Citrus Sinensis ID: 033355

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-
Protein Sequence
MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAGGAGAAPAAAEAKKEEKVEEKEESDDVRFTYLMPSIFYEPTF
Secondary Structure (PSIPRED)
cHHHHHHHHHHHcccccccHHHHHHHHHHccccccHHHHHHHHHHHccccHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHcccccccHHHHHHHHHHccccccHHHHHHHHHHHccccHHHHHHHcHHHHccccccccEEEEccccccccccccccHHcccccccccccccccccEEEccccEEEcccc
Coil and Loop (DISEMBL)
MKVVAAYLLAVLggntspsadDIKGIlgsvgadceDNRLELLLSEVKGKDITELIASGReklasvpsgggvavaaapsaggagaapaaaeakkeekveekeesddvrftylmpsifyeptf
Flexible Loop (DISEMBL)
MKVVAAYLLAVLggntspsaddIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAGGAGAAPAAaeakkeekveekeesddvrftylmpsifyeptf
Low Complexity Region (SEG)
MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLasvpsgggvavaaapsaggagaapaaaeakkeekveekeesDDVRFTYLMPSIFYEPTF
Disordered region (IsUnstruct)
**VVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIA**************************************************RFTYLMPSIFY****
Disordered Region (DISOPRED)
MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLA*********************************************TYLMPSIFYEPTF
Disordered Region (DISEMBL)
MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAA****************************DVRFTYLMPSIFYEPTF
Disordered Region (DISPRO)
MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAV*******************************DVRFTYLMPSIFYEPTF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAGGAGAAPAAAEAKKEEKVEEKEESDDVRFTYLMPSIFYEPTF
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	121	2.2.26 [Sep-21-2011]
Q9LXM8	111	60S acidic ribosomal prot	yes	no	0.603	0.657	0.767	1e-23
P41099	114	60S acidic ribosomal prot	N/A	no	0.553	0.587	0.761	3e-23
O24415	113	60S acidic ribosomal prot	N/A	no	0.578	0.619	0.728	3e-23
P46252	112	60S acidic ribosomal prot	N/A	no	0.545	0.589	0.696	2e-19
Q9SLF7	115	60S acidic ribosomal prot	no	no	0.537	0.565	0.753	2e-18
O01725	116	60S acidic ribosomal prot	yes	no	0.553	0.577	0.671	6e-18
P51407	115	60S acidic ribosomal prot	no	no	0.537	0.565	0.738	8e-18
Q9LH85	115	60S acidic ribosomal prot	no	no	0.867	0.913	0.490	8e-17
P08094	110	60S acidic ribosomal prot	yes	no	0.570	0.627	0.579	7e-16
Q9HFQ4	111	60S acidic ribosomal prot	N/A	no	0.545	0.594	0.621	2e-15

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

 Score =  108 bits (270), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 56/73 (76%), Positives = 63/73 (86%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MKV AA+LLAVLGGN +PSAD+IK I+G+VGAD +   +ELLL EV GKDI ELIASGRE
Sbjct: 1  MKVAAAFLLAVLGGNANPSADNIKDIIGAVGADVDGESIELLLKEVSGKDIAELIASGRE 60

Query: 61 KLASVPSGGGVAV 73
          KLASVPSGGGVAV
Sbjct: 61 KLASVPSGGGVAV 73

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

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

 Score =  107 bits (266), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 51/67 (76%), Positives = 63/67 (94%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MKV+AA+LLA+LGGNTSP+ +D+K IL SVGAD +D+++ELLLS+VKGKDITELIASGRE
Sbjct: 1  MKVIAAFLLALLGGNTSPTDEDLKSILASVGADADDDKIELLLSQVKGKDITELIASGRE 60

Query: 61 KLASVPS 67
          +LASVPS
Sbjct: 61 RLASVPS 67

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

Parthenium argentatum (taxid: 35935)

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

 Score =  107 bits (266), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 51/70 (72%), Positives = 64/70 (91%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MKV+AAYLLAVLGGNTSP+ADD+K IL SVGA+ ++ +LE LL+E+K KDITE+IA+GRE
Sbjct: 1  MKVIAAYLLAVLGGNTSPTADDVKSILESVGAEADEEKLEFLLTELKDKDITEVIAAGRE 60

Query: 61 KLASVPSGGG 70
          +L+SVPSGGG
Sbjct: 61 RLSSVPSGGG 70

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

Zea mays (taxid: 4577)

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

 Score = 94.4 bits (233), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/66 (69%), Positives = 55/66 (83%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MK VAAYLLAVL GN SPSADD+  IL SVG + ++ ++ELLLS++ GKDITELIA+GRE
Sbjct: 1  MKFVAAYLLAVLAGNASPSADDLTAILESVGCEVDNEKMELLLSQLSGKDITELIAAGRE 60

Query: 61 KLASVP 66
          K ASVP
Sbjct: 61 KFASVP 66

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

Zea mays (taxid: 4577)

>sp|Q9SLF7|RLA22_ARATH 60S acidic ribosomal protein P2-2 OS=Arabidopsis thaliana GN=RPP2B PE=1 SV=1

 Score = 90.9 bits (224), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 49/65 (75%), Positives = 57/65 (87%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MKVVAAYLLAVL G  SP++ DIK ILGSVGA+ ED+++ELLL EVKGKD+ ELIA+GRE
Sbjct: 1  MKVVAAYLLAVLSGKASPTSADIKTILGSVGAETEDSQIELLLKEVKGKDLAELIAAGRE 60

Query: 61 KLASV 65
          KLASV
Sbjct: 61 KLASV 65

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

Arabidopsis thaliana (taxid: 3702)

>sp|O01725|RLA2_BRAFL 60S acidic ribosomal protein P2 OS=Branchiostoma floridae PE=3 SV=1

 Score = 89.4 bits (220), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 45/67 (67%), Positives = 55/67 (82%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          M+ VAAYLLAVLGGN +PSA DIK ILGSVG D ED RL  ++ E+KGKDI E++A+GR 
Sbjct: 1  MRYVAAYLLAVLGGNANPSAGDIKKILGSVGIDAEDERLNKVIGELKGKDIEEVMAAGRG 60

Query: 61 KLASVPS 67
          KL+S+PS
Sbjct: 61 KLSSMPS 67

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

Branchiostoma floridae (taxid: 7739)

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

 Score = 89.0 bits (219), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 48/65 (73%), Positives = 56/65 (86%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MKVVAA+LLAVL G  SP+  DIK ILGSVGA+ ED+++ELLL EVKGKD+ ELIA+GRE
Sbjct: 1  MKVVAAFLLAVLSGKASPTTGDIKDILGSVGAETEDSQIELLLKEVKGKDLAELIAAGRE 60

Query: 61 KLASV 65
          KLASV
Sbjct: 61 KLASV 65

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 = 85.5 bits (210), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 52/106 (49%), Positives = 77/106 (72%), Gaps = 1/106 (0%)

Query: 1   MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
           MKV+AA+LLA LGGN +P+++D+K IL SVGA+ ++ +++LL S +K  D+TELIA+GRE
Sbjct: 1   MKVIAAFLLAKLGGNENPTSNDLKKILESVGAEIDETKIDLLFSLIKDHDVTELIAAGRE 60

Query: 61  KLASVPSGGGVAVAAAPSAGGAGAAPAAAEAKKEEKVEE-KEESDD 105
           K++++ SGG      A   GG  A+ A   A+ ++KVEE K+ES D
Sbjct: 61  KMSALSSGGPAVAMVAGGGGGGAASAAEPVAESKKKVEEVKDESSD 106

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 = 82.4 bits (202), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 40/69 (57%), Positives = 53/69 (76%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MK +AAYLL  +GG  SPSA DI+ +L +VG + E  R+E L++E+ GKDI ELIA+G E
Sbjct: 1  MKYLAAYLLLTVGGKDSPSASDIESVLSTVGIEAESERIETLINELNGKDIDELIAAGNE 60

Query: 61 KLASVPSGG 69
          KLA+VP+GG
Sbjct: 61 KLATVPTGG 69

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

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

>sp|Q9HFQ4|RLA4_CANAX 60S acidic ribosomal protein P2-B OS=Candida albicans GN=RPP2B PE=1 SV=1

 Score = 81.3 bits (199), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 41/66 (62%), Positives = 51/66 (77%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MK +AAYLL V GGNTSPSA DI  +L SVG + E++RL+ LL +++GKD+ ELIA G  
Sbjct: 1  MKYLAAYLLLVQGGNTSPSASDITALLESVGVEAEESRLQALLKDLEGKDLQELIAEGNT 60

Query: 61 KLASVP 66
          KLASVP
Sbjct: 61 KLASVP 66

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

Candida albicans (taxid: 5476)

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	121
255568554	108	60S acidic ribosomal protein P2, putativ	0.603	0.675	0.849	6e-26
448872696	112	60S acidic ribosomal protein P2B [Elaeis	0.578	0.625	0.871	1e-25
224105037	113	predicted protein [Populus trichocarpa]	0.578	0.619	0.857	3e-25
42565379	114	60s acidic ribosomal protein [Hyacinthus	0.570	0.605	0.884	4e-25
388516419	115	unknown [Lotus japonicus]	0.628	0.660	0.763	2e-24
147828208	110	hypothetical protein VITISV_042772 [Viti	0.867	0.954	0.733	2e-24
24473796	113	60s acidic ribosomal protein [Prunus dul	0.553	0.592	0.850	5e-24
225440938	114	PREDICTED: 60S acidic ribosomal protein	0.553	0.587	0.850	1e-23
47026878	114	acidic ribosomal protein [Hyacinthus ori	0.570	0.605	0.855	1e-23
77416939	162	unknown [Solanum tuberosum]	0.677	0.506	0.670	2e-23

>gi|255568554|ref|XP_002525251.1| 60S acidic ribosomal protein P2, putative [Ricinus communis] gi|223535548|gb|EEF37217.1| 60S acidic ribosomal protein P2, putative [Ricinus communis]

 Score =  121 bits (303), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 62/73 (84%), Positives = 69/73 (94%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MKVVAAYLLAVLG NTSPSAD+IK IL SVGADC+ +++ELLLS+V+GKDITELIASGRE
Sbjct: 1  MKVVAAYLLAVLGVNTSPSADNIKDILNSVGADCDGDKIELLLSQVEGKDITELIASGRE 60

Query: 61 KLASVPSGGGVAV 73
          KLASVPSGGGVAV
Sbjct: 61 KLASVPSGGGVAV 73

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|448872696|gb|AGE46033.1| 60S acidic ribosomal protein P2B [Elaeis guineensis]

 Score =  120 bits (301), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 61/70 (87%), Positives = 66/70 (94%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MKVVAAYLLAVLGGNT PSADD+K ILGSVGA+ +D+R+ELLLSEVKGKDITELIASGRE
Sbjct: 1  MKVVAAYLLAVLGGNTCPSADDLKDILGSVGAEADDDRIELLLSEVKGKDITELIASGRE 60

Query: 61 KLASVPSGGG 70
          K ASVPSGGG
Sbjct: 61 KFASVPSGGG 70

Source: Elaeis guineensis

Species: Elaeis guineensis

Genus: Elaeis

Family: Arecaceae

Order: Arecales

Class: Liliopsida

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 =  119 bits (297), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 60/70 (85%), Positives = 66/70 (94%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MKVVAAYLLAVLGGNT P+A+D+K ILGSVGAD +D+R+ELLLS VKGKDITELIASGRE
Sbjct: 1  MKVVAAYLLAVLGGNTCPTAEDLKNILGSVGADADDDRIELLLSSVKGKDITELIASGRE 60

Query: 61 KLASVPSGGG 70
          KLASVPSGGG
Sbjct: 61 KLASVPSGGG 70

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42565379|gb|AAS20966.1| 60s acidic ribosomal protein [Hyacinthus orientalis]

 Score =  118 bits (296), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 61/69 (88%), Positives = 65/69 (94%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MKVVAAYLLAVLGGNT+PSA+ IK ILGSVGAD ED+R+ELLLSEVKGKDITELIASGRE
Sbjct: 1  MKVVAAYLLAVLGGNTTPSAEVIKDILGSVGADAEDDRIELLLSEVKGKDITELIASGRE 60

Query: 61 KLASVPSGG 69
          K ASVPSGG
Sbjct: 61 KFASVPSGG 69

Source: Hyacinthus orientalis

Species: Hyacinthus orientalis

Genus: Hyacinthus

Family: Hyacinthaceae

Order: Asparagales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388516419|gb|AFK46271.1| unknown [Lotus japonicus]

 Score =  116 bits (290), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 58/76 (76%), Positives = 67/76 (88%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MKV+AAYLLAVLGGNT+PSADD+K IL SVGAD +D +L  LLSEVKGKD+ E+IASGRE
Sbjct: 1  MKVIAAYLLAVLGGNTAPSADDLKSILSSVGADADDEKLSFLLSEVKGKDLAEVIASGRE 60

Query: 61 KLASVPSGGGVAVAAA 76
          KL+SVP GGGVAVA +
Sbjct: 61 KLSSVPCGGGVAVAVS 76

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147828208|emb|CAN75514.1| hypothetical protein VITISV_042772 [Vitis vinifera]

 Score =  116 bits (290), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 80/109 (73%), Positives = 88/109 (80%), Gaps = 4/109 (3%)

Query: 1   MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
           MKV+AAYLLAVLGGN S  ADD+K ILGSVGA  +D+ +ELLL EVKG  ITELIASGRE
Sbjct: 1   MKVMAAYLLAVLGGNVSLCADDLKSILGSVGAGADDDGIELLLFEVKGIGITELIASGRE 60

Query: 61  KLASVPSGGGVAVAAAPSAGGAGAAPAAAEAKKEEKVEEKEESD-DVRF 108
           KLA VPSGGGVAVAA+    G GAAPAA E +KEEKVEEKE SD D+ F
Sbjct: 61  KLAXVPSGGGVAVAASD---GGGAAPAATEPRKEEKVEEKEGSDRDMGF 106

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|24473796|gb|AAL91663.1| 60s acidic ribosomal protein [Prunus dulcis] gi|111013714|gb|ABH03379.1| 60S acidic ribosomal protein [Prunus dulcis]

 Score =  114 bits (286), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 57/67 (85%), Positives = 65/67 (97%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MKVVAAYLLAVLGGNT+PSA+D+K ILGSVGA+ +D+R++LLLSEVKGKDITELIASGRE
Sbjct: 1  MKVVAAYLLAVLGGNTTPSAEDLKDILGSVGAETDDDRIQLLLSEVKGKDITELIASGRE 60

Query: 61 KLASVPS 67
          KLASVPS
Sbjct: 61 KLASVPS 67

Source: Prunus dulcis

Species: Prunus dulcis

Genus: Prunus

Family: Rosaceae

Order: Rosales

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 =  113 bits (283), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 57/67 (85%), Positives = 64/67 (95%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MKV+AAYLLAVLGGNT PSA+D+K ILGSVGA+ +D+R+ELLLSEVKGKDITELIASGRE
Sbjct: 1  MKVIAAYLLAVLGGNTCPSANDLKDILGSVGAEADDDRIELLLSEVKGKDITELIASGRE 60

Query: 61 KLASVPS 67
          KLASVPS
Sbjct: 61 KLASVPS 67

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|47026878|gb|AAT08664.1| acidic ribosomal protein [Hyacinthus orientalis]

 Score =  113 bits (283), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 59/69 (85%), Positives = 64/69 (92%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MKVVAAYLLAVLGGNT+PSA+ IK ILGSVGA+ ED+R+ LLLSEVKGKDITELIASGRE
Sbjct: 1  MKVVAAYLLAVLGGNTTPSAEVIKDILGSVGAEAEDDRILLLLSEVKGKDITELIASGRE 60

Query: 61 KLASVPSGG 69
          K ASVPSGG
Sbjct: 61 KFASVPSGG 69

Source: Hyacinthus orientalis

Species: Hyacinthus orientalis

Genus: Hyacinthus

Family: Hyacinthaceae

Order: Asparagales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|77416939|gb|ABA81865.1| unknown [Solanum tuberosum]

 Score =  113 bits (282), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 55/82 (67%), Positives = 67/82 (81%)

Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MKV+AAYLLAVLGGNT PS  D+K IL SVGA+ +D+R++LLLS+V GKDITELIA+GRE
Sbjct: 1  MKVIAAYLLAVLGGNTCPSEKDLKKILASVGAEADDDRIQLLLSQVDGKDITELIAAGRE 60

Query: 61 KLASVPSGGGVAVAAAPSAGGA 82
          KLASVP+GGG A  +  +   A
Sbjct: 61 KLASVPAGGGAACCSCCTWWCA 82

Source: Solanum tuberosum

Species: Solanum tuberosum

Genus: Solanum

Family: Solanaceae

Order: Solanales

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	121
TAIR|locus:2042062	115	AT2G27710 [Arabidopsis thalian	0.512	0.539	0.741	1.4e-18
TAIR|locus:2075993	111	AT3G44590 [Arabidopsis thalian	0.512	0.558	0.725	2.8e-18
ZFIN|ZDB-GENE-031018-2	115	rplp2 "ribosomal protein, larg	0.512	0.539	0.629	2e-15
ASPGD|ASPL0000000414	109	AN5996 [Emericella nidulans (t	0.512	0.568	0.629	6.9e-15
TAIR|locus:2098653	115	AT3G28500 [Arabidopsis thalian	0.512	0.539	0.564	1.4e-14
CGD|CAL0003308	111	RPP2B [Candida albicans (taxid	0.512	0.558	0.596	2.3e-14
UNIPROTKB|Q5ANH5	111	RPP2B "Cytosolic ribosomal aci	0.512	0.558	0.596	2.3e-14
POMBASE|SPBP8B7.06	110	rpp201 "60S acidic ribosomal p	0.512	0.563	0.564	6.2e-14
UNIPROTKB|F1RYZ0	115	RPLP2 "60S acidic ribosomal pr	0.512	0.539	0.596	7.9e-14
TAIR|locus:2042052	130	AT2G27720 [Arabidopsis thalian	0.512	0.476	0.571	7.9e-14

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

 Score = 224 (83.9 bits), Expect = 1.4e-18, P = 1.4e-18
 Identities = 46/62 (74%), Positives = 54/62 (87%)

Query:     1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
             MKVVAAYLLAVL G  SP++ DIK ILGSVGA+ ED+++ELLL EVKGKD+ ELIA+GRE
Sbjct:     1 MKVVAAYLLAVLSGKASPTSADIKTILGSVGAETEDSQIELLLKEVKGKDLAELIAAGRE 60

Query:    61 KL 62
             KL
Sbjct:    61 KL 62

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:2075993 AT3G44590 [Arabidopsis thaliana (taxid:3702)]

 Score = 221 (82.9 bits), Expect = 2.8e-18, P = 2.8e-18
 Identities = 45/62 (72%), Positives = 52/62 (83%)

Query:     1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
             MKV AA+LLAVLGGN +PSAD+IK I+G+VGAD +   +ELLL EV GKDI ELIASGRE
Sbjct:     1 MKVAAAFLLAVLGGNANPSADNIKDIIGAVGADVDGESIELLLKEVSGKDIAELIASGRE 60

Query:    61 KL 62
             KL
Sbjct:    61 KL 62

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

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

 Score = 194 (73.4 bits), Expect = 2.0e-15, P = 2.0e-15
 Identities = 39/62 (62%), Positives = 49/62 (79%)

Query:     1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
             M+ VAAYLLAVLGGNT+PSA DIK ILGSVG + +D RL  ++SE+ GKDI E++ +G  
Sbjct:     1 MRYVAAYLLAVLGGNTNPSAKDIKNILGSVGIEADDERLNKVVSELNGKDINEVMNAGLS 60

Query:    61 KL 62
             KL
Sbjct:    61 KL 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

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

 Score = 189 (71.6 bits), Expect = 6.9e-15, P = 6.9e-15
 Identities = 39/62 (62%), Positives = 46/62 (74%)

Query:     1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
             MK +AAYLL  L GN SPSA DIK +L SVG D +D RLE L++E++GKDI ELIA G  
Sbjct:     1 MKHLAAYLLLALAGNESPSASDIKEVLSSVGVDADDERLEKLIAELQGKDINELIAEGTT 60

Query:    61 KL 62
             KL
Sbjct:    61 KL 62

GO:0005829 "cytosol" evidence=IEA

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

GO:0005840 "ribosome" evidence=IEA

GO:0006414 "translational elongation" evidence=IEA

TAIR|locus:2098653 AT3G28500 [Arabidopsis thaliana (taxid:3702)]

 Score = 186 (70.5 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 35/62 (56%), Positives = 52/62 (83%)

Query:     1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
             MKV+AA+LLA LGGN +P+++D+K IL SVGA+ ++ +++LL S +K  D+TELIA+GRE
Sbjct:     1 MKVIAAFLLAKLGGNENPTSNDLKKILESVGAEIDETKIDLLFSLIKDHDVTELIAAGRE 60

Query:    61 KL 62
             K+
Sbjct:    61 KM 62

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:0022626 "cytosolic ribosome" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

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

 Score = 184 (69.8 bits), Expect = 2.3e-14, P = 2.3e-14
 Identities = 37/62 (59%), Positives = 47/62 (75%)

Query:     1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
             MK +AAYLL V GGNTSPSA DI  +L SVG + E++RL+ LL +++GKD+ ELIA G  
Sbjct:     1 MKYLAAYLLLVQGGNTSPSASDITALLESVGVEAEESRLQALLKDLEGKDLQELIAEGNT 60

Query:    61 KL 62
             KL
Sbjct:    61 KL 62

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

GO:0005840 "ribosome" evidence=IDA

GO:0006412 "translation" evidence=ISS

GO:0005829 "cytosol" evidence=IEA

UNIPROTKB|Q5ANH5 RPP2B "Cytosolic ribosomal acidic protein P2B" [Candida albicans SC5314 (taxid:237561)]

 Score = 184 (69.8 bits), Expect = 2.3e-14, P = 2.3e-14
 Identities = 37/62 (59%), Positives = 47/62 (75%)

Query:     1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
             MK +AAYLL V GGNTSPSA DI  +L SVG + E++RL+ LL +++GKD+ ELIA G  
Sbjct:     1 MKYLAAYLLLVQGGNTSPSASDITALLESVGVEAEESRLQALLKDLEGKDLQELIAEGNT 60

Query:    61 KL 62
             KL
Sbjct:    61 KL 62

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

GO:0005840 "ribosome" evidence=IDA

GO:0006412 "translation" evidence=ISS

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

 Score = 180 (68.4 bits), Expect = 6.2e-14, P = 6.2e-14
 Identities = 35/62 (56%), Positives = 46/62 (74%)

Query:     1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
             MK +AAYLL  +GG  SPSA DI+ +L +VG + E  R+E L++E+ GKDI ELIA+G E
Sbjct:     1 MKYLAAYLLLTVGGKDSPSASDIESVLSTVGIEAESERIETLINELNGKDIDELIAAGNE 60

Query:    61 KL 62
             KL
Sbjct:    61 KL 62

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

UNIPROTKB|F1RYZ0 RPLP2 "60S acidic ribosomal protein P2" [Sus scrofa (taxid:9823)]

 Score = 179 (68.1 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 37/62 (59%), Positives = 48/62 (77%)

Query:     1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
             M+ VA+YLLA LGGNTSPSA DIK IL SVG + +D+RL  ++SE+ GK+I ++IA G  
Sbjct:     1 MRYVASYLLAALGGNTSPSAKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIG 60

Query:    61 KL 62
             KL
Sbjct:    61 KL 62

GO:0006414 "translational elongation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

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

 Score = 179 (68.1 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 44/77 (57%), Positives = 52/77 (67%)

Query:     1 MKVVAAYLLAVLGGNTSPSADDIKGILGS---------------VGADCEDNRLELLLSE 45
             MKVVAA+LLAVL G  SP+  DIK ILGS                GA+ ED+++ELLL E
Sbjct:     1 MKVVAAFLLAVLSGKASPTTGDIKDILGSGIMVLVLDCVVIGDCFGAETEDSQIELLLKE 60

Query:    46 VKGKDITELIASGREKL 62
             VKGKD+ ELIA+GREKL
Sbjct:    61 VKGKDLAELIAAGREKL 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

---

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)
Q9LXM8	RLA24_ARATH	No assigned EC number	0.7671	0.6033	0.6576	yes	no
Q96UQ7	RLA2_RHOGU	No assigned EC number	0.5185	0.8760	0.9636	N/A	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	121
PLN00138	113	PLN00138, PLN00138, large subunit ribosomal protei	4e-46
cd05833	109	cd05833, Ribosomal_P2, Ribosomal protein P2	2e-39
PTZ00373	112	PTZ00373, PTZ00373, 60S Acidic ribosomal protein P	3e-25
pfam00428	88	pfam00428, Ribosomal_60s, 60s Acidic ribosomal pro	5e-15
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	1e-14
cd04411	105	cd04411, Ribosomal_P1_P2_L12p, Ribosomal protein P	1e-12
cd05831	103	cd05831, Ribosomal_P1, Ribosomal protein P1	7e-09
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	3e-06
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	3e-05
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	5e-05
PTZ00135	310	PTZ00135, PTZ00135, 60S acidic ribosomal protein P	6e-04

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

 Score =  144 bits (364), Expect = 4e-46
 Identities = 89/105 (84%), Positives = 95/105 (90%)

Query: 1   MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
           MKVVAAYLLAVLGGNT PSA+D+K ILGSVGAD +D+R+ELLLSEVKGKDITELIASGRE
Sbjct: 1   MKVVAAYLLAVLGGNTCPSAEDLKDILGSVGADADDDRIELLLSEVKGKDITELIASGRE 60

Query: 61  KLASVPSGGGVAVAAAPSAGGAGAAPAAAEAKKEEKVEEKEESDD 105
           KLASVPSGGGVAVAAA +    GAA  AAEAKKEEKVEEKEESDD
Sbjct: 61  KLASVPSGGGVAVAAAAAPAAGGAAAPAAEAKKEEKVEEKEESDD 105

Length = 113

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

 Score =  127 bits (321), Expect = 2e-39
 Identities = 67/106 (63%), Positives = 79/106 (74%), Gaps = 5/106 (4%)

Query: 1   MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
           MK VAAYLLAVLGGN SPSA D+K ILGSVG + +D +L  ++SE++GKD+ ELIA+G+E
Sbjct: 1   MKYVAAYLLAVLGGNASPSAADVKKILGSVGVEVDDEKLNKVISELEGKDVEELIAAGKE 60

Query: 61  KLASVPSGGGVAVAAAPSAGGAGAAPAAAEAKKEEKVEEKEESDDV 106
           KLASVP+G G A  AA     A AA AAA AKKEEK EE EE  D 
Sbjct: 61  KLASVPAGAGGAAPAA-----AAAAAAAAAAKKEEKKEESEEESDD 101

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

 Score = 91.5 bits (227), Expect = 3e-25
 Identities = 54/109 (49%), Positives = 75/109 (68%), Gaps = 2/109 (1%)

Query: 1   MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
           MK VAAYL+ VLGGN +P+  ++K +L +V AD ED+ L+     ++GK   ELIA+G +
Sbjct: 3   MKYVAAYLMCVLGGNENPTKKEVKNVLSAVNADVEDDVLDNFFKSLEGKTPHELIAAGMK 62

Query: 61  KLASVPSGGGVAVAAAPSAGGAGAAPAAAEAKKEEKVEEKEESDDVRFT 109
           KL ++  GGGVA AAAP+AG A A   A   K+E+K EE+EE DD+ F+
Sbjct: 63  KLQNI--GGGVAAAAAPAAGAATAGAKAEAKKEEKKEEEEEEEDDLGFS 109

Length = 112

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

 Score = 64.6 bits (158), Expect = 5e-15
 Identities = 40/89 (44%), Positives = 57/89 (64%), Gaps = 8/89 (8%)

Query: 17  SPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAA 76
            P+A DIK +L + G + E  RLELL+  ++GK+I ELIA+G  KL+        A AAA
Sbjct: 1   EPTAADIKHVLKAAGKEVEAERLELLVKFLEGKNIKELIANGSAKLS--------AAAAA 52

Query: 77  PSAGGAGAAPAAAEAKKEEKVEEKEESDD 105
            +A  A AA AAA  +++++ EE+EE DD
Sbjct: 53  AAAAAAAAAAAAAAEEEKKEEEEEEEEDD 81

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

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

 Score = 64.3 bits (157), Expect = 1e-14
 Identities = 35/104 (33%), Positives = 57/104 (54%), Gaps = 1/104 (0%)

Query: 1   MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
           M+ + AYLL  L G    + D++K +L + G + E+ R + L++ ++G DI E+I +  E
Sbjct: 1   MEYIYAYLLLHLAGK-EITEDNLKSVLEAAGVEVEEARAKALVAALEGVDIDEVIKNAAE 59

Query: 61  KLASVPSGGGVAVAAAPSAGGAGAAPAAAEAKKEEKVEEKEESD 104
             A+  + G  A AAA +   A A  A  E K+EE  EE ++  
Sbjct: 60  APAAAAAAGAAAAAAAGAEAAAEADEAEEEEKEEEAEEESDDDM 103

Length = 109

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

 Score = 58.8 bits (142), Expect = 1e-12
 Identities = 42/104 (40%), Positives = 59/104 (56%), Gaps = 3/104 (2%)

Query: 1   MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
           M+ VAAYLL   GG    + D IK +L + GA+ E  R++L LS + GK+I E+I+ G+E
Sbjct: 1   MEYVAAYLLLHKGGKE-LTEDKIKELLSAAGAEIEPERVKLFLSALNGKNIDEVISKGKE 59

Query: 61  KLASVPSGGGVAVAAAPSAGGAGAAPAAAEAKKEEKVEEKEESD 104
            +         A  AA +A  A  A  A EAK+EE+ EE E+  
Sbjct: 60  LM--SSQAAAAAAPAATAAATAEPAEKAEEAKEEEEEEEDEDFG 101

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|100109 cd05831, Ribosomal_P1, Ribosomal protein P1

 Score = 49.2 bits (118), Expect = 7e-09
 Identities = 39/101 (38%), Positives = 53/101 (52%), Gaps = 12/101 (11%)

Query: 5   AAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLAS 64
           AA +L         +AD+I  +L + G + E     L    ++GKDI +L+++       
Sbjct: 7   AALILH--DDGIEITADNINALLKAAGVNVEPYWPGLFAKALEGKDIKDLLSNV------ 58

Query: 65  VPSGGGVAVAAAPSAGGAGAAPAAAEAKKEEKVEEKEESDD 105
               GG    AAP+A  A AA AAAEAKKEEK EE+EE  D
Sbjct: 59  ----GGGGGGAAPAAAAAAAAAAAAEAKKEEKKEEEEEESD 95

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

 Score = 42.6 bits (101), Expect = 3e-06
 Identities = 29/87 (33%), Positives = 52/87 (59%), Gaps = 10/87 (11%)

Query: 19  SADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPS 78
           + D++K +L + G + ++ R++ L++ ++  +I E I    +K A+ P      VAAA +
Sbjct: 18  NEDNLKKVLEAAGVEVDEARVKALVAALEDVNIEEAI----KKAAAAP------VAAAAA 67

Query: 79  AGGAGAAPAAAEAKKEEKVEEKEESDD 105
           A  A AA AA E K+EE+ EE++E  +
Sbjct: 68  AAAAAAAAAAEEKKEEEEEEEEKEESE 94

Length = 106

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

 Score = 39.6 bits (93), Expect = 3e-05
 Identities = 26/85 (30%), Positives = 49/85 (57%), Gaps = 8/85 (9%)

Query: 21  DDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG 80
           +++K +L + G + ++ R++ L++ ++G +I E I    +K A+ P    VA AAA +A 
Sbjct: 20  ENLKAVLEAAGVEVDEARVKALVAALEGVNIEEAI----KKAAAAP----VAAAAAAAAA 71

Query: 81  GAGAAPAAAEAKKEEKVEEKEESDD 105
            A A     E ++EE+ EE+ E + 
Sbjct: 72  AAAAEEEEEEEEEEEEEEEESEEEA 96

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 = 39.0 bits (91), Expect = 5e-05
 Identities = 25/86 (29%), Positives = 47/86 (54%), Gaps = 10/86 (11%)

Query: 19  SADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPS 78
           + +++K +L + G + ++ R++ L++ ++  +I E I                A AAAP+
Sbjct: 18  NEENLKKVLEAAGIEVDEARVKALVAALEEVNIDEAIKKA----------AVAAAAAAPA 67

Query: 79  AGGAGAAPAAAEAKKEEKVEEKEESD 104
           A  A AA   AE K+EEK +E+E+ +
Sbjct: 68  AAAAAAAEEKAEEKEEEKKKEEEKEE 93

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

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 17/38 (44%), Positives = 22/38 (57%)

Query: 71  VAVAAAPSAGGAGAAPAAAEAKKEEKVEEKEESDDVRF 108
           +A  +A +A  A AA AAA A      EE+EE DD+ F
Sbjct: 269 LANPSAAAAAAAAAAAAAAAAAAAPAEEEEEEEDDMGF 306

Length = 310

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	121
PTZ00373	112	60S Acidic ribosomal protein P2; Provisional	100.0
PLN00138	113	large subunit ribosomal protein LP2; Provisional	100.0
KOG3449	112	consensus 60S acidic ribosomal protein P2 [Transla	100.0
cd05833	109	Ribosomal_P2 Ribosomal protein P2. This subfamily	100.0
cd04411	105	Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and	100.0
COG2058	109	RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Tr	99.96
PRK06402	106	rpl12p 50S ribosomal protein L12P; Reviewed	99.95
cd05831	103	Ribosomal_P1 Ribosomal protein P1. This subfamily	99.94
cd05832	106	Ribosomal_L12p Ribosomal protein L12p. This subfam	99.91
TIGR03685	105	L21P_arch 50S ribosomal protein L12P. This model r	99.91
KOG1762	114	consensus 60s acidic ribosomal protein P1 [Transla	99.9
PF00428	88	Ribosomal_60s: 60s Acidic ribosomal protein; Inter	99.84
PTZ00135	310	60S acidic ribosomal protein P0; Provisional	98.56
PTZ00240	323	60S ribosomal protein P0; Provisional	97.38
PRK06402	106	rpl12p 50S ribosomal protein L12P; Reviewed	96.4
cd04411	105	Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and	96.34
PRK04019	330	rplP0 acidic ribosomal protein P0; Validated	96.34
KOG3449	112	consensus 60S acidic ribosomal protein P2 [Transla	94.69
PTZ00373	112	60S Acidic ribosomal protein P2; Provisional	94.68
COG2058	109	RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Tr	93.11
cd05832	106	Ribosomal_L12p Ribosomal protein L12p. This subfam	93.11
TIGR03685	105	L21P_arch 50S ribosomal protein L12P. This model r	92.06
cd05833	109	Ribosomal_P2 Ribosomal protein P2. This subfamily	91.63
cd05831	103	Ribosomal_P1 Ribosomal protein P1. This subfamily	91.25
PLN00138	113	large subunit ribosomal protein LP2; Provisional	87.18

>PTZ00373 60S Acidic ribosomal protein P2; Provisional

Probab=100.00  E-value=4.6e-41  Score=241.23  Aligned_cols=108  Identities=53%  Similarity=0.799  Sum_probs=84.4

Q ss_pred             ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccCCCCC
Q 033355            1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG   80 (121)
Q Consensus         1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaaaa~a   80 (121)
                      ||||+||||++|+||.+||++||++||+++||+||++|+++|++.|+||||++||++|++||+|+  ||+++++++++++
T Consensus         3 MkyvaAYlL~~lgG~~~pTaddI~kIL~AaGveVd~~~~~l~~~~L~GKdI~ELIa~G~~kl~sv--gg~~~aa~a~a~~   80 (112)
T PTZ00373          3 MKYVAAYLMCVLGGNENPTKKEVKNVLSAVNADVEDDVLDNFFKSLEGKTPHELIAAGMKKLQNI--GGGVAAAAAPAAG   80 (112)
T ss_pred             hHHHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHHHHhcc--cCccccccccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999  3332211111111


Q ss_pred             CCCCCcchhhhhhhhhhhccccccccc-cccc
Q 033355           81 GAGAAPAAAEAKKEEKVEEKEESDDVR-FTYL  111 (121)
Q Consensus        81 ~~~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~  111 (121)
                      ++++++++ ++++++|+||+||||||| ||||
T Consensus        81 ~~~~~~~~-~~~~e~k~ee~ee~ddDmgf~LF  111 (112)
T PTZ00373         81 AATAGAKA-EAKKEEKKEEEEEEEDDLGFSLF  111 (112)
T ss_pred             ccccccch-hhhhhhccccccccccccccccc
Confidence            11122222 234444556667888899 9998

>PLN00138 large subunit ribosomal protein LP2; Provisional

Probab=100.00  E-value=2.1e-40  Score=238.08  Aligned_cols=110  Identities=82%  Similarity=1.105  Sum_probs=87.0

Q ss_pred             ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccCCCCC
Q 033355            1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG   80 (121)
Q Consensus         1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaaaa~a   80 (121)
                      ||||+||||++|+||.+||++||++||+++|++||++|+++|++.|+||||++||.+|++||+++|+||+++++++++++
T Consensus         1 mkyvaAyll~~l~g~~~pta~dI~~IL~AaGvevd~~~~~~f~~~L~gK~i~eLIa~G~~kl~sv~~gg~aa~a~a~a~~   80 (113)
T PLN00138          1 MKVVAAYLLAVLGGNTCPSAEDLKDILGSVGADADDDRIELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAAAPA   80 (113)
T ss_pred             ChHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCcccHHHHHHHHHHHcCCCHHHHHHhchhccccCCCCCccccccccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999987764432221111


Q ss_pred             C-CCCCcchhhhhhhhhhhccccccccc-cccc
Q 033355           81 G-AGAAPAAAEAKKEEKVEEKEESDDVR-FTYL  111 (121)
Q Consensus        81 ~-~~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~  111 (121)
                      + +++++++ ++++++|+|++||+|||| ||||
T Consensus        81 ~~~~~~~~~-~~~~e~k~e~eeE~ddDmGfgLF  112 (113)
T PLN00138         81 AGGAAAPAA-EAKKEEKVEEKEESDDDMGFSLF  112 (113)
T ss_pred             ccccccccc-chhhhhhcccccccccccccccc
Confidence            1 1111111 223344456667788888 9998

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

Probab=100.00  E-value=1.8e-39  Score=231.51  Aligned_cols=109  Identities=74%  Similarity=1.015  Sum_probs=89.6

Q ss_pred             ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccCC-CC
Q 033355            1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAP-SA   79 (121)
Q Consensus         1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaaa-a~   79 (121)
                      ||||+||||++|+||.+|++.||++||+++|+++|++|+++|++.|+||||+|||++|.+||+|||+||++++++++ ++
T Consensus         1 MkyvaAYLL~~lgGn~~psa~DikkIl~sVG~E~d~e~i~~visel~GK~i~ElIA~G~eklAsvpsGGa~~aaa~~aag   80 (112)
T KOG3449|consen    1 MKYVAAYLLAVLGGNASPSASDIKKILESVGAEIDDERINLVLSELKGKDIEELIAAGREKLASVPSGGAVAAAAAPAAG   80 (112)
T ss_pred             ChHHHHHHHHHhcCCCCCCHHHHHHHHHHhCcccCHHHHHHHHHHhcCCCHHHHHHHhHHHHhcCCCCCccccccCcCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999885432221 21


Q ss_pred             CCCCCCcchhhhhhhhhhhccccccccc-cccc
Q 033355           80 GGAGAAPAAAEAKKEEKVEEKEESDDVR-FTYL  111 (121)
Q Consensus        80 a~~~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~  111 (121)
                      +++++++.  ..++++|+||+||||||| |+||
T Consensus        81 gaa~aa~~--a~~~e~keEe~eesddDmgf~lF  111 (112)
T KOG3449|consen   81 GAAGAAPA--AAKEEEKEEEKEESDDDMGFGLF  111 (112)
T ss_pred             CCccCCcc--chhhhhhhhhccccccccccccc
Confidence            11212221  224455666668999999 9987

>cd05833 Ribosomal_P2 Ribosomal protein P2

Probab=100.00  E-value=3.3e-39  Score=230.53  Aligned_cols=107  Identities=61%  Similarity=0.864  Sum_probs=84.0

Q ss_pred             ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccCCCCC
Q 033355            1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG   80 (121)
Q Consensus         1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaaaa~a   80 (121)
                      ||||+||||++++||.+||++||++||+++||+||++|+++|++.|+||||++||++|++||+++|++++++++++++  
T Consensus         1 MkyvaAylL~~l~g~~~pTa~dI~~IL~AaGveVe~~~~~lf~~~L~GKdi~eLIa~g~~kl~s~~~~~~~aa~a~~~--   78 (109)
T cd05833           1 MKYVAAYLLAVLGGNASPSAADVKKILGSVGVEVDDEKLNKVISELEGKDVEELIAAGKEKLASVPAGAGGAAPAAAA--   78 (109)
T ss_pred             CHHHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHhhhcCCCcccccccccccc--
Confidence            999999999999999999999999999999999999999999999999999999999999999987543222111111  


Q ss_pred             CCCCCcchhhhhhhhhhhccccccccc-cccc
Q 033355           81 GAGAAPAAAEAKKEEKVEEKEESDDVR-FTYL  111 (121)
Q Consensus        81 ~~~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~  111 (121)
                       ++++++. ++++++|+|++||+|||| ||||
T Consensus        79 -~a~aa~~-~~~e~kkee~eee~ddDmGf~LF  108 (109)
T cd05833          79 -AAAAAAA-AKKEEKKEESEEESDDDMGFGLF  108 (109)
T ss_pred             -ccccccc-hhhhhhccCCccccccccCCCCC
Confidence             1111111 234444555666678899 9998

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

>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p

Probab=100.00  E-value=4.9e-37  Score=218.08  Aligned_cols=104  Identities=39%  Similarity=0.587  Sum_probs=84.6

Q ss_pred             ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccCCCCC
Q 033355            1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG   80 (121)
Q Consensus         1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaaaa~a   80 (121)
                      |+|++|||||+++|+. ||++||++||+++|++|+++|+++|++.|+||||++||++|+.||+++|+||++++ + ++ +
T Consensus         1 m~~v~A~Lll~~~g~~-~ta~~I~~IL~aaGveVe~~~~~~~~~aLaGk~V~eli~~g~~kl~~~~~~~~a~~-~-a~-~   76 (105)
T cd04411           1 MEYVAAYLLLHKGGKE-LTEDKIKELLSAAGAEIEPERVKLFLSALNGKNIDEVISKGKELMSSQAAAAAAPA-A-TA-A   76 (105)
T ss_pred             CHHHHHHHHHHhcCCC-CCHHHHHHHHHHcCCCcCHHHHHHHHHHHcCCCHHHHHHHHHhhccCCCCcccccc-c-cc-c
Confidence            9999999999999987 99999999999999999999999999999999999999999999999998765321 1 11 1


Q ss_pred             CCCCCcchhhhhhhhhhhccccccccc-cccc
Q 033355           81 GAGAAPAAAEAKKEEKVEEKEESDDVR-FTYL  111 (121)
Q Consensus        81 ~~~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~  111 (121)
                       ++++ ++ ++++++|+||+||||||| ||||
T Consensus        77 -~~~~-~~-~~~~e~k~ee~eE~dddmgf~LF  105 (105)
T cd04411          77 -ATAE-PA-EKAEEAKEEEEEEEDEDFGFGLF  105 (105)
T ss_pred             -cccc-ch-hhhhhhhcccccccccccCcccC
Confidence             1111 11 233444556667888899 9998

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

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

Probab=99.96  E-value=7.9e-30  Score=181.67  Aligned_cols=107  Identities=35%  Similarity=0.522  Sum_probs=81.5

Q ss_pred             ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccCCCCC
Q 033355            1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG   80 (121)
Q Consensus         1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaaaa~a   80 (121)
                      |+||++||||+++|+ +||++||++||+++||+||+.|++.|++.|+||||+++|.++..++..++.+++++++++++  
T Consensus         1 MeYi~a~llL~~agk-ei~e~~l~~vl~aaGveve~~r~k~lvaaLeg~~idE~i~~~~~~~~a~a~a~aaaa~~A~~--   77 (109)
T COG2058           1 MEYIYAYLLLHLAGK-EITEDNLKSVLEAAGVEVEEARAKALVAALEGVDIDEVIKNAAEAPAAAAAAGAAAAAAAGA--   77 (109)
T ss_pred             ChHHHHHHHHHHccC-cCCHHHHHHHHHHcCCCccHHHHHHHHHHhcCCCHHHHHHHhcccccccCCccccccccccc--
Confidence            999999999999998 69999999999999999999999999999999999999999988777776554433211111  


Q ss_pred             CCCCCcchhhhhhhhhhhccccccccc-cccc
Q 033355           81 GAGAAPAAAEAKKEEKVEEKEESDDVR-FTYL  111 (121)
Q Consensus        81 ~~~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~  111 (121)
                       ..+.++.++++++++++.+||+|+|| |+||
T Consensus        78 -~~a~~~~ea~eEe~eEe~~EE~~~~~lf~LF  108 (109)
T COG2058          78 -EAAAEADEAEEEEKEEEAEEESDDDMLFGLF  108 (109)
T ss_pred             -ccccchhhHHHHHhhhchhhcccccchhhcc
Confidence             11111111223334455667888888 9998

>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed

Probab=99.95  E-value=1.7e-27  Score=169.57  Aligned_cols=55  Identities=25%  Similarity=0.457  Sum_probs=54.1

Q ss_pred             ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHH
Q 033355            1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIA   56 (121)
Q Consensus         1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~   56 (121)
                      |||++|||||+++|+ +||++||++||+++|++||++|+++|++.|+||||++||.
T Consensus         1 M~yiyAaLLL~~~g~-~it~e~I~~IL~AAGveVee~~~k~~v~aL~GkdIeElI~   55 (106)
T PRK06402          1 MEYIYAALLLHSAGK-EINEDNLKKVLEAAGVEVDEARVKALVAALEDVNIEEAIK   55 (106)
T ss_pred             CHHHHHHHHHHhcCC-CCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHH
Confidence            999999999999998 7999999999999999999999999999999999999997

>cd05831 Ribosomal_P1 Ribosomal protein P1

Probab=99.94  E-value=5e-27  Score=166.15  Aligned_cols=99  Identities=37%  Similarity=0.484  Sum_probs=66.9

Q ss_pred             HHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccCCCCCCC
Q 033355            3 VVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAGGA   82 (121)
Q Consensus         3 yvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaaaa~a~~   82 (121)
                      |++|-|+|+.. +.+||++||++||+++|++|+++|+++|++.|+||||++||+       +++++|+++++++++++ +
T Consensus         4 c~yAaLiL~d~-~~~~Tae~I~~ilkAaGveve~~~~~~f~~~L~gk~i~elIa-------~~~~~~~~aap~a~~a~-~   74 (103)
T cd05831           4 CTYAALILHDD-GIEITADNINALLKAAGVNVEPYWPGLFAKALEGKDIKDLLS-------NVGGGGGGAAPAAAAAA-A   74 (103)
T ss_pred             HHHHHHHHccC-CCCCCHHHHHHHHHHcCCcccHHHHHHHHHHHcCCCHHHHhh-------ccccccccccccccccc-c
Confidence            45555555555 567999999999999999999999999999999999999998       44433332111111111 1


Q ss_pred             CCCcchhhhhhhhhhhccccccccc-cccc
Q 033355           83 GAAPAAAEAKKEEKVEEKEESDDVR-FTYL  111 (121)
Q Consensus        83 ~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~  111 (121)
                      +++.++ ++++++|+|++||+|||| ||||
T Consensus        75 ~~~~~~-~~~~~kk~e~eee~d~dmgfglF  103 (103)
T cd05831          75 AAAAAE-AKKEEKKEEEEEESDDDMGFGLF  103 (103)
T ss_pred             cccccc-chhhhcccccccccccccccccC
Confidence            111111 233445566667789999 9986

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

>cd05832 Ribosomal_L12p Ribosomal protein L12p

Probab=99.91  E-value=1e-24  Score=155.30  Aligned_cols=55  Identities=24%  Similarity=0.448  Sum_probs=54.1

Q ss_pred             ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHH
Q 033355            1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIA   56 (121)
Q Consensus         1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~   56 (121)
                      |||++|||||+++|+ +||.++|++||+++||+||++|+++|++.|+|+||+++|.
T Consensus         1 M~yvyAaLLL~~~G~-eITae~I~~IL~AAGveVd~~~~~ala~aL~gkdIeElIa   55 (106)
T cd05832           1 MEYIYAALLLHYAGK-EINEENLKKVLEAAGIEVDEARVKALVAALEEVNIDEAIK   55 (106)
T ss_pred             CHHHHHHHHHHhcCC-CCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHH
Confidence            999999999999998 7999999999999999999999999999999999999998

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

>TIGR03685 L21P_arch 50S ribosomal protein L12P

Probab=99.91  E-value=2.1e-24  Score=153.35  Aligned_cols=55  Identities=25%  Similarity=0.494  Sum_probs=54.1

Q ss_pred             ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHH
Q 033355            1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIA   56 (121)
Q Consensus         1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~   56 (121)
                      |||++|||||+++|+ +||.++|++||+++||+||++|+.+|++.|+||+|++||.
T Consensus         1 M~yvyA~Lll~~~g~-~iT~e~I~~IL~AAGv~ve~~~~~~la~~L~gk~i~eli~   55 (105)
T TIGR03685         1 MEYIYAALLLHSAGK-EINEENLKAVLEAAGVEVDEARVKALVAALEGVNIEEAIK   55 (105)
T ss_pred             CHHHHHHHHHHhcCC-CCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHH
Confidence            999999999999998 7999999999999999999999999999999999999997

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

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

Probab=99.90  E-value=3.3e-24  Score=153.91  Aligned_cols=102  Identities=35%  Similarity=0.484  Sum_probs=73.1

Q ss_pred             HHHHHHHHhc-CCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccC--CCC-
Q 033355            4 VAAYLLAVLG-GNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAA--PSA-   79 (121)
Q Consensus         4 vaAYlLl~l~-G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaa--aa~-   79 (121)
                      ...|.-++|. ....+|.++|++|+|++|++|+++||.+|++.|.++||.+||+       ++++||+++++++  +++ 
T Consensus         8 ac~yaalIL~d~~i~it~dki~tl~kaa~v~ve~~Wp~lfakale~vni~~li~-------n~gag~~a~a~~~~~~~~a   80 (114)
T KOG1762|consen    8 ACSYAALILHDDEIEVTADKINTLTKAAGVNVEPYWPGLFAKALEGVNIKELIC-------NVGAGGGALAAGAAAAGGA   80 (114)
T ss_pred             HHhhhhhhccccceeeehhhhhhHHHhccCcccccchhHHHHHhccCChHHHHH-------hcccCCccCCCcccccccc
Confidence            3445555554 2567999999999999999999999999999999999999999       6776555443221  111 


Q ss_pred             CCCCCCcchhhhhhhhhhhccccccccc-ccccc
Q 033355           80 GGAGAAPAAAEAKKEEKVEEKEESDDVR-FTYLM  112 (121)
Q Consensus        80 a~~~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~~  112 (121)
                      ++++++++.++++++.|+||.||+|||| ||||.
T Consensus        81 a~~~~aA~~~Ekk~eak~EeseesddDmgfGLfd  114 (114)
T KOG1762|consen   81 AAAGGAAAAEEKKEEAKKEESEESDDDMGFGLFD  114 (114)
T ss_pred             ccccccccchHHHHHhhhhhhcccccccccCCCC
Confidence            1111122222455566778889999999 99983

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

Probab=99.84  E-value=1.3e-22  Score=139.00  Aligned_cols=47  Identities=43%  Similarity=0.693  Sum_probs=44.2

Q ss_pred             CCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhc
Q 033355           17 SPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLA   63 (121)
Q Consensus        17 ~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~   63 (121)
                      +||.++|++||+++|++|+++|+.+|++.|+|++|++||++|..+|+
T Consensus         1 ~pT~~~i~~vl~aag~~v~~~~~~~~~~~l~~~~i~~li~~~~~~~~   47 (88)
T PF00428_consen    1 EPTAENIKKVLKAAGVEVEAIWLELFAKALEGKDIKELIANGSAGMA   47 (88)
T ss_dssp             S-SCCCHHHHHHHHTHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHhCCchhHHHHHHHHHHHcCCcHHHHHhccccccc
Confidence            48999999999999999999999999999999999999999988876

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.

>PTZ00135 60S acidic ribosomal protein P0; Provisional

Probab=98.56  E-value=6e-08  Score=79.96  Aligned_cols=28  Identities=18%  Similarity=0.230  Sum_probs=24.8

Q ss_pred             HHHHHHHHhcCCCcchhHHHHHHHHhCC
Q 033355           21 DDIKGILGSVGADCEDNRLELLLSEVKG   48 (121)
Q Consensus        21 e~I~kIl~AaGveVd~~~~~~f~~~L~g   48 (121)
                      .+|.+|..++|+.++..|+.+|++++++
T Consensus       220 ~~i~als~aag~pt~~s~p~~ia~a~k~  247 (310)
T PTZ00135        220 QNVAAISLAAGYPTEASAPHSILNAFKN  247 (310)
T ss_pred             HHHHHHHHHhCCCcHHHHHHHHHHHHHH
Confidence            4678899999999999999999999853

>PTZ00240 60S ribosomal protein P0; Provisional

Probab=97.38  E-value=0.0002  Score=59.73  Aligned_cols=15  Identities=33%  Similarity=0.322  Sum_probs=9.8

Q ss_pred             hhccccccccc-cccc
Q 033355           97 VEEKEESDDVR-FTYL  111 (121)
Q Consensus        97 ~eeeEE~ddDm-f~l~  111 (121)
                      +||+||+|||| ||-+
T Consensus       307 ~~~~e~~~~d~~~~~~  322 (323)
T PTZ00240        307 EEEEESDEDDFGMGAL  322 (323)
T ss_pred             cCCccCcccccCcccc
Confidence            45566677777 8754

>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed

Probab=96.40  E-value=0.01  Score=42.47  Aligned_cols=27  Identities=26%  Similarity=0.558  Sum_probs=17.4

Q ss_pred             HHHhcCCCcchhHHHHHHHHhCCCChHH
Q 033355           26 ILGSVGADCEDNRLELLLSEVKGKDITE   53 (121)
Q Consensus        26 Il~AaGveVd~~~~~~f~~~L~gk~i~e   53 (121)
                      ||.-.|.++...-++.++++. |.+|++
T Consensus         9 LL~~~g~~it~e~I~~IL~AA-GveVee   35 (106)
T PRK06402          9 LLHSAGKEINEDNLKKVLEAA-GVEVDE   35 (106)
T ss_pred             HHHhcCCCCCHHHHHHHHHHc-CCCccH
Confidence            456666777777777777664 455554

>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p

Probab=96.34  E-value=0.0096  Score=42.36  Aligned_cols=38  Identities=13%  Similarity=0.127  Sum_probs=26.9

Q ss_pred             HHHhcCCCCCCHHHHHHHHHh-cCCCcchhHHHHHHHHhCC
Q 033355            9 LAVLGGNTSPSADDIKGILGS-VGADCEDNRLELLLSEVKG   48 (121)
Q Consensus         9 Ll~l~G~~~~Tae~I~kIl~A-aGveVd~~~~~~f~~~L~g   48 (121)
                      +|...| .+++.+.++.++++ .|.+|+.-. ......|.+
T Consensus        25 IL~aaG-veVe~~~~~~~~~aLaGk~V~eli-~~g~~kl~~   63 (105)
T cd04411          25 LLSAAG-AEIEPERVKLFLSALNGKNIDEVI-SKGKELMSS   63 (105)
T ss_pred             HHHHcC-CCcCHHHHHHHHHHHcCCCHHHHH-HHHHhhccC
Confidence            445555 56999999999999 899987754 444444543

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

>PRK04019 rplP0 acidic ribosomal protein P0; Validated

Probab=96.34  E-value=0.011  Score=49.07  Aligned_cols=44  Identities=20%  Similarity=0.208  Sum_probs=35.0

Q ss_pred             HHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCC-CChHHHHH
Q 033355            6 AYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKG-KDITELIA   56 (121)
Q Consensus         6 AYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~g-k~i~eLI~   56 (121)
                      |..|.+-.|  =||.+.|..||..+     ..+...++..|.+ .++++-|.
T Consensus       245 a~aLa~~~~--~~t~e~~~~il~kA-----~~~~~ala~~~~~~~~~~~~~~  289 (330)
T PRK04019        245 AKALAVEAG--IVTPETADDILSKA-----VAQALALAAALADKDALDEELK  289 (330)
T ss_pred             HHHHHHHcC--CCChhhHHHHHHHH-----HHHHHHHHHHhcCcccccHHHH
Confidence            344444443  38999999999999     5677789999999 99999997

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

Probab=94.69  E-value=0.17  Score=36.67  Aligned_cols=22  Identities=14%  Similarity=0.132  Sum_probs=17.6

Q ss_pred             hcCCCCCCHHHHHHHHHhcCCCc
Q 033355           12 LGGNTSPSADDIKGILGSVGADC   34 (121)
Q Consensus        12 l~G~~~~Tae~I~kIl~AaGveV   34 (121)
                      -.| .+++.+.|+++|+.+...-
T Consensus        29 sVG-~E~d~e~i~~visel~GK~   50 (112)
T KOG3449|consen   29 SVG-AEIDDERINLVLSELKGKD   50 (112)
T ss_pred             HhC-cccCHHHHHHHHHHhcCCC
Confidence            345 4699999999999998753

>PTZ00373 60S Acidic ribosomal protein P2; Provisional

Probab=94.68  E-value=0.11  Score=37.45  Aligned_cols=26  Identities=8%  Similarity=0.054  Sum_probs=18.3

Q ss_pred             HHhcCCCCCCHHHHHHHHHhcCC-Ccch
Q 033355           10 AVLGGNTSPSADDIKGILGSVGA-DCED   36 (121)
Q Consensus        10 l~l~G~~~~Tae~I~kIl~AaGv-eVd~   36 (121)
                      |.-.| .++..+.++.+++.... +|+.
T Consensus        29 L~AaG-veVd~~~~~l~~~~L~GKdI~E   55 (112)
T PTZ00373         29 LSAVN-ADVEDDVLDNFFKSLEGKTPHE   55 (112)
T ss_pred             HHHcC-CCccHHHHHHHHHHHcCCCHHH
Confidence            44445 56899999999998854 4444

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

Probab=93.11  E-value=0.25  Score=35.64  Aligned_cols=27  Identities=22%  Similarity=0.491  Sum_probs=22.5

Q ss_pred             HHHhcCCCcchhHHHHHHHHhCCCChHH
Q 033355           26 ILGSVGADCEDNRLELLLSEVKGKDITE   53 (121)
Q Consensus        26 Il~AaGveVd~~~~~~f~~~L~gk~i~e   53 (121)
                      +|..+|-+++...++.+.+.. |.+|++
T Consensus         9 lL~~agkei~e~~l~~vl~aa-Gveve~   35 (109)
T COG2058           9 LLHLAGKEITEDNLKSVLEAA-GVEVEE   35 (109)
T ss_pred             HHHHccCcCCHHHHHHHHHHc-CCCccH
Confidence            688899999999999888865 777765

>cd05832 Ribosomal_L12p Ribosomal protein L12p

Probab=93.11  E-value=0.27  Score=35.22  Aligned_cols=27  Identities=22%  Similarity=0.486  Sum_probs=20.6

Q ss_pred             HHHhcCCCcchhHHHHHHHHhCCCChHH
Q 033355           26 ILGSVGADCEDNRLELLLSEVKGKDITE   53 (121)
Q Consensus        26 Il~AaGveVd~~~~~~f~~~L~gk~i~e   53 (121)
                      ||.-.|.++....++.+++.- |.++++
T Consensus         9 LL~~~G~eITae~I~~IL~AA-GveVd~   35 (106)
T cd05832           9 LLHYAGKEINEENLKKVLEAA-GIEVDE   35 (106)
T ss_pred             HHHhcCCCCCHHHHHHHHHHh-CCcccH
Confidence            677788899998888888864 566654

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

>TIGR03685 L21P_arch 50S ribosomal protein L12P

Probab=92.06  E-value=0.42  Score=33.99  Aligned_cols=27  Identities=26%  Similarity=0.553  Sum_probs=19.3

Q ss_pred             HHHhcCCCcchhHHHHHHHHhCCCChHH
Q 033355           26 ILGSVGADCEDNRLELLLSEVKGKDITE   53 (121)
Q Consensus        26 Il~AaGveVd~~~~~~f~~~L~gk~i~e   53 (121)
                      ||.-.|.++....++.++++- |.++++
T Consensus         9 ll~~~g~~iT~e~I~~IL~AA-Gv~ve~   35 (105)
T TIGR03685         9 LLHSAGKEINEENLKAVLEAA-GVEVDE   35 (105)
T ss_pred             HHHhcCCCCCHHHHHHHHHHh-CCcccH
Confidence            566677888888888887764 555554

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

>cd05833 Ribosomal_P2 Ribosomal protein P2

Probab=91.63  E-value=0.66  Score=33.18  Aligned_cols=37  Identities=3%  Similarity=0.036  Sum_probs=20.8

Q ss_pred             HHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhC
Q 033355           10 AVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVK   47 (121)
Q Consensus        10 l~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~   47 (121)
                      |.-.| .++..+.+..++++....--.+.+..-.+.|.
T Consensus        27 L~AaG-veVe~~~~~lf~~~L~GKdi~eLIa~g~~kl~   63 (109)
T cd05833          27 LGSVG-VEVDDEKLNKVISELEGKDVEELIAAGKEKLA   63 (109)
T ss_pred             HHHcC-CCccHHHHHHHHHHHcCCCHHHHHHHhHhhhc
Confidence            34444 45888888888887755333334443333343

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

>cd05831 Ribosomal_P1 Ribosomal protein P1

Probab=91.25  E-value=0.52  Score=33.29  Aligned_cols=27  Identities=22%  Similarity=0.421  Sum_probs=20.0

Q ss_pred             HHHhcCCCcchhHHHHHHHHhCCCChHH
Q 033355           26 ILGSVGADCEDNRLELLLSEVKGKDITE   53 (121)
Q Consensus        26 Il~AaGveVd~~~~~~f~~~L~gk~i~e   53 (121)
                      ||...|.++....++.++++. |.++++
T Consensus        10 iL~d~~~~~Tae~I~~ilkAa-Gveve~   36 (103)
T cd05831          10 ILHDDGIEITADNINALLKAA-GVNVEP   36 (103)
T ss_pred             HHccCCCCCCHHHHHHHHHHc-CCcccH
Confidence            677788888888888888765 466654

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

>PLN00138 large subunit ribosomal protein LP2; Provisional

Probab=87.18  E-value=0.46  Score=34.24  Aligned_cols=22  Identities=23%  Similarity=0.210  Sum_probs=16.0

Q ss_pred             HHhcCCCCCCHHHHHHHHHhcCC
Q 033355           10 AVLGGNTSPSADDIKGILGSVGA   32 (121)
Q Consensus        10 l~l~G~~~~Tae~I~kIl~AaGv   32 (121)
                      |.-.| .++..+.++.+++....
T Consensus        27 L~AaG-vevd~~~~~~f~~~L~g   48 (113)
T PLN00138         27 LGSVG-ADADDDRIELLLSEVKG   48 (113)
T ss_pred             HHHcC-CcccHHHHHHHHHHHcC
Confidence            33444 56899999999988754

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	121
3izr_v	113	Localization Of The Large Subunit Ribosomal Protein		8e-17
2w1o_A	70	Nmr Structure Of Dimerization Domain Of Human Ribos		2e-13
3izs_v	106	Localization Of The Large Subunit Ribosomal Protein		2e-05

>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 = 82.0 bits (201), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 39/62 (62%), Positives = 51/62 (82%)
Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MK +AAYLLA L GN SPSA+D+  IL SVG + ++ ++EL+LS+VKGKDITEL+A+GRE
Sbjct: 1  MKFIAAYLLAYLSGNASPSAEDLTSILESVGCEIDNEKMELMLSQVKGKDITELLAAGRE 60
Query: 61 KL 62
          K 
Sbjct: 61 KF 62

>pdb|2W1O|A Chain A, Nmr Structure Of Dimerization Domain Of Human Ribosomal Protein P2 Length = 70

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/62 (58%), Positives = 48/62 (77%)
Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          M+ VA+YLLA LGGN+SPSA DIK IL SVG + +D+RL  ++SE+ GK+I ++IA G  
Sbjct: 2  MRYVASYLLAALGGNSSPSAKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIG 61
Query: 61 KL 62
          KL
Sbjct: 62 KL 63

>pdb|3IZS|VV Chain v, Localization Of The Large Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 106

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 32/62 (51%), Positives = 40/62 (64%), Gaps = 1/62 (1%)
Query: 1  MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGRE 60
          MK +AAYLL    GNT P A  IK IL SVG + ED ++  +LS ++GK + ELI  G E
Sbjct: 1  MKYLAAYLLLNAAGNT-PDATKIKAILESVGIEIEDEKVSSVLSALEGKSVDELITEGNE 59
Query: 61 KL 62
          KL
Sbjct: 60 KL 61

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	121
3iz5_v	113	60S acidic ribosomal protein P21 - P2 (L12P); euka	100.0
3izc_v	106	60S acidic ribosomal protein (P2); eukaryotic ribo	100.0
3izc_t	106	60S acidic ribosomal protein RPP11 (P1); eukaryoti	99.98
3iz5_t	110	60S acidic ribosomal protein P11 - P1 (L12P); euka	99.97
2lbf_B	70	60S acidic ribosomal protein P2; ribosome, stalk,	99.95
3a1y_A	58	50S ribosomal protein P1 (L12P); stalk, helix SPIN	99.85
2lbf_A	69	60S acidic ribosomal protein P1; ribosome, stalk,	99.79
3iz5_s	319	60S acidic ribosomal protein P0 (L10P); eukaryotic	98.44
2zkr_g	317	60S acidic ribosomal protein P0; protein-RNA compl	98.36
3u5i_q	312	A0, L10E, 60S acidic ribosomal protein P0; transla	98.12
3iz5_t	110	60S acidic ribosomal protein P11 - P1 (L12P); euka	92.53
3iz5_v	113	60S acidic ribosomal protein P21 - P2 (L12P); euka	88.64
3izc_t	106	60S acidic ribosomal protein RPP11 (P1); eukaryoti	88.62
3j21_k	339	Acidic ribosomal protein P0 homolog; archaea, arch	86.16

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

Probab=99.95  E-value=1.4e-28  Score=162.81  Aligned_cols=69  Identities=61%  Similarity=0.964  Sum_probs=67.4

Q ss_pred             ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCC
Q 033355            1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGG   69 (121)
Q Consensus         1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg   69 (121)
                      |||+|||||++++|+.+||++||++||+++|++||++|+++|+++|+||||+|||++|.+||+|+|+||
T Consensus         2 M~yvyA~Lll~~~g~~~~ta~~I~~il~aaGvevd~~~~~~~~~aL~gk~i~elIa~g~~kl~s~p~gg   70 (70)
T 2lbf_B            2 MRYVASYLLAALGGNSSPSAKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIGKLASVPAGG   70 (70)
T ss_dssp             CCTHHHHHHHHHHTCSSCCHHHHHHHHHTTTCCCCTTHHHHHHHHHSSCCHHHHHTTCSSSCSSCCCCC
T ss_pred             cHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCC
Confidence            999999999999999789999999999999999999999999999999999999999999999999875

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

Probab=99.85  E-value=2.5e-21  Score=123.68  Aligned_cols=56  Identities=29%  Similarity=0.478  Sum_probs=54.1

Q ss_pred             ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHh
Q 033355            1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIAS   57 (121)
Q Consensus         1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~   57 (121)
                      |+|++||+||+..|+ +||++||++||+++|++||++|+++|++.|+||||++||++
T Consensus         1 m~~~yAallL~~~g~-~~t~~~I~~il~aaGveve~~~~~~~~~~L~gk~i~elI~~   56 (58)
T 3a1y_A            1 MEYVYAALLLHSVGK-EINEENLKAVLQAAGVEPEEARIKALVAALEGVNIDEVIEK   56 (58)
T ss_dssp             CHHHHHHHHHHHTTC-CCCHHHHHHHHHHTTCCCCHHHHHHHHHHHSSCCHHHHHHH
T ss_pred             CHHHHHHHHHHhCCC-CCCHHHHHHHHHHcCCCccHHHHHHHHHHHCCCCHHHHHHc
Confidence            999999999999986 79999999999999999999999999999999999999973

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

Probab=99.79  E-value=1.3e-19  Score=119.29  Aligned_cols=61  Identities=20%  Similarity=0.320  Sum_probs=54.7

Q ss_pred             ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCC
Q 033355            1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGG   69 (121)
Q Consensus         1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg   69 (121)
                      |.|++|.+||+..| .+||++||++||+++|++||++|+++|++.|+||||++||+       ++++||
T Consensus         7 la~~YAAllL~~~g-~~~ta~~I~~il~AaGveve~~~~~lf~~aL~gk~I~elI~-------~~g~g~   67 (69)
T 2lbf_A            7 LACIYSALILHDDE-VTVTEDKINALIKAAGVNVEPFWPGLFAKALANVNIGSLIC-------NVGAGG   67 (69)
T ss_dssp             HHHHHHHHHHHHHT-CCCCHHHHHHHHHHHTCCCCTHHHHHHHHHTTTSCGGGGGT-------TTTCCC
T ss_pred             HHHHHHHHHHHcCC-CCCCHHHHHHHHHHcCCCccHHHHHHHHHHHCCCCHHHHHH-------hccCCC
Confidence            35888888888887 47999999999999999999999999999999999999998       665554

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

Probab=98.36  E-value=3.8e-09  Score=86.03  Aligned_cols=20  Identities=45%  Similarity=0.498  Sum_probs=8.7

Q ss_pred             hhhhhhhccccccccc-cccc
Q 033355           92 KKEEKVEEKEESDDVR-FTYL  111 (121)
Q Consensus        92 ~~e~k~eeeEE~ddDm-f~l~  111 (121)
                      ++++++||+||||||| ||||
T Consensus       296 ~~~~~~ee~ee~d~d~gf~lf  316 (317)
T 2zkr_g          296 AKVEAKEESEESDEDMGFGLF  316 (317)
T ss_dssp             HSTTHHHHTSSCC--------
T ss_pred             ccccccCCccccccccCcCCC
Confidence            4455566678889999 9987

>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=98.12  E-value=3.4e-07  Score=74.37  Aligned_cols=20  Identities=45%  Similarity=0.577  Sum_probs=0.0

Q ss_pred             hhhhhhhccccccccc-cccc
Q 033355           92 KKEEKVEEKEESDDVR-FTYL  111 (121)
Q Consensus        92 ~~e~k~eeeEE~ddDm-f~l~  111 (121)
                      ++++++||+||||||| ||||
T Consensus       291 ~~~~~~e~~ee~d~d~gf~lf  311 (312)
T 3u5i_q          291 AEEAAAEEEEESDDDMGFGLF  311 (312)
T ss_dssp             ---------------------
T ss_pred             cccccccccccccccCCCCCC
Confidence            3445556677888899 9998

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

Probab=86.16  E-value=0.14  Score=41.59  Aligned_cols=11  Identities=9%  Similarity=0.042  Sum_probs=0.0

Q ss_pred             hCCCChHHHHH
Q 033355           46 VKGKDITELIA   56 (121)
Q Consensus        46 L~gk~i~eLI~   56 (121)
                      +.+.++++-+.
T Consensus       283 ~~~~~~~e~~~  293 (339)
T 3j21_k          283 LPEDVLDEKTK  293 (339)
T ss_dssp             -----------
T ss_pred             hccccchhHHh
Confidence            33444444443

---

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