Psyllid ID: psy17938

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-------290-------300-------
MSAKFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYPAIDAQYCSLLAQFGWSILILVVAVGTLHQCPGCRELRIILTFLDSIVSLKEVCKPDIIIALWEYFHKRLNSNFVLKSMPFAYTLSCLNSNRSVLEVLTHVEQMISSTRIQKNEENSYTLFLRMLGIYLLKYNHEQRIWNQVKGLKSPFTPAVGYYYYYCGQILLSVYTASFHFNCRYVAHIYLYRAHINYFGPL
cHHcHHHHHHHHHHHHHHHHHHHHHccccEEEEEEcccEEEEEEEEccccEEccccccHHHHHHHHHHHHHccccccEEEEEEEcccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHccccEEEEEEEEccccccccccHHHHHHHccccccccccccccEEEEEHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHcccccccccEEcEEEcccccccHHHHHHHHHHHHHHHHHcccccccEEEEEEEEcccccccccc
ccHHHHHcccHHHHHHHHHHHHHHHcccccEEEEEccccEEEEEEEEccccEccccccHHHHHHHHHHHHcccccccEEEEEEEcccccccHHHHHHHHHHHHHccccHHccHHHHHHHHHHHHHHccEEEEEEEEHccHcccccHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHcccHEEcccccEEEHHHccccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHccHHHHHHHcccccccccccEEEEEEEccHEEEEEEEEcEcccHHHHHHHHHHHHHHHccccc
MSAKFVADGVFRAELDEFLTRElaedgysgveirftpaRTEIIIMATRTqnvlgdkgrRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGglavrrypaiDAQYCSLLAQFGWSILILVVAVGtlhqcpgcrELRIILTFLDSIVSLKEVCKPDIIIALWEYFHKRLnsnfvlksmpFAYTLSCLNSNRSVLEVLTHVEQMISSTRIQKNEENSYTLFLRMLGIYLLKYNHEQRIWNqvkglkspftpavgyYYYYCGQILLSVYTASFHFNCRYVAHIYLYRAHINYFGPL
msakfvadgvfraELDEFLTrelaedgysgveirftparteIIIMAtrtqnvlgdkgrrIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYPAIDAQYCSLLAQFGWSILILVVAVGTLHQCPGCRELRIILTFLDSIVSLKEVCKPDIIIALWEYFHKRLNSNFVLKSMPFAYTLSCLNSNRSVLEVLTHVEQMIsstriqkneenSYTLFLRMLGIYLLKYNHEQRIWNQVKGLKSPFTPAVGYYYYYCGQILLSVYTASFHFNCRYVAHIYLYRAHINYFGPL
MSAKFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYPAIDAQYCSLLAQFGWSILILVVAVGTLHQCPGCRELRIILTFLDSIVSLKEVCKPDIIIALWEYFHKRLNSNFVLKSMPFAYTLSCLNSNRSVLEVLTHVEQMISSTRIQKNEENSYTLFLRMLGIYLLKYNHEQRIWNQVKGLKSPFTPAVGYYYYYCGQILLSVYTASFHFNCRYVAHIYLYRAHINYFGPL
****FVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYPAIDAQYCSLLAQFGWSILILVVAVGTLHQCPGCRELRIILTFLDSIVSLKEVCKPDIIIALWEYFHKRLNSNFVLKSMPFAYTLSCLNSNRSVLEVLTHVEQMISSTRIQKNEENSYTLFLRMLGIYLLKYNHEQRIWNQVKGLKSPFTPAVGYYYYYCGQILLSVYTASFHFNCRYVAHIYLYRAHINYF***
*SAKFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYPAIDAQYCSLLAQ*******LVVAVGTLHQCPGCRELRIILTFLDSIVSLKEVCKPDIIIALWEYFHKRLNSNFVLKSMPFAYTLSCLNSNRSVLEVLTHVEQ**************YTLFLRMLGIYLLKY*******NQVKGLKSPFTPAVGYYYYYCGQILLSVYTASFHFNCRYVAHIYLYRAHINYFGPL
MSAKFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYPAIDAQYCSLLAQFGWSILILVVAVGTLHQCPGCRELRIILTFLDSIVSLKEVCKPDIIIALWEYFHKRLNSNFVLKSMPFAYTLSCLNSNRSVLEVLTHVEQMISSTRIQKNEENSYTLFLRMLGIYLLKYNHEQRIWNQVKGLKSPFTPAVGYYYYYCGQILLSVYTASFHFNCRYVAHIYLYRAHINYFGPL
MSAKFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYPAIDAQYCSLLAQFGWSILILVVAVGTLHQCPGCRELRIILTFLDSIVSLKEVCKPDIIIALWEYFHKRLNSNFVLKSMPFAYTLSCLNSNRSVLEVLTHVEQMISSTRIQKNEENSYTLFLRMLGIYLLKYNHEQRIWNQVKGLKSPFTPAVGYYYYYCGQILLSVYTASFHFNCRYVAHIYLYRAHINYFGPL
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MSAKFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYPAIDAQYCSLLAQFGWSILILVVAVGTLHQCPGCRELRIILTFLDSIVSLKEVCKPDIIIALWEYFHKRLNSNFVLKSMPFAYTLSCLNSNRSVLEVLTHVEQMISSTRIQKNEENSYTLFLRMLGIYLLKYNHEQRIWNQVKGLKSPFTPAVGYYYYYCGQILLSVYTASFHFNCRYVAHIYLYRAHINYFGPL
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 ?
Query307 2.2.26 [Sep-21-2011]
P62909243 40S ribosomal protein S3 yes N/A 0.351 0.444 0.861 1e-49
P62908243 40S ribosomal protein S3 yes N/A 0.351 0.444 0.861 1e-49
E2RH47243 40S ribosomal protein S3 yes N/A 0.351 0.444 0.861 1e-49
Q0Z8U2243 40S ribosomal protein S3 yes N/A 0.351 0.444 0.861 1e-49
P23396243 40S ribosomal protein S3 yes N/A 0.351 0.444 0.861 1e-49
Q3T169243 40S ribosomal protein S3 yes N/A 0.351 0.444 0.861 1e-49
P02350246 40S ribosomal protein S3- N/A N/A 0.351 0.439 0.861 2e-49
P79891253 40S ribosomal protein S3 N/A N/A 0.351 0.426 0.861 2e-49
Q5R465243 40S ribosomal protein S3 yes N/A 0.351 0.444 0.851 4e-49
P47835246 40S ribosomal protein S3- N/A N/A 0.351 0.439 0.851 5e-49
>sp|P62909|RS3_RAT 40S ribosomal protein S3 OS=Rattus norvegicus GN=Rps3 PE=1 SV=1 Back     alignment and function desciption
 Score =  197 bits (500), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 93/108 (86%), Positives = 104/108 (96%)

