Citrus Sinensis ID: 033666

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----
MEQKVETTETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVDCSIDEQLSLLKVDQ
cccccccccccccccccccccccHHHHHHHHHcccEEEEEEEcccEEEEEEEEEcccccEEEEccEEEEEcccccccccccEEEEEEEEccccEEEEEEcccccHHcccccccc
ccHHHcccccccccccccccccccHHHHHHHHHHccEEEEEEcccEEEEEEEEEcccccEEEEcHHHHHcccccccccccccEEEEEEEccccEEEEEEEccHHHHHHHHcccc
MEQKVETTETLVEssagsdtkgsnHISRVRKLLCRRMLVgikdgrfflgsfhcidkqgniilqdaveyrstrrtspspmeqrclgiilipsscrtschvdcsiDEQLSLLKVDQ
meqkvettetlvessagsdtkgsnhisrVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRStrrtspspmeqrCLGIILIPSSCRTSCHVDCSIDEQLSLLKVDQ
MEQKVETTETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVDCSIDEQLSLLKVDQ
*************************ISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYR************RCLGIILIPSSCRTSCHVDCSIDEQLSL*****
*******************************LLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVE****************LGIILIPSSCRTSCHV***************
*************************ISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEY***********EQRCLGIILIPSSCRTSCHVDCSIDEQLSLLKVDQ
***********************NHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRT****MEQRCLGIILIPSSCRTSCHVDCSIDEQLSLLKV**
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MEQKVETTETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVDCSIDEQLSLLKVDQ
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 ?
Query114 2.2.26 [Sep-21-2011]
Q55A45 274 Small nuclear ribonucleop yes no 0.728 0.302 0.345 1e-05
Q6GQ67113 LSM domain-containing pro N/A no 0.754 0.761 0.318 0.0005
A2BIG9109 LSM domain-containing pro yes no 0.622 0.651 0.364 0.0008
A4IGZ4113 LSM domain-containing pro yes no 0.631 0.637 0.328 0.0008
>sp|Q55A45|RSMB_DICDI Small nuclear ribonucleoprotein-associated protein B OS=Dictyostelium discoideum GN=snrpb PE=3 SV=1 Back     alignment and function desciption
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 44/84 (52%), Gaps = 1/84 (1%)

Query: 27  SRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQ-RCLG 85
           S++ + +  RM V I+DGR  +G F   DK  N+++ DA E+R  R+      E+ R LG
Sbjct: 8   SKMLQYINYRMRVTIQDGRVIVGRFLAFDKHMNVVICDAEEFRRIRQKGKEDREEKRTLG 67

Query: 86  IILIPSSCRTSCHVDCSIDEQLSL 109
           +ILI      S  V+    E+  L
Sbjct: 68  MILIRGETVVSMSVEAPPPEEAKL 91
May have a functional role in the pre-mRNA splicing or in snRNP structure.
Dictyostelium discoideum (taxid: 44689)
>sp|Q6GQ67|LMD1A_XENLA LSM domain-containing protein 1-A OS=Xenopus laevis GN=lsmd1-a PE=3 SV=1 Back     alignment and function description
>sp|A2BIG9|LSMD1_DANRE LSM domain-containing protein 1 OS=Danio rerio GN=lsmd1 PE=2 SV=1 Back     alignment and function description
>sp|A4IGZ4|LSMD1_XENTR LSM domain-containing protein 1 OS=Xenopus tropicalis GN=lsmd1 PE=3 SV=2 Back     alignment and function description

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 ?
Query114
225429803116 PREDICTED: uncharacterized protein LOC10 0.982 0.965 0.75 9e-43
224136910109 predicted protein [Populus trichocarpa] 0.947 0.990 0.741 2e-41
22328770112 Small nuclear ribonucleoprotein family p 0.973 0.991 0.747 9e-41
297800232112 hypothetical protein ARALYDRAFT_914851 [ 0.973 0.991 0.747 1e-40
255557237118 conserved hypothetical protein [Ricinus 0.780 0.754 0.865 5e-40
357447241113 Small nuclear ribonucleoprotein-associat 0.964 0.973 0.714 1e-39
356549110107 PREDICTED: uncharacterized protein LOC10 0.842 0.897 0.786 2e-39
449439179112 PREDICTED: uncharacterized protein LOC10 0.982 1.0 0.705 3e-39
388502276111 unknown [Lotus japonicus] 0.719 0.738 0.890 2e-36
3856655078 At4g18372 [Arabidopsis thaliana] gi|4082 0.684 1.0 0.858 4e-33
>gi|225429803|ref|XP_002282858.1| PREDICTED: uncharacterized protein LOC100262900 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  177 bits (448), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 84/112 (75%), Positives = 95/112 (84%)

Query: 1   MEQKVETTETLVESSAGSDTKGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNI 60
           ME   E +   VESS GS+  GSN +++VR LL RRMLVG+ DGRFFLGSFHC+DKQGNI
Sbjct: 3   MEHDAEKSFIHVESSEGSNPNGSNPVTKVRMLLFRRMLVGVSDGRFFLGSFHCMDKQGNI 62

Query: 61  ILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVDCSIDEQLSLLKV 112
           ILQD VEYRSTRR+SPSPMEQRCLG+ILIP SCRTSCHVDCSI+EQLSLL +
Sbjct: 63  ILQDTVEYRSTRRSSPSPMEQRCLGLILIPFSCRTSCHVDCSIEEQLSLLSL 114

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224136910|ref|XP_002322446.1| predicted protein [Populus trichocarpa] gi|222869442|gb|EEF06573.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|22328770|ref|NP_680719.1| Small nuclear ribonucleoprotein family protein [Arabidopsis thaliana] gi|332658634|gb|AEE84034.1| Small nuclear ribonucleoprotein family protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297800232|ref|XP_002868000.1| hypothetical protein ARALYDRAFT_914851 [Arabidopsis lyrata subsp. lyrata] gi|297313836|gb|EFH44259.1| hypothetical protein ARALYDRAFT_914851 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|255557237|ref|XP_002519649.1| conserved hypothetical protein [Ricinus communis] gi|223541066|gb|EEF42622.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|357447241|ref|XP_003593896.1| Small nuclear ribonucleoprotein-associated protein B [Medicago truncatula] gi|357447245|ref|XP_003593898.1| Small nuclear ribonucleoprotein-associated protein B [Medicago truncatula] gi|355482944|gb|AES64147.1| Small nuclear ribonucleoprotein-associated protein B [Medicago truncatula] gi|355482946|gb|AES64149.1| Small nuclear ribonucleoprotein-associated protein B [Medicago truncatula] gi|388515765|gb|AFK45944.1| unknown [Medicago truncatula] Back     alignment and taxonomy information
>gi|356549110|ref|XP_003542940.1| PREDICTED: uncharacterized protein LOC100792908 [Glycine max] Back     alignment and taxonomy information
>gi|449439179|ref|XP_004137364.1| PREDICTED: uncharacterized protein LOC101206200 [Cucumis sativus] gi|449523864|ref|XP_004168943.1| PREDICTED: uncharacterized protein LOC101229488 [Cucumis sativus] Back     alignment and taxonomy information
>gi|388502276|gb|AFK39204.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|38566550|gb|AAR24165.1| At4g18372 [Arabidopsis thaliana] gi|40823882|gb|AAR92310.1| At4g18372 [Arabidopsis thaliana] 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 ?
Query114
TAIR|locus:504955489112 AT4G18372 "AT4G18372" [Arabido 0.973 0.991 0.747 4.2e-40
DICTYBASE|DDB_G0272320 274 snrpb "putative small nuclear 0.728 0.302 0.345 2.2e-06
GENEDB_PFALCIPARUM|PF14_0146 201 PF14_0146 "ribonucleoprotein, 0.578 0.328 0.405 9.6e-06
UNIPROTKB|Q8ILU8 201 PF14_0146 "Ribonucleoprotein, 0.578 0.328 0.405 9.6e-06
FB|FBgn0051950121 CG31950 [Drosophila melanogast 0.666 0.628 0.337 1.5e-05
UNIPROTKB|J3QLE5169 SNRPN "Small nuclear ribonucle 0.473 0.319 0.385 1.9e-05
UNIPROTKB|B3KVR1 244 SNRPN "Small nuclear ribonucle 0.614 0.286 0.346 2.8e-05
ZFIN|ZDB-GENE-040426-1819 239 snrpb "small nuclear ribonucle 0.473 0.225 0.403 3.4e-05
WB|WBGene00004915160 snr-2 [Caenorhabditis elegans 0.657 0.468 0.320 3.9e-05
UNIPROTKB|Q9PV94 240 SNRPB "Small nuclear ribonucle 0.473 0.225 0.403 4.5e-05
TAIR|locus:504955489 AT4G18372 "AT4G18372" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 427 (155.4 bits), Expect = 4.2e-40, P = 4.2e-40
 Identities = 86/115 (74%), Positives = 98/115 (85%)

Query:     1 MEQKVETTETLVES-SAGSDTKGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGN 59
             MEQ  E + T+V S S GSD    + ISR+RKLL R+MLVGIKDGRFFLG+FHCIDKQGN
Sbjct:     1 MEQAAERSSTIVASTSEGSDF---DPISRLRKLLFRQMLVGIKDGRFFLGNFHCIDKQGN 57

Query:    60 IILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVDCSIDEQLSLLKVDQ 114
             IILQD VEYRS RR+SPSP EQRCLG+ILIPSSCRTSCHVDCSIDEQLSL+++ +
Sbjct:    58 IILQDTVEYRSIRRSSPSPTEQRCLGMILIPSSCRTSCHVDCSIDEQLSLIQLKE 112
GO:0003674 "molecular_function" evidence=ND
GO:0005634 "nucleus" evidence=ISM
GO:0008150 "biological_process" evidence=ND
DICTYBASE|DDB_G0272320 snrpb "putative small nuclear ribonucleoparticle-associated protein" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
GENEDB_PFALCIPARUM|PF14_0146 PF14_0146 "ribonucleoprotein, putative" [Plasmodium falciparum (taxid:5833)] Back     alignment and assigned GO terms
UNIPROTKB|Q8ILU8 PF14_0146 "Ribonucleoprotein, putative" [Plasmodium falciparum 3D7 (taxid:36329)] Back     alignment and assigned GO terms
FB|FBgn0051950 CG31950 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|J3QLE5 SNRPN "Small nuclear ribonucleoprotein-associated protein N" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|B3KVR1 SNRPN "Small nuclear ribonucleoprotein-associated protein" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-040426-1819 snrpb "small nuclear ribonucleoprotein polypeptides B and B1" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
WB|WBGene00004915 snr-2 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
UNIPROTKB|Q9PV94 SNRPB "Small nuclear ribonucleoprotein-associated protein B'" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query114
cd0616873 cd06168, LSMD1, LSM domain containing 1 5e-24
cd0171780 cd01717, Sm_B, Sm protein B 6e-08
cd0172874 cd01728, LSm1, Like-Sm protein 1 7e-06
cd0060063 cd00600, Sm_like, Sm and related proteins 2e-05
COG195879 COG1958, LSM1, Small nuclear ribonucleoprotein (sn 3e-05
smart0065167 smart00651, Sm, snRNP Sm proteins 4e-05
cd0172791 cd01727, LSm8, Like-Sm protein 8 5e-05
pfam0142366 pfam01423, LSM, LSM domain 0.002
>gnl|CDD|212486 cd06168, LSMD1, LSM domain containing 1 Back     alignment and domain information 
 Score = 86.8 bits (216), Expect = 5e-24
 Identities = 31/75 (41%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 26  ISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLG 85
             ++RKLL R + V + DGR  +G+F C DK GNIIL +A EYR          E R LG
Sbjct: 1   RLKLRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSD--LGAEEPRSLG 58

Query: 86  IILIPSSCRTSCHVD 100
           ++++P     S  VD
Sbjct: 59  LVMVPGKHIVSIEVD 73

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSMD1 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes, forming heptameric and hexameric ring structures similar to those found in eukaryotes. Length = 73
>gnl|CDD|212464 cd01717, Sm_B, Sm protein B Back     alignment and domain information
>gnl|CDD|212475 cd01728, LSm1, Like-Sm protein 1 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|197820 smart00651, Sm, snRNP Sm proteins Back     alignment and domain information
>gnl|CDD|212474 cd01727, LSm8, Like-Sm protein 8 Back     alignment and domain information
>gnl|CDD|201787 pfam01423, LSM, LSM domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 114
cd0616875 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins 99.92
cd0171779 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins 99.91
cd0172981 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins 99.88
cd0173082 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins 99.87
cd0171972 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins 99.86
cd0172774 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins 99.86
cd0172874 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins 99.86
cd0173276 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins 99.86
cd0173168 archaeal_Sm1 The archaeal sm1 proteins: The Sm pro 99.85
PRK0073772 small nuclear ribonucleoprotein; Provisional 99.84
cd0172087 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins 99.84
cd0172667 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins 99.82
cd0172268 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins 99.82
PF0142367 LSM: LSM domain ; InterPro: IPR001163 This family 99.81
smart0065167 Sm snRNP Sm proteins. small nuclear ribonucleoprot 99.8
cd0171879 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins 99.79
cd0060063 Sm_like The eukaryotic Sm and Sm-like (LSm) protei 99.77
COG195879 LSM1 Small nuclear ribonucleoprotein (snRNP) homol 99.76
KOG178077 consensus Small Nuclear ribonucleoprotein G [RNA p 99.73
KOG3168177 consensus U1 snRNP component [Transcription] 99.73
PTZ0013889 small nuclear ribonucleoprotein; Provisional 99.71
cd0172376 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins 99.7
cd0172170 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins 99.7
KOG1781108 consensus Small Nuclear ribonucleoprotein splicing 99.67
cd0172490 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins 99.66
KOG178496 consensus Small Nuclear ribonucleoprotein splicing 99.64
cd0173378 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins 99.62
cd0172581 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins 99.6
KOG348279 consensus Small nuclear ribonucleoprotein (snRNP) 99.57
KOG346091 consensus Small nuclear ribonucleoprotein (snRNP) 99.56
KOG178377 consensus Small nuclear ribonucleoprotein F [RNA p 99.53
KOG1782129 consensus Small Nuclear ribonucleoprotein splicing 99.44
KOG177584 consensus U6 snRNA-associated Sm-like protein [RNA 99.38
KOG177488 consensus Small nuclear ribonucleoprotein E [RNA p 99.13
KOG344896 consensus Predicted snRNP core protein [RNA proces 98.55
KOG3459114 consensus Small nuclear ribonucleoprotein (snRNP) 98.36
KOG3428109 consensus Small nuclear ribonucleoprotein SMD1 and 98.17
KOG3293134 consensus Small nuclear ribonucleoprotein (snRNP) 98.08
cd0173966 LSm11_C The eukaryotic Sm and Sm-like (LSm) protei 98.06
PF1443877 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1. 97.94
KOG3172119 consensus Small nuclear ribonucleoprotein Sm D3 [R 97.61
PF1270196 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC 97.04
PF06372166 Gemin6: Gemin6 protein; InterPro: IPR009422 This f 96.8
PF0223748 BPL_C: Biotin protein ligase C terminal domain; In 96.73
PF1109580 Gemin7: Gem-associated protein 7 (Gemin7); InterPr 96.09
cd0173674 LSm14_N LSm14 (also known as RAP55) belongs to a f 96.02
PRK14638150 hypothetical protein; Provisional 95.75
PRK02001152 hypothetical protein; Validated 95.28
PRK14639140 hypothetical protein; Provisional 95.21
cd0173483 YlxS_C YxlS is a Bacillus subtilis gene of unknown 95.16
cd0173561 LSm12_N LSm12 belongs to a family of Sm-like prote 94.38
PF1084266 DUF2642: Protein of unknown function (DUF2642); In 94.09
PRK14633150 hypothetical protein; Provisional 93.53
PRK14640152 hypothetical protein; Provisional 93.14
PRK14636176 hypothetical protein; Provisional 93.1
PRK14632172 hypothetical protein; Provisional 93.07
PRK14645154 hypothetical protein; Provisional 92.92
PRK14644136 hypothetical protein; Provisional 92.85
PF02576141 DUF150: Uncharacterised BCR, YhbC family COG0779; 92.73
PRK00092154 ribosome maturation protein RimP; Reviewed 92.21
PRK14642197 hypothetical protein; Provisional 92.1
cd0171661 Hfq Hfq, an abundant, ubiquitous RNA-binding prote 92.08
TIGR0238361 Hfq RNA chaperone Hfq. This model represents the R 92.05
COG0779153 Uncharacterized protein conserved in bacteria [Fun 91.69
PRK14634155 hypothetical protein; Provisional 91.51
PRK14643164 hypothetical protein; Provisional 90.59
PRK14631174 hypothetical protein; Provisional 90.54
PRK0039579 hfq RNA-binding protein Hfq; Provisional 90.51
PRK14647159 hypothetical protein; Provisional 90.3
PRK14637151 hypothetical protein; Provisional 90.24
PRK14646155 hypothetical protein; Provisional 90.02
PRK14641173 hypothetical protein; Provisional 89.74
PRK06955300 biotin--protein ligase; Provisional 87.73
PF03614165 Flag1_repress: Repressor of phase-1 flagellin; Int 85.46
KOG1073 361 consensus Uncharacterized mRNA-associated protein 83.84
PRK13325 592 bifunctional biotin--[acetyl-CoA-carboxylase] liga 83.01
PF03614165 Flag1_repress: Repressor of phase-1 flagellin; Int 82.86
TIGR00121237 birA_ligase birA, biotin-[acetyl-CoA-carboxylase] 81.65
COG0340238 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenz 81.23
PRK14630143 hypothetical protein; Provisional 81.06
PRK11886319 bifunctional biotin--[acetyl-CoA-carboxylase] synt 80.42
PRK14635162 hypothetical protein; Provisional 80.06
>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 
Probab=99.92  E-value=1.1e-24  Score=143.12  Aligned_cols=74  Identities=41%  Similarity=0.681  Sum_probs=66.5

Q ss_pred             HHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEEEEEEc
Q 033666           26 ISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRTSCHVD  100 (114)
Q Consensus        26 ~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv~I~v~  100 (114)
                      ++.|++|++++|+|+|+|||.|+|+|.|||++|||||+||.|++..+++ ....+.|.+|+++|||++|++|+++
T Consensus         2 ~~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~-~~~~~~r~lGlv~IrG~~Iv~i~v~   75 (75)
T cd06168           2 RQKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDS-FSPTEPRVLGLVMIPGHHIVSIEVE   75 (75)
T ss_pred             HhHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCc-cCCccEEEeeeEEEeCCeEEEEEEC
Confidence            5789999999999999999999999999999999999999999866432 2446789999999999999999875

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. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
>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
>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
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>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
>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
>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
>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
>PRK00737 small nuclear ribonucleoprotein; Provisional 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
>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
>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
>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
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription] Back     alignment and domain information
>KOG1780 consensus Small Nuclear ribonucleoprotein G [RNA processing and modification] Back     alignment and domain information
>KOG3168 consensus U1 snRNP component [Transcription] Back     alignment and domain information
>PTZ00138 small nuclear ribonucleoprotein; Provisional 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
>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
>KOG1781 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] 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
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] 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 Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification] Back     alignment and domain information
>KOG3460 consensus Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification] Back     alignment and domain information
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification] Back     alignment and domain information
>KOG1782 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] Back     alignment and domain information
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification] Back     alignment and domain information
>KOG1774 consensus Small nuclear ribonucleoprotein E [RNA processing and modification] Back     alignment and domain information
>KOG3448 consensus Predicted snRNP core protein [RNA processing and modification] Back     alignment and domain information
>KOG3459 consensus Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification] Back     alignment and domain information
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification] Back     alignment and domain information
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification] Back     alignment and domain information
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1 Back     alignment and domain information
>KOG3172 consensus Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification] 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
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins 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
>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
>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
>PRK02001 hypothetical protein; Validated Back     alignment and domain information
>PRK14639 hypothetical protein; Provisional Back     alignment and domain information
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold Back     alignment and domain information
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation Back     alignment and domain information
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function Back     alignment and domain information
>PRK14633 hypothetical protein; Provisional Back     alignment and domain information
>PRK14640 hypothetical protein; Provisional Back     alignment and domain information
>PRK14636 hypothetical protein; Provisional Back     alignment and domain information
>PRK14632 hypothetical protein; Provisional Back     alignment and domain information
>PRK14645 hypothetical protein; Provisional Back     alignment and domain information
>PRK14644 hypothetical protein; Provisional Back     alignment and domain information
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [] Back     alignment and domain information
>PRK00092 ribosome maturation protein RimP; Reviewed Back     alignment and domain information
>PRK14642 hypothetical protein; Provisional Back     alignment and domain information
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others Back     alignment and domain information
>TIGR02383 Hfq RNA chaperone Hfq Back     alignment and domain information
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK14634 hypothetical protein; Provisional Back     alignment and domain information
>PRK14643 hypothetical protein; Provisional Back     alignment and domain information
>PRK14631 hypothetical protein; Provisional Back     alignment and domain information
>PRK00395 hfq RNA-binding protein Hfq; Provisional Back     alignment and domain information
>PRK14647 hypothetical protein; Provisional Back     alignment and domain information
>PRK14637 hypothetical protein; Provisional Back     alignment and domain information
>PRK14646 hypothetical protein; Provisional Back     alignment and domain information
>PRK14641 hypothetical protein; Provisional Back     alignment and domain information
>PRK06955 biotin--protein ligase; Provisional Back     alignment and domain information
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella Back     alignment and domain information
>KOG1073 consensus Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed Back     alignment and domain information
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella Back     alignment and domain information
>TIGR00121 birA_ligase birA, biotin-[acetyl-CoA-carboxylase] ligase region Back     alignment and domain information
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism] Back     alignment and domain information
>PRK14630 hypothetical protein; Provisional Back     alignment and domain information
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional Back     alignment and domain information
>PRK14635 hypothetical protein; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query114
2y9a_A95 Structure Of The Spliceosomal U4 Snrnp Core Domain 2e-04
1d3b_B91 Crystal Structure Of The D3b Subcomplex Of The Huma 2e-04
3pgw_B 231 Crystal Structure Of Human U1 Snrnp Length = 231 7e-04
3cw1_A174 Crystal Structure Of Human Spliceosomal U1 Snrnp Le 8e-04
>pdb|2Y9A|A Chain A, Structure Of The Spliceosomal U4 Snrnp Core Domain Length = 95 Back     alignment and structure 
Iteration: 1

 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 10/78 (12%)
Query: 15 SAGSDTKGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRT 74
          + G  +K   HI         RM   ++DGR F+G+F   DK  N+IL D  E+R  +  
Sbjct: 2  TVGKSSKMLQHIDY-------RMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPK 54
Query: 75 SPSPM---EQRCLGIILI 89
          +       E+R LG++L+
Sbjct: 55 NSKQAEREEKRVLGLVLL 72
>pdb|1D3B|B Chain B, Crystal Structure Of The D3b Subcomplex Of The Human Core Snrnp Domain At 2.0a Resolution Length = 91 Back     alignment and structure
>pdb|3PGW|B Chain B, Crystal Structure Of Human U1 Snrnp Length = 231 Back     alignment and structure
>pdb|3CW1|A Chain A, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 174 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query114
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 1e-18
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 1e-11
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 2e-10
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 1e-07
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 8e-07
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 4e-06
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 1e-05
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 2e-05
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 2e-05
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 3e-05
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 3e-05
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 3e-05
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 2e-04
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 3e-04
>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A Length = 91 Back     alignment and structure
 Score = 73.0 bits (179), Expect = 1e-18
 Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 3/80 (3%)

Query: 24  NHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRR---TSPSPME 80
              S++ + +  RM   ++DGR F+G+F   DK  N+IL D  E+R  +          E
Sbjct: 4   GKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREE 63

Query: 81  QRCLGIILIPSSCRTSCHVD 100
           +R LG++L+      S  V+
Sbjct: 64  KRVLGLVLLRGENLVSMTVE 83
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A Length = 231 Back     alignment and structure
>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C Length = 113 Back     alignment and structure
>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae} Length = 96 Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query114
4emk_C113 U6 snRNA-associated SM-like protein LSM7; SM fold, 99.9
3bw1_A96 SMX4 protein, U6 snRNA-associated SM-like protein 99.89
1d3b_B91 Protein (small nuclear ribonucleoprotein associat 99.88
3pgw_B 231 SM B; protein-RNA complex, U1 snRNA, SM fold, SM c 99.87
1h64_175 SnRNP SM-like protein; SM fold, spliceosome, snRNP 99.87
4emk_A94 U6 snRNA-associated SM-like protein LSM5; SM fold, 99.86
1mgq_A83 SM-like protein; LSM, RNA-binding, archea, RNA bin 99.86
2fwk_A121 U6 snRNA-associated SM-like protein LSM5; structur 99.86
1i4k_A77 Putative snRNP SM-like protein; core snRNP domain, 99.86
3s6n_G76 Small nuclear ribonucleoprotein G; SMN complex, SM 99.86
4emg_A93 Probable U6 snRNA-associated SM-like protein LSM3; 99.86
1th7_A81 SnRNP-2, small nuclear riboprotein protein; archae 99.86
1i8f_A81 Putative snRNP SM-like protein; beta barrel-like S 99.85
4emk_B75 U6 snRNA-associated SM-like protein LSM6; SM fold, 99.85
1ljo_A77 Archaeal SM-like protein AF-SM2; snRNP, core snRNP 99.85
3s6n_F86 Small nuclear ribonucleoprotein F; SMN complex, SM 99.84
1n9r_A93 SMF, small nuclear ribonucleoprotein F, snRNP-F, S 99.84
3s6n_E92 Small nuclear ribonucleoprotein E; SMN complex, SM 99.82
1b34_B118 Protein (small nuclear ribonucleoprotein SM D2); s 99.81
1d3b_A75 Protein (small nuclear ribonucleoprotein SM D3); s 99.81
4emh_A105 Probable U6 snRNA-associated SM-like protein LSM4; 99.81
1b34_A119 Protein (small nuclear ribonucleoprotein SM D1); s 99.78
2y9a_D126 Small nuclear ribonucleoprotein SM D3; splicing-RN 99.73
1m5q_A130 SMAP3, small nuclear ribonucleoprotein homolog, SM 99.72
1y96_A86 Gemin6, SIP2, GEM-associated protein 6; SM fold, p 99.05
2fb7_A95 SM-like protein, LSM-14_N (RAP55); DR.13312, BC055 96.62
2vxe_A88 CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA 96.58
4a53_A125 EDC3; RNA binding protein; NMR {Schizosaccharomyce 95.97
1y96_B85 Gemin7, SIP3, GEM-associated protein 7; SM fold, p 95.54
3ahu_A78 Protein HFQ; SM-like motif, protein-RNA complex, t 94.79
3hfo_A70 SSR3341 protein; HFQ, SM, RNA-binding protein, sRN 93.97
2vc8_A84 Enhancer of mRNA-decapping protein 3; P-BODY compo 93.79
1kq1_A77 HFQ, HOST factor for Q beta; hexamer, RNA binding 93.75
2ylb_A74 Protein HFQ; RNA-binding protein, LSM protein, RNA 93.61
3hfn_A72 ASL2047 protein; HFQ, SM, RNA-binding protein, sRN 93.4
1ib8_A164 Conserved protein SP14.3; nucleic acid binding pro 93.01
2qtx_A71 Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi 92.94
3sb2_A79 Protein HFQ; SM-like, RNA chaperone, chaperone; 2. 92.71
1ycy_A71 Conserved hypothetical protein; structural genomic 92.6
3rux_A270 BIRA bifunctional protein; biotin-protein ligase, 91.97
1u1s_A82 HFQ protein; SM-like bacterial protein, riken stru 91.43
2y90_A104 Protein HFQ; RNA-binding protein, SM-like, RNA cha 91.29
1bia_A321 BIRA bifunctional protein; transcription regulatio 84.94
2ej9_A237 Putative biotin ligase; biotin biosynthesis, monom 84.35
2rm4_A103 CG6311-PB, DM EDC3; enhancer of mRNA decapping, P- 83.24
2eay_A233 Biotin [acetyl-COA-carboxylase] ligase; biotin bio 82.95
2xk0_A69 Polycomb protein PCL; transcription, aromatic CAGE 80.32
2dxu_A235 Biotin--[acetyl-COA-carboxylase] ligase; biotin bi 80.31
>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=99.90  E-value=8.3e-24  Score=147.28  Aligned_cols=90  Identities=16%  Similarity=0.186  Sum_probs=56.7

Q ss_pred             cCCCCCCCchHHHHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCCCCCCceEeeeEEEEcCCCEE
Q 033666           16 AGSDTKGSNHISRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTSPSPMEQRCLGIILIPSSCRT   95 (114)
Q Consensus        16 ~~~~~~~~~~~~~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~~~~~~~r~lG~vlIrG~~Iv   95 (114)
                      +-+..++.++...|.+|++++|+|+|+|||.|+|+|.|||+||||||+||+|++............|.+|+++|||++|+
T Consensus        15 ~~~~~~kke~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv   94 (113)
T 4emk_C           15 QPTERPRKESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLV   94 (113)
T ss_dssp             -----------------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEE
T ss_pred             CCccCCccchHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEE
Confidence            44455668889999999999999999999999999999999999999999998754210011346899999999999999


Q ss_pred             EEEEccChhh
Q 033666           96 SCHVDCSIDE  105 (114)
Q Consensus        96 ~I~v~~~~~e  105 (114)
                      +|......+|
T Consensus        95 ~I~~~d~~ee  104 (113)
T 4emk_C           95 LIAPMDGSEE  104 (113)
T ss_dssp             EEEECC----
T ss_pred             EEEecCcccc
Confidence            9975544333
>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae} Back     alignment and structure
>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A Back     alignment and structure
>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
>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A* Back     alignment and structure
>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A Back     alignment and structure
>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
>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
>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_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G Back     alignment and structure
>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe} Back     alignment and structure
>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Back     alignment and structure
>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Back     alignment and structure
>4emk_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
>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
>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Back     alignment and structure
>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E Back     alignment and structure
>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B Back     alignment and structure
>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
>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
>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
>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens} 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
>2vxe_A CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA decay, LSM proteins, translational repression, transcription; NMR {Drosophila melanogaster} Back     alignment and structure
>4a53_A EDC3; RNA binding protein; NMR {Schizosaccharomyces pombe} PDB: 4a54_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
>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A Back     alignment and structure
>3hfo_A SSR3341 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 1.30A {Synechocystis SP} Back     alignment and structure
>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
>1kq1_A HFQ, HOST factor for Q beta; hexamer, RNA binding protein, translational regulator, SM motif; 1.55A {Staphylococcus aureus} SCOP: b.38.1.2 PDB: 1kq2_A Back     alignment and structure
>2ylb_A Protein HFQ; RNA-binding protein, LSM protein, RNA chaperone; 1.15A {Salmonella enterica subsp} PDB: 2yht_A 1hk9_A 2ylc_A* 3gib_A* 3rer_A* 3qo3_A* 3res_A* Back     alignment and structure
>3hfn_A ASL2047 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 2.31A {Nostoc SP} Back     alignment and structure
>1ib8_A Conserved protein SP14.3; nucleic acid binding protein, ribosomal protein, essential gene, structural genomics; NMR {Streptococcus pneumoniae} SCOP: b.38.2.1 d.52.4.1 Back     alignment and structure
>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii} Back     alignment and structure
>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2 Back     alignment and structure
>1ycy_A Conserved hypothetical protein; structural genomics, southeast collaboratory for structural genomics, secsg, protein structure initiative; 2.80A {Pyrococcus furiosus} SCOP: b.38.1.4 Back     alignment and structure
>3rux_A BIRA bifunctional protein; biotin-protein ligase, ligase-ligase inhibitor complex; HET: BS5; 1.70A {Mycobacterium tuberculosis} PDB: 3l1a_A 3l2z_A 2cgh_A Back     alignment and structure
>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
>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A {Escherichia coli} PDB: 3qhs_A Back     alignment and structure
>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A* Back     alignment and structure
>2ej9_A Putative biotin ligase; biotin biosynthesis, monomer, X-RAY diffraction, structural genomics, NPPSFA; HET: BTN; 2.00A {Methanocaldococcus jannaschii} Back     alignment and structure
>2rm4_A CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-BODY component, SM-like protein,, protein binding; NMR {Drosophila melanogaster} Back     alignment and structure
>2eay_A Biotin [acetyl-COA-carboxylase] ligase; biotin biosynthesis, dimer, X-RAY diffraction, structural genomics, NPPSFA; 1.95A {Aquifex aeolicus} PDB: 3efs_A* 3fjp_A 3efr_A* Back     alignment and structure
>2xk0_A Polycomb protein PCL; transcription, aromatic CAGE; NMR {Drosophila melanogaster} Back     alignment and structure
>2dxu_A Biotin--[acetyl-COA-carboxylase] ligase; biotin biosynthesis, dimer, X-RAY diffraction, structural genomics, NPPSFA; HET: BT5; 1.28A {Pyrococcus horikoshii} PDB: 2dzc_A 2ejg_A* 2e3y_A* 2e41_A* 2e64_A 2ejf_A* 2zgw_A* 1wqw_A* 1wpy_A* 1wq7_A 1wnl_A* 1x01_A* 2dkg_A* 2dth_A* 2dti_A* 2dto_A* 2fyk_A* 2djz_A* 2hni_A 2e10_A ... Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 114
d1d3bb_81 b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa 4e-16
d2fwka192 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr 3e-10
d1i4k1_72 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 3e-07
d1mgqa_74 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 4e-07
d1h641_71 b.38.1.1 (1:) Archaeal homoheptameric Sm protein { 6e-07
d1i8fa_71 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 2e-06
d1th7a176 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote 2e-06
d1b34b_93 b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s 2e-04
d1ljoa_75 b.38.1.1 (A:) Archaeal homoheptameric Sm protein { 9e-04
d1m5q1_127 b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch 0.001
>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 = 65.2 bits (159), Expect = 4e-16
 Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 3/77 (3%)

Query: 27  SRVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRT---SPSPMEQRC 83
           S++ + +  RM   ++DGR F+G+F   DK  N+IL D  E+R  +          E+R 
Sbjct: 1   SKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRV 60

Query: 84  LGIILIPSSCRTSCHVD 100
           LG++L+      S  V+
Sbjct: 61  LGLVLLRGENLVSMTVE 77
>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
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Length = 72 Back     information, alignment and structure
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 74 Back     information, alignment and structure
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Length = 71 Back     information, alignment and structure
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} 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
>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93 Back     information, alignment and structure
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Length = 75 Back     information, alignment and structure
>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 127 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 ?
Query114
d1d3bb_81 B core SNRNP protein {Human (Homo sapiens) [TaxId: 99.92
d2fwka192 U6 snRNA-associated sm-like protein LSM5 {Cryptosp 99.87
d1h641_71 Archaeal homoheptameric Sm protein {Archaeon Pyroc 99.86
d1i4k1_72 Archaeal homoheptameric Sm protein {Archaeon Archa 99.86
d1th7a176 Archaeal homoheptameric Sm protein {Sulfolobus sol 99.85
d1b34b_93 D2 core SNRNP protein {Human (Homo sapiens) [TaxId 99.85
d1mgqa_74 Archaeal homoheptameric Sm protein {Archaeon Metha 99.85
d1i8fa_71 Archaeal homoheptameric Sm protein {Archaeon Pyrob 99.84
d1ljoa_75 Archaeal homoheptameric Sm protein {Archaeon Archa 99.82
d1n9ra_68 Small nuclear ribonucleoprotein F, Smf {Baker's ye 99.78
d1d3ba_72 D3 core SNRNP protein {Human (Homo sapiens) [TaxId 99.75
d1b34a_80 D1 core SNRNP protein {Human (Homo sapiens) [TaxId 99.66
d1m5q1_127 Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul 99.56
d1biaa247 Biotin repressor/biotin holoenzyme synthetase, C-t 96.95
d2vxfa180 LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) 96.95
d1ib8a174 Hypothetical protein SP14.3 (SP0552) {Streptococcu 93.25
d1ycya166 Hypothetical protein PF1955 {Pyrococcus furiosus [ 92.54
d1kq1a_60 Pleiotropic translational regulator Hfq {Staphyloc 90.42
d1u1sa166 Pleiotropic translational regulator Hfq {Pseudomon 86.0
>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=99.92  E-value=4.6e-26  Score=148.34  Aligned_cols=75  Identities=31%  Similarity=0.524  Sum_probs=65.2

Q ss_pred             HHHHhcCCeEEEEEcCCeEEEEEEEEecCccceEecccEEEeecCCCC---CCCCceEeeeEEEEcCCCEEEEEEccC
Q 033666           28 RVRKLLCRRMLVGIKDGRFFLGSFHCIDKQGNIILQDAVEYRSTRRTS---PSPMEQRCLGIILIPSSCRTSCHVDCS  102 (114)
Q Consensus        28 ~L~~~l~k~V~V~L~dGR~i~G~L~~~D~~~NLvLsda~E~~~~~~~~---~~~~~~r~lG~vlIrG~~Iv~I~v~~~  102 (114)
                      +|.+|++++|+|+|+|||.|.|+|.|||+||||||+||+|++......   ......|.+|+++|||++|++|+++.+
T Consensus         2 ~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~~~~   79 (81)
T d1d3bb_           2 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVEGP   79 (81)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEEEC
T ss_pred             hhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEccCC
Confidence            478999999999999999999999999999999999999987654321   233467999999999999999998754
>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} Back     information, alignment and structure
>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Back     information, alignment and structure
>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Back     information, alignment and structure
>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} 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
>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Back     information, alignment and structure
>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Back     information, alignment and structure
>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>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
>d2vxfa1 b.38.1.5 (A:6-85) LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) [TaxId: 7955]} Back     information, alignment and structure
>d1ib8a1 b.38.2.1 (A:91-164) Hypothetical protein SP14.3 (SP0552) {Streptococcus pneumoniae [TaxId: 1313]} Back     information, alignment and structure
>d1ycya1 b.38.1.4 (A:5-70) Hypothetical protein PF1955 {Pyrococcus furiosus [TaxId: 2261]} 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