Citrus Sinensis ID: 033353

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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
MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMGFSLFD
Secondary Structure (PSIPRED)
ccEEEEEEEccccccccccccccccccccccHHHHHHHHHHHHHHHcccccEEEEEEEEcccccEEEEEEcccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEcccccEcHHHccccccccccccHHHHHHHHHHHHHHHccccccEEcEcEcccccEEEEEEEEccccHHHHccHccccccccccccccccHHHHHHHHHHHcccccccccccc
Coil and Loop (DISEMBL)
MGVFTYVCrknggewsgkqieggdleasAASTYELQRKLVQTSlsadssggvqssfslvtptsAVFQVIIGGavgsgfigggaaasapsggggaaaeapaaeekkeekeesdedmgfslfd
Flexible Loop (DISEMBL)
MGVFTYvcrknggewsgkqiegGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPaaeekkeekeesdedmgfslfd
Low Complexity Region (SEG)
MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQViiggavgsgfigggaaasapsggggaaaeapaaeekkeekeeSDEDMGFSLFD
Disordered region (IsUnstruct)
**VFTYVCRKNGGEW****************************************FSLVTPTSAVFQVIIGGAVGSGFIGGG***************************************
Disordered Region (DISOPRED)
MGVFTYVCRKNGGEW************SAASTYELQRKLV***************FSLVTPTSAVFQVIIGGAVGSGF************************************MGFSLFD
Disordered Region (DISEMBL)
MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQ***********QSSFSLVTPTSAVFQVIIGGAVGSGFIGGGA**************************************
Disordered Region (DISPRO)
*GVFTYVCRKNGGEWS********LEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAVGSGFIGG*************************************L**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMGFSLFD
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]
O24413	120	60S acidic ribosomal prot	N/A	no	0.991	1.0	0.619	5e-25
Q9LVC9	120	60S acidic ribosomal prot	yes	no	0.570	0.575	0.785	8e-25
Q9SVZ6	119	60S acidic ribosomal prot	no	no	0.570	0.579	0.8	9e-25
P56724	119	60S acidic ribosomal prot	yes	no	0.983	1.0	0.586	1e-12

>sp|O24413|RLA3_MAIZE 60S acidic ribosomal protein P3 OS=Zea mays GN=RPP3A PE=1 SV=3

 Score =  112 bits (281), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 75/121 (61%), Positives = 92/121 (76%), Gaps = 1/121 (0%)

Query: 1   MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
           MGV+T+VCR NGGEW+ KQ   G++EASAA+ YELQR+LV  + +ADS  GVQSSFS+VT
Sbjct: 1   MGVYTFVCRNNGGEWTAKQ-HSGEIEASAATPYELQRRLVAAASAADSRYGVQSSFSMVT 59

Query: 61  PTSAVFQVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMGFSLF 120
           P+SAVFQVI+G   G   +  G      +  GGAAAEAP  E+K+EEKEESD+DMGFSLF
Sbjct: 60  PSSAVFQVIVGAVGGGAMMVSGGGGGGAAASGGAAAEAPKEEKKEEEKEESDDDMGFSLF 119

Query: 121 D 121
           D
Sbjct: 120 D 120

Plays an important role in the elongation step of protein synthesis.
Zea mays (taxid: 4577)

>sp|Q9LVC9|RLA32_ARATH 60S acidic ribosomal protein P3-2 OS=Arabidopsis thaliana GN=RPP3B PE=1 SV=1

 Score =  112 bits (279), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 55/70 (78%), Positives = 64/70 (91%), Gaps = 1/70 (1%)

Query: 1  MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
          MGVF++VC+  GGEW+ KQ EG DLEASA+STY+LQRKLVQT+LSADSSGGVQSSFSLV+
Sbjct: 1  MGVFSFVCKSKGGEWTAKQHEG-DLEASASSTYDLQRKLVQTALSADSSGGVQSSFSLVS 59

Query: 61 PTSAVFQVII 70
          PTSAVF V+I
Sbjct: 60 PTSAVFVVVI 69

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SVZ6|RLA31_ARATH 60S acidic ribosomal protein P3-1 OS=Arabidopsis thaliana GN=RPP3A PE=1 SV=1

 Score =  112 bits (279), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 56/70 (80%), Positives = 63/70 (90%), Gaps = 1/70 (1%)

Query: 1  MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
          MGVFT+VC+  GG WS KQ EG +LE+SA+STYELQRKLVQ SLSADSSGGVQSSFSLV+
Sbjct: 1  MGVFTFVCKNGGGAWSAKQHEG-ELESSASSTYELQRKLVQVSLSADSSGGVQSSFSLVS 59

Query: 61 PTSAVFQVII 70
          PTSAVFQVI+
Sbjct: 60 PTSAVFQVIV 69

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

Arabidopsis thaliana (taxid: 3702)

>sp|P56724|RLA3_ORYSJ 60S acidic ribosomal protein P3 OS=Oryza sativa subsp. japonica GN=Os06g0701400 PE=3 SV=3

 Score = 72.0 bits (175), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 71/121 (58%), Positives = 93/121 (76%), Gaps = 2/121 (1%)

Query: 1   MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
           MGV+T+VCR +G EW+ KQ++G +LEASAA+ YELQR+LV  + +ADS+ GVQSSFS+V+
Sbjct: 1   MGVYTFVCRSSGDEWTAKQLKG-ELEASAATPYELQRRLVAAASAADSAAGVQSSFSMVS 59

Query: 61  PTSAVFQVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMGFSLF 120
           P+SAVFQVIIG   G   IGGGAAA A SGG  A A     ++++E++E  D D+GFSLF
Sbjct: 60  PSSAVFQVIIGAVGGGAAIGGGAAAGAASGGAAAEAPKAEEKKEEEKEESED-DLGFSLF 118

Query: 121 D 121
           D
Sbjct: 119 D 119

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

Oryza sativa subsp. japonica (taxid: 39947)

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
224106463	116	predicted protein [Populus trichocarpa]	0.958	1.0	0.652	2e-26
118485567	124	unknown [Populus trichocarpa]	1.0	0.975	0.677	8e-26
118481350	124	unknown [Populus trichocarpa]	1.0	0.975	0.637	5e-25
297796629	120	hypothetical protein ARALYDRAFT_918901 [	0.570	0.575	0.828	9e-25
162463825	120	60S acidic ribosomal protein P3 [Zea may	0.991	1.0	0.619	2e-23
15242089	120	60S acidic ribosomal protein P3-2 [Arabi	0.570	0.575	0.785	3e-23
15236029	119	60S acidic ribosomal protein P3-1 [Arabi	0.570	0.579	0.8	4e-23
147790496	121	hypothetical protein VITISV_010073 [Viti	0.991	0.991	0.754	4e-23
225446287	121	PREDICTED: 60S acidic ribosomal protein	0.991	0.991	0.745	7e-23
297799408	119	hypothetical protein ARALYDRAFT_492228 [	0.570	0.579	0.785	7e-23

>gi|224106463|ref|XP_002314174.1| predicted protein [Populus trichocarpa] gi|222850582|gb|EEE88129.1| predicted protein [Populus trichocarpa]

 Score =  122 bits (307), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 79/121 (65%), Positives = 90/121 (74%), Gaps = 5/121 (4%)

Query: 1   MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
           MGVFT+VCR +G EWS KQI  GD+EASA+ST+ELQRKLVQ++LSADSSGGVQSSFS VT
Sbjct: 1   MGVFTFVCRCSGNEWSAKQIAEGDIEASASSTFELQRKLVQSALSADSSGGVQSSFSYVT 60

Query: 61  PTSAVFQVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMGFSLF 120
           P+SAVFQVIIGG  G              G   AA    A E+KKEE+ ESD+DMGFSLF
Sbjct: 61  PSSAVFQVIIGGGCGG-----AFFGGGGGGAAAAAEAPAAEEKKKEEEPESDDDMGFSLF 115