Query: 4   KFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 63
           KFVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+KGRRIREL
Sbjct: 10  KFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIREL 69

Query: 64  TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 111
           T+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 70  TAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117

Rattus norvegicus (taxid: 10116)
>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
>sp|P79891|RS3_AMBME 40S ribosomal protein S3 OS=Ambystoma mexicanum GN=RPS3 PE=2 SV=1 Back     alignment and function description
>sp|Q5R465|RS3_PONAB 40S ribosomal protein S3 OS=Pongo abelii GN=RPS3 PE=2 SV=1 Back     alignment and function description
>sp|P47835|RS32_XENLA 40S ribosomal protein S3-B OS=Xenopus laevis GN=rps3-b PE=2 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query307
121543809248 putative ribosomal protein S3 [Maconelli 0.351 0.435 0.916 1e-49
121511934243 40S ribosomal protein S3 [Xenopsylla che 0.351 0.444 0.888 8e-49
312380148278 hypothetical protein AND_07881 [Anophele 0.355 0.392 0.880 4e-48
392881646245 40S ribosomal protein S3-like protein [C 0.351 0.440 0.870 5e-48
148684443243 ribosomal protein S3, isoform CRA_e [Mus 0.351 0.444 0.861 5e-48
209733852250 40S ribosomal protein S3 [Salmo salar] 0.351 0.432 0.861 5e-48
327281458243 PREDICTED: 40S ribosomal protein S3-like 0.351 0.444 0.861 5e-48
260833516226 hypothetical protein BRAFLDRAFT_56803 [B 0.351 0.477 0.879 6e-48
417409029251 Putative 40s ribosomal protein s3, parti 0.351 0.430 0.861 6e-48
296217041243 PREDICTED: 40S ribosomal protein S3-like 0.351 0.444 0.861 6e-48
>gi|121543809|gb|ABM55569.1| putative ribosomal protein S3 [Maconellicoccus hirsutus] Back     alignment and taxonomy information
 Score =  202 bits (515), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 99/108 (91%), Positives = 104/108 (96%)

Query: 4   KFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 63
           KFVADGVF+AEL+EFL RELAEDGYSGV+IR TP RTEIIIMATRTQNVLG+KGRRIREL
Sbjct: 10  KFVADGVFKAELNEFLMRELAEDGYSGVQIRVTPTRTEIIIMATRTQNVLGEKGRRIREL 69

Query: 64  TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 111
           TSVVQKRFKF DG+IELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR
Sbjct: 70  TSVVQKRFKFPDGSIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 117

Source: Maconellicoccus hirsutus

Species: Maconellicoccus hirsutus

Genus: Maconellicoccus

Family: Pseudococcidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|121511934|gb|ABM55418.1| 40S ribosomal protein S3 [Xenopsylla cheopis] Back     alignment and taxonomy information
>gi|312380148|gb|EFR26232.1| hypothetical protein AND_07881 [Anopheles darlingi] Back     alignment and taxonomy information
>gi|392881646|gb|AFM89655.1| 40S ribosomal protein S3-like protein [Callorhinchus milii] Back     alignment and taxonomy information
>gi|148684443|gb|EDL16390.1| ribosomal protein S3, isoform CRA_e [Mus musculus] Back     alignment and taxonomy information
>gi|209733852|gb|ACI67795.1| 40S ribosomal protein S3 [Salmo salar] Back     alignment and taxonomy information
>gi|327281458|ref|XP_003225465.1| PREDICTED: 40S ribosomal protein S3-like [Anolis carolinensis] Back     alignment and taxonomy information
>gi|260833516|ref|XP_002611703.1| hypothetical protein BRAFLDRAFT_56803 [Branchiostoma floridae] gi|229297074|gb|EEN67713.1| hypothetical protein BRAFLDRAFT_56803 [Branchiostoma floridae] Back     alignment and taxonomy information
>gi|417409029|gb|JAA51041.1| Putative 40s ribosomal protein s3, partial [Desmodus rotundus] Back     alignment and taxonomy information
>gi|296217041|ref|XP_002754860.1| PREDICTED: 40S ribosomal protein S3-like isoform 1 [Callithrix jacchus] gi|390470016|ref|XP_003734218.1| PREDICTED: 40S ribosomal protein S3-like isoform 2 [Callithrix jacchus] gi|390470018|ref|XP_003734219.1| PREDICTED: 40S ribosomal protein S3-like isoform 3 [Callithrix jacchus] gi|390470020|ref|XP_003734220.1| PREDICTED: 40S ribosomal protein S3-like isoform 4 [Callithrix jacchus] 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 ?
Query307
UNIPROTKB|H0YCJ7135 RPS3 "40S ribosomal protein S3 0.381 0.866 0.805 1.3e-45
UNIPROTKB|F1N9X5243 RPS3 "Uncharacterized protein" 0.351 0.444 0.861 1.6e-45
UNIPROTKB|Q3T169243 RPS3 "40S ribosomal protein S3 0.351 0.444 0.861 1.6e-45
UNIPROTKB|E2RH47243 RPS3 "40S ribosomal protein S3 0.351 0.444 0.861 1.6e-45
UNIPROTKB|E9PL45164 RPS3 "40S ribosomal protein S3 0.351 0.658 0.861 1.6e-45
UNIPROTKB|F2Z2S8117 RPS3 "40S ribosomal protein S3 0.351 0.923 0.861 1.6e-45
UNIPROTKB|P23396243 RPS3 "40S ribosomal protein S3 0.351 0.444 0.861 1.6e-45
UNIPROTKB|Q0Z8U2243 RPS3 "40S ribosomal protein S3 0.351 0.444 0.861 1.6e-45
MGI|MGI:1350917243 Rps3 "ribosomal protein S3" [M 0.351 0.444 0.861 1.6e-45
RGD|619888243 Rps3 "ribosomal protein S3" [R 0.351 0.444 0.861 1.6e-45
UNIPROTKB|H0YCJ7 RPS3 "40S ribosomal protein S3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
 Score = 479 (173.7 bits), Expect = 1.3e-45, P = 1.3e-45
 Identities = 95/118 (80%), Positives = 107/118 (90%)

