Psyllid ID: psy1175

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-----
MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDEIIDMVKEDQVQRTRQRDSNRGGRGGSNQRGRGGHNMRGMRANNAPKPTLNRNELFYYCGIILLITCLFQMLKSQVDLNMLRVMTMTTDINHGFCF
cEEEEEcccEEEEEEEEEcccccEEEEEEEEEcccccccccccEEEEEcccEEEEEcccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccEEEHHHHHHHHHHHHHHHHHccccEEEEEEEEccccccccc
cEEEEEcccEEcEEEEEccccEEEEEEEEEEEcccccEEEEccEEEEEccEEEEEEccHHHHHHHHHHHHHHHcccccHccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHccccccccccc
mlvelkngetynghlvncdhwmniNLREVICtsrdgdkfwrmpecyirgsmikylripDEIIDMVKedqvqrtrqrdsnrggrggsnqrgrgghnmrgmrannapkptlnrnelFYYCGIILLITCLFQMLKSQVDLNMLRVMTMttdinhgfcf
mlvelkngetynghlvncdhWMNINLREVIctsrdgdkfwRMPECYIRGSMIKYLRIPDEIIDMVkedqvqrtrqrdsnrggrggsnqrgrgghnmrgmrannapkptlNRNELFYYCGIILLITCLFQMLKSQVDLNMLRVMTMTTDINHGFCF
MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDEIIDMVKEDQVQRTrqrdsnrggrggsnqrgrgghnmrgmrannAPKPTLNRNELFYYCGIILLITCLFQMLKSQVDLNMLRVMTMTTDINHGFCF
********ETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDEIIDMV*********************************************RNELFYYCGIILLITCLFQMLKSQVDLNMLRVMTMTTDINHGFC*
MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDEIID****************************************************YYCGIILLITCLFQMLKSQVDLNMLRVMTMTTDINHGFCF
MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDEIIDMVKED************************GHNMRGMRANNAPKPTLNRNELFYYCGIILLITCLFQMLKSQVDLNMLRVMTMTTDINHGFCF
MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDEIIDMVKEDQVQ*************************************LNRNELFYYCGIILLITCLFQMLKSQVDLNMLRVMTMTTDINHGFCF
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiii
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MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDEIIDMVKEDQVQRTRQRDSNRGGRGGSNQRGRGGHNMRGMRANNAPKPTLNRNELFYYCGIILLITCLFQMLKSQVDLNMLRVMTMTTDINHGFCF
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 ?
Query155 2.2.26 [Sep-21-2011]
Q9Y4Z0139 U6 snRNA-associated Sm-li yes N/A 0.477 0.532 0.891 4e-34
Q3ZBK6139 U6 snRNA-associated Sm-li yes N/A 0.477 0.532 0.891 4e-34
Q9QXA5137 U6 snRNA-associated Sm-li yes N/A 0.522 0.591 0.764 4e-34
Q43582146 Probable U6 snRNA-associa N/A N/A 0.580 0.616 0.673 3e-32
Q9LGE6147 Probable U6 snRNA-associa yes N/A 0.438 0.462 0.852 1e-30
Q9ZRU9148 Probable U6 snRNA-associa N/A N/A 0.490 0.513 0.736 3e-30
Q54KX4177 Probable U6 snRNA-associa yes N/A 0.632 0.553 0.644 3e-27
Q19952123 Probable U6 snRNA-associa yes N/A 0.438 0.552 0.691 1e-23
O14352121 Probable U6 snRNA-associa yes N/A 0.464 0.595 0.666 3e-23
P40070187 U6 snRNA-associated Sm-li yes N/A 0.432 0.358 0.402 6e-09
>sp|Q9Y4Z0|LSM4_HUMAN U6 snRNA-associated Sm-like protein LSm4 OS=Homo sapiens GN=LSM4 PE=1 SV=1 Back     alignment and function desciption
 Score =  143 bits (361), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 66/74 (89%), Positives = 70/74 (94%)

Query: 1  MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDE 60
          MLVELKNGETYNGHLV+CD+WMNINLREVICTSRDGDKFWRMPECYIRGS IKYLRIPDE
Sbjct: 15 MLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRMPECYIRGSTIKYLRIPDE 74

Query: 61 IIDMVKEDQVQRTR 74
          IIDMVKE+ V + R
Sbjct: 75 IIDMVKEEVVAKGR 88
Binds specifically to the 3'-terminal U-tract of U6 snRNA.
Homo sapiens (taxid: 9606)
>sp|Q3ZBK6|LSM4_BOVIN U6 snRNA-associated Sm-like protein LSm4 OS=Bos taurus GN=LSM4 PE=2 SV=1 Back     alignment and function description
>sp|Q9QXA5|LSM4_MOUSE U6 snRNA-associated Sm-like protein LSm4 OS=Mus musculus GN=Lsm4 PE=2 SV=1 Back     alignment and function description
>sp|Q43582|LSM4_TOBAC Probable U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana tabacum PE=2 SV=1 Back     alignment and function description
>sp|Q9LGE6|LSM4_ORYSJ Probable U6 snRNA-associated Sm-like protein LSm4 OS=Oryza sativa subsp. japonica GN=Os01g0256900 PE=2 SV=1 Back     alignment and function description
>sp|Q9ZRU9|LSM4_FAGSY Probable U6 snRNA-associated Sm-like protein LSm4 OS=Fagus sylvatica GN=LSM4 PE=2 SV=1 Back     alignment and function description
>sp|Q54KX4|LSM4_DICDI Probable U6 snRNA-associated Sm-like protein LSm4 OS=Dictyostelium discoideum GN=lsm4 PE=3 SV=1 Back     alignment and function description
>sp|Q19952|LSM4_CAEEL Probable U6 snRNA-associated Sm-like protein LSm4 OS=Caenorhabditis elegans GN=lsm-4 PE=3 SV=1 Back     alignment and function description
>sp|O14352|LSM4_SCHPO Probable U6 snRNA-associated Sm-like protein LSm4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm4 PE=1 SV=1 Back     alignment and function description
>sp|P40070|LSM4_YEAST U6 snRNA-associated Sm-like protein LSm4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=LSM4 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 ?
Query155
332376551135 unknown [Dendroctonus ponderosae] 0.677 0.777 0.738 2e-38
91084013163 PREDICTED: similar to LSM4 homolog, U6 s 0.580 0.552 0.835 2e-37
270007999130 hypothetical protein TcasGA2_TC014750 [T 0.580 0.692 0.835 4e-37
357619535138 hypothetical protein KGM_17625 [Danaus p 0.703 0.789 0.714 3e-36
195434128 303 GK14878 [Drosophila willistoni] gi|19416 0.593 0.303 0.736 9e-36
194761808140 GF14101 [Drosophila ananassae] gi|190616 0.580 0.642 0.763 7e-35
405977571 697 UPF0632 protein A [Crassostrea gigas] 0.477 0.106 0.851 1e-34
195051225155 GH13613 [Drosophila grimshawi] gi|193900 0.593 0.593 0.736 2e-34
38047763152 similar to Drosophila melanogaster CG177 0.567 0.578 0.758 2e-34
25012547154 RE35747p [Drosophila melanogaster] 0.567 0.571 0.758 2e-34
>gi|332376551|gb|AEE63415.1| unknown [Dendroctonus ponderosae] Back     alignment and taxonomy information
 Score =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 79/107 (73%), Positives = 86/107 (80%), Gaps = 2/107 (1%)

Query: 1   MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDE 60
           MLVELKNGETYNGHLV+CD+WMNINLREVICTSRDGDKFWRMPECYIRGS IKYLRIPDE
Sbjct: 15  MLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRMPECYIRGSTIKYLRIPDE 74

Query: 61  IIDMVKEDQVQRTRQRDSNRGGRGGSNQRGRGGHNMRGMRANNAPKP 107
           +IDMVKE+ V + +Q    +GGRGG NQR R     RG     A KP
Sbjct: 75  VIDMVKEETVTKNKQSRDQKGGRGGQNQRNRPA--ARGNFGGRANKP 119

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|91084013|ref|XP_975325.1| PREDICTED: similar to LSM4 homolog, U6 small nuclear RNA associated [Tribolium castaneum] Back     alignment and taxonomy information
>gi|270007999|gb|EFA04447.1| hypothetical protein TcasGA2_TC014750 [Tribolium castaneum] Back     alignment and taxonomy information
>gi|357619535|gb|EHJ72069.1| hypothetical protein KGM_17625 [Danaus plexippus] Back     alignment and taxonomy information
>gi|195434128|ref|XP_002065055.1| GK14878 [Drosophila willistoni] gi|194161140|gb|EDW76041.1| GK14878 [Drosophila willistoni] Back     alignment and taxonomy information
>gi|194761808|ref|XP_001963115.1| GF14101 [Drosophila ananassae] gi|190616812|gb|EDV32336.1| GF14101 [Drosophila ananassae] Back     alignment and taxonomy information
>gi|405977571|gb|EKC42014.1| UPF0632 protein A [Crassostrea gigas] Back     alignment and taxonomy information
>gi|195051225|ref|XP_001993055.1| GH13613 [Drosophila grimshawi] gi|193900114|gb|EDV98980.1| GH13613 [Drosophila grimshawi] Back     alignment and taxonomy information
>gi|38047763|gb|AAR09784.1| similar to Drosophila melanogaster CG17768, partial [Drosophila yakuba] Back     alignment and taxonomy information
>gi|25012547|gb|AAN71375.1| RE35747p [Drosophila melanogaster] 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 ?
Query155
ZFIN|ZDB-GENE-040426-1652143 lsm4 "LSM4 homolog, U6 small n 0.464 0.503 0.902 5.2e-33
UNIPROTKB|Q3ZBK6139 LSM4 "U6 snRNA-associated Sm-l 0.464 0.517 0.902 6.7e-33
UNIPROTKB|Q9Y4Z0139 LSM4 "U6 snRNA-associated Sm-l 0.464 0.517 0.902 6.7e-33
MGI|MGI:1354692137 Lsm4 "LSM4 homolog, U6 small n 0.438 0.496 0.926 2.9e-32
FB|FBgn0032240154 CG17768 [Drosophila melanogast 0.438 0.441 0.897 9.8e-32
TAIR|locus:2180295129 emb1644 "AT5G27720" [Arabidops 0.458 0.550 0.802 3e-30
DICTYBASE|DDB_G0287053177 lsm4 "putative U6 small nuclea 0.470 0.412 0.675 1.6e-24
UNIPROTKB|G4MT14121 MGG_01509 "Glycine rich protei 0.458 0.586 0.704 1.6e-24
ASPGD|ASPL0000001547119 AN10781 [Emericella nidulans ( 0.445 0.579 0.724 2e-24
POMBASE|SPBC30D10.06121 lsm4 "U6 snRNP-associated prot 0.464 0.595 0.666 4.8e-23
ZFIN|ZDB-GENE-040426-1652 lsm4 "LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
 Score = 360 (131.8 bits), Expect = 5.2e-33, P = 5.2e-33
 Identities = 65/72 (90%), Positives = 69/72 (95%)

Query:     1 MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDE 60
             MLVELKNGETYNGHLV+CD+WMNINLREVICTSRDGDKFWRMPECYIRGS IKYLRIPDE
Sbjct:    15 MLVELKNGETYNGHLVSCDNWMNINLREVICTSRDGDKFWRMPECYIRGSTIKYLRIPDE 74

Query:    61 IIDMVKEDQVQR 72
             IIDMVKE+ V +
Sbjct:    75 IIDMVKEEVVSK 86
GO:0003674 "molecular_function" evidence=ND
UNIPROTKB|Q3ZBK6 LSM4 "U6 snRNA-associated Sm-like protein LSm4" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|Q9Y4Z0 LSM4 "U6 snRNA-associated Sm-like protein LSm4" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:1354692 Lsm4 "LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
FB|FBgn0032240 CG17768 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
TAIR|locus:2180295 emb1644 "AT5G27720" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0287053 lsm4 "putative U6 small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
UNIPROTKB|G4MT14 MGG_01509 "Glycine rich protein" [Magnaporthe oryzae 70-15 (taxid:242507)] Back     alignment and assigned GO terms
ASPGD|ASPL0000001547 AN10781 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
POMBASE|SPBC30D10.06 lsm4 "U6 snRNP-associated protein Lsm4 (predicted)" [Schizosaccharomyces pombe (taxid:4896)] 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) ?
Q9QXA5LSM4_MOUSENo assigned EC number0.76400.52250.5912yesN/A
Q54KX4LSM4_DICDINo assigned EC number0.64420.63220.5536yesN/A
Q9LGE6LSM4_ORYSJNo assigned EC number0.85290.43870.4625yesN/A
Q3ZBK6LSM4_BOVINNo assigned EC number0.89180.47740.5323yesN/A
O14352LSM4_SCHPONo assigned EC number0.66660.46450.5950yesN/A
Q9Y4Z0LSM4_HUMANNo assigned EC number0.89180.47740.5323yesN/A
Q19952LSM4_CAEELNo assigned EC number0.69110.43870.5528yesN/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 ?
Query155
cd0172376 cd01723, LSm4, Like-Sm protein 4 2e-44
smart0065167 smart00651, Sm, snRNP Sm proteins 3e-16
cd0172170 cd01721, Sm_D3, Sm protein D3 2e-14
cd0060063 cd00600, Sm_like, Sm and related proteins 4e-11
pfam0142366 pfam01423, LSM, LSM domain 8e-10
cd0172589 cd01725, LSm2, Like-Sm protein 2 5e-09
cd0173378 cd01733, LSm10, Like-Sm protein 10 1e-08
COG195879 COG1958, LSM1, Small nuclear ribonucleoprotein (sn 2e-08
cd0172492 cd01724, Sm_D1, Sm protein D1 2e-04
cd0172668 cd01726, LSm6, Like-Sm protein 6 4e-04
>gnl|CDD|212470 cd01723, LSm4, Like-Sm protein 4 Back     alignment and domain information 
 Score =  140 bits (354), Expect = 2e-44
 Identities = 51/63 (80%), Positives = 61/63 (96%)

Query: 1  MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDE 60
          +LVELKNGETYNGHLVNCD+WMNI+L+ VICTS+DGD+FW+MPECYIRG+ IKYLR+PDE
Sbjct: 14 VLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIRGNTIKYLRLPDE 73

Query: 61 IID 63
          +ID
Sbjct: 74 VID 76

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 76
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins Back     alignment and domain information
>gnl|CDD|212468 cd01721, Sm_D3, Sm protein D3 Back     alignment and domain information
>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins Back     alignment and domain information
>gnl|CDD|201787 pfam01423, LSM, LSM domain Back     alignment and domain information
>gnl|CDD|212472 cd01725, LSm2, Like-Sm protein 2 Back     alignment and domain information
>gnl|CDD|212480 cd01733, LSm10, Like-Sm protein 10 Back     alignment and domain information
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] Back     alignment and domain information
>gnl|CDD|212471 cd01724, Sm_D1, Sm protein D1 Back     alignment and domain information
>gnl|CDD|212473 cd01726, LSm6, Like-Sm protein 6 Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 155
KOG3293|consensus134 99.95
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.88
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.87
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.87
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.85
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.85
KOG3428|consensus109 99.8
KOG3172|consensus119 99.8
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.72
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.69
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.67
KOG3448|consensus96 99.66
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.63
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.63
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.63
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.61
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.57
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.55
KOG3482|consensus79 99.53
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.53
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.42
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 99.41
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.36
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.35
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.29
cd0171779 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins 99.28
cd0172874 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins 99.25
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.24
KOG1783|consensus77 99.21
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.1
KOG1780|consensus77 98.93
KOG1775|consensus84 98.55
KOG3460|consensus91 98.44
KOG1774|consensus88 98.26
KOG1781|consensus108 97.38
KOG3168|consensus177 96.89
KOG1784|consensus96 96.48
KOG1782|consensus129 96.39
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 95.69
PF1443877 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1. 94.87
PF1270196 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC 92.59
PTZ00034124 40S ribosomal protein S10; Provisional 92.3
cd0171661 Hfq Hfq, an abundant, ubiquitous RNA-binding prote 89.6
KOG3459|consensus114 89.51
TIGR0238361 Hfq RNA chaperone Hfq. This model represents the R 89.11
PRK0039579 hfq RNA-binding protein Hfq; Provisional 85.87
>KOG3293|consensus Back     alignment and domain information 
Probab=99.95  E-value=1.5e-28  Score=189.65  Aligned_cols=76  Identities=82%  Similarity=1.400  Sum_probs=72.2

Q ss_pred             CEEEecCCcEEEEEEEEeccccceEEeeEEEEcCCCceeccCCeEEEeCCeEEEEecCchhhhhHHHHHHhhhhcc
Q psy1175           1 MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDEIIDMVKEDQVQRTRQR   76 (155)
Q Consensus         1 VtVELKNG~~y~GtL~svD~~MNL~LknV~~t~~dG~~~~~l~~ifIRGnnIRyI~LPdeiid~~k~~~~~k~~~r   76 (155)
                      |.||||||++|.|.|++||.||||+|++|+++++||+.||.+++|||||++|+|+.+||+++|.+++|..++.+.|
T Consensus        15 mlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~iid~vkee~~~~~~~r   90 (134)
T KOG3293|consen   15 MLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEIIDKVKEECVSNNRNR   90 (134)
T ss_pred             EEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHHHHHHHHHHHHhccch
Confidence            5799999999999999999999999999999999999999999999999999999999999999999988765544

>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>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
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>KOG3428|consensus Back     alignment and domain information
>KOG3172|consensus 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
>KOG3448|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
>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
>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
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] 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
>KOG3482|consensus 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
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>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
>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
>PTZ00138 small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>KOG1783|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
>KOG1780|consensus Back     alignment and domain information
>KOG1775|consensus Back     alignment and domain information
>KOG3460|consensus 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
>KOG1784|consensus Back     alignment and domain information
>KOG1782|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
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1 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
>PTZ00034 40S ribosomal protein S10; Provisional 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
>KOG3459|consensus 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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query155
4emh_A105 Crystal Structure Of Splsm4 Length = 105 7e-24
3pgw_Z126 Crystal Structure Of Human U1 Snrnp Length = 126 1e-05
3cw1_D126 Crystal Structure Of Human Spliceosomal U1 Snrnp Le 8e-05
1d3b_A75 Crystal Structure Of The D3b Subcomplex Of The Huma 9e-05
>pdb|4EMH|A Chain A, Crystal Structure Of Splsm4 Length = 105 Back     alignment and structure 
Iteration: 1

 Score =  105 bits (263), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 47/72 (65%), Positives = 59/72 (81%)
Query: 1   MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDE 60
           +LVELKNGET+NGHL NCD++ N+ LREVI T  DGDKF+R+PECYIRG+ IKYLRI DE
Sbjct: 29  ILVELKNGETFNGHLENCDNYXNLTLREVIRTXPDGDKFFRLPECYIRGNNIKYLRIQDE 88
Query: 61  IIDMVKEDQVQR 72
           ++  V + Q Q+
Sbjct: 89  VLSQVAKQQAQQ 100
>pdb|3PGW|Z Chain Z, Crystal Structure Of Human U1 Snrnp Length = 126 Back     alignment and structure
>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 HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query155
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 99.92
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 99.9
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.85
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.83
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.73
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.72
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.71
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.7
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.69
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.68
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.67
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.65
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.65
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.62
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.61
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.6
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.57
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.55
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.55
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.5
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.47
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.45
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.44
3pgw_B231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.41
1y96_A86 Gemin6, SIP2, GEM-associated protein 6; SM fold, p 97.64
2qtx_A71 Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi 91.79
3ahu_A78 Protein HFQ; SM-like motif, protein-RNA complex, t 90.79
2ylb_A74 Protein HFQ; RNA-binding protein, LSM protein, RNA 90.7
1u1s_A82 HFQ protein; SM-like bacterial protein, riken stru 90.65
1kq1_A77 HFQ, HOST factor for Q beta; hexamer, RNA binding 89.93
3sb2_A79 Protein HFQ; SM-like, RNA chaperone, chaperone; 2. 88.91
4a53_A125 EDC3; RNA binding protein; NMR {Schizosaccharomyce 88.46
2y90_A104 Protein HFQ; RNA-binding protein, SM-like, RNA cha 87.92
2vc8_A84 Enhancer of mRNA-decapping protein 3; P-BODY compo 82.48
2vxe_A88 CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA 82.19
>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
Probab=99.92  E-value=1.4e-25  Score=168.58  Aligned_cols=71  Identities=30%  Similarity=0.521  Sum_probs=60.3

Q ss_pred             CEEEecCCcEEEEEEEEeccccceEEeeEEEEcCCCceeccCCeEEEeCCeEEEEecCchh-hhhHHHHHHhh
Q psy1175           1 MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDEI-IDMVKEDQVQR   72 (155)
Q Consensus         1 VtVELKNG~~y~GtL~svD~~MNL~LknV~~t~~dG~~~~~l~~ifIRGnnIRyI~LPdei-id~~k~~~~~k   72 (155)
                      |+||||||.+|.|+|.+||.|||++|+||+++.+++++. +++.+||||+||+||++||++ +|....++++|
T Consensus        15 V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~~~~-~lg~v~IRG~nI~~I~~pd~l~~d~~l~~~~pK   86 (119)
T 1b34_A           15 VTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPV-QLETLSIRGNNIRYFILPDSLPLDTLLVDVEPK   86 (119)
T ss_dssp             EEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCE-EEEEEEECGGGEEEEECCTTCCHHHHTC-----
T ss_pred             EEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCcee-EcceEEEcCCeEEEEEeccccccchhHhhhccc
Confidence            689999999999999999999999999999998777665 899999999999999999996 66666555444
>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
>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
>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Back     alignment and structure
>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A* Back     alignment and structure
>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A* Back     alignment and structure
>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
>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
>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
>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
>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Back     alignment and structure
>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B Back     alignment and structure
>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
>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
>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
>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
>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A Back     alignment and structure
>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E Back     alignment and structure
>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
>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
>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B Back     alignment and structure
>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C Back     alignment and structure
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Back     alignment and structure
>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} Back     alignment and structure
>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii} Back     alignment and structure
>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A Back     alignment and structure
>2ylb_A Protein HFQ; RNA-binding protein, LSM protein, RNA chaperone; 1.15A {Salmonella enterica subsp} PDB: 2yht_A 1hk9_A 2ylc_A* 3gib_A* 3rer_A* 3qo3_A* 3res_A* Back     alignment and structure
>1u1s_A HFQ protein; SM-like bacterial protein, riken structural genomics/proteomics initiative, RSGI, structural genomics, RNA binding protein; 1.60A {Pseudomonas aeruginosa} SCOP: b.38.1.2 PDB: 1u1t_A 3qui_A* 3m4g_A 3inz_A Back     alignment and structure
>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
>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2 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
>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
>2vxe_A CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA decay, LSM proteins, translational repression, transcription; NMR {Drosophila melanogaster} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 155
d1m5q1_127 b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch 2e-22
d1b34a_80 b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s 1e-19
d1d3ba_72 b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s 2e-17
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 8e-14
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 3e-13
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 4e-13
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 7e-13
d1n9ra_68 b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S 7e-13
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 9e-13
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 1e-11
d2fwka192 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr 4e-08
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 127 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: Sm-Like archaeal protein Smap3
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 84.0 bits (208), Expect = 2e-22
 Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 6/75 (8%)

Query: 1  MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDE 60
          + V L NGE Y G L   D+ +NI L      + +     +    +I    I ++   + 
Sbjct: 13 VQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGE-----KFNRVFIMYRYIVHIDSTER 67

Query: 61 IIDMVK-EDQVQRTR 74
           IDM +   Q ++  
Sbjct: 68 RIDMREFAKQAEKIF 82
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80 Back     information, alignment and structure
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72 Back     information, alignment and structure
>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
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Length = 71 Back     information, alignment and structure
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Length = 76 Back     information, alignment and structure
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 68 Back     information, alignment and structure
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 71 Back     information, alignment and structure
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Length = 75 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 ?
Query155
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.86
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.85
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.75
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 99.69
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.68
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.68
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.67
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.67
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.67
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.67
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.32
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.28
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.19
d1kq1a_60 Pleiotropic translational regulator Hfq {Staphyloc 86.81
d1u1sa166 Pleiotropic translational regulator Hfq {Pseudomon 85.74
d2vxfa180 LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) 83.51
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=2.4e-22  Score=140.32  Aligned_cols=60  Identities=32%  Similarity=0.569  Sum_probs=57.8

Q ss_pred             CEEEecCCcEEEEEEEEeccccceEEeeEEEEcCCCceeccCCeEEEeCCeEEEEecCchh
Q psy1175           1 MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDEI   61 (155)
Q Consensus         1 VtVELKNG~~y~GtL~svD~~MNL~LknV~~t~~dG~~~~~l~~ifIRGnnIRyI~LPdei   61 (155)
                      |+||||||.+|+|+|.++|+|||++|+||++++++|++. +++++||||++|+||++||++
T Consensus        14 V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~-~~~~v~IRG~~Ir~i~lPd~l   73 (80)
T d1b34a_          14 VTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPV-QLETLSIRGNNIRYFILPDSL   73 (80)
T ss_dssp             EEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCE-EEEEEEECGGGEEEEECCTTC
T ss_pred             EEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEE-EcccEEEcCCEEEEEECCCCc
Confidence            689999999999999999999999999999999999887 899999999999999999986
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {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
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Back     information, alignment and structure
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Back     information, alignment and structure
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Back     information, alignment and structure
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} 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
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} 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
>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