Citrus Sinensis ID: 034868

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80
Protein Sequence
MFSWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAAAAPAAEAKKEEKVEEKEESDDDMGFSLFD
Secondary Structure (PSIPRED)
cccEEEEEEccccccHHHHHHHHHHHccccHHHHHHHHHccccccccccccccccHHHHHHHHHHHHccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEEcccccHHHHHHHHHHHccccHHHHHHHccHHHccccccccccccHHHHHHHHHcHccccccccccccccc
Coil and Loop (DISEMBL)
MFSWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGReklasvpsggaaaapaaeakkeekveekeesdddmgfslfd
Flexible Loop (DISEMBL)
MFSWVFGFavgaeaddeRIEFLLSEVKGKDITELIASGreklasvpsggaaaapaaeakkeekveekeesdddmgfslfd
Low Complexity Region (SEG)
MFSWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLasvpsggaaaapaaeakkeekveekeeSDDDMGFSLFD
Disordered region (IsUnstruct)
**SWVFGFAVGAEADDERIEFLLSEVKGKDITELI*********************************************
Disordered Region (DISOPRED)
*FSWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLAS*****************************MGFSLFD
Disordered Region (DISEMBL)
MFSWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREK********************************MGFSLFD
Disordered Region (DISPRO)
MFSWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGRE*************************************L**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MFSWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAAAAPAAEAKKEEKVEEKEESDDDMGFSLFD
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	80	2.2.26 [Sep-21-2011]
Q9LXM8	111	60S acidic ribosomal prot	yes	no	0.887	0.639	0.658	7e-13
O24415	113	60S acidic ribosomal prot	N/A	no	0.9	0.637	0.682	1e-12
P41099	114	60S acidic ribosomal prot	N/A	no	0.487	0.342	0.820	2e-11
P46252	112	60S acidic ribosomal prot	N/A	no	0.9	0.642	0.654	1e-10
Q96UQ7	110	60S acidic ribosomal prot	N/A	no	0.9	0.654	0.560	2e-09
P51407	115	60S acidic ribosomal prot	no	no	0.9	0.626	0.597	7e-09
Q9LH85	115	60S acidic ribosomal prot	no	no	0.875	0.608	0.471	2e-08
P08094	110	60S acidic ribosomal prot	yes	no	0.512	0.372	0.658	3e-08
P42037	113	60S acidic ribosomal prot	N/A	no	0.9	0.637	0.517	1e-07
Q9C3Z5	111	60S acidic ribosomal prot	yes	no	0.9	0.648	0.542	1e-07

>sp|Q9LXM8|RLA24_ARATH 60S acidic ribosomal protein P2-4 OS=Arabidopsis thaliana GN=RPP2D PE=1 SV=1

 Score = 72.4 bits (176), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 54/82 (65%), Positives = 55/82 (67%), Gaps = 11/82 (13%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAAAA-----------PAAE 57
           AVGA+ D E IE LL EV GKDI ELIASGREKLASVPSGG  A             A  
Sbjct: 29  AVGADVDGESIELLLKEVSGKDIAELIASGREKLASVPSGGGVAVSAAPSSGGGGAAAPA 88

Query: 58  AKKEEKVEEKEESDDDMGFSLF 79
            KKE K EEKEESDDDMGFSLF
Sbjct: 89  EKKEAKKEEKEESDDDMGFSLF 110

Plays an important role in the elongation step of protein synthesis.
Arabidopsis thaliana (taxid: 3702)

>sp|O24415|RLA2B_MAIZE 60S acidic ribosomal protein P2B OS=Zea mays GN=RPP2B PE=1 SV=1

 Score = 72.0 bits (175), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 58/85 (68%), Positives = 69/85 (81%), Gaps = 13/85 (15%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAA-------------AAPA 55
           +VGAEAD+E++EFLL+E+K KDITE+IA+GRE+L+SVPSGG A             AAPA
Sbjct: 29  SVGAEADEEKLEFLLTELKDKDITEVIAAGRERLSSVPSGGGAIDMGAPAAVAGGGAAPA 88

Query: 56  AEAKKEEKVEEKEESDDDMGFSLFD 80
            EAKKEEKVEEKEESD+DMGFSLFD
Sbjct: 89  EEAKKEEKVEEKEESDEDMGFSLFD 113

Plays an important role in the elongation step of protein synthesis.

Zea mays (taxid: 4577)

>sp|P41099|RLA2_PARAR 60S acidic ribosomal protein P2 OS=Parthenium argentatum PE=3 SV=1

 Score = 67.8 bits (164), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/39 (82%), Positives = 38/39 (97%)

Query: 9  AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPS 47
          +VGA+ADD++IE LLS+VKGKDITELIASGRE+LASVPS
Sbjct: 29 SVGADADDDKIELLLSQVKGKDITELIASGRERLASVPS 67

Plays an important role in the elongation step of protein synthesis.

Parthenium argentatum (taxid: 35935)

>sp|P46252|RLA2A_MAIZE 60S acidic ribosomal protein P2A OS=Zea mays GN=RPP2A PE=1 SV=3

 Score = 65.5 bits (158), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 55/84 (65%), Positives = 62/84 (73%), Gaps = 12/84 (14%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPS------------GGAAAAPAA 56
           +VG E D+E++E LLS++ GKDITELIA+GREK ASVP                 AAPAA
Sbjct: 29  SVGCEVDNEKMELLLSQLSGKDITELIAAGREKFASVPCGGGGVAVAAAAPAAGGAAPAA 88

Query: 57  EAKKEEKVEEKEESDDDMGFSLFD 80
           EAKKEEKVEEKEESDDDMGFSLFD
Sbjct: 89  EAKKEEKVEEKEESDDDMGFSLFD 112

Plays an important role in the elongation step of protein synthesis.

Zea mays (taxid: 4577)

>sp|Q96UQ7|RLA2_RHOGU 60S acidic ribosomal protein P2 OS=Rhodotorula glutinis PE=1 SV=1

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 46/82 (56%), Positives = 56/82 (68%), Gaps = 10/82 (12%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPS---------GGAAAAPAAEAK 59
           A   +AD+ER+  L+ E++GKD+ E+IA G +KLASVPS         GGAAA  AAE K
Sbjct: 29  AADIQADEERLSVLIKELEGKDVNEVIAEGSKKLASVPSGGAAPAAAAGGAAAGGAAEEK 88

Query: 60  KEEKVEEK-EESDDDMGFSLFD 80
            E+K  EK EESDDDMGF LFD
Sbjct: 89  AEDKPAEKDEESDDDMGFGLFD 110

Probable bifunctional protein. The phosphorylated protein plays an important role in the elongation step of protein synthesis (By similarity). The phosphopantetheinylated protein acts as an acyl carrier protein.

Rhodotorula glutinis (taxid: 5535)

>sp|P51407|RLA21_ARATH 60S acidic ribosomal protein P2-1 OS=Arabidopsis thaliana GN=RPP2A PE=2 SV=2

 Score = 59.3 bits (142), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 52/87 (59%), Positives = 60/87 (68%), Gaps = 15/87 (17%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLA---------------SVPSGGAAAA 53
           +VGAE +D +IE LL EVKGKD+ ELIA+GREKLA               +   GG   A
Sbjct: 29  SVGAETEDSQIELLLKEVKGKDLAELIAAGREKLASVPSGGGGGVAVASATSGGGGGGGA 88

Query: 54  PAAEAKKEEKVEEKEESDDDMGFSLFD 80
           PAAE+KKEEK EEKEESDDDMGFSLF+
Sbjct: 89  PAAESKKEEKKEEKEESDDDMGFSLFE 115

Plays an important role in the elongation step of protein synthesis.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LH85|RLA23_ARATH 60S acidic ribosomal protein P2-3 OS=Arabidopsis thaliana GN=RPP2C PE=1 SV=1

 Score = 57.8 bits (138), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 42/89 (47%), Positives = 55/89 (61%), Gaps = 19/89 (21%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAAAA--------------- 53
           +VGAE D+ +I+ L S +K  D+TELIA+GREK++++ SGG A A               
Sbjct: 29  SVGAEIDETKIDLLFSLIKDHDVTELIAAGREKMSALSSGGPAVAMVAGGGGGGAASAAE 88

Query: 54  PAAEAKKEEKVEE-KEESDDDMG-FSLFD 80
           P AE+KK  KVEE K+ES DD G   LFD
Sbjct: 89  PVAESKK--KVEEVKDESSDDAGMMGLFD 115

Plays an important role in the elongation step of protein synthesis.

Arabidopsis thaliana (taxid: 3702)

>sp|P08094|RLA2_SCHPO 60S acidic ribosomal protein P2-alpha OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpp201 PE=1 SV=1

 Score = 57.4 bits (137), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 27/41 (65%), Positives = 34/41 (82%)

Query: 9  AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGG 49
           VG EA+ ERIE L++E+ GKDI ELIA+G EKLA+VP+GG
Sbjct: 29 TVGIEAESERIETLINELNGKDIDELIAAGNEKLATVPTGG 69

Plays an important role in the elongation step of protein synthesis.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|P42037|RLA2_ALTAL 60S acidic ribosomal protein P2 OS=Alternaria alternata GN=ALTA5 PE=1 SV=1

 Score = 55.5 bits (132), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 44/85 (51%), Positives = 55/85 (64%), Gaps = 13/85 (15%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVP-------------SGGAAAAPA 55
           +VG EAD +R++ L+SE++GKDI ELIASG EKLASVP             +    +A A
Sbjct: 29  SVGIEADSDRLDKLISELEGKDINELIASGSEKLASVPSGGAGGAAASGGAAAAGGSAQA 88

Query: 56  AEAKKEEKVEEKEESDDDMGFSLFD 80
             A +  K EEKEESD+DMGF LFD
Sbjct: 89  EAAPEAAKEEEKEESDEDMGFGLFD 113

Plays an important role in the elongation step of protein synthesis.

Alternaria alternata (taxid: 5599)

>sp|Q9C3Z5|RLA2_PODAS 60S acidic ribosomal protein P2 OS=Podospora anserina PE=3 SV=1

 Score = 55.1 bits (131), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 45/83 (54%), Positives = 54/83 (65%), Gaps = 11/83 (13%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPS-----------GGAAAAPAAE 57
           +VG EAD +R++ L+SE++GKD+ ELIA G  KLASVPS             AA   A  
Sbjct: 29  SVGIEADSDRLDKLISELEGKDVNELIAEGSSKLASVPSGGAGGAAAAGGAAAAGGAAEA 88

Query: 58  AKKEEKVEEKEESDDDMGFSLFD 80
           A +E K EEKEESDDDMGF LFD
Sbjct: 89  APEEAKEEEKEESDDDMGFGLFD 111

Plays an important role in the elongation step of protein synthesis.

Podospora anserina (taxid: 5145)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	80
449521190	115	PREDICTED: 60S acidic ribosomal protein	0.887	0.617	0.545	2e-13
449451120	107	PREDICTED: LOW QUALITY PROTEIN: 60S acid	0.887	0.663	0.545	2e-13
224105037	113	predicted protein [Populus trichocarpa]	0.9	0.637	0.764	2e-13
297815582	111	hypothetical protein ARALYDRAFT_484870 [	0.9	0.648	0.686	5e-13
225465704	113	PREDICTED: 60S acidic ribosomal protein	0.887	0.628	0.666	8e-13
147819575	113	hypothetical protein VITISV_026175 [Viti	0.887	0.628	0.666	8e-13
225440938	114	PREDICTED: 60S acidic ribosomal protein	0.9	0.631	0.720	8e-13
121955995	113	60S acidic ribosomal protein P2 [Juglans	0.9	0.637	0.729	1e-12
297734823	145	unnamed protein product [Vitis vinifera]	0.9	0.496	0.764	1e-12
449516276	131	PREDICTED: 60S acidic ribosomal protein	0.912	0.557	0.747	2e-12

>gi|449521190|ref|XP_004167613.1| PREDICTED: 60S acidic ribosomal protein P2B-like [Cucumis sativus]

 Score = 80.1 bits (196), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 48/88 (54%), Positives = 58/88 (65%), Gaps = 17/88 (19%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAA----------------A 52
           +VG EA+DERIE LLS+VKGKD+ EL+A GREK+A VP GG+A                 
Sbjct: 29  SVGVEAEDERIELLLSQVKGKDVAELVACGREKMACVPCGGSAIPVAAGSDSGGGAAAAV 88

Query: 53  APAAEAKKEEKVEEKEESDDDMGFSLFD 80
             AAE  KE+K +E EESD+DM FSLFD
Sbjct: 89  VVAAEPVKEDK-KEVEESDEDMCFSLFD 115

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449451120|ref|XP_004143310.1| PREDICTED: LOW QUALITY PROTEIN: 60S acidic ribosomal protein P2B-like [Cucumis sativus]

 Score = 79.7 bits (195), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 48/88 (54%), Positives = 58/88 (65%), Gaps = 17/88 (19%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAA----------------A 52
           +VG EA+DERIE LLS+VKGKD+ EL+A GREK+A VP GG+A                 
Sbjct: 21  SVGVEAEDERIELLLSQVKGKDVAELVACGREKMACVPCGGSAIPVAAGSDSGGGAAAAV 80

Query: 53  APAAEAKKEEKVEEKEESDDDMGFSLFD 80
             AAE  KE+K +E EESD+DM FSLFD
Sbjct: 81  VVAAEPVKEDK-KEVEESDEDMCFSLFD 107

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224105037|ref|XP_002313663.1| predicted protein [Populus trichocarpa] gi|118484510|gb|ABK94130.1| unknown [Populus trichocarpa] gi|118485202|gb|ABK94462.1| unknown [Populus trichocarpa] gi|118487376|gb|ABK95516.1| unknown [Populus trichocarpa] gi|118488119|gb|ABK95879.1| unknown [Populus trichocarpa] gi|222850071|gb|EEE87618.1| predicted protein [Populus trichocarpa]

 Score = 79.7 bits (195), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/85 (76%), Positives = 68/85 (80%), Gaps = 13/85 (15%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGA-------------AAAPA 55
           +VGA+ADD+RIE LLS VKGKDITELIASGREKLASVPSGG               AAPA
Sbjct: 29  SVGADADDDRIELLLSSVKGKDITELIASGREKLASVPSGGGVAVSAGAAPAAAGGAAPA 88

Query: 56  AEAKKEEKVEEKEESDDDMGFSLFD 80
           AEAKKEEKVEEKEESDDDMGFSLFD
Sbjct: 89  AEAKKEEKVEEKEESDDDMGFSLFD 113

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297815582|ref|XP_002875674.1| hypothetical protein ARALYDRAFT_484870 [Arabidopsis lyrata subsp. lyrata] gi|297321512|gb|EFH51933.1| hypothetical protein ARALYDRAFT_484870 [Arabidopsis lyrata subsp. lyrata]

 Score = 78.6 bits (192), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 57/83 (68%), Positives = 59/83 (71%), Gaps = 11/83 (13%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAAA-----------APAAE 57
           AVGA+ D E IE LL EV GKDI ELIASGREKLASVPSGG  A           APAA 
Sbjct: 29  AVGADVDGESIELLLKEVSGKDIAELIASGREKLASVPSGGGGAVSAALSSGGGGAPAAV 88

Query: 58  AKKEEKVEEKEESDDDMGFSLFD 80
            KKE K EEKEESDDDMGFSLF+
Sbjct: 89  EKKEAKKEEKEESDDDMGFSLFE 111

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225465704|ref|XP_002273733.1| PREDICTED: 60S acidic ribosomal protein P2B [Vitis vinifera] gi|296085335|emb|CBI29067.3| unnamed protein product [Vitis vinifera]

 Score = 77.8 bits (190), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 56/84 (66%), Positives = 59/84 (70%), Gaps = 13/84 (15%)

Query: 10  VGAEADDERIEFLLSEVKGKDITELIASGREKLASVPS-------------GGAAAAPAA 56
           VGA ADD  IE LL EVKGKDITELIASGREKLASVPS             GG AA  A 
Sbjct: 30  VGAGADDVGIELLLFEVKGKDITELIASGREKLASVPSGGGAAVATVAASDGGGAAPAAT 89

Query: 57  EAKKEEKVEEKEESDDDMGFSLFD 80
           E +KE+KVEEKE SD+DMGF LFD
Sbjct: 90  EPRKEKKVEEKEGSDEDMGFGLFD 113

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147819575|emb|CAN61098.1| hypothetical protein VITISV_026175 [Vitis vinifera]

 Score = 77.8 bits (190), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 56/84 (66%), Positives = 59/84 (70%), Gaps = 13/84 (15%)

Query: 10  VGAEADDERIEFLLSEVKGKDITELIASGREKLASVPS-------------GGAAAAPAA 56
           VGA ADD  IE LL EVKGKDITELIASGREKLASVPS             GG AA  A 
Sbjct: 30  VGAGADDVGIELLLFEVKGKDITELIASGREKLASVPSGGGAAVAXVAASDGGGAAPAAT 89

Query: 57  EAKKEEKVEEKEESDDDMGFSLFD 80
           E +KE+KVEEKE SD+DMGF LFD
Sbjct: 90  EPRKEKKVEEKEGSDEDMGFGLFD 113

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225440938|ref|XP_002283025.1| PREDICTED: 60S acidic ribosomal protein P2B [Vitis vinifera] gi|297740089|emb|CBI30271.3| unnamed protein product [Vitis vinifera]

 Score = 77.8 bits (190), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 62/86 (72%), Positives = 64/86 (74%), Gaps = 14/86 (16%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPS--------------GGAAAAP 54
           +VGAEADD+RIE LLSEVKGKDITELIASGREKLASVPS               G  A  
Sbjct: 29  SVGAEADDDRIELLLSEVKGKDITELIASGREKLASVPSGGGVAVAATAVGGASGGGAPA 88

Query: 55  AAEAKKEEKVEEKEESDDDMGFSLFD 80
           A E KKEEKVEEKEESDDDMGFSLFD
Sbjct: 89  APEPKKEEKVEEKEESDDDMGFSLFD 114

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|121955995|gb|ABM65702.1| 60S acidic ribosomal protein P2 [Juglans regia]

 Score = 77.0 bits (188), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/85 (72%), Positives = 67/85 (78%), Gaps = 13/85 (15%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPS-------------GGAAAAPA 55
           +VGAEADD++IE LLSEVKGKDITELIA+GREKLASVPS               AAAA A
Sbjct: 29  SVGAEADDDKIELLLSEVKGKDITELIAAGREKLASVPSGGGGIAVAAAAGGAPAAAAAA 88

Query: 56  AEAKKEEKVEEKEESDDDMGFSLFD 80
           AE KKEEKVEEK+ESDDDMGFSLFD
Sbjct: 89  AEPKKEEKVEEKKESDDDMGFSLFD 113

Source: Juglans regia

Species: Juglans regia

Genus: Juglans

Family: Juglandaceae

Order: Fagales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297734823|emb|CBI17057.3| unnamed protein product [Vitis vinifera]

 Score = 77.0 bits (188), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 65/85 (76%), Positives = 68/85 (80%), Gaps = 13/85 (15%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPS-------------GGAAAAPA 55
           +VGAEADD+RIE LL+EVKGKDITELIASGREKLASVPS             GGAAA  A
Sbjct: 61  SVGAEADDDRIELLLAEVKGKDITELIASGREKLASVPSGGGAAVAVAAPGGGGAAAPAA 120

Query: 56  AEAKKEEKVEEKEESDDDMGFSLFD 80
           AE KKEEKVEEKEESDDDMGFSLFD
Sbjct: 121 AEPKKEEKVEEKEESDDDMGFSLFD 145

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449516276|ref|XP_004165173.1| PREDICTED: 60S acidic ribosomal protein P2-4-like isoform 1 [Cucumis sativus]

 Score = 76.6 bits (187), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 65/87 (74%), Positives = 66/87 (75%), Gaps = 14/87 (16%)

Query: 8   FAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPS--------------GGAAAA 53
           FAVGAE D+ERI  LLS VKGKDITELIASGREKLASVPS              GGAAA 
Sbjct: 45  FAVGAEVDEERINLLLSNVKGKDITELIASGREKLASVPSGGGAAVAVAAGGGGGGAAAP 104

Query: 54  PAAEAKKEEKVEEKEESDDDMGFSLFD 80
             AEAKKEEKVEEKEESDDDMGFSLFD
Sbjct: 105 APAEAKKEEKVEEKEESDDDMGFSLFD 131

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	80
ZFIN|ZDB-GENE-031018-2	115	rplp2 "ribosomal protein, larg	0.425	0.295	0.529	9.2e-09
TAIR|locus:2075993	111	AT3G44590 [Arabidopsis thalian	0.9	0.648	0.433	9.7e-09
TAIR|locus:2042062	115	AT2G27710 [Arabidopsis thalian	0.9	0.626	0.390	6.8e-08
TAIR|locus:2042052	130	AT2G27720 [Arabidopsis thalian	0.475	0.292	0.657	6.8e-08
ASPGD|ASPL0000000414	109	AN5996 [Emericella nidulans (t	0.9	0.660	0.370	1.4e-07
POMBASE|SPBP8B7.06	110	rpp201 "60S acidic ribosomal p	0.887	0.645	0.382	1.8e-07
POMBASE|SPBC23G7.15c	110	rpp202 "60S acidic ribosomal p	0.887	0.645	0.370	4.8e-07
POMBASE|SPAC1071.08	110	rpp203 "60S acidic ribosomal p	0.887	0.645	0.358	7.8e-07
SGD|S000005399	106	RPP2A "Ribosomal protein P2 al	0.9	0.679	0.329	2.6e-06
CGD|CAL0003308	111	RPP2B [Candida albicans (taxid	0.9	0.648	0.325	3.4e-06

ZFIN|ZDB-GENE-031018-2 rplp2 "ribosomal protein, large P2" [Danio rerio (taxid:7955)]

 Score = 92 (37.4 bits), Expect = 9.2e-09, Sum P(2) = 9.2e-09
 Identities = 18/34 (52%), Positives = 26/34 (76%)

Query:     9 AVGAEADDERIEFLLSEVKGKDITELIASGREKL 42
             +VG EADDER+  ++SE+ GKDI E++ +G  KL
Sbjct:    29 SVGIEADDERLNKVVSELNGKDINEVMNAGLSKL 62

GO:0005840 "ribosome" evidence=IEA

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0006414 "translational elongation" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

TAIR|locus:2075993 AT3G44590 [Arabidopsis thaliana (taxid:3702)]

 Score = 131 (51.2 bits), Expect = 9.7e-09, P = 9.7e-09
 Identities = 36/83 (43%), Positives = 38/83 (45%)

Query:     9 AVGAEADDERIEFLLSEVKGKDITELIASGREKLXXXXXXXXXXXXXXXXXXXXXXXXXX 68
             AVGA+ D E IE LL EV GKDI ELIASGREKL                          
Sbjct:    29 AVGADVDGESIELLLKEVSGKDIAELIASGREKLASVPSGGGVAVSAAPSSGGGGAAAPA 88

Query:    69 X-----------SDDDMGFSLFD 80
                         SDDDMGFSLF+
Sbjct:    89 EKKEAKKEEKEESDDDMGFSLFE 111

GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006414 "translational elongation" evidence=IEA;ISS

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0001510 "RNA methylation" evidence=RCA

TAIR|locus:2042062 AT2G27710 [Arabidopsis thaliana (taxid:3702)]

 Score = 123 (48.4 bits), Expect = 6.8e-08, P = 6.8e-08
 Identities = 34/87 (39%), Positives = 40/87 (45%)

Query:     9 AVGAEADDERIEFLLSEVKGKDITELIASGREKLXXXXXXXXXXXXXXXXXXXXXXXXXX 68
             +VGAE +D +IE LL EVKGKD+ ELIA+GREKL                          
Sbjct:    29 SVGAETEDSQIELLLKEVKGKDLAELIAAGREKLASVPSGGGGGVAVASATSGGGGGGGA 88

Query:    69 X---------------SDDDMGFSLFD 80
                             SDDDMGFSLF+
Sbjct:    89 SAAESKKEEKKEEKEESDDDMGFSLFE 115

GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006414 "translational elongation" evidence=IEA;ISS

GO:0005730 "nucleolus" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0009409 "response to cold" evidence=IEP

GO:0005886 "plasma membrane" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

GO:0001510 "RNA methylation" evidence=RCA

TAIR|locus:2042052 AT2G27720 [Arabidopsis thaliana (taxid:3702)]

 Score = 123 (48.4 bits), Expect = 6.8e-08, P = 6.8e-08
 Identities = 25/38 (65%), Positives = 29/38 (76%)

Query:     5 VFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKL 42
             V G   GAE +D +IE LL EVKGKD+ ELIA+GREKL
Sbjct:    40 VIGDCFGAETEDSQIELLLKEVKGKDLAELIAAGREKL 77

GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006414 "translational elongation" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=IDA

GO:0009409 "response to cold" evidence=IEP

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

ASPGD|ASPL0000000414 AN5996 [Emericella nidulans (taxid:162425)]

 Score = 120 (47.3 bits), Expect = 1.4e-07, P = 1.4e-07
 Identities = 30/81 (37%), Positives = 38/81 (46%)

Query:     9 AVGAEADDERIEFLLSEVKGKDITELIASGREKLXXXXXXXXXXXXXXXXXXXXXXXXXX 68
             +VG +ADDER+E L++E++GKDI ELIA G  KL                          
Sbjct:    29 SVGVDADDERLEKLIAELQGKDINELIAEGTTKLASVPSGGAGGAAPAAAAGGAAAAEAP 88

Query:    69 X---------SDDDMGFSLFD 80
                       SD+DMGF LFD
Sbjct:    89 AAEKEEEKEESDEDMGFGLFD 109

GO:0005829 "cytosol" evidence=IEA

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006414 "translational elongation" evidence=IEA

POMBASE|SPBP8B7.06 rpp201 "60S acidic ribosomal protein P2A subunit (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 119 (46.9 bits), Expect = 1.8e-07, P = 1.8e-07
 Identities = 31/81 (38%), Positives = 37/81 (45%)

Query:    10 VGAEADDERIEFLLSEVKGKDITELIASGREKLXXXXXXXXXXXXXXXXXXXXXXXXXXX 69
             VG EA+ ERIE L++E+ GKDI ELIA+G EKL                           
Sbjct:    30 VGIEAESERIETLINELNGKDIDELIAAGNEKLATVPTGGAASAAPAAAAGGAAPAAEEA 89

Query:    70 ----------SDDDMGFSLFD 80
                       SD+DMGF LFD
Sbjct:    90 AKEEAKEEEESDEDMGFGLFD 110

GO:0002182 "cytoplasmic translational elongation" evidence=NAS

GO:0003735 "structural constituent of ribosome" evidence=ISO

GO:0005829 "cytosol" evidence=IDA

GO:0006414 "translational elongation" evidence=ISO

GO:0022625 "cytosolic large ribosomal subunit" evidence=ISO

POMBASE|SPBC23G7.15c rpp202 "60S acidic ribosomal protein P2B subunit" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 115 (45.5 bits), Expect = 4.8e-07, P = 4.8e-07
 Identities = 30/81 (37%), Positives = 37/81 (45%)

Query:    10 VGAEADDERIEFLLSEVKGKDITELIASGREKLXXXXXXXXXXXXXXXXXXXXXXXXXXX 69
             VG EA+ ER+E L+SE+ GK+I ELIA+G EKL                           
Sbjct:    30 VGIEAEAERVESLISELNGKNIEELIAAGNEKLSTVPSAGAVATPAAGGAAGAEATSAAE 89

Query:    70 ----------SDDDMGFSLFD 80
                       SD+DMGF LFD
Sbjct:    90 EAKEEEAAEESDEDMGFGLFD 110

GO:0002182 "cytoplasmic translational elongation" evidence=NAS

GO:0003735 "structural constituent of ribosome" evidence=ISO

GO:0005829 "cytosol" evidence=IDA

GO:0006414 "translational elongation" evidence=ISO

GO:0022625 "cytosolic large ribosomal subunit" evidence=ISO

POMBASE|SPAC1071.08 rpp203 "60S acidic ribosomal protein P2C subunit" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 113 (44.8 bits), Expect = 7.8e-07, P = 7.8e-07
 Identities = 29/81 (35%), Positives = 36/81 (44%)

Query:    10 VGAEADDERIEFLLSEVKGKDITELIASGREKLXXXXXXXXXXXXXXXXXXXXXXXXXXX 69
             VG E++ ER+E L+ E+ GKDI ELIA+G EKL                           
Sbjct:    30 VGIESESERVEALIKELDGKDIDELIAAGNEKLATVPSGGAAAAAAPAAAGGAAPAAEEA 89

Query:    70 ----------SDDDMGFSLFD 80
                       SD+DMGF LFD
Sbjct:    90 AKEEAKEEEESDEDMGFGLFD 110

GO:0002182 "cytoplasmic translational elongation" evidence=NAS

GO:0003735 "structural constituent of ribosome" evidence=ISO

GO:0005829 "cytosol" evidence=IDA

GO:0006414 "translational elongation" evidence=ISO

GO:0022625 "cytosolic large ribosomal subunit" evidence=ISO

SGD|S000005399 RPP2A "Ribosomal protein P2 alpha" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 108 (43.1 bits), Expect = 2.6e-06, P = 2.6e-06
 Identities = 26/79 (32%), Positives = 34/79 (43%)

Query:     9 AVGAEADDERIEFLLSEVKGKDITELIASGREKLXXXXXXXXXXXXXXXXXXXXXXX--- 65
             +VG E +DE++  +LS ++GK + ELI  G EKL                          
Sbjct:    28 SVGIEIEDEKVSSVLSALEGKSVDELITEGNEKLAAVPAAGPASAGGAAAASGDAAAEEE 87

Query:    66 ----XXXXSDDDMGFSLFD 80
                     SDDDMGF LFD
Sbjct:    88 KEEEAAEESDDDMGFGLFD 106

GO:0005840 "ribosome" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0002181 "cytoplasmic translation" evidence=TAS

GO:0006414 "translational elongation" evidence=IEA;ISS

GO:0003735 "structural constituent of ribosome" evidence=IEA;TAS

GO:0022625 "cytosolic large ribosomal subunit" evidence=TAS

GO:0005622 "intracellular" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

CGD|CAL0003308 RPP2B [Candida albicans (taxid:5476)]

 Score = 107 (42.7 bits), Expect = 3.4e-06, P = 3.4e-06
 Identities = 27/83 (32%), Positives = 36/83 (43%)

Query:     9 AVGAEADDERIEFLLSEVKGKDITELIASGREKLXXXXXXXXXXXXXXXXXXXXXXXXXX 68
             +VG EA++ R++ LL +++GKD+ ELIA G  KL                          
Sbjct:    29 SVGVEAEESRLQALLKDLEGKDLQELIAEGNTKLASVPSGGAAAGGASASAGAAAGGAAE 88

Query:    69 X-----------SDDDMGFSLFD 80
                         SDDDMGF LFD
Sbjct:    89 AEEEKEEEAKEESDDDMGFGLFD 111

GO:0003735 "structural constituent of ribosome" evidence=ISS;IDA

GO:0005840 "ribosome" evidence=IDA

GO:0006412 "translation" evidence=ISS

GO:0005829 "cytosol" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P42899	RLA2_BOVIN	No assigned EC number	0.5057	0.9	0.6260	yes	no
Q9UUZ6	RLA2_ASPFU	No assigned EC number	0.5421	0.9	0.6486	yes	no
Q9LXM8	RLA24_ARATH	No assigned EC number	0.6585	0.8875	0.6396	yes	no
Q9C3Z5	RLA2_PODAS	No assigned EC number	0.5421	0.9	0.6486	yes	no

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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	80
PLN00138	113	PLN00138, PLN00138, large subunit ribosomal protei	7e-29
cd05833	109	cd05833, Ribosomal_P2, Ribosomal protein P2	2e-24
pfam00428	88	pfam00428, Ribosomal_60s, 60s Acidic ribosomal pro	9e-13
PTZ00373	112	PTZ00373, PTZ00373, 60S Acidic ribosomal protein P	9e-12
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	9e-10
cd05831	103	cd05831, Ribosomal_P1, Ribosomal protein P1	5e-09
PTZ00135	310	PTZ00135, PTZ00135, 60S acidic ribosomal protein P	6e-09
cd04411	105	cd04411, Ribosomal_P1_P2_L12p, Ribosomal protein P	1e-08
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	2e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	3e-04
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	3e-04

>gnl|CDD|165706 PLN00138, PLN00138, large subunit ribosomal protein LP2; Provisional

 Score = 99.0 bits (246), Expect = 7e-29
 Identities = 67/85 (78%), Positives = 70/85 (82%), Gaps = 13/85 (15%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGG-------------AAAAPA 55
           +VGA+ADD+RIE LLSEVKGKDITELIASGREKLASVPSGG              AAAPA
Sbjct: 29  SVGADADDDRIELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAAAPAAGGAAAPA 88

Query: 56  AEAKKEEKVEEKEESDDDMGFSLFD 80
           AEAKKEEKVEEKEESDDDMGFSLFD
Sbjct: 89  AEAKKEEKVEEKEESDDDMGFSLFD 113

Length = 113

>gnl|CDD|100111 cd05833, Ribosomal_P2, Ribosomal protein P2

 Score = 87.3 bits (217), Expect = 2e-24
 Identities = 49/81 (60%), Positives = 61/81 (75%), Gaps = 9/81 (11%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAAAAPAA--------EAKK 60
           +VG E DDE++  ++SE++GKD+ ELIA+G+EKLASVP+G   AAPAA         AKK
Sbjct: 29  SVGVEVDDEKLNKVISELEGKDVEELIAAGKEKLASVPAGAGGAAPAAAAAAAAAAAAKK 88

Query: 61  EEKVEE-KEESDDDMGFSLFD 80
           EEK EE +EESDDDMGF LFD
Sbjct: 89  EEKKEESEEESDDDMGFGLFD 109

This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and P2B, which form P1A/P2B and P1B/P2A heterodimers. Some plants have a third P-protein, called P3, which is not homologous to P1 and P2. In humans, P1 and P2 are strongly autoimmunogenic. They play a significant role in the etiology and pathogenesis of systemic lupus erythema (SLE). In addition, the ribosome-inactivating protein trichosanthin (TCS) interacts with human P0, P1, and P2, with its primary binding site in the C-terminal region of P2. TCS inactivates the ribosome by depurinating a specific adenine in the sarcin-ricin loop of 28S rRNA. Length = 109

>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein

 Score = 57.2 bits (139), Expect = 9e-13
 Identities = 36/76 (47%), Positives = 52/76 (68%), Gaps = 5/76 (6%)

Query: 9  AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAAAAPAAEA-----KKEEK 63
          A G E + ER+E L+  ++GK+I ELIA+G  KL++  +  AAAA AA A     +++++
Sbjct: 13 AAGKEVEAERLELLVKFLEGKNIKELIANGSAKLSAAAAAAAAAAAAAAAAAAAEEEKKE 72

Query: 64 VEEKEESDDDMGFSLF 79
           EE+EE DDDMGF LF
Sbjct: 73 EEEEEEEDDDMGFGLF 88

This family includes archaebacterial L12, eukaryotic P0, P1 and P2. Length = 88

>gnl|CDD|185582 PTZ00373, PTZ00373, 60S Acidic ribosomal protein P2; Provisional

 Score = 55.3 bits (133), Expect = 9e-12
 Identities = 39/82 (47%), Positives = 53/82 (64%), Gaps = 10/82 (12%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSG-GAAAAPAA---------EA 58
           AV A+ +D+ ++     ++GK   ELIA+G +KL ++  G  AAAAPAA         EA
Sbjct: 31  AVNADVEDDVLDNFFKSLEGKTPHELIAAGMKKLQNIGGGVAAAAAPAAGAATAGAKAEA 90

Query: 59  KKEEKVEEKEESDDDMGFSLFD 80
           KKEEK EE+EE +DD+GFSLF 
Sbjct: 91  KKEEKKEEEEEEEDDLGFSLFG 112

Length = 112

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 50.1 bits (120), Expect = 9e-10
 Identities = 32/82 (39%), Positives = 48/82 (58%), Gaps = 10/82 (12%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAAAAPAAEA---------- 58
           A G E ++ R + L++ ++G DI E+I +  E  A+  + GAAAA AA A          
Sbjct: 28  AAGVEVEEARAKALVAALEGVDIDEVIKNAAEAPAAAAAAGAAAAAAAGAEAAAEADEAE 87

Query: 59  KKEEKVEEKEESDDDMGFSLFD 80
           ++E++ E +EESDDDM F LF 
Sbjct: 88  EEEKEEEAEEESDDDMLFGLFG 109

Length = 109

>gnl|CDD|100109 cd05831, Ribosomal_P1, Ribosomal protein P1

 Score = 48.1 bits (115), Expect = 5e-09
 Identities = 31/57 (54%), Positives = 38/57 (66%), Gaps = 4/57 (7%)

Query: 27  KGKDITELIASGREKLAS---VPSGGAAAAPAAEAKKEEKVEE-KEESDDDMGFSLF 79
           +GKDI +L+++            +  AAAA AAEAKKEEK EE +EESDDDMGF LF
Sbjct: 47  EGKDIKDLLSNVGGGGGGAAPAAAAAAAAAAAAEAKKEEKKEEEEEESDDDMGFGLF 103

This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers) and bacteria may have four or six copies (two or three homodimers), depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and P2B, which form P1A/P2B and P1B/P2A heterodimers. Some plant species have a third P-protein, called P3, which is not homologous to P1 and P2. In humans, P1 and P2 are strongly autoimmunogenic. They play a significant role in the etiology and pathogenesis of systemic lupus erythema (SLE). In addition, the ribosome-inactivating protein trichosanthin (TCS) interacts with human P0, P1, and P2, with its primary binding site located in the C-terminal region of P2. TCS inactivates the ribosome by depurinating a specific adenine in the sarcin-ricin loop of 28S rRNA. Length = 103

>gnl|CDD|240285 PTZ00135, PTZ00135, 60S acidic ribosomal protein P0; Provisional

 Score = 50.0 bits (120), Expect = 6e-09
 Identities = 19/37 (51%), Positives = 23/37 (62%)

Query: 44  SVPSGGAAAAPAAEAKKEEKVEEKEESDDDMGFSLFD 80
           +  +  AAAA AA A      EE+EE +DDMGF LFD
Sbjct: 274 AAAAAAAAAAAAAAAAAAAPAEEEEEEEDDMGFGLFD 310

Length = 310

>gnl|CDD|100108 cd04411, Ribosomal_P1_P2_L12p, Ribosomal protein P1, P2, and L12p

 Score = 47.3 bits (112), Expect = 1e-08
 Identities = 33/78 (42%), Positives = 47/78 (60%), Gaps = 7/78 (8%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAAAAPAAEA-------KKE 61
           A GAE + ER++  LS + GK+I E+I+ G+E ++S  +  AA A  A A        +E
Sbjct: 28  AAGAEIEPERVKLFLSALNGKNIDEVISKGKELMSSQAAAAAAPAATAAATAEPAEKAEE 87

Query: 62  EKVEEKEESDDDMGFSLF 79
            K EE+EE D+D GF LF
Sbjct: 88  AKEEEEEEEDEDFGFGLF 105

Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have two copies each of P1 and P2 (two heterodimers). Bacteria may have four or six copies (two or three homodimers), depending on the species. As in bacteria, the stalk is crucial for binding of initiation, elongation, and release factors in eukaryotes and archaea. Length = 105

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 36.2 bits (84), Expect = 2e-04
 Identities = 23/65 (35%), Positives = 39/65 (60%)

Query: 9  AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAAAAPAAEAKKEEKVEEKE 68
          A G E D+ R++ L++ ++G +I E I        +  +  AAAA AAE ++EE+ EE+E
Sbjct: 28 AAGVEVDEARVKALVAALEGVNIEEAIKKAAAAPVAAAAAAAAAAAAAEEEEEEEEEEEE 87

Query: 69 ESDDD 73
          E ++ 
Sbjct: 88 EEEES 92

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 35.9 bits (83), Expect = 3e-04
 Identities = 20/65 (30%), Positives = 36/65 (55%)

Query: 9  AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAAAAPAAEAKKEEKVEEKE 68
          A G E D+ R++ L++ ++  +I E I       A+     AAAA A E  +E++ E+K+
Sbjct: 28 AAGIEVDEARVKALVAALEEVNIDEAIKKAAVAAAAAAPAAAAAAAAEEKAEEKEEEKKK 87

Query: 69 ESDDD 73
          E + +
Sbjct: 88 EEEKE 92

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 35.7 bits (83), Expect = 3e-04
 Identities = 20/65 (30%), Positives = 38/65 (58%)

Query: 9  AVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAAAAPAAEAKKEEKVEEKE 68
          A G E D+ R++ L++ ++  +I E I        +  +  AAAA AA A+++++ EE+E
Sbjct: 28 AAGVEVDEARVKALVAALEDVNIEEAIKKAAAAPVAAAAAAAAAAAAAAAEEKKEEEEEE 87

Query: 69 ESDDD 73
          E  ++
Sbjct: 88 EEKEE 92

Length = 106

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	80
cd05833	109	Ribosomal_P2 Ribosomal protein P2. This subfamily	99.94
PTZ00373	112	60S Acidic ribosomal protein P2; Provisional	99.93
KOG3449	112	consensus 60S acidic ribosomal protein P2 [Transla	99.93
cd04411	105	Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and	99.93
PLN00138	113	large subunit ribosomal protein LP2; Provisional	99.92
cd05831	103	Ribosomal_P1 Ribosomal protein P1. This subfamily	99.86
PF00428	88	Ribosomal_60s: 60s Acidic ribosomal protein; Inter	99.82
COG2058	109	RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Tr	99.82
KOG1762	114	consensus 60s acidic ribosomal protein P1 [Transla	99.81
PRK06402	106	rpl12p 50S ribosomal protein L12P; Reviewed	99.63
TIGR03685	105	L21P_arch 50S ribosomal protein L12P. This model r	99.4
cd05832	106	Ribosomal_L12p Ribosomal protein L12p. This subfam	99.32
PTZ00135	310	60S acidic ribosomal protein P0; Provisional	98.86
PTZ00240	323	60S ribosomal protein P0; Provisional	97.87
PRK06402	106	rpl12p 50S ribosomal protein L12P; Reviewed	96.87
TIGR03685	105	L21P_arch 50S ribosomal protein L12P. This model r	96.04
COG2058	109	RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Tr	95.96
cd05831	103	Ribosomal_P1 Ribosomal protein P1. This subfamily	95.71
PRK04019	330	rplP0 acidic ribosomal protein P0; Validated	95.62
KOG1762	114	consensus 60s acidic ribosomal protein P1 [Transla	95.58
cd05832	106	Ribosomal_L12p Ribosomal protein L12p. This subfam	95.51
cd04411	105	Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and	89.1

>cd05833 Ribosomal_P2 Ribosomal protein P2

Probab=99.94  E-value=7.6e-27  Score=152.09  Aligned_cols=78  Identities=56%  Similarity=0.810  Sum_probs=59.7

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccccccccccCCCCC----C-C--cc--hhhhhhhhhhhhcccccC
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAA----A-A--PA--AEAKKEEKVEEKEESDDD   73 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~~~~~g~a----a-a--~a--~~~~~~~k~eeeEE~ddD   73 (80)
                      +++||+++|++|+++|+.+|++.|+||||++||++|..+++++|+++++    + +  ++  .++++++|+|++||+|||
T Consensus        23 I~~IL~AaGveVe~~~~~lf~~~L~GKdi~eLIa~g~~kl~s~~~~~~~aa~a~~~~a~aa~~~~~e~kkee~eee~ddD  102 (109)
T cd05833          23 VKKILGSVGVEVDDEKLNKVISELEGKDVEELIAAGKEKLASVPAGAGGAAPAAAAAAAAAAAAKKEEKKEESEEESDDD  102 (109)
T ss_pred             HHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHhhhcCCCccccccccccccccccccchhhhhhccCCccccccc
Confidence            5799999999999999999999999999999999999998875432211    1 1  11  122344445555667999


Q ss_pred             CCCCCCC
Q 034868           74 MGFSLFD   80 (80)
Q Consensus        74 mgfgLFd   80 (80)
                      |||||||
T Consensus       103 mGf~LFd  109 (109)
T cd05833         103 MGFGLFD  109 (109)
T ss_pred             cCCCCCC
Confidence            9999998

This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2

>PTZ00373 60S Acidic ribosomal protein P2; Provisional

Probab=99.93  E-value=8.4e-27  Score=152.61  Aligned_cols=78  Identities=45%  Similarity=0.614  Sum_probs=60.0

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccccccccccCCCCC------C--C--cchhhhhhhhhhhhccccc
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAA------A--A--PAAEAKKEEKVEEKEESDD   72 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~~~~~g~a------a--a--~a~~~~~~~k~eeeEE~dd   72 (80)
                      +++||+++|++|+++|+++|++.|+||||++||++|..+|++++.++++      +  +  +++++++++|+|++||+||
T Consensus        25 I~kIL~AaGveVd~~~~~l~~~~L~GKdI~ELIa~G~~kl~svgg~~~aa~a~a~~~~~~~~~~~~~~e~k~ee~ee~dd  104 (112)
T PTZ00373         25 VKNVLSAVNADVEDDVLDNFFKSLEGKTPHELIAAGMKKLQNIGGGVAAAAAPAAGAATAGAKAEAKKEEKKEEEEEEED  104 (112)
T ss_pred             HHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHHHHhcccCcccccccccccccccccchhhhhhhcccccccccc
Confidence            6899999999999999999999999999999999999999886222111      1  1  1112333344555678889


Q ss_pred             CCCCCCCC
Q 034868           73 DMGFSLFD   80 (80)
Q Consensus        73 DmgfgLFd   80 (80)
                      ||||||||
T Consensus       105 Dmgf~LFd  112 (112)
T PTZ00373        105 DLGFSLFG  112 (112)
T ss_pred             cccccccC
Confidence            99999998

>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]

Probab=99.93  E-value=1.5e-26  Score=150.67  Aligned_cols=78  Identities=73%  Similarity=0.946  Sum_probs=64.5

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccccccccccCCCCC--C----C----c--chhhhhhhhhhhhccc
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAA--A----A----P--AAEAKKEEKVEEKEES   70 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~~~~~g~a--a----a----~--a~~~~~~~k~eeeEE~   70 (80)
                      +++||.++|++++++|+++|++.|+||||.+||+.|..+|+++|++|++  +    +    +  ..++++++|+|++||+
T Consensus        23 ikkIl~sVG~E~d~e~i~~visel~GK~i~ElIA~G~eklAsvpsGGa~~aaa~~aaggaa~aa~~a~~~e~keEe~ees  102 (112)
T KOG3449|consen   23 IKKILESVGAEIDDERINLVLSELKGKDIEELIAAGREKLASVPSGGAVAAAAAPAAGGAAGAAPAAAKEEEKEEEKEES  102 (112)
T ss_pred             HHHHHHHhCcccCHHHHHHHHHHhcCCCHHHHHHHhHHHHhcCCCCCccccccCcCCCCCccCCccchhhhhhhhhcccc
Confidence            5899999999999999999999999999999999999999999988872  1    1    1  1112344555556899


Q ss_pred             ccCCCCCCCC
Q 034868           71 DDDMGFSLFD   80 (80)
Q Consensus        71 ddDmgfgLFd   80 (80)
                      ||||||+|||
T Consensus       103 ddDmgf~lFd  112 (112)
T KOG3449|consen  103 DDDMGFGLFD  112 (112)
T ss_pred             cccccccccC
Confidence            9999999998

>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p

Probab=99.93  E-value=4.4e-26  Score=147.62  Aligned_cols=77  Identities=42%  Similarity=0.629  Sum_probs=60.9

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccccccccccCCCCC---C---C-cchhhhhhhhhhhhcccccCCC
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAA---A---A-PAAEAKKEEKVEEKEESDDDMG   75 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~~~~~g~a---a---a-~a~~~~~~~k~eeeEE~ddDmg   75 (80)
                      +++||+++|++|+++|+++|+++|+||||++||++|..+++++|++|++   +   + +++++++++|+|++||+|||||
T Consensus        22 I~~IL~aaGveVe~~~~~~~~~aLaGk~V~eli~~g~~kl~~~~~~~~a~~~a~~~~~~~~~~~~e~k~ee~eE~dddmg  101 (105)
T cd04411          22 IKELLSAAGAEIEPERVKLFLSALNGKNIDEVISKGKELMSSQAAAAAAPAATAAATAEPAEKAEEAKEEEEEEEDEDFG  101 (105)
T ss_pred             HHHHHHHcCCCcCHHHHHHHHHHHcCCCHHHHHHHHHhhccCCCCccccccccccccccchhhhhhhhcccccccccccC
Confidence            6899999999999999999999999999999999999998877655432   1   1 1112333444556677899999


Q ss_pred             CCCC
Q 034868           76 FSLF   79 (80)
Q Consensus        76 fgLF   79 (80)
                      ||||
T Consensus       102 f~LF  105 (105)
T cd04411         102 FGLF  105 (105)
T ss_pred             cccC
Confidence            9999

Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain

>PLN00138 large subunit ribosomal protein LP2; Provisional

Probab=99.92  E-value=8.1e-26  Score=148.10  Aligned_cols=78  Identities=83%  Similarity=1.046  Sum_probs=60.9

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccccccccccCCCCC-----C---C--cc--h-hhhhhhhhhhhcc
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAA-----A---A--PA--A-EAKKEEKVEEKEE   69 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~~~~~g~a-----a---a--~a--~-~~~~~~k~eeeEE   69 (80)
                      +++||+++|++|+++|+++|++.|+||||++||++|..+|+++|++|++     +   +  ++  + +++++++++++||
T Consensus        23 I~~IL~AaGvevd~~~~~~f~~~L~gK~i~eLIa~G~~kl~sv~~gg~aa~a~a~a~~~~~~~~~~~~~~~e~k~e~eeE  102 (113)
T PLN00138         23 LKDILGSVGADADDDRIELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAAAPAAGGAAAPAAEAKKEEKVEEKEE  102 (113)
T ss_pred             HHHHHHHcCCcccHHHHHHHHHHHcCCCHHHHHHhchhccccCCCCCccccccccccccccccccccchhhhhhcccccc
Confidence            6899999999999999999999999999999999999999887765431     1   0  11  1 1123333455577


Q ss_pred             cccCCCCCCCC
Q 034868           70 SDDDMGFSLFD   80 (80)
Q Consensus        70 ~ddDmgfgLFd   80 (80)
                      +||||||+|||
T Consensus       103 ~ddDmGfgLFd  113 (113)
T PLN00138        103 SDDDMGFSLFD  113 (113)
T ss_pred             ccccccccccC
Confidence            88999999998

>cd05831 Ribosomal_P1 Ribosomal protein P1

Probab=99.86  E-value=5.4e-22  Score=128.07  Aligned_cols=77  Identities=38%  Similarity=0.494  Sum_probs=55.2

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccccccc-cccCCCCCCCc---chhhhhhhhhhhhcccccCCCCCC
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLA-SVPSGGAAAAP---AAEAKKEEKVEEKEESDDDMGFSL   78 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~-~~~~~g~aaa~---a~~~~~~~k~eeeEE~ddDmgfgL   78 (80)
                      +++||+++|++|+++|+++|++.|+||+|++||.+++...+ +.|++++++++   ++++++++|++++||+|+||||||
T Consensus        23 I~~ilkAaGveve~~~~~~f~~~L~gk~i~elIa~~~~~~~~aap~a~~a~~~~~~~~~~~~~kk~e~eee~d~dmgfgl  102 (103)
T cd05831          23 INALLKAAGVNVEPYWPGLFAKALEGKDIKDLLSNVGGGGGGAAPAAAAAAAAAAAAEAKKEEKKEEEEEESDDDMGFGL  102 (103)
T ss_pred             HHHHHHHcCCcccHHHHHHHHHHHcCCCHHHHhhccccccccccccccccccccccccchhhhccccccccccccccccc
Confidence            58999999999999999999999999999999988653211 13322222111   112234445566677899999999


Q ss_pred             C
Q 034868           79 F   79 (80)
Q Consensus        79 F   79 (80)
                      |
T Consensus       103 F  103 (103)
T cd05831         103 F  103 (103)
T ss_pred             C
Confidence            9

This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers) and bacteria may have four or six copies (two or three homodimers), depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and

>PF00428 Ribosomal_60s: 60s Acidic ribosomal protein; InterPro: IPR001813 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.82  E-value=1.6e-21  Score=121.97  Aligned_cols=77  Identities=45%  Similarity=0.611  Sum_probs=53.8

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHcccccccc---ccCCCCCCCcchhh-hhhhhhhhh-cccccCCCCC
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLAS---VPSGGAAAAPAAEA-KKEEKVEEK-EESDDDMGFS   77 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~---~~~~g~aaa~a~~~-~~~~k~eee-EE~ddDmgfg   77 (80)
                      +++||+++|++|+++|+.+|++.|+|++|++||+++..++++   ++++++++.+++++ ++++|++++ ||+|+|||||
T Consensus         7 i~~vl~aag~~v~~~~~~~~~~~l~~~~i~~li~~~~~~~~~~aaa~aaa~aa~~~a~a~~e~kkEeeeeEEed~dmGf~   86 (88)
T PF00428_consen    7 IKKVLKAAGVEVEAIWLELFAKALEGKDIKELIANGSAGMAAAAAAAAAAAAAAAAAAAAEEEKKEEEEEEEEDDDMGFG   86 (88)
T ss_dssp             HHHHHHHHTHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHHHSTTHHHHT--SS-SSSSSTT
T ss_pred             HHHHHHHhCCchhHHHHHHHHHHHcCCcHHHHHhcccccccccccccccccccccccccchhcccccccccccccccCcC
Confidence            578999999999999999999999999999999998876532   12222111122222 222333333 5889999999


Q ss_pred             CC
Q 034868           78 LF   79 (80)
Q Consensus        78 LF   79 (80)
                      ||
T Consensus        87 LF   88 (88)
T PF00428_consen   87 LF   88 (88)
T ss_dssp             TT
T ss_pred             CC
Confidence            99

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The 60S acidic ribosomal protein plays an important role in the elongation step of protein synthesis. This family includes archaebacterial L12, eukaryotic P0, P1 and P2 []. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Alt a 6, Alt a 12, Cla h 3, Cla h 4 and Cla h 12.; GO: 0003735 structural constituent of ribosome, 0006414 translational elongation, 0005622 intracellular, 0005840 ribosome; PDB: 3A1Y_C 3N2D_B 2LBF_A 3IZS_t 3IZR_t 1S4J_A 2JDL_C 2W1O_B 1S4H_A 2ZKR_g.

>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

Probab=99.82  E-value=2.3e-20  Score=121.43  Aligned_cols=78  Identities=37%  Similarity=0.495  Sum_probs=59.2

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccccccccccCCCCCC---C-----cc--hhhhhhhhhhhhccccc
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAAA---A-----PA--AEAKKEEKVEEKEESDD   72 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~~~~~g~aa---a-----~a--~~~~~~~k~eeeEE~dd   72 (80)
                      .++||+++|++|++.|++.|+++|+||||+++|.++..++++++++++++   +     +.  .+++++++++.+||+++
T Consensus        22 l~~vl~aaGveve~~r~k~lvaaLeg~~idE~i~~~~~~~~a~a~a~aaaa~~A~~~~a~~~~ea~eEe~eEe~~EE~~~  101 (109)
T COG2058          22 LKSVLEAAGVEVEEARAKALVAALEGVDIDEVIKNAAEAPAAAAAAGAAAAAAAGAEAAAEADEAEEEEKEEEAEEESDD  101 (109)
T ss_pred             HHHHHHHcCCCccHHHHHHHHHHhcCCCHHHHHHHhcccccccCCcccccccccccccccchhhHHHHHhhhchhhcccc
Confidence            57899999999999999999999999999999999988776655444421   1     11  11222234455577889


Q ss_pred             CCCCCCCC
Q 034868           73 DMGFSLFD   80 (80)
Q Consensus        73 DmgfgLFd   80 (80)
                      ||+|+|||
T Consensus       102 ~~lf~LF~  109 (109)
T COG2058         102 DMLFGLFG  109 (109)
T ss_pred             cchhhccC
Confidence            99999998

>KOG1762 consensus 60s acidic ribosomal protein P1 [Translation, ribosomal structure and biogenesis]

Probab=99.81  E-value=3.6e-20  Score=121.30  Aligned_cols=77  Identities=42%  Similarity=0.542  Sum_probs=55.1

Q ss_pred             hhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHcccccccc-----ccCCCCC----CCcchhhhhhhhhhhhcccccCC
Q 034868            4 WVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLAS-----VPSGGAA----AAPAAEAKKEEKVEEKEESDDDM   74 (80)
Q Consensus         4 ~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~-----~~~~g~a----aa~a~~~~~~~k~eeeEE~ddDm   74 (80)
                      .+|++++|++|+++|+.+|+++|.++||.+||.+.+.+...     +|+++++    ++++++++++.|+|+.||+||||
T Consensus        29 ~tl~kaa~v~ve~~Wp~lfakale~vni~~li~n~gag~~a~a~~~~~~~~aa~~~~aA~~~Ekk~eak~EeseesddDm  108 (114)
T KOG1762|consen   29 NTLTKAAGVNVEPYWPGLFAKALEGVNIKELICNVGAGGGALAAGAAAAGGAAAAGGAAAAEEKKEEAKKEESEESDDDM  108 (114)
T ss_pred             hhHHHhccCcccccchhHHHHHhccCChHHHHHhcccCCccCCCccccccccccccccccchHHHHHhhhhhhccccccc
Confidence            46788999999999999999999999999999985542211     1111111    12233344445566678899999


Q ss_pred             CCCCCC
Q 034868           75 GFSLFD   80 (80)
Q Consensus        75 gfgLFd   80 (80)
                      ||||||
T Consensus       109 gfGLfd  114 (114)
T KOG1762|consen  109 GFGLFD  114 (114)
T ss_pred             ccCCCC
Confidence            999997

>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed

Probab=99.63  E-value=4.4e-16  Score=101.19  Aligned_cols=38  Identities=24%  Similarity=0.282  Sum_probs=35.0

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHcccc
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGRE   40 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~   40 (80)
                      +++||+++|++|+++|+++|+++|+|+||++||.+.+.
T Consensus        22 I~~IL~AAGveVee~~~k~~v~aL~GkdIeElI~~a~~   59 (106)
T PRK06402         22 LKKVLEAAGVEVDEARVKALVAALEDVNIEEAIKKAAA   59 (106)
T ss_pred             HHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHhccc
Confidence            68999999999999999999999999999999986443

>TIGR03685 L21P_arch 50S ribosomal protein L12P

Probab=99.40  E-value=4.2e-13  Score=86.98  Aligned_cols=37  Identities=27%  Similarity=0.364  Sum_probs=34.5

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccc
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGR   39 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~   39 (80)
                      +++||+++||+|+++|+..|++.|+|++|.+||.+-.
T Consensus        22 I~~IL~AAGv~ve~~~~~~la~~L~gk~i~eli~~~~   58 (105)
T TIGR03685        22 LKAVLEAAGVEVDEARVKALVAALEGVNIEEAIKKAA   58 (105)
T ss_pred             HHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHHhhh
Confidence            5799999999999999999999999999999997644

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.

>cd05832 Ribosomal_L12p Ribosomal protein L12p

Probab=99.32  E-value=2.5e-12  Score=83.60  Aligned_cols=37  Identities=24%  Similarity=0.274  Sum_probs=34.7

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccc
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGR   39 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~   39 (80)
                      +++||+++|++|++.|++.|++.|+|+||++||++..
T Consensus        22 I~~IL~AAGveVd~~~~~ala~aL~gkdIeElIa~~~   58 (106)
T cd05832          22 LKKVLEAAGIEVDEARVKALVAALEEVNIDEAIKKAA   58 (106)
T ss_pred             HHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHHhcc
Confidence            6899999999999999999999999999999998744

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera

>PTZ00135 60S acidic ribosomal protein P0; Provisional

Probab=98.86  E-value=2.4e-09  Score=80.00  Aligned_cols=74  Identities=30%  Similarity=0.381  Sum_probs=42.9

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCC---------C---ChHHHH---HccccccccccCCCCCCCcchhhhhhhhhhhh
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKG---------K---DITELI---ASGREKLASVPSGGAAAAPAAEAKKEEKVEEK   67 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~g---------k---~i~eLI---~~g~~~~~~~~~~g~aaa~a~~~~~~~k~eee   67 (80)
                      +.+|..++|+++.+.|+..|++++++         -   .+..++   +... +.+++|+++   ++++++++++++++|
T Consensus       222 i~als~aag~pt~~s~p~~ia~a~k~~~a~a~~~~~~~~~~~~~~~~~a~~~-~~~~~~~~~---~~~~~~~~~~~~~~~  297 (310)
T PTZ00135        222 VAAISLAAGYPTEASAPHSILNAFKNLAAIGLESGFTFPLAEKIKEALANPS-AAAAAAAAA---AAAAAAAAAAPAEEE  297 (310)
T ss_pred             HHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHhhcCCCChhhHHHHHhhcCch-hhccCcccc---Ccccccccccccccc
Confidence            46788999999999999999986532         1   111111   1111 112222211   111112233345667


Q ss_pred             cccccCCCCCCCC
Q 034868           68 EESDDDMGFSLFD   80 (80)
Q Consensus        68 EE~ddDmgfgLFd   80 (80)
                      ||+||||||||||
T Consensus       298 ee~~~~~g~~lf~  310 (310)
T PTZ00135        298 EEEEDDMGFGLFD  310 (310)
T ss_pred             cCcchhccccCCC
Confidence            7889999999998

>PTZ00240 60S ribosomal protein P0; Provisional

Probab=97.87  E-value=1.3e-05  Score=60.49  Aligned_cols=18  Identities=50%  Similarity=0.876  Sum_probs=13.0

Q ss_pred             hhhhhhcccccCCCCC-CC
Q 034868           62 EKVEEKEESDDDMGFS-LF   79 (80)
Q Consensus        62 ~k~eeeEE~ddDmgfg-LF   79 (80)
                      ++++++||+|+||||| ||
T Consensus       305 ~~~~~~e~~~~d~~~~~~~  323 (323)
T PTZ00240        305 AKEEEEESDEDDFGMGALF  323 (323)
T ss_pred             cccCCccCcccccCccccC
Confidence            3355667788899997 55

>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed

Probab=96.87  E-value=0.0019  Score=42.05  Aligned_cols=31  Identities=16%  Similarity=0.443  Sum_probs=26.0

Q ss_pred             hHhhhhhhcCCCcCHHHHHHHHHHhCCCChHH
Q 034868            2 FSWVFGFAVGAEADDERIEFLLSEVKGKDITE   33 (80)
Q Consensus         2 ~~~~iL~aaGveV~~~~~~~~~kaL~gk~i~e   33 (80)
                      +.-.||+..|.+|+.+.|+.++++. |.+|++
T Consensus         5 yAaLLL~~~g~~it~e~I~~IL~AA-GveVee   35 (106)
T PRK06402          5 YAALLLHSAGKEINEDNLKKVLEAA-GVEVDE   35 (106)
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHc-CCCccH
Confidence            3457899999999999999999987 666654

>TIGR03685 L21P_arch 50S ribosomal protein L12P

Probab=96.04  E-value=0.009  Score=38.69  Aligned_cols=31  Identities=19%  Similarity=0.463  Sum_probs=25.2

Q ss_pred             hHhhhhhhcCCCcCHHHHHHHHHHhCCCChHH
Q 034868            2 FSWVFGFAVGAEADDERIEFLLSEVKGKDITE   33 (80)
Q Consensus         2 ~~~~iL~aaGveV~~~~~~~~~kaL~gk~i~e   33 (80)
                      +.-.||+..|.+|+.+.++.++++- |.+|++
T Consensus         5 yA~Lll~~~g~~iT~e~I~~IL~AA-Gv~ve~   35 (105)
T TIGR03685         5 YAALLLHSAGKEINEENLKAVLEAA-GVEVDE   35 (105)
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHh-CCcccH
Confidence            3457899999999999999999987 555543

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.

>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

Probab=95.96  E-value=0.014  Score=38.27  Aligned_cols=29  Identities=14%  Similarity=0.415  Sum_probs=24.1

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChH
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDIT   32 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~   32 (80)
                      .-.+|+.+|-+++.++|..++++. |.+|+
T Consensus         6 a~llL~~agkei~e~~l~~vl~aa-Gveve   34 (109)
T COG2058           6 AYLLLHLAGKEITEDNLKSVLEAA-GVEVE   34 (109)
T ss_pred             HHHHHHHccCcCCHHHHHHHHHHc-CCCcc
Confidence            346899999999999999999976 66654

>cd05831 Ribosomal_P1 Ribosomal protein P1

Probab=95.71  E-value=0.025  Score=36.44  Aligned_cols=31  Identities=19%  Similarity=0.318  Sum_probs=26.6

Q ss_pred             hHhhhhhhcCCCcCHHHHHHHHHHhCCCChHH
Q 034868            2 FSWVFGFAVGAEADDERIEFLLSEVKGKDITE   33 (80)
Q Consensus         2 ~~~~iL~aaGveV~~~~~~~~~kaL~gk~i~e   33 (80)
                      |.-.||++.|++|+.+.|+.++++. |.+++.
T Consensus         6 yAaLiL~d~~~~~Tae~I~~ilkAa-Gveve~   36 (103)
T cd05831           6 YAALILHDDGIEITADNINALLKAA-GVNVEP   36 (103)
T ss_pred             HHHHHHccCCCCCCHHHHHHHHHHc-CCcccH
Confidence            5678999999999999999999987 566653

This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers) and bacteria may have four or six copies (two or three homodimers), depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and

>PRK04019 rplP0 acidic ribosomal protein P0; Validated

Probab=95.62  E-value=0.014  Score=43.85  Aligned_cols=20  Identities=10%  Similarity=0.126  Sum_probs=14.2

Q ss_pred             HHHHHHHHhCC-CChHHHHHc
Q 034868           18 RIEFLLSEVKG-KDITELIAS   37 (80)
Q Consensus        18 ~~~~~~kaL~g-k~i~eLI~~   37 (80)
                      ++..++..+.+ .++.+-|.+
T Consensus       270 ~~~ala~~~~~~~~~~~~~~~  290 (330)
T PRK04019        270 QALALAAALADKDALDEELKE  290 (330)
T ss_pred             HHHHHHHHhcCcccccHHHHh
Confidence            44455567888 888888875

>KOG1762 consensus 60s acidic ribosomal protein P1 [Translation, ribosomal structure and biogenesis]

Probab=95.58  E-value=0.0077  Score=39.77  Aligned_cols=30  Identities=13%  Similarity=0.231  Sum_probs=25.3

Q ss_pred             hHhhhhhhcCCCcCHHHHHHHHHHhCCCChH
Q 034868            2 FSWVFGFAVGAEADDERIEFLLSEVKGKDIT   32 (80)
Q Consensus         2 ~~~~iL~aaGveV~~~~~~~~~kaL~gk~i~   32 (80)
                      +.-.||++.+++|+.++++.++|+. |.|+.
T Consensus        11 yaalIL~d~~i~it~dki~tl~kaa-~v~ve   40 (114)
T KOG1762|consen   11 YAALILHDDEIEVTADKINTLTKAA-GVNVE   40 (114)
T ss_pred             hhhhhccccceeeehhhhhhHHHhc-cCccc
Confidence            3457999999999999999999988 55554

>cd05832 Ribosomal_L12p Ribosomal protein L12p

Probab=95.51  E-value=0.021  Score=37.17  Aligned_cols=30  Identities=17%  Similarity=0.387  Sum_probs=24.6

Q ss_pred             hHhhhhhhcCCCcCHHHHHHHHHHhCCCChH
Q 034868            2 FSWVFGFAVGAEADDERIEFLLSEVKGKDIT   32 (80)
Q Consensus         2 ~~~~iL~aaGveV~~~~~~~~~kaL~gk~i~   32 (80)
                      +.-.||+..|.+|+.+.++.++++- |.+++
T Consensus         5 yAaLLL~~~G~eITae~I~~IL~AA-GveVd   34 (106)
T cd05832           5 YAALLLHYAGKEINEENLKKVLEAA-GIEVD   34 (106)
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHh-CCccc
Confidence            3457899999999999999999986 54444

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera

>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p

Probab=89.10  E-value=0.55  Score=30.31  Aligned_cols=30  Identities=27%  Similarity=0.461  Sum_probs=24.7

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChHH
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDITE   33 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~e   33 (80)
                      .-.||+..|.+|+.+.|+.+++.. |.+|++
T Consensus         6 A~Lll~~~g~~~ta~~I~~IL~aa-GveVe~   35 (105)
T cd04411           6 AYLLLHKGGKELTEDKIKELLSAA-GAEIEP   35 (105)
T ss_pred             HHHHHHhcCCCCCHHHHHHHHHHc-CCCcCH
Confidence            456899999999999999999987 566653

Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	80
3izr_v	113	Localization Of The Large Subunit Ribosomal Protein		1e-07

>pdb|3IZR|VV Chain v, Localization Of The Large Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 113

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/33 (66%), Positives = 30/33 (90%)
Query: 9  AVGAEADDERIEFLLSEVKGKDITELIASGREK 41
          +VG E D+E++E +LS+VKGKDITEL+A+GREK
Sbjct: 29 SVGCEIDNEKMELMLSQVKGKDITELLAAGREK 61

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	80
3iz5_v	113	60S acidic ribosomal protein P21 - P2 (L12P); euka	99.95
3izc_v	106	60S acidic ribosomal protein (P2); eukaryotic ribo	99.95
3iz5_t	110	60S acidic ribosomal protein P11 - P1 (L12P); euka	99.92
3izc_t	106	60S acidic ribosomal protein RPP11 (P1); eukaryoti	99.92
2lbf_B	70	60S acidic ribosomal protein P2; ribosome, stalk,	99.56
2lbf_A	69	60S acidic ribosomal protein P1; ribosome, stalk,	99.18
3a1y_A	58	50S ribosomal protein P1 (L12P); stalk, helix SPIN	99.17
3u5i_q	312	A0, L10E, 60S acidic ribosomal protein P0; transla	99.0
3iz5_s	319	60S acidic ribosomal protein P0 (L10P); eukaryotic	98.93
2zkr_g	317	60S acidic ribosomal protein P0; protein-RNA compl	98.82
3iz5_t	110	60S acidic ribosomal protein P11 - P1 (L12P); euka	97.14
3izc_t	106	60S acidic ribosomal protein RPP11 (P1); eukaryoti	96.82
3j21_k	339	Acidic ribosomal protein P0 homolog; archaea, arch	88.48

>2lbf_B 60S acidic ribosomal protein P2; ribosome, stalk, P1/P2; NMR {Homo sapiens} PDB: 2w1o_A

Probab=99.56  E-value=2.2e-15  Score=90.78  Aligned_cols=47  Identities=49%  Similarity=0.703  Sum_probs=45.0

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccccccccccCCC
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGG   49 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~~~~~g   49 (80)
                      +++||+++|++|+++|+++|+++|+||||++||++|..+++++|+||
T Consensus        24 I~~il~aaGvevd~~~~~~~~~aL~gk~i~elIa~g~~kl~s~p~gg   70 (70)
T 2lbf_B           24 IKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIGKLASVPAGG   70 (70)
T ss_dssp             HHHHHHTTTCCCCTTHHHHHHHHHSSCCHHHHHTTCSSSCSSCCCCC
T ss_pred             HHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCC
Confidence            57899999999999999999999999999999999999999999875

>2lbf_A 60S acidic ribosomal protein P1; ribosome, stalk, P1/P2; NMR {Homo sapiens}

Probab=99.18  E-value=1.2e-11  Score=74.05  Aligned_cols=35  Identities=14%  Similarity=0.097  Sum_probs=33.5

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHc
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIAS   37 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~   37 (80)
                      +++||+++|++|+++|+.+|+++|+||||++||.+
T Consensus        28 I~~il~AaGveve~~~~~lf~~aL~gk~I~elI~~   62 (69)
T 2lbf_A           28 INALIKAAGVNVEPFWPGLFAKALANVNIGSLICN   62 (69)
T ss_dssp             HHHHHHHHTCCCCTHHHHHHHHHTTTSCGGGGGTT
T ss_pred             HHHHHHHcCCCccHHHHHHHHHHHCCCCHHHHHHh
Confidence            57899999999999999999999999999999976

>3a1y_A 50S ribosomal protein P1 (L12P); stalk, helix SPIN, ribonucleoprotein; 2.13A {Pyrococcus horikoshii}

Probab=99.17  E-value=2.9e-11  Score=70.16  Aligned_cols=35  Identities=29%  Similarity=0.422  Sum_probs=33.4

Q ss_pred             HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHc
Q 034868            3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIAS   37 (80)
Q Consensus         3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~   37 (80)
                      +++||+++|++|+++|+.+|+++|+||||++||++
T Consensus        22 I~~il~aaGveve~~~~~~~~~~L~gk~i~elI~~   56 (58)
T 3a1y_A           22 LKAVLQAAGVEPEEARIKALVAALEGVNIDEVIEK   56 (58)
T ss_dssp             HHHHHHHTTCCCCHHHHHHHHHHHSSCCHHHHHHH
T ss_pred             HHHHHHHcCCCccHHHHHHHHHHHCCCCHHHHHHc
Confidence            57899999999999999999999999999999975

>3u5i_q A0, L10E, 60S acidic ribosomal protein P0; translation, ribosome, ribosomal R ribosomal protein, STM1; 3.00A {Saccharomyces cerevisiae} PDB: 4b6a_q 3izc_s 3izs_s 3j16_G* 3o5h_M 3jyw_8

Probab=99.00  E-value=4e-11  Score=88.48  Aligned_cols=53  Identities=42%  Similarity=0.603  Sum_probs=0.0

Q ss_pred             CCChHHHHHccccccccccCCCCCCCcchhhhhhhhhhhhcccccCCCCCCCC
Q 034868           28 GKDITELIASGREKLASVPSGGAAAAPAAEAKKEEKVEEKEESDDDMGFSLFD   80 (80)
Q Consensus        28 gk~i~eLI~~g~~~~~~~~~~g~aaa~a~~~~~~~k~eeeEE~ddDmgfgLFd   80 (80)
                      -..|.++|++.+.-.+++|++++++++++++++++++|++||+||||||||||
T Consensus       260 ~~~ik~~la~p~a~a~aa~~a~~~~~~~~~~~~~~~~e~~ee~d~d~gf~lfd  312 (312)
T 3u5i_q          260 IEDLVDRIENPEKYAAAAPAATSAASGDAAPAEEAAAEEEEESDDDMGFGLFD  312 (312)
T ss_dssp             -----------------------------------------------------
T ss_pred             chhHHHHHhChhhhhcccccccccccccccccccccccccccccccCCCCCCC
Confidence            34566777664433222232222112222233445556677889999999998

>2zkr_g 60S acidic ribosomal protein P0; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}

Probab=98.82  E-value=7.9e-11  Score=87.07  Aligned_cols=54  Identities=39%  Similarity=0.533  Sum_probs=21.2

Q ss_pred             CCCChHHHHHcccccccc-ccCCCCCCC--cchhhhhhhhhhhhcccccCCCCCCCC
Q 034868           27 KGKDITELIASGREKLAS-VPSGGAAAA--PAAEAKKEEKVEEKEESDDDMGFSLFD   80 (80)
Q Consensus        27 ~gk~i~eLI~~g~~~~~~-~~~~g~aaa--~a~~~~~~~k~eeeEE~ddDmgfgLFd   80 (80)
                      ++++|.++|.+.+...++ +|+++++++  ++++++++++++++||+||||||||||
T Consensus       261 ea~~vk~~l~~~~~~~~a~a~~a~~~~~~~~~~~~~~~~~~ee~ee~d~d~gf~lfd  317 (317)
T 2zkr_g          261 LAEKVKAFLADPSAFVAAAPVAAATTAAPAAAAAPAKVEAKEESEESDEDMGFGLFD  317 (317)
T ss_dssp             CHHHHHTTTHHHHHHHHHHHHHTTSSHHHHHHHHHHSTTHHHHTSSCC---------
T ss_pred             hhhhHHHHHhccCccccccccccccccccccccccccccccCCccccccccCcCCCC
Confidence            466778888765432211 222211111  112223444556677889999999998

>3j21_k Acidic ribosomal protein P0 homolog; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=88.48  E-value=0.087  Score=38.88  Aligned_cols=12  Identities=8%  Similarity=0.086  Sum_probs=0.0

Q ss_pred             HhCCCChHHHHH
Q 034868           25 EVKGKDITELIA   36 (80)
Q Consensus        25 aL~gk~i~eLI~   36 (80)
                      .+...++.+-|.
T Consensus       282 ~~~~~~~~e~~~  293 (339)
T 3j21_k          282 QLPEDVLDEKTK  293 (339)
T ss_dssp             ------------
T ss_pred             hhccccchhHHh
Confidence            334444444444

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Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

No hit with probability above 80.00