Query:     4 KFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 63
             KFVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+KGRRIREL
Sbjct:     7 KFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIREL 66

Query:    64 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRY-PAIDAQYC 120
             T+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR  P     +C
Sbjct:    67 TAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRVGPKAARLWC 124
GO:0003723 "RNA binding" evidence=IEA
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|E9PL45 RPS3 "40S ribosomal protein S3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F2Z2S8 RPS3 "40S ribosomal protein S3" [Homo sapiens (taxid:9606)] 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 number0.85180.35170.4444yesN/A
P05750RS3_YEASTNo assigned EC number0.70370.35170.45yesN/A
P48152RS3_CAEELNo assigned EC number0.75920.35170.4372yesN/A
O60128RS3_SCHPONo assigned EC number0.75920.35170.4337yesN/A
E2RH47RS3_CANFANo assigned EC number0.86110.35170.4444yesN/A
Q0Z8U2RS3_PIGNo assigned EC number0.86110.35170.4444yesN/A
P23396RS3_HUMANNo assigned EC number0.86110.35170.4444yesN/A
Q3T169RS3_BOVINNo assigned EC number0.86110.35170.4444yesN/A
P62909RS3_RATNo assigned EC number0.86110.35170.4444yesN/A
P62908RS3_MOUSENo assigned EC number0.86110.35170.4444yesN/A
Q9FJA6RS33_ARATHNo assigned EC number0.85180.35170.4354yesN/A
Q06559RS3_DROMENo assigned EC number0.83330.35170.4390yesN/A
P90526RS3_DICDINo assigned EC number0.61460.35170.4954yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query307
PTZ00084220 PTZ00084, PTZ00084, 40S ribosomal protein S3; Prov 2e-64
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, 9e-24
cd0241185 cd02411, archeal_30S_S3_KH, K homology RNA-binding 7e-18
PRK04191207 PRK04191, rps3p, 30S ribosomal protein S3P; Review 8e-17
pfam0765077 pfam07650, KH_2, KH domain 8e-15
cd0240968 cd02409, KH-II, KH-II (K homology RNA-binding doma 2e-10
>gnl|CDD|240260 PTZ00084, PTZ00084, 40S ribosomal protein S3; Provisional Back     alignment and domain information 
 Score =  202 bits (515), Expect = 2e-64
 Identities = 84/108 (77%), Positives = 96/108 (88%)

Query: 4   KFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 63
           KFVADGVF AEL+EFL+RELAEDGYSGVE+R TP RTEIII ATRT+ VLGDKGRRIREL
Sbjct: 10  KFVADGVFYAELNEFLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIREL 69

Query: 64  TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 111
           TS++QKRF F +G +EL+AE+V  RGLCA+AQAESLRYKL+ GL VRR
Sbjct: 70  TSLLQKRFGFPEGKVELFAERVENRGLCAMAQAESLRYKLLEGLPVRR 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 307
PF14910 704 MMS22L_N: S-phase genomic integrity recombination 100.0
COG0092233 RpsC Ribosomal protein S3 [Translation, ribosomal 100.0
PTZ00084220 40S ribosomal protein S3; Provisional 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 99.97
PRK00310232 rpsC 30S ribosomal protein S3; Reviewed 99.97
KOG3181|consensus244 99.9
cd0241381 40S_S3_KH K homology RNA-binding (KH) domain of th 99.84
cd0241185 archeal_30S_S3_KH K homology RNA-binding domain (K 99.82
cd02412109 30S_S3_KH K homology RNA-binding (KH) domain of th 99.72
PF0765078 KH_2: KH domain syndrome, contains KH motifs.; Int 99.56
cd0240968 KH-II KH-II (K homology RNA-binding domain, type I 98.86
PF0018985 Ribosomal_S3_C: Ribosomal protein S3, C-terminal d 97.88
smart0032269 KH K homology RNA-binding domain. 97.54
cd0241477 jag_KH jag_K homology RNA-binding domain. The KH d 96.98
PF1308373 KH_4: KH domain; PDB: 3GKU_B. 96.76
PRK0106478 hypothetical protein; Provisional 95.88
COG1847208 Jag Predicted RNA-binding protein [General functio 95.01
cd0213461 NusA_KH NusA_K homology RNA-binding domain (KH). N 94.61
PRK0282177 hypothetical protein; Provisional 94.39
COG1159298 Era GTPase [General function prediction only] 93.66
PRK08406140 transcription elongation factor NusA-like protein; 93.45
cd02410145 archeal_CPSF_KH The archaeal cleavage and polyaden 93.22
PRK0046875 hypothetical protein; Provisional 92.56
TIGR00436270 era GTP-binding protein Era. Era is an essential G 91.34
PRK15494339 era GTPase Era; Provisional 91.1
COG183776 Predicted RNA-binding protein (contains KH domain) 90.69
PRK00089292 era GTPase Era; Reviewed 90.47
COG1782 637 Predicted metal-dependent RNase, consists of a met 86.62
TIGR01952141 nusA_arch NusA family KH domain protein, archaeal. 85.34
TIGR03675 630 arCOG00543 arCOG00543 universal archaeal KH-domain 82.99
>PF14910 MMS22L_N: S-phase genomic integrity recombination mediator, N-terminal Back     alignment and domain information 
Probab=100.00  E-value=4.7e-43  Score=359.12  Aligned_cols=148  Identities=28%  Similarity=0.362  Sum_probs=138.9

Q ss_pred             ecCC--CcccceEeeehhHHHHhhcCCCCccchhhhhhhhhhccCCCccccccccccccccccccccHHHHHHHHhhccc
Q psy17938        141 HQCP--GCRELRIILTFLDSIVSLKEVCKPDIIIALWEYFHKRLNSNFVLKSMPFAYTLSCLNSNRSVLEVLTHVEQMIS  218 (307)
Q Consensus       141 ar~e--~~~e~~i~l~~l~~i~~~w~~~~~~~v~~LWeyfsK~Lns~F~~~~~~l~~~~~~~~~~~s~l~~~~~c~~~~~  218 (307)
                      +.+.  .|+++||.|.++.|+.++|+| |+++|++|||||||||||||++||+|++++.+++|||.+++|.+++||++.+
T Consensus       366 ~~q~~~~EeqlRm~L~c~l~L~~~W~p-n~~iv~~LWEYfsK~LNssF~v~~~~l~~L~~i~kS~~~~le~~~~~c~~~~  444 (704)
T PF14910_consen  366 NSQDGILEEQLRMYLHCCLPLCQWWEP-NTDIVTILWEYFSKNLNSSFSVPWLGLKGLACICKSPLSMLEQAKSCCSPQQ  444 (704)
T ss_pred             ccCCcccHHHHHHHHHHHHHHHhhcCC-ChHHHHHHHHHHHhhcCCCCccCccchhhhhhhcCCHHHHHHHHHHHhCCCc
Confidence            4444  899999999999999888888 9999999999999999999999999999999999999999999999999999


Q ss_pred             cchhccCCchhHHHHHHHHHHHHhhc--ccCcccccccccc-cCCCCc-------hhhHHHHHHHHHHHHHHhccccccc
Q psy17938        219 STRIQKNEENSYTLFLRMLGIYLLKY--NHEQRIWNQVKGL-KSPFTP-------AVGYYYYYCGQILLSVYTASFHFNC  288 (307)
Q Consensus       219 ~~~~~~~~~~Sy~~FL~iLa~~l~~~--~~~~~~w~qikgR-yskf~~-------e~gl~nf~~lfl~la~~~~~~~~~~  288 (307)
                      .+++++ ++|||+|||++||+|||+.  +++++||+||||| ||||||       |+|||||++||||||.+||.-...+
T Consensus       445 ~~~L~~-~~sSf~iFL~lLa~~lk~~~~~~~~~~wkQiKGRIYSKF~~kKm~ELtE~GL~Nf~~LFLtLa~~ad~eDvas  523 (704)
T PF14910_consen  445 HDDLYK-SESSFHIFLRLLAKMLKKLYSNSGPHPWKQIKGRIYSKFSQKKMEELTEVGLYNFISLFLTLASVADFEDVAS  523 (704)
T ss_pred             cccccc-ccCcHHHHHHHHHHHHHHHHhcCCCChHHHhcCeehhhcCHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            888998 9999999999999999973  5789999999999 999999       9999999999999999999888777


Q ss_pred             hh
Q psy17938        289 RY  290 (307)
Q Consensus       289 ~~  290 (307)
                      |.
T Consensus       524 r~  525 (704)
T PF14910_consen  524 RV  525 (704)
T ss_pred             HH
Confidence            64

>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PTZ00084 40S ribosomal protein S3; Provisional 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 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
>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
>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
>PF13083 KH_4: KH domain; PDB: 3GKU_B 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
>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
>PRK00468 hypothetical protein; Provisional Back     alignment and domain information
>TIGR00436 era GTP-binding protein Era 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
>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
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal Back     alignment and domain information
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein 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 ?
Query307
2zkq_c243 Structure Of A Mammalian Ribosomal 40s Subunit With 8e-51
3iz6_B227 Localization Of The Small Subunit Ribosomal Protein 7e-47
3izb_B240 Localization Of The Small Subunit Ribosomal Protein 2e-39
1s1h_C192 Structure Of The Ribosomal 80s-Eef2-Sordarin Comple 3e-39
3jyv_C188 Structure Of The 40s Rrna And Proteins And PE TRNA 3e-39
1wh9_A92 Solution Structure Of The Kh Domain Of Human Riboso 7e-35
3zey_X214 High-resolution Cryo-electron Microscopy Structure 2e-33
2xzm_C243 Crystal Structure Of The Eukaryotic 40s Ribosomal S 7e-27
3j20_C210 Promiscuous Behavior Of Proteins In Archaeal Riboso 6e-11
>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 
Iteration: 1

 Score =  197 bits (500), Expect = 8e-51,   Method: Compositional matrix adjust.
 Identities = 93/108 (86%), Positives = 104/108 (96%)
Query: 4   KFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 63
           KFVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+KGRRIREL
Sbjct: 10  KFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIREL 69
Query: 64  TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 111
           T+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 70  TAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117
>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
>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|1WH9|A Chain A, Solution Structure Of The Kh Domain Of Human Ribosomal Protein S3 Length = 92 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|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 ?
Query307
3u5c_D240 RP13, YS3, 40S ribosomal protein S3; translation, 9e-50
2zkq_c243 40S ribosomal protein S3E; protein-RNA complex, 40 3e-49
3iz6_B227 40S ribosomal protein S3 (S3P); eukaryotic ribosom 1e-48
2xzm_C243 KH domain containing protein; ribosome, translatio 7e-46
1wh9_A92 40S ribosomal protein S3; KH domain, structural ge 1e-42
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-04
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 4e-04
>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 =  164 bits (417), Expect = 9e-50
 Identities = 76/108 (70%), Positives = 92/108 (85%)