Query: 121 D 121
           D
Sbjct: 116 D 116

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118485567|gb|ABK94635.1| unknown [Populus trichocarpa]

 Score =  120 bits (302), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 84/124 (67%), Positives = 96/124 (77%), Gaps = 3/124 (2%)

Query: 1   MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
           MGVFT+VCR +G EWS KQI  GD+EASA+ST+ELQRKLVQ++LSADSSGGVQSSFS VT
Sbjct: 1   MGVFTFVCRCSGNEWSAKQIAEGDIEASASSTFELQRKLVQSALSADSSGGVQSSFSYVT 60

Query: 61  PTSAVFQVII---GGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMGF 117
           P+SAVFQVII    G    G  GGGAAA+   G   AA    A E+KKEE+ ESD+DMGF
Sbjct: 61  PSSAVFQVIIGGGCGGAFFGGGGGGAAAAPAGGAAAAAEAPAAEEKKKEEEPESDDDMGF 120

Query: 118 SLFD 121
           SLFD
Sbjct: 121 SLFD 124

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118481350|gb|ABK92618.1| unknown [Populus trichocarpa]

 Score =  118 bits (295), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 79/124 (63%), Positives = 93/124 (75%), Gaps = 3/124 (2%)

Query: 1   MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
           MGVFT+VCR +  EWS KQI  G++EASA+ST+ELQRKLVQ++LSADSSG VQSSFS VT
Sbjct: 1   MGVFTFVCRSSSNEWSAKQISDGNIEASASSTFELQRKLVQSALSADSSGAVQSSFSYVT 60

Query: 61  PTSAVFQVII---GGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMGF 117
           P+SAVFQV+I    G    G  GGGA A+   G   AA    A E+KKEE+ ESD+DMGF
Sbjct: 61  PSSAVFQVVIGGSAGGAFFGGGGGGAVAAPAGGATAAAEAPAAEEKKKEEEPESDDDMGF 120

Query: 118 SLFD 121
           SLFD
Sbjct: 121 SLFD 124

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297796629|ref|XP_002866199.1| hypothetical protein ARALYDRAFT_918901 [Arabidopsis lyrata subsp. lyrata] gi|297312034|gb|EFH42458.1| hypothetical protein ARALYDRAFT_918901 [Arabidopsis lyrata subsp. lyrata]

 Score =  117 bits (293), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 58/70 (82%), Positives = 65/70 (92%), Gaps = 1/70 (1%)

Query: 1  MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
          MGVFT+VC+  GGEW+ KQ EG DLEASA+STY+LQRKLVQT+LSADSSGGVQSSFSLV+
Sbjct: 1  MGVFTFVCKSKGGEWTAKQHEG-DLEASASSTYDLQRKLVQTALSADSSGGVQSSFSLVS 59

Query: 61 PTSAVFQVII 70
          PTSAVFQVII
Sbjct: 60 PTSAVFQVII 69

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|162463825|ref|NP_001105389.1| 60S acidic ribosomal protein P3 [Zea mays] gi|6226016|sp|O24413.3|RLA3_MAIZE RecName: Full=60S acidic ribosomal protein P3; AltName: Full=P1/P2-like; AltName: Full=P3A gi|2431767|gb|AAB71078.1| acidic ribosomal protein P3a [Zea mays]

 Score =  112 bits (281), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 75/121 (61%), Positives = 92/121 (76%), Gaps = 1/121 (0%)

Query: 1   MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
           MGV+T+VCR NGGEW+ KQ   G++EASAA+ YELQR+LV  + +ADS  GVQSSFS+VT
Sbjct: 1   MGVYTFVCRNNGGEWTAKQ-HSGEIEASAATPYELQRRLVAAASAADSRYGVQSSFSMVT 59

Query: 61  PTSAVFQVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMGFSLF 120
           P+SAVFQVI+G   G   +  G      +  GGAAAEAP  E+K+EEKEESD+DMGFSLF
Sbjct: 60  PSSAVFQVIVGAVGGGAMMVSGGGGGGAAASGGAAAEAPKEEKKEEEKEESDDDMGFSLF 119

Query: 121 D 121
           D
Sbjct: 120 D 120

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15242089|ref|NP_200539.1| 60S acidic ribosomal protein P3-2 [Arabidopsis thaliana] gi|75264272|sp|Q9LVC9.1|RLA32_ARATH RecName: Full=60S acidic ribosomal protein P3-2 gi|8777362|dbj|BAA96952.1| 60S acidic ribosomal protein P3 [Arabidopsis thaliana] gi|21617903|gb|AAM66953.1| 60S acidic ribosomal protein P3 [Arabidopsis thaliana] gi|98961057|gb|ABF59012.1| At5g57290 [Arabidopsis thaliana] gi|332009494|gb|AED96877.1| 60S acidic ribosomal protein P3-2 [Arabidopsis thaliana]

 Score =  112 bits (279), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 55/70 (78%), Positives = 64/70 (91%), Gaps = 1/70 (1%)

Query: 1  MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
          MGVF++VC+  GGEW+ KQ EG DLEASA+STY+LQRKLVQT+LSADSSGGVQSSFSLV+
Sbjct: 1  MGVFSFVCKSKGGEWTAKQHEG-DLEASASSTYDLQRKLVQTALSADSSGGVQSSFSLVS 59

Query: 61 PTSAVFQVII 70
          PTSAVF V+I
Sbjct: 60 PTSAVFVVVI 69

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15236029|ref|NP_194319.1| 60S acidic ribosomal protein P3-1 [Arabidopsis thaliana] gi|75266431|sp|Q9SVZ6.1|RLA31_ARATH RecName: Full=60S acidic ribosomal protein P3-1 gi|4539307|emb|CAB39610.1| putative acidic ribosomal protein [Arabidopsis thaliana] gi|7269440|emb|CAB79444.1| putative acidic ribosomal protein [Arabidopsis thaliana] gi|17979039|gb|AAL49787.1| putative acidic ribosomal protein [Arabidopsis thaliana] gi|20259603|gb|AAM14158.1| putative acidic ribosomal protein [Arabidopsis thaliana] gi|332659730|gb|AEE85130.1| 60S acidic ribosomal protein P3-1 [Arabidopsis thaliana]

 Score =  112 bits (279), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 56/70 (80%), Positives = 63/70 (90%), Gaps = 1/70 (1%)

Query: 1  MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
          MGVFT+VC+  GG WS KQ EG +LE+SA+STYELQRKLVQ SLSADSSGGVQSSFSLV+
Sbjct: 1  MGVFTFVCKNGGGAWSAKQHEG-ELESSASSTYELQRKLVQVSLSADSSGGVQSSFSLVS 59

Query: 61 PTSAVFQVII 70
          PTSAVFQVI+
Sbjct: 60 PTSAVFQVIV 69

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147790496|emb|CAN65458.1| hypothetical protein VITISV_010073 [Vitis vinifera]

 Score =  111 bits (278), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 92/122 (75%), Positives = 104/122 (85%), Gaps = 2/122 (1%)

Query: 1   MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
           MGVFT+VCR +G EW+ KQ+  GDLE SAASTY+LQRK VQ++LSADSSGGVQSSFS VT
Sbjct: 1   MGVFTFVCRSSGKEWTAKQM-NGDLEESAASTYDLQRKCVQSALSADSSGGVQSSFSYVT 59

Query: 61  PTSAVFQVII-GGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMGFSL 119
           P+S VFQVI+ GG  G  F GGGAAA+APSGGG  AA+AP AEEKKEEKEESD+DMGFSL
Sbjct: 60  PSSGVFQVIVGGGGGGGFFGGGGAAAAAPSGGGAPAADAPPAEEKKEEKEESDDDMGFSL 119

Query: 120 FD 121
           FD
Sbjct: 120 FD 121

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225446287|ref|XP_002269613.1| PREDICTED: 60S acidic ribosomal protein P3-2 [Vitis vinifera] gi|296090308|emb|CBI40127.3| unnamed protein product [Vitis vinifera]

 Score =  111 bits (277), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 91/122 (74%), Positives = 104/122 (85%), Gaps = 2/122 (1%)

Query: 1   MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
           MGVFT+VCR +G EW+ KQ+  GDLE SAASTY+LQR+ VQ++LSADSSGGVQSSFS VT
Sbjct: 1   MGVFTFVCRSSGKEWTAKQM-NGDLEESAASTYDLQRRCVQSALSADSSGGVQSSFSYVT 59

Query: 61  PTSAVFQVII-GGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMGFSL 119
           P+SAV QVI+ GG  G  F GGGAAA+APSGGG  AA+AP AEEKKEEKEESD+DMGFSL
Sbjct: 60  PSSAVIQVIVGGGGGGGFFGGGGAAAAAPSGGGAPAADAPPAEEKKEEKEESDDDMGFSL 119

Query: 120 FD 121
           FD
Sbjct: 120 FD 121

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297799408|ref|XP_002867588.1| hypothetical protein ARALYDRAFT_492228 [Arabidopsis lyrata subsp. lyrata] gi|297313424|gb|EFH43847.1| hypothetical protein ARALYDRAFT_492228 [Arabidopsis lyrata subsp. lyrata]

 Score =  110 bits (276), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 55/70 (78%), Positives = 63/70 (90%), Gaps = 1/70 (1%)

Query: 1  MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
          MGVFT+VC+  GG W+ KQ EG +LEASA+STYELQRKLVQ +LSADSSGGVQSSFSLV+
Sbjct: 1  MGVFTFVCKNGGGAWTAKQHEG-ELEASASSTYELQRKLVQAALSADSSGGVQSSFSLVS 59

Query: 61 PTSAVFQVII 70
          PTSAVFQVI+
Sbjct: 60 PTSAVFQVIV 69

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

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:2117562	119	AT4G25890 [Arabidopsis thalian	0.553	0.563	0.808	1.8e-23
TAIR|locus:2165620	120	AT5G57290 [Arabidopsis thalian	0.553	0.558	0.794	2.9e-23

TAIR|locus:2117562 AT4G25890 [Arabidopsis thaliana (taxid:3702)]

 Score = 270 (100.1 bits), Expect = 1.8e-23, P = 1.8e-23
 Identities = 55/68 (80%), Positives = 61/68 (89%)

Query:     1 MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
             MGVFT+VC+  GG WS KQ EG +LE+SA+STYELQRKLVQ SLSADSSGGVQSSFSLV+
Sbjct:     1 MGVFTFVCKNGGGAWSAKQHEG-ELESSASSTYELQRKLVQVSLSADSSGGVQSSFSLVS 59

Query:    61 PTSAVFQV 68
             PTSAVFQV
Sbjct:    60 PTSAVFQV 67

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:0005886 "plasma membrane" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

TAIR|locus:2165620 AT5G57290 [Arabidopsis thaliana (taxid:3702)]

 Score = 268 (99.4 bits), Expect = 2.9e-23, P = 2.9e-23
 Identities = 54/68 (79%), Positives = 62/68 (91%)

Query:     1 MGVFTYVCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSFSLVT 60
             MGVF++VC+  GGEW+ KQ EG DLEASA+STY+LQRKLVQT+LSADSSGGVQSSFSLV+
Sbjct:     1 MGVFSFVCKSKGGEWTAKQHEG-DLEASASSTYDLQRKLVQTALSADSSGGVQSSFSLVS 59

Query:    61 PTSAVFQV 68
             PTSAVF V
Sbjct:    60 PTSAVFVV 67


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.312   0.127   0.357    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      121        79   0.00091  102 3  11 23  0.44    29
                                                     29  0.39    30


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  2
  No. of states in DFA:  502 (53 KB)
  Total size of DFA:  90 KB (2067 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  8.70u 0.19s 8.89t   Elapsed:  00:00:01
  Total cpu time:  8.70u 0.19s 8.89t   Elapsed:  00:00:01
  Start:  Sat May 11 00:14:56 2013   End:  Sat May 11 00:14:57 2013

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

---

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)
P56724	RLA3_ORYSJ	No assigned EC number	0.5867	0.9834	1.0	yes	no
O24413	RLA3_MAIZE	No assigned EC number	0.6198	0.9917	1.0	N/A	no
Q9LVC9	RLA32_ARATH	No assigned EC number	0.7857	0.5702	0.575	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	121
cd05833	109	cd05833, Ribosomal_P2, Ribosomal protein P2	8e-11
cd05831	103	cd05831, Ribosomal_P1, Ribosomal protein P1	4e-10
pfam00428	88	pfam00428, Ribosomal_60s, 60s Acidic ribosomal pro	6e-10
PLN00138	113	PLN00138, PLN00138, large subunit ribosomal protei	5e-08
PTZ00135	310	PTZ00135, PTZ00135, 60S acidic ribosomal protein P	2e-07
PTZ00373	112	PTZ00373, PTZ00373, 60S Acidic ribosomal protein P	7e-07
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	7e-06
cd04411	105	cd04411, Ribosomal_P1_P2_L12p, Ribosomal protein P	4e-05
PTZ00240	323	PTZ00240, PTZ00240, 60S ribosomal protein P0; Prov	1e-04

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

 Score = 54.6 bits (132), Expect = 8e-11
 Identities = 24/48 (50%), Positives = 30/48 (62%)

Query: 74  VGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMGFSLFD 121
           + S   G G AA A +    AAA A   E+K+E +EESD+DMGF LFD
Sbjct: 62  LASVPAGAGGAAPAAAAAAAAAAAAKKEEKKEESEEESDDDMGFGLFD 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|100109 cd05831, Ribosomal_P1, Ribosomal protein P1

 Score = 52.3 bits (126), Expect = 4e-10
 Identities = 24/46 (52%), Positives = 29/46 (63%), Gaps = 4/46 (8%)

Query: 79  IGGGAAASAP---SGGGGAAAEAPAAEEKKEE-KEESDEDMGFSLF 120
           +GGG   +AP   +    AAA     EEKKEE +EESD+DMGF LF
Sbjct: 58  VGGGGGGAAPAAAAAAAAAAAAEAKKEEKKEEEEEESDDDMGFGLF 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|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein

 Score = 51.5 bits (124), Expect = 6e-10
 Identities = 19/48 (39%), Positives = 28/48 (58%)

Query: 73  AVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMGFSLF 120
              +      AAA+A +    AAA A   ++++EE+EE D+DMGF LF
Sbjct: 41  NGSAKLSAAAAAAAAAAAAAAAAAAAEEEKKEEEEEEEEDDDMGFGLF 88

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

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

 Score = 47.4 bits (112), Expect = 5e-08
 Identities = 28/46 (60%), Positives = 31/46 (67%), Gaps = 4/46 (8%)

Query: 80  GGGAAASAPSGGGGAAAEAPAAEEKKEEK----EESDEDMGFSLFD 121
           GGG A +A +      A APAAE KKEEK    EESD+DMGFSLFD
Sbjct: 68  GGGVAVAAAAAPAAGGAAAPAAEAKKEEKVEEKEESDDDMGFSLFD 113

Length = 113

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

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 21/39 (53%), Positives = 26/39 (66%), Gaps = 2/39 (5%)

Query: 83  AAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMGFSLFD 121
           AAA+A +    AAA A AA    EE+EE ++DMGF LFD
Sbjct: 274 AAAAAAAAA--AAAAAAAAAAPAEEEEEEEDDMGFGLFD 310

Length = 310

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

 Score = 44.1 bits (104), Expect = 7e-07
 Identities = 26/46 (56%), Positives = 31/46 (67%), Gaps = 3/46 (6%)

Query: 79  IGGGAAASAPSGGGGAAAEAPAA---EEKKEEKEESDEDMGFSLFD 121
           IGGG AA+A    G A A A A    EEKKEE+EE ++D+GFSLF 
Sbjct: 67  IGGGVAAAAAPAAGAATAGAKAEAKKEEKKEEEEEEEDDLGFSLFG 112

