Citrus Sinensis ID: 045484

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-------18
MWATCYVRQSEIDRRNQNLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKLNQLVMTLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGKPCKWCKTASRKKKRKFSCLIILSFCAI
cccccccEEEEEcccccccccccccccccEEEEcccccccccccccccccccccEEEEcccccccccHHHHHHHHHHHccccEEEEEEccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccc
ccEEEEEEEEcccccEEEEEEccccEcccEEEEccccccccccccccccccccEEEEEEEEcccccHHHHHHHHHHHHHHccEEEEEEcccccccccccEEEccccccccccccccccHHHccHHHccccccccccccccccccccccccccccccccccccccccccccEEEEEEccc
mwatcyvrqseidrrnqnlgnrdteRDRQKWLGAEYAQLhrhsslgfsalpfstitllnaispvkLNQLVMTLILKLEVACHLLVCmlgpssttlSHEAKVLRKAGqshwlgqrpvirgvpmnpvdhprgrgegrgkssgnhgrcsltpwgkpckwcktasrkkkrkfSCLIILSFCAI
mwatcyvrqseidrrnqnlgnrdteRDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKLNQLVMTLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKagqshwlgqrpvirgvpmnpvdhprgrgegrgkssgnhgrcsltpwgkpckwcktasrkkkrkfscliilsfcai
MWATCYVRQSEIDRRNQNLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKLNQLVMTLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPrgrgegrgKSSGNHGRCSLTPWGKPCKWCKTASRKKKRKFSCLIILSFCAI
****CY***********************KWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKLNQLVMTLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIR**************************CSLTPWGKPCKWCKTASRKKKRKFSCLIILSFCA*
*****YVRQSEIDRRNQNLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKLNQLVMTLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHP*********************WGKPCKWCKTAS*****KFSCLIILSFCA*
MWATCYVRQSEIDRRNQNLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKLNQLVMTLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRG************GRCSLTPWGKPCKWCKTASRKKKRKFSCLIILSFCAI
MWATCYVRQSEIDRRNQNLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKLNQLVMTLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRG**************CSLTPWGKPCKWCKTAS***KRKFSCLIILSFCAI
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MWATCYVRQSEIDRRNQNLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKLNQLVMTLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGKPCKWCKTASRKKKRKFSCLIILSFCAI
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 ?
Query179 2.2.26 [Sep-21-2011]
Q3A9R9274 50S ribosomal protein L2 yes no 0.491 0.321 0.469 2e-14
B3EP58279 50S ribosomal protein L2 yes no 0.519 0.333 0.46 5e-14
B1I1J1275 50S ribosomal protein L2 yes no 0.463 0.301 0.462 6e-14
Q8K953273 50S ribosomal protein L2 yes no 0.469 0.307 0.462 1e-13
Q2RFQ0276 50S ribosomal protein L2 yes no 0.508 0.329 0.435 3e-13
Q89A71273 50S ribosomal protein L2 yes no 0.469 0.307 0.451 3e-13
B8D846273 50S ribosomal protein L2 yes no 0.469 0.307 0.451 3e-13
P57588273 50S ribosomal protein L2 yes no 0.469 0.307 0.451 3e-13
B8D9U4273 50S ribosomal protein L2 yes no 0.469 0.307 0.451 3e-13
P60428273 50S ribosomal protein L2 yes no 0.469 0.307 0.440 6e-13
>sp|Q3A9R9|RL2_CARHZ 50S ribosomal protein L2 OS=Carboxydothermus hydrogenoformans (strain Z-2901 / DSM 6008) GN=rplB PE=3 SV=1 Back     alignment and function desciption
 Score = 78.6 bits (192), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 46/98 (46%), Positives = 56/98 (57%), Gaps = 10/98 (10%)

Query: 76  KLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGR 135
           K+ + C   +  +G     L HE   + KAG++ WLG RP +RGV MNPVDHP G GEGR
Sbjct: 183 KVLLECRATIGQVG----NLEHENITIGKAGRARWLGIRPTVRGVVMNPVDHPHGGGEGR 238

Query: 136 GKSSGNHGRCSLTPWGKPCKWCKTASRKKKRKFSCLII 173
                  GR  +TPWGKP    KT  RKK +  S LII
Sbjct: 239 SPI----GRHPVTPWGKPTLGVKT--RKKNKASSKLII 270
One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.
Carboxydothermus hydrogenoformans (strain Z-2901 / DSM 6008) (taxid: 246194)
>sp|B3EP58|RL2_CHLPB 50S ribosomal protein L2 OS=Chlorobium phaeobacteroides (strain BS1) GN=rplB PE=3 SV=1 Back     alignment and function description
>sp|B1I1J1|RL2_DESAP 50S ribosomal protein L2 OS=Desulforudis audaxviator (strain MP104C) GN=rplB PE=3 SV=1 Back     alignment and function description
>sp|Q8K953|RL2_BUCAP 50S ribosomal protein L2 OS=Buchnera aphidicola subsp. Schizaphis graminum (strain Sg) GN=rplB PE=3 SV=1 Back     alignment and function description
>sp|Q2RFQ0|RL2_MOOTA 50S ribosomal protein L2 OS=Moorella thermoacetica (strain ATCC 39073) GN=rplB PE=3 SV=1 Back     alignment and function description
>sp|Q89A71|RL2_BUCBP 50S ribosomal protein L2 OS=Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp) GN=rplB PE=3 SV=1 Back     alignment and function description
>sp|B8D846|RL2_BUCAT 50S ribosomal protein L2 OS=Buchnera aphidicola subsp. Acyrthosiphon pisum (strain Tuc7) GN=rplB PE=3 SV=1 Back     alignment and function description
>sp|P57588|RL2_BUCAI 50S ribosomal protein L2 OS=Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) GN=rplB PE=3 SV=1 Back     alignment and function description
>sp|B8D9U4|RL2_BUCA5 50S ribosomal protein L2 OS=Buchnera aphidicola subsp. Acyrthosiphon pisum (strain 5A) GN=rplB PE=3 SV=1 Back     alignment and function description
>sp|P60428|RL2_SALTY 50S ribosomal protein L2 OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=rplB 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 ?
Query179
225434185193 PREDICTED: 60S ribosomal protein L2, mit 0.335 0.310 0.766 1e-19
224141127159 predicted protein [Populus trichocarpa] 0.581 0.654 0.478 1e-19
255586439241 50S ribosomal protein L2, putative [Rici 0.430 0.319 0.623 2e-19
17644114191 ribosomal protein L2 [Gossypium arboreum 0.396 0.371 0.680 2e-19
296084340204 unnamed protein product [Vitis vinifera] 0.396 0.348 0.690 2e-19
17644112202 ribosomal protein L2 [Solanum lycopersic 0.541 0.480 0.538 3e-19
224092860159 predicted protein [Populus trichocarpa] 0.620 0.698 0.456 2e-18
449459236216 PREDICTED: 60S ribosomal protein L2, mit 0.391 0.324 0.676 4e-18
297824397214 ribosomal protein L2 family protein [Ara 0.335 0.280 0.683 3e-16
21592449214 unknown [Arabidopsis thaliana] 0.335 0.280 0.683 3e-16
>gi|225434185|ref|XP_002279271.1| PREDICTED: 60S ribosomal protein L2, mitochondrial-like [Vitis vinifera] Back     alignment and taxonomy information
 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 46/60 (76%), Positives = 50/60 (83%)

Query: 97  HEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGKPCKW 156
           H AK LRKAGQS WLG+RPV+RGV MNPVDHP G GEGR KS G+HGR SLTPWGKP K+
Sbjct: 134 HGAKKLRKAGQSRWLGRRPVVRGVAMNPVDHPHGGGEGRSKSGGSHGRGSLTPWGKPTKY 193

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224141127|ref|XP_002323926.1| predicted protein [Populus trichocarpa] gi|222866928|gb|EEF04059.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|255586439|ref|XP_002533864.1| 50S ribosomal protein L2, putative [Ricinus communis] gi|223526186|gb|EEF28514.1| 50S ribosomal protein L2, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|17644114|gb|AAK95391.1| ribosomal protein L2 [Gossypium arboreum] Back     alignment and taxonomy information
>gi|296084340|emb|CBI24728.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|17644112|gb|AAK95390.1| ribosomal protein L2 [Solanum lycopersicum] Back     alignment and taxonomy information
>gi|224092860|ref|XP_002309726.1| predicted protein [Populus trichocarpa] gi|222852629|gb|EEE90176.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449459236|ref|XP_004147352.1| PREDICTED: 60S ribosomal protein L2, mitochondrial-like [Cucumis sativus] gi|449530285|ref|XP_004172126.1| PREDICTED: 60S ribosomal protein L2, mitochondrial-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297824397|ref|XP_002880081.1| ribosomal protein L2 family protein [Arabidopsis lyrata subsp. lyrata] gi|297325920|gb|EFH56340.1| ribosomal protein L2 family protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|21592449|gb|AAM64400.1| unknown [Arabidopsis thaliana] 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 ?
Query179
TAIR|locus:505006316214 AT2G44065 [Arabidopsis thalian 0.402 0.336 0.602 2.8e-18
TIGR_CMR|GSU_2854274 GSU_2854 "ribosomal protein L2 0.486 0.317 0.445 2.3e-13
TIGR_CMR|CPS_0870274 CPS_0870 "ribosomal protein L2 0.474 0.310 0.440 9.2e-13
UNIPROTKB|P0C8K6502 RPL2 "60S ribosomal protein L2 0.312 0.111 0.55 3.5e-12
UNIPROTKB|P92812502 RPL2 "60S ribosomal protein L2 0.312 0.111 0.55 3.5e-12
UNIPROTKB|Q2F969502 RPL2 "60S ribosomal protein L2 0.312 0.111 0.55 3.5e-12
TIGR_CMR|CHY_2306274 CHY_2306 "ribosomal protein L2 0.491 0.321 0.418 3.6e-12
TIGR_CMR|APH_0283276 APH_0283 "ribosomal protein L2 0.458 0.297 0.494 3.8e-12
TIGR_CMR|ECH_0412276 ECH_0412 "ribosomal protein L2 0.379 0.246 0.486 1.1e-11
TIGR_CMR|SO_0234274 SO_0234 "ribosomal protein L2" 0.379 0.248 0.472 3.1e-11
TAIR|locus:505006316 AT2G44065 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 221 (82.9 bits), Expect = 2.8e-18, P = 2.8e-18
 Identities = 44/73 (60%), Positives = 50/73 (68%)

Query:    96 SHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPXXXXXXXXKSSGNHGRCSLTPWGKPCK 155
             SH  K L KAGQS WLG RP +RGV MNP DHP        KSSG+ GR S++PWGKPCK
Sbjct:   133 SHGTKKLYKAGQSRWLGIRPKVRGVAMNPCDHPHGGGEGKSKSSGSRGRTSVSPWGKPCK 192

Query:   156 W-CKTASRKKKRK 167
                K+AS KKK+K
Sbjct:   193 GGYKSASVKKKKK 205
GO:0003723 "RNA binding" evidence=IEA
GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS
GO:0005622 "intracellular" evidence=IEA
GO:0005840 "ribosome" evidence=IEA
GO:0006412 "translation" evidence=IEA;ISS
GO:0009507 "chloroplast" evidence=ISM
GO:0015934 "large ribosomal subunit" evidence=IEA;ISS
GO:0016740 "transferase activity" evidence=IEA
GO:0006354 "DNA-dependent transcription, elongation" evidence=RCA
GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=RCA
GO:0009853 "photorespiration" evidence=RCA
GO:0051788 "response to misfolded protein" evidence=RCA
GO:0080129 "proteasome core complex assembly" evidence=RCA
TIGR_CMR|GSU_2854 GSU_2854 "ribosomal protein L2" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
TIGR_CMR|CPS_0870 CPS_0870 "ribosomal protein L2" [Colwellia psychrerythraea 34H (taxid:167879)] Back     alignment and assigned GO terms
UNIPROTKB|P0C8K6 RPL2 "60S ribosomal protein L2, mitochondrial" [Oryza sativa (taxid:4530)] Back     alignment and assigned GO terms
UNIPROTKB|P92812 RPL2 "60S ribosomal protein L2, mitochondrial" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
UNIPROTKB|Q2F969 RPL2 "60S ribosomal protein L2, mitochondrial" [Oryza sativa Indica Group (taxid:39946)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_2306 CHY_2306 "ribosomal protein L2" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
TIGR_CMR|APH_0283 APH_0283 "ribosomal protein L2" [Anaplasma phagocytophilum HZ (taxid:212042)] Back     alignment and assigned GO terms
TIGR_CMR|ECH_0412 ECH_0412 "ribosomal protein L2" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)] Back     alignment and assigned GO terms
TIGR_CMR|SO_0234 SO_0234 "ribosomal protein L2" [Shewanella oneidensis MR-1 (taxid:211586)] 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:
fgenesh4_pm.C_LG_XVII000007
hypothetical protein (159 aa)
(Populus trichocarpa)
Predicted Functional Partners:
gw1.16155.2.1
Predicted protein (206 aa)
• ••  • 0.926
fgenesh4_pm.C_LG_XIII000297
hypothetical protein (222 aa)
• ••• • 0.849
gw1.II.2942.1
SubName- Full=Putative uncharacterized protein; (218 aa)
• • • • 0.847
gw1.IV.3048.1
SubName- Full=Putative uncharacterized protein; (227 aa)
• ••  • 0.847
rpl22
50S ribosomal protein L22 ; This protein binds specifically to 23S rRNA (By similarity) (129 aa)
•  •• • 0.813
eugene3.00141000
hypothetical protein (227 aa)
•  •• • 0.809
eugene3.15590001
hypothetical protein (142 aa)
• • • • 0.804
gw1.8701.6.1
Predicted protein (100 aa)
•  •  • 0.780
fgenesh4_pg.C_scaffold_166000032
hypothetical protein (285 aa)
•   • • 0.754
fgenesh4_pm.C_LG_VI000651
hypothetical protein (279 aa)
•   • • 0.735

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 ?
Query179
PRK09374276 PRK09374, rplB, 50S ribosomal protein L2; Validate 1e-23
TIGR01171273 TIGR01171, rplB_bact, ribosomal protein L2, bacter 2e-23
CHL00052273 CHL00052, rpl2, ribosomal protein L2 5e-21
pfam03947130 pfam03947, Ribosomal_L2_C, Ribosomal Proteins L2, 1e-19
COG0090275 COG0090, RplB, Ribosomal protein L2 [Translation, 7e-19
PTZ00031317 PTZ00031, PTZ00031, ribosomal protein L2; Provisio 9e-15
PTZ00180260 PTZ00180, PTZ00180, 60S ribosomal protein L8; Prov 7e-04
PRK09612238 PRK09612, rpl2p, 50S ribosomal protein L2P; Valida 0.001
>gnl|CDD|236488 PRK09374, rplB, 50S ribosomal protein L2; Validated Back     alignment and domain information 
 Score = 93.6 bits (234), Expect = 1e-23
 Identities = 43/77 (55%), Positives = 50/77 (64%), Gaps = 6/77 (7%)

Query: 97  HEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGKPCKW 156
           H    L KAG+S WLG RP +RGV MNPVDHP G GEGR  +SG  GR  +TPWGKP K 
Sbjct: 200 HSNISLGKAGRSRWLGIRPTVRGVAMNPVDHPHGGGEGR--TSG--GRHPVTPWGKPTKG 255

Query: 157 CKTASRKKKRKFSCLII 173
            KT  RKK ++    I+
Sbjct: 256 YKT--RKKNKRSDKFIV 270

Length = 276
>gnl|CDD|162234 TIGR01171, rplB_bact, ribosomal protein L2, bacterial/organellar Back     alignment and domain information
>gnl|CDD|176993 CHL00052, rpl2, ribosomal protein L2 Back     alignment and domain information
>gnl|CDD|202823 pfam03947, Ribosomal_L2_C, Ribosomal Proteins L2, C-terminal domain Back     alignment and domain information
>gnl|CDD|223168 COG0090, RplB, Ribosomal protein L2 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|173329 PTZ00031, PTZ00031, ribosomal protein L2; Provisional Back     alignment and domain information
>gnl|CDD|173464 PTZ00180, PTZ00180, 60S ribosomal protein L8; Provisional Back     alignment and domain information
>gnl|CDD|236589 PRK09612, rpl2p, 50S ribosomal protein L2P; Validated Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 179
TIGR01171273 rplB_bact ribosomal protein L2, bacterial/organell 100.0
PRK09374276 rplB 50S ribosomal protein L2; Validated 100.0
PTZ00031317 ribosomal protein L2; Provisional 100.0
CHL00052273 rpl2 ribosomal protein L2 100.0
COG0090275 RplB Ribosomal protein L2 [Translation, ribosomal 100.0
PF03947130 Ribosomal_L2_C: Ribosomal Proteins L2, C-terminal 100.0
PRK09612238 rpl2p 50S ribosomal protein L2P; Validated 100.0
PTZ00180260 60S ribosomal protein L8; Provisional 100.0
KOG2309248 consensus 60s ribosomal protein L2/L8 [Translation 99.97
KOG0438312 consensus Mitochondrial/chloroplast ribosomal prot 99.97
>TIGR01171 rplB_bact ribosomal protein L2, bacterial/organellar Back     alignment and domain information 
Probab=100.00  E-value=2.6e-53  Score=368.95  Aligned_cols=142  Identities=35%  Similarity=0.575  Sum_probs=128.5

Q ss_pred             cCCCCCccccCcEEEeecCCccCCCCeeccCCCCcccccccceEeeccc-----hhhhh---------------------
Q 045484           18 NLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKL-----NQLVM---------------------   71 (179)
Q Consensus        18 ~~~~~~~~~~Gq~I~~G~~A~i~~GN~LPlsalPlg~IP~Gt~I~nIE~-----Gql~r---------------------   71 (179)
                      -+=++|.+++||+|++|++|++++||+|     ||.+||+||.|||||+     |||+|                     
T Consensus       101 YIlap~gl~~Gd~I~~g~~~~i~~Gn~l-----pL~~IP~Gt~I~NIE~~pg~Ggkl~RsAGt~A~ii~k~~~~~~vkLP  175 (273)
T TIGR01171       101 YILAPKGLKVGDTVISGPEAPIKPGNAL-----PLRNIPVGTTVHNIELKPGKGGQLARSAGTSAQILAKEGGYVTLRLP  175 (273)
T ss_pred             EEEccCCCCCCCEEEECCCCCCCCcCCc-----ccccCCCCCEEEEEEecCCCCceEEEecCCeEEEEEecCCEEEEECC
Confidence            4568999999999999999999999999     5789999999999998     88886                     


Q ss_pred             -hhhheEeccceEeEeeeecCCCchhhhhhhhhhhhhcccCCCCCeeeeeeCCCCcCCCCCCCCCCCCCCCCCCCCCCCC
Q 045484           72 -TLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPW  150 (179)
Q Consensus        72 -~~ik~v~~~CrAtIG~Va~ggsN~~h~~k~lgKAGr~r~lg~RP~VRGvaMNpvdHPhGGG~gk~~~~~~~g~~~~tpW  150 (179)
                       +++++|+++|+||||+|    ||.+|.+++++|||++||+++||+||||||||||||||||||+++    +|++|+|||
T Consensus       176 SGe~r~i~~~c~AtiG~V----sn~~~~~~~~gKAG~~r~lg~rP~VRGvAMNpvDHPHGGGegk~~----~g~~~~spw  247 (273)
T TIGR01171       176 SGEMRMVLKECRATIGEV----GNEDHNNIVLGKAGRSRWLGIRPTVRGVAMNPVDHPHGGGEGRTP----GGRHPVTPW  247 (273)
T ss_pred             CCCeEEECCcCeEEEEEc----cCCchhccEeccchhheeCCCCCccccEecCcccCCCCCCCCcCC----CCCCCCCCC
Confidence             56789999999999999    899999999999999999999999999999999999999999997    568999999


Q ss_pred             CccccceecCccccCccccceeeee
Q 045484          151 GKPCKWCKTASRKKKRKFSCLIILS  175 (179)
Q Consensus       151 G~~~kg~kTr~~kk~~k~~~~~i~~  175 (179)
                      |+++||+|||++   +|+++.+|++
T Consensus       248 G~~~kg~kTr~~---~k~~~~~i~~  269 (273)
T TIGR01171       248 GKPTKGYKTRKK---KKYSDKFIVR  269 (273)
T ss_pred             eeeccccccCCC---CCCCCceEEE
Confidence            999999999976   4444445543

This model distinguishes bacterial and organellar ribosomal protein L2 from its counterparts in the archaea nad in the eukaryotic cytosol. Plant mitochondrial examples tend to have long, variable inserts.
>PRK09374 rplB 50S ribosomal protein L2; Validated Back     alignment and domain information
>PTZ00031 ribosomal protein L2; Provisional Back     alignment and domain information
>CHL00052 rpl2 ribosomal protein L2 Back     alignment and domain information
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF03947 Ribosomal_L2_C: Ribosomal Proteins L2, C-terminal domain; InterPro: IPR022669 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated Back     alignment and domain information
>PTZ00180 60S ribosomal protein L8; Provisional Back     alignment and domain information
>KOG2309 consensus 60s ribosomal protein L2/L8 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG0438 consensus Mitochondrial/chloroplast ribosomal protein L2 [Translation, ribosomal structure and biogenesis] 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 ?
Query179
1nwx_A274 Complex Of The Large Ribosomal Subunit From Deinoco 9e-11
1nkw_A275 Crystal Structure Of The Large Ribosomal Subunit Fr 1e-10
1pnu_A270 Crystal Structure Of A Streptomycin Dependent Ribos 1e-10
3fik_C271 Ternary Complex-Bound E.Coli 70s Ribosome. This Ent 1e-10
2aw4_C273 Crystal Structure Of The Bacterial Ribosome From Es 1e-10
3e1b_N270 Structure Of The 50s Subunit Of E. Coli Ribosome In 1e-10
2j28_C267 Model Of E. Coli Srp Bound To 70s Rncs Length = 267 1e-10
1p85_A272 Real Space Refined Coordinates Of The 50s Subunit F 1e-10
3fin_D272 T. Thermophilus 70s Ribosome In Complex With Mrna, 3e-10
2j01_D276 Structure Of The Thermus Thermophilus 70s Ribosome 3e-10
3pyo_C271 Crystal Structure Of A Complex Containing Domain 3 3e-10
3mrz_C275 Recognition Of The Amber Stop Codon By Release Fact 4e-10
2gya_A227 Structure Of The 50s Subunit Of A Pre-Translocation 5e-10
3bbo_E269 Homology Model For The Spinach Chloroplast 50s Subu 2e-08
>pdb|1NWX|A Chain A, Complex Of The Large Ribosomal Subunit From Deinococcus Radiodurans With Abt-773 Length = 274 Back     alignment and structure 
Iteration: 1

 Score = 62.8 bits (151), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 37/95 (38%), Positives = 50/95 (52%), Gaps = 11/95 (11%)
Query: 81  CHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPXXXXXXXXKSSG 140
           C+  +  +G       H+  VL KAG+S WLG++P  RG  MNPVDHP         +  
Sbjct: 188 CYATIGAVG----NAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTGAG- 242
Query: 141 NHGRCSLTPWGKPCKWCKTASRKKKRKFSCLIILS 175
              R  +TPWGKP K  KT   ++KRK S   I++
Sbjct: 243 ---RVPVTPWGKPTKGLKT---RRKRKTSDRFIVT 271
>pdb|1NKW|A Chain A, Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Length = 275 Back     alignment and structure
>pdb|1PNU|A Chain A, 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 = 270 Back     alignment and structure
>pdb|3FIK|C Chain C, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry Consists Of The 50s Subunit. Length = 271 Back     alignment and structure
>pdb|2AW4|C Chain C, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli At 3.5 A Resolution. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. Length = 273 Back     alignment and structure
>pdb|3E1B|N Chain N, Structure Of The 50s Subunit Of E. Coli Ribosome In Pre-Accommodation State Length = 270 Back     alignment and structure
>pdb|2J28|C Chain C, Model Of E. Coli Srp Bound To 70s Rncs Length = 267 Back     alignment and structure
>pdb|1P85|A Chain A, 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 = 272 Back     alignment and structure
>pdb|3FIN|D Chain D, 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 = 272 Back     alignment and structure
>pdb|2J01|D Chain D, 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 = 276 Back     alignment and structure
>pdb|3PYO|C Chain C, 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 = 271 Back     alignment and structure
>pdb|3MRZ|C Chain C, Recognition Of The Amber Stop Codon By Release Factor Rf1. This Entry 3mrz Contains 50s Ribosomal Subunit. The 30s Ribosomal Subunit Can Be Found In Pdb Entry 3ms0. Molecule A In The Same Asymmetric Unit Is Deposited As 3mr8 (50s) And 3ms1 (30s). Length = 275 Back     alignment and structure
>pdb|2GYA|A Chain A, 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 = 227 Back     alignment and structure
>pdb|3BBO|E Chain E, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 269 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 ?
Query179
3bbo_E269 Ribosomal protein L2; large ribosomal subunit, spi 4e-24
3v2d_D276 50S ribosomal protein L2; ribosome associated inhi 4e-24
3r8s_C271 50S ribosomal protein L2; protein biosynthesis, RN 6e-22
1vq8_A240 50S ribosomal protein L2P; ribosome 50S, protein-p 5e-19
3iz5_B261 60S ribosomal protein L2 (L2P); eukaryotic ribosom 2e-18
4a17_A264 RPL8; eukaryotic ribosome, ribosome, eukaryotic in 3e-18
3jyw_B243 60S ribosomal protein L2; eukaryotic ribosome, RAC 1e-15
1giy_D178 50S ribosomal protein L2; ribosome assembly, prote 7e-10
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 4e-04
>3bbo_E Ribosomal protein L2; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 269 Back     alignment and structure
 Score = 94.1 bits (235), Expect = 4e-24
 Identities = 34/77 (44%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 97  HEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGKPCKW 156
              K L +AG   WLG+RPV+RGV MNPVDHP G GEGR            TPWG P   
Sbjct: 196 VNQKRLGRAGSKRWLGKRPVVRGVVMNPVDHPHGGGEGRAPIGRKS---PTTPWGYPALG 252

Query: 157 CKTASRKKKRKFSCLII 173
            ++  RK+ +     II
Sbjct: 253 RRS--RKRNKYSDNFII 267
>3v2d_D 50S ribosomal protein L2; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_B 2hgj_D 2hgq_D 2hgu_D 1vsa_B 2j03_D 2jl6_D 2jl8_D 2v47_D 2v49_D 2wdi_D 2wdj_D 2wdl_D 2wdn_D 2wh2_D 2wh4_D 2wrj_D 2wrl_D 2wro_D 2wrr_D ... Length = 276 Back     alignment and structure
>3r8s_C 50S ribosomal protein L2; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 3fik_C 2wwq_C 3oat_C* 3oas_C* 3ofd_C 3ofc_C 3ofr_C* 3ofz_C* 3og0_C 3ofq_C 3r8t_C 3i1n_C 1vs8_C 1vs6_C 2aw4_C 2awb_C 2vhm_C 2vhn_C 3bbx_C 3df2_C ... Length = 271 Back     alignment and structure
>1vq8_A 50S ribosomal protein L2P; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: b.34.5.3 b.40.4.5 PDB: 1vq4_A* 1vq5_A* 1vq6_A* 1vq7_A* 1s72_A* 1vq9_A* 1vqk_A* 1vql_A* 1vqm_A* 1vqn_A* 1vqo_A* 1vqp_A* 1yhq_A* 1yi2_A* 1yij_A* 1yit_A* 1yj9_A* 1yjn_A* 1yjw_A* 2otj_A* ... Length = 240 Back     alignment and structure
>4a17_A RPL8; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_A 4a1c_A 4a1e_A Length = 264 Back     alignment and structure
>3jyw_B 60S ribosomal protein L2; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 3izc_B 3izs_B 3o58_B 3o5h_B 3u5e_A 3u5i_A 1s1i_B Length = 243 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query179
3v2d_D276 50S ribosomal protein L2; ribosome associated inhi 100.0
3r8s_C271 50S ribosomal protein L2; protein biosynthesis, RN 100.0
3bbo_E269 Ribosomal protein L2; large ribosomal subunit, spi 100.0
1vq8_A240 50S ribosomal protein L2P; ribosome 50S, protein-p 100.0
3j21_B239 50S ribosomal protein L2P; archaea, archaeal, KINK 100.0
3iz5_B261 60S ribosomal protein L2 (L2P); eukaryotic ribosom 100.0
3jyw_B243 60S ribosomal protein L2; eukaryotic ribosome, RAC 100.0
4a17_A264 RPL8; eukaryotic ribosome, ribosome, eukaryotic in 100.0
1giy_D178 50S ribosomal protein L2; ribosome assembly, prote 100.0
2ftc_B136 Mitochondrial ribosomal protein L2; mitochondrial 99.84
1rl2_A137 Protein (ribosomal protein L2); RNA-binding domain 99.73
>3v2d_D 50S ribosomal protein L2; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_B 2hgj_D 2hgq_D 2hgu_D 1vsa_B 2j03_D 2jl6_D 2jl8_D 2v47_D 2v49_D 2wdi_D 2wdj_D 2wdl_D 2wdn_D 2wh2_D 2wh4_D 2wrj_D 2wrl_D 2wro_D 2wrr_D ... Back     alignment and structure
Probab=100.00  E-value=4e-55  Score=379.57  Aligned_cols=142  Identities=36%  Similarity=0.550  Sum_probs=129.6

Q ss_pred             cCCCCCccccCcEEEeecCCccCCCCeeccCCCCcccccccceEeeccc-----hhhhh---------------------
Q 045484           18 NLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKL-----NQLVM---------------------   71 (179)
Q Consensus        18 ~~~~~~~~~~Gq~I~~G~~A~i~~GN~LPlsalPlg~IP~Gt~I~nIE~-----Gql~r---------------------   71 (179)
                      -+=++|.+++||+|++|.+|++++||+|     ||++||+||.|||||+     |||+|                     
T Consensus       104 yIlAp~gl~~Gd~I~sg~~a~i~~GN~l-----PL~~IP~GT~IhNIE~~pG~Gg~laRsAGt~A~ii~k~~~~~~vrLP  178 (276)
T 3v2d_D          104 YIIAPDGLQVGQQVVAGPDAPIQVGNAL-----PLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLP  178 (276)
T ss_dssp             EEECBTTCCTTCEECBSTTCCSSTTCEE-----EGGGSCTTCEEESEESSTTSCEEESCSTTCCEEEEEEETTEEEEECT
T ss_pred             EEEeeCCCcCCCEEEeCCCCCCCCCCee-----hhhhCCCCCEEEEEEecCCCCceEEEeCCCeEEEEEecCCEEEEECC
Confidence            3558999999999999999999999999     5789999999999998     88886                     


Q ss_pred             -hhhheEeccceEeEeeeecCCCchhhhhhhhhhhhhcccCCCCCeeeeeeCCCCcCCCCCCCCCCCCCCCCCCCCCCCC
Q 045484           72 -TLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPW  150 (179)
Q Consensus        72 -~~ik~v~~~CrAtIG~Va~ggsN~~h~~k~lgKAGr~r~lg~RP~VRGvaMNpvdHPhGGG~gk~~~~~~~g~~~~tpW  150 (179)
                       +++++|+++|+||||+|    +|.+|.+++++|||++||+++||+||||||||||||||||||+++    +|++|+|||
T Consensus       179 SGe~r~i~~~c~AtIG~V----sn~~~~~~~lgKAGr~rw~g~rP~VRGVAMNPVDHPHGGGeGr~~----~g~~p~spw  250 (276)
T 3v2d_D          179 SGELRKVHGECYATVGAV----GNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAP----RGRPPASPW  250 (276)
T ss_dssp             TSCEEEEETTCEEEESCB----SCGGGGGCCCCSHHHHHHTTBCCCCCGGGSCTTTCTTCCCSSCCC----CCSSCBCTT
T ss_pred             CCCeEEEcccCeEEEEee----cCcchhhcEeccCcccccCCCCCccCeEecCCccCCCcCcCCCCC----CCCCCcCcc
Confidence             46789999999999999    899999999999999999999999999999999999999999997    568999999


Q ss_pred             CccccceecCccccCccccceeeee
Q 045484          151 GKPCKWCKTASRKKKRKFSCLIILS  175 (179)
Q Consensus       151 G~~~kg~kTr~~kk~~k~~~~~i~~  175 (179)
                      |+++||+|||++   +|++|.+|++
T Consensus       251 G~~~kG~kTr~~---~k~s~~~iv~  272 (276)
T 3v2d_D          251 GWQTKGLKTRKR---RKPSSRFIIA  272 (276)
T ss_dssp             SCBCSSCCCSCT---TCGGGGGEEE
T ss_pred             cccccCCCCCCC---CCCCCCEEEe
Confidence            999999999986   4555555654
>3r8s_C 50S ribosomal protein L2; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 3fik_C 3j19_C 2wwq_C 3oat_C* 3oas_C* 3ofd_C 3ofc_C 3ofr_C* 3ofz_C* 3og0_C 3ofq_C 3r8t_C 3i1n_C 1vs8_C 1vs6_C 2aw4_C 2awb_C 2vhm_C 2vhn_C 3bbx_C ... Back     alignment and structure
>3bbo_E Ribosomal protein L2; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>1vq8_A 50S ribosomal protein L2P; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: b.34.5.3 b.40.4.5 PDB: 1vq4_A* 1vq5_A* 1vq6_A* 1vq7_A* 1s72_A* 1vq9_A* 1vqk_A* 1vql_A* 1vqm_A* 1vqn_A* 1vqo_A* 1vqp_A* 1yhq_A* 1yi2_A* 1yij_A* 1yit_A* 1yj9_A* 1yjn_A* 1yjw_A* 2otj_A* ... Back     alignment and structure
>3j21_B 50S ribosomal protein L2P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>3jyw_B 60S ribosomal protein L2; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 3izc_B 3izs_B 3o58_B 3o5h_B 3u5e_A 3u5i_A 4b6a_A 1s1i_B Back     alignment and structure
>4a17_A RPL8; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_A 4a1c_A 4a1e_A Back     alignment and structure
>2ftc_B Mitochondrial ribosomal protein L2; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_B Back     alignment and structure
>1rl2_A Protein (ribosomal protein L2); RNA-binding domain, peptidyltransferease center, X-RAY diffraction; 2.30A {Geobacillus stearothermophilus} SCOP: b.34.5.3 b.40.4.5 PDB: 1c04_A 487d_I 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 179
d2qamc1145 b.34.5.3 (C:125-269) C-terminal domain of ribosoma 6e-16
d2j01d1147 b.34.5.3 (D:127-273) C-terminal domain of ribosoma 2e-15
d1vqoa1147 b.34.5.3 (A:91-237) C-terminal domain of ribosomal 3e-11
>d2qamc1 b.34.5.3 (C:125-269) C-terminal domain of ribosomal protein L2 {Escherichia coli [TaxId: 562]} Length = 145 Back     information, alignment and structure

class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: C-terminal domain of ribosomal protein L2
domain: C-terminal domain of ribosomal protein L2
species: Escherichia coli [TaxId: 562]

 Score = 68.8 bits (168), Expect = 6e-16
 Identities = 38/83 (45%), Positives = 44/83 (53%), Gaps = 6/83 (7%)

Query: 86  CMLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRC 145
             LG       H  +VL KAG + W G RP +RG  MNPVDHP G GEGR       G+ 
Sbjct: 65  ATLGEVGNA-EHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRN-----FGKH 118

Query: 146 SLTPWGKPCKWCKTASRKKKRKF 168
            +TPWG   K  KT S K+  KF
Sbjct: 119 PVTPWGVQTKGKKTRSNKRTDKF 141
>d2j01d1 b.34.5.3 (D:127-273) C-terminal domain of ribosomal protein L2 {Thermus thermophilus [TaxId: 274]} Length = 147 Back     information, alignment and structure
>d1vqoa1 b.34.5.3 (A:91-237) C-terminal domain of ribosomal protein L2 {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 147 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 ?
Query179
d2j01d1147 C-terminal domain of ribosomal protein L2 {Thermus 100.0
d2qamc1145 C-terminal domain of ribosomal protein L2 {Escheri 100.0
d1vqoa1147 C-terminal domain of ribosomal protein L2 {Archaeo 100.0
d1rl2a170 C-terminal domain of ribosomal protein L2 {Bacillu 99.25
d1vqoa290 N-terminal domain of ribosomal protein L2 {Archaeo 92.71
d1rl2a266 N-terminal domain of ribosomal protein L2 {Bacillu 87.8
d2qamc264 N-terminal domain of ribosomal protein L2 {Escheri 85.72
d2zjra295 N-terminal domain of ribosomal protein L2 {Deinoco 81.65
>d2j01d1 b.34.5.3 (D:127-273) C-terminal domain of ribosomal protein L2 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
class: All beta proteins
fold: SH3-like barrel
superfamily: Translation proteins SH3-like domain
family: C-terminal domain of ribosomal protein L2
domain: C-terminal domain of ribosomal protein L2
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=2.8e-49  Score=315.10  Aligned_cols=115  Identities=40%  Similarity=0.681  Sum_probs=105.5

Q ss_pred             CCCeeccCCCCcccccccceEeeccc-----hhhhh----------------------hhhheEeccceEeEeeeecCCC
Q 045484           41 RHSSLGFSALPFSTITLLNAISPVKL-----NQLVM----------------------TLILKLEVACHLLVCMLGPSST   93 (179)
Q Consensus        41 ~GN~LPlsalPlg~IP~Gt~I~nIE~-----Gql~r----------------------~~ik~v~~~CrAtIG~Va~ggs   93 (179)
                      +||+|     ||++||+||.|||||+     |||+|                      +++++|+++|+||||+|    +
T Consensus         1 iGN~l-----PL~~IP~Gt~I~NIE~~PG~Ggkl~RsAGt~A~Ii~k~~~~~~vkLPSGe~r~i~~~c~AtiG~v----s   71 (147)
T d2j01d1           1 VGNAL-----PLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSGELRKVHGECYATVGAV----G   71 (147)
T ss_dssp             TTCEE-----EGGGSCTTCEEESEESSTTSCEEESCSSSCCEEECCCBTTEEEEECTTSCEEEEETTSEEEESCC----S
T ss_pred             Ccccc-----cHhhCCCCCEEEEEEecCCCCceEEEeccceEEEEEecCCeEEEEecCCceEEecccceEEEeEe----c
Confidence            59999     5799999999999999     78886                      46688999999999999    8


Q ss_pred             chhhhhhhhhhhhhcccCCCCCeeeeeeCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCccccceecCcccc-Cccc
Q 045484           94 TLSHEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGKPCKWCKTASRKK-KRKF  168 (179)
Q Consensus        94 N~~h~~k~lgKAGr~r~lg~RP~VRGvaMNpvdHPhGGG~gk~~~~~~~g~~~~tpWG~~~kg~kTr~~kk-~~k~  168 (179)
                      |.+|.+++++|||++||+++||+||||||||||||||||||+++    ++++|+||||+++||+|||+++| +++|
T Consensus        72 n~~~~~~~~gKAG~~r~~g~rP~VRGvaMNpvdHPhGGG~g~~~----~g~~~~spwG~~~kg~ktRk~~k~~~~~  143 (147)
T d2j01d1          72 NADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAP----RGRPPASPWGWQTKGLKTRKRRKPSSRF  143 (147)
T ss_dssp             CGGGGGCCCCSHHHHTTTTBCCCCCSSSSCTTTCSSCCSSSSCC----CSSSCBCTTCCBCSSCCCSCTTSSCCSS
T ss_pred             chhhhhhhhhhhHHHHhccCccccceeeccCccCCCCCCCCCcC----CCCCCCCCCcccCCCccCCCCCCCCCCe
Confidence            99999999999999999999999999999999999999999987    57899999999999999999754 4444
>d2qamc1 b.34.5.3 (C:125-269) C-terminal domain of ribosomal protein L2 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vqoa1 b.34.5.3 (A:91-237) C-terminal domain of ribosomal protein L2 {Archaeon Haloarcula marismortui [TaxId: 2238]} Back     information, alignment and structure
>d1rl2a1 b.34.5.3 (A:126-195) C-terminal domain of ribosomal protein L2 {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1vqoa2 b.40.4.5 (A:1-90) N-terminal domain of ribosomal protein L2 {Archaeon Haloarcula marismortui [TaxId: 2238]} Back     information, alignment and structure
>d1rl2a2 b.40.4.5 (A:60-125) N-terminal domain of ribosomal protein L2 {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d2qamc2 b.40.4.5 (C:61-124) N-terminal domain of ribosomal protein L2 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2zjra2 b.40.4.5 (A:33-127) N-terminal domain of ribosomal protein L2 {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure