Citrus Sinensis ID: 022312

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-------30
MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVVRSTTQSFLIYYYFLDFDFKKI
cHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccEEEEEEcccccEEEEEEEccccccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccHHHHHHHHHHHHHHHHHcccEEEEEccccccccHHHHHHHHHHcccccEEEEEEccccHHHHHHHHccccccEEEEcccccccccccHHHHHHccccccc
ccHHHHHHHHHHcccHHHHcccccccccHHHHcccccEEEEEcccccccHHHHHHHHHHHccccccccccccccccccHHHcccccccccccccccEEEEEEEEEccccEEEEEEEcHHHccccccHHHHHHHHHHHHHHHHcccccccccccEccccccccccccccccccccccccccccccEEEcccccccHccccHHHHHHHHHHHHHHHHHcccEEEEEccccccccHHHHHHHHHHccccccEEEEEcccccHHHHHHHHcccccEEEEccccccccccEEEEEHHHcccccc
MALTVSRRLLRRfgsfsafgryespsltsrsirsppdlyvacsgdnlfplksglsflasrkfsttiltpdssegafpsdlllkktvltpditiglhqdlvipvtnffnedkgfmvlagdvfdvpirkDIIHRVVRWQLakrqqgthstktisevsgtgkkpwrqkgtgrarhgtlrgpqfrggttmhgpkprshaIKLNKKVRRLGLKIALSARAAEGKLLvfedlevpshktKFIVNYYNQMENTKKVllcdggcihekLKLATQNLHYVNVLPSVVRSTTQSFLIYYYFldfdfkki
maltvsrrllrrfgsfsafgryespsltsrsirspPDLYVACSGDNLFPLKSGLSFLASRKFSTTiltpdssegafpsDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWqlakrqqgthstktisevsgtgkkpwrqkgtgrarhgtlrgpqfrggttmhgpkprshaiklnKKVRRLGLKIALSAraaegkllvfedlevpshKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVVRSTTQSFLIYYYFLDFDFKKI
MALTVSrrllrrFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVVRSTTQSfliyyyfldfdfkki
*********LRRFGSFSAF*****************DLYVACSGDNLFPLKSGLSFLASRKFSTTILTP****GAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLA*********************************************************KLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVVRSTTQSFLIYYYFLDFDF***
*****SRRLLRRFGSFSAFGRYESPSLTSRSIRSPP********************************************LLKKTVLT**ITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTH*********GTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVVRSTTQSFLIYYYFLDFDFKKI
MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQL*********************************HGTLRGPQFRGG**********HAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVVRSTTQSFLIYYYFLDFDFKKI
*********L*RFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTI*****SEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQ*********************************RGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVVRSTTQSFLIYYYFLDFDFKKI
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooo
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MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVVRSTTQSFLIYYYFLDFDFKKI
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 ?
Query299 2.2.26 [Sep-21-2011]
B6IRQ7206 50S ribosomal protein L4 yes no 0.578 0.839 0.522 6e-44
Q2W2J2206 50S ribosomal protein L4 yes no 0.578 0.839 0.511 2e-42
Q2RQW1206 50S ribosomal protein L4 yes no 0.578 0.839 0.511 4e-42
Q11HQ3206 50S ribosomal protein L4 yes no 0.581 0.844 0.48 1e-39
Q1RHM2207 50S ribosomal protein L4 yes no 0.581 0.840 0.5 1e-39
A8GVB5207 50S ribosomal protein L4 yes no 0.581 0.840 0.5 1e-39
Q68W79207 50S ribosomal protein L4 yes no 0.581 0.840 0.477 1e-38
Q4UMS8207 50S ribosomal protein L4 yes no 0.581 0.840 0.477 3e-38
A8GT68207 50S ribosomal protein L4 yes no 0.581 0.840 0.477 2e-37
B0BUQ9207 50S ribosomal protein L4 yes no 0.581 0.840 0.477 2e-37
>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 =  177 bits (450), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 91/174 (52%), Positives = 115/174 (66%), Gaps = 1/174 (0%)

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 RQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLV 222
           RQKGTGRAR G+ R PQFRGG  + GP  RSH   L KKVR+L LK ALS +AAEGKL V
Sbjct: 65  RQKGTGRARQGSTRSPQFRGGARIFGPVVRSHEHDLTKKVRKLALKTALSTKAAEGKLFV 124

Query: 223 FEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPS 276
            E  +  +HKTK +      +  T   L+ DG  + E    A +N+ +++VLP 
Sbjct: 125 LEAAKADTHKTKALAAQLKTLGLT-SALIIDGANLDETFVRAARNIPHLDVLPE 177
Forms part of the polypeptide exit tunnel.
Rhodospirillum centenum (strain ATCC 51521 / SW) (taxid: 414684)
>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|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|Q11HQ3|RL4_MESSB 50S ribosomal protein L4 OS=Mesorhizobium sp. (strain BNC1) 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
>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|Q4UMS8|RL4_RICFE 50S ribosomal protein L4 OS=Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) GN=rplD PE=3 SV=1 Back     alignment and function description
>sp|A8GT68|RL4_RICRS 50S ribosomal protein L4 OS=Rickettsia rickettsii (strain Sheila Smith) GN=rplD PE=3 SV=1 Back     alignment and function description
>sp|B0BUQ9|RL4_RICRO 50S ribosomal protein L4 OS=Rickettsia rickettsii (strain Iowa) 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 ?
Query299
18399235300 large subunit ribosomal protein L4 [Arab 0.879 0.876 0.740 1e-115
21553676300 50S ribosomal protein L4 [Arabidopsis th 0.879 0.876 0.740 1e-115
449433990315 PREDICTED: 50S ribosomal protein L4-like 0.926 0.879 0.734 1e-112
255554769294 50S ribosomal protein L4, putative [Rici 0.872 0.887 0.747 1e-112
359494830315 PREDICTED: 50S ribosomal protein L4-like 0.926 0.879 0.734 1e-110
297836242297 50S ribosomal protein L4 [Arabidopsis ly 0.869 0.875 0.718 1e-110
363807964312 uncharacterized protein LOC100804238 [Gl 0.923 0.884 0.717 1e-108
356532241310 PREDICTED: 50S ribosomal protein L4-like 0.916 0.883 0.717 1e-107
147767815278 hypothetical protein VITISV_027648 [Viti 0.719 0.773 0.855 1e-102
224118096285 predicted protein [Populus trichocarpa] 0.822 0.863 0.681 1e-101
>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
 Score =  420 bits (1079), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 208/281 (74%), Positives = 236/281 (83%), Gaps = 18/281 (6%)

Query: 1   MALTVSRRLLRRFGSFSAFGRYESPSLTSRSIRSPPDLYVACSGDNLFPL----KSGLSF 56
           MA ++SRR+ R FGSFSA GR  SP+L++ +           SG+ L  L    K G++ 
Sbjct: 1   MAASISRRIFRTFGSFSALGRSSSPNLSANT-----------SGNGLASLTNDLKYGMAL 49

Query: 57  LASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNEDKGFMVL 116
           L++RK ST+ILTPD S   FPSDLL KKTVLTPD TIG +QDLVIPVTNF NE+KGFMVL
Sbjct: 50  LSNRKLSTSILTPDDS---FPSDLLTKKTVLTPDRTIGQYQDLVIPVTNFQNEEKGFMVL 106

Query: 117 AGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLR 176
           AGDVFDVPIRKDIIH VVRWQLAKRQQGTHSTKT+SEVSGTG+KPW QKGTGRARHGTLR
Sbjct: 107 AGDVFDVPIRKDIIHNVVRWQLAKRQQGTHSTKTLSEVSGTGRKPWNQKGTGRARHGTLR 166

Query: 177 GPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFI 236
           GPQFRGG  MHGPKPRSHAIK+NK+VRRLGLKIAL+ARAAEGKLLVF+DL +P+HKTK I
Sbjct: 167 GPQFRGGCVMHGPKPRSHAIKMNKQVRRLGLKIALTARAAEGKLLVFDDLGLPTHKTKNI 226

Query: 237 VNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSV 277
           VNYYNQMENTKKVL+ +GG I EKLKLATQNLHYVN++PS+
Sbjct: 227 VNYYNQMENTKKVLVVEGGPIDEKLKLATQNLHYVNIIPSI 267

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|21553676|gb|AAM62769.1| 50S ribosomal protein L4 [Arabidopsis thaliana] Back     alignment and taxonomy information
>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
>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|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|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|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|147767815|emb|CAN77922.1| hypothetical protein VITISV_027648 [Vitis vinifera] 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 ?
Query299
TAIR|locus:2061659300 AT2G20060 [Arabidopsis thalian 0.892 0.89 0.740 3.7e-103
TIGR_CMR|APH_0281208 APH_0281 "ribosomal protein L4 0.588 0.846 0.463 7.2e-36
TIGR_CMR|ECH_0410205 ECH_0410 "ribosomal protein L4 0.561 0.819 0.456 6.7e-33
TIGR_CMR|NSE_0267214 NSE_0267 "ribosomal protein L4 0.548 0.766 0.471 6e-32
TIGR_CMR|BA_0111207 BA_0111 "ribosomal protein L4" 0.578 0.835 0.419 5.4e-31
DICTYBASE|DDB_G0283275258 DDB_G0283275 "ribosomal protei 0.739 0.856 0.355 8.8e-31
UNIPROTKB|Q3A9R7206 rplD "50S ribosomal protein L4 0.588 0.854 0.396 1.8e-30
TIGR_CMR|CHY_2308206 CHY_2308 "ribosomal protein L4 0.588 0.854 0.396 1.8e-30
TIGR_CMR|SPO_3824205 SPO_3824 "ribosomal protein L4 0.521 0.760 0.449 1.6e-29
ZFIN|ZDB-GENE-050522-388302 zgmrpl4 "mitochondrial ribosom 0.568 0.562 0.406 9.1e-29
TAIR|locus:2061659 AT2G20060 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1022 (364.8 bits), Expect = 3.7e-103, P = 3.7e-103
 Identities = 205/277 (74%), Positives = 233/277 (84%)

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 RGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYY 240
             RGG  MHGPKPRSHAIK+NK+VRRLGLKIAL+ARAAEGKLLVF+DL +P+HKTK IVNYY
Sbjct:   171 RGGCVMHGPKPRSHAIKMNKQVRRLGLKIALTARAAEGKLLVFDDLGLPTHKTKNIVNYY 230

Query:   241 NQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSV 277
             NQMENTKKVL+ +GG I EKLKLATQNLHYVN++PS+
Sbjct:   231 NQMENTKKVLVVEGGPIDEKLKLATQNLHYVNIIPSI 267
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|ECH_0410 ECH_0410 "ribosomal protein L4" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)] 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|BA_0111 BA_0111 "ribosomal protein L4" [Bacillus anthracis str. Ames (taxid:198094)] 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
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
TIGR_CMR|SPO_3824 SPO_3824 "ribosomal protein L4" [Ruegeria pomeroyi DSS-3 (taxid:246200)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-050522-388 zgmrpl4 "mitochondrial ribosomal protein L4" [Danio rerio (taxid:7955)] 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 ?
Query299
PRK05319205 PRK05319, rplD, 50S ribosomal protein L4; Provisio 7e-82
TIGR03953188 TIGR03953, rplD_bact, 50S ribosomal protein L4, ba 3e-77
pfam00573190 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 f 1e-73
COG0088214 COG0088, RplD, Ribosomal protein L4 [Translation, 5e-63
PRK14547298 PRK14547, rplD, 50S ribosomal protein L4; Provisio 8e-44
CHL00147215 CHL00147, rpl4, ribosomal protein L4; Validated 4e-36
PRK14907295 PRK14907, rplD, 50S ribosomal protein L4; Provisio 4e-28
PRK04042254 PRK04042, rpl4lp, 50S ribosomal protein L4P; Provi 2e-11
TIGR03672251 TIGR03672, rpl4p_arch, 50S ribosomal protein L4P 2e-10
>gnl|CDD|235404 PRK05319, rplD, 50S ribosomal protein L4; Provisional Back     alignment and domain information 
 Score =  245 bits (628), Expect = 7e-82
 Identities = 87/175 (49%), Positives = 118/175 (67%), Gaps = 2/175 (1%)

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

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

Query: 221 LVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLP 275
           +V +DL + + KTK +      +   KKVL+     + E L L+ +NL  V+VLP
Sbjct: 123 VVVDDLSLEAPKTKELAAKLKNL-GLKKVLIVTDE-VDENLYLSARNLPNVDVLP 175

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 299
CHL00147215 rpl4 ribosomal protein L4; Validated 100.0
PRK05319205 rplD 50S ribosomal protein L4; Provisional 100.0
PRK14547298 rplD 50S ribosomal protein L4; Provisional 100.0
PF00573192 Ribosomal_L4: Ribosomal protein L4/L1 family; Inte 100.0
PRK14907295 rplD 50S ribosomal protein L4; Provisional 100.0
COG0088214 RplD Ribosomal protein L4 [Translation, ribosomal 100.0
PRK04042254 rpl4lp 50S ribosomal protein L4P; Provisional 100.0
KOG1624290 consensus Mitochondrial/chloroplast ribosomal prot 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 99.96
PTZ00428 381 60S ribosomal protein L4; Provisional 95.49
>CHL00147 rpl4 ribosomal protein L4; Validated Back     alignment and domain information 
Probab=100.00  E-value=2.8e-68  Score=483.31  Aligned_cols=197  Identities=34%  Similarity=0.505  Sum_probs=187.0

Q ss_pred             ceeeEEEccCCCe-eeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeeeecCCCCCccccCCCCccCCCCCC
Q 022312           98 DLVIPVTNFFNED-KGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLR  176 (299)
Q Consensus        98 ~~~v~V~n~~ge~-~g~ieLp~~VF~~pir~dilh~vv~~q~anrRqGta~TKtRaEVsGsGrKp~rQKGTGrAR~Gs~r  176 (299)
                      .++++|+|++|+. +|+++|+++|| .+++.|+||++|+||++++|||||+||||+||+|||||||||||||||||||+|
T Consensus         6 ~~~~~v~~~~g~~~~~~~~l~~~vf-~~~~~~ll~~~v~~~~a~~R~gt~~tKtR~eV~G~grKp~~QKGTGrAR~Gs~r   84 (215)
T CHL00147          6 FLNYPVIDLTGKEKSETIKLKLNVL-EKSGNYLLHRALVRQNNNQRQGTASTKTRSEVRGGGRKPWKQKGTGRARAGSNR   84 (215)
T ss_pred             eeeEEEEccCCCeecceEEeCHHHh-CCchHhHHHHHHHHHHHHHhhcccccCccccccCCCCCCcccCCCCccCCCCCc
Confidence            4689999999999 89999999999 557799999999999999999999999999999999999999999999999999


Q ss_pred             CCcccCcccccCCCCccccccccHHHHHHHHHHHHHHHHHcCCeEEEecCC--CCCCCHHHHHHHHHhccCC--CcEEEE
Q 022312          177 GPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLE--VPSHKTKFIVNYYNQMENT--KKVLLC  252 (299)
Q Consensus       177 sP~~rGGG~afGPkPR~y~~klNKK~rrlAlksALSak~~~g~LiVVD~l~--~~~~KTK~~~~~Lk~l~~~--k~~LiV  252 (299)
                      ||+|||||++|||+||+|+++||||+|++|+++|||+|  +++|+|||+++  ++.+|||+++++|++++..  +++|||
T Consensus        85 sP~~rgGG~afgP~pR~y~~klnKKvrrlAl~sALS~k--~~~l~VVd~~~~~~~~~KTK~~~~~L~~l~~~~~~~~L~V  162 (215)
T CHL00147         85 SPLWKGGGVIFGPKPKTYSNKLNKKERRLALRTLLYNK--SNNITVVENFESSITNPKTKAFINLLKKLNINLDQKILII  162 (215)
T ss_pred             CCcccCCEeecCCCCcchhhhcCHHHHHHHHHHHHHHh--hCCeEEEcccccccCCCCHHHHHHHHHHcCCCcCCceEEE
Confidence            99999999999999999999999999999999999998  45899999999  9999999999999999863  579999


Q ss_pred             ecCCcchhHHHHhhCCCCceEEecCCCccccccccceEEEeeeccC
Q 022312          253 DGGCIHEKLKLATQNLHYVNVLPSVVRSTTQSFLIYYYFLDFDFKK  298 (299)
Q Consensus       253 ~~~~~~enl~~A~RNIp~V~v~~~~~LNv~dLl~~~~ifI~~~a~~  298 (299)
                      + ++.|+|+.+|+||||+|+++++++|||||||.+++++|+++|.+
T Consensus       163 ~-~~~~~nl~~S~rNlp~V~v~~~~~lNv~dLL~~~~vvit~~Al~  207 (215)
T CHL00147        163 V-PEKTENLYLSTRNLKNVELISADTLNIKSLLKAKQIIITKEALK  207 (215)
T ss_pred             E-CCCchHHHHHHhCCCCcEEEecCCccHHHHhcCCcEEEEHHHHH
Confidence            8 46789999999999999999999999999999999999999863

>PRK05319 rplD 50S ribosomal protein L4; Provisional Back     alignment and domain information
>PRK14547 rplD 50S ribosomal protein L4; Provisional 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
>COG0088 RplD 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
>KOG1624 consensus Mitochondrial/chloroplast ribosomal protein L4 [Translation, ribosomal structure and biogenesis] 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 ?
Query299
1pnu_C197 Crystal Structure Of A Streptomycin Dependent Ribos 4e-28
1nwx_C204 Complex Of The Large Ribosomal Subunit From Deinoco 4e-28
1vor_F198 Crystal Structure Of Five 70s Ribosomes From Escher 4e-28
1jzx_K205 Structural Basis For The Interaction Of Antibiotics 4e-28
2j01_F210 Structure Of The Thermus Thermophilus 70s Ribosome 2e-27
1vsa_D205 Crystal Structure Of A 70s Ribosome-Trna Complex Re 2e-27
3d5b_F210 Structural Basis For Translation Termination On The 2e-27
3uxq_F205 The Structure Of Thermorubin In Complex With The 70 2e-27
3pyo_E202 Crystal Structure Of A Complex Containing Domain 3 2e-27
3fin_F208 T. Thermophilus 70s Ribosome In Complex With Mrna, 2e-27
3tve_F202 Crystal Structure Analysis Of Ribosomal Decoding. T 2e-27
1p85_C201 Real Space Refined Coordinates Of The 50s Subunit F 8e-25
2gya_C198 Structure Of The 50s Subunit Of A Pre-Translocation 1e-24
2ftc_D175 Structural Model For The Large Subunit Of The Mamma 7e-24
1dmg_A225 Crystal Structure Of Ribosomal Protein L4 Length = 6e-19
3bbo_G293 Homology Model For The Spinach Chloroplast 50s Subu 2e-16
3cc2_C246 The Refined Crystal Structure Of The Haloarcula Mar 2e-05
1ffk_C246 Crystal Structure Of The Large Ribosomal Subunit Fr 4e-05
1jj2_C246 Fully Refined Crystal Structure Of The Haloarcula M 4e-05
>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 
Iteration: 1

 Score =  121 bits (304), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 64/153 (41%), Positives = 97/153 (63%), Gaps = 5/153 (3%)
Query: 125 IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQFRGGT 184
           +   ++H VV WQLA R++GT ST+T ++VS TG+K + QKGTG ARHG    P F GG 
Sbjct: 21  VNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGDRSVPTFVGGG 80
Query: 185 TMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYYNQ-- 242
              GPKPRS+   L ++VR+LGL +A+++R   GKL+  +  ++   KTK  +++  Q  
Sbjct: 81  VAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAVDGFDIADAKTKNFISWAKQNG 140
Query: 243 MENTKKVLLCDGGCIHEKLKLATQNLHYVNVLP 275
           ++ T+KVLL       E  + A +N+ +V+VLP
Sbjct: 141 LDGTEKVLLV---TDDENTRRAARNVSWVSVLP 170
>pdb|1NWX|C Chain C, Complex Of The Large Ribosomal Subunit From Deinococcus Radiodurans With Abt-773 Length = 204 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|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|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|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|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
>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|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|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|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|2FTC|D Chain D, Structural Model For The Large Subunit Of The Mammalian Mitochondrial Ribosome Length = 175 Back     alignment and structure
>pdb|1DMG|A Chain A, Crystal Structure Of Ribosomal Protein L4 Length = 225 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 ?
Query299
3bbo_G293 Ribosomal protein L4; large ribosomal subunit, spi 2e-81
1dmg_A225 Ribosomal protein L4; alpha-beta, ribosome, RNA, S 3e-81
3r8s_E201 50S ribosomal protein L4; protein biosynthesis, RN 6e-81
2zjr_C205 50S ribosomal protein L4; ribosome, large ribosoma 5e-79
3v2d_F210 50S ribosomal protein L4; ribosome associated inhi 2e-78
2ftc_D175 Mitochondrial ribosomal protein L4 isoform A, mito 1e-72
1vq8_C246 50S ribosomal protein L4E; ribosome 50S, protein-p 2e-38
2wwb_H 362 60S ribosomal protein L4-B; ribosome, protein EXIT 1e-32
4a17_C 410 RPL4, ribosomal protein L3; eukaryotic ribosome, r 9e-30
3iz5_D 405 60S ribosomal protein L4 (L4P); eukaryotic ribosom 1e-25
2zkr_c 421 60S ribosomal protein L4; protein-RNA complex, 60S 3e-25
>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
 Score =  247 bits (631), Expect = 2e-81
 Identities = 60/224 (26%), Positives = 97/224 (43%), Gaps = 6/224 (2%)

Query: 58  ASRKFSTTILTPDSSEGAFPSDLLLK---KTVLTPDITIGLHQDLVIPVTNFFNEDKGFM 114
            S  F ++ L    S       +L         T        + + +P+ NF  E  G  
Sbjct: 9   LSLSFFSSSLFSSKSRNFSSKPILKLPSSSHSQTSLSLSIKSELIPLPILNFSGEKVGET 68

Query: 115 VLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGT 174
            L          + ++HR +   L  +++GT ST T +EV G G+KP+ QK TGRAR G+
Sbjct: 69  FLNLKTAPPEKARAVVHRGLITHLQNKRRGTASTLTRAEVRGGGRKPYPQKKTGRARRGS 128

Query: 175 LRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTK 234
              P   GG  + GPKPR   IK+NKK RRL L  A+++      ++          KTK
Sbjct: 129 QGSPLRPGGGVIFGPKPRDWTIKMNKKERRLALSTAIASAVGNSFVVEEFAENFEKPKTK 188

Query: 235 FIVNYYNQM--ENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPS 276
             +    +   +  +K L      + E ++ + +N+  + +L  
Sbjct: 189 DFIAAMQRWGLDPAEKSLFFLMD-LVENVEKSGRNIRTLKLLTP 231
>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
>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
>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 ?
Query299
1dmg_A225 Ribosomal protein L4; alpha-beta, ribosome, RNA, S 100.0
3v2d_F210 50S ribosomal protein L4; ribosome associated inhi 100.0
3r8s_E201 50S ribosomal protein L4; protein biosynthesis, RN 100.0
3bbo_G293 Ribosomal protein L4; large ribosomal subunit, spi 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=2.7e-71  Score=504.71  Aligned_cols=199  Identities=39%  Similarity=0.563  Sum_probs=139.9

Q ss_pred             eeeEEEccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeeeecCCCCCccccCCCCccCCCCCCCC
Q 022312           99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP  178 (299)
Q Consensus        99 ~~v~V~n~~ge~~g~ieLp~~VF~~pir~dilh~vv~~q~anrRqGta~TKtRaEVsGsGrKp~rQKGTGrAR~Gs~rsP  178 (299)
                      |+++|||++|+++|+++||++||+.|+|.||||+||+||++|+|||||+||||+||||||||||||||||||||||+|+|
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             cccCcccccCCCCccccccccHHHHHHHHHHHHHHHHHcCCeEEEecCCCCCCCHHHHHHHHHhccCC-CcEEEEecCCc
Q 022312          179 QFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYYNQMENT-KKVLLCDGGCI  257 (299)
Q Consensus       179 ~~rGGG~afGPkPR~y~~klNKK~rrlAlksALSak~~~g~LiVVD~l~~~~~KTK~~~~~Lk~l~~~-k~~LiV~~~~~  257 (299)
                      +|||||++|||+||+|+++||||+|++|+++|||+++.+++|+|||+++++.+|||+++++|++++++ +++|||++ +.
T Consensus        81 ~~rGGG~~fgPkpR~~~~klnkK~rrlAl~sALs~k~~~~~LvVvd~~~~~~~KTK~~~~~L~~l~~~~~~~LiV~~-~~  159 (225)
T 1dmg_A           81 IWRHGGVVHGPKPRDWSKKLNKKMKKLALRSALSVKYRENKLLVLDDLKLERPKTKSLKEILQNLQLSDKKTLIVLP-WK  159 (225)
T ss_dssp             --------------CHHHHHHHHHHHHHHHHHHHHHHHTTCEEEESCCCCSSCCHHHHHHHHHHTTCTTSCEEEEEC-CC
T ss_pred             ceecCceecCCcCccccccCCHHHHHHHHHHHHHHHHhCCCEEEEeecccCCCCHHHHHHHHHHcCCCCCCEEEEEC-CC
Confidence            99999999999999999999999999999999999999999999999999999999999999999986 78999984 55


Q ss_pred             ch---hHHHHhhCCCCceEEecCC---------------CccccccccceEEEeeeccC
Q 022312          258 HE---KLKLATQNLHYVNVLPSVV---------------RSTTQSFLIYYYFLDFDFKK  298 (299)
Q Consensus       258 ~e---nl~~A~RNIp~V~v~~~~~---------------LNv~dLl~~~~ifI~~~a~~  298 (299)
                      |+   |+.+|+||||+|+++++++               ||+||||+++.++|+++|.+
T Consensus       160 ~~~~~n~~~a~RNip~v~v~~~~~~~~~~~~~~~~~~~~lNv~dll~~~~lv~t~~Al~  218 (225)
T 1dmg_A          160 EEGYMNVKLSGRNLPDVKVIIADNPNNSKNGEKAVRIDGLNVFDMLKYDYLVLTRDMVS  218 (225)
T ss_dssp             SHHHHHHHHHHTTCTTEEEEECCCCSSCCSSCCCCCCTTCCHHHHHHSSEEEEEHHHHH
T ss_pred             ccchHHHHHHHhCCCCCEEEecCCcccccccccccCcCcEEHHHHhCCCcEEEeHHHHH
Confidence            78   9999999999999999999               99999999999999998853
>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
>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
>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} 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 299
d2gycc1198 c.22.1.1 (C:1-198) Ribosomal protein L4 {Escherich 7e-41
d1dmga_225 c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga mar 3e-40
d2zjrc1197 c.22.1.1 (C:2-198) Ribosomal protein L4 {Deinococc 3e-37
d1vqoc1246 c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon 2e-35
d2j01f1208 c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus t 2e-31
>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 =  138 bits (349), Expect = 7e-41
 Identities = 58/168 (34%), Positives = 92/168 (54%), Gaps = 2/168 (1%)

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

Query: 168 GRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLE 227
           GRAR G+++ P +R G      +P+ H+ K+NKK+ R  LK  LS    + +L+V E   
Sbjct: 66  GRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFS 125

Query: 228 VPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLP 275
           V + KTK +      M     +++      +  L LA +NLH V+V  
Sbjct: 126 VEAPKTKLLAQKLKDMALEDVLIITGELDEN--LFLAARNLHKVDVRD 171
>d1dmga_ c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga maritima [TaxId: 2336]} Length = 225 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
>d1vqoc1 c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 246 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 ?
Query299
d2gycc1198 Ribosomal protein L4 {Escherichia coli [TaxId: 562 100.0
d2zjrc1197 Ribosomal protein L4 {Deinococcus radiodurans [Tax 100.0
d1dmga_225 Ribosomal protein L4 {Thermotoga maritima [TaxId: 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=4.7e-69  Score=479.17  Aligned_cols=194  Identities=33%  Similarity=0.497  Sum_probs=185.8

Q ss_pred             eeeEEEccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeeeecCCCCCccccCCCCccCCCCCCCC
Q 022312           99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP  178 (299)
Q Consensus        99 ~~v~V~n~~ge~~g~ieLp~~VF~~pir~dilh~vv~~q~anrRqGta~TKtRaEVsGsGrKp~rQKGTGrAR~Gs~rsP  178 (299)
                      |++.|.|..    |+++|+++||+.++|.||||+||+||++|+|||||+||||+||+|||||||+|||||||||||+|||
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            678888765    5699999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCcccccCCCCccccccccHHHHHHHHHHHHHHHHHcCCeEEEecCCCCCCCHHHHHHHHHhccCCCcEEEEecCCcc
Q 022312          179 QFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGCIH  258 (299)
Q Consensus       179 ~~rGGG~afGPkPR~y~~klNKK~rrlAlksALSak~~~g~LiVVD~l~~~~~KTK~~~~~Lk~l~~~k~~LiV~~~~~~  258 (299)
                      +|||||++|||+||+|+++||||+|++|+++|||.|+++++|+|||++.++++|||++.++|++++. .++|||+ ++.|
T Consensus        77 ~~~gGGva~GP~pr~~~~kl~kK~r~~al~~aLs~k~~~~~l~vvd~~~~~~~kTk~~~~~l~~~~~-~~~Liv~-~~~~  154 (198)
T d2gycc1          77 IWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMAL-EDVLIIT-GELD  154 (198)
T ss_dssp             SSSSCCCSSCSCCSSSCCCCCTTTHHHHHHHHHHHTTSSSSCCEECGGGGTCCSSHHHHHHHHTTTC-GGGTTTC-CCCS
T ss_pred             hcccCceecCccccCeEeeHHHHHHHHHHHHHHHHHHhcCCeEEEeeccccCCcHHHHHHHHhhhcc-ceeEEec-Cccc
Confidence            9999999999999999999999999999999999999999999999999999999999999999987 4688888 4789


Q ss_pred             hhHHHHhhCCCCceEEecCCCccccccccceEEEeeeccC
Q 022312          259 EKLKLATQNLHYVNVLPSVVRSTTQSFLIYYYFLDFDFKK  298 (299)
Q Consensus       259 enl~~A~RNIp~V~v~~~~~LNv~dLl~~~~ifI~~~a~~  298 (299)
                      +|+.+|+||||+|+++++++|||||||++++|+|+++|.+
T Consensus       155 enl~~S~RNI~~v~v~~~~~lNvydlLk~~~lVit~~Al~  194 (198)
T d2gycc1         155 ENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVK  194 (198)
T ss_dssp             SSCCGGGSSSSSCCCCCSSSCCHHHHTTTSCCCEEHHHHH
T ss_pred             HHHHHHHhCcCCceEeecCCccHHHHhcCCeEEEEHHHHH
Confidence            9999999999999999999999999999999999998864
>d2zjrc1 c.22.1.1 (C:2-198) Ribosomal protein L4 {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d1dmga_ c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga maritima [TaxId: 2336]} 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