Citrus Sinensis ID: 033937

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------11
MSSRPMEEDNVKNEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK
ccccccHHHHcccccHHcccccHHHHHHHHHccEEEEEEEccccEEEEEEEEEccccccEEccEEEEEEEccccccccccccccEEEEEEcEEEEcccEEEEEEcccc
ccccccHHHHHHHHHHHcccccHHHHHHHHHcccEEEEEEccccEEEEEEEHHHHHHHHHHHcHHHHEcEccccccccccccccccccEEcEEEEEccEEEEEEEccc
mssrpmeednvkneeeefntgplSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTelpktgkgkkkalpvnkdrFISKMFLRGDSVIIVLRNPK
mssrpmeednvkneeeefntgplSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMwtelpktgkgkkkalpvnkdrfiskmflrgdsviivlrnpk
MSSRPMeednvkneeeefnTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK
**********************LSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKT*****KALPVNKDRFISKMFLRGDSVIIVL****
*********************PLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREM********************RFISKMFLRGDSVIIVLRNP*
*****************FNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTEL*********ALPVNKDRFISKMFLRGDSVIIVLRNPK
*****MEEDNVKNEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGK*KKKALPVNKDRFISKMFLRGDSVIIVLRNP*
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MSSRPMEEDNVKNEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK
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 ?
Query108 2.2.26 [Sep-21-2011]
Q9VI10119 Probable small nuclear ri yes no 0.833 0.756 0.911 6e-36
Q18786118 Probable small nuclear ri yes no 0.925 0.847 0.8 1e-34
P62317118 Small nuclear ribonucleop no no 0.833 0.762 0.888 2e-34
P62316118 Small nuclear ribonucleop yes no 0.833 0.762 0.888 2e-34
Q3SZF8118 Small nuclear ribonucleop yes no 0.833 0.762 0.888 2e-34
Q54NC5112 Probable small nuclear ri yes no 0.935 0.901 0.754 1e-33
O14036115 Small nuclear ribonucleop yes no 0.861 0.808 0.712 3e-33
Q06217110 Small nuclear ribonucleop yes no 0.740 0.727 0.563 2e-21
Q9Y7M493 Probable U6 snRNA-associa no no 0.731 0.849 0.341 1e-06
Q54HH8257 Small nuclear ribonucleop no no 0.861 0.361 0.297 3e-06
>sp|Q9VI10|SMD2_DROME Probable small nuclear ribonucleoprotein Sm D2 OS=Drosophila melanogaster GN=SmD2 PE=3 SV=1 Back     alignment and function desciption
 Score =  149 bits (376), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 82/90 (91%), Positives = 86/90 (95%)

Query: 18  FNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKG 77
           FNTGPLSVL  SVKNNTQVLINCRNNKKLLGRV+AFDRHCNMVLENV+EMWTELP+TGKG
Sbjct: 23  FNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTELPRTGKG 82

Query: 78  KKKALPVNKDRFISKMFLRGDSVIIVLRNP 107
           KKK  PVNKDRFISKMFLRGDSVI+VLRNP
Sbjct: 83  KKKVKPVNKDRFISKMFLRGDSVILVLRNP 112
Required for pre-mRNA splicing. Required for snRNP biogenesis.
Drosophila melanogaster (taxid: 7227)
>sp|Q18786|SMD2_CAEEL Probable small nuclear ribonucleoprotein Sm D2 OS=Caenorhabditis elegans GN=snr-4 PE=1 SV=1 Back     alignment and function description
>sp|P62317|SMD2_MOUSE Small nuclear ribonucleoprotein Sm D2 OS=Mus musculus GN=Snrpd2 PE=2 SV=1 Back     alignment and function description
>sp|P62316|SMD2_HUMAN Small nuclear ribonucleoprotein Sm D2 OS=Homo sapiens GN=SNRPD2 PE=1 SV=1 Back     alignment and function description
>sp|Q3SZF8|SMD2_BOVIN Small nuclear ribonucleoprotein Sm D2 OS=Bos taurus GN=SNRPD2 PE=3 SV=1 Back     alignment and function description
>sp|Q54NC5|SMD2_DICDI Probable small nuclear ribonucleoprotein Sm D2 OS=Dictyostelium discoideum GN=snrpd2 PE=3 SV=1 Back     alignment and function description
>sp|O14036|SMD2_SCHPO Small nuclear ribonucleoprotein Sm D2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=smd2 PE=1 SV=1 Back     alignment and function description
>sp|Q06217|SMD2_YEAST Small nuclear ribonucleoprotein Sm D2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SMD2 PE=1 SV=2 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|Q54HH8|SMDL_DICDI Small nuclear ribonucleoprotein Sm D-like protein OS=Dictyostelium discoideum GN=DDB_G0289453 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 ?
Query108
449457536107 PREDICTED: probable small nuclear ribonu 0.981 0.990 0.962 4e-52
356513032108 PREDICTED: probable small nuclear ribonu 0.981 0.981 0.962 3e-51
357521397108 Small nuclear ribonucleoprotein-like pro 0.981 0.981 0.962 4e-51
359806642108 uncharacterized protein LOC100793233 [Gl 0.981 0.981 0.953 8e-51
225424416107 PREDICTED: probable small nuclear ribonu 0.981 0.990 0.943 8e-51
351727138117 uncharacterized protein LOC100500203 [Gl 0.981 0.905 0.943 2e-50
255573198103 small nuclear ribonucleoprotein sm d2, p 0.953 1.0 0.961 2e-50
30690747108 small nuclear ribonucleoprotein D2 [Arab 0.981 0.981 0.934 4e-50
224068340108 predicted protein [Populus trichocarpa] 0.981 0.981 0.943 4e-50
297821194109 predicted protein [Arabidopsis lyrata su 0.981 0.972 0.916 6e-50
>gi|449457536|ref|XP_004146504.1| PREDICTED: probable small nuclear ribonucleoprotein Sm D2-like [Cucumis sativus] gi|449499984|ref|XP_004160970.1| PREDICTED: probable small nuclear ribonucleoprotein Sm D2-like [Cucumis sativus] Back     alignment and taxonomy information
 Score =  208 bits (529), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 102/106 (96%), Positives = 103/106 (97%)

Query: 3   SRPMEEDNVKNEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLE 62
           SRPMEED  KNEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLE
Sbjct: 2   SRPMEEDTSKNEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLE 61

Query: 63  NVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNPK 108
           NVREMWTE+PKTGKGKKKA PVNKDRFISKMFLRGDSVIIVLRNPK
Sbjct: 62  NVREMWTEVPKTGKGKKKAQPVNKDRFISKMFLRGDSVIIVLRNPK 107

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|356513032|ref|XP_003525218.1| PREDICTED: probable small nuclear ribonucleoprotein Sm D2-like [Glycine max] Back     alignment and taxonomy information
>gi|357521397|ref|XP_003630987.1| Small nuclear ribonucleoprotein-like protein [Medicago truncatula] gi|355525009|gb|AET05463.1| Small nuclear ribonucleoprotein-like protein [Medicago truncatula] gi|388506390|gb|AFK41261.1| unknown [Medicago truncatula] Back     alignment and taxonomy information
>gi|359806642|ref|NP_001241022.1| uncharacterized protein LOC100793233 [Glycine max] gi|255633912|gb|ACU17317.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|225424416|ref|XP_002285043.1| PREDICTED: probable small nuclear ribonucleoprotein Sm D2-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|351727138|ref|NP_001238430.1| uncharacterized protein LOC100500203 [Glycine max] gi|255629692|gb|ACU15195.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|255573198|ref|XP_002527528.1| small nuclear ribonucleoprotein sm d2, putative [Ricinus communis] gi|223533078|gb|EEF34837.1| small nuclear ribonucleoprotein sm d2, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|30690747|ref|NP_850477.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|42571273|ref|NP_973710.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|145332931|ref|NP_001078331.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|7362764|emb|CAB83134.1| small nuclear ribonucleoprotein-like protein [Arabidopsis thaliana] gi|28466881|gb|AAO44049.1| At2g47640 [Arabidopsis thaliana] gi|110743879|dbj|BAE99774.1| putative small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|330255774|gb|AEC10868.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|330255775|gb|AEC10869.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] gi|332646880|gb|AEE80401.1| small nuclear ribonucleoprotein D2 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|224068340|ref|XP_002302713.1| predicted protein [Populus trichocarpa] gi|224128478|ref|XP_002320342.1| predicted protein [Populus trichocarpa] gi|118481477|gb|ABK92681.1| unknown [Populus trichocarpa] gi|222844439|gb|EEE81986.1| predicted protein [Populus trichocarpa] gi|222861115|gb|EEE98657.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|297821194|ref|XP_002878480.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297324318|gb|EFH54739.1| predicted protein [Arabidopsis lyrata subsp. lyrata] 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 ?
Query108
TAIR|locus:2043323109 AT2G47640 "AT2G47640" [Arabido 0.824 0.816 0.966 9.3e-43
TAIR|locus:2081685109 AT3G62840 "AT3G62840" [Arabido 0.824 0.816 0.966 9.3e-43
FB|FBgn0261789119 SmD2 "Small ribonucleoprotein 0.814 0.739 0.909 8.7e-40
UNIPROTKB|G3X6Z3117 SNRPD2 "Small nuclear ribonucl 0.814 0.752 0.886 2.9e-39
UNIPROTKB|Q3SZF8118 SNRPD2 "Small nuclear ribonucl 0.814 0.745 0.886 2.9e-39
UNIPROTKB|F1PSI7118 SNRPD2 "Uncharacterized protei 0.814 0.745 0.886 2.9e-39
UNIPROTKB|P62316118 SNRPD2 "Small nuclear ribonucl 0.814 0.745 0.886 2.9e-39
MGI|MGI:98345118 Snrpd2 "small nuclear ribonucl 0.814 0.745 0.886 2.9e-39
RGD|1593018118 Snrpd2 "small nuclear ribonucl 0.814 0.745 0.886 2.9e-39
ZFIN|ZDB-GENE-040914-10118 snrpd2 "small nuclear ribonucl 0.814 0.745 0.886 2.9e-39
TAIR|locus:2043323 AT2G47640 "AT2G47640" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 452 (164.2 bits), Expect = 9.3e-43, P = 9.3e-43
 Identities = 86/89 (96%), Positives = 89/89 (100%)

Query:    20 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKK 79
             TGPLSVLMMSVKNNTQVLINCRNN+KLLGRVRAFDRHCNMVLENVREMWTE+PKTGKGKK
Sbjct:    21 TGPLSVLMMSVKNNTQVLINCRNNRKLLGRVRAFDRHCNMVLENVREMWTEVPKTGKGKK 80

Query:    80 KALPVNKDRFISKMFLRGDSVIIVLRNPK 108
             KALPVN+DRFISKMFLRGDSVIIVLRNPK
Sbjct:    81 KALPVNRDRFISKMFLRGDSVIIVLRNPK 109
GO:0003674 "molecular_function" evidence=ND
GO:0005634 "nucleus" evidence=ISM;ISS
GO:0005732 "small nucleolar ribonucleoprotein complex" evidence=ISS
GO:0005730 "nucleolus" evidence=IDA
GO:0005829 "cytosol" evidence=IDA
GO:0001510 "RNA methylation" evidence=RCA
TAIR|locus:2081685 AT3G62840 "AT3G62840" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
FB|FBgn0261789 SmD2 "Small ribonucleoprotein particle protein SmD2" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|G3X6Z3 SNRPD2 "Small nuclear ribonucleoprotein Sm D2" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|Q3SZF8 SNRPD2 "Small nuclear ribonucleoprotein Sm D2" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|F1PSI7 SNRPD2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|P62316 SNRPD2 "Small nuclear ribonucleoprotein Sm D2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:98345 Snrpd2 "small nuclear ribonucleoprotein D2" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1593018 Snrpd2 "small nuclear ribonucleoprotein D2 polypeptide" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-040914-10 snrpd2 "small nuclear ribonucleoprotein D2 polypeptide" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q06217SMD2_YEASTNo assigned EC number0.56320.74070.7272yesno
P62316SMD2_HUMANNo assigned EC number0.88880.83330.7627yesno
Q18786SMD2_CAEELNo assigned EC number0.80.92590.8474yesno
Q9VI10SMD2_DROMENo assigned EC number0.91110.83330.7563yesno
Q3SZF8SMD2_BOVINNo assigned EC number0.88880.83330.7627yesno
Q54NC5SMD2_DICDINo assigned EC number0.75490.93510.9017yesno
O14036SMD2_SCHPONo assigned EC number0.71270.86110.8086yesno

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_kg.C_LG_XIV0024
SubName- Full=Putative uncharacterized protein; (108 aa)
(Populus trichocarpa)
Predicted Functional Partners:
eugene3.00180816
hypothetical protein (88 aa)
   •••• 0.590
eugene3.00440042
hypothetical protein (2357 aa)
   •••• 0.536
estExt_fgenesh4_kg.C_LG_III0001
SubName- Full=Putative uncharacterized protein; (93 aa)
   •••• 0.508
estExt_fgenesh4_kg.C_1630004
SubName- Full=Putative uncharacterized protein; (93 aa)
   •••• 0.508
estExt_Genewise1_v1.C_LG_V0812
hypothetical protein (113 aa)
   •••• 0.485
estExt_fgenesh4_pm.C_LG_II0256
SubName- Full=Putative uncharacterized protein; (116 aa)
   •••• 0.484
estExt_Genewise1_v1.C_LG_XVIII2933
SubName- Full=Putative uncharacterized protein; (88 aa)
   •••• 0.480
estExt_Genewise1_v1.C_1710010
SubName- Full=Putative uncharacterized protein; (88 aa)
   •••• 0.480
estExt_Genewise1_v1.C_LG_XIII3357
hypothetical protein (820 aa)
    ••  0.460
estExt_Genewise1_v1.C_LG_VI0793
SubName- Full=Putative uncharacterized protein; (80 aa)
   •••• 0.456

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 ?
Query108
cd0172089 cd01720, Sm_D2, Sm protein D2 7e-57
cd0173082 cd01730, LSm3, Like-Sm protein 3 2e-15
smart0065167 smart00651, Sm, snRNP Sm proteins 3e-14
pfam0142366 pfam01423, LSM, LSM domain 3e-12
COG195879 COG1958, LSM1, Small nuclear ribonucleoprotein (sn 3e-11
cd0173169 cd01731, archaeal_Sm1, archaeal Sm protein 1 1e-08
cd0060063 cd00600, Sm_like, Sm and related proteins 4e-08
PRK0073772 PRK00737, PRK00737, small nuclear ribonucleoprotei 3e-04
cd0173963 cd01739, LSm11_M, Like-Sm protein 11, middle domai 0.003
cd0173276 cd01732, LSm5, Like-Sm protein 5 0.004
>gnl|CDD|212467 cd01720, Sm_D2, Sm protein D2 Back     alignment and domain information 
 Score =  170 bits (432), Expect = 7e-57
 Identities = 79/90 (87%), Positives = 84/90 (93%), Gaps = 1/90 (1%)

Query: 18  FNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKG 77
           FNTGPLS+L  SVKNNTQVLINCRNNKKLL RV+AFDRHCNMVLENV+EMWTE+PKTGKG
Sbjct: 1   FNTGPLSLLTQSVKNNTQVLINCRNNKKLLARVKAFDRHCNMVLENVKEMWTEVPKTGKG 60

Query: 78  KKKALPVNKDRFISKMFLRGDSVIIVLRNP 107
           KK   PVNKDRFISKMFLRGDSVI+VLRNP
Sbjct: 61  KKSK-PVNKDRFISKMFLRGDSVILVLRNP 89

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, 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. 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. Length = 89
>gnl|CDD|212477 cd01730, LSm3, Like-Sm protein 3 Back     alignment and domain information
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins Back     alignment and domain information
>gnl|CDD|201787 pfam01423, LSM, LSM domain Back     alignment and domain information
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] Back     alignment and domain information
>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1 Back     alignment and domain information
>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins Back     alignment and domain information
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>gnl|CDD|212485 cd01739, LSm11_M, Like-Sm protein 11, middle domain Back     alignment and domain information
>gnl|CDD|212479 cd01732, LSm5, Like-Sm protein 5 Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 108
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.95
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.93
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.91
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.91
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.91
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 99.89
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.88
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.88
cd0171779 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins 99.87
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.87
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.87
cd0172874 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins 99.86
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.86
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.85
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.85
KOG346091 consensus Small nuclear ribonucleoprotein (snRNP) 99.84
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.84
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.83
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.82
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.82
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.82
KOG3459114 consensus Small nuclear ribonucleoprotein (snRNP) 99.78
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.78
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.75
KOG177488 consensus Small nuclear ribonucleoprotein E [RNA p 99.74
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.73
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.72
KOG177584 consensus U6 snRNA-associated Sm-like protein [RNA 99.7
KOG178077 consensus Small Nuclear ribonucleoprotein G [RNA p 99.68
KOG1781108 consensus Small Nuclear ribonucleoprotein splicing 99.65
KOG348279 consensus Small nuclear ribonucleoprotein (snRNP) 99.63
KOG3168177 consensus U1 snRNP component [Transcription] 99.56
KOG178496 consensus Small Nuclear ribonucleoprotein splicing 99.43
KOG178377 consensus Small nuclear ribonucleoprotein F [RNA p 99.42
KOG1782129 consensus Small Nuclear ribonucleoprotein splicing 99.38
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 99.38
KOG3293134 consensus Small nuclear ribonucleoprotein (snRNP) 99.28
KOG344896 consensus Predicted snRNP core protein [RNA proces 99.15
KOG3172119 consensus Small nuclear ribonucleoprotein Sm D3 [R 99.07
KOG3428109 consensus Small nuclear ribonucleoprotein SMD1 and 98.52
cd0171661 Hfq Hfq, an abundant, ubiquitous RNA-binding prote 97.43
TIGR0238361 Hfq RNA chaperone Hfq. This model represents the R 97.37
PF1443877 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1. 97.36
PRK0039579 hfq RNA-binding protein Hfq; Provisional 97.18
COG192377 Hfq Uncharacterized host factor I protein [General 96.36
PRK14091165 RNA-binding protein Hfq; Provisional 95.85
PRK14091165 RNA-binding protein Hfq; Provisional 95.82
cd0173561 LSm12_N LSm12 belongs to a family of Sm-like prote 95.12
PF1270196 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC 94.81
PF0223748 BPL_C: Biotin protein ligase C terminal domain; In 94.71
PF1109580 Gemin7: Gem-associated protein 7 (Gemin7); InterPr 93.37
PF03614165 Flag1_repress: Repressor of phase-1 flagellin; Int 92.06
PRK14638150 hypothetical protein; Provisional 91.69
cd0173674 LSm14_N LSm14 (also known as RAP55) belongs to a f 91.12
PRK02001152 hypothetical protein; Validated 90.33
PRK14639140 hypothetical protein; Provisional 89.93
PF06372166 Gemin6: Gemin6 protein; InterPro: IPR009422 This f 86.15
PRK14644136 hypothetical protein; Provisional 85.86
cd0173483 YlxS_C YxlS is a Bacillus subtilis gene of unknown 84.65
PF03614165 Flag1_repress: Repressor of phase-1 flagellin; Int 83.94
PRK14640152 hypothetical protein; Provisional 83.59
PRK14642197 hypothetical protein; Provisional 82.83
PRK14636176 hypothetical protein; Provisional 82.53
PF02576141 DUF150: Uncharacterised BCR, YhbC family COG0779; 82.26
PRK14633150 hypothetical protein; Provisional 82.21
PF11607101 DUF3247: Protein of unknown function (DUF3247); In 82.0
PRK14643164 hypothetical protein; Provisional 81.92
COG0779153 Uncharacterized protein conserved in bacteria [Fun 81.27
PRK14645154 hypothetical protein; Provisional 80.79
PRK14646155 hypothetical protein; Provisional 80.12
>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=99.95  E-value=4.5e-28  Score=159.72  Aligned_cols=87  Identities=90%  Similarity=1.381  Sum_probs=72.6

Q ss_pred             CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCc
Q 033937           20 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS   99 (108)
Q Consensus        20 ~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~   99 (108)
                      .||+++|.+++..+++|+|.|++|+.+.|+|+|||+||||+|+||+|++...++++.+. +.+....++++|.+|||||+
T Consensus         1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~-~~~~~~~~r~lg~v~iRGd~   79 (87)
T cd01720           1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGK-KAKPVNKDRFISKMFLRGDS   79 (87)
T ss_pred             CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccc-cccceeeeeEcccEEEeCCE
Confidence            48999999999889999999999999999999999999999999999987644332210 11112356789999999999


Q ss_pred             EEEEEeCC
Q 033937          100 VIIVLRNP  107 (108)
Q Consensus       100 Iv~I~~~~  107 (108)
                      |++|+++|
T Consensus        80 Vv~Is~~~   87 (87)
T cd01720          80 VILVLRNP   87 (87)
T ss_pred             EEEEecCC
Confidence            99999987

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
>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
>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
>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
>PTZ00138 small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] 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
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification] Back     alignment and domain information
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins Back     alignment and domain information
>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
>smart00651 Sm snRNP Sm proteins Back     alignment and domain information
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>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
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core 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
>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
>KOG1774 consensus Small nuclear ribonucleoprotein E [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
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification] Back     alignment and domain information
>KOG1780 consensus Small Nuclear ribonucleoprotein G [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
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [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
>KOG1783 consensus Small nuclear ribonucleoprotein F [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
>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
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification] Back     alignment and domain information
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification] Back     alignment and domain information
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification] Back     alignment and domain information
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification] Back     alignment and domain information
>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
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1 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
>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
>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
>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
>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
>PRK14638 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
>PRK02001 hypothetical protein; Validated Back     alignment and domain information
>PRK14639 hypothetical protein; Provisional Back     alignment and domain information
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins Back     alignment and domain information
>PRK14644 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
>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
>PRK14636 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
>PRK14633 hypothetical protein; Provisional Back     alignment and domain information
>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris Back     alignment and domain information
>PRK14643 hypothetical protein; Provisional Back     alignment and domain information
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK14645 hypothetical protein; Provisional Back     alignment and domain information
>PRK14646 hypothetical protein; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query108
1b34_B118 Crystal Structure Of The D1d2 Sub-Complex From The 3e-34
4emg_A93 Crystal Structure Of Splsm3 Length = 93 2e-07
1th7_A81 Crystal Structure Of An Archaeal Sm Protein From Su 6e-05
3bw1_A96 Crystal Structure Of Homomeric Yeast Lsm3 Exhibitin 8e-05
>pdb|1B34|B Chain B, Crystal Structure Of The D1d2 Sub-Complex From The Human Snrnp Core Domain Length = 118 Back     alignment and structure 
Iteration: 1

 Score =  139 bits (351), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 78/88 (88%), Positives = 85/88 (96%)
Query: 20  TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKK 79
           TGPLSVL  SVKNNTQVLINCRNNKKLLGRV+AFDRHCNMVLENV+EMWTE+PK+GKGKK
Sbjct: 26  TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKK 85
Query: 80  KALPVNKDRFISKMFLRGDSVIIVLRNP 107
           K+ PVNKDR+ISKMFLRGDSVI+VLRNP
Sbjct: 86  KSKPVNKDRYISKMFLRGDSVIVVLRNP 113
>pdb|4EMG|A Chain A, Crystal Structure Of Splsm3 Length = 93 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|3BW1|A Chain A, Crystal Structure Of Homomeric Yeast Lsm3 Exhibiting Novel Octameric Ring Organisation Length = 96 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 ?
Query108
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 8e-41
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 1e-25
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 9e-23
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 3e-20
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 1e-08
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 2e-08
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 2e-07
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 2e-07
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 2e-07
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 3e-07
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 4e-07
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 6e-07
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 5e-06
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 2e-05
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 1e-04
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 2e-04
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 6e-04
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 8e-04
>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
 Score =  130 bits (327), Expect = 8e-41
 Identities = 87/105 (82%), Positives = 95/105 (90%)

Query: 3   SRPMEEDNVKNEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLE 62
           S    E+  K EEEEFNTGPLSVL  SVKNNTQVLINCRNNKKLLGRV+AFDRHCNMVLE
Sbjct: 9   SEMTPEELQKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLE 68

Query: 63  NVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDSVIIVLRNP 107
           NV+EMWTE+PK+GKGKKK+ PVNKDR+ISKMFLRGDSVI+VLRNP
Sbjct: 69  NVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNP 113
>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
>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
>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_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
>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
>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
>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_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
>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
>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
>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G Length = 76 Back     alignment and structure
>4emk_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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query108
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.95
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.92
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.92
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.91
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.91
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.91
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.91
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.91
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.9
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.9
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.9
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.9
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.9
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.9
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.89
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.89
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.88
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.88
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.88
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.86
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.86
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 99.85
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 99.82
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.79
1y96_A86 Gemin6, SIP2, GEM-associated protein 6; SM fold, p 98.31
1u1s_A82 HFQ protein; SM-like bacterial protein, riken stru 97.47
2ylb_A74 Protein HFQ; RNA-binding protein, LSM protein, RNA 97.38
3sb2_A79 Protein HFQ; SM-like, RNA chaperone, chaperone; 2. 97.34
3ahu_A78 Protein HFQ; SM-like motif, protein-RNA complex, t 97.28
2y90_A104 Protein HFQ; RNA-binding protein, SM-like, RNA cha 97.2
1kq1_A77 HFQ, HOST factor for Q beta; hexamer, RNA binding 97.18
2qtx_A71 Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi 97.14
3hfo_A70 SSR3341 protein; HFQ, SM, RNA-binding protein, sRN 95.85
3hfn_A72 ASL2047 protein; HFQ, SM, RNA-binding protein, sRN 95.49
1y96_B85 Gemin7, SIP3, GEM-associated protein 7; SM fold, p 93.76
1ycy_A71 Conserved hypothetical protein; structural genomic 93.12
4a53_A125 EDC3; RNA binding protein; NMR {Schizosaccharomyce 89.17
1ib8_A164 Conserved protein SP14.3; nucleic acid binding pro 84.05
2vxe_A88 CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA 83.73
2fb7_A95 SM-like protein, LSM-14_N (RAP55); DR.13312, BC055 81.71
2e12_A101 SM-like motif, hypothetical protein XCC3642; novel 81.65
3rux_A270 BIRA bifunctional protein; biotin-protein ligase, 81.19
>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
Probab=99.95  E-value=1.2e-28  Score=168.90  Aligned_cols=98  Identities=87%  Similarity=1.318  Sum_probs=67.0

Q ss_pred             hcccccccCCCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeee
Q 033937           11 VKNEEEEFNTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFI   90 (108)
Q Consensus        11 ~~~~~~~~~~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~l   90 (108)
                      ++.|+..+..+|+++|++++..+++|+|+|++|+.|.|+|+|||+||||+|+||+|++...++.+++.+..+....+|++
T Consensus        17 ~~~e~~~~~~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~l   96 (118)
T 1b34_B           17 QKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYI   96 (118)
T ss_dssp             ---------CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEE
T ss_pred             hhhhhhhcccChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCc
Confidence            55677889999999999999667999999999999999999999999999999999986543333221111122345789


Q ss_pred             ceEEEeCCcEEEEEeCCC
Q 033937           91 SKMFLRGDSVIIVLRNPK  108 (108)
Q Consensus        91 g~i~IRGd~Iv~I~~~~~  108 (108)
                      |.+||||+||++|++.|+
T Consensus        97 g~v~IRG~nVv~I~~~~~  114 (118)
T 1b34_B           97 SKMFLRGDSVIVVLRNPL  114 (118)
T ss_dssp             EEEEECGGGEEEEEECCC
T ss_pred             CeEEEcCCEEEEEEeCch
Confidence            999999999999999874
>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
>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
>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
>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
>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
>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
>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Back     alignment and structure
>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B Back     alignment and structure
>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Back     alignment and structure
>3s6n_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
>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
>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
>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
>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
>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
>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A {Escherichia coli} PDB: 3qhs_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
>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
>1y96_B Gemin7, SIP3, GEM-associated protein 7; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} 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
>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
>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
>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
>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

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 108
d1b34b_93 b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s 1e-34
d2fwka192 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr 2e-18
d1d3bb_81 b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa 5e-14
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 1e-12
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 6e-11
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 1e-10
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 2e-10
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 4e-10
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 2e-06
d1d3ba_72 b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s 6e-05
d1m5q1_127 b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch 0.001
d1n9ra_68 b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S 0.001
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93 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]

 Score =  112 bits (281), Expect = 1e-34
 Identities = 78/89 (87%), Positives = 85/89 (95%)

Query: 20  TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKK 79
           TGPLSVL  SVKNNTQVLINCRNNKKLLGRV+AFDRHCNMVLENV+EMWTE+PK+GKGKK
Sbjct: 1   TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKK 60

Query: 80  KALPVNKDRFISKMFLRGDSVIIVLRNPK 108
           K+ PVNKDR+ISKMFLRGDSVI+VLRNP 
Sbjct: 61  KSKPVNKDRYISKMFLRGDSVIVVLRNPL 89
>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
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 81 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
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 74 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
>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
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72 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
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query108
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.97
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.93
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.92
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.91
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.91
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.9
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.9
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.89
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.89
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.86
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.84
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.73
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 99.65
d1u1sa166 Pleiotropic translational regulator Hfq {Pseudomon 97.18
d1kq1a_60 Pleiotropic translational regulator Hfq {Staphyloc 97.17
d1ycya166 Hypothetical protein PF1955 {Pyrococcus furiosus [ 92.72
d1biaa247 Biotin repressor/biotin holoenzyme synthetase, C-t 92.2
d2vxfa180 LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) 89.84
d1ib8a174 Hypothetical protein SP14.3 (SP0552) {Streptococcu 87.77
>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=99.97  E-value=4.4e-31  Score=173.18  Aligned_cols=89  Identities=88%  Similarity=1.350  Sum_probs=67.8

Q ss_pred             CCcHHHHHhhhhCCcEEEEEecCCeEEEEEEEEecCccceEeeceEEEeecCCCCCCCccccccCcceeeeceEEEeCCc
Q 033937           20 TGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTELPKTGKGKKKALPVNKDRFISKMFLRGDS   99 (108)
Q Consensus        20 ~~Pl~~L~~~~~~~krV~V~l~~gr~i~G~L~~fD~hmNlvL~d~~E~~~~~~~~~k~~~~~~~~~~~r~lg~i~IRGd~   99 (108)
                      .|||++|++|++++++|+|+|++||.+.|+|+|||+||||+|+||+|+|...++..+..+..+....+|++|++||||||
T Consensus         1 tGPl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdn   80 (93)
T d1b34b_           1 TGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDS   80 (93)
T ss_dssp             CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGG
T ss_pred             CCcHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCE
Confidence            48999999999999999999999999999999999999999999999988755433222222223456899999999999


Q ss_pred             EEEEEeCCC
Q 033937          100 VIIVLRNPK  108 (108)
Q Consensus       100 Iv~I~~~~~  108 (108)
                      |++|.+.|+
T Consensus        81 Vv~I~~~p~   89 (93)
T d1b34b_          81 VIVVLRNPL   89 (93)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEcChh
Confidence            999999995
>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
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} 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
>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
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} 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
>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