Query: 4   KFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 63
           K VADGVF AEL+EF TRELAE+GYSGVE+R TP +TE+II ATRTQ+VLG+ GRRI EL
Sbjct: 10  KLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENGRRINEL 69

Query: 64  TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 111
           T +VQKRFK+A G I LYAE+V  RGL A+AQAES+++KL+ GLA+RR
Sbjct: 70  TLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRR 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
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query307
2zkq_c243 40S ribosomal protein S3E; protein-RNA complex, 40 100.0
3iz6_B227 40S ribosomal protein S3 (S3P); eukaryotic ribosom 100.0
3j20_C210 30S ribosomal protein S3P; archaea, archaeal, KINK 100.0
3u5c_D240 RP13, YS3, 40S ribosomal protein S3; translation, 100.0
2xzm_C243 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
3bbn_C218 Ribosomal protein S3; small ribosomal subunit, spi 100.0
2vqe_C239 30S ribosomal protein S3; tRNA-binding, rRNA-bindi 100.0
1wh9_A92 40S ribosomal protein S3; KH domain, structural ge 99.91
2pt7_G152 HP1451, hypothetical protein; ATPase, protein-prot 95.73
3gku_A225 Probable RNA-binding protein; APC21302, clostridiu 90.09
1ec6_A87 RNA-binding protein NOVA-2; KH domain, alpha-beta 83.02
1ega_A301 Protein (GTP-binding protein ERA); GTPase, RNA-bin 81.57
3iev_A308 GTP-binding protein ERA; ERA, GTPase, KH domain, a 81.22
>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure
Probab=100.00  E-value=3.2e-39  Score=297.40  Aligned_cols=141  Identities=69%  Similarity=1.025  Sum_probs=136.4

Q ss_pred             cccchhhhhHHHHHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEE
Q psy17938          2 SAKFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELY   81 (307)
Q Consensus         2 ~kkfI~d~~i~~kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~   81 (307)
                      +++||+||+++.+|||||.+++.+||||+|||+|+++.++|+|||++||++||++|+++++|++.|+|.|+..+++++|+
T Consensus         8 ~rkfv~dgv~~~~IR~~l~k~l~~agis~IeIeRt~~~i~I~I~tarPg~vIGkkG~~I~~L~~~L~k~~~~~~~~v~I~   87 (243)
T 2zkq_c            8 KRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFPEGSVELY   87 (243)
T ss_dssp             TTTHHHHHHHHHHHHHHHHHHTCTTTEEEEECBEETTEECCEEEESCHHHHHCGGGHHHHHHHHHHHHHSCTTTCCCCCE
T ss_pred             hhHHHhcChHHHHHHHHHHHHHHHCCcceEEEEEcCCcEEEEEEeCCCceEEcCCchHHHHHHHHHHHHhCcCCceEEEE
Confidence            58999999999999999999999999999999999999999999999999999999999999999999998878899999


Q ss_pred             EEEecCCCcCHHHHHHHHHHHHHcChhhhhhh--------hcCCceeEEeeeccceeeEEEeeeeee----ecCCCcccc
Q psy17938         82 AEKVATRGLCAIAQAESLRYKLIGGLAVRRYP--------AIDAQYCSLLAQFGWSILILVVAVGTL----HQCPGCREL  149 (307)
Q Consensus        82 I~eVknP~l~A~lLAe~IA~QLE~Rv~FRRAM--------kaGAkGIKI~~~~~~~~~~~~~~sgrl----ar~e~~~e~  149 (307)
                      +.||++|++||+++|++||+|||+|++|||||        ++||+||||+            +||||    ||+|.|+|+
T Consensus        88 i~eV~~p~l~A~lvAe~IA~qLe~rv~FRRa~k~ai~~am~aGakGikI~------------iSGRL~GaiARtE~~~eG  155 (243)
T 2zkq_c           88 AEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVV------------VSGKLRGQRAKSMKFVDG  155 (243)
T ss_dssp             EEECSCGGGCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHSSCSEEEEE------------ECSSGGGSSCCCBCCEEE
T ss_pred             EEEecCcccCHHHHHHHHHHHHHcchhHHHHHHHHHHHHHhcCCceEEEE------------EecchhhHhhhhhhhcCc
Confidence            99999999999999999999999999999975        8999999999            99999    999999999


Q ss_pred             eEeeeh
Q psy17938        150 RIILTF  155 (307)
Q Consensus       150 ~i~l~~  155 (307)
                      +| |--
T Consensus       156 ~v-LhT  160 (243)
T 2zkq_c          156 LM-IHS  160 (243)
T ss_dssp             SS-HHH
T ss_pred             EE-eec
Confidence            99 644
>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
>3j20_C 30S ribosomal protein S3P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>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
>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
>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} 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
>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

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 307
d1wh9a_92 d.52.3.1 (A:) Ribosomal protein S3 N-terminal doma 2e-37
d2uubc1105 d.52.3.1 (C:2-106) Ribosomal protein S3 N-terminal 1e-04
d2qalc1105 d.52.3.1 (C:1-105) Ribosomal protein S3 N-terminal 3e-04
>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 =  126 bits (319), Expect = 2e-37
 Identities = 66/87 (75%), Positives = 76/87 (87%)

Query: 8  DGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVV 67
             F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+KGRRIRELT+VV
Sbjct: 5  SSGFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVV 64

Query: 68 QKRFKFADGAIELYAEKVATRGLCAIA 94
          QKRF F +G++ELYAEKVATRG    +
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 ?
Query307
d1wh9a_92 Ribosomal protein S3 N-terminal domain {Mouse (Mus 99.87
d2uubc1105 Ribosomal protein S3 N-terminal domain {Thermus th 99.68
d2qalc1105 Ribosomal protein S3 N-terminal domain {Escherichi 99.67
d2qalc2101 Ribosomal protein S3 C-terminal domain {Escherichi 99.52
d2uubc2101 Ribosomal protein S3 C-terminal domain {Thermus th 99.44
d1egaa2113 GTPase Era C-terminal domain {Escherichia coli [Ta 91.71
d1wf3a2118 GTPase Era C-terminal domain {Thermus thermophilus 89.37
d1hh2p368 Transcription factor NusA, C-terminal domains {The 88.8
d2asba367 Transcription factor NusA, C-terminal domains {Myc 86.87
d1tuaa184 Hypothetical protein APE0754 {Aeropyrum pernix [Ta 85.85
>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=99.87  E-value=1.2e-22  Score=160.85  Aligned_cols=82  Identities=79%  Similarity=1.163  Sum_probs=80.2

Q ss_pred             HHHHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcC
Q psy17938         12 RAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLC   91 (307)
Q Consensus        12 ~~kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~eVknP~l~   91 (307)
                      +++|||||.+++.+||||+|+|+|++++++|+|||+|||++||++|+++++|++.|+|+|+..+++|+|++++|++++|+
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            89999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HH
Q psy17938         92 AI   93 (307)
Q Consensus        92 A~   93 (307)
                      |.
T Consensus        89 ~~   90 (92)
T d1wh9a_          89 PS   90 (92)
T ss_dssp             SC
T ss_pred             cc
Confidence            73
>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
>d2qalc2 d.53.1.1 (C:106-206) Ribosomal protein S3 C-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
>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
>d1hh2p3 d.52.3.1 (P:277-344) Transcription factor NusA, C-terminal domains {Thermotoga maritima [TaxId: 2336]} 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
>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure