Citrus Sinensis ID: 034340

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-------
MASEEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSPPLRTA
ccccccccccccHHHHHHHcccEEEEEEccccEEEEEEEEEcccccEEEEcEEEEEEEEcccccHHHHHHccccEEccEEEEEccEEEEEEcccccc
cccccccccccHHHHHHHHcccEEEEEEccccEEEEEEEEEcccccEEEEEEEEEEEEEEcccccccEEEEEEEEEEEEEEEEccEEEEEccccccc
MASEEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTrrtvpflfvrgdgvilvspplrta
maseeesavkepldlirlslderIYVKLrsdrelrgkLHAYDQHLNMILGDVEEVVTTVEIDdetyeeivrttrrtvpflfvrgdgvilvspplrta
MASEEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGdveevvttveiddetyeeivRTTRRTVPFLFVRGDGVILVSPPLRTA
************LDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILV*******
*************DLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTV************TTRRTVPFLFVRGDGVILVSPPL***
**********EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSPPLRTA
********VKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSPP****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
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MASEEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGVILVSPPLRTA
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 ?
Query97 2.2.26 [Sep-21-2011]
P62311102 U6 snRNA-associated Sm-li yes no 0.938 0.892 0.780 1e-37
P62310102 U6 snRNA-associated Sm-li yes no 0.938 0.892 0.780 1e-37
Q32PE9102 U6 snRNA-associated Sm-li yes no 0.938 0.892 0.780 1e-37
Q1ZXK397 Probable U6 snRNA-associa yes no 1.0 1.0 0.721 4e-35
Q9Y7M493 Probable U6 snRNA-associa yes no 0.927 0.967 0.588 3e-25
P5774389 U6 snRNA-associated Sm-li yes no 0.783 0.853 0.439 1e-12
O2674581 Putative snRNP Sm-like pr yes no 0.793 0.950 0.344 5e-08
O2938677 Putative snRNP Sm-like pr yes no 0.701 0.883 0.382 4e-07
Q0W8R972 Putative snRNP Sm-like pr yes no 0.721 0.972 0.325 6e-07
Q9YEQ577 Putative snRNP Sm-like pr yes no 0.608 0.766 0.383 2e-06
>sp|P62311|LSM3_MOUSE U6 snRNA-associated Sm-like protein LSm3 OS=Mus musculus GN=Lsm3 PE=3 SV=2 Back     alignment and function desciption
 Score =  154 bits (390), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 71/91 (78%), Positives = 84/91 (92%)

Query: 7   SAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETY 66
           + V+EPLDLIRLSLDERIYVK+R+DRELRG+LHAYDQHLNMILGDVEE VTT+EID+ETY
Sbjct: 12  NTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEIDEETY 71

Query: 67  EEIVRTTRRTVPFLFVRGDGVILVSPPLRTA 97
           EEI ++T+R +P LFVRGDGV+LV+PPLR  
Sbjct: 72  EEIYKSTKRNIPMLFVRGDGVVLVAPPLRVG 102
Binds specifically to the 3'-terminal U-tract of U6 snRNA.
Mus musculus (taxid: 10090)
>sp|P62310|LSM3_HUMAN U6 snRNA-associated Sm-like protein LSm3 OS=Homo sapiens GN=LSM3 PE=1 SV=2 Back     alignment and function description
>sp|Q32PE9|LSM3_BOVIN U6 snRNA-associated Sm-like protein LSm3 OS=Bos taurus GN=LSM3 PE=3 SV=3 Back     alignment and function description
>sp|Q1ZXK3|LSM3_DICDI Probable U6 snRNA-associated Sm-like protein LSm3 OS=Dictyostelium discoideum GN=lsm3 PE=3 SV=1 Back     alignment and function description
>sp|Q9Y7M4|LSM3_SCHPO Probable U6 snRNA-associated Sm-like protein LSm3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm3 PE=1 SV=2 Back     alignment and function description
>sp|P57743|LSM3_YEAST U6 snRNA-associated Sm-like protein LSm3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=LSM3 PE=1 SV=1 Back     alignment and function description
>sp|O26745|RUXX_METTH Putative snRNP Sm-like protein OS=Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) GN=MTH_649 PE=1 SV=1 Back     alignment and function description
>sp|O29386|RUXX_ARCFU Putative snRNP Sm-like protein OS=Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) GN=AF_0875 PE=1 SV=1 Back     alignment and function description
>sp|Q0W8R9|RUXX_UNCMA Putative snRNP Sm-like protein OS=Uncultured methanogenic archaeon RC-I GN=UNCMA_29510 PE=3 SV=1 Back     alignment and function description
>sp|Q9YEQ5|RUXX_AERPE Putative snRNP Sm-like protein OS=Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) GN=APE_0525a PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query97
22408511197 predicted protein [Populus trichocarpa] 1.0 1.0 0.989 4e-47
25558334297 snrnp sm protein, putative [Ricinus comm 1.0 1.0 0.979 1e-46
22406289297 predicted protein [Populus trichocarpa] 1.0 1.0 0.979 1e-46
38849393297 unknown [Lotus japonicus] gi|388511495|g 1.0 1.0 0.969 2e-46
35172234397 uncharacterized protein LOC100499782 [Gl 1.0 1.0 0.969 2e-46
35172477197 uncharacterized protein LOC100306547 [Gl 1.0 1.0 0.938 2e-45
35747505398 U6 snRNA-associated Sm-like protein LSm3 0.989 0.979 0.958 3e-45
24205935198 hypothetical protein SORBIDRAFT_03g04093 0.989 0.979 0.958 4e-45
35712602998 PREDICTED: U6 snRNA-associated Sm-like p 0.989 0.979 0.947 8e-45
44949708897 PREDICTED: U6 snRNA-associated Sm-like p 1.0 1.0 0.948 9e-45
>gi|224085111|ref|XP_002307496.1| predicted protein [Populus trichocarpa] gi|359493111|ref|XP_002266320.2| PREDICTED: U6 snRNA-associated Sm-like protein LSm3-like isoform 1 [Vitis vinifera] gi|222856945|gb|EEE94492.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  191 bits (485), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 96/97 (98%), Positives = 97/97 (100%)

