Citrus Sinensis ID: 040226

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-------
MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILIISQILSNKALRSCGLM
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEcccEEEEEEEEcccccccccccHHHHHHHHHHHHHHccccccEEEEEEEcccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHccccEEEEc
ccHHHHHHHHHHHcccHHHHHHHHHHHHHHHcccccEEEEEccccEEEEEEEEccccEccccccHHHHHHHHHHHHcccccccEEEEEEEcccccccHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHcccccEEEc
MATQISKKRKFVADGVFFAELNEVLTRELaedgysgvevrvtPVRTEIIIRATRTqnvlgekgrRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILIISQILSNKalrscglm
matqiskkrkfvadgvFFAELNEVLTrelaedgysgvevrvtpvrteiiiratrtqnvlgekgrrireltsvvqkrfkfpensVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILIISqilsnkalrscglm
MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILIISQILSNKALRSCGLM
*********KFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILIISQILSNKAL******
******K*RKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILIISQILSNKALRSCGLM
MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILIISQILSNKALRSCGLM
*ATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILIISQILSNKALRSCGLM
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MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILIISQILSNKALRSCGLM
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 ?
Query137 2.2.26 [Sep-21-2011]
Q9SIP7 250 40S ribosomal protein S3- yes no 0.978 0.536 0.843 6e-60
Q9FJA6 248 40S ribosomal protein S3- no no 0.978 0.540 0.835 1e-59
Q9M339 249 40S ribosomal protein S3- no no 0.978 0.538 0.835 4e-59
P62909 243 40S ribosomal protein S3 yes no 0.978 0.551 0.798 3e-55
P62908 243 40S ribosomal protein S3 yes no 0.978 0.551 0.798 3e-55
E2RH47 243 40S ribosomal protein S3 yes no 0.978 0.551 0.798 3e-55
Q0Z8U2 243 40S ribosomal protein S3 yes no 0.978 0.551 0.798 3e-55
P23396 243 40S ribosomal protein S3 yes no 0.978 0.551 0.798 3e-55
Q3T169 243 40S ribosomal protein S3 yes no 0.978 0.551 0.798 3e-55
P02350 246 40S ribosomal protein S3- N/A no 0.978 0.544 0.798 5e-55
>sp|Q9SIP7|RS31_ARATH 40S ribosomal protein S3-1 OS=Arabidopsis thaliana GN=RPS3A PE=1 SV=1 Back     alignment and function desciption
 Score =  228 bits (582), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 113/134 (84%), Positives = 121/134 (90%)

Query: 1   MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
           MATQISKKRKFVADGVF+AELNEVLTRELAEDGYSGVEVRVTP+RTEIIIRATRTQNVLG
Sbjct: 1   MATQISKKRKFVADGVFYAELNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLG 60

Query: 61  EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL 120
           EKGRRIRELTS+VQKRFKFP +SVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRR   
Sbjct: 61  EKGRRIRELTSLVQKRFKFPVDSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACY 120

Query: 121 IISQILSNKALRSC 134
            + + +     + C
Sbjct: 121 GVLRFVMESGAKGC 134

Arabidopsis thaliana (taxid: 3702)
>sp|Q9FJA6|RS33_ARATH 40S ribosomal protein S3-3 OS=Arabidopsis thaliana GN=RPS3C PE=1 SV=1 Back     alignment and function description
>sp|Q9M339|RS32_ARATH 40S ribosomal protein S3-2 OS=Arabidopsis thaliana GN=RPS3B PE=1 SV=1 Back     alignment and function description
>sp|P62909|RS3_RAT 40S ribosomal protein S3 OS=Rattus norvegicus GN=Rps3 PE=1 SV=1 Back     alignment and function description
>sp|P62908|RS3_MOUSE 40S ribosomal protein S3 OS=Mus musculus GN=Rps3 PE=1 SV=1 Back     alignment and function description
>sp|E2RH47|RS3_CANFA 40S ribosomal protein S3 OS=Canis familiaris GN=RPS3 PE=1 SV=1 Back     alignment and function description
>sp|Q0Z8U2|RS3_PIG 40S ribosomal protein S3 OS=Sus scrofa GN=RPS3 PE=2 SV=1 Back     alignment and function description
>sp|P23396|RS3_HUMAN 40S ribosomal protein S3 OS=Homo sapiens GN=RPS3 PE=1 SV=2 Back     alignment and function description
>sp|Q3T169|RS3_BOVIN 40S ribosomal protein S3 OS=Bos taurus GN=RPS3 PE=2 SV=1 Back     alignment and function description
>sp|P02350|RS31_XENLA 40S ribosomal protein S3-A OS=Xenopus laevis GN=rps3-a PE=2 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 ?
Query137
449446618 243 PREDICTED: 40S ribosomal protein S3-3-li 0.978 0.551 0.865 1e-59
449447888236 PREDICTED: 40S ribosomal protein S3-3-li 0.978 0.567 0.865 1e-59
224121646178 predicted protein [Populus trichocarpa] 0.861 0.662 0.974 2e-59
225444782234 PREDICTED: 40S ribosomal protein S3-3 [V 0.978 0.572 0.858 2e-59
359476269235 PREDICTED: 40S ribosomal protein S3-3-li 0.978 0.570 0.858 3e-59
225442156234 PREDICTED: 40S ribosomal protein S3-3 [V 0.978 0.572 0.858 3e-59
224141685234 predicted protein [Populus trichocarpa] 0.978 0.572 0.858 5e-59
224088766236 predicted protein [Populus trichocarpa] 0.978 0.567 0.858 5e-59
118488288232 unknown [Populus trichocarpa] 0.978 0.577 0.858 6e-59
224135747233 predicted protein [Populus trichocarpa] 0.978 0.575 0.858 6e-59
>gi|449446618|ref|XP_004141068.1| PREDICTED: 40S ribosomal protein S3-3-like [Cucumis sativus] gi|449488075|ref|XP_004157933.1| PREDICTED: 40S ribosomal protein S3-3-like [Cucumis sativus] Back     alignment and taxonomy information
 Score =  234 bits (596), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 116/134 (86%), Positives = 122/134 (91%)

