Citrus Sinensis ID: 025562

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-
MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKVSLSVSLSLFLRPSFSLSLKNTDTHVHIVSSI
cHHHHHHHHHHHcccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccEEEEEEcccccEEEEEEEccccccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccHHHHHHHHHHHHHHHHHcccEEEEEccccccccccHHHcccHHHHHHHHHcc
ccHHHHHHHHHHcccHHHHcccccccccHHHccccccEEEEEcccccccHHccHHHHHHHcccccccccccccccccccccEEccccccccccccccEEEEEEEEccccEEEEEEEcHHHccccccHHHHHHHHHHHHHHHccccccccccccEccccccccccccccccccccccccccccccEEEcccccccHccccHHHHHHHHHHHHHHHHHcccEEEEEcccccccccHHHHcHHHHHHHHHHHcc
MALTVSRRLLRRfgsfsafgryespsltsrsirsppdlyvacsgdnlfplksglsflasrkfsttiltpdssegafpsdlllkktvltpditiglhqdlvipvtnffnedkgfmvlagdvfdvpirkDIIHRVVRWQLakrqqgthstktisevsgtgkkpwrqkgtgrarhgtlrgpqfrggttmhgpkprshaIKLNKKVRRLGLKIALSARAAEGKVSLSVSLslflrpsfslslkntdTHVHIVSSI
maltvsrrllrrfgsfsafgryespsltsrsirspPDLYVACSGDNLFPLKSGLSFLASRKFSTTiltpdssegafpsDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWqlakrqqgthstktisevsgtgkkpwrqkgtgrarhgtlrgpqfrggttmhgpkprshaiklnKKVRRLGLKIALSARAAEGKVSLSVSLSLFLrpsfslslkntdthvhivssi
MALTVSrrllrrFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKvslsvslslflrpsfslslKNTDTHVHIVSSI
*********LRRFGSFSAF*****************DLYVACSGDNLFPLKSGLSFLASRKFSTTILTP****GAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLA**********************************************************LNKKVRRLGLKIALSARAAEGKVSLSVSLSLFLRPSFSLSLKNT***V******
*****SRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLY*****************************************************IGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTH*********GTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKVSLSVSLSLFLRPSFSLSLKNTDTHVHIVSSI
MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQL*********************************HGTLRGPQFRGG**********HAIKLNKKVRRLGLKIALSARAAEGKVSLSVSLSLFLRPSFSLSLKNTDTHVHIVSSI
*********L*RFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTT*******EGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQ*********************************RGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKVSLSVSLSLFLRPSFSLSLKNTDTHVHIVSSI
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKVSLSVSLSLFLRPSFSLSLKNTDTHVHIVSSI
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 ?
Query251 2.2.26 [Sep-21-2011]
B6IRQ7206 50S ribosomal protein L4 yes no 0.513 0.626 0.556 2e-36
Q5PA59208 50S ribosomal protein L4 yes no 0.549 0.663 0.524 1e-34
B9KJ69208 50S ribosomal protein L4 yes no 0.549 0.663 0.524 1e-34
Q2RQW1206 50S ribosomal protein L4 yes no 0.470 0.572 0.593 3e-34
Q2W2J2206 50S ribosomal protein L4 yes no 0.470 0.572 0.601 1e-33
Q2GL58208 50S ribosomal protein L4 yes no 0.529 0.639 0.526 5e-33
Q11HQ3206 50S ribosomal protein L4 yes no 0.509 0.621 0.531 1e-31
Q68W79207 50S ribosomal protein L4 yes no 0.482 0.584 0.590 2e-31
Q1RHM2207 50S ribosomal protein L4 yes no 0.501 0.608 0.574 2e-31
A8GVB5207 50S ribosomal protein L4 yes no 0.501 0.608 0.574 2e-31
>sp|B6IRQ7|RL4_RHOCS 50S ribosomal protein L4 OS=Rhodospirillum centenum (strain ATCC 51521 / SW) GN=rplD PE=3 SV=1 Back     alignment and function desciption
 Score =  152 bits (384), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 79/142 (55%), Positives = 93/142 (65%), Gaps = 13/142 (9%)

Query: 103 VTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPW 162
           V N  NE  G + LA +VF +P R+DI+ R+V WQLAKR+QGTH TK ISE++GT KKPW
Sbjct: 5   VKNLNNETVGEIELADEVFGLPTRQDILTRMVLWQLAKRRQGTHKTKGISEIAGTTKKPW 64

Query: 163 RQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKVSL 222
           RQKGTGRAR G+ R PQFRGG  + GP  RSH   L KKVR+L LK ALS +AAEGK+  
Sbjct: 65  RQKGTGRARQGSTRSPQFRGGARIFGPVVRSHEHDLTKKVRKLALKTALSTKAAEGKL-- 122

Query: 223 SVSLSLFLRPSFSLSLKNTDTH 244
                      F L     DTH
Sbjct: 123 -----------FVLEAAKADTH 133
Forms part of the polypeptide exit tunnel.
Rhodospirillum centenum (strain ATCC 51521 / SW) (taxid: 414684)
>sp|Q5PA59|RL4_ANAMM 50S ribosomal protein L4 OS=Anaplasma marginale (strain St. Maries) GN=rplD PE=3 SV=1 Back     alignment and function description
>sp|B9KJ69|RL4_ANAMF 50S ribosomal protein L4 OS=Anaplasma marginale (strain Florida) GN=rplD PE=3 SV=1 Back     alignment and function description
>sp|Q2RQW1|RL4_RHORT 50S ribosomal protein L4 OS=Rhodospirillum rubrum (strain ATCC 11170 / NCIB 8255) GN=rplD PE=3 SV=1 Back     alignment and function description
>sp|Q2W2J2|RL4_MAGSA 50S ribosomal protein L4 OS=Magnetospirillum magneticum (strain AMB-1 / ATCC 700264) GN=rplD PE=3 SV=1 Back     alignment and function description
>sp|Q2GL58|RL4_ANAPZ 50S ribosomal protein L4 OS=Anaplasma phagocytophilum (strain HZ) GN=rplD PE=3 SV=1 Back     alignment and function description
>sp|Q11HQ3|RL4_MESSB 50S ribosomal protein L4 OS=Mesorhizobium sp. (strain BNC1) GN=rplD PE=3 SV=1 Back     alignment and function description
>sp|Q68W79|RL4_RICTY 50S ribosomal protein L4 OS=Rickettsia typhi (strain ATCC VR-144 / Wilmington) GN=rplD PE=3 SV=1 Back     alignment and function description
>sp|Q1RHM2|RL4_RICBR 50S ribosomal protein L4 OS=Rickettsia bellii (strain RML369-C) GN=rplD PE=3 SV=1 Back     alignment and function description
>sp|A8GVB5|RL4_RICB8 50S ribosomal protein L4 OS=Rickettsia bellii (strain OSU 85-389) GN=rplD PE=3 SV=1 Back     alignment and function description

