Citrus Sinensis ID: 023289

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280----
MPLSTGCLTSLVVHLYVCQVKLLNFLILSFLFSTSQLLLLTHYNSLGLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAAA
cccccccHHHHHHEEEEHHHHHHHHHHHHHHHcccccccccccccccEEEccccccccccccccHHHHHHHHHccccccHHHHHHHHHccEEEEccEEEcccccccccEEEEEEccccccEEEEEcccccEEEEEccHHHccEEEEEEEEEEEEEcccEEEEEEccEEEEEcccccccccEEEEEcccccEEEEEEEEcccEEEEEccccEEEEEEEEEEEEEEccccEEEEEcccccEEEEEEcEEEEEEcccccEEEccccccEEEEHHHHHHHHHHHHHHc
ccccccHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHccEEEccEEccccccccccEEEEEEccccccEEEEEccccEEEEEEccHHHHcEEEEEEEEEEEcccccEEEEEccccEEEcccccEEEccEEEEEcccccEEEEEEEccccEEEEEccccccEEEEEEEEEcccccccEEEEEEccccEEEEEcccEEEEEcccccEEEccccccEEEHHHHHHHHHHHHHHcc
MPLSTGCLTSLVVHLYVCQVKLLNFLILSFLFSTSQLLLLTHYnslglqapkpssgphksreclPLILVLRNRLKYALTYREVIAILMQRHVLvdgkvrtdktypagfmdvvsipktnenFRLLYDtkgrfrlhsLRDEEAKFKLCKvrsvqfgqkgipyintydgrtirypdplikandtikldleenkitdfikfdvGNIVMVTggrnrgrvgiiknrekhkgsfeTIHIQDALGHEFATRLGNvftigkgskpwvslpkgkgikLSIIEEARKRQAAQAAA
MPLSTGCLTSLVVHLYVCQVKLLNFLILSFLFSTSQLLLLTHYNSLGLQapkpssgphksrECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDktypagfmdvvsipktnenFRLLYDTKGRFRLHSLRDEEAkfklckvrsvqfgqkgipyintydgrtirypdplIKANDTIKLDLEENKitdfikfdvgnivmvtggrnrgrvgiiknrekhkgsFETIHIQDALGHEFATRLGNVFTigkgskpwvslpkgkGIKLSIIEEARKRQAAQAAA
MPLSTGCLTSLVVHLYVCQVKllnflilsflfstsqllllTHYNSLGLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEarkrqaaqaaa
*****GCLTSLVVHLYVCQVKLLNFLILSFLFSTSQLLLLTHYNSLGL*************ECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSII*************
****TGCLTSLVVHLYVCQVKLLNFLILSFLFSTSQLLLLTHYNSLGLQAPKPSSG*H*SRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE***********
MPLSTGCLTSLVVHLYVCQVKLLNFLILSFLFSTSQLLLLTHYNSLGLQ***********RECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEA**********
***STGCLTSLVVHLYVCQVKLLNFLILSFLFSTSQLLLLTHYNSLGLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQA*****
iiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
SSSSSSSSSSSSSSSoooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MPLSTGCLTSLVVHLYVCQVKLLNFLILSFLFSTSQLLLLTHYNSLGLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAAA
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 ?
Query284 2.2.26 [Sep-21-2011]
P46300264 40S ribosomal protein S4 N/A no 0.838 0.901 0.894 1e-128
P49204262 40S ribosomal protein S4- yes no 0.838 0.908 0.894 1e-127
Q8VYK6262 40S ribosomal protein S4- yes no 0.838 0.908 0.890 1e-127
Q93VH9261 40S ribosomal protein S4- yes no 0.834 0.908 0.894 1e-127
P46299262 40S ribosomal protein S4 N/A no 0.838 0.908 0.903 1e-125
O22424265 40S ribosomal protein S4 N/A no 0.816 0.875 0.892 1e-124
P49398265 40S ribosomal protein S4 no no 0.816 0.875 0.887 1e-123
O81363261 40S ribosomal protein S4 N/A no 0.799 0.869 0.874 1e-117
P47961263 40S ribosomal protein S4 yes no 0.838 0.904 0.676 6e-95
P79103263 40S ribosomal protein S4 yes no 0.838 0.904 0.676 1e-94
>sp|P46300|RS4_SOLTU 40S ribosomal protein S4 OS=Solanum tuberosum GN=RPS4 PE=2 SV=1 Back     alignment and function desciption
 Score =  456 bits (1173), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 213/238 (89%), Positives = 230/238 (96%)

Query: 47  GLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA 106
           G  APKPSSGPHKSRECLPL++++RNRLKYALTYREVI+ILMQR V+VDGKVRTDKTYPA
Sbjct: 25  GAFAPKPSSGPHKSRECLPLVIIMRNRLKYALTYREVISILMQRQVMVDGKVRTDKTYPA 84

Query: 107 GFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDG 166
           GFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEE+KFKLCKVRSVQFGQKGIPY+NTYDG
Sbjct: 85  GFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEESKFKLCKVRSVQFGQKGIPYLNTYDG 144

Query: 167 RTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGS 226
           RTIRYPDPLIKANDTIKLDLE NKI DFIKFDVGN+VMVTGGRNRGRVG+IKNREKHKGS
Sbjct: 145 RTIRYPDPLIKANDTIKLDLESNKIVDFIKFDVGNVVMVTGGRNRGRVGVIKNREKHKGS 204

Query: 227 FETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAAA 284
           FET+HIQD+ GHEFATRLGNVFT+GKG+KPWVSLPKGKGIKL+IIE+ARKR AAQ+A 
Sbjct: 205 FETLHIQDSQGHEFATRLGNVFTLGKGTKPWVSLPKGKGIKLTIIEDARKRLAAQSAT 262