Query: 1   MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
           MATQ+SKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTP+RTEIIIRATRTQNVLG
Sbjct: 1   MATQMSKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLG 60

Query: 61  EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL 120
           EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRR   
Sbjct: 61  EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACY 120

Query: 121 IISQILSNKALRSC 134
            + + +     + C
Sbjct: 121 GVLRFVMESGAKGC 134

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|449447888|ref|XP_004141698.1| PREDICTED: 40S ribosomal protein S3-3-like [Cucumis sativus] gi|449521735|ref|XP_004167885.1| PREDICTED: 40S ribosomal protein S3-3-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|224121646|ref|XP_002318635.1| predicted protein [Populus trichocarpa] gi|222859308|gb|EEE96855.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|225444782|ref|XP_002279950.1| PREDICTED: 40S ribosomal protein S3-3 [Vitis vinifera] gi|297738588|emb|CBI27833.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|359476269|ref|XP_002281141.2| PREDICTED: 40S ribosomal protein S3-3-like [Vitis vinifera] gi|296081703|emb|CBI20708.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|225442156|ref|XP_002275541.1| PREDICTED: 40S ribosomal protein S3-3 [Vitis vinifera] gi|297743020|emb|CBI35887.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|224141685|ref|XP_002324195.1| predicted protein [Populus trichocarpa] gi|118483222|gb|ABK93514.1| unknown [Populus trichocarpa] gi|118487214|gb|ABK95435.1| unknown [Populus trichocarpa] gi|222865629|gb|EEF02760.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224088766|ref|XP_002308530.1| predicted protein [Populus trichocarpa] gi|118483836|gb|ABK93809.1| unknown [Populus trichocarpa] gi|118485378|gb|ABK94546.1| unknown [Populus trichocarpa] gi|222854506|gb|EEE92053.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|118488288|gb|ABK95963.1| unknown [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224135747|ref|XP_002322150.1| predicted protein [Populus trichocarpa] gi|222869146|gb|EEF06277.1| predicted protein [Populus trichocarpa] 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 ?
Query137
TAIR|locus:2065863 250 AT2G31610 [Arabidopsis thalian 0.978 0.536 0.843 7e-54
TAIR|locus:2084490 249 AT3G53870 [Arabidopsis thalian 0.978 0.538 0.835 1.9e-53
TAIR|locus:2169518 248 AT5G35530 [Arabidopsis thalian 0.978 0.540 0.835 1.9e-53
UNIPROTKB|F1N9X5 243 RPS3 "Uncharacterized protein" 0.978 0.551 0.798 9.5e-50
UNIPROTKB|Q3T169 243 RPS3 "40S ribosomal protein S3 0.978 0.551 0.798 9.5e-50
UNIPROTKB|E2RH47 243 RPS3 "40S ribosomal protein S3 0.978 0.551 0.798 9.5e-50
UNIPROTKB|P23396 243 RPS3 "40S ribosomal protein S3 0.978 0.551 0.798 9.5e-50
UNIPROTKB|Q0Z8U2 243 RPS3 "40S ribosomal protein S3 0.978 0.551 0.798 9.5e-50
MGI|MGI:1350917 243 Rps3 "ribosomal protein S3" [M 0.978 0.551 0.798 9.5e-50
RGD|619888 243 Rps3 "ribosomal protein S3" [R 0.978 0.551 0.798 9.5e-50
TAIR|locus:2065863 AT2G31610 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 557 (201.1 bits), Expect = 7.0e-54, P = 7.0e-54
 Identities = 113/134 (84%), Positives = 121/134 (90%)

Query:     1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
             MATQISKKRKFVADGVF+AELNEVLTRELAEDGYSGVEVRVTP+RTEIIIRATRTQNVLG
Sbjct:     1 MATQISKKRKFVADGVFYAELNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLG 60