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query251
449433990315 PREDICTED: 50S ribosomal protein L4-like 0.876 0.698 0.728 3e-86
21553676300 50S ribosomal protein L4 [Arabidopsis th 0.820 0.686 0.727 3e-86
18399235300 large subunit ribosomal protein L4 [Arab 0.852 0.713 0.711 3e-86
255554769294 50S ribosomal protein L4, putative [Rici 0.812 0.693 0.731 2e-83
297836242297 50S ribosomal protein L4 [Arabidopsis ly 0.840 0.710 0.685 2e-81
359494830315 PREDICTED: 50S ribosomal protein L4-like 0.876 0.698 0.706 3e-81
363807964312 uncharacterized protein LOC100804238 [Gl 0.876 0.705 0.686 2e-79
356532241310 PREDICTED: 50S ribosomal protein L4-like 0.868 0.703 0.690 2e-79
255635335224 unknown [Glycine max] 0.868 0.973 0.690 1e-78
224118096285 predicted protein [Populus trichocarpa] 0.725 0.638 0.686 6e-75
>gi|449433990|ref|XP_004134779.1| PREDICTED: 50S ribosomal protein L4-like [Cucumis sativus] gi|449531047|ref|XP_004172499.1| PREDICTED: 50S ribosomal protein L4-like [Cucumis sativus] Back     alignment and taxonomy information
 Score =  323 bits (829), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 164/225 (72%), Positives = 183/225 (81%), Gaps = 5/225 (2%)

Query: 1   MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDN-LFPLKSGL----S 55
           MA++VSRRLLR  GS S FG+  S    SRS  +P ++Y   SG +  F  +S L    S
Sbjct: 1   MAISVSRRLLRSVGSLSTFGQCNSSCTMSRSFSNPHEIYGHVSGSSSTFASRSTLLKAGS 60

Query: 56  FLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMV 115
           FLASR F T+ILTP+SS  AFPS+LL  K V + +  IGL+QDL+IPVTNF NEDKGFMV
Sbjct: 61  FLASRGFCTSILTPESSNNAFPSELLSAKPVASEERKIGLYQDLMIPVTNFENEDKGFMV 120

Query: 116 LAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTL 175
           LAGDVFD+PIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTG+KPW+QKGTGRARHGTL
Sbjct: 121 LAGDVFDLPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGRKPWKQKGTGRARHGTL 180

Query: 176 RGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKV 220
           RGPQFRGG TMHGPKPRSHA KLNKKVRRLGL IALSAR AEGK+
Sbjct: 181 RGPQFRGGATMHGPKPRSHAFKLNKKVRRLGLMIALSARVAEGKL 225

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|21553676|gb|AAM62769.1| 50S ribosomal protein L4 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|18399235|ref|NP_565463.1| large subunit ribosomal protein L4 [Arabidopsis thaliana] gi|18252969|gb|AAL62411.1| 50S ribosomal protein L4 [Arabidopsis thaliana] gi|20197568|gb|AAD24390.2| 50S ribosomal protein L4 [Arabidopsis thaliana] gi|25084070|gb|AAN72167.1| 50S ribosomal protein L4 [Arabidopsis thaliana] gi|330251866|gb|AEC06960.1| large subunit ribosomal protein L4 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|255554769|ref|XP_002518422.1| 50S ribosomal protein L4, putative [Ricinus communis] gi|223542267|gb|EEF43809.1| 50S ribosomal protein L4, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|297836242|ref|XP_002886003.1| 50S ribosomal protein L4 [Arabidopsis lyrata subsp. lyrata] gi|297331843|gb|EFH62262.1| 50S ribosomal protein L4 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|359494830|ref|XP_003634850.1| PREDICTED: 50S ribosomal protein L4-like [Vitis vinifera] gi|297741766|emb|CBI32995.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|363807964|ref|NP_001242456.1| uncharacterized protein LOC100804238 [Glycine max] gi|255635327|gb|ACU18017.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|356532241|ref|XP_003534682.1| PREDICTED: 50S ribosomal protein L4-like [Glycine max] Back     alignment and taxonomy information
>gi|255635335|gb|ACU18021.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|224118096|ref|XP_002331557.1| predicted protein [Populus trichocarpa] gi|222873781|gb|EEF10912.1| 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 ?
Query251
TAIR|locus:2061659300 AT2G20060 [Arabidopsis thalian 0.832 0.696 0.730 1e-77
TIGR_CMR|APH_0281208 APH_0281 "ribosomal protein L4 0.474 0.572 0.563 5.4e-31
TIGR_CMR|NSE_0267214 NSE_0267 "ribosomal protein L4 0.438 0.514 0.560 1.3e-27
TIGR_CMR|ECH_0410205 ECH_0410 "ribosomal protein L4 0.426 0.521 0.583 2.8e-27
DICTYBASE|DDB_G0283275258 DDB_G0283275 "ribosomal protei 0.661 0.643 0.387 1.4e-25
TIGR_CMR|BA_0111207 BA_0111 "ribosomal protein L4" 0.466 0.565 0.495 2.9e-25
UNIPROTKB|Q3A9R7206 rplD "50S ribosomal protein L4 0.466 0.567 0.470 5.9e-25
TIGR_CMR|CHY_2308206 CHY_2308 "ribosomal protein L4 0.466 0.567 0.470 5.9e-25
UNIPROTKB|P60729223 rplD "50S ribosomal protein L4 0.430 0.484 0.527 7.6e-25
UNIPROTKB|K7ELQ0220 MRPL4 "39S ribosomal protein L 0.657 0.75 0.424 5.3e-24
TAIR|locus:2061659 AT2G20060 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 782 (280.3 bits), Expect = 1.0e-77, P = 1.0e-77
 Identities = 160/219 (73%), Positives = 180/219 (82%)

