Citrus Sinensis ID: 034752

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-----
MASEEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFKL
ccccccccccccHHHHHHHcccEEEEEEcccEEEEEEEEEEcccccEEEEcEEEEEEEEEcccccccEEEEEEEEEEEEEEEEEc
cccccccccccHHHHHHHHcccEEEEEEcccEEEEEEEEEEcccccEEEEEEEEEEEEEEccccccEEEEEEccccEEEEEEEcc
MASEEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFKL
maseeesavkepldlirlslderIYVKLrsdrelrgkLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFKL
MASEEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGdveevvttveiddetyeeivRVCCNLKILLLNFKL
************LDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNF**
************LDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEI**********VCCNLKILLLNFKL
**********EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFKL
********VKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFKL
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MASEEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEEIVRVCCNLKILLLNFKL
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 ?
Query85 2.2.26 [Sep-21-2011]
P62311102 U6 snRNA-associated Sm-li yes no 0.882 0.735 0.736 1e-25
P62310102 U6 snRNA-associated Sm-li yes no 0.882 0.735 0.736 1e-25
Q32PE9102 U6 snRNA-associated Sm-li yes no 0.882 0.735 0.736 1e-25
Q1ZXK397 Probable U6 snRNA-associa yes no 0.952 0.835 0.682 4e-24
Q9Y7M493 Probable U6 snRNA-associa yes no 0.717 0.655 0.693 1e-17
P5774389 U6 snRNA-associated Sm-li yes no 0.705 0.674 0.467 1e-08
O2674581 Putative snRNP Sm-like pr yes no 0.623 0.654 0.415 2e-06
Q0W8R972 Putative snRNP Sm-like pr yes no 0.541 0.638 0.391 3e-05
O2938677 Putative snRNP Sm-like pr yes no 0.541 0.597 0.434 4e-05
Q8PZZ972 Putative snRNP Sm-like pr yes no 0.517 0.611 0.431 5e-05
>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 =  114 bits (286), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 56/76 (73%), Positives = 67/76 (88%), Gaps = 1/76 (1%)

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

Query: 67 EEIVRVCC-NLKILLL 81
          EEI +    N+ +L +
Sbjct: 72 EEIYKSTKRNIPMLFV 87
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|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|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|Q8PZZ9|RUXX_METMA Putative snRNP Sm-like protein OS=Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88) GN=MM_0339 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 ?
Query85
359493113109 PREDICTED: U6 snRNA-associated Sm-like p 0.847 0.660 0.986 2e-32
22408511197 predicted protein [Populus trichocarpa] 0.858 0.752 0.958 8e-32
22406289297 predicted protein [Populus trichocarpa] 0.858 0.752 0.958 8e-32
25558334297 snrnp sm protein, putative [Ricinus comm 0.858 0.752 0.958 1e-31
35172234397 uncharacterized protein LOC100499782 [Gl 0.858 0.752 0.945 1e-31
38849393297 unknown [Lotus japonicus] gi|388511495|g 0.858 0.752 0.945 2e-31
35172477197 uncharacterized protein LOC100306547 [Gl 0.858 0.752 0.917 5e-31
212723246107 uncharacterized protein LOC100194361 [Ze 0.858 0.682 0.945 6e-31
14890826597 unknown [Picea sitchensis] 0.858 0.752 0.917 1e-30
44949708897 PREDICTED: U6 snRNA-associated Sm-like p 0.858 0.752 0.931 2e-30
>gi|359493113|ref|XP_003634512.1| PREDICTED: U6 snRNA-associated Sm-like protein LSm3-like isoform 2 [Vitis vinifera] gi|296081172|emb|CBI18198.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  142 bits (359), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 71/72 (98%), Positives = 72/72 (100%)

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

Query: 61 IDDETYEEIVRV 72
          IDDETYEEIVRV
Sbjct: 61 IDDETYEEIVRV 72

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>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
>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|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|351722343|ref|NP_001235961.1| uncharacterized protein LOC100499782 [Glycine max] gi|255626487|gb|ACU13588.1| unknown [Glycine max] 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|351724771|ref|NP_001236557.1| uncharacterized protein LOC100306547 [Glycine max] gi|255628849|gb|ACU14769.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|212723246|ref|NP_001132868.1| uncharacterized protein LOC100194361 [Zea mays] gi|194695618|gb|ACF81893.1| unknown [Zea mays] Back     alignment and taxonomy information
>gi|148908265|gb|ABR17247.1| unknown [Picea sitchensis] 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 ?
Query85
TAIR|locus:203625798 LSM3B "AT1G76860" [Arabidopsis 0.588 0.510 0.88 6.5e-19
TAIR|locus:201492297 LSM3A "AT1G21190" [Arabidopsis 0.588 0.515 0.82 9.5e-18
DICTYBASE|DDB_G027710797 lsm3 "putative U6 small nuclea 0.576 0.505 0.816 1.4e-16
UNIPROTKB|F1P28096 LSM3 "Uncharacterized protein" 0.517 0.458 0.863 3.7e-16
UNIPROTKB|Q32PE9102 LSM3 "U6 snRNA-associated Sm-l 0.517 0.431 0.863 3.7e-16
UNIPROTKB|P62310102 LSM3 "U6 snRNA-associated Sm-l 0.517 0.431 0.863 3.7e-16
UNIPROTKB|F2Z5S4102 LSM3 "Uncharacterized protein" 0.517 0.431 0.863 3.7e-16
MGI|MGI:1914928102 Lsm3 "LSM3 homolog, U6 small n 0.517 0.431 0.863 3.7e-16
RGD|1305971102 Lsm3 "LSM3 homolog, U6 small n 0.517 0.431 0.863 3.7e-16
FB|FBgn0051184103 LSm3 [Drosophila melanogaster 0.494 0.407 0.809 4.2e-15
TAIR|locus:2036257 LSM3B "AT1G76860" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 227 (85.0 bits), Expect = 6.5e-19, P = 6.5e-19
 Identities = 44/50 (88%), Positives = 48/50 (96%)

Query:     1 MASEEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILG 50
             M+ EEE+ V+EPLDLIRLSLDERIYVKLRSDRELRGKLHA+DQHLNMILG
Sbjct:     1 MSGEEEATVREPLDLIRLSLDERIYVKLRSDRELRGKLHAFDQHLNMILG 50
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
DICTYBASE|DDB_G0277107 lsm3 "putative U6 small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)] 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
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) ?
P62311LSM3_MOUSENo assigned EC number0.73680.88230.7352yesno
Q9Y7M4LSM3_SCHPONo assigned EC number0.69350.71760.6559yesno
P62310LSM3_HUMANNo assigned EC number0.73680.88230.7352yesno
Q1ZXK3LSM3_DICDINo assigned EC number0.68290.95290.8350yesno
Q32PE9LSM3_BOVINNo assigned EC number0.73680.88230.7352yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
estExt_fgenesh4_pm.C_LG_V0415
hypothetical protein (98 aa)
(Populus trichocarpa)
Predicted Functional Partners:
grail3.0053017102
SubName- Full=Putative uncharacterized protein; (88 aa)
  ••••• 0.700
eugene3.00090932
SubName- Full=Putative uncharacterized protein; (88 aa)
  ••••• 0.700
grail3.0053017202
SubName- Full=Putative uncharacterized protein; (99 aa)
   •• • 0.698
gw1.X.1452.1
annotation not avaliable (75 aa)
  ••••• 0.683
estExt_fgenesh4_pm.C_LG_VIII0306
SubName- Full=Putative uncharacterized protein; (92 aa)
  ••••• 0.667
estExt_fgenesh4_kg.C_LG_III0001
SubName- Full=Putative uncharacterized protein; (93 aa)
   •••• 0.589
estExt_fgenesh4_kg.C_1630004
SubName- Full=Putative uncharacterized protein; (93 aa)
   •••• 0.589
gw1.IX.2304.1
hypothetical protein (321 aa)
  ••    0.525
eugene3.00180816
hypothetical protein (88 aa)
  ••• • 0.503
estExt_Genewise1_v1.C_1580060
hypothetical protein (128 aa)
  ••••• 0.494

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 ?
Query85
cd0173082 cd01730, LSm3, Like-Sm protein 3 7e-37
COG195879 COG1958, LSM1, Small nuclear ribonucleoprotein (sn 6e-12
cd0173169 cd01731, archaeal_Sm1, archaeal Sm protein 1 5e-11
smart0065167 smart00651, Sm, snRNP Sm proteins 6e-11
pfam0142366 pfam01423, LSM, LSM domain 3e-10
PRK0073772 PRK00737, PRK00737, small nuclear ribonucleoprotei 9e-10
cd0060063 cd00600, Sm_like, Sm and related proteins 6e-07
cd0173276 cd01732, LSm5, Like-Sm protein 5 2e-06
cd0172668 cd01726, LSm6, Like-Sm protein 6 5e-06
cd0172989 cd01729, LSm7, Like-Sm protein 7 1e-05
cd0172089 cd01720, Sm_D2, Sm protein D2 3e-05
cd0171780 cd01717, Sm_B, Sm protein B 2e-04
cd0616873 cd06168, LSMD1, LSM domain containing 1 4e-04
cd0172874 cd01728, LSm1, Like-Sm protein 1 0.003
>gnl|CDD|212477 cd01730, LSm3, Like-Sm protein 3 Back     alignment and domain information 
 Score =  118 bits (298), Expect = 7e-37
 Identities = 53/62 (85%), Positives = 58/62 (93%)

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

Query: 71 RV 72
          + 
Sbjct: 61 KT 62

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|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] Back     alignment and domain information
>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1 Back     alignment and domain information
>gnl|CDD|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|212462 cd00600, Sm_like, Sm and related proteins Back     alignment and domain information
>gnl|CDD|212479 cd01732, LSm5, Like-Sm protein 5 Back     alignment and domain information
>gnl|CDD|212473 cd01726, LSm6, Like-Sm protein 6 Back     alignment and domain information
>gnl|CDD|212476 cd01729, LSm7, Like-Sm protein 7 Back     alignment and domain information
>gnl|CDD|212467 cd01720, Sm_D2, Sm protein D2 Back     alignment and domain information
>gnl|CDD|212464 cd01717, Sm_B, Sm protein B Back     alignment and domain information
>gnl|CDD|212486 cd06168, LSMD1, LSM domain containing 1 Back     alignment and domain information
>gnl|CDD|212475 cd01728, LSm1, Like-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 85
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.88
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.87
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.86
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.85
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.84
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.83
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.82
cd0171779 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins 99.81
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.81
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.81
cd0172874 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins 99.79
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.78
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 99.78
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.77
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.77
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.76
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.74
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.73
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.73
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.72
KOG177584 consensus U6 snRNA-associated Sm-like protein [RNA 99.71
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.7
KOG346091 consensus Small nuclear ribonucleoprotein (snRNP) 99.69
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.65
KOG348279 consensus Small nuclear ribonucleoprotein (snRNP) 99.65
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.63
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.63
KOG1781108 consensus Small Nuclear ribonucleoprotein splicing 99.61
KOG178077 consensus Small Nuclear ribonucleoprotein G [RNA p 99.6
KOG177488 consensus Small nuclear ribonucleoprotein E [RNA p 99.47
KOG178377 consensus Small nuclear ribonucleoprotein F [RNA p 99.33
KOG3459114 consensus Small nuclear ribonucleoprotein (snRNP) 99.33
KOG3168 177 consensus U1 snRNP component [Transcription] 99.25
KOG178496 consensus Small Nuclear ribonucleoprotein splicing 99.03
KOG3293134 consensus Small nuclear ribonucleoprotein (snRNP) 99.02
KOG3172119 consensus Small nuclear ribonucleoprotein Sm D3 [R 98.77
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 98.67
KOG1782129 consensus Small Nuclear ribonucleoprotein splicing 98.64
KOG344896 consensus Predicted snRNP core protein [RNA proces 98.62
KOG3428109 consensus Small nuclear ribonucleoprotein SMD1 and 97.83
PF1443877 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1. 97.66
cd0171661 Hfq Hfq, an abundant, ubiquitous RNA-binding prote 96.94
TIGR0238361 Hfq RNA chaperone Hfq. This model represents the R 96.84
PRK0039579 hfq RNA-binding protein Hfq; Provisional 96.62
COG192377 Hfq Uncharacterized host factor I protein [General 95.7
PRK14091165 RNA-binding protein Hfq; Provisional 95.29
cd0173561 LSm12_N LSm12 belongs to a family of Sm-like prote 95.11
PF1270196 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC 94.96
PF06372166 Gemin6: Gemin6 protein; InterPro: IPR009422 This f 94.92
PF0223748 BPL_C: Biotin protein ligase C terminal domain; In 94.8
PRK14091165 RNA-binding protein Hfq; Provisional 94.51
PRK14638150 hypothetical protein; Provisional 94.16
PRK02001152 hypothetical protein; Validated 93.21
PRK14639140 hypothetical protein; Provisional 93.15
cd0173674 LSm14_N LSm14 (also known as RAP55) belongs to a f 92.9
PF1109580 Gemin7: Gem-associated protein 7 (Gemin7); InterPr 91.43
PRK14644136 hypothetical protein; Provisional 91.41
PRK14640152 hypothetical protein; Provisional 89.54
cd0173483 YlxS_C YxlS is a Bacillus subtilis gene of unknown 89.45
PRK14633150 hypothetical protein; Provisional 89.22
PRK14645154 hypothetical protein; Provisional 88.88
PRK14642197 hypothetical protein; Provisional 88.55
PF02576141 DUF150: Uncharacterised BCR, YhbC family COG0779; 88.49
PRK14636176 hypothetical protein; Provisional 87.83
PRK14632172 hypothetical protein; Provisional 87.23
PRK14634155 hypothetical protein; Provisional 87.22
PRK14646155 hypothetical protein; Provisional 86.96
PRK14643164 hypothetical protein; Provisional 86.85
PRK00092154 ribosome maturation protein RimP; Reviewed 86.74
COG0779153 Uncharacterized protein conserved in bacteria [Fun 85.93
PRK14647159 hypothetical protein; Provisional 84.61
PRK14631174 hypothetical protein; Provisional 83.11
PRK14637151 hypothetical protein; Provisional 81.85
PRK14641173 hypothetical protein; Provisional 81.45
>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 
Probab=99.88  E-value=2.4e-22  Score=126.59  Aligned_cols=74  Identities=73%  Similarity=1.101  Sum_probs=62.8

Q ss_pred             ChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccce-eeeeeeeeeeEEecCC
Q 034752           11 EPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEE-IVRVCCNLKILLLNFK   84 (85)
Q Consensus        11 ~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~~-~~~~~r~lg~ill~G~   84 (85)
                      .|+++|+.+++++|+|+|++||.|.|+|.|||+||||+|+||+|++......++...+ .....|+||+++|||+
T Consensus         1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd   75 (82)
T cd01730           1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGD   75 (82)
T ss_pred             CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCC
Confidence            4999999999999999999999999999999999999999999999876544322212 2235789999999997

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. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
>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
>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
>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
>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
>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
>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
>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
>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
>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
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] 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
>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
>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
>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
>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
>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
>PTZ00138 small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification] Back     alignment and domain information
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification] Back     alignment and domain information
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification] 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
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification] Back     alignment and domain information
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification] Back     alignment and domain information
>KOG1783 consensus Small nuclear ribonucleoprotein F [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
>KOG3168 consensus U1 snRNP component [Transcription] Back     alignment and domain information
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification] Back     alignment and domain information
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification] Back     alignment and domain information
>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
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification] Back     alignment and domain information
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification] Back     alignment and domain information
>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
>PRK14091 RNA-binding protein Hfq; Provisional Back     alignment and domain information
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A Back     alignment and domain information
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins 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
>PRK14091 RNA-binding protein Hfq; Provisional Back     alignment and domain information
>PRK14638 hypothetical protein; Provisional Back     alignment and domain information
>PRK02001 hypothetical protein; Validated Back     alignment and domain information
>PRK14639 hypothetical protein; Provisional 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
>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
>PRK14644 hypothetical protein; Provisional Back     alignment and domain information
>PRK14640 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
>PRK14642 hypothetical protein; Provisional Back     alignment and domain information
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [] Back     alignment and domain information
>PRK14636 hypothetical protein; Provisional Back     alignment and domain information
>PRK14632 hypothetical protein; Provisional Back     alignment and domain information
>PRK14634 hypothetical protein; Provisional Back     alignment and domain information
>PRK14646 hypothetical protein; Provisional Back     alignment and domain information
>PRK14643 hypothetical protein; Provisional Back     alignment and domain information
>PRK00092 ribosome maturation protein RimP; Reviewed Back     alignment and domain information
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK14647 hypothetical protein; Provisional Back     alignment and domain information
>PRK14631 hypothetical protein; Provisional Back     alignment and domain information
>PRK14637 hypothetical protein; Provisional Back     alignment and domain information
>PRK14641 hypothetical protein; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query85
4emg_A93 Crystal Structure Of Splsm3 Length = 93 2e-14
3bw1_A96 Crystal Structure Of Homomeric Yeast Lsm3 Exhibitin 4e-08
1i81_A83 Crystal Structure Of A Heptameric Lsm Protein From 1e-05
1jbm_A86 Heptameric Crystal Structure Of Mth649, An Sm-Like 1e-05
1loj_A87 Crystal Structure Of A Methanobacterial Sm-Like Arc 1e-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 9e-05
2fwk_A121 Crystal Structure Of Cryptosporidium Parvum U6 Snrn 3e-04
1m8v_A77 Structure Of Pyrococcus Abyssii Sm Protein In Compl 4e-04
1h64_175 Crystal Structure Of The Sm-Related Protein Of P. A 4e-04
1th7_A81 Crystal Structure Of An Archaeal Sm Protein From Su 5e-04
>pdb|4EMG|A Chain A, Crystal Structure Of Splsm3 Length = 93 Back     alignment and structure 
Iteration: 1

 Score = 73.9 bits (180), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 34/47 (72%), Positives = 39/47 (82%)
Query: 4  EEESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILG 50
          E   AV EPLDL+RLSLDE +YVKLR DREL G+LHAYD+HLN +LG
Sbjct: 2  ESAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNXVLG 48
>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|1JBM|A Chain A, Heptameric Crystal Structure Of Mth649, An Sm-Like Archaeal Protein From Methanobacterium Thermautotrophicum Length = 86 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|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
>pdb|1TH7|A Chain A, Crystal Structure Of An Archaeal Sm Protein From Sulfolobus Solfataricus Length = 81 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 ?
Query85
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 7e-23
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 8e-21
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 4e-20
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 6e-20
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 8e-18
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 6e-17
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 8e-17
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 2e-16
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 2e-16
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 7e-16
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 2e-12
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 2e-11
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 3e-11
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 7e-11
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 4e-10
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 2e-09
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 2e-09
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 9e-09
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 4e-07
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 8e-07
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 1e-06
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 2e-05
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); 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 = 83.0 bits (205), Expect = 7e-23
 Identities = 40/69 (57%), Positives = 53/69 (76%)

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

Query: 64 ETYEEIVRV 72
             ++ ++ 
Sbjct: 62 TDKDKALKT 70
>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
>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
>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
>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
>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
>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
>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A* Length = 77 Back     alignment and structure
>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A Length = 94 Back     alignment and structure
>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A* Length = 75 Back     alignment and structure
>4emk_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
>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
>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
>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
>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
>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
>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
>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
>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Length = 93 Back     alignment and structure
>1b34_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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query85
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.89
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.89
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.88
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.87
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.87
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.87
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.86
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.85
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.85
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.85
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.85
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.84
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.84
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.84
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.84
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.84
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.83
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.83
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.81
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.8
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.79
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 99.77
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 99.74
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.66
1y96_A86 Gemin6, SIP2, GEM-associated protein 6; SM fold, p 98.61
3sb2_A79 Protein HFQ; SM-like, RNA chaperone, chaperone; 2. 97.45
1u1s_A82 HFQ protein; SM-like bacterial protein, riken stru 97.43
2ylb_A74 Protein HFQ; RNA-binding protein, LSM protein, RNA 97.42
2y90_A104 Protein HFQ; RNA-binding protein, SM-like, RNA cha 97.26
3ahu_A78 Protein HFQ; SM-like motif, protein-RNA complex, t 97.12
1kq1_A77 HFQ, HOST factor for Q beta; hexamer, RNA binding 97.1
2qtx_A71 Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi 96.86
1ycy_A71 Conserved hypothetical protein; structural genomic 95.53
4a53_A125 EDC3; RNA binding protein; NMR {Schizosaccharomyce 95.28
3hfn_A72 ASL2047 protein; HFQ, SM, RNA-binding protein, sRN 94.76
3hfo_A70 SSR3341 protein; HFQ, SM, RNA-binding protein, sRN 94.41
2vxe_A88 CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA 93.03
2fb7_A95 SM-like protein, LSM-14_N (RAP55); DR.13312, BC055 90.61
1y96_B85 Gemin7, SIP3, GEM-associated protein 7; SM fold, p 89.87
1ib8_A164 Conserved protein SP14.3; nucleic acid binding pro 88.88
2vc8_A84 Enhancer of mRNA-decapping protein 3; P-BODY compo 87.97
3rux_A270 BIRA bifunctional protein; biotin-protein ligase, 85.27
2xk0_A69 Polycomb protein PCL; transcription, aromatic CAGE 84.46
>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=99.89  E-value=3.9e-23  Score=132.11  Aligned_cols=79  Identities=51%  Similarity=0.833  Sum_probs=58.7

Q ss_pred             ccccCChHHHHHhhcCCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCccccc-eeeeeeeeeeeEEecCC
Q 034752            6 ESAVKEPLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYE-EIVRVCCNLKILLLNFK   84 (85)
Q Consensus         6 ~~~~~~Pl~~L~~~l~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~~-~~~~~~r~lg~ill~G~   84 (85)
                      ......|+++|+.+++++|+|+|++|+.|+|+|.|||+||||+|+||.|++...+++.+..+ ......|+||+++|||+
T Consensus         4 ~~~~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~   83 (93)
T 4emg_A            4 AQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGD   83 (93)
T ss_dssp             -----CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGG
T ss_pred             ccccCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCC
Confidence            35678999999999999999999999999999999999999999999999987544322111 11235799999999996
>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
>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
>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
>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
>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
>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
>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
>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
>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
>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Back     alignment and structure
>4emk_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
>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
>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_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F Back     alignment and structure
>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Back     alignment and structure
>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_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
>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
>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
>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2 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
>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A {Escherichia coli} PDB: 3qhs_A Back     alignment and structure
>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A Back     alignment and structure
>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
>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii} 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
>3hfn_A ASL2047 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 2.31A {Nostoc SP} 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
>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
>1y96_B Gemin7, SIP3, GEM-associated protein 7; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} 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
>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
>2xk0_A Polycomb protein PCL; transcription, aromatic CAGE; NMR {Drosophila melanogaster} 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 85
d2fwka192 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr 2e-16
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 2e-14
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 7e-14
d1b34b_93 b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s 7e-14
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 1e-13
d1d3bb_81 b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa 3e-12
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 9e-12
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 4e-11
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 2e-10
d1d3ba_72 b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s 2e-09
d1n9ra_68 b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S 6e-07
d1m5q1_127 b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch 9e-07
d1b34a_80 b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s 2e-04
>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 = 65.3 bits (159), Expect = 2e-16
 Identities = 20/57 (35%), Positives = 33/57 (57%)

Query: 12 PLDLIRLSLDERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETYEE 68
          PL LI   +  RIYV ++ D+E  G L  +D+++NM+L DV+E     + +D +   
Sbjct: 6  PLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGN 62
>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
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93 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 ?
Query85
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.87
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.87
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.85
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.84
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.84
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.83
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.83
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.81
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.8
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.77
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.74
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.62
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 99.5
d1u1sa166 Pleiotropic translational regulator Hfq {Pseudomon 96.93
d1kq1a_60 Pleiotropic translational regulator Hfq {Staphyloc 96.67
d1ycya166 Hypothetical protein PF1955 {Pyrococcus furiosus [ 95.43
d1biaa247 Biotin repressor/biotin holoenzyme synthetase, C-t 94.3
d2vxfa180 LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) 93.61
d1ib8a174 Hypothetical protein SP14.3 (SP0552) {Streptococcu 92.08
>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=99.87  E-value=1.4e-22  Score=128.19  Aligned_cols=75  Identities=24%  Similarity=0.426  Sum_probs=55.8

Q ss_pred             CChHHHHHhhc--CCEEEEEEcCCeEEEEEEEEEcCccceEecceEEEEeccccCcccc--ceeeeeeeeeeeEEecCC
Q 034752           10 KEPLDLIRLSL--DERIYVKLRSDRELRGKLHAYDQHLNMILGDVEEVVTTVEIDDETY--EEIVRVCCNLKILLLNFK   84 (85)
Q Consensus        10 ~~Pl~~L~~~l--~k~V~V~L~~g~~~~G~L~~fD~~mNlvL~n~~E~~~~~~~~~~~~--~~~~~~~r~lg~ill~G~   84 (85)
                      .+|+++|.+++  +++|+|.+++|+.+.|+|.|||+||||+|+||.|++...+...+..  .......|+||+++|||+
T Consensus         1 tGPl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGd   79 (93)
T d1b34b_           1 TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGD   79 (93)
T ss_dssp             CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGG
T ss_pred             CCcHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCC
Confidence            37999999999  8999999999999999999999999999999999988765543221  223345799999999997
>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
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [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
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} 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
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d1u1sa1 b.38.1.2 (A:6-71) Pleiotropic translational regulator Hfq {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1kq1a_ b.38.1.2 (A:) Pleiotropic translational regulator Hfq {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d1ycya1 b.38.1.4 (A:5-70) Hypothetical protein PF1955 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1biaa2 b.34.1.1 (A:271-317) Biotin repressor/biotin holoenzyme synthetase, C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2vxfa1 b.38.1.5 (A:6-85) LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) [TaxId: 7955]} 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