Psyllid ID: psy1140

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--
MTTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISSSTRSPVPDPQLTDNFILLPQIWGIERRTLSFMRFGYRPSVDVLHLSASALKVESMAFIMGLTLPCVLSHDLFLPPWNS
cEEEEEEEcEEEEEEEEEccccccEEEEccEEEEEEccccEEEEEEEEEEEEcccEEEEEccccccccccccccccHHHHHcccHHHHHHHHHHHHHcccccccHHHHccHHHHHHHHHHHHHcccccEEEEcccccccccc
ccEEEHHHHHHHHHHHHHHHHHHHEEEHccEEEEEEccccccEEccEEEEEEccEEEEEEEEccHHccccccccEcHHHHHHHHHHHHHHHHHHHHHccccccccEEEEcHHHHHHHHHHHHccccccEEEccccccccccc
MTTFTILSLIFFQgtlkgfdqTINIilddshervysptagVEQVVLGLHIirgdnikiptkissstrspvpdpqltdnfillpqiwgierRTLSfmrfgyrpsvDVLHLSASALKVESMAFIMGLtlpcvlshdlflppwns
MTTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIptkissstrspvpdpqltdnfillpQIWGIERRTLSFMRFGYRPSVDVLHLSASALKVESMAFIMGLTLPCVLSHDlflppwns
MTTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISSSTRSPVPDPQLTDNFILLPQIWGIERRTLSFMRFGYRPSVDVLHLSASALKVESMAFIMGLTLPCVLSHDLFLPPWNS
**TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPT**************LTDNFILLPQIWGIERRTLSFMRFGYRPSVDVLHLSASALKVESMAFIMGLTLPCVLSHDLFLPP***
*TTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISSSTRSPVPDPQLTDNFIL**********************VDVLHLSASALKVESMAFIMGLTLPCVLSHDLFLPPW**
MTTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKI********PDPQLTDNFILLPQIWGIERRTLSFMRFGYRPSVDVLHLSASALKVESMAFIMGLTLPCVLSHDLFLPPWNS
MTTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISSSTRSPVPDPQLTDNFILLPQIWGIERRTLSFMRFGYRPSVDVLHLSASALKVESMAFIMGLTLPCVLSHDLFLPPWNS
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooo
SSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MTTFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISSSTRSPVPDPQLTDNFILLPQIWGIERRTLSFMRFGYRPSVDVLHLSASALKVESMAFIMGLTLPCVLSHDLFLPPWNS
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 ?
Query142 2.2.26 [Sep-21-2011]
Q5RCP396 N-alpha-acetyltransferase yes N/A 0.408 0.604 0.637 4e-16
Q6ZWM496 N-alpha-acetyltransferase yes N/A 0.408 0.604 0.637 4e-16
O9577796 N-alpha-acetyltransferase yes N/A 0.408 0.604 0.637 4e-16
Q3ZCE096 N-alpha-acetyltransferase yes N/A 0.408 0.604 0.637 4e-16
Q1ZXD594 N-alpha-acetyltransferase yes N/A 0.359 0.542 0.461 3e-08
O7448394 U6 snRNA-associated Sm-li yes N/A 0.408 0.617 0.379 7e-06
>sp|Q5RCP3|NAA38_PONAB N-alpha-acetyltransferase 38, NatC auxiliary subunit OS=Pongo abelii GN=NAA38 PE=3 SV=3 Back     alignment and function desciption
 Score = 83.2 bits (204), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 37/58 (63%), Positives = 47/58 (81%)

Query: 14 GTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISSSTRSPVP 71
          GTLKGFDQTIN+ILD+SHERV+S + GVEQVVLGL+I+RGDN+ +  +I   T S + 
Sbjct: 25 GTLKGFDQTINLILDESHERVFSSSQGVEQVVLGLYIVRGDNVAVIGEIDEETDSALD 82
Binds specifically to the 3'-terminal U-tract of U6 snRNA.
Pongo abelii (taxid: 9601)
>sp|Q6ZWM4|NAA38_MOUSE N-alpha-acetyltransferase 38, NatC auxiliary subunit OS=Mus musculus GN=Naa38 PE=3 SV=3 Back     alignment and function description
>sp|O95777|NAA38_HUMAN N-alpha-acetyltransferase 38, NatC auxiliary subunit OS=Homo sapiens GN=NAA38 PE=1 SV=3 Back     alignment and function description
>sp|Q3ZCE0|NAA38_BOVIN N-alpha-acetyltransferase 38, NatC auxiliary subunit OS=Bos taurus GN=NAA38 PE=3 SV=3 Back     alignment and function description
>sp|Q1ZXD5|NAA38_DICDI N-alpha-acetyltransferase 38, NatC auxiliary subunit OS=Dictyostelium discoideum GN=lsm8 PE=3 SV=1 Back     alignment and function description
>sp|O74483|LSM8_SCHPO U6 snRNA-associated Sm-like protein LSm8 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=lsm8 PE=3 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 ?
Query142
170041123123 conserved hypothetical protein [Culex qu 0.626 0.723 0.486 3e-17
3124053395 AGAP011837-PA [Anopheles gambiae str. PE 0.415 0.621 0.711 3e-16
17006088095 LSM8 protein [Culex quinquefasciatus] gi 0.415 0.621 0.711 3e-16
19371626196 PREDICTED: n-alpha-acetyltransferase 38, 0.415 0.614 0.677 3e-16
30720383396 U6 snRNA-associated Sm-like protein LSm8 0.330 0.489 0.893 9e-16
322784412102 hypothetical protein SINV_13023 [Solenop 0.330 0.460 0.872 1e-15
6653378396 PREDICTED: n-alpha-acetyltransferase 38, 0.330 0.489 0.872 1e-15
33202490996 U6 snRNA-associated Sm-like protein LSm8 0.359 0.531 0.803 1e-15
157104024162 small nuclear ribonucleoprotein, core, p 0.415 0.364 0.694 2e-15
30717407385 U6 snRNA-associated Sm-like protein LSm8 0.330 0.552 0.872 2e-15
>gi|170041123|ref|XP_001848324.1| conserved hypothetical protein [Culex quinquefasciatus] gi|167864689|gb|EDS28072.1| conserved hypothetical protein [Culex quinquefasciatus] Back     alignment and taxonomy information
 Score = 93.2 bits (230), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 55/113 (48%), Positives = 69/113 (61%), Gaps = 24/113 (21%)

Query: 12  FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISSSTRSPV- 70
           F GTLKGFDQT+NIILD+SHERVYS TAG+EQVVLGLHIIRGDN+ I  ++  S  S + 
Sbjct: 22  FVGTLKGFDQTVNIILDESHERVYSMTAGIEQVVLGLHIIRGDNVAIIGQLDESVDSKLD 81

Query: 71  ----------PDPQLTDNFILLPQIWGIERRTLSFMRFGYRPSVD-VLHLSAS 112
                     P+ QLT        + G+ +R     R G +  +D V HL+A 
Sbjct: 82  FSSIRGMPLEPNLQLT--------LGGLVQRN----RLGLQALIDHVQHLAAE 122

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|31240533|ref|XP_320680.1| AGAP011837-PA [Anopheles gambiae str. PEST] gi|21288006|gb|EAA00327.1| AGAP011837-PA [Anopheles gambiae str. PEST] Back     alignment and taxonomy information
>gi|170060880|ref|XP_001865997.1| LSM8 protein [Culex quinquefasciatus] gi|167879234|gb|EDS42617.1| LSM8 protein [Culex quinquefasciatus] Back     alignment and taxonomy information
>gi|193716261|ref|XP_001944890.1| PREDICTED: n-alpha-acetyltransferase 38, NatC auxiliary subunit-like [Acyrthosiphon pisum] Back     alignment and taxonomy information
>gi|307203833|gb|EFN82769.1| U6 snRNA-associated Sm-like protein LSm8 [Harpegnathos saltator] Back     alignment and taxonomy information
>gi|322784412|gb|EFZ11383.1| hypothetical protein SINV_13023 [Solenopsis invicta] Back     alignment and taxonomy information
>gi|66533783|ref|XP_624537.1| PREDICTED: n-alpha-acetyltransferase 38, NatC auxiliary subunit-like [Apis mellifera] gi|340726388|ref|XP_003401541.1| PREDICTED: n-alpha-acetyltransferase 38, NatC auxiliary subunit-like [Bombus terrestris] gi|350423978|ref|XP_003493651.1| PREDICTED: N-alpha-acetyltransferase 38, NatC auxiliary subunit-like [Bombus impatiens] gi|380024341|ref|XP_003695959.1| PREDICTED: N-alpha-acetyltransferase 38, NatC auxiliary subunit-like [Apis florea] gi|383847985|ref|XP_003699633.1| PREDICTED: N-alpha-acetyltransferase 38, NatC auxiliary subunit-like [Megachile rotundata] Back     alignment and taxonomy information
>gi|332024909|gb|EGI65097.1| U6 snRNA-associated Sm-like protein LSm8 [Acromyrmex echinatior] Back     alignment and taxonomy information
>gi|157104024|ref|XP_001648223.1| small nuclear ribonucleoprotein, core, putative [Aedes aegypti] gi|108880439|gb|EAT44664.1| AAEL003985-PA [Aedes aegypti] Back     alignment and taxonomy information
>gi|307174073|gb|EFN64760.1| U6 snRNA-associated Sm-like protein LSm8 [Camponotus floridanus] 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 ?
Query142
FB|FBgn003527195 CG2021 [Drosophila melanogaste 0.330 0.494 0.765 9.8e-16
UNIPROTKB|Q3ZCE096 NAA38 "N-alpha-acetyltransfera 0.387 0.572 0.672 2e-15
UNIPROTKB|O9577796 NAA38 "N-alpha-acetyltransfera 0.387 0.572 0.672 2e-15
MGI|MGI:192377296 Naa38 "N(alpha)-acetyltransfer 0.387 0.572 0.672 2e-15
DICTYBASE|DDB_G028847994 lsm8 "putative U6 small nuclea 0.309 0.468 0.533 1.4e-09
GENEDB_PFALCIPARUM|MAL8P1.995 MAL8P1.9 "u6 snRNA-associated 0.316 0.473 0.531 1.2e-08
UNIPROTKB|C0H4Y995 MAL8P1.9 "U6 snRNA-associated 0.316 0.473 0.531 1.2e-08
POMBASE|SPCC1840.1094 lsm8 "U6 snRNP-associated prot 0.401 0.606 0.385 1.4e-07
POMBASE|SPCC285.12113 lsm7 "U6 snRNP-associated prot 0.408 0.513 0.360 3.9e-05
UNIPROTKB|E1BHK892 SNRPE "Small nuclear ribonucle 0.345 0.532 0.365 0.0001
FB|FBgn0035271 CG2021 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 197 (74.4 bits), Expect = 9.8e-16, P = 9.8e-16
 Identities = 36/47 (76%), Positives = 43/47 (91%)

Query:    12 FQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKI 58
             F GTLKGFDQTINII+D+ HERV+S T+G+EQ+VLGLHIIRGDNI +
Sbjct:    22 FIGTLKGFDQTINIIIDECHERVFSTTSGIEQIVLGLHIIRGDNIAV 68
GO:0005688 "U6 snRNP" evidence=ISS;NAS
GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;ISS
GO:0030532 "small nuclear ribonucleoprotein complex" evidence=ISS
GO:0005681 "spliceosomal complex" evidence=ISS
GO:0071011 "precatalytic spliceosome" evidence=IDA
UNIPROTKB|Q3ZCE0 NAA38 "N-alpha-acetyltransferase 38, NatC auxiliary subunit" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|O95777 NAA38 "N-alpha-acetyltransferase 38, NatC auxiliary subunit" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:1923772 Naa38 "N(alpha)-acetyltransferase 38, NatC auxiliary subunit" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0288479 lsm8 "putative U6 small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
GENEDB_PFALCIPARUM|MAL8P1.9 MAL8P1.9 "u6 snRNA-associated sm-like protein, putative" [Plasmodium falciparum (taxid:5833)] Back     alignment and assigned GO terms
UNIPROTKB|C0H4Y9 MAL8P1.9 "U6 snRNA-associated Sm-like protein, putative" [Plasmodium falciparum 3D7 (taxid:36329)] Back     alignment and assigned GO terms
POMBASE|SPCC1840.10 lsm8 "U6 snRNP-associated protein Lsm8 (predicted)" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
POMBASE|SPCC285.12 lsm7 "U6 snRNP-associated protein Lsm7 (predicted)" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
UNIPROTKB|E1BHK8 SNRPE "Small nuclear ribonucleoprotein E" [Bos taurus (taxid:9913)] 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) ?
O95777NAA38_HUMANNo assigned EC number0.63790.40840.6041yesN/A
Q6ZWM4NAA38_MOUSENo assigned EC number0.63790.40840.6041yesN/A
Q3ZCE0NAA38_BOVINNo assigned EC number0.63790.40840.6041yesN/A
Q5RCP3NAA38_PONABNo assigned EC number0.63790.40840.6041yesN/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 ?
Query142
cd0172791 cd01727, LSm8, Like-Sm protein 8 5e-26
pfam0142366 pfam01423, LSM, LSM domain 6e-10
smart0065167 smart00651, Sm, snRNP Sm proteins 1e-09
cd0060063 cd00600, Sm_like, Sm and related proteins 8e-09
COG195879 COG1958, LSM1, Small nuclear ribonucleoprotein (sn 7e-08
cd0173169 cd01731, archaeal_Sm1, archaeal Sm protein 1 4e-07
cd0172874 cd01728, LSm1, Like-Sm protein 1 3e-06
cd0171780 cd01717, Sm_B, Sm protein B 2e-05
cd0171970 cd01719, Sm_G, Sm protein G 6e-05
cd0171879 cd01718, Sm_E, Sm protein E 1e-04
PRK0073772 PRK00737, PRK00737, small nuclear ribonucleoprotei 3e-04
cd0172989 cd01729, LSm7, Like-Sm protein 7 4e-04
cd0172269 cd01722, Sm_F, Sm protein F 0.002
cd0173276 cd01732, LSm5, Like-Sm protein 5 0.002
cd1167869 cd11678, archaeal_LSm, archaeal Like-Sm protein 0.003
PTZ0013889 PTZ00138, PTZ00138, small nuclear ribonucleoprotei 0.004
>gnl|CDD|212474 cd01727, LSm8, Like-Sm protein 8 Back     alignment and domain information 
 Score = 93.4 bits (233), Expect = 5e-26
 Identities = 29/46 (63%), Positives = 36/46 (78%)

Query: 11 FFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNI 56
             GTLKGFDQT N+IL + HERVYS   GVE+V LGL+++RGDN+
Sbjct: 21 VIVGTLKGFDQTTNLILSNCHERVYSSDEGVEEVPLGLYLLRGDNV 66

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. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. 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 = 91
>gnl|CDD|201787 pfam01423, LSM, LSM domain Back     alignment and domain information
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins Back     alignment and domain information
>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins Back     alignment and domain information
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] Back     alignment and domain information
>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1 Back     alignment and domain information
>gnl|CDD|212475 cd01728, LSm1, Like-Sm protein 1 Back     alignment and domain information
>gnl|CDD|212464 cd01717, Sm_B, Sm protein B Back     alignment and domain information
>gnl|CDD|212466 cd01719, Sm_G, Sm protein G Back     alignment and domain information
>gnl|CDD|212465 cd01718, Sm_E, Sm protein E Back     alignment and domain information
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>gnl|CDD|212476 cd01729, LSm7, Like-Sm protein 7 Back     alignment and domain information
>gnl|CDD|212469 cd01722, Sm_F, Sm protein F Back     alignment and domain information
>gnl|CDD|212479 cd01732, LSm5, Like-Sm protein 5 Back     alignment and domain information
>gnl|CDD|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein Back     alignment and domain information
>gnl|CDD|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 142
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.82
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.8
KOG1782|consensus129 99.78
cd0172874 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins 99.78
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.76
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.76
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.76
cd0171779 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins 99.72
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.72
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 99.72
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.71
KOG1784|consensus96 99.7
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.68
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.68
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.65
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.65
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.64
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.61
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.6
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.59
KOG1780|consensus77 99.56
KOG1781|consensus108 99.55
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.53
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.44
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.42
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.39
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.32
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.31
KOG3482|consensus79 99.22
KOG3168|consensus177 99.22
KOG3460|consensus91 99.21
KOG1775|consensus84 99.12
KOG1774|consensus88 99.05
KOG1783|consensus77 98.77
KOG3448|consensus96 97.59
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 97.36
KOG3293|consensus134 97.11
KOG3428|consensus109 97.04
KOG3172|consensus119 96.93
KOG3459|consensus114 96.74
PF1443877 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1. 94.18
cd0171661 Hfq Hfq, an abundant, ubiquitous RNA-binding prote 88.53
TIGR0238361 Hfq RNA chaperone Hfq. This model represents the R 87.63
PRK0039579 hfq RNA-binding protein Hfq; Provisional 86.0
PF0223748 BPL_C: Biotin protein ligase C terminal domain; In 82.5
>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 
Probab=99.82  E-value=8.2e-20  Score=126.01  Aligned_cols=62  Identities=60%  Similarity=0.860  Sum_probs=55.7

Q ss_pred             EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCCCeeeEEeceEEEecCcEEEeeeCCC
Q psy1140           3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTAGVEQVVLGLHIIRGDNIKIPTKISS   64 (142)
Q Consensus         3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~~~~~r~LGlvlIRGdNIVlIg~vDe   64 (142)
                      .|++++||.++|+|+|||+|||+||++|+|++..++++..++.+|.+++||+||++|+++|+
T Consensus        13 ~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~   74 (74)
T cd01727          13 SVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE   74 (74)
T ss_pred             EEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence            57899999999999999999999999999997655445568899999999999999999885

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. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
>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
>KOG1782|consensus 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
>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
>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
>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
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences Back     alignment and domain information
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>PRK00737 small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>KOG1784|consensus 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
>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
>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
>PTZ00138 small nuclear ribonucleoprotein; Provisional Back     alignment and domain information
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>smart00651 Sm snRNP Sm proteins 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
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] Back     alignment and domain information
>KOG1780|consensus Back     alignment and domain information
>KOG1781|consensus Back     alignment and domain information
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>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
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>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
>KOG3482|consensus Back     alignment and domain information
>KOG3168|consensus Back     alignment and domain information
>KOG3460|consensus Back     alignment and domain information
>KOG1775|consensus Back     alignment and domain information
>KOG1774|consensus Back     alignment and domain information
>KOG1783|consensus Back     alignment and domain information
>KOG3448|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
>KOG3293|consensus Back     alignment and domain information
>KOG3428|consensus Back     alignment and domain information
>KOG3172|consensus Back     alignment and domain information
>KOG3459|consensus Back     alignment and domain information
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1 Back     alignment and domain information
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others Back     alignment and domain information
>TIGR02383 Hfq RNA chaperone Hfq Back     alignment and domain information
>PRK00395 hfq RNA-binding protein Hfq; Provisional Back     alignment and domain information
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown Back     alignment and domain information

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 ?
Query142
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 6e-13
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 2e-12
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 1e-11
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 8e-11
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 2e-10
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 2e-09
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 4e-08
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 1e-07
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 1e-07
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 2e-07
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 8e-07
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 1e-06
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 3e-06
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 6e-06
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 6e-06
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 9e-06
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 1e-05
>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae} Length = 96 Back     alignment and structure
 Score = 59.7 bits (145), Expect = 6e-13
 Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 3/48 (6%)

Query: 12 FQGTLKGFDQTINIILDDSHERVYSP---TAGVEQVVLGLHIIRGDNI 56
            GTL+ FD   NI+L D+ E +Y          +    +  IRGD +
Sbjct: 33 LVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTV 80
>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 Length = 76 Back     alignment and structure
>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C Length = 113 Back     alignment and structure
>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A Length = 91 Back     alignment and structure
>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Length = 81 Back     alignment and structure
>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Length = 81 Back     alignment and structure
>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A* Length = 75 Back     alignment and structure
>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A Length = 83 Back     alignment and structure
>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A* Length = 77 Back     alignment and structure
>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Length = 77 Back     alignment and structure
>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F Length = 86 Back     alignment and structure
>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B Length = 75 Back     alignment and structure
>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe} Length = 93 Back     alignment and structure
>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 Length = 92 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 Length = 94 Back     alignment and structure
>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Length = 93 Back     alignment and structure
>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Length = 121 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query142
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.82
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.81
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.76
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.75
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.75
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.74
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.74
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.74
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.73
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.73
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.73
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.72
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.72
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.7
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.7
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.69
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.69
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.68
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.65
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.63
3pgw_B231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.62
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 99.62
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.54
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 99.5
1y96_A86 Gemin6, SIP2, GEM-associated protein 6; SM fold, p 96.29
3ahu_A78 Protein HFQ; SM-like motif, protein-RNA complex, t 88.77
2qtx_A71 Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi 88.49
2ylb_A74 Protein HFQ; RNA-binding protein, LSM protein, RNA 86.85
1u1s_A82 HFQ protein; SM-like bacterial protein, riken stru 86.53
1kq1_A77 HFQ, HOST factor for Q beta; hexamer, RNA binding 83.28
3sb2_A79 Protein HFQ; SM-like, RNA chaperone, chaperone; 2. 82.5
>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
Probab=99.82  E-value=2.4e-20  Score=137.74  Aligned_cols=72  Identities=32%  Similarity=0.457  Sum_probs=52.7

Q ss_pred             EEEEcCCeEEEEEEEEecceecEEecceEEEEecCCC---CeeeEEeceEEEecCcEEEeeeCCCCCCCCCCCcc
Q psy1140           3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPTA---GVEQVVLGLHIIRGDNIKIPTKISSSTRSPVPDPQ   74 (142)
Q Consensus         3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~~---~~~~r~LGlvlIRGdNIVlIg~vDee~e~~v~~~~   74 (142)
                      .|.+++||+|+|+|+|||+||||||+||+|++..+++   ...++.+|+++|||+||++|+++|.+++..+||.+
T Consensus        37 ~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~~ee~~~p~~~  111 (113)
T 4emk_C           37 QATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPMDGSEEIPNPFVQ  111 (113)
T ss_dssp             EEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEECC-----------
T ss_pred             EEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEecCccccccCcccc
Confidence            6899999999999999999999999999998754321   24689999999999999999999999998888754
>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
>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
>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
>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F Back     alignment and structure
>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A* Back     alignment and structure
>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
>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G Back     alignment and structure
>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A Back     alignment and structure
>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like P; OB-like fold, B-sheet toroid, 14-MER, cadmium-binding site, translation; 2.00A {Pyrobaculum aerophilum} SCOP: b.38.1.1 Back     alignment and structure
>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D Back     alignment and structure
>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} Back     alignment and structure
>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A Back     alignment and structure
>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii} Back     alignment and structure
>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

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 142
d1d3bb_81 b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa 4e-10
d1n9ra_68 b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S 9e-09
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 2e-08
d2fwka192 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr 2e-08
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 2e-08
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 4e-08
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 5e-08
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 6e-08
d1b34b_93 b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s 6e-08
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 5e-07
d1d3ba_72 b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s 0.002
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 81 Back     information, alignment and structure

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.0 bits (122), Expect = 4e-10
 Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 6/51 (11%)

Query: 12 FQGTLKGFDQTINIILDDSHERV------YSPTAGVEQVVLGLHIIRGDNI 56
          F GT K FD+ +N+IL D  E               E+ VLGL ++RG+N+
Sbjct: 21 FIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENL 71
>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
>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
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Length = 76 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
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 74 Back     information, alignment and structure
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Length = 72 Back     information, alignment and structure
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93 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
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72 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 ?
Query142
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.73
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.71
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.71
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.7
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.7
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.7
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.68
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.68
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.67
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.66
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.51
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.35
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 99.22
d1kq1a_60 Pleiotropic translational regulator Hfq {Staphyloc 85.28
d1u1sa166 Pleiotropic translational regulator Hfq {Pseudomon 81.7
>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=3.7e-18  Score=116.85  Aligned_cols=59  Identities=34%  Similarity=0.439  Sum_probs=51.0

Q ss_pred             EEEEcCCeEEEEEEEEecceecEEecceEEEEecCC------CCeeeEEeceEEEecCcEEEeee
Q psy1140           3 TFTILSLIFFQGTLKGFDQTINIILDDSHERVYSPT------AGVEQVVLGLHIIRGDNIKIPTK   61 (142)
Q Consensus         3 ~~~l~sGR~ivG~L~gFDqfmNLVL~davEri~~~~------~~~~~r~LGlvlIRGdNIVlIg~   61 (142)
                      .|++++||.|+|+|+|||+||||||++|+|++....      ....+|.+|+++|||+||++|+.
T Consensus        12 ~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~   76 (81)
T d1d3bb_          12 RCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTV   76 (81)
T ss_dssp             EEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEE
T ss_pred             EEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEc
Confidence            588999999999999999999999999999864321      12457899999999999999975
>d1b34b_ b.38.1.1 (B:) D2 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
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Back     information, alignment and structure
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Back     information, alignment and structure
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Back     information, alignment and structure
>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} Back     information, alignment and structure
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Back     information, alignment and structure
>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Back     information, alignment and structure
>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