Query:     1 MALTVSXXXXXXFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASR 60
             MA ++S      FGSFSA GR  SP+L++ +  S   L  + + D    LK G++ L++R
Sbjct:     1 MAASISRRIFRTFGSFSALGRSSSPNLSANT--SGNGL-ASLTND----LKYGMALLSNR 53

Query:    61 KFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDV 120
             K ST+ILTPD S   FPSDLL KKTVLTPD TIG +QDLVIPVTNF NE+KGFMVLAGDV
Sbjct:    54 KLSTSILTPDDS---FPSDLLTKKTVLTPDRTIGQYQDLVIPVTNFQNEEKGFMVLAGDV 110

Query:   121 FDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQF 180
             FDVPIRKDIIH VVRWQLAKRQQGTHSTKT+SEVSGTG+KPW QKGTGRARHGTLRGPQF
Sbjct:   111 FDVPIRKDIIHNVVRWQLAKRQQGTHSTKTLSEVSGTGRKPWNQKGTGRARHGTLRGPQF 170

Query:   181 RGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGK 219
             RGG  MHGPKPRSHAIK+NK+VRRLGLKIAL+ARAAEGK
Sbjct:   171 RGGCVMHGPKPRSHAIKMNKQVRRLGLKIALTARAAEGK 209
GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS
GO:0005739 "mitochondrion" evidence=ISM
GO:0005840 "ribosome" evidence=IEA
GO:0006412 "translation" evidence=IEA;ISS
GO:0015934 "large ribosomal subunit" evidence=ISS
GO:0006354 "DNA-dependent transcription, elongation" evidence=RCA
TIGR_CMR|APH_0281 APH_0281 "ribosomal protein L4" [Anaplasma phagocytophilum HZ (taxid:212042)] Back     alignment and assigned GO terms
TIGR_CMR|NSE_0267 NSE_0267 "ribosomal protein L4" [Neorickettsia sennetsu str. Miyayama (taxid:222891)] Back     alignment and assigned GO terms
TIGR_CMR|ECH_0410 ECH_0410 "ribosomal protein L4" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0283275 DDB_G0283275 "ribosomal protein L4P family protein" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
TIGR_CMR|BA_0111 BA_0111 "ribosomal protein L4" [Bacillus anthracis str. Ames (taxid:198094)] Back     alignment and assigned GO terms
UNIPROTKB|Q3A9R7 rplD "50S ribosomal protein L4" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_2308 CHY_2308 "ribosomal protein L4" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
UNIPROTKB|P60729 rplD "50S ribosomal protein L4" [Mycobacterium tuberculosis (taxid:1773)] Back     alignment and assigned GO terms
UNIPROTKB|K7ELQ0 MRPL4 "39S ribosomal protein L4, mitochondrial" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
AT2G20060
ribosomal protein L4 family protein; ribosomal protein L4 family protein; FUNCTIONS IN- structural constituent of ribosome; INVOLVED IN- translation; LOCATED IN- ribosome, intracellular, chloroplast, large ribosomal subunit; EXPRESSED IN- 22 plant structures; EXPRESSED DURING- 13 growth stages; CONTAINS InterPro DOMAIN/s- Ribosomal protein L4 (InterPro-IPR015498), Ribosomal protein L4/L1e, bacterial-type (InterPro-IPR013005), Ribosomal protein L4/L1e (InterPro-IPR002136); BEST Arabidopsis thaliana protein match is- RPL4; poly(U) binding / structural constituent of ribosome (TAIR-AT1G07 [...] (300 aa)
(Arabidopsis thaliana)
Predicted Functional Partners:
AT5G23535
KOW domain-containing protein; KOW domain-containing protein; FUNCTIONS IN- structural constitu [...] (159 aa)
•  •• • 0.997
RPL3A
ribosomal protein L3 family protein; ribosomal protein L3 family protein; FUNCTIONS IN- structu [...] (271 aa)
• ••• • 0.996
AT3G13120
30S ribosomal protein S10, chloroplast, putative; 30S ribosomal protein S10, chloroplast, putat [...] (191 aa)
• ••• • 0.996
AT2G33800
ribosomal protein S5 family protein; ribosomal protein S5 family protein; FUNCTIONS IN- structu [...] (303 aa)
•  •• • 0.994
ATCG00790.1-P
unknown protein; chloroplast gene encoding a ribosomal protein L16, which is a constituent of 5 [...] (135 aa)
• ••• • 0.993
RPL2.2
unknown protein; encodes a chloroplast ribosomal protein L2, a constituent of the large subunit [...] (274 aa)
• ••• • 0.993
RPL2.1
unknown protein; encodes a chloroplast ribosomal protein L2, a constituent of the large subunit [...] (274 aa)
• ••• • 0.993
emb2394
emb2394 (embryo defective 2394); structural constituent of ribosome; embryo defective 2394 (emb [...] (223 aa)
•  •• • 0.991
AT1G48350
ribosomal protein L18 family protein; ribosomal protein L18 family protein; FUNCTIONS IN- struc [...] (170 aa)
•  •• • 0.990
ATCG00800.1-P
unknown protein; encodes a chloroplast ribosomal protein S3, a constituent of the small subunit [...] (218 aa)
• ••• • 0.990

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 ?
Query251
PRK05319205 PRK05319, rplD, 50S ribosomal protein L4; Provisio 3e-67
TIGR03953188 TIGR03953, rplD_bact, 50S ribosomal protein L4, ba 4e-61
pfam00573190 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 f 5e-60
COG0088214 COG0088, RplD, Ribosomal protein L4 [Translation, 2e-51
PRK14547 298 PRK14547, rplD, 50S ribosomal protein L4; Provisio 3e-39
CHL00147215 CHL00147, rpl4, ribosomal protein L4; Validated 2e-31
PRK14907295 PRK14907, rplD, 50S ribosomal protein L4; Provisio 1e-25
PRK04042254 PRK04042, rpl4lp, 50S ribosomal protein L4P; Provi 4e-11
TIGR03672251 TIGR03672, rpl4p_arch, 50S ribosomal protein L4P 3e-09
>gnl|CDD|235404 PRK05319, rplD, 50S ribosomal protein L4; Provisional Back     alignment and domain information 
 Score =  206 bits (526), Expect = 3e-67
 Identities = 67/120 (55%), Positives = 88/120 (73%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           + V N   ++ G + L+  VF V   + ++H+VV  QLA  +QGTH+TKT SEVSG GKK
Sbjct: 3   LKVLNLDGKEAGEVELSDAVFGVEPNEALLHQVVVAQLANARQGTHATKTRSEVSGGGKK 62

Query: 161 PWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKV 220
           PWRQKGTGRAR G++R PQ+RGG  + GPKPR ++ KLNKKVRRL L+ ALS +A EG++
Sbjct: 63  PWRQKGTGRARQGSIRSPQWRGGGVVFGPKPRDYSQKLNKKVRRLALRSALSEKAREGRL 122

Length = 205
>gnl|CDD|234414 TIGR03953, rplD_bact, 50S ribosomal protein L4, bacterial/organelle Back     alignment and domain information
>gnl|CDD|215999 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family Back     alignment and domain information
>gnl|CDD|223166 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|184735 PRK14547, rplD, 50S ribosomal protein L4; Provisional Back     alignment and domain information
>gnl|CDD|214375 CHL00147, rpl4, ribosomal protein L4; Validated Back     alignment and domain information
>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional Back     alignment and domain information
>gnl|CDD|235211 PRK04042, rpl4lp, 50S ribosomal protein L4P; Provisional Back     alignment and domain information
>gnl|CDD|234305 TIGR03672, rpl4p_arch, 50S ribosomal protein L4P Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 251
PRK05319205 rplD 50S ribosomal protein L4; Provisional 100.0
PRK14547 298 rplD 50S ribosomal protein L4; Provisional 100.0
CHL00147215 rpl4 ribosomal protein L4; Validated 100.0
COG0088214 RplD Ribosomal protein L4 [Translation, ribosomal 100.0
PF00573192 Ribosomal_L4: Ribosomal protein L4/L1 family; Inte 100.0
PRK14907295 rplD 50S ribosomal protein L4; Provisional 100.0
KOG1624290 consensus Mitochondrial/chloroplast ribosomal prot 100.0
PRK04042254 rpl4lp 50S ribosomal protein L4P; Provisional 100.0
TIGR03672251 rpl4p_arch 50S ribosomal protein L4P. One of the p 100.0
PLN00185 405 60S ribosomal protein L4-1; Provisional 100.0
PTZ00428 381 60S ribosomal protein L4; Provisional 100.0
KOG1475 363 consensus Ribosomal protein RPL1/RPL2/RL4L4 [RNA p 99.8
PTZ00428 381 60S ribosomal protein L4; Provisional 82.52
>PRK05319 rplD 50S ribosomal protein L4; Provisional Back     alignment and domain information 
Probab=100.00  E-value=4.7e-52  Score=365.00  Aligned_cols=144  Identities=51%  Similarity=0.765  Sum_probs=139.1

Q ss_pred             eeeEEEccCCCeeeeEEcCccccCCCCchHHHHHHHHHHHHHcccCCcccceeeeecCCCCCccccCCCCcccCCCCCCC
Q 025562           99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP  178 (251)
Q Consensus        99 m~v~V~~i~Ge~~g~ieLp~~VF~~piR~dllh~vV~~q~a~rRqGta~tKtRaEV~GsGrKp~rQKGTGrAR~Gs~rsP  178 (251)
                      |+++|||++|++.|+++||++||+.|+|.||||++|+||++++||||++||+|+||+|+|||||+||||||||+|++++|
T Consensus         1 ~~~~v~~~~g~~~~~i~l~~~vF~~~~r~dll~~~v~~~~~~~Rqgta~tk~r~ev~GsgrK~~~QKGTGrAR~Gs~rsP   80 (205)
T PRK05319          1 MELKVLNLDGKEAGEVELSDAVFGVEPNEALLHQVVVAQLANARQGTHATKTRSEVSGGGKKPWRQKGTGRARQGSIRSP   80 (205)
T ss_pred             CeeEEEcCCCCCcceEEcCHHHhCCCccHHHHHHHHHHHHHhcccCcccCCcccccCCCCCCCCCCCCCCccCcCcccCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccceeccCCCCccccccccHHHHHHHHHHHHHHHHhCCCeEEEecccCCCCCchh---hhhcCCcc
Q 025562          179 QFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKVSLSVSLSLFLRPSFS---LSLKNTDT  243 (251)
Q Consensus       179 ~~rGGG~afgPkPR~~~~klNKK~rrlAlrsALSaK~~qg~L~VVd~l~~~~~pkTk---~~lk~~~~  243 (251)
                      +|||||+||||+||+|++|||||+|++|+++|||+++++++|+|||+|.+ +.||||   ..|+++|.
T Consensus        81 ~~rGGg~afgpkpr~~~~klnkK~~~lAl~~aLs~k~~~~~l~Vvd~~~~-~~~KTk~~~~~l~~lg~  147 (205)
T PRK05319         81 QWRGGGVVFGPKPRDYSQKLNKKVRRLALRSALSEKAREGRLVVVDDLSL-EAPKTKELAAKLKNLGL  147 (205)
T ss_pred             cccCCeeeCCCCccchhhhcCHHHHHHHHHHHHHHHHhcCCeEEEecccc-CCCCHHHHHHHHHHcCC
Confidence            99999999999999999999999999999999999999999999999976 889999   56677664

>PRK14547 rplD 50S ribosomal protein L4; Provisional Back     alignment and domain information
>CHL00147 rpl4 ribosomal protein L4; Validated Back     alignment and domain information
>COG0088 RplD Ribosomal protein L4 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF00573 Ribosomal_L4: Ribosomal protein L4/L1 family; InterPro: IPR002136 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PRK14907 rplD 50S ribosomal protein L4; Provisional Back     alignment and domain information
>KOG1624 consensus Mitochondrial/chloroplast ribosomal protein L4 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK04042 rpl4lp 50S ribosomal protein L4P; Provisional Back     alignment and domain information
>TIGR03672 rpl4p_arch 50S ribosomal protein L4P Back     alignment and domain information
>PLN00185 60S ribosomal protein L4-1; Provisional Back     alignment and domain information
>PTZ00428 60S ribosomal protein L4; Provisional Back     alignment and domain information
>KOG1475 consensus Ribosomal protein RPL1/RPL2/RL4L4 [RNA processing and modification] Back     alignment and domain information
>PTZ00428 60S ribosomal protein L4; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query251
3d5b_F210 Structural Basis For Translation Termination On The 3e-22
2j01_F210 Structure Of The Thermus Thermophilus 70s Ribosome 3e-22
3fin_F208 T. Thermophilus 70s Ribosome In Complex With Mrna, 3e-22
3tve_F202 Crystal Structure Analysis Of Ribosomal Decoding. T 4e-22
3pyo_E202 Crystal Structure Of A Complex Containing Domain 3 4e-22
3uxq_F205 The Structure Of Thermorubin In Complex With The 70 4e-22
1vsa_D205 Crystal Structure Of A 70s Ribosome-Trna Complex Re 4e-22
1vor_F198 Crystal Structure Of Five 70s Ribosomes From Escher 5e-20
1pnu_C197 Crystal Structure Of A Streptomycin Dependent Ribos 5e-20
1jzx_K205 Structural Basis For The Interaction Of Antibiotics 6e-20
1nwx_C204 Complex Of The Large Ribosomal Subunit From Deinoco 6e-20
1dmg_A225 Crystal Structure Of Ribosomal Protein L4 Length = 2e-18
2ftc_D175 Structural Model For The Large Subunit Of The Mamma 3e-18
1p85_C201 Real Space Refined Coordinates Of The 50s Subunit F 3e-17
2gya_C198 Structure Of The 50s Subunit Of A Pre-Translocation 3e-17
3bbo_G293 Homology Model For The Spinach Chloroplast 50s Subu 8e-16
3cc2_C246 The Refined Crystal Structure Of The Haloarcula Mar 2e-05
1ffk_C246 Crystal Structure Of The Large Ribosomal Subunit Fr 3e-05
1jj2_C246 Fully Refined Crystal Structure Of The Haloarcula M 3e-05
>pdb|3D5B|F Chain F, Structural Basis For Translation Termination On The 70s Ribosome. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes As Described In Remark 400. Length = 210 Back     alignment and structure 
Iteration: 1

 Score =  101 bits (252), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 54/100 (54%), Positives = 70/100 (70%), Gaps = 2/100 (2%)
Query: 122 DVP--IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQ 179
           D+P  I   ++  VVRWQLAKR++GT STKT  EV+ +G+K W QK TGRARHG +  P 
Sbjct: 23  DLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHGDIGAPI 82
Query: 180 FRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGK 219
           F GG  + GPKPR ++  L KKVR+ GL +A++ RA EGK
Sbjct: 83  FVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGK 122
>pdb|2J01|F Chain F, Structure Of The Thermus Thermophilus 70s Ribosome Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4). This File Contains The 50s Subunit From Molecule I. Length = 210 Back     alignment and structure
>pdb|3FIN|F Chain F, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A 6.4 A Cryo-Em Map. This File Contains The 50s Subunit. Length = 208 Back     alignment and structure
>pdb|3TVE|F Chain F, Crystal Structure Analysis Of Ribosomal Decoding. This Entry Contains The 50s Ribosomal Subunit Of The First 70s Molecule In The Asymmetric Unit For The Cognate Trna-Leu Complex Length = 202 Back     alignment and structure
>pdb|3PYO|E Chain E, Crystal Structure Of A Complex Containing Domain 3 From The Psiv Igr Ires Rna Bound To The 70s Ribosome. This File Contains The 50s Subunit Of The First 70s Ribosome. Length = 202 Back     alignment and structure
>pdb|3UXQ|F Chain F, The Structure Of Thermorubin In Complex With The 70s Ribosome From Thermus Thermophilus. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes. Length = 205 Back     alignment and structure
>pdb|1VSA|D Chain D, Crystal Structure Of A 70s Ribosome-Trna Complex Reveals Functional Interactions And Rearrangements. This File, 1vsa, Contains The 50s Ribosome Subunit. 30s Ribosome Subunit Is In The File 2ow8 Length = 205 Back     alignment and structure
>pdb|1VOR|F Chain F, Crystal Structure Of Five 70s Ribosomes From Escherichia Coli In Complex With Protein Y. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Five 70s Ribosomes And Is Described In Remark 400. Length = 198 Back     alignment and structure
>pdb|1PNU|C Chain C, Crystal Structure Of A Streptomycin Dependent Ribosome From Escherichia Coli, 50s Subunit Of 70s Ribosome. This File, 1pnu, Contains Only Molecules Of The 50s Ribosomal Subunit. The 30s Subunit, Mrna, P-Site Trna, And A-Site Trna Are In The Pdb File 1pns. Length = 197 Back     alignment and structure
>pdb|1JZX|K Chain K, Structural Basis For The Interaction Of Antibiotics With The Peptidyl Transferase Center In Eubacteria Length = 205 Back     alignment and structure
>pdb|1NWX|C Chain C, Complex Of The Large Ribosomal Subunit From Deinococcus Radiodurans With Abt-773 Length = 204 Back     alignment and structure
>pdb|1DMG|A Chain A, Crystal Structure Of Ribosomal Protein L4 Length = 225 Back     alignment and structure
>pdb|2FTC|D Chain D, Structural Model For The Large Subunit Of The Mammalian Mitochondrial Ribosome Length = 175 Back     alignment and structure
>pdb|1P85|C Chain C, Real Space Refined Coordinates Of The 50s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome Length = 201 Back     alignment and structure
>pdb|2GYA|C Chain C, Structure Of The 50s Subunit Of A Pre-Translocational E. Coli Ribosome Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1056 Length = 198 Back     alignment and structure
>pdb|3BBO|G Chain G, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 293 Back     alignment and structure
>pdb|3CC2|C Chain C, The Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution With Rrna Sequence For The 23s Rrna And Genome-Derived Sequences For R-Proteins Length = 246 Back     alignment and structure
>pdb|1FFK|C Chain C, Crystal Structure Of The Large Ribosomal Subunit From Haloarcula Marismortui At 2.4 Angstrom Resolution Length = 246 Back     alignment and structure
>pdb|1JJ2|C Chain C, Fully Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution Length = 246 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 ?
Query251
1dmg_A225 Ribosomal protein L4; alpha-beta, ribosome, RNA, S 4e-65
3r8s_E201 50S ribosomal protein L4; protein biosynthesis, RN 3e-64
3bbo_G293 Ribosomal protein L4; large ribosomal subunit, spi 3e-64
2zjr_C205 50S ribosomal protein L4; ribosome, large ribosoma 1e-62
3v2d_F210 50S ribosomal protein L4; ribosome associated inhi 1e-61
2ftc_D175 Mitochondrial ribosomal protein L4 isoform A, mito 1e-54
1vq8_C246 50S ribosomal protein L4E; ribosome 50S, protein-p 3e-35
2wwb_H 362 60S ribosomal protein L4-B; ribosome, protein EXIT 5e-30
4a17_C 410 RPL4, ribosomal protein L3; eukaryotic ribosome, r 3e-27
2zkr_c 421 60S ribosomal protein L4; protein-RNA complex, 60S 7e-24
3iz5_D 405 60S ribosomal protein L4 (L4P); eukaryotic ribosom 4e-23
>1dmg_A Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon, gene regulation; HET: CIT; 1.70A {Thermotoga maritima} SCOP: c.22.1.1 Length = 225 Back     alignment and structure
 Score =  201 bits (512), Expect = 4e-65
 Identities = 56/120 (46%), Positives = 79/120 (65%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           + + N   E  G + ++  VF++    D++ R V  QL+ R+ GT STKT  EVSG G+K
Sbjct: 3   VDLLNVKGEKVGTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTASTKTRGEVSGGGRK 62

Query: 161 PWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKV 220
           PW QK TGRARHG++R P +R G  +HGPKPR  + KLNKK+++L L+ ALS +  E K+
Sbjct: 63  PWPQKHTGRARHGSIRSPIWRHGGVVHGPKPRDWSKKLNKKMKKLALRSALSVKYRENKL 122
>3r8s_E 50S ribosomal protein L4; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_C 1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E 2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E* 2qbk_E* 2qov_E 2qox_E 2qoz_E* ... Length = 201 Back     alignment and structure
>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 293 Back     alignment and structure
>2zjr_C 50S ribosomal protein L4; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: c.22.1.1 PDB: 1j5a_K* 1jzy_K* 1jzz_K* 1k01_K* 1nkw_C 1sm1_C* 2zjp_C* 2zjq_C 1jzx_K 3cf5_C* 3dll_C* 3pio_C* 3pip_C* 1nwy_C* 1nwx_C* 1xbp_C* 1pnu_C 1pny_C 1vor_F 1vou_F ... Length = 205 Back     alignment and structure
>3v2d_F 50S ribosomal protein L4; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgq_F 2hgj_F 2hgu_F 2j03_F 2jl6_F 2jl8_F 2v47_F 2v49_F 2wdi_F 2wdj_F 2wdl_F 2wdn_F 2wh2_F 2wh4_F 2wrj_F 2wrl_F 2wro_F 2wrr_F 2x9s_F 2x9u_F ... Length = 210 Back     alignment and structure
>2ftc_D Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_D Length = 175 Back     alignment and structure
>1vq8_C 50S ribosomal protein L4E; 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: c.22.1.1 PDB: 1k73_E* 1k8a_E* 1k9m_E* 1kc8_E* 1kd1_E* 1kqs_C* 1m1k_E* 1m90_E* 1n8r_E* 1nji_E* 1q7y_E* 1q81_E* 1q82_E* 1q86_E* 1qvf_C 1qvg_C 1s72_C* 1vq4_C* 1vq5_C* 1vq6_C* ... Length = 246 Back     alignment and structure
>2wwb_H 60S ribosomal protein L4-B; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 2wwa_H 2ww9_H 3izc_D 3izs_D 3o58_D 3o5h_D 3u5e_C 3u5i_C 1s1i_D 3jyw_D Length = 362 Back     alignment and structure
>4a17_C RPL4, ribosomal protein L3; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_C 4a1c_C 4a1e_C Length = 410 Back     alignment and structure
>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 421 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query251
1dmg_A225 Ribosomal protein L4; alpha-beta, ribosome, RNA, S 100.0
3v2d_F210 50S ribosomal protein L4; ribosome associated inhi 100.0
3bbo_G293 Ribosomal protein L4; large ribosomal subunit, spi 100.0
3r8s_E201 50S ribosomal protein L4; protein biosynthesis, RN 100.0
2zjr_C205 50S ribosomal protein L4; ribosome, large ribosoma 100.0
2ftc_D175 Mitochondrial ribosomal protein L4 isoform A, mito 100.0
3j21_D255 50S ribosomal protein L4P; archaea, archaeal, KINK 100.0
1vq8_C246 50S ribosomal protein L4E; ribosome 50S, protein-p 100.0
2zkr_c 421 60S ribosomal protein L4; protein-RNA complex, 60S 100.0
4a17_C 410 RPL4, ribosomal protein L3; eukaryotic ribosome, r 100.0
3iz5_D 405 60S ribosomal protein L4 (L4P); eukaryotic ribosom 100.0
2wwb_H 362 60S ribosomal protein L4-B; ribosome, protein EXIT 100.0
>1dmg_A Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon, gene regulation; HET: CIT; 1.70A {Thermotoga maritima} SCOP: c.22.1.1 Back     alignment and structure
Probab=100.00  E-value=2.4e-55  Score=389.92  Aligned_cols=145  Identities=43%  Similarity=0.644  Sum_probs=88.1

Q ss_pred             eeeEEEccCCCeeeeEEcCccccCCCCchHHHHHHHHHHHHHcccCCcccceeeeecCCCCCccccCCCCcccCCCCCCC
Q 025562           99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP  178 (251)
Q Consensus        99 m~v~V~~i~Ge~~g~ieLp~~VF~~piR~dllh~vV~~q~a~rRqGta~tKtRaEV~GsGrKp~rQKGTGrAR~Gs~rsP  178 (251)
                      |+++|||++|+++|+++||++||+.|+|.||||++|+||++++||||++||||+||||+||||||||||||||+|++++|
T Consensus         1 ~~~~v~~~~g~~~g~v~L~~~vF~~~~r~dlih~~v~~~~a~~Rqgt~~tktRaEv~G~GrKp~rQKGTGrAR~Gs~rsP   80 (225)
T 1dmg_A            1 AQVDLLNVKGEKVGTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTASTKTRGEVSGGGRKPWPQKHTGRARHGSIRSP   80 (225)
T ss_dssp             CEEEEECTTSCEEEEEECCHHHHSSCCCHHHHHHHHHHHHC---------------------------------------
T ss_pred             CeeEEEcCCCCEeeEEEcCHHHhCCCccHHHHHHHHHHHHHhccCCccccceeeEeecCCCCCCCCCCCCccccccccCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccceeccCCCCccccccccHHHHHHHHHHHHHHHHhCCCeEEEecccCCCCCchh---hhhcCCccc
Q 025562          179 QFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKVSLSVSLSLFLRPSFS---LSLKNTDTH  244 (251)
Q Consensus       179 ~~rGGG~afgPkPR~~~~klNKK~rrlAlrsALSaK~~qg~L~VVd~l~~~~~pkTk---~~lk~~~~~  244 (251)
                      +|||||++|||+||+|+++||||+|++||+||||+++++++|+|||+|++ +.||||   ..|++++.+
T Consensus        81 ~~rGGG~~fgPkpR~~~~klnkK~rrlAl~sALs~k~~~~~LvVvd~~~~-~~~KTK~~~~~L~~l~~~  148 (225)
T 1dmg_A           81 IWRHGGVVHGPKPRDWSKKLNKKMKKLALRSALSVKYRENKLLVLDDLKL-ERPKTKSLKEILQNLQLS  148 (225)
T ss_dssp             --------------CHHHHHHHHHHHHHHHHHHHHHHHTTCEEEESCCCC-SSCCHHHHHHHHHHTTCT
T ss_pred             ceecCceecCCcCccccccCCHHHHHHHHHHHHHHHHhCCCEEEEeeccc-CCCCHHHHHHHHHHcCCC
Confidence            99999999999999999999999999999999999999999999999976 899999   678888875
>3v2d_F 50S ribosomal protein L4; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgq_F 2hgj_F 2hgu_F 2j03_F 2jl6_F 2jl8_F 2v47_F 2v49_F 2wdi_F 2wdj_F 2wdl_F 2wdn_F 2wh2_F 2wh4_F 2wrj_F 2wrl_F 2wro_F 2wrr_F 2x9s_F 2x9u_F ... Back     alignment and structure
>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>3r8s_E 50S ribosomal protein L4; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_C 1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E 2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E* 2qbk_E* 2qov_E 2qox_E 2qoz_E* ... Back     alignment and structure
>2zjr_C 50S ribosomal protein L4; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: c.22.1.1 PDB: 1j5a_K* 1jzy_K* 1jzz_K* 1k01_K* 1nkw_C 1sm1_C* 2zjp_C* 2zjq_C 1jzx_K 3cf5_C* 3dll_C* 3pio_C* 3pip_C* 1nwy_C* 1nwx_C* 1xbp_C* 1pnu_C 1pny_C 1vor_F 1vou_F ... Back     alignment and structure
>2ftc_D Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_D Back     alignment and structure
>3j21_D 50S ribosomal protein L4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>1vq8_C 50S ribosomal protein L4E; 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: c.22.1.1 PDB: 1k73_E* 1k8a_E* 1k9m_E* 1kc8_E* 1kd1_E* 1kqs_C* 1m1k_E* 1m90_E* 1n8r_E* 1nji_E* 1q7y_E* 1q81_E* 1q82_E* 1q86_E* 1qvf_C 1qvg_C 1s72_C* 1vq4_C* 1vq5_C* 1vq6_C* ... Back     alignment and structure
>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure
>4a17_C RPL4, ribosomal protein L3; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_C 4a1c_C 4a1e_C Back     alignment and structure
>2wwb_H 60S ribosomal protein L4-B; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 2wwa_H 2ww9_H 3izc_D 3izs_D 3o58_D 3o5h_D 3u5e_C 3u5i_C 1s1i_D 3jyw_D 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 251
d2gycc1198 c.22.1.1 (C:1-198) Ribosomal protein L4 {Escherich 3e-32
d1dmga_225 c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga mar 1e-31
d1vqoc1246 c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon 6e-31
d2zjrc1197 c.22.1.1 (C:2-198) Ribosomal protein L4 {Deinococc 3e-30
d2j01f1208 c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus t 2e-25
>d2gycc1 c.22.1.1 (C:1-198) Ribosomal protein L4 {Escherichia coli [TaxId: 562]} Length = 198 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L4
superfamily: Ribosomal protein L4
family: Ribosomal protein L4
domain: Ribosomal protein L4
species: Escherichia coli [TaxId: 562]

 Score =  115 bits (288), Expect = 3e-32
 Identities = 43/122 (35%), Positives = 71/122 (58%)

Query: 108 NEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGT 167
            + +  + ++   F     + ++H+VV    A  +QGT + KT +EV+G+GKKPWRQKGT
Sbjct: 6   KDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGT 65

Query: 168 GRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKVSLSVSLS 227
           GRAR G+++ P +R G      +P+ H+ K+NKK+ R  LK  LS    + ++ +    S
Sbjct: 66  GRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFS 125

Query: 228 LF 229
           + 
Sbjct: 126 VE 127
>d1dmga_ c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga maritima [TaxId: 2336]} Length = 225 Back     information, alignment and structure
>d1vqoc1 c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 246 Back     information, alignment and structure
>d2zjrc1 c.22.1.1 (C:2-198) Ribosomal protein L4 {Deinococcus radiodurans [TaxId: 1299]} Length = 197 Back     information, alignment and structure
>d2j01f1 c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus thermophilus [TaxId: 274]} Length = 208 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 ?
Query251
d2gycc1198 Ribosomal protein L4 {Escherichia coli [TaxId: 562 100.0
d1dmga_225 Ribosomal protein L4 {Thermotoga maritima [TaxId: 100.0
d2zjrc1197 Ribosomal protein L4 {Deinococcus radiodurans [Tax 100.0
d2j01f1208 Ribosomal protein L4 {Thermus thermophilus [TaxId: 100.0
d1vqoc1246 Ribosomal protein L4 {Archaeon Haloarcula marismor 100.0
>d2gycc1 c.22.1.1 (C:1-198) Ribosomal protein L4 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L4
superfamily: Ribosomal protein L4
family: Ribosomal protein L4
domain: Ribosomal protein L4
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=3.7e-52  Score=360.27  Aligned_cols=140  Identities=33%  Similarity=0.536  Sum_probs=132.8

Q ss_pred             eeeEEEccCCCeeeeEEcCccccCCCCchHHHHHHHHHHHHHcccCCcccceeeeecCCCCCccccCCCCcccCCCCCCC
Q 025562           99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP  178 (251)
Q Consensus        99 m~v~V~~i~Ge~~g~ieLp~~VF~~piR~dllh~vV~~q~a~rRqGta~tKtRaEV~GsGrKp~rQKGTGrAR~Gs~rsP  178 (251)
                      |+++|.|..    |+|+||++||+.++|.||||+||+||++|+|||||+||+|+||+|+|||||+||||||||||++++|
T Consensus         1 m~l~~~~~~----~~i~l~~~vF~~~~~~~llh~~v~~~~a~~R~gt~~tKtRseV~g~gkKp~~QKGTGrAR~Gs~rsP   76 (198)
T d2gycc1           1 MELVLKDAQ----SALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSP   76 (198)
T ss_dssp             CCEEEECTT----CCSCCCEECCCSCCCHHHHTTTSSSCTTCCSCCCCSSCSCCCCCCSCSSCSCCCCCCCBTTBCCSCS
T ss_pred             CeeEecCCC----CeEEeCHHHhCCCcCHHHHHHHHHHHHHhccCCCcccceehhccCCccCcccccCCCCCCCcCcchh
Confidence            688888866    4699999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccceeccCCCCccccccccHHHHHHHHHHHHHHHHhCCCeEEEecccCCCCCchh---hhhcCCcc
Q 025562          179 QFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKVSLSVSLSLFLRPSFS---LSLKNTDT  243 (251)
Q Consensus       179 ~~rGGG~afgPkPR~~~~klNKK~rrlAlrsALSaK~~qg~L~VVd~l~~~~~pkTk---~~lk~~~~  243 (251)
                      +|+|||++|||+||+|+++||||+|++||++|||+|+++++|+|||+|.+ ++||||   ..|++++.
T Consensus        77 ~~~gGGva~GP~pr~~~~kl~kK~r~~al~~aLs~k~~~~~l~vvd~~~~-~~~kTk~~~~~l~~~~~  143 (198)
T d2gycc1          77 IWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSV-EAPKTKLLAQKLKDMAL  143 (198)
T ss_dssp             SSSSCCCSSCSCCSSSCCCCCTTTHHHHHHHHHHHTTSSSSCCEECGGGG-TCCSSHHHHHHHHTTTC
T ss_pred             hcccCceecCccccCeEeeHHHHHHHHHHHHHHHHHHhcCCeEEEeeccc-cCCcHHHHHHHHhhhcc
Confidence            99999999999999999999999999999999999999999999999987 899999   55666654
>d1dmga_ c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2zjrc1 c.22.1.1 (C:2-198) Ribosomal protein L4 {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d2j01f1 c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1vqoc1 c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon Haloarcula marismortui [TaxId: 2238]} Back     information, alignment and structure