Psyllid ID: psy1222

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
MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA
cccccEEEEEEEEEcccccEEEcccEEEccccccccccccccccEEEEEEEEEccccccc
cccccEEEEEEEEccccccEEEEcHHHHccccccccccccccccccEEEEEEEccccccc
MTDGRVLVGTflctdrdanvilgscgeylspevfeskeenGAQEARLLGLvmvpgqhipa
MTDGRVLVGTflctdrdanVILGSCGEYLSPEVFESKEENGAQEARLLglvmvpgqhipa
MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA
****RVLVGTFLCTDRDANVILGSCGEYLSPEVF************LLGLVM********
MTDGRVLVGTFLCTDRDANVILGSCGE********************LGLVMVPGQHIP*
MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA
**DGRVLVGTFLCTDRDANVILGSCGEYLSPE************ARLLGLVMVPGQ****
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MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA
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 ?
Query60 2.2.26 [Sep-21-2011]
Q9BRA0125 LSM domain-containing pro no N/A 0.883 0.424 0.620 3e-12
Q9D2U5125 LSM domain-containing pro yes N/A 0.883 0.424 0.620 3e-12
Q6GQ67113 LSM domain-containing pro N/A N/A 0.883 0.469 0.586 1e-11
A4IGZ4113 LSM domain-containing pro yes N/A 0.883 0.469 0.586 1e-11
Q6NU60111 LSM domain-containing pro N/A N/A 0.883 0.477 0.586 1e-11
A2BIG9109 LSM domain-containing pro yes N/A 0.883 0.486 0.568 4e-11
P91918160 Probable small nuclear ri yes N/A 0.95 0.356 0.379 5e-05
Q9PV94 240 Small nuclear ribonucleop no N/A 0.95 0.237 0.379 0.0003
P27048 231 Small nuclear ribonucleop no N/A 0.95 0.246 0.362 0.0005
P14678 240 Small nuclear ribonucleop no N/A 0.95 0.237 0.362 0.0005
>sp|Q9BRA0|LSMD1_HUMAN LSM domain-containing protein 1 OS=Homo sapiens GN=LSMD1 PE=1 SV=1 Back     alignment and function desciption
 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 36/58 (62%), Positives = 39/58 (67%), Gaps = 5/58 (8%)

Query: 1   MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58
           MTDGR LVG FLCTDRD NVILGS  E+L P      +   A E R+LGL MVPG HI
Sbjct: 57  MTDGRTLVGCFLCTDRDCNVILGSAQEFLKP-----SDSFSAGEPRVLGLAMVPGHHI 109
Component of the N-terminal acetyltransferase C (NatC) complex which may catalyze acetylation of N-terminal methionine residues.
Homo sapiens (taxid: 9606)
>sp|Q9D2U5|LSMD1_MOUSE LSM domain-containing protein 1 OS=Mus musculus GN=Lsmd1 PE=2 SV=1 Back     alignment and function description
>sp|Q6GQ67|LMD1A_XENLA LSM domain-containing protein 1-A OS=Xenopus laevis GN=lsmd1-a PE=3 SV=1 Back     alignment and function description
>sp|A4IGZ4|LSMD1_XENTR LSM domain-containing protein 1 OS=Xenopus tropicalis GN=lsmd1 PE=3 SV=2 Back     alignment and function description
>sp|Q6NU60|LMD1B_XENLA LSM domain-containing protein 1-B OS=Xenopus laevis GN=lsmd1-b PE=3 SV=1 Back     alignment and function description
>sp|A2BIG9|LSMD1_DANRE LSM domain-containing protein 1 OS=Danio rerio GN=lsmd1 PE=2 SV=1 Back     alignment and function description
>sp|P91918|RSMB_CAEEL Probable small nuclear ribonucleoprotein-associated protein B OS=Caenorhabditis elegans GN=snr-2 PE=3 SV=1 Back     alignment and function description
>sp|Q9PV94|RSMB_CHICK Small nuclear ribonucleoprotein-associated protein B' OS=Gallus gallus GN=SNRPB PE=2 SV=1 Back     alignment and function description
>sp|P27048|RSMB_MOUSE Small nuclear ribonucleoprotein-associated protein B OS=Mus musculus GN=Snrpb PE=1 SV=1 Back     alignment and function description
>sp|P14678|RSMB_HUMAN Small nuclear ribonucleoprotein-associated proteins B and B' OS=Homo sapiens GN=SNRPB PE=1 SV=2 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 ?
Query60
332031609115 LSM domain-containing protein 1-A [Acrom 0.816 0.426 0.706 4e-14
390335271122 PREDICTED: LSM domain-containing protein 0.883 0.434 0.655 3e-13
380029708103 PREDICTED: LSM domain-containing protein 0.816 0.475 0.655 4e-13
110760136103 PREDICTED: LSM domain-containing protein 0.816 0.475 0.655 4e-13
91081025134 PREDICTED: similar to GA16583-PA [Tribol 0.866 0.388 0.672 4e-13
340719457101 PREDICTED: LSM domain-containing protein 0.816 0.485 0.637 6e-13
357624151105 putative small nuclear ribonucleoprotein 0.85 0.485 0.661 8e-13
30719277456 LSM domain-containing protein 1 [Harpegn 0.816 0.875 0.689 1e-12
345491540109 PREDICTED: LSM domain-containing protein 0.8 0.440 0.689 1e-12
383847078101 PREDICTED: LSM domain-containing protein 0.816 0.485 0.637 3e-12
>gi|332031609|gb|EGI71081.1| LSM domain-containing protein 1-A [Acromyrmex echinatior] Back     alignment and taxonomy information
 Score = 82.0 bits (201), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 41/58 (70%), Positives = 43/58 (74%), Gaps = 9/58 (15%)

Query: 1   MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58
           MTDGRVL G FLCTDRDANVILGSC EYLS E           EAR+LGLVMVPG+HI
Sbjct: 60  MTDGRVLRGAFLCTDRDANVILGSCTEYLSTE---------HTEARVLGLVMVPGRHI 108

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|390335271|ref|XP_001198253.2| PREDICTED: LSM domain-containing protein 1-like [Strongylocentrotus purpuratus] Back     alignment and taxonomy information
>gi|380029708|ref|XP_003698509.1| PREDICTED: LSM domain-containing protein 1-A-like [Apis florea] Back     alignment and taxonomy information
>gi|110760136|ref|XP_001120034.1| PREDICTED: LSM domain-containing protein 1-A-like [Apis mellifera] Back     alignment and taxonomy information
>gi|91081025|ref|XP_975319.1| PREDICTED: similar to GA16583-PA [Tribolium castaneum] gi|270005993|gb|EFA02441.1| hypothetical protein TcasGA2_TC008128 [Tribolium castaneum] Back     alignment and taxonomy information
>gi|340719457|ref|XP_003398170.1| PREDICTED: LSM domain-containing protein 1-A-like [Bombus terrestris] gi|350410451|ref|XP_003489044.1| PREDICTED: LSM domain-containing protein 1-A-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|357624151|gb|EHJ75030.1| putative small nuclear ribonucleoprotein, core [Danaus plexippus] Back     alignment and taxonomy information
>gi|307192774|gb|EFN75864.1| LSM domain-containing protein 1 [Harpegnathos saltator] Back     alignment and taxonomy information
>gi|345491540|ref|XP_001607580.2| PREDICTED: LSM domain-containing protein 1-like [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|383847078|ref|XP_003699182.1| PREDICTED: LSM domain-containing protein 1-like [Megachile rotundata] 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 ?
Query60
UNIPROTKB|Q9BRA0125 LSMD1 "LSM domain-containing p 0.883 0.424 0.620 1.2e-12
MGI|MGI:1925554125 Lsmd1 "LSM domain containing 1 0.883 0.424 0.620 1.2e-12
FB|FBgn0051950121 CG31950 [Drosophila melanogast 0.8 0.396 0.603 2.8e-11
WB|WBGene00004915160 snr-2 [Caenorhabditis elegans 0.95 0.356 0.379 1.6e-06
TAIR|locus:2163416 254 AT5G44500 "AT5G44500" [Arabido 0.933 0.220 0.396 3.9e-06
UNIPROTKB|J3QLE5169 SNRPN "Small nuclear ribonucle 0.95 0.337 0.344 1.5e-05
UNIPROTKB|Q9PV94 240 SNRPB "Small nuclear ribonucle 0.95 0.237 0.379 1.6e-05
TAIR|locus:2128610 257 smB "small nuclear ribonucleop 0.933 0.217 0.403 1.9e-05
UNIPROTKB|E2R1C4 231 SNRPB "Small nuclear ribonucle 0.95 0.246 0.362 1.9e-05
MGI|MGI:98342 231 Snrpb "small nuclear ribonucle 0.95 0.246 0.362 1.9e-05
UNIPROTKB|Q9BRA0 LSMD1 "LSM domain-containing protein 1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 36/58 (62%), Positives = 39/58 (67%)

Query:     1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58
             MTDGR LVG FLCTDRD NVILGS  E+L P      +   A E R+LGL MVPG HI
Sbjct:    57 MTDGRTLVGCFLCTDRDCNVILGSAQEFLKPS-----DSFSAGEPRVLGLAMVPGHHI 109
GO:0005634 "nucleus" evidence=IEA
GO:0005737 "cytoplasm" evidence=IEA
MGI|MGI:1925554 Lsmd1 "LSM domain containing 1" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
FB|FBgn0051950 CG31950 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
WB|WBGene00004915 snr-2 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
TAIR|locus:2163416 AT5G44500 "AT5G44500" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|J3QLE5 SNRPN "Small nuclear ribonucleoprotein-associated protein N" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q9PV94 SNRPB "Small nuclear ribonucleoprotein-associated protein B'" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
TAIR|locus:2128610 smB "small nuclear ribonucleoprotein associated protein B" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|E2R1C4 SNRPB "Small nuclear ribonucleoprotein-associated protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
MGI|MGI:98342 Snrpb "small nuclear ribonucleoprotein B" [Mus musculus (taxid:10090)] 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) ?
A2BIG9LSMD1_DANRENo assigned EC number0.56890.88330.4862yesN/A
A4IGZ4LSMD1_XENTRNo assigned EC number0.58620.88330.4690yesN/A
Q9D2U5LSMD1_MOUSENo assigned EC number0.62060.88330.424yesN/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 ?
Query60
cd0616873 cd06168, LSMD1, LSM domain containing 1 4e-24
cd0171780 cd01717, Sm_B, Sm protein B 7e-13
cd0060063 cd00600, Sm_like, Sm and related proteins 1e-05
smart0065167 smart00651, Sm, snRNP Sm proteins 7e-05
cd0172791 cd01727, LSm8, Like-Sm protein 8 0.003
>gnl|CDD|212486 cd06168, LSMD1, LSM domain containing 1 Back     alignment and domain information 
 Score = 84.9 bits (211), Expect = 4e-24
 Identities = 34/58 (58%), Positives = 42/58 (72%), Gaps = 6/58 (10%)

Query: 1  MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58
          +TDGRVLVGTF+CTD+D N+IL +  EY  P       + GA+E R LGLVMVPG+HI
Sbjct: 16 LTDGRVLVGTFVCTDKDGNIILSNAEEYRKP------SDLGAEEPRSLGLVMVPGKHI 67

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. 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. LSMD1 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes, forming heptameric and hexameric ring structures similar to those found in eukaryotes. Length = 73
>gnl|CDD|212464 cd01717, Sm_B, Sm protein B Back     alignment and domain information
>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins Back     alignment and domain information
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins Back     alignment and domain information
>gnl|CDD|212474 cd01727, LSm8, Like-Sm protein 8 Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 60
cd0171779 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins 99.87
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.86
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.86
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.85
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.84
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.81
cd0172874 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins 99.81
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.8
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.79
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.78
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.78
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 99.78
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.75
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.73
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.72
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.72
KOG3168|consensus177 99.71
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.69
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.67
KOG1780|consensus77 99.67
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.67
KOG1781|consensus108 99.62
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.55
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.55
KOG3460|consensus91 99.54
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.5
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.47
KOG1782|consensus129 99.45
KOG1784|consensus96 99.4
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.4
KOG1774|consensus88 99.31
KOG3482|consensus79 99.24
KOG1775|consensus84 99.19
KOG3459|consensus114 99.15
KOG1783|consensus77 99.08
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 98.67
KOG3448|consensus96 97.73
KOG3293|consensus134 97.72
KOG3172|consensus119 97.4
KOG3428|consensus109 97.36
PF1443877 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1. 96.67
cd0171661 Hfq Hfq, an abundant, ubiquitous RNA-binding prote 92.23
TIGR0238361 Hfq RNA chaperone Hfq. This model represents the R 91.6
PRK0039579 hfq RNA-binding protein Hfq; Provisional 90.97
PF0223748 BPL_C: Biotin protein ligase C terminal domain; In 89.86
PF1456342 DUF4444: Domain of unknown function (DUF4444); PDB 89.13
COG192377 Hfq Uncharacterized host factor I protein [General 87.47
cd0173674 LSm14_N LSm14 (also known as RAP55) belongs to a f 80.74
KOG3382|consensus151 80.09
>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 
Probab=99.87  E-value=6.2e-23  Score=112.89  Aligned_cols=59  Identities=37%  Similarity=0.683  Sum_probs=47.6

Q ss_pred             CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCCC
Q psy1222           1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA   60 (60)
Q Consensus         1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv~   60 (60)
                      |+|||++.|+|+|||+||||||++|+|++...+..+. .....+.|.+|+++|||++|+|
T Consensus        17 l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~-~~~~~~~r~lG~v~iRG~~Vv~   75 (79)
T cd01717          17 LQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSK-NSEREEKRTLGLVLLRGENIVS   75 (79)
T ss_pred             ECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccc-cccCcceeEeeeEEEcCCEEEE
Confidence            5899999999999999999999999999875432210 0113467899999999999985

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 B heterodimerizes with subunit D3 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. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
>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
>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
>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
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>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
>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
>PRK00737 small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences Back     alignment and domain information
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>PTZ00138 small nuclear ribonucleoprotein; Provisional 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
>smart00651 Sm snRNP Sm proteins Back     alignment and domain information
>KOG3168|consensus 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
>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
>KOG1780|consensus Back     alignment and domain information
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] Back     alignment and domain information
>KOG1781|consensus Back     alignment and domain information
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>KOG3460|consensus 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
>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
>KOG1782|consensus Back     alignment and domain information
>KOG1784|consensus 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
>KOG1774|consensus Back     alignment and domain information
>KOG3482|consensus Back     alignment and domain information
>KOG1775|consensus Back     alignment and domain information
>KOG3459|consensus Back     alignment and domain information
>KOG1783|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
>KOG3448|consensus Back     alignment and domain information
>KOG3293|consensus Back     alignment and domain information
>KOG3172|consensus Back     alignment and domain information
>KOG3428|consensus Back     alignment and domain information
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1 Back     alignment and domain information
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others Back     alignment and domain information
>TIGR02383 Hfq RNA chaperone Hfq Back     alignment and domain information
>PRK00395 hfq RNA-binding protein Hfq; Provisional Back     alignment and domain information
>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
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A Back     alignment and domain information
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only] 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
>KOG3382|consensus 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 ?
Query60
2y9a_A95 Structure Of The Spliceosomal U4 Snrnp Core Domain 2e-05
1d3b_B91 Crystal Structure Of The D3b Subcomplex Of The Huma 2e-05
3pgw_B 231 Crystal Structure Of Human U1 Snrnp Length = 231 4e-05
3cw1_A174 Crystal Structure Of Human Spliceosomal U1 Snrnp Le 5e-05
>pdb|2Y9A|A Chain A, Structure Of The Spliceosomal U4 Snrnp Core Domain Length = 95 Back     alignment and structure 
Iteration: 1

 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 1  MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58
          + DGR+ +GTF   D+  N+IL  C E+   +   SK+    +E R+LGLV++ G+++
Sbjct: 21 LQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAE-REEKRVLGLVLLRGENL 77
>pdb|1D3B|B Chain B, Crystal Structure Of The D3b Subcomplex Of The Human Core Snrnp Domain At 2.0a Resolution Length = 91 Back     alignment and structure
>pdb|3PGW|B Chain B, Crystal Structure Of Human U1 Snrnp Length = 231 Back     alignment and structure
>pdb|3CW1|A Chain A, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 174 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 ?
Query60
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 8e-14
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 7e-09
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 4e-06
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 5e-06
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 2e-05
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 2e-05
>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A Length = 91 Back     alignment and structure
 Score = 58.7 bits (142), Expect = 8e-14
 Identities = 21/58 (36%), Positives = 36/58 (62%), Gaps = 1/58 (1%)

Query: 1  MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58
          + DGR+ +GTF   D+  N+IL  C E+   +   SK+    +E R+LGLV++ G+++
Sbjct: 21 LQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAER-EEKRVLGLVLLRGENL 77
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231 Back     alignment and structure
>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C Length = 113 Back     alignment and structure
>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae} Length = 96 Back     alignment and structure
>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Length = 121 Back     alignment and structure
>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe} Length = 93 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query60
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.83
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.83
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.82
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.82
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.82
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.81
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.8
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.8
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.8
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.8
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.79
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.79
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.79
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.78
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.78
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.77
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.77
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.75
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.74
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.71
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.7
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 99.69
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.62
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 99.59
1y96_A86 Gemin6, SIP2, GEM-associated protein 6; SM fold, p 97.21
1u1s_A82 HFQ protein; SM-like bacterial protein, riken stru 95.13
2ylb_A74 Protein HFQ; RNA-binding protein, LSM protein, RNA 94.92
3sb2_A79 Protein HFQ; SM-like, RNA chaperone, chaperone; 2. 94.84
2y90_A104 Protein HFQ; RNA-binding protein, SM-like, RNA cha 94.09
3ahu_A78 Protein HFQ; SM-like motif, protein-RNA complex, t 93.02
2qtx_A71 Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi 92.39
1kq1_A77 HFQ, HOST factor for Q beta; hexamer, RNA binding 90.52
1x4r_A99 PARP14 protein; WWE domain, structural genomics, N 83.43
3hfo_A70 SSR3341 protein; HFQ, SM, RNA-binding protein, sRN 80.39
>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe} Back     alignment and structure
Probab=99.83  E-value=1.7e-21  Score=109.34  Aligned_cols=60  Identities=18%  Similarity=0.241  Sum_probs=44.4

Q ss_pred             CCCCceEEEEEEeecCCCceEecccccccCccccccccc--cchhhheeeeeeeecCCCCCC
Q psy1222           1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEE--NGAQEARLLGLVMVPGQHIPA   60 (60)
Q Consensus         1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~--~~~~~~r~lG~v~irG~~Iv~   60 (60)
                      |+|||+|.|+|+|||+||||||+||+|++...+++.+..  ......|.+|+++|||+||++
T Consensus        26 l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~iRG~nVv~   87 (93)
T 4emg_A           26 LRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRGDSVIL   87 (93)
T ss_dssp             ETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEECGGGEEE
T ss_pred             ECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEECCCeEEE
Confidence            579999999999999999999999999987643321100  112357999999999999974
>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
>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
>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
>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
>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
>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
>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
>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
>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
>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B Back     alignment and structure
>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Back     alignment and structure
>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
>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
>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
>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
>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Back     alignment and structure
>3s6n_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
>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
>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
>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
>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
>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
>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} Back     alignment and structure
>1u1s_A HFQ protein; SM-like bacterial protein, riken structural genomics/proteomics initiative, RSGI, structural genomics, RNA binding protein; 1.60A {Pseudomonas aeruginosa} SCOP: b.38.1.2 PDB: 1u1t_A 3qui_A* 3m4g_A 3inz_A Back     alignment and structure
>2ylb_A Protein HFQ; RNA-binding protein, LSM protein, RNA chaperone; 1.15A {Salmonella enterica subsp} PDB: 2yht_A 1hk9_A 2ylc_A* 3gib_A* 3rer_A* 3qo3_A* 3res_A* Back     alignment and structure
>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2 Back     alignment and structure
>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A {Escherichia coli} PDB: 3qhs_A Back     alignment and structure
>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A Back     alignment and structure
>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii} 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
>1x4r_A PARP14 protein; WWE domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} 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

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 60
d1d3bb_81 b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa 2e-13
d2fwka192 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr 8e-10
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 2e-06
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 2e-06
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 3e-06
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 8e-06
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 2e-05
d1b34b_93 b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s 5e-04
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 0.004
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 81 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: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.4 bits (136), Expect = 2e-13
 Identities = 21/58 (36%), Positives = 36/58 (62%), Gaps = 1/58 (1%)

Query: 1  MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58
          + DGR+ +GTF   D+  N+IL  C E+   +   SK+    +E R+LGLV++ G+++
Sbjct: 15 LQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAER-EEKRVLGLVLLRGENL 71
>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
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Length = 71 Back     information, alignment and structure
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Length = 72 Back     information, alignment and structure
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 74 Back     information, alignment and structure
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Length = 76 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
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93 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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query60
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.89
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.86
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.83
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.79
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.78
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.77
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.77
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.76
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.73
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.72
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.62
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.5
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 99.37
d1u1sa166 Pleiotropic translational regulator Hfq {Pseudomon 94.49
d1biaa247 Biotin repressor/biotin holoenzyme synthetase, C-t 91.78
d1kq1a_60 Pleiotropic translational regulator Hfq {Staphyloc 91.37
d1rqpa1106 5'-fluoro-5'-deoxyadenosine synthase {Streptomyces 85.59
>d1d3bb_ b.38.1.1 (B:) B 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: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=1.4e-24  Score=117.89  Aligned_cols=59  Identities=36%  Similarity=0.685  Sum_probs=48.1

Q ss_pred             CCCCceEEEEEEeecCCCceEecccccccCccccccccccchhhheeeeeeeecCCCCCC
Q psy1222           1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHIPA   60 (60)
Q Consensus         1 l~dgR~~~G~l~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~~r~lG~v~irG~~Iv~   60 (60)
                      |+|||.|+|+|+|||+||||||++|+|++....++.+. ......|.+|+++|||+||+|
T Consensus        15 l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~-~~~~~~r~lG~v~IRG~~Iv~   73 (81)
T d1d3bb_          15 LQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQ-AEREEKRVLGLVLLRGENLVS   73 (81)
T ss_dssp             ETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTS-CCEEEEEEEEEEEECGGGEEE
T ss_pred             EcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccc-cccceEEEeeeEEEeCCEEEE
Confidence            57999999999999999999999999998654433221 123567999999999999975
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} 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
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} 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
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} 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
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} 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
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Back     information, alignment and structure
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Back     information, alignment and structure
>d1u1sa1 b.38.1.2 (A:6-71) Pleiotropic translational regulator Hfq {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>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
>d1rqpa1 b.141.1.1 (A:193-298) 5'-fluoro-5'-deoxyadenosine synthase {Streptomyces cattleya [TaxId: 29303]} Back     information, alignment and structure