Psyllid ID: psy14196

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--------8
MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRWATQE
cccccHHHHHHHHcccEEEEEEccccEEEEEEccccccccEEEEEEEEEccccccccccEEEEEccccccccEEEEEcc
cccccHHHHHHHHcccEEEEEEccccEEEEEEEEEcccccEEEEEEEEEcccccEEcccEEEEEEEEcccccEEEEccc
MSIGIPIKLLHEaeghiitcettngdlfrgklveaednmncamadvtvtfrdgtyylpalvpiagmwngtsglRWATQE
MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRWATQE
MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRWATQE
***GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRW****
*SIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRWA***
MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRWATQE
*SIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRWAT**
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYYLPALVPIAGMWNGTSGLRWATQE
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 ?
Query79 2.2.26 [Sep-21-2011]
P62323126 Small nuclear ribonucleop N/A N/A 0.670 0.420 0.735 2e-20
P62320126 Small nuclear ribonucleop yes N/A 0.670 0.420 0.735 2e-20
P62318126 Small nuclear ribonucleop yes N/A 0.670 0.420 0.735 2e-20
O44437151 Small nuclear ribonucleop yes N/A 0.670 0.350 0.754 8e-20
Q17348136 Small nuclear ribonucleop yes N/A 0.696 0.404 0.636 6e-17
Q9UUC697 Small nuclear ribonucleop yes N/A 0.594 0.484 0.680 1e-13
P43321101 Small nuclear ribonucleop yes N/A 0.632 0.495 0.56 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 = 97.8 bits (242), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 39/53 (73%), Positives = 50/53 (94%)

Query: 1  MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
          MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG
Sbjct: 1  MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG 53
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

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 ?
Query79
443687679135 hypothetical protein CAPTEDRAFT_221674 [ 0.670 0.392 0.792 1e-19
291235317123 PREDICTED: small nuclear ribonucleoprote 0.670 0.430 0.773 2e-19
241690470122 small nuclear ribonucleoprotein Sm D3, p 0.670 0.434 0.773 3e-19
405976315131 Small nuclear ribonucleoprotein Sm D3 [C 0.670 0.404 0.773 4e-19
346472269122 hypothetical protein [Amblyomma maculatu 0.670 0.434 0.754 4e-19
115497280125 small nuclear ribonucleoprotein Sm D3 [B 0.721 0.456 0.701 6e-19
308321147128 small nuclear ribonucleoprotein sm d3 [I 0.670 0.414 0.735 6e-19
41054297128 small nuclear ribonucleoprotein D3 polyp 0.822 0.507 0.646 6e-19
432888006117 PREDICTED: small nuclear ribonucleoprote 0.822 0.555 0.646 7e-19
47211785127 unnamed protein product [Tetraodon nigro 0.670 0.417 0.735 7e-19
>gi|443687679|gb|ELT90579.1| hypothetical protein CAPTEDRAFT_221674 [Capitella teleta] Back     alignment and taxonomy information
 Score =  100 bits (249), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 42/53 (79%), Positives = 52/53 (98%)

Query: 1  MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
          MSIG+PIK+LHEAEGHI+TCETT+G+++RGKLVEAEDNMNC MA++TVT+RDG
Sbjct: 1  MSIGVPIKVLHEAEGHIVTCETTSGEVYRGKLVEAEDNMNCQMANITVTYRDG 53

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota
>gi|291235317|ref|XP_002737590.1| PREDICTED: small nuclear ribonucleoprotein polypeptide D3-like [Saccoglossus kowalevskii] Back     alignment and taxonomy information
>gi|241690470|ref|XP_002411764.1| small nuclear ribonucleoprotein Sm D3, putative [Ixodes scapularis] gi|215504603|gb|EEC14097.1| small nuclear ribonucleoprotein Sm D3, putative [Ixodes scapularis] Back     alignment and taxonomy information
>gi|405976315|gb|EKC40827.1| Small nuclear ribonucleoprotein Sm D3 [Crassostrea gigas] Back     alignment and taxonomy information
>gi|346472269|gb|AEO35979.1| hypothetical protein [Amblyomma maculatum] Back     alignment and taxonomy information
>gi|115497280|ref|NP_001069947.1| small nuclear ribonucleoprotein Sm D3 [Bos taurus] gi|86437979|gb|AAI12525.1| Small nuclear ribonucleoprotein D3 polypeptide 18kDa [Bos taurus] Back     alignment and taxonomy information
>gi|308321147|gb|ADO27727.1| small nuclear ribonucleoprotein sm d3 [Ictalurus furcatus] Back     alignment and taxonomy information
>gi|41054297|ref|NP_956054.1| small nuclear ribonucleoprotein D3 polypeptide, like [Danio rerio] gi|28278495|gb|AAH45929.1| Small nuclear ribonucleoprotein D3 polypeptide, like [Danio rerio] gi|182889668|gb|AAI65492.1| Snrpd3l protein [Danio rerio] Back     alignment and taxonomy information
>gi|432888006|ref|XP_004075020.1| PREDICTED: small nuclear ribonucleoprotein Sm D3-like, partial [Oryzias latipes] Back     alignment and taxonomy information
>gi|47211785|emb|CAF93753.1| unnamed protein product [Tetraodon nigroviridis] 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 ?
Query79
UNIPROTKB|Q5ZL58126 SNRPD3 "Uncharacterized protei 0.670 0.420 0.735 1.2e-19
UNIPROTKB|F1MZ00126 SNRPD3 "Uncharacterized protei 0.670 0.420 0.735 1.2e-19
UNIPROTKB|B4DJP7120 SNRPD3 "Small nuclear ribonucl 0.670 0.441 0.735 1.2e-19
UNIPROTKB|P62318126 SNRPD3 "Small nuclear ribonucl 0.670 0.420 0.735 1.2e-19
UNIPROTKB|F2Z4Y0126 SNRPD3 "Uncharacterized protei 0.670 0.420 0.735 1.2e-19
UNIPROTKB|P62323126 snrpd3 "Small nuclear ribonucl 0.670 0.420 0.735 1.2e-19
MGI|MGI:1914582126 Snrpd3 "small nuclear ribonucl 0.670 0.420 0.735 1.2e-19
ZFIN|ZDB-GENE-030131-5219171 snrpd3l "small nuclear ribonuc 0.670 0.309 0.735 1.2e-19
ZFIN|ZDB-GENE-040625-55127 snrpd3 "small nuclear ribonucl 0.670 0.417 0.735 1.5e-19
FB|FBgn0023167151 SmD3 "Small ribonucleoprotein 0.670 0.350 0.754 1.9e-19
UNIPROTKB|Q5ZL58 SNRPD3 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
 Score = 234 (87.4 bits), Expect = 1.2e-19, P = 1.2e-19
 Identities = 39/53 (73%), Positives = 50/53 (94%)

Query:     1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
             MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG
Sbjct:     1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG 53
GO:0005683 "U7 snRNP" evidence=IEA
GO:0005689 "U12-type spliceosomal complex" evidence=IEA
GO:0005737 "cytoplasm" evidence=IEA
GO:0019899 "enzyme binding" evidence=IEA
GO:0071013 "catalytic step 2 spliceosome" evidence=IEA
GO:0071208 "histone pre-mRNA DCP binding" evidence=IEA
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
MGI|MGI:1914582 Snrpd3 "small nuclear ribonucleoprotein D3" [Mus musculus (taxid:10090)] 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
ZFIN|ZDB-GENE-040625-55 snrpd3 "small nuclear ribonucleoprotein D3 polypeptide" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
FB|FBgn0023167 SmD3 "Small ribonucleoprotein particle protein SmD3" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q17348SMD3_CAEELNo assigned EC number0.63630.69620.4044yesN/A
P62318SMD3_HUMANNo assigned EC number0.73580.67080.4206yesN/A
O44437SMD3_DROMENo assigned EC number0.75470.67080.3509yesN/A
Q9UUC6SMD3_SCHPONo assigned EC number0.68080.59490.4845yesN/A
P62320SMD3_MOUSENo assigned EC number0.73580.67080.4206yesN/A
P43321SMD3_YEASTNo assigned EC number0.560.63290.4950yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query79
cd0172170 cd01721, Sm_D3, Sm protein D3 4e-30
smart0065167 smart00651, Sm, snRNP Sm proteins 1e-09
pfam0142366 pfam01423, LSM, LSM domain 6e-09
COG195879 COG1958, LSM1, Small nuclear ribonucleoprotein (sn 4e-07
cd0060063 cd00600, Sm_like, Sm and related proteins 7e-07
cd0172376 cd01723, LSm4, Like-Sm protein 4 3e-06
cd0173378 cd01733, LSm10, Like-Sm protein 10 4e-06
>gnl|CDD|212468 cd01721, Sm_D3, Sm protein D3 Back     alignment and domain information 
 Score =  100 bits (252), Expect = 4e-30
 Identities = 35/48 (72%), Positives = 41/48 (85%)

Query: 6  PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
          PIKLLHEAEGHI+T E   G+++RGKL+EAEDNMNC + DVTVT RDG
Sbjct: 1  PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDG 48

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|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] Back     alignment and domain information
>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins 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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 79
KOG3172|consensus119 99.92
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.87
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.84
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.84
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.83
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.82
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.81
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.78
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.77
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.74
KOG3482|consensus79 99.69
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.69
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.64
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.64
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.64
KOG3293|consensus134 99.64
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.59
KOG3448|consensus96 99.58
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.57
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.52
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.49
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.38
KOG1783|consensus77 99.37
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 99.34
cd0172874 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins 99.32
cd0171779 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins 99.29
KOG3428|consensus109 99.24
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.22
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.21
KOG1775|consensus84 99.15
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.02
KOG3460|consensus91 98.8
KOG1780|consensus77 98.78
PF1443877 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1. 98.11
KOG1774|consensus88 97.96
KOG1781|consensus108 97.66
KOG3168|consensus177 97.6
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 97.09
KOG1784|consensus96 96.49
KOG1782|consensus129 95.6
cd0171661 Hfq Hfq, an abundant, ubiquitous RNA-binding prote 95.36
TIGR0238361 Hfq RNA chaperone Hfq. This model represents the R 95.28
PF1270196 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC 95.17
PRK0039579 hfq RNA-binding protein Hfq; Provisional 94.46
PRK14638150 hypothetical protein; Provisional 94.36
PRK14639140 hypothetical protein; Provisional 93.9
PRK02001152 hypothetical protein; Validated 93.18
PF0223748 BPL_C: Biotin protein ligase C terminal domain; In 93.15
KOG3459|consensus114 93.14
cd0173561 LSm12_N LSm12 belongs to a family of Sm-like prote 93.1
PRK14644136 hypothetical protein; Provisional 92.85
PF1084266 DUF2642: Protein of unknown function (DUF2642); In 92.42
COG192377 Hfq Uncharacterized host factor I protein [General 92.37
PF1109580 Gemin7: Gem-associated protein 7 (Gemin7); InterPr 92.07
PRK14640152 hypothetical protein; Provisional 91.22
cd0173674 LSm14_N LSm14 (also known as RAP55) belongs to a f 91.16
COG0779153 Uncharacterized protein conserved in bacteria [Fun 90.34
PRK14632172 hypothetical protein; Provisional 89.53
cd0173483 YlxS_C YxlS is a Bacillus subtilis gene of unknown 89.3
PRK14636176 hypothetical protein; Provisional 89.23
PRK14645154 hypothetical protein; Provisional 89.14
PRK14642197 hypothetical protein; Provisional 88.98
PRK14647159 hypothetical protein; Provisional 88.89
PRK00092154 ribosome maturation protein RimP; Reviewed 88.81
PRK14634155 hypothetical protein; Provisional 88.55
PRK14633150 hypothetical protein; Provisional 88.23
PF02576141 DUF150: Uncharacterised BCR, YhbC family COG0779; 87.56
PF06372166 Gemin6: Gemin6 protein; InterPro: IPR009422 This f 87.13
PRK14091165 RNA-binding protein Hfq; Provisional 86.7
PRK14091165 RNA-binding protein Hfq; Provisional 85.86
PRK14646155 hypothetical protein; Provisional 85.55
PRK14631174 hypothetical protein; Provisional 84.78
PRK14641173 hypothetical protein; Provisional 83.47
PRK14637151 hypothetical protein; Provisional 83.25
PF0707380 ROF: Modulator of Rho-dependent transcription term 81.85
PRK14643164 hypothetical protein; Provisional 81.41
smart0033357 TUDOR Tudor domain. Domain of unknown function pre 80.28
PF10618119 Tail_tube: Phage tail tube protein; InterPro: IPR0 80.1
>KOG3172|consensus Back     alignment and domain information 
Probab=99.92  E-value=9.3e-26  Score=148.86  Aligned_cols=72  Identities=57%  Similarity=0.971  Sum_probs=68.4

Q ss_pred             CCcCchHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeE----------------ecCcccccc
Q psy14196          1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTY----------------YLPALVPIA   64 (79)
Q Consensus         1 m~~~~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~----------------~lp~~l~~~   64 (79)
                      ||+++|+++|++++|+.|++|+++|..|+|+|+++|++||++|+|++.|.+||++                ++||||++|
T Consensus         1 ~s~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPdmLKnA   80 (119)
T KOG3172|consen    1 MSVGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPDMLKNA   80 (119)
T ss_pred             CccccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECchHhhcC
Confidence            7899999999999999999999999999999999999999999999999999965                999999999


Q ss_pred             ccccccce
Q psy14196         65 GMWNGTSG   72 (79)
Q Consensus        65 p~~~~~~~   72 (79)
                      ||||..++
T Consensus        81 PmFkk~~~   88 (119)
T KOG3172|consen   81 PMFKKGKS   88 (119)
T ss_pred             cccccccC
Confidence            99997543

>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
>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
>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
>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
>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
>PRK00737 small nuclear ribonucleoprotein; Provisional 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
>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
>KOG3482|consensus Back     alignment and domain information
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] 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
>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
>KOG3293|consensus 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
>KOG3448|consensus Back     alignment and domain information
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>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
>KOG1783|consensus 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
>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
>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
>KOG3428|consensus Back     alignment and domain information
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>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
>KOG1775|consensus Back     alignment and domain information
>PTZ00138 small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>KOG3460|consensus Back     alignment and domain information
>KOG1780|consensus Back     alignment and domain information
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1 Back     alignment and domain information
>KOG1774|consensus Back     alignment and domain information
>KOG1781|consensus Back     alignment and domain information
>KOG3168|consensus Back     alignment and domain information
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>KOG1784|consensus Back     alignment and domain information
>KOG1782|consensus 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
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A Back     alignment and domain information
>PRK00395 hfq RNA-binding protein Hfq; Provisional Back     alignment and domain information
>PRK14638 hypothetical protein; Provisional Back     alignment and domain information
>PRK14639 hypothetical protein; Provisional Back     alignment and domain information
>PRK02001 hypothetical protein; Validated 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
>KOG3459|consensus 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
>PRK14644 hypothetical protein; Provisional Back     alignment and domain information
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function Back     alignment and domain information
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only] 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
>PRK14640 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
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK14632 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
>PRK14636 hypothetical protein; Provisional Back     alignment and domain information
>PRK14645 hypothetical protein; Provisional Back     alignment and domain information
>PRK14642 hypothetical protein; Provisional Back     alignment and domain information
>PRK14647 hypothetical protein; Provisional Back     alignment and domain information
>PRK00092 ribosome maturation protein RimP; Reviewed Back     alignment and domain information
>PRK14634 hypothetical protein; Provisional Back     alignment and domain information
>PRK14633 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
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins 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
>PRK14646 hypothetical protein; Provisional Back     alignment and domain information
>PRK14631 hypothetical protein; Provisional Back     alignment and domain information
>PRK14641 hypothetical protein; Provisional Back     alignment and domain information
>PRK14637 hypothetical protein; Provisional Back     alignment and domain information
>PF07073 ROF: Modulator of Rho-dependent transcription termination (ROF); InterPro: IPR009778 This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins Back     alignment and domain information
>PRK14643 hypothetical protein; Provisional Back     alignment and domain information
>smart00333 TUDOR Tudor domain Back     alignment and domain information
>PF10618 Tail_tube: Phage tail tube protein; InterPro: IPR019596 This entry is represented by Bacteriophage Mu, GpM tail tube protein 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 ?
Query79
3pgw_Z126 Crystal Structure Of Human U1 Snrnp Length = 126 1e-21
3cw1_D126 Crystal Structure Of Human Spliceosomal U1 Snrnp Le 2e-21
1d3b_A75 Crystal Structure Of The D3b Subcomplex Of The Huma 6e-21
>pdb|3PGW|Z Chain Z, Crystal Structure Of Human U1 Snrnp Length = 126 Back     alignment and structure 
Iteration: 1

 Score = 97.8 bits (242), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 39/53 (73%), Positives = 50/53 (94%)
Query: 1  MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
          MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG
Sbjct: 1  MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG 53
>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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query79
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 5e-22
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 8e-22
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 8e-18
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 2e-16
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 6e-05
>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
 Score = 79.8 bits (197), Expect = 5e-22
 Identities = 39/53 (73%), Positives = 50/53 (94%)

Query: 1  MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
          MSIG+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG
Sbjct: 1  MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG 53
>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D Length = 126 Back     alignment and structure
>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe} Length = 105 Back     alignment and structure
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query79
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 99.89
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.88
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.86
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 99.79
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.78
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.76
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.76
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.75
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.73
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.73
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.73
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.73
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.72
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.72
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.68
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.65
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.63
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.55
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.52
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.52
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.51
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.5
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.39
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.36
1y96_A86 Gemin6, SIP2, GEM-associated protein 6; SM fold, p 98.33
1kq1_A77 HFQ, HOST factor for Q beta; hexamer, RNA binding 96.82
2ylb_A74 Protein HFQ; RNA-binding protein, LSM protein, RNA 96.79
3ahu_A78 Protein HFQ; SM-like motif, protein-RNA complex, t 96.75
1u1s_A82 HFQ protein; SM-like bacterial protein, riken stru 96.67
4a53_A125 EDC3; RNA binding protein; NMR {Schizosaccharomyce 96.29
2y90_A104 Protein HFQ; RNA-binding protein, SM-like, RNA cha 96.24
2qtx_A71 Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi 96.14
3sb2_A79 Protein HFQ; SM-like, RNA chaperone, chaperone; 2. 95.88
2vc8_A84 Enhancer of mRNA-decapping protein 3; P-BODY compo 93.8
3hfo_A70 SSR3341 protein; HFQ, SM, RNA-binding protein, sRN 90.64
1y96_B85 Gemin7, SIP3, GEM-associated protein 7; SM fold, p 89.86
1ib8_A164 Conserved protein SP14.3; nucleic acid binding pro 89.47
2vxe_A88 CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA 89.17
3hfn_A72 ASL2047 protein; HFQ, SM, RNA-binding protein, sRN 88.43
3rux_A270 BIRA bifunctional protein; biotin-protein ligase, 83.97
2fb7_A95 SM-like protein, LSM-14_N (RAP55); DR.13312, BC055 81.9
>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=99.89  E-value=1.8e-23  Score=139.29  Aligned_cols=69  Identities=62%  Similarity=1.104  Sum_probs=62.6

Q ss_pred             CCcCchHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeE----------------ecCcccccc
Q psy14196          1 MSIGIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTY----------------YLPALVPIA   64 (79)
Q Consensus         1 m~~~~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~----------------~lp~~l~~~   64 (79)
                      ||+..|++||++++|++|+||||||.+|+|+|.+||+|||++|+||+++.++|+.                ++||++..+
T Consensus         1 ~~~~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~IRGnnI~~I~lpd~l~~~   80 (126)
T 2y9a_D            1 MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDMLKNA   80 (126)
T ss_dssp             ---CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCSSCSSS
T ss_pred             CCcccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEEEeCCEEEEEEccccccch
Confidence            8999999999999999999999999999999999999999999999999877743                999999999


Q ss_pred             ccccc
Q psy14196         65 GMWNG   69 (79)
Q Consensus        65 p~~~~   69 (79)
                      |+|+.
T Consensus        81 ~~l~~   85 (126)
T 2y9a_D           81 PMLKS   85 (126)
T ss_dssp             SHHHH
T ss_pred             HHhhh
Confidence            99974
>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
>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
>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
>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A* Back     alignment and structure
>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A* Back     alignment and structure
>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
>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
>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
>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Back     alignment and structure
>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A Back     alignment and structure
>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
>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
>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
>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae} Back     alignment and structure
>3s6n_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
>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
>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
>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
>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
>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
>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
>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_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
>4a53_A EDC3; RNA binding protein; NMR {Schizosaccharomyces pombe} PDB: 4a54_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
>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2 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
>3hfo_A SSR3341 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 1.30A {Synechocystis 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
>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
>3hfn_A ASL2047 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 2.31A {Nostoc SP} 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
>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

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 79
d1d3ba_72 b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s 4e-17
d1b34a_80 b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s 5e-13
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 8e-13
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 1e-11
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 1e-11
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 2e-11
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 3e-11
d1m5q1_127 b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch 2e-09
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 4e-09
d1n9ra_68 b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S 3e-05
d2fwka192 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr 1e-04
>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 = 66.3 bits (162), Expect = 4e-17
 Identities = 36/50 (72%), Positives = 47/50 (94%)

Query: 4  GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
          G+PIK+LHEAEGHI+TCET  G+++RGKL+EAEDNMNC M+++TVT+RDG
Sbjct: 1  GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDG 50
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80 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
>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
>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
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 127 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
>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
>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 ?
Query79
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.87
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.83
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.82
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.79
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.79
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.78
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.76
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.69
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.69
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 99.61
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.54
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.4
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.28
d1kq1a_60 Pleiotropic translational regulator Hfq {Staphyloc 94.55
d1u1sa166 Pleiotropic translational regulator Hfq {Pseudomon 93.89
d2vxfa180 LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) 90.54
d1ib8a174 Hypothetical protein SP14.3 (SP0552) {Streptococcu 86.59
d2qqra159 Jumonji domain-containing protein 2A {Human (Homo 85.58
d1biaa247 Biotin repressor/biotin holoenzyme synthetase, C-t 81.76
>d1d3ba_ b.38.1.1 (A:) D3 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: D3 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=2.4e-22  Score=120.52  Aligned_cols=68  Identities=56%  Similarity=1.036  Sum_probs=61.7

Q ss_pred             CchHHHHhhcCCCeEEEEecCCcEEEEEEeEeCCccceEEeeeEEEccCCeE-ecCccccccccccccceeEEee
Q psy14196          4 GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTY-YLPALVPIAGMWNGTSGLRWAT   77 (79)
Q Consensus         4 ~~Pl~lL~~~~g~~V~VeLKnG~~y~G~L~~~D~~MNv~L~n~~~~~~~G~~-~lp~~l~~~p~~~~~~~~~~~~   77 (79)
                      ++|+++|++++|+.|+||||||++|+|+|.+||+|||++|+||+++.++|+. .+|.      +|-|++++||..
T Consensus         1 g~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~------v~IRG~~I~~i~   69 (72)
T d1d3ba_           1 GVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ------VYIRGCKIRFLI   69 (72)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEE------EEECGGGEEEEE
T ss_pred             CCchHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCcEeEcCe------EEEECCEEEEEE
Confidence            5899999999999999999999999999999999999999999999888865 4443      688999999874
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Back     information, alignment and structure
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Back     information, alignment and structure
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Back     information, alignment and structure
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>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
>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
>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
>d2qqra1 b.34.9.1 (A:897-955) Jumonji domain-containing protein 2A {Human (Homo sapiens) [TaxId: 9606]} 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