Query: 1  MASEEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVE 60
          MASEEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEE+VTTVE
Sbjct: 1  MASEEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEIVTTVE 60

Query: 61 IDDETYEEIVRTTRRTVPFLFVRGDGVILVSPPLRTA 97
          IDDETYEEIVRTTRRTVPFLFVRGDGVILVSPPLRTA
Sbjct: 61 IDDETYEEIVRTTRRTVPFLFVRGDGVILVSPPLRTA 97

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255583342|ref|XP_002532432.1| snrnp sm protein, putative [Ricinus communis] gi|223527852|gb|EEF29947.1| snrnp sm protein, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|224062892|ref|XP_002300922.1| predicted protein [Populus trichocarpa] gi|222842648|gb|EEE80195.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|388493932|gb|AFK35032.1| unknown [Lotus japonicus] gi|388511495|gb|AFK43809.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|351722343|ref|NP_001235961.1| uncharacterized protein LOC100499782 [Glycine max] gi|255626487|gb|ACU13588.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|351724771|ref|NP_001236557.1| uncharacterized protein LOC100306547 [Glycine max] gi|255628849|gb|ACU14769.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|357475053|ref|XP_003607812.1| U6 snRNA-associated Sm-like protein LSm3 [Medicago truncatula] gi|355508867|gb|AES90009.1| U6 snRNA-associated Sm-like protein LSm3 [Medicago truncatula] Back     alignment and taxonomy information
>gi|242059351|ref|XP_002458821.1| hypothetical protein SORBIDRAFT_03g040930 [Sorghum bicolor] gi|194699902|gb|ACF84035.1| unknown [Zea mays] gi|195628156|gb|ACG35908.1| U6 snRNA-associated Sm-like protein LSm3 [Zea mays] gi|195643108|gb|ACG41022.1| U6 snRNA-associated Sm-like protein LSm3 [Zea mays] gi|241930796|gb|EES03941.1| hypothetical protein SORBIDRAFT_03g040930 [Sorghum bicolor] Back     alignment and taxonomy information
>gi|357126029|ref|XP_003564691.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm3-like isoform 1 [Brachypodium distachyon] Back     alignment and taxonomy information
>gi|449497088|ref|XP_004160308.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm3-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 ?
Query97
TAIR|locus:203625798 LSM3B "AT1G76860" [Arabidopsis 1.0 0.989 0.701 2.3e-30
TAIR|locus:201492297 LSM3A "AT1G21190" [Arabidopsis 0.989 0.989 0.687 1.3e-29
UNIPROTKB|F1P28096 LSM3 "Uncharacterized protein" 0.917 0.927 0.617 3.6e-25
UNIPROTKB|Q32PE9102 LSM3 "U6 snRNA-associated Sm-l 0.917 0.872 0.617 3.6e-25
UNIPROTKB|P62310102 LSM3 "U6 snRNA-associated Sm-l 0.917 0.872 0.617 3.6e-25
UNIPROTKB|F2Z5S4102 LSM3 "Uncharacterized protein" 0.917 0.872 0.617 3.6e-25
MGI|MGI:1914928102 Lsm3 "LSM3 homolog, U6 small n 0.917 0.872 0.617 3.6e-25
RGD|1305971102 Lsm3 "LSM3 homolog, U6 small n 0.917 0.872 0.617 3.6e-25
DICTYBASE|DDB_G027710797 lsm3 "putative U6 small nuclea 1.0 1.0 0.597 4.6e-25
FB|FBgn0051184103 LSm3 [Drosophila melanogaster 0.896 0.844 0.609 7.6e-25
TAIR|locus:2036257 LSM3B "AT1G76860" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 68/97 (70%), Positives = 74/97 (76%)

Query:     1 MASEEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGXXXXXXXXXX 60
             M+ EEE+ V+EPLDLIRLSLDERIYVKLRSDRELRGKLHA+DQHLNMILG          
Sbjct:     1 MSGEEEATVREPLDLIRLSLDERIYVKLRSDRELRGKLHAFDQHLNMILGDVEETITTVE 60

Query:    61 XXXXXXXXXXRTTRRTVPFLFVRGDGVILVSPPLRTA 97
                       RTT+RT+ FLFVRGDGVILVSPPLRTA
Sbjct:    61 IDDETYEEIVRTTKRTIEFLFVRGDGVILVSPPLRTA 97
GO:0003674 "molecular_function" evidence=ND
GO:0005634 "nucleus" evidence=ISM;ISS
GO:0005732 "small nucleolar ribonucleoprotein complex" evidence=ISS
GO:0008150 "biological_process" evidence=ND
TAIR|locus:2014922 LSM3A "AT1G21190" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|F1P280 LSM3 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q32PE9 LSM3 "U6 snRNA-associated Sm-like protein LSm3" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|P62310 LSM3 "U6 snRNA-associated Sm-like protein LSm3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F2Z5S4 LSM3 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:1914928 Lsm3 "LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1305971 Lsm3 "LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0277107 lsm3 "putative U6 small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
FB|FBgn0051184 LSm3 [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) ?
Q32PE9LSM3_BOVINNo assigned EC number0.78020.93810.8921yesno
P62310LSM3_HUMANNo assigned EC number0.78020.93810.8921yesno
P62311LSM3_MOUSENo assigned EC number0.78020.93810.8921yesno
Q9Y7M4LSM3_SCHPONo assigned EC number0.58880.92780.9677yesno
Q1ZXK3LSM3_DICDINo assigned EC number0.72161.01.0yesno

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

Fail to connect to STRING server

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 ?
Query97
cd0173082 cd01730, LSm3, Like-Sm protein 3 2e-51
cd0173169 cd01731, archaeal_Sm1, archaeal Sm protein 1 5e-16
COG195879 COG1958, LSM1, Small nuclear ribonucleoprotein (sn 2e-15
smart0065167 smart00651, Sm, snRNP Sm proteins 6e-15
pfam0142366 pfam01423, LSM, LSM domain 7e-14
PRK0073772 PRK00737, PRK00737, small nuclear ribonucleoprotei 9e-13
cd0172089 cd01720, Sm_D2, Sm protein D2 5e-10
cd0060063 cd00600, Sm_like, Sm and related proteins 3e-08
cd0171780 cd01717, Sm_B, Sm protein B 3e-07
cd0172989 cd01729, LSm7, Like-Sm protein 7 6e-07
cd0172668 cd01726, LSm6, Like-Sm protein 6 1e-06
cd0173276 cd01732, LSm5, Like-Sm protein 5 2e-06
cd0172874 cd01728, LSm1, Like-Sm protein 1 2e-05
cd0616873 cd06168, LSMD1, LSM domain containing 1 4e-04
cd0171970 cd01719, Sm_G, Sm protein G 0.001
>gnl|CDD|212477 cd01730, LSm3, Like-Sm protein 3 Back     alignment and domain information 
 Score =  155 bits (394), Expect = 2e-51
 Identities = 70/82 (85%), Positives = 77/82 (93%)

Query: 11 EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIV 70
          EPLDLIRLSLDER+YVKLR DRELRG+LHAYDQHLNMILGDVEE +TTVEID+ETYEEI 
Sbjct: 1  EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIY 60

Query: 71 RTTRRTVPFLFVRGDGVILVSP 92
          +TT+R +P LFVRGDGVILVSP
Sbjct: 61 KTTKRNIPMLFVRGDGVILVSP 82

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. 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 = 82
>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1 Back     alignment and domain information
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] 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|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>gnl|CDD|212467 cd01720, Sm_D2, Sm protein D2 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|212473 cd01726, LSm6, Like-Sm protein 6 Back     alignment and domain information
>gnl|CDD|212479 cd01732, LSm5, Like-Sm protein 5 Back     alignment and domain information
>gnl|CDD|212475 cd01728, LSm1, Like-Sm protein 1 Back     alignment and domain information
>gnl|CDD|212486 cd06168, LSMD1, LSM domain containing 1 Back     alignment and domain information
>gnl|CDD|212466 cd01719, Sm_G, Sm protein G Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 97
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.94
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.94
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.92
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.92
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.92
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.91
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.91
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.9
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.9
cd0171779 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins 99.9
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 99.89
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.88
cd0172874 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins 99.88
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.88
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.88
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.87
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.87
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.86
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.86
KOG346091 consensus Small nuclear ribonucleoprotein (snRNP) 99.86
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.85
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.83
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.83
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.82
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.81
KOG178077 consensus Small Nuclear ribonucleoprotein G [RNA p 99.78
KOG348279 consensus Small nuclear ribonucleoprotein (snRNP) 99.77
KOG1781108 consensus Small Nuclear ribonucleoprotein splicing 99.7
KOG3168177 consensus U1 snRNP component [Transcription] 99.66
KOG178377 consensus Small nuclear ribonucleoprotein F [RNA p 99.66
KOG177584 consensus U6 snRNA-associated Sm-like protein [RNA 99.63
KOG177488 consensus Small nuclear ribonucleoprotein E [RNA p 99.57
KOG178496 consensus Small Nuclear ribonucleoprotein splicing 99.53
KOG1782129 consensus Small Nuclear ribonucleoprotein splicing 99.5
KOG3459114 consensus Small nuclear ribonucleoprotein (snRNP) 99.46
KOG3293134 consensus Small nuclear ribonucleoprotein (snRNP) 99.42
KOG344896 consensus Predicted snRNP core protein [RNA proces 99.36
KOG3172119 consensus Small nuclear ribonucleoprotein Sm D3 [R 99.28
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 98.95
KOG3428109 consensus Small nuclear ribonucleoprotein SMD1 and 98.85
PF1443877 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1. 98.16
PF1270196 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC 96.89
PF0223748 BPL_C: Biotin protein ligase C terminal domain; In 96.74
TIGR0238361 Hfq RNA chaperone Hfq. This model represents the R 96.68
cd0171661 Hfq Hfq, an abundant, ubiquitous RNA-binding prote 96.66
PRK0039579 hfq RNA-binding protein Hfq; Provisional 96.4
PF1109580 Gemin7: Gem-associated protein 7 (Gemin7); InterPr 96.39
cd0173561 LSm12_N LSm12 belongs to a family of Sm-like prote 96.27
cd0173674 LSm14_N LSm14 (also known as RAP55) belongs to a f 95.83
PF06372166 Gemin6: Gemin6 protein; InterPro: IPR009422 This f 95.43
COG192377 Hfq Uncharacterized host factor I protein [General 95.25
PRK14091165 RNA-binding protein Hfq; Provisional 95.12
PRK14638150 hypothetical protein; Provisional 94.49
PF1084266 DUF2642: Protein of unknown function (DUF2642); In 93.79
PRK02001152 hypothetical protein; Validated 93.34
PRK14091165 RNA-binding protein Hfq; Provisional 93.26
PRK14639140 hypothetical protein; Provisional 93.03
PRK14644136 hypothetical protein; Provisional 91.01
PF03614165 Flag1_repress: Repressor of phase-1 flagellin; Int 89.89
PRK14640152 hypothetical protein; Provisional 89.87
PRK14642197 hypothetical protein; Provisional 89.8
cd0173483 YlxS_C YxlS is a Bacillus subtilis gene of unknown 89.74
PRK14633150 hypothetical protein; Provisional 89.52
PRK14645154 hypothetical protein; Provisional 89.42
PRK14636176 hypothetical protein; Provisional 88.69
COG0779153 Uncharacterized protein conserved in bacteria [Fun 88.42
PF02576141 DUF150: Uncharacterised BCR, YhbC family COG0779; 87.5
PRK14643164 hypothetical protein; Provisional 86.95
PF1456342 DUF4444: Domain of unknown function (DUF4444); PDB 86.88
PRK14632172 hypothetical protein; Provisional 86.85
PRK14634155 hypothetical protein; Provisional 86.8
PRK00092154 ribosome maturation protein RimP; Reviewed 86.61
PRK14646155 hypothetical protein; Provisional 85.96
PRK14647159 hypothetical protein; Provisional 85.05
PRK14631174 hypothetical protein; Provisional 84.68
KOG1073 361 consensus Uncharacterized mRNA-associated protein 84.57
PRK06955300 biotin--protein ligase; Provisional 84.34
PRK14637151 hypothetical protein; Provisional 82.42
PRK14641173 hypothetical protein; Provisional 81.29
PRK11886319 bifunctional biotin--[acetyl-CoA-carboxylase] synt 81.11
>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 
Probab=99.94  E-value=1.7e-26  Score=145.38  Aligned_cols=85  Identities=29%  Similarity=0.518  Sum_probs=70.5

Q ss_pred             CCcHHHHHHhC--CCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcCCcE
Q 034340           10 KEPLDLIRLSL--DERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRGDGV   87 (97)
Q Consensus        10 ~~P~~lL~~~l--~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~~I   87 (97)
                      .+|+++|+.++  +++|.|+|++|+.+.|+|.|||+||||+|+||.|.+...++++++.+.......+++|.+||||++|
T Consensus         1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~V   80 (87)
T cd01720           1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSV   80 (87)
T ss_pred             CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEE
Confidence            48999999997  7999999999999999999999999999999999987644332211122235678899999999999


Q ss_pred             EEEecCC
Q 034340           88 ILVSPPL   94 (97)
Q Consensus        88 v~I~~~~   94 (97)
                      ++|+..|
T Consensus        81 v~Is~~~   87 (87)
T cd01720          81 ILVLRNP   87 (87)
T ss_pred             EEEecCC
Confidence            9998754

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
>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
>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
>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
>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
>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
>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
>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
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>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
>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
>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
>smart00651 Sm snRNP Sm proteins Back     alignment and domain information
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] 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
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification] Back     alignment and domain information
>PTZ00138 small nuclear ribonucleoprotein; Provisional 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
>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
>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
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification] Back     alignment and domain information
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification] Back     alignment and domain information
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information
>KOG3168 consensus U1 snRNP component [Transcription] Back     alignment and domain information
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification] Back     alignment and domain information
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification] Back     alignment and domain information
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification] Back     alignment and domain information
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification] Back     alignment and domain information
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification] Back     alignment and domain information
>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
>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 Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification] Back     alignment and domain information
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1 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
>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
>TIGR02383 Hfq RNA chaperone Hfq 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
>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
>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
>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
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins Back     alignment and domain information
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only] Back     alignment and domain information
>PRK14091 RNA-binding protein Hfq; Provisional Back     alignment and domain information
>PRK14638 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
>PRK02001 hypothetical protein; Validated Back     alignment and domain information
>PRK14091 RNA-binding protein Hfq; Provisional Back     alignment and domain information
>PRK14639 hypothetical protein; Provisional Back     alignment and domain information
>PRK14644 hypothetical protein; Provisional Back     alignment and domain information
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella Back     alignment and domain information
>PRK14640 hypothetical protein; Provisional Back     alignment and domain information
>PRK14642 hypothetical protein; Provisional Back     alignment and domain information
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold Back     alignment and domain information
>PRK14633 hypothetical protein; Provisional Back     alignment and domain information
>PRK14645 hypothetical protein; Provisional Back     alignment and domain information
>PRK14636 hypothetical protein; Provisional Back     alignment and domain information
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown] 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
>PRK14643 hypothetical protein; Provisional Back     alignment and domain information
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A Back     alignment and domain information
>PRK14632 hypothetical protein; Provisional Back     alignment and domain information
>PRK14634 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
>PRK14647 hypothetical protein; Provisional Back     alignment and domain information
>PRK14631 hypothetical protein; Provisional Back     alignment and domain information
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>PRK06955 biotin--protein ligase; Provisional Back     alignment and domain information
>PRK14637 hypothetical protein; Provisional Back     alignment and domain information
>PRK14641 hypothetical protein; Provisional Back     alignment and domain information
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; 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 ?
Query97
4emg_A93 Crystal Structure Of Splsm3 Length = 93 1e-20
3bw1_A96 Crystal Structure Of Homomeric Yeast Lsm3 Exhibitin 8e-11
1i81_A83 Crystal Structure Of A Heptameric Lsm Protein From 3e-06
1th7_A81 Crystal Structure Of An Archaeal Sm Protein From Su 5e-06
1loj_A87 Crystal Structure Of A Methanobacterial Sm-Like Arc 2e-05
1jbm_A86 Heptameric Crystal Structure Of Mth649, An Sm-Like 2e-05
1jri_A85 The Crystal Structure Of An Sm-Like Archaeal Protei 2e-05
1i5l_A77 Crystal Structure Of An Sm-Like Protein (Af-Sm1) Fr 3e-05
2fwk_A121 Crystal Structure Of Cryptosporidium Parvum U6 Snrn 2e-04
1m8v_A77 Structure Of Pyrococcus Abyssii Sm Protein In Compl 3e-04
1h64_175 Crystal Structure Of The Sm-Related Protein Of P. A 4e-04
>pdb|4EMG|A Chain A, Crystal Structure Of Splsm3 Length = 93 Back     alignment and structure 
Iteration: 1

 Score = 94.7 bits (234), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 47/90 (52%), Positives = 56/90 (62%)
Query: 4  EEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGXXXXXXXXXXXXX 63
          E   AV EPLDL+RLSLDE +YVKLR DREL G+LHAYD+HLN +LG             
Sbjct: 2  ESAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNXVLGDAEEIVTIFDDEE 61
Query: 64 XXXXXXXRTTRRTVPFLFVRGDGVILVSPP 93
                 +T R+    LFVRGD VIL++PP
Sbjct: 62 TDKDKALKTIRKHYEXLFVRGDSVILIAPP 91
>pdb|3BW1|A Chain A, Crystal Structure Of Homomeric Yeast Lsm3 Exhibiting Novel Octameric Ring Organisation Length = 96 Back     alignment and structure
>pdb|1I81|A Chain A, Crystal Structure Of A Heptameric Lsm Protein From Methanobacterium Thermoautotrophicum Length = 83 Back     alignment and structure
>pdb|1TH7|A Chain A, Crystal Structure Of An Archaeal Sm Protein From Sulfolobus Solfataricus Length = 81 Back     alignment and structure
>pdb|1LOJ|A Chain A, Crystal Structure Of A Methanobacterial Sm-Like Archaeal Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump) Length = 87 Back     alignment and structure
>pdb|1JBM|A Chain A, Heptameric Crystal Structure Of Mth649, An Sm-Like Archaeal Protein From Methanobacterium Thermautotrophicum Length = 86 Back     alignment and structure
>pdb|1JRI|A Chain A, The Crystal Structure Of An Sm-Like Archaeal Protein With Two Heptamers In The Asymmetric Unit. Length = 85 Back     alignment and structure
>pdb|1I5L|A Chain A, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From Archaeoglobus Fulgidus Complexed With Short Poly-U Rna Length = 77 Back     alignment and structure
>pdb|2FWK|A Chain A, Crystal Structure Of Cryptosporidium Parvum U6 Snrna- Associated Sm-Like Protein Lsm5 Length = 121 Back     alignment and structure
>pdb|1M8V|A Chain A, Structure Of Pyrococcus Abyssii Sm Protein In Complex With A Uridine Heptamer Length = 77 Back     alignment and structure
>pdb|1H64|1 Chain 1, Crystal Structure Of The Sm-Related Protein Of P. Abyssi The Biological Unit Is A Heptamer Length = 75 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query97
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 3e-35
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 2e-29
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 6e-29
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 3e-28
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 1e-26
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 3e-22
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 6e-22
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 2e-21
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 3e-21
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 4e-21
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 3e-18
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 4e-16
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 5e-16
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 9e-16
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 2e-15
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 4e-14
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 3e-12
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 7e-10
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 9e-09
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 9e-09
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 3e-07
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 4e-06
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 3e-05
>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
 Score =  114 bits (287), Expect = 3e-35
 Identities = 53/90 (58%), Positives = 69/90 (76%)

Query: 4  EEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDD 63
          E   AV EPLDL+RLSLDE +YVKLR DREL G+LHAYD+HLNM+LGD EE+VT  + ++
Sbjct: 2  ESAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEE 61

Query: 64 ETYEEIVRTTRRTVPFLFVRGDGVILVSPP 93
             ++ ++T R+    LFVRGD VIL++PP
Sbjct: 62 TDKDKALKTIRKHYEMLFVRGDSVILIAPP 91
>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Length = 121 Back     alignment and structure
>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae} Length = 96 Back     alignment and structure
>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
>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A Length = 83 Back     alignment and structure
>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Length = 81 Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>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_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
>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
>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
>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
>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
>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
>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D Length = 126 Back     alignment and structure
>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 Length = 75 Back     alignment and structure
>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A Length = 119 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query97
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.94
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.94
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.94
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.93
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.93
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.93
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.93
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.93
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.92
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.92
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.92
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.92
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.92
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.92
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.91
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.91
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.91
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.91
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.9
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.9
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 99.88
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.88
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 99.87
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.82
1y96_A86 Gemin6, SIP2, GEM-associated protein 6; SM fold, p 98.85
2qtx_A71 Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi 97.04
1u1s_A82 HFQ protein; SM-like bacterial protein, riken stru 96.92
2ylb_A74 Protein HFQ; RNA-binding protein, LSM protein, RNA 96.87
3sb2_A79 Protein HFQ; SM-like, RNA chaperone, chaperone; 2. 96.81
3ahu_A78 Protein HFQ; SM-like motif, protein-RNA complex, t 96.73
1kq1_A77 HFQ, HOST factor for Q beta; hexamer, RNA binding 96.68
2y90_A104 Protein HFQ; RNA-binding protein, SM-like, RNA cha 96.31
1y96_B85 Gemin7, SIP3, GEM-associated protein 7; SM fold, p 96.29
2vxe_A88 CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA 96.23
2fb7_A95 SM-like protein, LSM-14_N (RAP55); DR.13312, BC055 95.63
1ycy_A71 Conserved hypothetical protein; structural genomic 95.53
4a53_A125 EDC3; RNA binding protein; NMR {Schizosaccharomyce 95.42
3hfo_A70 SSR3341 protein; HFQ, SM, RNA-binding protein, sRN 94.61
3hfn_A72 ASL2047 protein; HFQ, SM, RNA-binding protein, sRN 94.16
2vc8_A84 Enhancer of mRNA-decapping protein 3; P-BODY compo 92.76
3rux_A270 BIRA bifunctional protein; biotin-protein ligase, 91.43
1ib8_A164 Conserved protein SP14.3; nucleic acid binding pro 87.6
2eay_A233 Biotin [acetyl-COA-carboxylase] ligase; biotin bio 85.12
2e12_A101 SM-like motif, hypothetical protein XCC3642; novel 84.29
1bia_A321 BIRA bifunctional protein; transcription regulatio 83.89
2ej9_A237 Putative biotin ligase; biotin biosynthesis, monom 81.19
>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
Probab=99.94  E-value=4.7e-27  Score=148.49  Aligned_cols=90  Identities=58%  Similarity=0.976  Sum_probs=66.6

Q ss_pred             cccccCCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchhheeeceeeEecCeEEEcC
Q 034340            5 EESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRTTRRTVPFLFVRG   84 (97)
Q Consensus         5 ~~~~~~~P~~lL~~~l~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG   84 (97)
                      +.+....|+++|+.+++++|+|+|++||.|.|+|.|||+||||+|+||.|++..++.+++..+.......+.+|.+||||
T Consensus         3 ~~~~~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG   82 (93)
T 4emg_A            3 SAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRG   82 (93)
T ss_dssp             ------CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECG
T ss_pred             cccccCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECC
Confidence            34667899999999999999999999999999999999999999999999987543222100001124578999999999


Q ss_pred             CcEEEEecCC
Q 034340           85 DGVILVSPPL   94 (97)
Q Consensus        85 ~~Iv~I~~~~   94 (97)
                      +||++|+++.
T Consensus        83 ~nVv~I~p~~   92 (93)
T 4emg_A           83 DSVILIAPPR   92 (93)
T ss_dssp             GGEEEEECCC
T ss_pred             CeEEEEEecC
Confidence            9999999863
>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
>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
>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
>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_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
>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
>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A Back     alignment and structure
>4emk_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
>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
>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
>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
>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
>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
>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
>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
>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe} Back     alignment and structure
>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A Back     alignment and structure
>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
>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
>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
>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
>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2 Back     alignment and structure
>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A Back     alignment and structure
>1kq1_A HFQ, HOST factor for Q beta; hexamer, RNA binding protein, translational regulator, SM motif; 1.55A {Staphylococcus aureus} SCOP: b.38.1.2 PDB: 1kq2_A Back     alignment and structure
>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
>2vxe_A CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA decay, LSM proteins, translational repression, transcription; NMR {Drosophila melanogaster} 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
>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
>4a53_A EDC3; RNA binding protein; NMR {Schizosaccharomyces pombe} PDB: 4a54_A 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
>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
>2eay_A Biotin [acetyl-COA-carboxylase] ligase; biotin biosynthesis, dimer, X-RAY diffraction, structural genomics, NPPSFA; 1.95A {Aquifex aeolicus} PDB: 3efs_A* 3fjp_A 3efr_A* Back     alignment and structure
>2e12_A SM-like motif, hypothetical protein XCC3642; novel SM-like motif, LSM motif, X- RAY crystallography, translation; 1.70A {Xanthomonas campestris PV} Back     alignment and structure
>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A* Back     alignment and structure
>2ej9_A Putative biotin ligase; biotin biosynthesis, monomer, X-RAY diffraction, structural genomics, NPPSFA; HET: BTN; 2.00A {Methanocaldococcus jannaschii} 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 97
d2fwka192 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr 3e-24
d1b34b_93 b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s 2e-22
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 1e-19
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 8e-19
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 1e-18
d1d3bb_81 b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa 1e-17
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 3e-17
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 9e-16
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 5e-15
d1d3ba_72 b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s 6e-13
d1n9ra_68 b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S 1e-09
d1m5q1_127 b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch 2e-07
d1b34a_80 b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s 8e-06
>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

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: U6 snRNA-associated sm-like protein LSM5
species: Cryptosporidium parvum [TaxId: 5807]

 Score = 85.7 bits (212), Expect = 3e-24
 Identities = 24/83 (28%), Positives = 46/83 (55%), Gaps = 2/83 (2%)

Query: 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDET--YEEI 69
          PL LI   +  RIYV ++ D+E  G L  +D+++NM+L DV+E     + +D +   +++
Sbjct: 6  PLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKL 65

Query: 70 VRTTRRTVPFLFVRGDGVILVSP 92
           R     +  + + G+ V ++ P
Sbjct: 66 KRVMVNRLETILLSGNNVAMLVP 88
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93 Back     information, alignment and structure
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 74 Back     information, alignment and structure
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Length = 71 Back     information, alignment and structure
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Length = 72 Back     information, alignment and structure
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 81 Back     information, alignment and structure
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Length = 76 Back     information, alignment and structure
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Length = 75 Back     information, alignment and structure
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 71 Back     information, alignment and structure
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72 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
>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 ?
Query97
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.95
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.94
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.93
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.93
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.93
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.92
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.92
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.92
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.91
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.89
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.89
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.81
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 99.75
d1biaa247 Biotin repressor/biotin holoenzyme synthetase, C-t 96.63
d1kq1a_60 Pleiotropic translational regulator Hfq {Staphyloc 96.35
d2vxfa180 LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) 96.33
d1u1sa166 Pleiotropic translational regulator Hfq {Pseudomon 96.13
d1ycya166 Hypothetical protein PF1955 {Pyrococcus furiosus [ 95.78
d1ib8a174 Hypothetical protein SP14.3 (SP0552) {Streptococcu 92.35
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D2 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=9.8e-28  Score=150.20  Aligned_cols=87  Identities=29%  Similarity=0.495  Sum_probs=66.0

Q ss_pred             CcHHHHHHhC--CCeEEEEEcCCeEEEEEEEEECCccCeEEeceEEEEeecccCcchh-heeeceeeEecCeEEEcCCcE
Q 034340           11 EPLDLIRLSL--DERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETY-EEIVRTTRRTVPFLFVRGDGV   87 (97)
Q Consensus        11 ~P~~lL~~~l--~k~V~V~l~~gr~i~G~L~~fD~~mNlvL~d~~e~~~~~~~~~~~~-~~~~~~~~r~lg~v~IRG~~I   87 (97)
                      +|+++|..++  +++|+|.|++||.+.|+|.|||+||||+|+||+|++...+...+.. ..+.....|.+|++||||+||
T Consensus         2 GPl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdnV   81 (93)
T d1b34b_           2 GPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSV   81 (93)
T ss_dssp             CHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGE
T ss_pred             CcHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCEE
Confidence            7999999999  8999999999999999999999999999999999987654322111 112235678999999999999


Q ss_pred             EEEecCCCCC
Q 034340           88 ILVSPPLRTA   97 (97)
Q Consensus        88 v~I~~~~~~~   97 (97)
                      ++|..+|.-|
T Consensus        82 v~I~~~p~~~   91 (93)
T d1b34b_          82 IVVLRNPLIA   91 (93)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEcChhhc
Confidence            9999998754
>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} Back     information, alignment and structure
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Back     information, alignment and structure
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Back     information, alignment and structure
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Back     information, alignment and structure
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Back     information, alignment and structure
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d1kq1a_ b.38.1.2 (A:) Pleiotropic translational regulator Hfq {Staphylococcus aureus [TaxId: 1280]} 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
>d1u1sa1 b.38.1.2 (A:6-71) Pleiotropic translational regulator Hfq {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1ycya1 b.38.1.4 (A:5-70) Hypothetical protein PF1955 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1ib8a1 b.38.2.1 (A:91-164) Hypothetical protein SP14.3 (SP0552) {Streptococcus pneumoniae [TaxId: 1313]} Back     information, alignment and structure