Solanum tuberosum (taxid: 4113)
>sp|P49204|RS42_ARATH 40S ribosomal protein S4-2 OS=Arabidopsis thaliana GN=RPS4B PE=2 SV=4 Back     alignment and function description
>sp|Q8VYK6|RS43_ARATH 40S ribosomal protein S4-3 OS=Arabidopsis thaliana GN=RPS4D PE=2 SV=2 Back     alignment and function description
>sp|Q93VH9|RS41_ARATH 40S ribosomal protein S4-1 OS=Arabidopsis thaliana GN=RPS4A PE=2 SV=1 Back     alignment and function description
>sp|P46299|RS4_GOSHI 40S ribosomal protein S4 OS=Gossypium hirsutum GN=RPS4 PE=2 SV=1 Back     alignment and function description
>sp|O22424|RS4_MAIZE 40S ribosomal protein S4 OS=Zea mays GN=RPS4 PE=2 SV=1 Back     alignment and function description
>sp|P49398|RS4_ORYSJ 40S ribosomal protein S4 OS=Oryza sativa subsp. japonica GN=RPS4 PE=2 SV=3 Back     alignment and function description
>sp|O81363|RS4_PRUAR 40S ribosomal protein S4 OS=Prunus armeniaca GN=RPS4 PE=2 SV=1 Back     alignment and function description
>sp|P47961|RS4_CRIGR 40S ribosomal protein S4 OS=Cricetulus griseus GN=RPS4 PE=2 SV=2 Back     alignment and function description
>sp|P79103|RS4_BOVIN 40S ribosomal protein S4 OS=Bos taurus GN=RPS4 PE=2 SV=3 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 ?
Query284
357468567264 40S ribosomal protein S4 [Medicago trunc 0.827 0.890 0.936 1e-129
356559288264 PREDICTED: 40S ribosomal protein S4-1-li 0.834 0.897 0.928 1e-129
255647667264 unknown [Glycine max] 0.834 0.897 0.924 1e-129
224087813263 predicted protein [Populus trichocarpa] 0.838 0.904 0.924 1e-128
356551387264 PREDICTED: 40S ribosomal protein S4-1-li 0.834 0.897 0.924 1e-128
297736557246 unnamed protein product [Vitis vinifera] 0.838 0.967 0.924 1e-128
225448546264 PREDICTED: 40S ribosomal protein S4-like 0.838 0.901 0.924 1e-128
449465358264 PREDICTED: 40S ribosomal protein S4-like 0.830 0.893 0.936 1e-128
351725821264 40S ribosomal S4 protein [Glycine max] g 0.834 0.897 0.924 1e-128
449465362264 PREDICTED: 40S ribosomal protein S4-like 0.834 0.897 0.928 1e-128
>gi|357468567|ref|XP_003604568.1| 40S ribosomal protein S4 [Medicago truncatula] gi|355505623|gb|AES86765.1| 40S ribosomal protein S4 [Medicago truncatula] Back     alignment and taxonomy information
 Score =  466 bits (1199), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 220/235 (93%), Positives = 231/235 (98%)

Query: 47  GLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA 106
           G  APKPSSGPHKSRECLPLIL+LRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA
Sbjct: 25  GAFAPKPSSGPHKSRECLPLILILRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA 84

Query: 107 GFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDG 166
           GFMDVVSIPKTNENFRLLYDTKGRFRLHS+RD+EAKFKLCKVRSVQFGQKGIPY+NTYDG
Sbjct: 85  GFMDVVSIPKTNENFRLLYDTKGRFRLHSVRDDEAKFKLCKVRSVQFGQKGIPYLNTYDG 144

Query: 167 RTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGS 226
           RTIRYPDPLIKANDTIKLDLE NKITDFIKFDVGN+VMVTGGRNRGRVG+IKNREKHKG+
Sbjct: 145 RTIRYPDPLIKANDTIKLDLENNKITDFIKFDVGNVVMVTGGRNRGRVGVIKNREKHKGT 204

Query: 227 FETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQ 281
           FETIH+QDA GHEFATRLGNVFTIGKG+KPWVSLPKGKGIKL++IEEARKRQAAQ
Sbjct: 205 FETIHVQDASGHEFATRLGNVFTIGKGTKPWVSLPKGKGIKLTVIEEARKRQAAQ 259

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|356559288|ref|XP_003547932.1| PREDICTED: 40S ribosomal protein S4-1-like [Glycine max] Back     alignment and taxonomy information
>gi|255647667|gb|ACU24295.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|224087813|ref|XP_002308235.1| predicted protein [Populus trichocarpa] gi|222854211|gb|EEE91758.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356551387|ref|XP_003544057.1| PREDICTED: 40S ribosomal protein S4-1-like [Glycine max] Back     alignment and taxonomy information
>gi|297736557|emb|CBI25428.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|225448546|ref|XP_002276986.1| PREDICTED: 40S ribosomal protein S4-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|449465358|ref|XP_004150395.1| PREDICTED: 40S ribosomal protein S4-like [Cucumis sativus] gi|449496881|ref|XP_004160252.1| PREDICTED: 40S ribosomal protein S4-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|351725821|ref|NP_001235826.1| 40S ribosomal S4 protein [Glycine max] gi|22138108|gb|AAM93434.1| 40S ribosomal S4 protein [Glycine max] gi|255641970|gb|ACU21252.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|449465362|ref|XP_004150397.1| PREDICTED: 40S ribosomal protein S4-like [Cucumis sativus] gi|449496878|ref|XP_004160251.1| PREDICTED: 40S ribosomal protein S4-like [Cucumis sativus] 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 ?
Query284
TAIR|locus:2827612261 AT2G17360 [Arabidopsis thalian 0.799 0.869 0.903 8.4e-113
TAIR|locus:2169339262 AT5G07090 [Arabidopsis thalian 0.799 0.866 0.903 8.4e-113
TAIR|locus:2171198262 AT5G58420 [Arabidopsis thalian 0.799 0.866 0.898 3.6e-112
UNIPROTKB|P79103263 RPS4 "40S ribosomal protein S4 0.799 0.863 0.691 2e-86
UNIPROTKB|F2Z4Q1263 RPS4X "Uncharacterized protein 0.799 0.863 0.691 2e-86
UNIPROTKB|J9P5V0267 J9P5V0 "Uncharacterized protei 0.799 0.850 0.691 2e-86
UNIPROTKB|P62701263 RPS4X "40S ribosomal protein S 0.799 0.863 0.691 2e-86
UNIPROTKB|F1RQ91263 RPS4X "Uncharacterized protein 0.799 0.863 0.691 2e-86
UNIPROTKB|P62704263 RPS4X "40S ribosomal protein S 0.799 0.863 0.691 2e-86
UNIPROTKB|P62705263 RPS4X "40S ribosomal protein S 0.799 0.863 0.691 2e-86
TAIR|locus:2827612 AT2G17360 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1113 (396.9 bits), Expect = 8.4e-113, P = 8.4e-113
 Identities = 205/227 (90%), Positives = 221/227 (97%)

Query:    47 GLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA 106
             G  APKPSSGPHKSRECLPL+L++RNRLKYALTYREVI+ILMQRH+ VDGKVRTDKTYPA
Sbjct:    25 GAFAPKPSSGPHKSRECLPLVLIIRNRLKYALTYREVISILMQRHIQVDGKVRTDKTYPA 84

Query:   107 GFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDG 166
             GFMDVVSIPKTNENFRLLYDTKGRFRLHS++DEEAKFKLCKVRS+QFGQKGIPY+NTYDG
Sbjct:    85 GFMDVVSIPKTNENFRLLYDTKGRFRLHSIKDEEAKFKLCKVRSIQFGQKGIPYLNTYDG 144

Query:   167 RTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGS 226
             RTIRYPDPLIK NDTIKLDLEENKI +FIKFDVGN+VMVTGGRNRGRVG+IKNREKHKGS
Sbjct:   145 RTIRYPDPLIKPNDTIKLDLEENKIVEFIKFDVGNVVMVTGGRNRGRVGVIKNREKHKGS 204

Query:   227 FETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 273
             FETIHIQD+ GHEFATRLGNV+TIGKG+KPWVSLPKGKGIKL+IIEE
Sbjct:   205 FETIHIQDSTGHEFATRLGNVYTIGKGTKPWVSLPKGKGIKLTIIEE 251
GO:0003723 "RNA binding" evidence=IEA
GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS
GO:0005622 "intracellular" evidence=IEA
GO:0005737 "cytoplasm" evidence=ISM
GO:0005840 "ribosome" evidence=IEA
GO:0006412 "translation" evidence=IEA;ISS
GO:0022627 "cytosolic small ribosomal subunit" evidence=ISS;IDA
GO:0009507 "chloroplast" evidence=IDA
GO:0005774 "vacuolar membrane" evidence=IDA
GO:0005886 "plasma membrane" evidence=IDA
GO:0005829 "cytosol" evidence=IDA
GO:0005794 "Golgi apparatus" evidence=RCA
GO:0001510 "RNA methylation" evidence=RCA
TAIR|locus:2169339 AT5G07090 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2171198 AT5G58420 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|P79103 RPS4 "40S ribosomal protein S4" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|F2Z4Q1 RPS4X "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|J9P5V0 J9P5V0 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|P62701 RPS4X "40S ribosomal protein S4, X isoform" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1RQ91 RPS4X "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|P62704 RPS4X "40S ribosomal protein S4, X isoform" [Mesocricetus auratus (taxid:10036)] Back     alignment and assigned GO terms
UNIPROTKB|P62705 RPS4X "40S ribosomal protein S4, X isoform" [Felis catus (taxid:9685)] 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) ?
O81363RS4_PRUARNo assigned EC number0.87440.79920.8697N/Ano
Q76N24RS4X_CHLAENo assigned EC number0.67640.83800.9049N/Ano
Q861U7RS4Y1_PONPYNo assigned EC number0.63440.83800.9049N/Ano
Q9N3X2RS4_CAEELNo assigned EC number0.60420.82740.9073yesno
P47836RS4_CHICKNo assigned EC number0.67220.83800.9049yesno
P47837RS4_CANAXNo assigned EC number0.64550.83090.9007N/Ano
O59950RS4_YARLINo assigned EC number0.66800.82740.9038yesno
Q8VYK6RS43_ARATHNo assigned EC number0.89070.83800.9083yesno
Q95V34RS4_SPOFRNo assigned EC number0.64700.83800.9049N/Ano
Q56FH2RS4_LYSTENo assigned EC number0.65820.83450.9045N/Ano
P49204RS42_ARATHNo assigned EC number0.89490.83800.9083yesno
Q9P4W9RS4C_SCHPONo assigned EC number0.68480.83800.9083yesno
P0CX36RS4B_YEASTNo assigned EC number0.66520.83090.9042yesno
P49401RS4_XENLANo assigned EC number0.67220.83800.9049N/Ano
Q76MY1RS4X_MACFUNo assigned EC number0.67640.83800.9049N/Ano
Q861V0RS4Y1_PANPANo assigned EC number0.63020.83800.9049N/Ano
Q4GXU6RS4_CARGRNo assigned EC number0.65250.83090.9042N/Ano
Q90YS0RS4_ICTPUNo assigned EC number0.65540.83800.9049N/Ano
Q5UAP0RS4_BOMMONo assigned EC number0.66380.83800.9049N/Ano
P0C233RS4_TETTHNo assigned EC number0.53210.81330.8918N/Ano
P79103RS4_BOVINNo assigned EC number0.67640.83800.9049yesno
O22424RS4_MAIZENo assigned EC number0.89220.81690.8754N/Ano
P47961RS4_CRIGRNo assigned EC number0.67640.83800.9049yesno
P79183RS4Y1_MACFUNo assigned EC number0.64280.83800.9049N/Ano
P46300RS4_SOLTUNo assigned EC number0.89490.83800.9015N/Ano
O62739RS4Y1_MONDONo assigned EC number0.66380.83800.9049yesno
O62738RS4X_MONDONo assigned EC number0.67650.82740.8935yesno
P49398RS4_ORYSJNo assigned EC number0.88790.81690.8754nono
Q93VH9RS41_ARATHNo assigned EC number0.89450.83450.9080yesno
P41042RS4_DROMENo assigned EC number0.65100.82740.9003yesno
Q861U8RS4Y1_GORGONo assigned EC number0.63020.83800.9049N/Ano
Q6PBC4RS4_XENTRNo assigned EC number0.67220.83800.9049yesno
P62703RS4X_RATNo assigned EC number0.67640.83800.9049yesno
P62702RS4X_MOUSENo assigned EC number0.67640.83800.9049yesno
P62705RS4X_FELCANo assigned EC number0.67640.83800.9049N/Ano
P62704RS4X_MESAUNo assigned EC number0.67640.83800.9049N/Ano
P51405RS4_DICDINo assigned EC number0.64950.81330.8651yesno
Q9USW5RS4B_SCHPONo assigned EC number0.68480.83800.9083yesno
P62701RS4X_HUMANNo assigned EC number0.67640.83800.9049yesno
P0CX35RS4A_YEASTNo assigned EC number0.66520.83090.9042yesno
P46299RS4_GOSHINo assigned EC number0.90330.83800.9083N/Ano
Q4PMB3RS4_IXOSCNo assigned EC number0.63980.83090.9007N/Ano
Q642H9RS4X_DANRENo assigned EC number0.66380.83800.9049yesno
P87158RS4A_SCHPONo assigned EC number0.68480.83800.9083yesno

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

Your Input:
estExt_fgenesh4_pm.C_LG_VI0361
40S ribosomal protein S4 (RPS4A) (263 aa)
(Populus trichocarpa)
Predicted Functional Partners:
fgenesh4_pg.C_LG_VI001257
SubName- Full=Putative uncharacterized protein; (180 aa)
• ••  • 0.755
grail3.0071003601
SubName- Full=Putative uncharacterized protein; (181 aa)
• ••  • 0.755
estExt_fgenesh4_pg.C_LG_VI1248
SubName- Full=Putative uncharacterized protein; (181 aa)
• ••  • 0.755
estExt_Genewise1_v1.C_LG_XI3222
SubName- Full=Putative uncharacterized protein; (181 aa)
• ••  • 0.755
estExt_fgenesh4_pg.C_LG_VII0552
SubName- Full=Putative uncharacterized protein; (146 aa)
• ••    0.741
estExt_fgenesh4_pm.C_LG_III0216
SubName- Full=Putative uncharacterized protein; (146 aa)
• ••    0.728
estExt_fgenesh4_pg.C_LG_V0222
SubName- Full=Putative uncharacterized protein; (147 aa)
• ••    0.711
gw1.57.264.1
SubName- Full=Putative uncharacterized protein; (258 aa)
• ••• • 0.677
estExt_Genewise1_v1.C_LG_VII3915
SubName- Full=Putative uncharacterized protein; (260 aa)
• ••• • 0.675
estExt_fgenesh4_kg.C_LG_XVII0009
SubName- Full=Putative uncharacterized protein; (144 aa)
  •• •• 0.664

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 ?
Query284
PLN00036261 PLN00036, PLN00036, 40S ribosomal protein S4; Prov 1e-167
PTZ00118262 PTZ00118, PTZ00118, 40S ribosomal protein S4; Prov 1e-109
COG1471241 COG1471, RPS4A, Ribosomal protein S4E [Translation 1e-102
PTZ00223273 PTZ00223, PTZ00223, 40S ribosomal protein S4; Prov 3e-82
PRK04313237 PRK04313, PRK04313, 30S ribosomal protein S4e; Val 1e-68
pfam0090077 pfam00900, Ribosomal_S4e, Ribosomal family S4e 1e-36
cd0608755 cd06087, KOW_RPS4, KOW motif of Ribosomal Protein 7e-30
cd0016570 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding d 1e-05
smart0036360 smart00363, S4, S4 RNA-binding domain 2e-04
pfam0147948 pfam01479, S4, S4 domain 6e-04
pfam0046732 pfam00467, KOW, KOW motif 6e-04
smart0073928 smart00739, KOW, KOW (Kyprides, Ouzounis, Woese) m 0.002
>gnl|CDD|177670 PLN00036, PLN00036, 40S ribosomal protein S4; Provisional Back     alignment and domain information 
 Score =  463 bits (1192), Expect = e-167
 Identities = 207/238 (86%), Positives = 221/238 (92%)

Query: 46  LGLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYP 105
            G  APKPSSGPHK RECLPL+L+LRNRLKYALTYREV AILMQRHV VDGKVRTDKTYP
Sbjct: 24  GGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYP 83

Query: 106 AGFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYD 165
           AGFMDV+SIPKTNENFRLLYDTKGRFRLH + DEEAKFKLCKVR +QFGQKGIPY+NT+D
Sbjct: 84  AGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHD 143

Query: 166 GRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKG 225
           GRTIRYPDPLIKANDTIK+DLE NKI DFIKFDVGN+VMVTGGRNRGRVG+IKNREKHKG
Sbjct: 144 GRTIRYPDPLIKANDTIKIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKG 203

Query: 226 SFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAA 283
           SFE IH++DA GHEFATRLGNVF IGKG+KPW+SLPKGKGIKLSIIEEARKR AA  A
Sbjct: 204 SFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPKGKGIKLSIIEEARKRLAAGQA 261

Length = 261
>gnl|CDD|240277 PTZ00118, PTZ00118, 40S ribosomal protein S4; Provisional Back     alignment and domain information
>gnl|CDD|224388 COG1471, RPS4A, Ribosomal protein S4E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|140250 PTZ00223, PTZ00223, 40S ribosomal protein S4; Provisional Back     alignment and domain information
>gnl|CDD|179820 PRK04313, PRK04313, 30S ribosomal protein S4e; Validated Back     alignment and domain information
>gnl|CDD|189761 pfam00900, Ribosomal_S4e, Ribosomal family S4e Back     alignment and domain information
>gnl|CDD|240511 cd06087, KOW_RPS4, KOW motif of Ribosomal Protein S4 (RPS4) Back     alignment and domain information
>gnl|CDD|238095 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes Back     alignment and domain information
>gnl|CDD|214638 smart00363, S4, S4 RNA-binding domain Back     alignment and domain information
>gnl|CDD|201819 pfam01479, S4, S4 domain Back     alignment and domain information
>gnl|CDD|144165 pfam00467, KOW, KOW motif Back     alignment and domain information
>gnl|CDD|128978 smart00739, KOW, KOW (Kyprides, Ouzounis, Woese) motif Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 284
PLN00036261 40S ribosomal protein S4; Provisional 100.0
PTZ00118262 40S ribosomal protein S4; Provisional 100.0
PTZ00223273 40S ribosomal protein S4; Provisional 100.0
PRK04313237 30S ribosomal protein S4e; Validated 100.0
COG1471241 RPS4A Ribosomal protein S4E [Translation, ribosoma 100.0
KOG0378263 consensus 40S ribosomal protein S4 [Translation, r 100.0
PF0090077 Ribosomal_S4e: Ribosomal family S4e; InterPro: IPR 100.0
PF0147948 S4: S4 domain; InterPro: IPR002942 Ribosomes are t 98.51
PF0807138 RS4NT: RS4NT (NUC023) domain; InterPro: IPR013843 98.09
cd0016570 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The 97.52
smart0036360 S4 S4 RNA-binding domain. 97.18
PF0046732 KOW: KOW motif; InterPro: IPR005824 Ribosomes are 96.72
smart0073928 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif i 96.7
COG0522205 RpsD Ribosomal protein S4 and related proteins [Tr 96.68
TIGR0298859 YaaA_near_RecF S4 domain protein YaaA. This small 96.64
PF1327565 S4_2: S4 domain; PDB: 1P9K_A. 95.71
TIGR01018162 rpsD_arch ribosomal protein S4(archaeal type)/S9(e 95.32
PRK1150770 ribosome-associated protein; Provisional 95.2
PTZ00155181 40S ribosomal protein S9; Provisional 95.12
PLN00189194 40S ribosomal protein S9; Provisional 95.0
TIGR01017200 rpsD_bact ribosomal protein S4, bacterial/organell 94.78
TIGR00005299 rluA_subfam pseudouridine synthase, RluA family. m 94.73
PRK04051177 rps4p 30S ribosomal protein S4P; Validated 94.73
PRK05327203 rpsD 30S ribosomal protein S4; Validated 94.55
TIGR01080114 rplX_A_E ribosomal protein L24p/L26e, archaeal/euk 94.47
CHL00113201 rps4 ribosomal protein S4; Reviewed 94.42
TIGR03069257 PS_II_S4 photosystem II S4 domain protein. Members 94.08
TIGR00478228 tly hemolysin TlyA family protein. Hemolysins are 93.03
COG250173 S4-like RNA binding protein [Replication, recombin 91.84
PRK11180325 rluD 23S rRNA pseudouridine synthase D; Provisiona 91.74
COG0564289 RluA Pseudouridylate synthases, 23S RNA-specific [ 91.61
PRK01191120 rpl24p 50S ribosomal protein L24P; Validated 90.48
PRK05912408 tyrosyl-tRNA synthetase; Validated 90.26
PRK10700289 23S rRNA pseudouridylate synthase B; Provisional 90.05
PRK10348133 ribosome-associated heat shock protein Hsp15; Prov 89.03
PRK1228176 rplX 50S ribosomal protein L24; Reviewed 88.62
COG1187248 RsuA 16S rRNA uridine-516 pseudouridylate synthase 88.54
PRK10475290 23S rRNA pseudouridine synthase F; Provisional 88.17
CHL0014183 rpl24 ribosomal protein L24; Validated 87.98
PRK11025317 23S rRNA pseudouridylate synthase C; Provisional 87.74
PRK00004105 rplX 50S ribosomal protein L24; Reviewed 87.02
PRK10839232 16S rRNA pseudouridylate synthase A; Provisional 86.9
PLN00051267 RNA-binding S4 domain-containing protein; Provisio 85.31
PRK13354410 tyrosyl-tRNA synthetase; Provisional 84.98
COG2302257 Uncharacterized conserved protein, contains S4-lik 84.79
COG1189245 Predicted rRNA methylase [Translation, ribosomal s 84.59
PTZ00194143 60S ribosomal protein L26; Provisional 84.01
TIGR01079104 rplX_bact ribosomal protein L24, bacterial/organel 82.35
>PLN00036 40S ribosomal protein S4; Provisional Back     alignment and domain information 
Probab=100.00  E-value=2.2e-103  Score=722.82  Aligned_cols=240  Identities=86%  Similarity=1.333  Sum_probs=236.7

Q ss_pred             ecccceeecCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEE
Q 023289           43 YNSLGLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFR  122 (284)
Q Consensus        43 ~k~~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yR  122 (284)
                      +|++++||||||||||+++|||||++||||+||||+|+|||++||+||+|+||||||||++||||||||||||++|||||
T Consensus        21 ~kk~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~yR  100 (261)
T PLN00036         21 DKLGGAFAPKPSSGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPKTNENFR  100 (261)
T ss_pred             ccccCeeccCCCCCCCccccccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcCCCCeEE
Confidence            68899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCCCceEEEEcChhhhcceeEEEEeEEEeeCCeeEEEccCCeeeecCCCCCcCCCeEEEecCCceeeeEEeecCCcE
Q 023289          123 LLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNI  202 (284)
Q Consensus       123 vl~D~kGrf~l~~I~~eEA~~KLcKV~~Kt~~kgG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~~kI~d~ikfe~G~~  202 (284)
                      |+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||+||+||||+||+|+|||+||+|||+||+
T Consensus       101 vl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~l  180 (261)
T PLN00036        101 LLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDTIKIDLETNKIVDFIKFDVGNL  180 (261)
T ss_pred             EEECCCceEEEEEcChHHccceEEEEEEEEEecCCeEEEEecCCceeccCCCccccCCEEEEeCCCCceeeEEecCCCCE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeeeEeeceEEEEccCCCceEecCCCCceeeehHHHHHHHHHHHH
Q 023289          203 VMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQA  282 (284)
Q Consensus       203 ~~VtgG~n~GrvG~I~~I~~~~gs~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kGi~~~~~e~r~~~~~~~~  282 (284)
                      ||||||+|+|++|+|.+|+++++++++||++|++|++|+|+++||||||++++||||||++||||++++|||++++++.+
T Consensus       181 ~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~~g~~F~T~~~~vfvIG~~~kp~isLp~~~gi~~~~~e~r~~~~~~~~  260 (261)
T PLN00036        181 VMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLPKGKGIKLSIIEEARKRLAAGQ  260 (261)
T ss_pred             EEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCcCCCCcccchHHHHHHhhhhhc
Confidence            99999999999999999999999999999999999999999999999998899999999999999999999999998764

>PTZ00118 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PTZ00223 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PRK04313 30S ribosomal protein S4e; Validated Back     alignment and domain information
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG0378 consensus 40S ribosomal protein S4 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF00900 Ribosomal_S4e: Ribosomal family S4e; InterPro: IPR013845 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PF08071 RS4NT: RS4NT (NUC023) domain; InterPro: IPR013843 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes Back     alignment and domain information
>smart00363 S4 S4 RNA-binding domain Back     alignment and domain information
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif Back     alignment and domain information
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA Back     alignment and domain information
>PF13275 S4_2: S4 domain; PDB: 1P9K_A Back     alignment and domain information
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type) Back     alignment and domain information
>PRK11507 ribosome-associated protein; Provisional Back     alignment and domain information
>PTZ00155 40S ribosomal protein S9; Provisional Back     alignment and domain information
>PLN00189 40S ribosomal protein S9; Provisional Back     alignment and domain information
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type Back     alignment and domain information
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family Back     alignment and domain information
>PRK04051 rps4p 30S ribosomal protein S4P; Validated Back     alignment and domain information
>PRK05327 rpsD 30S ribosomal protein S4; Validated Back     alignment and domain information
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic Back     alignment and domain information
>CHL00113 rps4 ribosomal protein S4; Reviewed Back     alignment and domain information
>TIGR03069 PS_II_S4 photosystem II S4 domain protein Back     alignment and domain information
>TIGR00478 tly hemolysin TlyA family protein Back     alignment and domain information
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair] Back     alignment and domain information
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated Back     alignment and domain information
>PRK05912 tyrosyl-tRNA synthetase; Validated Back     alignment and domain information
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional Back     alignment and domain information
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional Back     alignment and domain information
>PRK12281 rplX 50S ribosomal protein L24; Reviewed Back     alignment and domain information
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK10475 23S rRNA pseudouridine synthase F; Provisional Back     alignment and domain information
>CHL00141 rpl24 ribosomal protein L24; Validated Back     alignment and domain information
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>PRK00004 rplX 50S ribosomal protein L24; Reviewed Back     alignment and domain information
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional Back     alignment and domain information
>PLN00051 RNA-binding S4 domain-containing protein; Provisional Back     alignment and domain information
>PRK13354 tyrosyl-tRNA synthetase; Provisional Back     alignment and domain information
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown] Back     alignment and domain information
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PTZ00194 60S ribosomal protein L26; Provisional Back     alignment and domain information
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle 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 ?
Query284
3iz6_D265 Localization Of The Small Subunit Ribosomal Protein 1e-121
3izb_D261 Localization Of The Small Subunit Ribosomal Protein 2e-89
2xzm_W260 Crystal Structure Of The Eukaryotic 40s Ribosomal S 7e-69
3zey_1273 High-resolution Cryo-electron Microscopy Structure 1e-62
3j20_E243 Promiscuous Behavior Of Proteins In Archaeal Riboso 4e-26
3kbg_A213 Crystal Structure Of The 30s Ribosomal Protein S4e 1e-19
>pdb|3IZ6|D Chain D, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 265 Back     alignment and structure 
Iteration: 1

 Score =  431 bits (1108), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 203/227 (89%), Positives = 220/227 (96%)
Query: 47  GLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPA 106
           G  APKPSSGPHKSRECLPLIL++RNRLKYALTYREVI+ILMQRHVLVDGKVRTDKTYPA
Sbjct: 25  GAFAPKPSSGPHKSRECLPLILIIRNRLKYALTYREVISILMQRHVLVDGKVRTDKTYPA 84
Query: 107 GFMDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDG 166
           GFMDV+SIPKT EN+RLLYDTKGRFRL S++DE+AKFKLCKVRSVQFGQKGIPY+NTYDG
Sbjct: 85  GFMDVISIPKTGENYRLLYDTKGRFRLQSVKDEDAKFKLCKVRSVQFGQKGIPYLNTYDG 144
Query: 167 RTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGS 226
           RTIRYPDP+IKANDTIK+DLE NKI DFIKFDVGN+VMVTGGRN GRVG+IKNREKHKGS
Sbjct: 145 RTIRYPDPIIKANDTIKIDLETNKIVDFIKFDVGNVVMVTGGRNTGRVGVIKNREKHKGS 204
Query: 227 FETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEE 273
           FETIH++DALGH+FATRLGNVFTIGKG+KPWVSLPKGKGIKLSIIEE
Sbjct: 205 FETIHVEDALGHQFATRLGNVFTIGKGNKPWVSLPKGKGIKLSIIEE 251
>pdb|3IZB|D Chain D, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 261 Back     alignment and structure
>pdb|2XZM|W Chain W, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit In Complex With Initiation Factor 1. This File Contains The 40s Subunit And Initiation Factor For Molecule 1 Length = 260 Back     alignment and structure
>pdb|3ZEY|1 Chain 1, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 273 Back     alignment and structure
>pdb|3J20|E Chain E, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (30s Ribosomal Subunit) Length = 243 Back     alignment and structure
>pdb|3KBG|A Chain A, Crystal Structure Of The 30s Ribosomal Protein S4e From Thermoplasma Acidophilum. Northeast Structural Genomics Consortium Target Tar28 Length = 213 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 ?
Query284
3iz6_D265 40S ribosomal protein S4 (S4E); eukaryotic ribosom 1e-116
3u5c_E261 RP5, S7, YS6, 40S ribosomal protein S4-A; translat 1e-115
2xzm_W260 40S ribosomal protein S4; ribosome, translation; 3 1e-109
3kbg_A213 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2 4e-90
>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Length = 265 Back     alignment and structure
 Score =  332 bits (853), Expect = e-116
 Identities = 209/235 (88%), Positives = 226/235 (96%)

Query: 50  APKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFM 109
           APKPSSGPHKSRECLPLIL++RNRLKYALTYREVI+ILMQRHVLVDGKVRTDKTYPAGFM
Sbjct: 28  APKPSSGPHKSRECLPLILIIRNRLKYALTYREVISILMQRHVLVDGKVRTDKTYPAGFM 87

Query: 110 DVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTI 169
           DV+SIPKT EN+RLLYDTKGRFRL S++DE+AKFKLCKVRSVQFGQKGIPY+NTYDGRTI
Sbjct: 88  DVISIPKTGENYRLLYDTKGRFRLQSVKDEDAKFKLCKVRSVQFGQKGIPYLNTYDGRTI 147

Query: 170 RYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFET 229
           RYPDP+IKANDTIK+DLE NKI DFIKFDVGN+VMVTGGRN GRVG+IKNREKHKGSFET
Sbjct: 148 RYPDPIIKANDTIKIDLETNKIVDFIKFDVGNVVMVTGGRNTGRVGVIKNREKHKGSFET 207

Query: 230 IHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQAAA 284
           IH++DALGH+FATRLGNVFTIGKG+KPWVSLPKGKGIKLSIIEE RKR AA  AA
Sbjct: 208 IHVEDALGHQFATRLGNVFTIGKGNKPWVSLPKGKGIKLSIIEEQRKRDAAAQAA 262
>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_D 3u5g_E Length = 261 Back     alignment and structure
>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W Length = 260 Back     alignment and structure
>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} Length = 213 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query284
3iz6_D265 40S ribosomal protein S4 (S4E); eukaryotic ribosom 100.0
3u5c_E261 RP5, S7, YS6, 40S ribosomal protein S4-A; translat 100.0
2xzm_W260 40S ribosomal protein S4; ribosome, translation; 3 100.0
3j20_E243 30S ribosomal protein S4E; archaea, archaeal, KINK 100.0
3kbg_A213 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2 100.0
1p9k_A79 ORF, hypothetical protein; alfal motif, RNA-bindin 96.76
2cqj_A71 BRMS2, U3 small nucleolar ribonucleoprotein protei 96.72
3j20_D180 30S ribosomal protein S4P; archaea, archaeal, KINK 96.0
1c05_A159 Ribosomal protein S4 delta 41; two subdomains, uni 95.86
3bbn_D201 Ribosomal protein S4; small ribosomal subunit, spi 95.82
2vqe_D209 30S ribosomal protein S4; tRNA-binding, rRNA-bindi 95.2
2do3_A69 Transcription elongation factor SPT5; KOW motif, s 94.94
3u5c_J197 40S ribosomal protein S9-A; translation, ribosome, 94.88
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; 94.88
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergen 94.87
2ckk_A127 KIN17; beta barrel, ribosomal protein, ribonucleop 94.86
2xzm_D181 Ribosomal protein S4 containing protein; ribosome, 94.83
3r8n_D205 30S ribosomal protein S4; protein biosynthesis, RN 94.45
1vio_A243 Ribosomal small subunit pseudouridine synthase A; 94.07
3dh3_A290 Ribosomal large subunit pseudouridine synthase F; 93.49
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RN 93.29
2ktl_A164 Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA s 91.68
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; 91.49
3iz6_C195 40S ribosomal protein S9 (S4P); eukaryotic ribosom 90.85
2jan_A432 Tyrosyl-tRNA synthetase; protein biosynthesis, ami 90.45
3hp7_A291 Hemolysin, putative; structural genomics, APC64019 89.39
1h3f_A432 Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy 88.92
1jil_A420 Tyrrs, tyrosyl-tRNA synthetase; truncation, based 83.88
1vq8_T120 50S ribosomal protein L24P; ribosome 50S, protein- 82.09
1nz9_A58 Transcription antitermination protein NUSG; transc 80.63
3j21_U121 50S ribosomal protein L24P; archaea, archaeal, KIN 80.38
>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Back     alignment and structure
Probab=100.00  E-value=1.8e-107  Score=749.81  Aligned_cols=242  Identities=87%  Similarity=1.359  Sum_probs=199.3

Q ss_pred             ecccceeecCCCCCCCCCcccchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEE
Q 023289           43 YNSLGLQAPKPSSGPHKSRECLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFR  122 (284)
Q Consensus        43 ~k~~g~~a~rpspGPH~~~eslPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yR  122 (284)
                      +|++++||||||||||+++|||||++||||+||||+|++||++||+||+|+||||||||++||||||||||||+|||+||
T Consensus        21 ~kk~~~fa~rpspGPHkl~eslPL~i~LRd~LkyA~t~~EakkIl~q~~VkVDGkvrtD~~~PvG~MDVIsI~kt~e~fR  100 (265)
T 3iz6_D           21 DKLGGAFAPKPSSGPHKSRECLPLILIIRNRLKYALTYREVISILMQRHVLVDGKVRTDKTYPAGFMDVISIPKTGENYR  100 (265)
T ss_dssp             ----------------------CHHHHHHHHHTTSSCSSSTHHHHHTTCCEETTEECCCTTCCCCTTCEEECCSSCCEEE
T ss_pred             ccccceeccCCCCCCCcchhheeeHHHhhhhhcccccHHHHHHHHHCCcEEECCEEeccCCCCCcEEEEEEEcCCCCEEE
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcCCCceEEEEcChhhhcceeEEEEeEEEeeCCeeEEEccCCeeeecCCCCCcCCCeEEEecCCceeeeEEeecCCcE
Q 023289          123 LLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNI  202 (284)
Q Consensus       123 vl~D~kGrf~l~~I~~eEA~~KLcKV~~Kt~~kgG~~ql~thDGrni~~~dp~ik~~DTv~i~l~~~kI~d~ikfe~G~~  202 (284)
                      |+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+||||.||+||||+||+|++||+||||||+||+
T Consensus       101 ll~D~kGrf~l~~I~~eEA~~KLcKV~~k~~~~~G~pql~tHDGrti~~~dp~ik~~DTv~idl~~~kI~d~ikfe~Gnl  180 (265)
T 3iz6_D          101 LLYDTKGRFRLQSVKDEDAKFKLCKVRSVQFGQKGIPYLNTYDGRTIRYPDPIIKANDTIKIDLETNKIVDFIKFDVGNV  180 (265)
T ss_dssp             EEECTTSCEEEEEECHHHHTCEEEEEEEEECCSSSCCEEEETTSCCCBSCSSCCCTTCEEEECSSSCCEEEEECCSTTCE
T ss_pred             EEECCCCcEEEEECChHHcceEEEEEEEEEEccCCceEEEeecceEEecCCCCcccCCEEEEECCCCceeeEEEccCCCE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeeeEeeceEEEEccCCCceEecCCCCceeeehHHHHHHHHHHHH
Q 023289          203 VMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLSIIEEARKRQAAQA  282 (284)
Q Consensus       203 ~~VtgG~n~GrvG~I~~I~~~~gs~~iV~ikd~~g~~F~T~~~nVfvIGk~~kp~IsLp~~kGi~~~~~e~r~~~~~~~~  282 (284)
                      ||||||+|+||+|+|++|++|+||+++||++|++|++|+|+++||||||++++||||||++||||++++|||++|+++++
T Consensus       181 ~mvtgG~n~GriG~I~~ie~~~gs~~iV~vkd~~g~~F~T~~~nvfvIGk~~kp~IsLp~~kg~~~~~~eer~~~~~~~~  260 (265)
T 3iz6_D          181 VMVTGGRNTGRVGVIKNREKHKGSFETIHVEDALGHQFATRLGNVFTIGKGNKPWVSLPKGKGIKLSIIEEQRKRDAAAQ  260 (265)
T ss_dssp             EEECSSSSCSCEEEEEEEECCSSSCCEEEECCCSSCCEEEEGGGEEEEECSSCCCCCCCCCC------------------
T ss_pred             EEEEcCCcceEEEEEEEEEEecCCCcEEEEEECCCCeEEEEeCeEEEEccCCCeeEeCCCCCceeeehHHhHHHHHHHhh
Confidence            99999999999999999999999999999999999999999999999999889999999999999999999999999887


Q ss_pred             hC
Q 023289          283 AA  284 (284)
Q Consensus       283 ~~  284 (284)
                      ++
T Consensus       261 ~~  262 (265)
T 3iz6_D          261 AA  262 (265)
T ss_dssp             --
T ss_pred             hh
Confidence            53
>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_D 3u5g_E Back     alignment and structure
>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W Back     alignment and structure
>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} Back     alignment and structure
>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston structural genomics initiative, BSGI; NMR {Escherichia coli} SCOP: d.66.1.6 Back     alignment and structure
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3j20_D 30S ribosomal protein S4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C Back     alignment and structure
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ... Back     alignment and structure
>2do3_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: b.34.5.5 Back     alignment and structure
>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D* Back     alignment and structure
>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A* Back     alignment and structure
>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A Back     alignment and structure
>2ckk_A KIN17; beta barrel, ribosomal protein, ribonucleoprotein, nuclear protein; 1.45A {Homo sapiens} Back     alignment and structure
>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D Back     alignment and structure
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5 Back     alignment and structure
>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} Back     alignment and structure
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} Back     alignment and structure
>2ktl_A Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA synthetase, ligase; NMR {Aspergillus nidulans fgsc A4} Back     alignment and structure
>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A Back     alignment and structure
>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Back     alignment and structure
>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis} Back     alignment and structure
>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein STR initiative, midwest center for structural genomics, MCSG; HET: MSE; 1.53A {Streptococcus thermophilus} Back     alignment and structure
>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYE; 2.00A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4 PDB: 1h3e_A* Back     alignment and structure
>1jil_A Tyrrs, tyrosyl-tRNA synthetase; truncation, based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A* Back     alignment and structure
>1vq8_T 50S ribosomal protein L24P; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: b.34.5.1 PDB: 1vq4_T* 1vq5_T* 1vq6_T* 1vq7_T* 1s72_T* 1vq9_T* 1vqk_T* 1vql_T* 1vqm_T* 1vqn_T* 1vqo_T* 1vqp_T* 1yhq_T* 1yi2_T* 1yij_T* 1yit_T* 1yj9_T* 1yjn_T* 1yjw_T* 2otj_T* ... Back     alignment and structure
>1nz9_A Transcription antitermination protein NUSG; transcription elongation, riken structural genomics/proteomics initiative, RSGI; NMR {Thermus thermophilus} SCOP: b.34.5.4 Back     alignment and structure
>3j21_U 50S ribosomal protein L24P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query284
d1p9ka_79 Hypothetical protein YbcJ {Escherichia coli [TaxId 97.19
d1vioa258 Pseudouridine synthase RsuA N-terminal domain {Hae 97.14
d1kska359 Pseudouridine synthase RsuA N-terminal domain {Esc 96.94
d1h3fa281 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 96.93
d1c06a_159 Ribosomal protein S4 {Bacillus stearothermophilus 96.9
d1jh3a_99 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 96.76
d2uubd1208 Ribosomal protein S4 {Thermus thermophilus [TaxId: 96.39
d1dm9a_104 Heat shock protein 15 kD {Escherichia coli [TaxId: 96.3
d2gy9d1204 Ribosomal protein S4 {Escherichia coli [TaxId: 562 96.05
d2do3a162 Transcription elongation factor SPT5 {Human (Homo 95.62
d1nz9a_58 N-utilization substance G protein NusG, C-terminal 86.45
d1nppa258 N-utilization substance G protein NusG, C-terminal 82.67
d1vqot1119 Ribosomal proteins L24 (L24p) {Archaeon Haloarcula 82.22
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: YbcJ-like
domain: Hypothetical protein YbcJ
species: Escherichia coli [TaxId: 562]

Probab=97.19  E-value=6.9e-05  Score=55.38  Aligned_cols=59  Identities=19%  Similarity=0.173  Sum_probs=52.1

Q ss_pred             cchhHHHHHhhhcccccHHHHHHHHhCceEEECCEEeccccCCCcceeEEEeccCCceEEEE
Q 023289           63 CLPLILVLRNRLKYALTYREVIAILMQRHVLVDGKVRTDKTYPAGFMDVVSIPKTNENFRLL  124 (284)
Q Consensus        63 slPL~i~LRd~LkyA~t~rEakkIl~~g~VkVDGkvrtD~kfPVG~MDVIsI~kt~e~yRvl  124 (284)
                      -+-|.=||-. .+++.+.+||++.+.+|.|.|||++.+++.+.|--=|+|+++  |+.++++
T Consensus        20 ~irL~k~L~~-~gl~~Sr~eAk~lI~~G~V~VNG~~~~~p~~~V~~~d~I~vd--G~~i~iv   78 (79)
T d1p9ka_          20 HVELCDLLKL-EGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFA--GHSVQVV   78 (79)
T ss_dssp             CCCHHHHHHH-HTSCSSSSTTSHHHHHHHHEETTBCCCCSSCCCCSSEEEEET--TEEEEEE
T ss_pred             cEEHHHHHHH-CCCccCHHHHHHHHHhCCcccCCEEeccccccCCCCCEEEEC--CEEEEEE
Confidence            3667777776 589999999999999999999999999999999999999996  7877765
>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2do3a1 b.34.5.5 (A:462-523) Transcription elongation factor SPT5 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1nz9a_ b.34.5.4 (A:) N-utilization substance G protein NusG, C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1nppa2 b.34.5.4 (A:191-248) N-utilization substance G protein NusG, C-terminal domain {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1vqot1 b.34.5.1 (T:1-119) Ribosomal proteins L24 (L24p) {Archaeon Haloarcula marismortui [TaxId: 2238]} Back     information, alignment and structure