Psyllid ID: psy9158

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---
MTAVFDSPKEQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSRELTFESLFIQSRNVMFIHIPRHVSIVNKVEDALQSKPRQSSSAGRTLKQKRANLMQQEVLEKIQALKKQKMAQGVM
ccccccccHHHHHHHHHHHHHHHHccccEEEEEcccccEEEEEEEEEcccccEEEccEEEEcEEEEEcccEEEEEccccccHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
cccccccHHHHHHHHHHHHHHHHHHcccEEEEEEccccEEEEEEEEccccEEEEEcccEEccEEEEEccEEEEEEccccccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccc
mtavfdspkeqflSFNTLACLAKSLVGMITCVDlrnessvsgrleHVDGFMNIYMSRELTFESLFIQSRNVMFIHIPRHVSIVNKVEDalqskprqsssagrTLKQKRANLMQQEVLEKIQALKKQKMAQGVM
mtavfdspkeqfLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSRELTFESLFIQSRNVMFIHIPRHVSIVNKVEDalqskprqsssagrtlkQKRANLMQQEVLEKIQALKKQKMAQGVM
MTAVFDSPKEQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSRELTFESLFIQSRNVMFIHIPRHVSIVNKVEDALQSKPRQSSSAGRTLKQKRANLMQQEVLEKIQALKKQKMAQGVM
**********QFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSRELTFESLFIQSRNVMFIHIPRHVSIVNKV***********************************************
***********FLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSRELTFESLFIQSRNVMFIHIPRHVSIVNK************************************************
MTAVFDSPKEQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSRELTFESLFIQSRNVMFIHIPRHVSIVNKVEDA*****************KRANLMQQEVLEKIQA***********
******SPKEQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSRELTFESLFIQSRNVMFIHIPRHVSIVNKVEDALQSKPRQ****GRTLKQKR*NLMQQEVLEKIQALKKQK******
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MTAVFDSPKEQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSRELTFESLFIQSRNVMFIHIPRHVSIVNKVEDALQSKPRQSSSAGRTLKQKRANLMQQEVLEKIQALKKQKMAQGVM
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 ?
Query133 2.2.26 [Sep-21-2011]
Q969L4123 U7 snRNA-associated Sm-li yes N/A 0.751 0.813 0.376 5e-14
Q8QZX5122 U7 snRNA-associated Sm-li yes N/A 0.751 0.819 0.394 2e-13
Q54F84137 Putative uncharacterized yes N/A 0.511 0.496 0.287 6e-05
>sp|Q969L4|LSM10_HUMAN U7 snRNA-associated Sm-like protein LSm10 OS=Homo sapiens GN=LSM10 PE=1 SV=1 Back     alignment and function desciption
 Score = 76.3 bits (186), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 41/109 (37%), Positives = 64/109 (58%), Gaps = 9/109 (8%)

Query: 3   AVFDSPKEQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR----- 57
           AV  S KE+ +S N+L  L + L G +T VDLR+ES   GR+++VD FMNI +++     
Sbjct: 2   AVSHSVKERTISENSLIILLQGLQGRVTTVDLRDESVAHGRIDNVDAFMNIRLAKVTYTD 61

Query: 58  ----ELTFESLFIQSRNVMFIHIPRHVSIVNKVEDALQSKPRQSSSAGR 102
               ++  + LF+  RNV ++HIP  V+I + +E  LQ   R  +  G+
Sbjct: 62  RWGHQVKLDDLFVTGRNVRYVHIPDDVNITSTIEQQLQIIHRVRNFGGK 110
Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Increases U7 snRNA levels but not histone 3'-end pre-mRNA processing activity, when overexpressed. Required for cell cycle progression from G1 to S phases. Binds specifically to U7 snRNA. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner.
Homo sapiens (taxid: 9606)
>sp|Q8QZX5|LSM10_MOUSE U7 snRNA-associated Sm-like protein LSm10 OS=Mus musculus GN=Lsm10 PE=1 SV=1 Back     alignment and function description
>sp|Q54F84|Y1015_DICDI Putative uncharacterized protein DDB_G0291015 OS=Dictyostelium discoideum GN=DDB_G0291015 PE=4 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 ?
Query133
389613644173 unknown unsecreted protein [Papilio xuth 0.774 0.595 0.437 1e-18
157135921141 hypothetical protein AaeL_AAEL013425 [Ae 0.842 0.794 0.393 3e-14
307186087145 U7 snRNA-associated Sm-like protein LSm1 0.887 0.813 0.338 6e-13
354477407122 PREDICTED: U7 snRNA-associated Sm-like p 0.751 0.819 0.403 1e-12
321468738153 hypothetical protein DAPPUDRAFT_304272 [ 0.864 0.751 0.312 1e-12
348571487123 PREDICTED: U7 snRNA-associated Sm-like p 0.669 0.723 0.408 2e-12
444706872156 U7 snRNA-associated Sm-like protein LSm1 0.669 0.570 0.418 3e-12
351714204123 U7 snRNA-associated Sm-like protein LSm1 0.669 0.723 0.408 3e-12
403293073123 PREDICTED: U7 snRNA-associated Sm-like p 0.751 0.813 0.394 3e-12
149694668123 PREDICTED: u7 snRNA-associated Sm-like p 0.751 0.813 0.394 3e-12
>gi|389613644|dbj|BAM20150.1| unknown unsecreted protein [Papilio xuthus] Back     alignment and taxonomy information
 Score = 97.8 bits (242), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 68/112 (60%), Gaps = 9/112 (8%)

Query: 7   SPKEQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS---------R 57
           +PKE+F  FNTL CL KSL G    VDLRN+S+V G L  VDGFMN+  S          
Sbjct: 47  TPKEKFAFFNTLLCLVKSLQGQYVNVDLRNDSNVCGLLLTVDGFMNLSFSTAVYCDPQGN 106

Query: 58  ELTFESLFIQSRNVMFIHIPRHVSIVNKVEDALQSKPRQSSSAGRTLKQKRA 109
           E  FE++F+Q RNV ++HIP HVSI+N +++ +  + R   +     K ++A
Sbjct: 107 EFFFENIFVQCRNVRYVHIPEHVSIINNIKNEVAREVRNKPTGTAMNKSRKA 158

Source: Papilio xuthus

Species: Papilio xuthus

Genus: Papilio

Family: Papilionidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|157135921|ref|XP_001663620.1| hypothetical protein AaeL_AAEL013425 [Aedes aegypti] gi|403183364|gb|EJY58040.1| AAEL013425-PB [Aedes aegypti] Back     alignment and taxonomy information
>gi|307186087|gb|EFN71819.1| U7 snRNA-associated Sm-like protein LSm10 [Camponotus floridanus] Back     alignment and taxonomy information
>gi|354477407|ref|XP_003500912.1| PREDICTED: U7 snRNA-associated Sm-like protein LSm10-like [Cricetulus griseus] gi|344245005|gb|EGW01109.1| U7 snRNA-associated Sm-like protein LSm10 [Cricetulus griseus] Back     alignment and taxonomy information
>gi|321468738|gb|EFX79721.1| hypothetical protein DAPPUDRAFT_304272 [Daphnia pulex] Back     alignment and taxonomy information
>gi|348571487|ref|XP_003471527.1| PREDICTED: U7 snRNA-associated Sm-like protein LSm10-like [Cavia porcellus] Back     alignment and taxonomy information
>gi|444706872|gb|ELW48189.1| U7 snRNA-associated Sm-like protein LSm10 [Tupaia chinensis] Back     alignment and taxonomy information
>gi|351714204|gb|EHB17123.1| U7 snRNA-associated Sm-like protein LSm10 [Heterocephalus glaber] Back     alignment and taxonomy information
>gi|403293073|ref|XP_003937547.1| PREDICTED: U7 snRNA-associated Sm-like protein LSm10 [Saimiri boliviensis boliviensis] Back     alignment and taxonomy information
>gi|149694668|ref|XP_001499097.1| PREDICTED: u7 snRNA-associated Sm-like protein LSm10-like [Equus caballus] 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 ?
Query133
UNIPROTKB|Q969L4123 LSM10 "U7 snRNA-associated Sm- 0.751 0.813 0.394 1.3e-13
UNIPROTKB|E2R7Q3123 LSM10 "Uncharacterized protein 0.751 0.813 0.396 2.7e-13
RGD|1584914122 Lsm10 "LSM10, U7 small nuclear 0.751 0.819 0.394 4.4e-13
UNIPROTKB|A4IFN1122 LSM10 "Uncharacterized protein 0.661 0.721 0.412 5.6e-13
MGI|MGI:2151045122 Lsm10 "U7 snRNP-specific Sm-li 0.751 0.819 0.394 5.6e-13
UNIPROTKB|E1BY33122 LSM10 "Uncharacterized protein 0.736 0.803 0.376 6.4e-12
FB|FBgn0033554141 Lsm10 "Lsm10" [Drosophila mela 0.909 0.858 0.311 1.3e-11
DICTYBASE|DDB_G0291015137 DDB_G0291015 "putative small n 0.751 0.729 0.275 3e-05
DICTYBASE|DDB_G0281779117 lsm2 "putative U6 small nuclea 0.654 0.743 0.272 0.00013
UNIPROTKB|Q969L4 LSM10 "U7 snRNA-associated Sm-like protein LSm10" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
 Score = 177 (67.4 bits), Expect = 1.3e-13, P = 1.3e-13
 Identities = 43/109 (39%), Positives = 63/109 (57%)

Query:     3 AVFDSPKEQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNI------YMS 56
             AV  S KE+ +S N+L  L + L G +T VDLR+ES   GR+++VD FMNI      Y  
Sbjct:     2 AVSHSVKERTISENSLIILLQGLQGRVTTVDLRDESVAHGRIDNVDAFMNIRLAKVTYTD 61

Query:    57 R---ELTFESLFIQSRNVMFIHIPRHVSIVNKVEDALQSKPRQSSSAGR 102
             R   ++  + LF+  RNV ++HIP  V+I + +E  LQ   R  +  G+
Sbjct:    62 RWGHQVKLDDLFVTGRNVRYVHIPDDVNITSTIEQQLQIIHRVRNFGGK 110
GO:0008380 "RNA splicing" evidence=IEA
GO:0005683 "U7 snRNP" evidence=IDA
GO:0005515 "protein binding" evidence=IPI
GO:0071208 "histone pre-mRNA DCP binding" evidence=ISS
GO:0000084 "S phase of mitotic cell cycle" evidence=IMP
GO:0015030 "Cajal body" evidence=IDA
GO:0005654 "nucleoplasm" evidence=TAS
GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS
GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS
GO:0006397 "mRNA processing" evidence=TAS
GO:0008334 "histone mRNA metabolic process" evidence=TAS
GO:0010467 "gene expression" evidence=TAS
UNIPROTKB|E2R7Q3 LSM10 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
RGD|1584914 Lsm10 "LSM10, U7 small nuclear RNA associated" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|A4IFN1 LSM10 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
MGI|MGI:2151045 Lsm10 "U7 snRNP-specific Sm-like protein LSM10" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|E1BY33 LSM10 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
FB|FBgn0033554 Lsm10 "Lsm10" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0291015 DDB_G0291015 "putative small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0281779 lsm2 "putative U6 small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)] 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) ?
Q8QZX5LSM10_MOUSENo assigned EC number0.39440.75180.8196yesN/A
Q969L4LSM10_HUMANNo assigned EC number0.37610.75180.8130yesN/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 ?
Query133
cd0173378 cd01733, LSm10, Like-Sm protein 10 1e-24
cd0172668 cd01726, LSm6, Like-Sm protein 6 0.001
>gnl|CDD|212480 cd01733, LSm10, Like-Sm protein 10 Back     alignment and domain information 
 Score = 89.5 bits (223), Expect = 1e-24
 Identities = 33/78 (42%), Positives = 53/78 (67%), Gaps = 9/78 (11%)

Query: 9  KEQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS---------REL 59
          +E++ S N+L CL ++L G +T V+LRNE+SV G +++VDGFMNI +S         ++ 
Sbjct: 1  RERYRSENSLVCLLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQH 60

Query: 60 TFESLFIQSRNVMFIHIP 77
           F+  F+Q RN+ ++HIP
Sbjct: 61 HFDEFFVQGRNIRYVHIP 78

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. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-membered ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing. Length = 78
>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 133
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.95
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.94
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.89
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.88
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.86
KOG3172|consensus119 99.8
KOG3428|consensus109 99.78
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.77
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.75
KOG3293|consensus134 99.74
KOG3448|consensus96 99.71
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.69
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.68
KOG3482|consensus79 99.67
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.67
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.64
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.63
KOG1783|consensus77 99.59
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.56
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.52
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.52
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.38
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.37
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.36
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 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 99.22
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.2
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.14
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.12
KOG3460|consensus91 98.68
KOG1780|consensus77 98.37
KOG1774|consensus88 97.87
KOG1775|consensus84 97.84
PF1443877 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1. 97.59
KOG1781|consensus108 97.25
KOG1782|consensus129 96.97
KOG3168|consensus177 96.65
KOG1784|consensus96 95.97
PF1109580 Gemin7: Gem-associated protein 7 (Gemin7); InterPr 95.87
PF1270196 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC 95.59
TIGR0238361 Hfq RNA chaperone Hfq. This model represents the R 94.42
cd0171661 Hfq Hfq, an abundant, ubiquitous RNA-binding prote 94.39
PRK0039579 hfq RNA-binding protein Hfq; Provisional 93.52
KOG3459|consensus114 93.34
PF0223748 BPL_C: Biotin protein ligase C terminal domain; In 91.94
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 91.44
COG192377 Hfq Uncharacterized host factor I protein [General 91.28
PF1084266 DUF2642: Protein of unknown function (DUF2642); In 90.63
PRK14091165 RNA-binding protein Hfq; Provisional 83.67
cd0173674 LSm14_N LSm14 (also known as RAP55) belongs to a f 83.56
PRK14638150 hypothetical protein; Provisional 83.28
PRK14091165 RNA-binding protein Hfq; Provisional 82.74
PRK14639140 hypothetical protein; Provisional 81.98
PF11607101 DUF3247: Protein of unknown function (DUF3247); In 81.59
>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 
Probab=99.95  E-value=6.7e-28  Score=166.54  Aligned_cols=69  Identities=42%  Similarity=0.749  Sum_probs=66.8

Q ss_pred             hhhhcccCcHHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEEEcC
Q psy9158           9 KEQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFIHIP   77 (133)
Q Consensus         9 ~Ek~~~~nsL~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI~lP   77 (133)
                      ||+++.+|||+|||++++|+.|+||||||.+|+|+|.+||+|||++|+|         ..+++++||||++|+|||||
T Consensus         1 ~e~~~~~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP   78 (78)
T cd01733           1 KERTLLENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP   78 (78)
T ss_pred             CccchhhchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence            6999999999999999999999999999999999999999999999999         35789999999999999999

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. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
>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
>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
>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
>KOG3172|consensus Back     alignment and domain information
>KOG3428|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
>KOG3293|consensus 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
>smart00651 Sm snRNP Sm proteins Back     alignment and domain information
>KOG3482|consensus 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
>KOG1783|consensus Back     alignment and domain information
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] 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
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>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
>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
>PTZ00138 small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>KOG3460|consensus Back     alignment and domain information
>KOG1780|consensus Back     alignment and domain information
>KOG1774|consensus Back     alignment and domain information
>KOG1775|consensus Back     alignment and domain information
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1 Back     alignment and domain information
>KOG1781|consensus Back     alignment and domain information
>KOG1782|consensus Back     alignment and domain information
>KOG3168|consensus Back     alignment and domain information
>KOG1784|consensus Back     alignment and domain information
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins Back     alignment and domain information
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A Back     alignment and domain information
>TIGR02383 Hfq RNA chaperone Hfq 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
>PRK00395 hfq RNA-binding protein Hfq; Provisional Back     alignment and domain information
>KOG3459|consensus 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
>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
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only] Back     alignment and domain information
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function Back     alignment and domain information
>PRK14091 RNA-binding protein Hfq; Provisional Back     alignment and domain information
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>PRK14638 hypothetical protein; Provisional Back     alignment and domain information
>PRK14091 RNA-binding protein Hfq; Provisional Back     alignment and domain information
>PRK14639 hypothetical protein; Provisional Back     alignment and domain information
>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query133
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 2e-11
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 8e-11
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 5e-09
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 2e-08
>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe} Length = 105 Back     alignment and structure
 Score = 55.5 bits (134), Expect = 2e-11
 Identities = 20/101 (19%), Positives = 39/101 (38%), Gaps = 12/101 (11%)

Query: 7   SPKEQFLSFNTLACLA--KSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS-------- 56
           S      S + +  L    +  G    V+L+N  + +G LE+ D +MN+ +         
Sbjct: 4   SHHHHHHSQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPD 63

Query: 57  --RELTFESLFIQSRNVMFIHIPRHVSIVNKVEDALQSKPR 95
             +       +I+  N+ ++ I   V      + A Q + R
Sbjct: 64  GDKFFRLPECYIRGNNIKYLRIQDEVLSQVAKQQAQQRENR 104
>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A Length = 119 Back     alignment and structure
>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D Length = 126 Back     alignment and structure
>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 Length = 75 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query133
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 99.89
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.87
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.85
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 99.84
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.76
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.76
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.76
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.75
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.74
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.73
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.72
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.71
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.69
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.69
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.66
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.61
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.54
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.54
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.52
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.49
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.49
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.47
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.45
3pgw_B231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.3
1y96_A86 Gemin6, SIP2, GEM-associated protein 6; SM fold, p 98.22
3ahu_A78 Protein HFQ; SM-like motif, protein-RNA complex, t 95.83
1u1s_A82 HFQ protein; SM-like bacterial protein, riken stru 95.75
1kq1_A77 HFQ, HOST factor for Q beta; hexamer, RNA binding 95.73
1y96_B85 Gemin7, SIP3, GEM-associated protein 7; SM fold, p 95.5
2ylb_A74 Protein HFQ; RNA-binding protein, LSM protein, RNA 95.45
2qtx_A71 Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi 95.39
4a53_A125 EDC3; RNA binding protein; NMR {Schizosaccharomyce 95.37
2y90_A104 Protein HFQ; RNA-binding protein, SM-like, RNA cha 93.72
3sb2_A79 Protein HFQ; SM-like, RNA chaperone, chaperone; 2. 93.71
2vxe_A88 CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA 90.17
2fb7_A95 SM-like protein, LSM-14_N (RAP55); DR.13312, BC055 90.05
2vc8_A84 Enhancer of mRNA-decapping protein 3; P-BODY compo 89.25
2e12_A101 SM-like motif, hypothetical protein XCC3642; novel 83.27
>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D Back     alignment and structure
Probab=99.89  E-value=4.6e-23  Score=152.74  Aligned_cols=75  Identities=16%  Similarity=0.249  Sum_probs=70.3

Q ss_pred             cHHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEEEcCCCCCchhHHH
Q psy9158          17 TLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFIHIPRHVSIVNKVE   87 (133)
Q Consensus        17 sL~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI~lPd~ld~~~~l~   87 (133)
                      ...+||+.+.|++|+||||||.+|+|+|.+||+||||+|+|         ..+++++|||||+|+||++||+++++++|+
T Consensus         5 ~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~IRGnnI~~I~lpd~l~~~~~l~   84 (126)
T 2y9a_D            5 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDMLKNAPMLK   84 (126)
T ss_dssp             CSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCSSCSSSSHHH
T ss_pred             cHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEEEeCCEEEEEEccccccchHHhh
Confidence            45789999999999999999999999999999999999999         467889999999999999999999999999


Q ss_pred             HHHh
Q psy9158          88 DALQ   91 (133)
Q Consensus        88 ~~l~   91 (133)
                      ++-.
T Consensus        85 ~~~~   88 (126)
T 2y9a_D           85 SMKN   88 (126)
T ss_dssp             HHHH
T ss_pred             hhhh
Confidence            8654
>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 Back     alignment and structure
>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe} Back     alignment and structure
>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A Back     alignment and structure
>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
>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
>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
>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
>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
>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B Back     alignment and structure
>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Back     alignment and structure
>3s6n_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
>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
>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
>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B Back     alignment and structure
>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A Back     alignment and structure
>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe} Back     alignment and structure
>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Back     alignment and structure
>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
>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
>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A Back     alignment and structure
>1u1s_A HFQ protein; SM-like bacterial protein, riken structural genomics/proteomics initiative, RSGI, structural genomics, RNA binding protein; 1.60A {Pseudomonas aeruginosa} SCOP: b.38.1.2 PDB: 1u1t_A 3qui_A* 3m4g_A 3inz_A Back     alignment and structure
>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
>1y96_B Gemin7, SIP3, GEM-associated protein 7; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} Back     alignment and structure
>2ylb_A Protein HFQ; RNA-binding protein, LSM protein, RNA chaperone; 1.15A {Salmonella enterica subsp} PDB: 2yht_A 1hk9_A 2ylc_A* 3gib_A* 3rer_A* 3qo3_A* 3res_A* Back     alignment and structure
>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii} 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
>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2 Back     alignment and structure
>2vxe_A CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA decay, LSM proteins, translational repression, transcription; NMR {Drosophila melanogaster} Back     alignment and structure
>2fb7_A SM-like protein, LSM-14_N (RAP55); DR.13312, BC055387, AAH55387, stronGly BENT five-stranded antiparallel beta- sheet, structural genomics, PSI; NMR {Danio rerio} SCOP: b.38.1.5 PDB: 2vxf_A Back     alignment and structure
>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
>2e12_A SM-like motif, hypothetical protein XCC3642; novel SM-like motif, LSM motif, X- RAY crystallography, translation; 1.70A {Xanthomonas campestris PV} Back     alignment and structure

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 133
d1b34a_80 b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s 2e-09
d1d3ba_72 b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s 2e-08
d1m5q1_127 b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch 2e-07
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 1e-05
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 6e-04
d1n9ra_68 b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S 7e-04
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 0.001
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 0.002
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 0.002
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 0.004
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80 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]

 Score = 48.9 bits (117), Expect = 2e-09
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 9/74 (12%)

Query: 18 LACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS---------RELTFESLFIQS 68
          L      L      ++L+N + V G +  VD  MN ++            +  E+L I+ 
Sbjct: 2  LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRG 61

Query: 69 RNVMFIHIPRHVSI 82
           N+ +  +P  + +
Sbjct: 62 NNIRYFILPDSLPL 75
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72 Back     information, alignment and structure
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 127 Back     information, alignment and structure
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} 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
>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
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Length = 71 Back     information, alignment and structure
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Length = 76 Back     information, alignment and structure
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 74 Back     information, alignment and structure
>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 ?
Query133
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.94
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.88
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 99.8
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.78
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.78
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.73
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.71
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.71
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.71
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.68
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.47
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.31
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.28
d1kq1a_60 Pleiotropic translational regulator Hfq {Staphyloc 93.18
d1u1sa166 Pleiotropic translational regulator Hfq {Pseudomon 92.83
d2vxfa180 LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) 90.52
d1biaa247 Biotin repressor/biotin holoenzyme synthetase, C-t 82.44
>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=99.94  E-value=4.1e-27  Score=160.25  Aligned_cols=69  Identities=22%  Similarity=0.362  Sum_probs=66.4

Q ss_pred             HHHHHHhcCCCeEEEEecCCcEEEEEEEEeccccceEEec---------ccccccEEEecCeeEEEEcCCCCCchhHH
Q psy9158          18 LACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR---------ELTFESLFIQSRNVMFIHIPRHVSIVNKV   86 (133)
Q Consensus        18 L~~lL~~l~G~~VtVELKNg~~~~G~L~~vD~~MNl~L~n---------~~~l~~ifIRGsnIryI~lPd~ld~~~~l   86 (133)
                      |.|||++++|+.|+||||||.+|+|+|.+||+|||++|+|         ..+++++||||++|||||+||++|++++|
T Consensus         2 lv~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~~Ir~i~lPd~l~~~~~L   79 (80)
T d1b34a_           2 LVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLL   79 (80)
T ss_dssp             HHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTTCCHHHHT
T ss_pred             HHHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEEEcccEEEcCCEEEEEECCCCccccccc
Confidence            7899999999999999999999999999999999999999         67789999999999999999999999875
>d1d3ba_ b.38.1.1 (A:) D3 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
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Back     information, alignment and structure
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Back     information, alignment and structure
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Back     information, alignment and structure
>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
>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