Query:    61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL 120
             EKGRRIRELTS+VQKRFKFP +SVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRR   
Sbjct:    61 EKGRRIRELTSLVQKRFKFPVDSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACY 120

Query:   121 IISQILSNKALRSC 134
              + + +     + C
Sbjct:   121 GVLRFVMESGAKGC 134
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:0015935 "small ribosomal subunit" evidence=IEA
GO:0022627 "cytosolic small ribosomal subunit" evidence=ISS;IDA
GO:0009507 "chloroplast" evidence=IDA
GO:0005773 "vacuole" evidence=IDA
GO:0022626 "cytosolic ribosome" evidence=IDA
GO:0005774 "vacuolar membrane" evidence=IDA
GO:0016020 "membrane" evidence=IDA
GO:0009651 "response to salt stress" evidence=IEP
GO:0005829 "cytosol" evidence=IDA
GO:0009506 "plasmodesma" evidence=IDA
GO:0005794 "Golgi apparatus" evidence=RCA
TAIR|locus:2084490 AT3G53870 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2169518 AT5G35530 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|F1N9X5 RPS3 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q3T169 RPS3 "40S ribosomal protein S3" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2RH47 RPS3 "40S ribosomal protein S3" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|P23396 RPS3 "40S ribosomal protein S3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q0Z8U2 RPS3 "40S ribosomal protein S3" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:1350917 Rps3 "ribosomal protein S3" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|619888 Rps3 "ribosomal protein S3" [Rattus norvegicus (taxid:10116)] 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) ?
Q5R465RS3_PONABNo assigned EC number0.79100.97810.5514yesno
P48152RS3_CAEELNo assigned EC number0.76990.82480.4574yesno
O60128RS3_SCHPONo assigned EC number0.82750.84670.4658yesno
E2RH47RS3_CANFANo assigned EC number0.79850.97810.5514yesno
Q0Z8U2RS3_PIGNo assigned EC number0.79850.97810.5514yesno
P23396RS3_HUMANNo assigned EC number0.79850.97810.5514yesno
Q3T169RS3_BOVINNo assigned EC number0.79850.97810.5514yesno
P62909RS3_RATNo assigned EC number0.79850.97810.5514yesno
P62908RS3_MOUSENo assigned EC number0.79850.97810.5514yesno
Q06559RS3_DROMENo assigned EC number0.73070.94890.5284yesno
P90526RS3_DICDINo assigned EC number0.60600.95620.6009yesno
Q9SIP7RS31_ARATHNo assigned EC number0.84320.97810.536yesno

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:
GSVIVG00016476001
SubName- Full=Chromosome chr11 scaffold_13, whole genome shotgun sequence; (234 aa)
(Vitis vinifera)
Predicted Functional Partners:
GSVIVG00025575001
SubName- Full=Chromosome chr8 scaffold_34, whole genome shotgun sequence; (307 aa)
•  •••• 0.989
GSVIVG00016417001
SubName- Full=Chromosome chr11 scaffold_13, whole genome shotgun sequence; (83 aa)
•  •••• 0.976
GSVIVG00023139001
SubName- Full=Chromosome chr8 scaffold_29, whole genome shotgun sequence; (136 aa)
   •••• 0.960
GSVIVG00018552001
SubName- Full=Chromosome chr13 scaffold_17, whole genome shotgun sequence; (155 aa)
•  •••• 0.952
GSVIVG00031140001
SubName- Full=Chromosome chr14 scaffold_54, whole genome shotgun sequence; (234 aa)
   •••• 0.951
GSVIVG00034206001
SubName- Full=Putative uncharacterized protein (Chromosome chr9 scaffold_7, whole genome shotgu [...] (129 aa)
•  •••• 0.946
GSVIVG00018776001
SubName- Full=Chromosome chr12 scaffold_18, whole genome shotgun sequence; (173 aa)
•  •••• 0.944
GSVIVG00035844001
SubName- Full=Chromosome chr10 scaffold_81, whole genome shotgun sequence; (173 aa)
•  •••• 0.942
GSVIVG00024035001
SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (246 aa)
•  •••• 0.939
GSVIVG00028518001
SubName- Full=Chromosome chr5 scaffold_2, whole genome shotgun sequence (Chromosome chr7 scaffo [...] (125 aa)
•  • •• 0.939

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 ?
Query137
PTZ00084220 PTZ00084, PTZ00084, 40S ribosomal protein S3; Prov 3e-71
cd0241381 cd02413, 40S_S3_KH, K homology RNA-binding (KH) do 2e-49
TIGR01008195 TIGR01008, rpsC_E_A, ribosomal protein S3, eukaryo 4e-34
COG0092233 COG0092, RpsC, Ribosomal protein S3 [Translation, 3e-24
cd0241185 cd02411, archeal_30S_S3_KH, K homology RNA-binding 6e-15
PRK04191207 PRK04191, rps3p, 30S ribosomal protein S3P; Review 5e-14
pfam0765077 pfam07650, KH_2, KH domain 6e-14
cd0240968 cd02409, KH-II, KH-II (K homology RNA-binding doma 3e-08
>gnl|CDD|240260 PTZ00084, PTZ00084, 40S ribosomal protein S3; Provisional Back     alignment and domain information 
 Score =  212 bits (542), Expect = 3e-71
 Identities = 96/115 (83%), Positives = 106/115 (92%)

Query: 3   TQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEK 62
            QISKKRKFVADGVF+AELNE L+RELAEDGYSGVEVRVTP+RTEIIIRATRT+ VLG+K
Sbjct: 3   GQISKKRKFVADGVFYAELNEFLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDK 62

Query: 63  GRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRR 117
           GRRIRELTS++QKRF FPE  VEL+AE+V NRGLCA+AQAESLRYKLL GL VRR
Sbjct: 63  GRRIRELTSLLQKRFGFPEGKVELFAERVENRGLCAMAQAESLRYKLLEGLPVRR 117

Length = 220
>gnl|CDD|239096 cd02413, 40S_S3_KH, K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3 Back     alignment and domain information
>gnl|CDD|130081 TIGR01008, rpsC_E_A, ribosomal protein S3, eukaryotic/archaeal type Back     alignment and domain information
>gnl|CDD|223170 COG0092, RpsC, Ribosomal protein S3 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|239094 cd02411, archeal_30S_S3_KH, K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein Back     alignment and domain information
>gnl|CDD|235247 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed Back     alignment and domain information
>gnl|CDD|203707 pfam07650, KH_2, KH domain Back     alignment and domain information
>gnl|CDD|239092 cd02409, KH-II, KH-II (K homology RNA-binding domain, type II) Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 137
PTZ00084220 40S ribosomal protein S3; Provisional 100.0
COG0092233 RpsC Ribosomal protein S3 [Translation, ribosomal 100.0
TIGR01008195 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal 100.0
PRK04191207 rps3p 30S ribosomal protein S3P; Reviewed 100.0
CHL00048214 rps3 ribosomal protein S3 100.0
TIGR01009211 rpsC_bact ribosomal protein S3, bacterial type. TI 100.0
PRK00310232 rpsC 30S ribosomal protein S3; Reviewed 100.0
KOG3181 244 consensus 40S ribosomal protein S3 [Translation, r 99.95
cd0241381 40S_S3_KH K homology RNA-binding (KH) domain of th 99.91
cd0241185 archeal_30S_S3_KH K homology RNA-binding domain (K 99.89
cd02412109 30S_S3_KH K homology RNA-binding (KH) domain of th 99.85
PF0765078 KH_2: KH domain syndrome, contains KH motifs.; Int 99.7
cd0240968 KH-II KH-II (K homology RNA-binding domain, type I 99.09
smart0032269 KH K homology RNA-binding domain. 98.07
cd0241477 jag_KH jag_K homology RNA-binding domain. The KH d 97.56
PF0018985 Ribosomal_S3_C: Ribosomal protein S3, C-terminal d 97.51
PF1308373 KH_4: KH domain; PDB: 3GKU_B. 97.43
cd02410145 archeal_CPSF_KH The archaeal cleavage and polyaden 96.92
PRK0106478 hypothetical protein; Provisional 96.61
COG1847208 Jag Predicted RNA-binding protein [General functio 96.56
cd0213461 NusA_KH NusA_K homology RNA-binding domain (KH). N 95.49
PRK0282177 hypothetical protein; Provisional 95.21
COG1159298 Era GTPase [General function prediction only] 95.2
PRK08406140 transcription elongation factor NusA-like protein; 95.14
PRK0046875 hypothetical protein; Provisional 94.19
PRK15494339 era GTPase Era; Provisional 93.45
COG183776 Predicted RNA-binding protein (contains KH domain) 93.22
TIGR00436270 era GTP-binding protein Era. Era is an essential G 93.17
PRK00089292 era GTPase Era; Reviewed 92.95
COG1782 637 Predicted metal-dependent RNase, consists of a met 92.7
TIGR03675 630 arCOG00543 arCOG00543 universal archaeal KH-domain 92.57
TIGR01952141 nusA_arch NusA family KH domain protein, archaeal. 90.04
cd0239361 PNPase_KH Polynucleotide phosphorylase (PNPase) K 88.14
PRK06418166 transcription elongation factor NusA-like protein; 85.64
PF1301443 KH_3: KH domain 85.16
>PTZ00084 40S ribosomal protein S3; Provisional Back     alignment and domain information 
Probab=100.00  E-value=1.7e-43  Score=280.03  Aligned_cols=134  Identities=73%  Similarity=1.141  Sum_probs=130.0

Q ss_pred             cchhhhHhHHHhhHHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCC
Q 040226            3 TQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPEN   82 (137)
Q Consensus         3 ~~~~~~~~fi~~~~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~   82 (137)
                      .|++++++|++|++.+++||+||.++|.++|||+|+|+|+++.++|+|||++||++||++|+++++|++.|++.|+++++
T Consensus         3 ~~~~~~k~fi~~~~~~~~~re~l~k~~~~agis~ieI~Rt~~~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~~~~~~   82 (220)
T PTZ00084          3 GQISKKRKFVADGVFYAELNEFLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIRELTSLLQKRFGFPEG   82 (220)
T ss_pred             cccchhhHHHHcchhhHHHHHHHHHHHHHCCcceEEEEEcCCcEEEEEEECCCccEEcCCchHHHHHHHHHHHHhCCCCc
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999998889


Q ss_pred             eEEEEEEEecCCCcCHHHHHHHHHHHHHcChHHHHHHH-HHHHHHhcccccccccC
Q 040226           83 SVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL-IISQILSNKALRSCGLM  137 (137)
Q Consensus        83 ~i~I~i~ev~~P~l~A~liA~~ia~qLe~Rv~fRRa~k-ai~~a~~~ga~kG~~~~  137 (137)
                      +++|+|.||++|++||.++|++||+|||+|+||||||+ ++++||++|| +||++.
T Consensus        83 ~i~i~v~ev~~P~l~A~lvA~~IA~qLe~rv~FRRa~k~ai~~~m~aGa-kGikI~  137 (220)
T PTZ00084         83 KVELFAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESGA-KGCEVI  137 (220)
T ss_pred             eEEEEEEEecCCCcCHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHcCC-ceEEEE
Confidence            99999999999999999999999999999999999999 9999999996 999873

>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type Back     alignment and domain information
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed Back     alignment and domain information
>CHL00048 rps3 ribosomal protein S3 Back     alignment and domain information
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type Back     alignment and domain information
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed Back     alignment and domain information
>KOG3181 consensus 40S ribosomal protein S3 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3 Back     alignment and domain information
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein Back     alignment and domain information
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3 Back     alignment and domain information
>PF07650 KH_2: KH domain syndrome, contains KH motifs Back     alignment and domain information
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II) Back     alignment and domain information
>smart00322 KH K homology RNA-binding domain Back     alignment and domain information
>cd02414 jag_KH jag_K homology RNA-binding domain Back     alignment and domain information
>PF00189 Ribosomal_S3_C: Ribosomal protein S3, C-terminal domain; InterPro: IPR001351 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PF13083 KH_4: KH domain; PDB: 3GKU_B Back     alignment and domain information
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH) Back     alignment and domain information
>PRK01064 hypothetical protein; Provisional Back     alignment and domain information
>COG1847 Jag Predicted RNA-binding protein [General function prediction only] Back     alignment and domain information
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH) Back     alignment and domain information
>PRK02821 hypothetical protein; Provisional Back     alignment and domain information
>COG1159 Era GTPase [General function prediction only] Back     alignment and domain information
>PRK08406 transcription elongation factor NusA-like protein; Validated Back     alignment and domain information
>PRK00468 hypothetical protein; Provisional Back     alignment and domain information
>PRK15494 era GTPase Era; Provisional Back     alignment and domain information
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only] Back     alignment and domain information
>TIGR00436 era GTP-binding protein Era Back     alignment and domain information
>PRK00089 era GTPase Era; Reviewed Back     alignment and domain information
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only] Back     alignment and domain information
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein Back     alignment and domain information
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal Back     alignment and domain information
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH) Back     alignment and domain information
>PRK06418 transcription elongation factor NusA-like protein; Validated Back     alignment and domain information
>PF13014 KH_3: KH domain 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 ?
Query137
3iz6_B227 Localization Of The Small Subunit Ribosomal Protein 2e-57
2zkq_c 243 Structure Of A Mammalian Ribosomal 40s Subunit With 3e-56
3izb_B 240 Localization Of The Small Subunit Ribosomal Protein 4e-45
1s1h_C192 Structure Of The Ribosomal 80s-Eef2-Sordarin Comple 1e-44
3jyv_C188 Structure Of The 40s Rrna And Proteins And PE TRNA 4e-44
3zey_X214 High-resolution Cryo-electron Microscopy Structure 2e-38
1wh9_A92 Solution Structure Of The Kh Domain Of Human Riboso 7e-34
2xzm_C 243 Crystal Structure Of The Eukaryotic 40s Ribosomal S 1e-29
3j20_C210 Promiscuous Behavior Of Proteins In Archaeal Riboso 2e-10
>pdb|3IZ6|B Chain B, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 227 Back     alignment and structure 
Iteration: 1

 Score =  217 bits (552), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 109/134 (81%), Positives = 118/134 (88%)
Query: 1   MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
           MATQISKK+KFV+DGVF+AELNE+LTRELAEDGYSGVEVRVTP+RTEIIIRATRTQNVLG
Sbjct: 1   MATQISKKKKFVSDGVFYAELNEMLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLG 60
Query: 61  EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL 120
           EKGRRIRELTSVVQKRF F EN VELYAEKV NRGLCAIAQAESLRYKLLGGLAVRR   
Sbjct: 61  EKGRRIRELTSVVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRACY 120
Query: 121 IISQILSNKALRSC 134
            + + +     + C
Sbjct: 121 GVLRFVMESGAKGC 134
>pdb|2ZKQ|CC Chain c, Structure Of A Mammalian Ribosomal 40s Subunit Within An 80s Complex Obtained By Docking Homology Models Of The Rna And Proteins Into An 8.7 A Cryo-Em Map Length = 243 Back     alignment and structure
>pdb|3IZB|B Chain B, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 240 Back     alignment and structure
>pdb|1S1H|C Chain C, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From Yeast Obtained By Docking Atomic Models For Rna And Protein Components Into A 11.7 A Cryo-Em Map. This File, 1s1h, Contains 40s Subunit. The 60s Ribosomal Subunit Is In File 1s1i Length = 192 Back     alignment and structure
>pdb|3JYV|C Chain C, Structure Of The 40s Rrna And Proteins And PE TRNA FOR EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution Length = 188 Back     alignment and structure
>pdb|3ZEY|X Chain X, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 214 Back     alignment and structure
>pdb|1WH9|A Chain A, Solution Structure Of The Kh Domain Of Human Ribosomal Protein S3 Length = 92 Back     alignment and structure
>pdb|2XZM|C Chain C, 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 = 243 Back     alignment and structure
>pdb|3J20|C Chain C, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (30s Ribosomal Subunit) Length = 210 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 ?
Query137
3u5c_D 240 RP13, YS3, 40S ribosomal protein S3; translation, 2e-53
2zkq_c 243 40S ribosomal protein S3E; protein-RNA complex, 40 1e-52
3iz6_B227 40S ribosomal protein S3 (S3P); eukaryotic ribosom 2e-52
2xzm_C 243 KH domain containing protein; ribosome, translatio 7e-49
1wh9_A92 40S ribosomal protein S3; KH domain, structural ge 2e-39
>3u5c_D RP13, YS3, 40S ribosomal protein S3; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_B 3o30_C 3o2z_C 3u5g_D 1s1h_C 3jyv_C* Length = 240 Back     alignment and structure
 Score =  167 bits (424), Expect = 2e-53
 Identities = 84/117 (71%), Positives = 100/117 (85%)

Query: 1   MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
           M   ISKKRK VADGVF+AELNE  TRELAE+GYSGVEVRVTP +TE+IIRATRTQ+VLG
Sbjct: 1   MVALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLG 60

Query: 61  EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRR 117
           E GRRI ELT +VQKRFK+   ++ LYAE+V +RGL A+AQAES+++KLL GLA+RR
Sbjct: 61  ENGRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRR 117
>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 243 Back     alignment and structure
>3iz6_B 40S ribosomal protein S3 (S3P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} PDB: 1s1h_C 3jyv_C* Length = 227 Back     alignment and structure
>2xzm_C KH domain containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_C Length = 243 Back     alignment and structure
>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Homo sapiens} SCOP: d.52.3.1 Length = 92 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query137
3u5c_D 240 RP13, YS3, 40S ribosomal protein S3; translation, 100.0
3iz6_B227 40S ribosomal protein S3 (S3P); eukaryotic ribosom 100.0
2zkq_c 243 40S ribosomal protein S3E; protein-RNA complex, 40 100.0
3j20_C210 30S ribosomal protein S3P; archaea, archaeal, KINK 100.0
2xzm_C 243 KH domain containing protein; ribosome, translatio 100.0
3r8n_C206 30S ribosomal protein S3; protein biosynthesis, RN 100.0
3i1m_C233 30S ribosomal protein S3; ribosome structure, prot 100.0
2vqe_C239 30S ribosomal protein S3; tRNA-binding, rRNA-bindi 100.0
3bbn_C218 Ribosomal protein S3; small ribosomal subunit, spi 100.0
1wh9_A92 40S ribosomal protein S3; KH domain, structural ge 99.95
2pt7_G152 HP1451, hypothetical protein; ATPase, protein-prot 97.02
3gku_A225 Probable RNA-binding protein; APC21302, clostridiu 95.1
1ec6_A87 RNA-binding protein NOVA-2; KH domain, alpha-beta 91.62
1ega_A301 Protein (GTP-binding protein ERA); GTPase, RNA-bin 88.5
3iev_A308 GTP-binding protein ERA; ERA, GTPase, KH domain, a 88.42
2cxc_A144 NUSA; transcription termination, RNA binding prote 87.07
1dtj_A76 RNA-binding neurooncological ventral antigen 2; KH 84.12
2opv_A85 KHSRP protein; KH domain, RNA binding protein, KSR 84.12
2axy_A73 Poly(RC)-binding protein 2; protein-DNA complex, D 82.85
1zzk_A82 Heterogeneous nuclear ribonucleoprotein K; KH domi 82.79
1we8_A104 Tudor and KH domain containing protein; structural 82.09
1wvn_A82 Poly(RC)-binding protein 1; KH domain, RNA binding 81.72
1wf3_A301 GTP-binding protein; GTPase, riken structural geno 80.92
1x4m_A94 FAR upstream element binding protein 1; KH domain, 80.9
2hh3_A106 KH-type splicing regulatory protein; KH-RNA bindin 80.81
2hh2_A107 KH-type splicing regulatory protein; KH-RNA bindin 80.81
2p2r_A76 Poly(RC)-binding protein 2; protein-DNA complex, R 80.13
>3u5c_D RP13, YS3, 40S ribosomal protein S3; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_B 3o30_C 3o2z_C 3u5g_D 1s1h_C 3jyv_C* Back     alignment and structure
Probab=100.00  E-value=8.1e-44  Score=283.29  Aligned_cols=135  Identities=64%  Similarity=1.010  Sum_probs=130.6

Q ss_pred             CccchhhhHhHHHhhHHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCC
Q 040226            1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFP   80 (137)
Q Consensus         1 m~~~~~~~~~fi~~~~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~   80 (137)
                      |+.+++.+++|++|+.++++||+||.++|.++|||+|+|+|++++++|+||+++||+|||++|+++++|++.|+++|++.
T Consensus         1 ~~~~~~~~~k~vadg~~~~~ire~l~k~l~~agis~IeI~Rt~~~i~I~I~t~rPg~VIGkkG~~I~~L~~~l~k~~~~~   80 (240)
T 3u5c_D            1 MVALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENGRRINELTLLVQKRFKYA   80 (240)
T ss_dssp             --CCCCHHHHHHHHHHHHHHHHHHHHHHTGGGTEEEEEEEECSSCEEEEEEESCHHHHHTTTTCTHHHHHHHHHHHHTCC
T ss_pred             CcccccccceEeecCchHHHHHHHHHHHHHhCCcceEEEEEcCCeEEEEEEeCCCceEEcCCchhHHHHHHHHHHHhCCC
Confidence            78888999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CCeEEEEEEEecCCCcCHHHHHHHHHHHHHcChHHHHHHH-HHHHHHhccccccccc
Q 040226           81 ENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL-IISQILSNKALRSCGL  136 (137)
Q Consensus        81 ~~~i~I~i~ev~~P~l~A~liA~~ia~qLe~Rv~fRRa~k-ai~~a~~~ga~kG~~~  136 (137)
                      ++++.|++.||++|++||.++|++||+|||+|++|||||+ +++++|++|| +||++
T Consensus        81 ~~~v~I~i~eV~~p~l~A~lvAe~IA~qLe~rv~FRRA~k~ai~~am~aGa-kGikI  136 (240)
T 3u5c_D           81 PGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVRYVMESGA-KGCEV  136 (240)
T ss_dssp             TTSSEEEEECCSCGGGCHHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHTTC-SEEEE
T ss_pred             CCeEEEEEEEecCCCcCHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCC-ceeEE
Confidence            8999999999999999999999999999999999999999 9999999996 99987
>3iz6_B 40S ribosomal protein S3 (S3P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Back     alignment and structure
>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure
>3j20_C 30S ribosomal protein S3P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>2xzm_C KH domain containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_C Back     alignment and structure
>3i1m_C 30S ribosomal protein S3; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C 3i1q_C 3i1s_C 3i1z_C 3i21_C 3izv_G* 3izw_G* 3kc4_C 3or9_C 3ora_C 3sfs_C* 3uoq_C* 4gaq_C* 4gas_C* 2qal_C* 1p6g_C ... Back     alignment and structure
>2vqe_C 30S ribosomal protein S3; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C* 1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F* 1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C 1xmo_C* 1xmq_C* 1xnq_C* ... Back     alignment and structure
>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Homo sapiens} SCOP: d.52.3.1 Back     alignment and structure
>2pt7_G HP1451, hypothetical protein; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} Back     alignment and structure
>3gku_A Probable RNA-binding protein; APC21302, clostridium symbiosum ATCC 14 structural genomics, PSI-2, protein structure initiative; 2.95A {Clostridium symbiosum atcc 14940} Back     alignment and structure
>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1 Back     alignment and structure
>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8 d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X Back     alignment and structure
>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome ASSE GTP-binding, nucleotide-binding; HET: GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A* Back     alignment and structure
>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal NUS domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix} PDB: 2cy1_A Back     alignment and structure
>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A Back     alignment and structure
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens} Back     alignment and structure
>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A* Back     alignment and structure
>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A Back     alignment and structure
>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1 Back     alignment and structure
>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1 Back     alignment and structure
>1wf3_A GTP-binding protein; GTPase, riken structural genomics/prote initiative, RSGI, structural genomics, hydrolase; HET: GNP; 1.88A {Thermus thermophilus} SCOP: c.37.1.8 d.52.3.1 Back     alignment and structure
>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 Back     alignment and structure
>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Back     alignment and structure
>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens} Back     alignment and structure
>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens} 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 137
d1wh9a_92 d.52.3.1 (A:) Ribosomal protein S3 N-terminal doma 2e-34
d2uubc1105 d.52.3.1 (C:2-106) Ribosomal protein S3 N-terminal 2e-04
d2qalc1105 d.52.3.1 (C:1-105) Ribosomal protein S3 N-terminal 0.001
>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 92 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  112 bits (283), Expect = 2e-34
 Identities = 70/87 (80%), Positives = 72/87 (82%)

Query: 14  DGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVV 73
              F AELNE LTRELAEDGYSGVEVRVTP RTEIII ATRTQNVLGEKGRRIRELT+VV
Sbjct: 5   SSGFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVV 64

Query: 74  QKRFKFPENSVELYAEKVNNRGLCAIA 100
           QKRF FPE SVELYAEKV  RG    +
Sbjct: 65  QKRFGFPEGSVELYAEKVATRGSGPSS 91
>d2uubc1 d.52.3.1 (C:2-106) Ribosomal protein S3 N-terminal domain {Thermus thermophilus [TaxId: 274]} Length = 105 Back     information, alignment and structure
>d2qalc1 d.52.3.1 (C:1-105) Ribosomal protein S3 N-terminal domain {Escherichia coli [TaxId: 562]} Length = 105 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 ?
Query137
d1wh9a_92 Ribosomal protein S3 N-terminal domain {Mouse (Mus 99.93
d2uubc1105 Ribosomal protein S3 N-terminal domain {Thermus th 99.83
d2qalc1105 Ribosomal protein S3 N-terminal domain {Escherichi 99.83
d2uubc2101 Ribosomal protein S3 C-terminal domain {Thermus th 99.58
d2qalc2101 Ribosomal protein S3 C-terminal domain {Escherichi 99.53
d1egaa2113 GTPase Era C-terminal domain {Escherichia coli [Ta 94.75
d1wf3a2118 GTPase Era C-terminal domain {Thermus thermophilus 93.38
d1tuaa184 Hypothetical protein APE0754 {Aeropyrum pernix [Ta 92.53
d2asba367 Transcription factor NusA, C-terminal domains {Myc 87.1
d1hh2p368 Transcription factor NusA, C-terminal domains {The 85.95
d2axya171 Poly(RC)-binding protein 2 {Human (Homo sapiens) [ 84.04
d1dtja_74 Neuro-oncological ventral antigen 2, nova-2, KH3 { 83.84
d1zzka175 HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} 83.37
d1j4wa174 Far upstream binding element, FBP {Human (Homo sap 81.43
d1j4wa271 Far upstream binding element, FBP {Human (Homo sap 80.85
>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.93  E-value=4.6e-26  Score=156.44  Aligned_cols=82  Identities=84%  Similarity=1.108  Sum_probs=80.3

Q ss_pred             HHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcC
Q 040226           18 FAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLC   97 (137)
Q Consensus        18 ~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~P~l~   97 (137)
                      +++|||||.++|.+||||+|+|+|++++++|+|||+|||+|||++|+++++|++.|+++|++.+++++|++++|.+.+||
T Consensus         9 ~a~Ire~l~k~l~~Agis~ieI~Rt~~~i~I~I~tarPGivIGrkG~~I~~L~~~l~k~~~~~~~~i~lnae~Ia~r~l~   88 (92)
T d1wh9a_           9 KAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGSG   88 (92)
T ss_dssp             HHHHHHHHHHHTTTTTEEEEEEEECSSCEEEEEEESCHHHHHCGGGHHHHHHHHHHHHHHCCCTTSEEEEEEECCCSCCC
T ss_pred             HHHHHHHHHHHHHhCCcceEEEEECCCeEEEEEEeCCCceeeccCchhHHHHHHHHHHHHCCCCCcEEEEEEeecccCCC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HH
Q 040226           98 AI   99 (137)
Q Consensus        98 A~   99 (137)
                      |.
T Consensus        89 ~~   90 (92)
T d1wh9a_          89 PS   90 (92)
T ss_dssp             SC
T ss_pred             cc
Confidence            83
>d2uubc1 d.52.3.1 (C:2-106) Ribosomal protein S3 N-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2qalc1 d.52.3.1 (C:1-105) Ribosomal protein S3 N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2uubc2 d.53.1.1 (C:107-207) Ribosomal protein S3 C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2qalc2 d.53.1.1 (C:106-206) Ribosomal protein S3 C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1egaa2 d.52.3.1 (A:183-295) GTPase Era C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1wf3a2 d.52.3.1 (A:181-298) GTPase Era C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d2asba3 d.52.3.1 (A:263-329) Transcription factor NusA, C-terminal domains {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, KH3 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1j4wa1 d.51.1.1 (A:1-74) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure