Citrus Sinensis ID: 032863

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130--
MSRSLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDMLKNAPMFKRLDARIKGKSSSIGVGRGRAVAMRAKAAAAGRGAAPGRGVVPPVRR
cccccccHHHHHHHHcccEEEEEEccccEEEEEEEEEcccccEEEEEEEEEcccccEEccccEEEEccEEEEEEcccccccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHccccccccccccccccc
cccccccHHHHHHHHcccEEEEEEccccEEEEEEEEEcccccEEEEEEEEEcccccEEEEEEEEEcHHHEEEEEEccHHHcccHHcccccccccccccccccccHHHHHHHHHHHccccccccccccccccc
msrslgipvkllheasgHVVTVELksgelyrgsmvecednwncqlenitytakdgkvsqLEHVFIrgskvrfmvipdmlknapmfkrldarikgksssigvgRGRAVAMRAKAAAagrgaapgrgvvppvrr
msrslgipvkllheasghvvtvELKSGELYRGSMVECEDNWNCQLENITYtakdgkvsqLEHVFIRGSKVRFMVIPDMLKNAPMFKrldarikgksssigvgrgRAVAMRAKAaaagrgaapgrgvvppvrr
MSRSLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDMLKNAPMFKRLDARIKGKSSSIgvgrgravamrakaaaagrgaapgrgvvppvrr
******IPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDMLKNAPMFKRLDAR*****************************************
****LGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDMLKNA**************************************************
MSRSLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDMLKNAPMFKRLDARIKGKSSSIGVG******************************
***SLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDMLKNAPMFKR*********************************************
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSRSLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDMLKNAPMFKRLDARIKGKSSSIGVGRGRAVAMRAKAAAAGRGAAPGRGVVPPVRR
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 ?
Query132 2.2.26 [Sep-21-2011]
P62323126 Small nuclear ribonucleop N/A no 0.818 0.857 0.562 2e-35
P62320126 Small nuclear ribonucleop yes no 0.818 0.857 0.562 2e-35
P62318126 Small nuclear ribonucleop yes no 0.818 0.857 0.562 2e-35
O44437151 Small nuclear ribonucleop yes no 0.803 0.701 0.527 5e-32
Q17348136 Small nuclear ribonucleop yes no 0.787 0.764 0.530 1e-29
Q9UUC697 Small nuclear ribonucleop yes no 0.621 0.845 0.573 4e-27
P43321101 Small nuclear ribonucleop yes no 0.651 0.851 0.511 4e-24
Q54KX4177 Probable U6 snRNA-associa no no 0.848 0.632 0.355 9e-14
Q43582146 Probable U6 snRNA-associa N/A no 0.886 0.801 0.314 1e-11
Q9QXA5137 U6 snRNA-associated Sm-li no no 0.530 0.510 0.424 3e-10
>sp|P62323|SMD3_XENLA Small nuclear ribonucleoprotein Sm D3 OS=Xenopus laevis GN=snrpd3 PE=2 SV=1 Back     alignment and function desciption
 Score =  147 bits (370), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 63/112 (56%), Positives = 87/112 (77%), Gaps = 4/112 (3%)

Query: 4   SLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHV 63
           S+G+P+K+LHEA GH+VT E  +GE+YRG ++E EDN NCQ+ NIT T +DG+V+QLE V
Sbjct: 2   SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQV 61

Query: 64  FIRGSKVRFMVIPDMLKNAPMFKRLDARIKGKSSSIGVGRGRAVAMRAKAAA 115
           +IRGSK+RF+++PDMLKNAPM K +    K K+   G GRG+A  ++A+ AA
Sbjct: 62  YIRGSKIRFLILPDMLKNAPMLKSM----KNKNQGSGAGRGKAAILKAQVAA 109
Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Binds to RNA.
Xenopus laevis (taxid: 8355)
>sp|P62320|SMD3_MOUSE Small nuclear ribonucleoprotein Sm D3 OS=Mus musculus GN=Snrpd3 PE=1 SV=1 Back     alignment and function description
>sp|P62318|SMD3_HUMAN Small nuclear ribonucleoprotein Sm D3 OS=Homo sapiens GN=SNRPD3 PE=1 SV=1 Back     alignment and function description
>sp|O44437|SMD3_DROME Small nuclear ribonucleoprotein Sm D3 OS=Drosophila melanogaster GN=SmD3 PE=1 SV=1 Back     alignment and function description
>sp|Q17348|SMD3_CAEEL Small nuclear ribonucleoprotein Sm D3 OS=Caenorhabditis elegans GN=snr-1 PE=2 SV=2 Back     alignment and function description
>sp|Q9UUC6|SMD3_SCHPO Small nuclear ribonucleoprotein Sm D3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=smd3 PE=1 SV=1 Back     alignment and function description
>sp|P43321|SMD3_YEAST Small nuclear ribonucleoprotein Sm D3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SMD3 PE=1 SV=1 Back     alignment and function description
>sp|Q54KX4|LSM4_DICDI Probable U6 snRNA-associated Sm-like protein LSm4 OS=Dictyostelium discoideum GN=lsm4 PE=3 SV=1 Back     alignment and function description
>sp|Q43582|LSM4_TOBAC Probable U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana tabacum PE=2 SV=1 Back     alignment and function description
>sp|Q9QXA5|LSM4_MOUSE U6 snRNA-associated Sm-like protein LSm4 OS=Mus musculus GN=Lsm4 PE=2 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 ?
Query132
224065689132 predicted protein [Populus trichocarpa] 1.0 1.0 0.939 2e-67
224083270132 predicted protein [Populus trichocarpa] 1.0 1.0 0.931 2e-66
351721470131 uncharacterized protein LOC100305856 [Gl 0.992 1.0 0.939 1e-65
255539216131 small nuclear ribonucleoprotein, putativ 0.992 1.0 0.916 2e-64
357519697131 Small nuclear ribonucleoprotein Sm D3 [M 0.992 1.0 0.924 2e-64
449512675132 PREDICTED: small nuclear ribonucleoprote 1.0 1.0 0.909 3e-64
388502716133 unknown [Lotus japonicus] 0.992 0.984 0.909 4e-64
449455595132 PREDICTED: small nuclear ribonucleoprote 1.0 1.0 0.901 1e-63
116780936133 unknown [Picea sitchensis] 1.0 0.992 0.864 2e-59
302811572135 hypothetical protein SELMODRAFT_183167 [ 0.992 0.970 0.830 5e-57
>gi|224065689|ref|XP_002301922.1| predicted protein [Populus trichocarpa] gi|222843648|gb|EEE81195.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  259 bits (663), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 124/132 (93%), Positives = 130/132 (98%)

Query: 1   MSRSLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQL 60
           MSRSLGIPVKLLHEASGH+VTVELKSGELYRGSMVECEDNWNCQLE+ITYTAKDGKVSQL
Sbjct: 1   MSRSLGIPVKLLHEASGHIVTVELKSGELYRGSMVECEDNWNCQLESITYTAKDGKVSQL 60

Query: 61  EHVFIRGSKVRFMVIPDMLKNAPMFKRLDARIKGKSSSIGVGRGRAVAMRAKAAAAGRGA 120
           EHVFIRGSKVRFMVIPDMLKNAPMFKRLDARIKGKS+S+GVGRGR+VAMR+KA A GRGA
Sbjct: 61  EHVFIRGSKVRFMVIPDMLKNAPMFKRLDARIKGKSASLGVGRGRSVAMRSKAQATGRGA 120

Query: 121 APGRGVVPPVRR 132
           APGRGVVPPVRR
Sbjct: 121 APGRGVVPPVRR 132

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224083270|ref|XP_002306975.1| predicted protein [Populus trichocarpa] gi|222856424|gb|EEE93971.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|351721470|ref|NP_001237722.1| uncharacterized protein LOC100305856 [Glycine max] gi|356525557|ref|XP_003531391.1| PREDICTED: small nuclear ribonucleoprotein Sm D3-like [Glycine max] gi|255626793|gb|ACU13741.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|255539216|ref|XP_002510673.1| small nuclear ribonucleoprotein, putative [Ricinus communis] gi|223551374|gb|EEF52860.1| small nuclear ribonucleoprotein, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|357519697|ref|XP_003630137.1| Small nuclear ribonucleoprotein Sm D3 [Medicago truncatula] gi|355524159|gb|AET04613.1| Small nuclear ribonucleoprotein Sm D3 [Medicago truncatula] gi|388503694|gb|AFK39913.1| unknown [Medicago truncatula] Back     alignment and taxonomy information
>gi|449512675|ref|XP_004164112.1| PREDICTED: small nuclear ribonucleoprotein Sm D3-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|388502716|gb|AFK39424.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|449455595|ref|XP_004145538.1| PREDICTED: small nuclear ribonucleoprotein Sm D3-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|116780936|gb|ABK21888.1| unknown [Picea sitchensis] Back     alignment and taxonomy information
>gi|302811572|ref|XP_002987475.1| hypothetical protein SELMODRAFT_183167 [Selaginella moellendorffii] gi|300144881|gb|EFJ11562.1| hypothetical protein SELMODRAFT_183167 [Selaginella moellendorffii] 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 ?
Query132
TAIR|locus:2030442131 AT1G20580 "AT1G20580" [Arabido 0.75 0.755 0.939 8.8e-47
TAIR|locus:2014589128 SmD3 "AT1G76300" [Arabidopsis 0.734 0.757 0.868 1.5e-42
DICTYBASE|DDB_G0273003146 snrpD3 "putative small nuclear 0.727 0.657 0.653 2.5e-33
ZFIN|ZDB-GENE-030131-5219171 snrpd3l "small nuclear ribonuc 0.689 0.532 0.604 2.7e-29
UNIPROTKB|Q5ZL58126 SNRPD3 "Uncharacterized protei 0.712 0.746 0.574 4.4e-29
UNIPROTKB|F1MZ00126 SNRPD3 "Uncharacterized protei 0.712 0.746 0.574 4.4e-29
UNIPROTKB|B4DJP7120 SNRPD3 "Small nuclear ribonucl 0.712 0.783 0.574 4.4e-29
UNIPROTKB|P62318126 SNRPD3 "Small nuclear ribonucl 0.712 0.746 0.574 4.4e-29
UNIPROTKB|F2Z4Y0126 SNRPD3 "Uncharacterized protei 0.712 0.746 0.574 4.4e-29
UNIPROTKB|P62323126 snrpd3 "Small nuclear ribonucl 0.712 0.746 0.574 4.4e-29
TAIR|locus:2030442 AT1G20580 "AT1G20580" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 490 (177.5 bits), Expect = 8.8e-47, P = 8.8e-47
 Identities = 93/99 (93%), Positives = 99/99 (100%)

Query:     1 MSRSLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQL 60
             MSRSLGIPVKLLHEASGH+VTVELKSGELYRGSM+ECEDNWNCQLE+ITYTAKDGKVSQL
Sbjct:     1 MSRSLGIPVKLLHEASGHIVTVELKSGELYRGSMIECEDNWNCQLEDITYTAKDGKVSQL 60

Query:    61 EHVFIRGSKVRFMVIPDMLKNAPMFKRLDARIKGKSSSI 99
             EHVFIRGSKVRFMVIPD+LK+APMFKRLDARIKGKSSS+
Sbjct:    61 EHVFIRGSKVRFMVIPDILKHAPMFKRLDARIKGKSSSL 99
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:2014589 SmD3 "AT1G76300" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0273003 snrpD3 "putative small nuclear ribonucleoprotein D3" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-5219 snrpd3l "small nuclear ribonucleoprotein D3 polypeptide, like" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|Q5ZL58 SNRPD3 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1MZ00 SNRPD3 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|B4DJP7 SNRPD3 "Small nuclear ribonucleoprotein Sm D3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|P62318 SNRPD3 "Small nuclear ribonucleoprotein Sm D3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F2Z4Y0 SNRPD3 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|P62323 snrpd3 "Small nuclear ribonucleoprotein Sm D3" [Xenopus laevis (taxid:8355)] 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) ?
Q17348SMD3_CAEELNo assigned EC number0.53040.78780.7647yesno
P62323SMD3_XENLANo assigned EC number0.56250.81810.8571N/Ano
P62320SMD3_MOUSENo assigned EC number0.56250.81810.8571yesno
Q9UUC6SMD3_SCHPONo assigned EC number0.57310.62120.8453yesno
O44437SMD3_DROMENo assigned EC number0.52720.80300.7019yesno
P62318SMD3_HUMANNo assigned EC number0.56250.81810.8571yesno
P43321SMD3_YEASTNo assigned EC number0.51160.65150.8514yesno

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:
eugene3.00020086
hypothetical protein (133 aa)
(Populus trichocarpa)
Predicted Functional Partners:
eugene3.00440042
hypothetical protein (2357 aa)
    ••• 0.527
estExt_Genewise1_v1.C_LG_XIII3357
hypothetical protein (820 aa)
    ••  0.484
gw1.202.37.1
annotation not avaliable (151 aa)
   •••• 0.454
estExt_fgenesh4_kg.C_LG_VII0024
SubName- Full=Putative uncharacterized protein; (143 aa)
   •••  0.437
estExt_Genewise1_v1.C_LG_VI0793
SubName- Full=Putative uncharacterized protein; (80 aa)
   •••• 0.427
estExt_Genewise1_v1.C_LG_XVIII2933
SubName- Full=Putative uncharacterized protein; (88 aa)
   •••• 0.425
estExt_Genewise1_v1.C_1710010
SubName- Full=Putative uncharacterized protein; (88 aa)
   •••• 0.425
estExt_Genewise1_v1.C_LG_XVI2449
hypothetical protein (80 aa)
   •••• 0.421
grail3.0014029901
hypothetical protein (52 aa)
   • •  0.413
eugene3.00180816
hypothetical protein (88 aa)
   •••• 0.413

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 ?
Query132
cd0172170 cd01721, Sm_D3, Sm protein D3 1e-47
smart0065167 smart00651, Sm, snRNP Sm proteins 4e-19
pfam0142366 pfam01423, LSM, LSM domain 6e-18
cd0172376 cd01723, LSm4, Like-Sm protein 4 2e-15
cd0173378 cd01733, LSm10, Like-Sm protein 10 4e-13
cd0060063 cd00600, Sm_like, Sm and related proteins 4e-11
COG195879 COG1958, LSM1, Small nuclear ribonucleoprotein (sn 2e-10
cd0172492 cd01724, Sm_D1, Sm protein D1 2e-08
cd0172589 cd01725, LSm2, Like-Sm protein 2 2e-05
cd0172668 cd01726, LSm6, Like-Sm protein 6 2e-04
cd0173169 cd01731, archaeal_Sm1, archaeal Sm protein 1 0.004
>gnl|CDD|212468 cd01721, Sm_D3, Sm protein D3 Back     alignment and domain information 
 Score =  146 bits (372), Expect = 1e-47
 Identities = 47/70 (67%), Positives = 64/70 (91%)

Query: 8  PVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRG 67
          P+KLLHEA GH+VTVELK+GE+YRG ++E EDN NCQL+++T TA+DGKVS+LE V+IRG
Sbjct: 1  PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGKVSKLEQVYIRG 60

Query: 68 SKVRFMVIPD 77
          S++RF+++PD
Sbjct: 61 SQIRFIILPD 70

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 D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Length = 70
>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|212470 cd01723, LSm4, Like-Sm protein 4 Back     alignment and domain information
>gnl|CDD|212480 cd01733, LSm10, Like-Sm protein 10 Back     alignment and domain information
>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins Back     alignment and domain information
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] Back     alignment and domain information
>gnl|CDD|212471 cd01724, Sm_D1, Sm protein D1 Back     alignment and domain information
>gnl|CDD|212472 cd01725, LSm2, Like-Sm protein 2 Back     alignment and domain information
>gnl|CDD|212473 cd01726, LSm6, Like-Sm protein 6 Back     alignment and domain information
>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1 Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 132
KOG3172119 consensus Small nuclear ribonucleoprotein Sm D3 [R 100.0
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.97
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.95
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.94
KOG3293134 consensus Small nuclear ribonucleoprotein (snRNP) 99.94
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.94
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.93
KOG3428109 consensus Small nuclear ribonucleoprotein SMD1 and 99.9
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.9
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.89
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.87
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.86
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.83
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.83
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.82
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.8
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.8
KOG344896 consensus Predicted snRNP core protein [RNA proces 99.77
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.76
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.72
KOG348279 consensus Small nuclear ribonucleoprotein (snRNP) 99.72
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.72
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.66
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 99.66
KOG178377 consensus Small nuclear ribonucleoprotein F [RNA p 99.62
cd0171779 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins 99.6
cd0172874 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins 99.58
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.53
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.53
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.52
KOG178077 consensus Small Nuclear ribonucleoprotein G [RNA p 99.42
KOG346091 consensus Small nuclear ribonucleoprotein (snRNP) 99.41
KOG177584 consensus U6 snRNA-associated Sm-like protein [RNA 99.3
KOG177488 consensus Small nuclear ribonucleoprotein E [RNA p 98.57
KOG3168177 consensus U1 snRNP component [Transcription] 98.51
KOG1781108 consensus Small Nuclear ribonucleoprotein splicing 98.4
PF1443877 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1. 98.09
KOG178496 consensus Small Nuclear ribonucleoprotein splicing 97.87
KOG1782129 consensus Small Nuclear ribonucleoprotein splicing 97.61
PF1270196 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC 97.41
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 97.08
KOG3459114 consensus Small nuclear ribonucleoprotein (snRNP) 97.07
PF1109580 Gemin7: Gem-associated protein 7 (Gemin7); InterPr 96.4
cd0173674 LSm14_N LSm14 (also known as RAP55) belongs to a f 96.04
PF1084266 DUF2642: Protein of unknown function (DUF2642); In 95.97
PF0223748 BPL_C: Biotin protein ligase C terminal domain; In 95.49
cd0171661 Hfq Hfq, an abundant, ubiquitous RNA-binding prote 95.34
TIGR0238361 Hfq RNA chaperone Hfq. This model represents the R 95.03
PRK0039579 hfq RNA-binding protein Hfq; Provisional 94.74
KOG1073 361 consensus Uncharacterized mRNA-associated protein 93.24
PF06372166 Gemin6: Gemin6 protein; InterPro: IPR009422 This f 92.63
PRK14644136 hypothetical protein; Provisional 92.2
cd0173561 LSm12_N LSm12 belongs to a family of Sm-like prote 91.68
COG192377 Hfq Uncharacterized host factor I protein [General 91.54
PRK02001152 hypothetical protein; Validated 90.38
PRK14638150 hypothetical protein; Provisional 89.85
PRK14639140 hypothetical protein; Provisional 88.64
cd0173483 YlxS_C YxlS is a Bacillus subtilis gene of unknown 88.61
PF05918556 API5: Apoptosis inhibitory protein 5 (API5); Inter 86.91
PRK00092154 ribosome maturation protein RimP; Reviewed 86.73
PRK14642197 hypothetical protein; Provisional 86.72
PRK14091165 RNA-binding protein Hfq; Provisional 86.66
PRK14091165 RNA-binding protein Hfq; Provisional 85.8
PRK14632172 hypothetical protein; Provisional 84.99
PF02576141 DUF150: Uncharacterised BCR, YhbC family COG0779; 84.65
PRK14633150 hypothetical protein; Provisional 84.12
COG0779153 Uncharacterized protein conserved in bacteria [Fun 83.71
PRK14640152 hypothetical protein; Provisional 83.58
PRK14647159 hypothetical protein; Provisional 82.31
PRK14636176 hypothetical protein; Provisional 81.98
PRK14645154 hypothetical protein; Provisional 81.39
PRK14643164 hypothetical protein; Provisional 80.84
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification] Back     alignment and domain information 
Probab=100.00  E-value=4.4e-41  Score=240.07  Aligned_cols=118  Identities=70%  Similarity=1.162  Sum_probs=100.1

Q ss_pred             CCCcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEecCccccccc
Q 032863            4 SLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDMLKNAP   83 (132)
Q Consensus         4 ~i~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lpd~l~~ap   83 (132)
                      ++++|++||||++||.|++|+++|++|+|+|.++||+|||+|+|+++|.+||+.+++++||||||+|||+++||+|++||
T Consensus         2 s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdmLKnAP   81 (119)
T KOG3172|consen    2 SVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDMLKNAP   81 (119)
T ss_pred             ccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchHhhcCc
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhchhhhhcCCCCCcccccchhHHHHHHHhhcCCCCCCCCCCCCCCCC
Q 032863           84 MFKRLDARIKGKSSSIGVGRGRAVAMRAKAAAAGRGAAPGRGVVPPVRR  132 (132)
Q Consensus        84 ~l~~~~~~~~~~~~~~~~~rg~~~~~~~~~~~~~~~~~~g~~~~~~~~~  132 (132)
                      ||+.      +++++.+.+.+|+.+.+    ++|+| +||||.++++||
T Consensus        82 mFkk------~~~~~~g~~~~RG~~~~----~~grg-~g~rg~~~p~~r  119 (119)
T KOG3172|consen   82 MFKK------GKSRSLGGGPGRGRARR----ARGRG-RGGRGAGPPVRR  119 (119)
T ss_pred             cccc------ccCCcCCCCCCcccccc----ccCCC-CCCCCCCCCCCC
Confidence            9993      33444444444443333    33333 556888888775

>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
>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
>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
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification] 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
>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
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification] Back     alignment and domain information
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>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
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins Back     alignment and domain information
>smart00651 Sm snRNP Sm proteins Back     alignment and domain information
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] Back     alignment and domain information
>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
>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
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification] 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
>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
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification] Back     alignment and domain information
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>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
>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
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification] 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
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>PTZ00138 small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification] Back     alignment and domain information
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification] Back     alignment and domain information
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification] Back     alignment and domain information
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification] Back     alignment and domain information
>KOG3168 consensus U1 snRNP component [Transcription] Back     alignment and domain information
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1 Back     alignment and domain information
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A 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
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification] Back     alignment and domain information
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins Back     alignment and domain information
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function 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
>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
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport] 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
>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
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only] Back     alignment and domain information
>PRK02001 hypothetical protein; Validated Back     alignment and domain information
>PRK14638 hypothetical protein; Provisional Back     alignment and domain information
>PRK14639 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
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms Back     alignment and domain information
>PRK00092 ribosome maturation protein RimP; Reviewed Back     alignment and domain information
>PRK14642 hypothetical protein; Provisional 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
>PRK14632 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
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK14640 hypothetical protein; Provisional Back     alignment and domain information
>PRK14647 hypothetical protein; Provisional Back     alignment and domain information
>PRK14636 hypothetical protein; Provisional Back     alignment and domain information
>PRK14645 hypothetical protein; Provisional Back     alignment and domain information
>PRK14643 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 ?
Query132
3pgw_Z126 Crystal Structure Of Human U1 Snrnp Length = 126 9e-33
3cw1_D126 Crystal Structure Of Human Spliceosomal U1 Snrnp Le 4e-32
1d3b_A75 Crystal Structure Of The D3b Subcomplex Of The Huma 6e-26
1b34_A119 Crystal Structure Of The D1d2 Sub-Complex From The 8e-08
4emh_A105 Crystal Structure Of Splsm4 Length = 105 1e-07
>pdb|3PGW|Z Chain Z, Crystal Structure Of Human U1 Snrnp Length = 126 Back     alignment and structure 
Iteration: 1

 Score =  135 bits (339), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 54/94 (57%), Positives = 76/94 (80%)
Query: 4  SLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHV 63
          S+G+P+K+LHEA GH+VT E  +GE+YRG ++E EDN NCQ+ NIT T +DG+V+QLE V
Sbjct: 2  SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQV 61
Query: 64 FIRGSKVRFMVIPDMLKNAPMFKRLDARIKGKSS 97
          +IRGSK+RF+++PDMLKNAPM K +  + +G  +
Sbjct: 62 YIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGA 95
>pdb|3CW1|D Chain D, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 126 Back     alignment and structure
>pdb|1D3B|A Chain A, Crystal Structure Of The D3b Subcomplex Of The Human Core Snrnp Domain At 2.0a Resolution Length = 75 Back     alignment and structure
>pdb|1B34|A Chain A, Crystal Structure Of The D1d2 Sub-Complex From The Human Snrnp Core Domain Length = 119 Back     alignment and structure
>pdb|4EMH|A Chain A, Crystal Structure Of Splsm4 Length = 105 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 ?
Query132
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 2e-42
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 1e-36
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 7e-36
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 2e-35
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 3e-13
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 6e-13
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 7e-12
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 6e-10
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 6e-08
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 8e-08
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 1e-07
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 2e-06
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 1e-05
>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
 Score =  135 bits (341), Expect = 2e-42
 Identities = 70/129 (54%), Positives = 96/129 (74%), Gaps = 4/129 (3%)

Query: 4   SLGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHV 63
           S+G+P+K+LHEA GH+VT E  +GE+YRG ++E EDN NCQ+ NIT T +DG+V+QLE V
Sbjct: 2   SIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQV 61

Query: 64  FIRGSKVRFMVIPDMLKNAPMFKRLDARIKGKSSSIGVGRGRAVAMRAKAAAAGRGAAPG 123
           +IRGSK+RF+++PDMLKNAPM K +  + +G     G GRG+A  ++A+ AA GRG   G
Sbjct: 62  YIRGSKIRFLILPDMLKNAPMLKSMKNKNQGS----GAGRGKAAILKAQVAARGRGRGMG 117

Query: 124 RGVVPPVRR 132
           RG +   RR
Sbjct: 118 RGNIFQKRR 126
>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
>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
>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F Length = 86 Back     alignment and structure
>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B Length = 75 Back     alignment and structure
>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
>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Length = 93 Back     alignment and structure
>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Length = 77 Back     alignment and structure
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query132
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 100.0
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 100.0
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.96
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.95
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.9
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.9
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.9
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.9
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.9
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.89
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.88
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.88
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.87
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.86
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.86
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.83
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.82
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.8
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.79
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.78
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.76
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.75
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.71
3pgw_B231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.66
1y96_A86 Gemin6, SIP2, GEM-associated protein 6; SM fold, p 98.72
2vxe_A88 CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA 97.07
4a53_A125 EDC3; RNA binding protein; NMR {Schizosaccharomyce 96.78
2vc8_A84 Enhancer of mRNA-decapping protein 3; P-BODY compo 96.57
1kq1_A77 HFQ, HOST factor for Q beta; hexamer, RNA binding 96.4
2fb7_A95 SM-like protein, LSM-14_N (RAP55); DR.13312, BC055 96.36
1y96_B85 Gemin7, SIP3, GEM-associated protein 7; SM fold, p 96.33
2ylb_A74 Protein HFQ; RNA-binding protein, LSM protein, RNA 96.31
1u1s_A82 HFQ protein; SM-like bacterial protein, riken stru 96.28
2y90_A104 Protein HFQ; RNA-binding protein, SM-like, RNA cha 95.69
2qtx_A71 Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi 95.56
3ahu_A78 Protein HFQ; SM-like motif, protein-RNA complex, t 95.55
3hfo_A70 SSR3341 protein; HFQ, SM, RNA-binding protein, sRN 94.83
3sb2_A79 Protein HFQ; SM-like, RNA chaperone, chaperone; 2. 94.03
3hfn_A72 ASL2047 protein; HFQ, SM, RNA-binding protein, sRN 93.64
1ycy_A71 Conserved hypothetical protein; structural genomic 92.11
2rm4_A103 CG6311-PB, DM EDC3; enhancer of mRNA decapping, P- 91.16
1ib8_A164 Conserved protein SP14.3; nucleic acid binding pro 84.29
>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
Probab=100.00  E-value=6e-38  Score=229.79  Aligned_cols=120  Identities=56%  Similarity=1.027  Sum_probs=85.1

Q ss_pred             CCcHHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEecCcccccccc
Q 032863            5 LGIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDMLKNAPM   84 (132)
Q Consensus         5 i~~P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lpd~l~~ap~   84 (132)
                      ++.|++||++++|++|+||||||++|+|+|.+||+||||+|+||+++.++++..+++++||||++|+||++||+++++|+
T Consensus         3 ~~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~IRGnnI~~I~lpd~l~~~~~   82 (126)
T 2y9a_D            3 IGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDMLKNAPM   82 (126)
T ss_dssp             -CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCSSCSSSSH
T ss_pred             cccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEEEeCCEEEEEEccccccchHH
Confidence            78999999999999999999999999999999999999999999999989999999999999999999999999999999


Q ss_pred             hhchhhhhcCCCCCcccccchhHHHHHHHhhcCCCCCCCCCCCC
Q 032863           85 FKRLDARIKGKSSSIGVGRGRAVAMRAKAAAAGRGAAPGRGVVP  128 (132)
Q Consensus        85 l~~~~~~~~~~~~~~~~~rg~~~~~~~~~~~~~~~~~~g~~~~~  128 (132)
                      |+++.++.|++    +.++|++++.+++++++|+|.+.|||.++
T Consensus        83 l~~~~~k~~~~----~~~~g~~~~~~~~~~~~~~~~~~~~~~~~  122 (126)
T 2y9a_D           83 LKSMKNKNQGS----GAGRGKAAILKAQVAARGRGRGMGRGNIF  122 (126)
T ss_dssp             HHHHHHHHC-----------------------------------
T ss_pred             hhhhhhccccc----ccCcCchhhhhcccccCCCCCCCCCCCCC
Confidence            99987775543    35689999888876666666555555444
>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A Back     alignment and structure
>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 Back     alignment and structure
>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
>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
>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
>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
>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_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
>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Back     alignment and structure
>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} Back     alignment and structure
>2vxe_A CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA decay, LSM proteins, translational repression, transcription; NMR {Drosophila melanogaster} Back     alignment and structure
>4a53_A EDC3; RNA binding protein; NMR {Schizosaccharomyces pombe} PDB: 4a54_A 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
>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
>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
>2ylb_A Protein HFQ; RNA-binding protein, LSM protein, RNA chaperone; 1.15A {Salmonella enterica subsp} PDB: 2yht_A 1hk9_A 2ylc_A* 3gib_A* 3rer_A* 3qo3_A* 3res_A* Back     alignment and structure
>1u1s_A HFQ protein; SM-like bacterial protein, riken structural genomics/proteomics initiative, RSGI, structural genomics, RNA binding protein; 1.60A {Pseudomonas aeruginosa} SCOP: b.38.1.2 PDB: 1u1t_A 3qui_A* 3m4g_A 3inz_A Back     alignment and structure
>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A {Escherichia coli} PDB: 3qhs_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
>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A Back     alignment and structure
>3hfo_A SSR3341 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 1.30A {Synechocystis SP} Back     alignment and structure
>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2 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
>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
>2rm4_A CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-BODY component, SM-like protein,, protein binding; NMR {Drosophila melanogaster} Back     alignment and structure
>1ib8_A Conserved protein SP14.3; nucleic acid binding protein, ribosomal protein, essential gene, structural genomics; NMR {Streptococcus pneumoniae} SCOP: b.38.2.1 d.52.4.1 Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 132
d1d3ba_72 b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s 2e-30
d1b34a_80 b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s 4e-30
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 2e-20
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 2e-20
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 2e-20
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 3e-20
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 1e-19
d1m5q1_127 b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch 4e-18
d1n9ra_68 b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S 1e-16
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 4e-16
d2fwka192 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr 3e-05
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72 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: D3 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  102 bits (256), Expect = 2e-30
 Identities = 43/72 (59%), Positives = 60/72 (83%)

Query: 6  GIPVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFI 65
          G+P+K+LHEA GH+VT E  +GE+YRG ++E EDN NCQ+ NIT T +DG+V+QLE V+I
Sbjct: 1  GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYI 60

Query: 66 RGSKVRFMVIPD 77
          RG K+RF+++PD
Sbjct: 61 RGCKIRFLILPD 72
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80 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
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Length = 76 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
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Length = 72 Back     information, alignment and structure
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Length = 75 Back     information, alignment and structure
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 127 Back     information, alignment and structure
>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
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 71 Back     information, alignment and structure
>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} Length = 92 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query132
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.96
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.96
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.9
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.9
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.89
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.89
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.88
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.87
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.86
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 99.84
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.75
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.64
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.56
d2vxfa180 LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) 96.83
d1biaa247 Biotin repressor/biotin holoenzyme synthetase, C-t 93.82
d1kq1a_60 Pleiotropic translational regulator Hfq {Staphyloc 93.81
d1u1sa166 Pleiotropic translational regulator Hfq {Pseudomon 93.56
d1ycya166 Hypothetical protein PF1955 {Pyrococcus furiosus [ 92.83
d1ib8a174 Hypothetical protein SP14.3 (SP0552) {Streptococcu 85.78
d2d6fa172 Glutamyl-tRNA(Gln) amidotransferase subunit D, Gat 80.88
>d1b34a_ b.38.1.1 (A:) D1 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: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=1.3e-29  Score=170.70  Aligned_cols=78  Identities=31%  Similarity=0.527  Sum_probs=75.8

Q ss_pred             HHHHHHhhCCCEEEEEeCCCcEEEEEEEeeCCceeeEEeeeEEEccCCceeeeeeEEEeCCeEEEEecCcccccccch
Q 032863            8 PVKLLHEASGHVVTVELKSGELYRGSMVECEDNWNCQLENITYTAKDGKVSQLEHVFIRGSKVRFMVIPDMLKNAPMF   85 (132)
Q Consensus         8 P~~lL~~~~g~~V~VELknG~~y~G~L~~vD~~MNi~L~dv~~t~~dg~~~~l~~vfIRGs~Ir~I~lpd~l~~ap~l   85 (132)
                      .++||++++|++|+||||||.+|+|+|.+||+|||++|+||+++.++++..+++++||||++|+||++||+++.+|+|
T Consensus         2 lv~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~~Ir~i~lPd~l~~~~~L   79 (80)
T d1b34a_           2 LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLL   79 (80)
T ss_dssp             HHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTTCCHHHHT
T ss_pred             HHHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEEEcccEEEcCCEEEEEECCCCccccccc
Confidence            479999999999999999999999999999999999999999999999999999999999999999999999999987
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} 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
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} 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
>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
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} 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
>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} Back     information, alignment and structure
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} 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
>d1biaa2 b.34.1.1 (A:271-317) Biotin repressor/biotin holoenzyme synthetase, C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1kq1a_ b.38.1.2 (A:) Pleiotropic translational regulator Hfq {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d1u1sa1 b.38.1.2 (A:6-71) Pleiotropic translational regulator Hfq {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1ycya1 b.38.1.4 (A:5-70) Hypothetical protein PF1955 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1ib8a1 b.38.2.1 (A:91-164) Hypothetical protein SP14.3 (SP0552) {Streptococcus pneumoniae [TaxId: 1313]} Back     information, alignment and structure
>d2d6fa1 b.38.3.1 (A:2-73) Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD {Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure