi|307212313|gb|EFN88119.1| U6 snRNA-associated Sm-like protein LSm1 [Harpegnathos saltator] Back     alignment and taxonomy information
>gi|357609556|gb|EHJ66513.1| LSM1-like protein [Danaus plexippus] Back     alignment and taxonomy information
>gi|389609539|dbj|BAM18381.1| Sm protein G, putative [Papilio xuthus] Back     alignment and taxonomy information
>gi|157136994|ref|XP_001656966.1| Sm protein G, putative [Aedes aegypti] gi|108884233|gb|EAT48458.1| AAEL000478-PA [Aedes aegypti] Back     alignment and taxonomy information
>gi|307172327|gb|EFN63815.1| U6 snRNA-associated Sm-like protein LSm1 [Camponotus floridanus] Back     alignment and taxonomy information
>gi|148298867|ref|NP_001091827.1| LSM1-like protein [Bombyx mori] gi|95102704|gb|ABF51290.1| LSM1-like protein [Bombyx mori] Back     alignment and taxonomy information
>gi|242021605|ref|XP_002431235.1| lsm1, putative [Pediculus humanus corporis] gi|212516484|gb|EEB18497.1| lsm1, putative [Pediculus humanus corporis] 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 ?
Query116
FB|FBgn0261067137 LSm1 [Drosophila melanogaster 0.982 0.832 0.710 3.3e-40
UNIPROTKB|Q5E9Z8133 LSM1 "U6 snRNA-associated Sm-l 0.922 0.804 0.675 2.4e-35
UNIPROTKB|E2R7S6133 LSM1 "Uncharacterized protein" 0.922 0.804 0.675 2.4e-35
UNIPROTKB|O15116133 LSM1 "U6 snRNA-associated Sm-l 0.922 0.804 0.675 2.4e-35
ZFIN|ZDB-GENE-040801-68133 lsm1 "LSM1 homolog, U6 small n 0.956 0.834 0.663 2.4e-35
UNIPROTKB|I3LCU8133 LSM1 "Uncharacterized protein" 0.922 0.804 0.666 5.1e-35
RGD|1304967133 Lsm1 "LSM1 homolog, U6 small n 0.922 0.804 0.666 8.3e-35
MGI|MGI:1914457133 Lsm1 "LSM1 homolog, U6 small n 0.922 0.804 0.657 1.1e-34
UNIPROTKB|E1C962133 E1C962 "Uncharacterized protei 0.75 0.654 0.647 1.1e-25
POMBASE|SPBC3D6.08c140 lsm1 "mRNA decapping complex s 0.982 0.814 0.483 2.1e-22
FB|FBgn0261067 LSm1 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 428 (155.7 bits), Expect = 3.3e-40, P = 3.3e-40
 Identities = 81/114 (71%), Positives = 103/114 (90%)

Query:     1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60
             MVLLRDGRTLIGYLRSVDQFANLVL +TIERIHVGN+YGDIPRG+FIIRGENVVL+GE+D
Sbjct:    22 MVLLRDGRTLIGYLRSVDQFANLVLQRTIERIHVGNEYGDIPRGVFIIRGENVVLLGEID 81

Query:    61 KEKEHCPQLQQVSVEDILNAQRKEQEVKQERSRMLAKRLKERGLSFVPDLINDD 114
             +EKE    L+++SV++IL+AQR+EQE +QE+ R+++K LKERGL+   ++IN+D
Sbjct:    82 REKEQKLPLKEISVDEILDAQRREQEQRQEKHRLVSKALKERGLAVDANIINED 135
GO:0030532 "small nuclear ribonucleoprotein complex" evidence=ISS
GO:0005681 "spliceosomal complex" evidence=ISS
GO:0006396 "RNA processing" evidence=ISS
GO:0000398 "mRNA splicing, via spliceosome" evidence=ISS
GO:0033962 "cytoplasmic mRNA processing body assembly" evidence=IMP
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
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
UNIPROTKB|I3LCU8 LSM1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] 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
UNIPROTKB|E1C962 E1C962 "Uncharacterized protein" [Gallus gallus (taxid:9031)] 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

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 number0.67920.91370.7969yesN/A
P47017LSM1_YEASTNo assigned EC number0.39160.98270.6627yesN/A
Q8VC85LSM1_MOUSENo assigned EC number0.66030.91370.7969yesN/A
Q54W83LSM1_DICDINo assigned EC number0.43580.99130.8914yesN/A
Q5E9Z8LSM1_BOVINNo assigned EC number0.67920.91370.7969yesN/A
P87173LSM1_SCHPONo assigned EC number0.48300.98270.8142yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query116
cd0172874 cd01728, LSm1, Like-Sm protein 1 2e-35
cd0172791 cd01727, LSm8, Like-Sm protein 8 4e-14
smart0065167 smart00651, Sm, snRNP Sm proteins 1e-12
pfam0142366 pfam01423, LSM, LSM domain 4e-12
COG195879 COG1958, LSM1, Small nuclear ribonucleoprotein (sn 1e-08
cd0171970 cd01719, Sm_G, Sm protein G 2e-05
cd0172668 cd01726, LSm6, Like-Sm protein 6 3e-05
cd0171780 cd01717, Sm_B, Sm protein B 9e-05
cd0060063 cd00600, Sm_like, Sm and related proteins 6e-04
cd0173169 cd01731, archaeal_Sm1, archaeal Sm protein 1 0.001
>gnl|CDD|212475 cd01728, LSm1, Like-Sm protein 1 Back     alignment and domain information 
 Score =  115 bits (291), Expect = 2e-35
 Identities = 47/59 (79%), Positives = 53/59 (89%)

Query: 1  MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 59
          +V+LRDGR LIG LRS DQFANLVL  T+ERI VGNQYGDIPRG+FIIRGENVVL+GE+
Sbjct: 16 LVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQYGDIPRGLFIIRGENVVLLGEI 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|212473 cd01726, LSm6, Like-Sm protein 6 Back     alignment and domain information
>gnl|CDD|212464 cd01717, Sm_B, Sm protein B Back     alignment and domain information
>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins Back     alignment and domain information
>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1 Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 116
KOG1782|consensus129 100.0
cd0172874 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins 99.83
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.82
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.81
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.78
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.78
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.77
cd0171779 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins 99.75
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.74
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 99.72
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.71
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.71
KOG1784|consensus96 99.7
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.66
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.66
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.66
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.64
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.63
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.63
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.62
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.56
KOG1780|consensus77 99.56
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.48
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.47
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.41
KOG1781|consensus108 99.35
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.34
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.32
KOG3460|consensus91 99.25
KOG3482|consensus79 99.24
KOG1775|consensus84 99.17
KOG3168|consensus177 99.16
KOG1774|consensus88 98.97
KOG1783|consensus77 98.68
KOG3459|consensus114 98.2
KOG3448|consensus96 97.89
KOG3293|consensus134 97.69
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 97.19
KOG3428|consensus109 96.84
KOG3172|consensus119 96.56
PF1443877 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1. 95.46
cd0171661 Hfq Hfq, an abundant, ubiquitous RNA-binding prote 90.64
TIGR0238361 Hfq RNA chaperone Hfq. This model represents the R 89.81
PRK0039579 hfq RNA-binding protein Hfq; Provisional 88.39
COG192377 Hfq Uncharacterized host factor I protein [General 81.69
PF0223748 BPL_C: Biotin protein ligase C terminal domain; In 80.72
>KOG1782|consensus Back     alignment and domain information 
Probab=100.00  E-value=2.4e-34  Score=206.36  Aligned_cols=106  Identities=60%  Similarity=0.913  Sum_probs=101.7

Q ss_pred             CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCcccceeecceEEEeeccEEEEeecCCccccCCCCcccCHHHHHHH
Q psy10177          1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDKEKEHCPQLQQVSVEDILNA   80 (116)
Q Consensus         1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~~~~~~~~G~~lIRG~nVv~ig~id~~~e~~~~~~~v~~~~~~~~   80 (116)
                      +|.|||||+++|+|+|||||+|+||++|+||++.++.|+++++|+|+|||+||+++|++|.++| +.|++++|+++++..
T Consensus        23 lVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE-~~~l~~i~~~e~~~~  101 (129)
T KOG1782|consen   23 LVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKE-EEPLEQISFEEALNE  101 (129)
T ss_pred             EEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchh-hccceeCCHHHHHHH
Confidence            5899999999999999999999999999999999999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHHHHHHhHHHHHHHHHcCCCCCC
Q psy10177         81 QRKEQEVKQERSRMLAKRLKERGLSFVP  108 (116)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~l~~~g~~~~~  108 (116)
                      ++.+++++++.+..|. .|+++|++.+.
T Consensus       102 ~~~~q~~k~e~~~lkg-~m~~rg~~~D~  128 (129)
T KOG1782|consen  102 IKREQEAKKEEERLKG-TMAERGEFLDF  128 (129)
T ss_pred             HHHHHHHhhhHHHHHH-HHHHhcccccC
Confidence            9999999999999888 99999999854

>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
>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
>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
>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
>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
>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
>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
>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
>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
>KOG1784|consensus 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
>PTZ00138 small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>smart00651 Sm snRNP Sm proteins 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
>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
>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
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>KOG1780|consensus 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
>KOG1781|consensus 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 Back     alignment and domain information
>KOG3482|consensus Back     alignment and domain information
>KOG1775|consensus Back     alignment and domain information
>KOG3168|consensus Back     alignment and domain information
>KOG1774|consensus Back     alignment and domain information
>KOG1783|consensus Back     alignment and domain information
>KOG3459|consensus Back     alignment and domain information
>KOG3448|consensus Back     alignment and domain information
>KOG3293|consensus 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
>KOG3428|consensus Back     alignment and domain information
>KOG3172|consensus Back     alignment and domain information
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1 Back     alignment and domain information
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others Back     alignment and domain information
>TIGR02383 Hfq RNA chaperone Hfq Back     alignment and domain information
>PRK00395 hfq RNA-binding protein Hfq; Provisional Back     alignment and domain information
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only] Back     alignment and domain information
>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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query116
1i8f_A81 The Crystal Structure Of A Heptameric Archaeal Sm P 3e-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 = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 1  MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 59
          +V LRD   + G LRS DQ  NL+L    E I  GN Y    RG  ++RGENV+ +  V
Sbjct: 25 LVKLRDSHEIRGILRSFDQHVNLLLEDA-EEIIDGNVY---KRGTMVVRGENVLFISPV 79

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query116
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 1e-16
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 2e-15
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 5e-15
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 8e-15
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 6e-13
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 6e-12
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 3e-10
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 7e-10
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 2e-09
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 9e-09
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 1e-08
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 2e-08
3pgw_B231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 7e-08
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 3e-07
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 3e-06
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 4e-06
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 1e-05
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 3e-04
>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
 Score = 67.8 bits (166), Expect = 1e-16
 Identities = 26/60 (43%), Positives = 33/60 (55%), Gaps = 4/60 (6%)

Query: 1  MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60
          +V LRD   + G LRS DQ  NL+L    E I  GN Y    RG  ++RGENV+ +  V 
Sbjct: 25 LVKLRDSHEIRGILRSFDQHVNLLLEDAEEIID-GNVY---KRGTMVVRGENVLFISPVP 80
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query116
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.84
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.81
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.76
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.75
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.75
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.74
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.74
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.74
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.73
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.73
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.73
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.73
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.73
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.73
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.72
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.71
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.7
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.69
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.66
3pgw_B231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.66
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 99.64
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.63
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.57
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 99.51
1y96_A86 Gemin6, SIP2, GEM-associated protein 6; SM fold, p 97.38
3ahu_A78 Protein HFQ; SM-like motif, protein-RNA complex, t 91.88
2qtx_A71 Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi 91.61
1u1s_A82 HFQ protein; SM-like bacterial protein, riken stru 91.01
1kq1_A77 HFQ, HOST factor for Q beta; hexamer, RNA binding 89.54
3sb2_A79 Protein HFQ; SM-like, RNA chaperone, chaperone; 2. 89.39
2ylb_A74 Protein HFQ; RNA-binding protein, LSM protein, RNA 89.31
2y90_A104 Protein HFQ; RNA-binding protein, SM-like, RNA cha 87.45
>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=99.84  E-value=3.4e-21  Score=135.81  Aligned_cols=71  Identities=27%  Similarity=0.412  Sum_probs=52.1

Q ss_pred             CEEecCCcEEEEEEEEeccccceEEcceEEEEEcCc----ccceeecceEEEeeccEEEEeecCCccccCCCCcc
Q psy10177          1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGN----QYGDIPRGIFIIRGENVVLMGEVDKEKEHCPQLQQ   71 (116)
Q Consensus         1 lV~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~----~~~~~~~G~~lIRG~nVv~ig~id~~~e~~~~~~~   71 (116)
                      .|.|+|||+|.|+|+|||+||||||++|+|++...+    ....+.+|.++|||+||++|+++|.+.+.+.||.+
T Consensus        37 ~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~ee~~~p~~~  111 (113)
T 4emk_C           37 QATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPMDGSEEIPNPFVQ  111 (113)
T ss_dssp             EEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEECC-----------
T ss_pred             EEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEecCccccccCcccc
Confidence            488999999999999999999999999999876432    24578999999999999999999999988888754
>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_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
>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
>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
>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Back     alignment and structure
>3s6n_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
>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
>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe} Back     alignment and structure
>3s6n_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
>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
>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
>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
>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
>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_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
>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
>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} 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
>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii} Back     alignment and structure
>1u1s_A HFQ protein; SM-like bacterial protein, riken structural genomics/proteomics initiative, RSGI, structural genomics, RNA binding protein; 1.60A {Pseudomonas aeruginosa} SCOP: b.38.1.2 PDB: 1u1t_A 3qui_A* 3m4g_A 3inz_A Back     alignment and structure
>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
>2ylb_A Protein HFQ; RNA-binding protein, LSM protein, RNA chaperone; 1.15A {Salmonella enterica subsp} PDB: 2yht_A 1hk9_A 2ylc_A* 3gib_A* 3rer_A* 3qo3_A* 3res_A* Back     alignment and structure
>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A {Escherichia coli} PDB: 3qhs_A Back     alignment and structure

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 116
d1d3bb_81 b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa 5e-14
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 9e-14
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 2e-12
d2fwka192 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr 3e-12
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 3e-12
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 2e-11
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 2e-11
d1n9ra_68 b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S 4e-10
d1b34b_93 b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s 4e-10
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 1e-09
d1m5q1_127 b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch 3e-08
d1d3ba_72 b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s 6e-05
d1b34a_80 b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s 0.003
>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 = 60.2 bits (146), Expect = 5e-14
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 7/63 (11%)

Query: 1  MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPR-------GIFIIRGENV 53
            +L+DGR  IG  ++ D+  NL+L    E   +  +             G+ ++RGEN+
Sbjct: 12 RCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENL 71

Query: 54 VLM 56
          V M
Sbjct: 72 VSM 74
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 71 Back     information, alignment and structure
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Length = 72 Back     information, alignment and structure
>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
>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
>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
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 127 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 ?
Query116
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.75
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.74
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.73
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.71
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.71
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.7
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.69
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.69
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.67
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.66
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.52
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.35
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 99.33
d1kq1a_60 Pleiotropic translational regulator Hfq {Staphyloc 88.52
d1u1sa166 Pleiotropic translational regulator Hfq {Pseudomon 87.93
d1biaa247 Biotin repressor/biotin holoenzyme synthetase, C-t 83.83
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1e-18  Score=114.46  Aligned_cols=57  Identities=32%  Similarity=0.501  Sum_probs=49.5

Q ss_pred             EEecCCcEEEEEEEEeccccceEEcceEEEEEcCc-------ccceeecceEEEeeccEEEEee
Q psy10177          2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGN-------QYGDIPRGIFIIRGENVVLMGE   58 (116)
Q Consensus         2 V~LrdGR~l~G~L~~fDqf~NLVL~d~~Eri~~~~-------~~~~~~~G~~lIRG~nVv~ig~   58 (116)
                      |.|+|||.|.|+|+|||+||||||++|+|++....       ....+.+|+++|||+||++|+.
T Consensus        13 V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~   76 (81)
T d1d3bb_          13 CILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTV   76 (81)
T ss_dssp             EEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEE
T ss_pred             EEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEc
Confidence            78999999999999999999999999999865322       1245789999999999999963
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Back     information, alignment and structure
>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
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Back     information, alignment and structure
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Back     information, alignment and structure
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Back     information, alignment and structure
>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
>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