Length = 112

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

 Score = 41.6 bits (98), Expect = 7e-06
 Identities = 25/58 (43%), Positives = 32/58 (55%), Gaps = 3/58 (5%)

Query: 67  QVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEE---KKEEKEESDEDMGFSLFD 121
           +VI   A          AA+A + G  AAAEA  AEE   ++E +EESD+DM F LF 
Sbjct: 52  EVIKNAAEAPAAAAAAGAAAAAAAGAEAAAEADEAEEEEKEEEAEEESDDDMLFGLFG 109

Length = 109

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

 Score = 39.6 bits (92), Expect = 4e-05
 Identities = 22/54 (40%), Positives = 26/54 (48%)

Query: 67  QVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMGFSLF 120
           +VI  G          AAA A +    A     A E K+EE+EE DED GF LF
Sbjct: 52  EVISKGKELMSSQAAAAAAPAATAAATAEPAEKAEEAKEEEEEEEDEDFGFGLF 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|140267 PTZ00240, PTZ00240, 60S ribosomal protein P0; Provisional

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 18/44 (40%), Positives = 27/44 (61%)

Query: 73  AVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMG 116
           A   G +GGG +A+A +     AA + AA+E++EE +E D  MG
Sbjct: 277 AALEGLLGGGGSAAAEAAAAAPAAASAAAKEEEEESDEDDFGMG 320

Length = 323

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	121
KOG1762	114	consensus 60s acidic ribosomal protein P1 [Transla	99.88
cd05833	109	Ribosomal_P2 Ribosomal protein P2. This subfamily	99.76
PTZ00373	112	60S Acidic ribosomal protein P2; Provisional	99.73
PLN00138	113	large subunit ribosomal protein LP2; Provisional	99.71
cd04411	105	Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and	99.69
cd05831	103	Ribosomal_P1 Ribosomal protein P1. This subfamily	99.63
KOG3449	112	consensus 60S acidic ribosomal protein P2 [Transla	99.48
PF00428	88	Ribosomal_60s: 60s Acidic ribosomal protein; Inter	99.43
COG2058	109	RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Tr	99.37
PRK06402	106	rpl12p 50S ribosomal protein L12P; Reviewed	99.02
TIGR03685	105	L21P_arch 50S ribosomal protein L12P. This model r	98.46
PTZ00135	310	60S acidic ribosomal protein P0; Provisional	98.44
cd05832	106	Ribosomal_L12p Ribosomal protein L12p. This subfam	98.42
PTZ00240	323	60S ribosomal protein P0; Provisional	97.27
KOG3449	112	consensus 60S acidic ribosomal protein P2 [Transla	92.92
cd05833	109	Ribosomal_P2 Ribosomal protein P2. This subfamily	89.46
cd04411	105	Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and	88.25
cd05831	103	Ribosomal_P1 Ribosomal protein P1. This subfamily	83.55
PLN00138	113	large subunit ribosomal protein LP2; Provisional	82.2

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

Probab=99.88  E-value=2e-23  Score=153.01  Aligned_cols=91  Identities=35%  Similarity=0.464  Sum_probs=66.6

Q ss_pred             cchHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCCCCCcc-CCCCCCCCCCCCCCCC-CCCchhhhhccc
Q 033353           30 ASTYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAVGSGFI-GGGAAASAPSGGGGAA-AEAPAAEEKKEE  107 (121)
Q Consensus        30 ~~~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~g~~~~-gggaAa~aaagg~~aa-a~~~k~EekkEE  107 (121)
                      ..|-+.-.+|++++. ++|++|||.||++.|+++||.++|+|+|.|++++ ++.++++.|+++++++ ++++|+|.||||
T Consensus        22 ~it~dki~tl~kaa~-v~ve~~Wp~lfakale~vni~~li~n~gag~~a~a~~~~~~~~aa~~~~aA~~~Ekk~eak~Ee  100 (114)
T KOG1762|consen   22 EVTADKINTLTKAAG-VNVEPYWPGLFAKALEGVNIKELICNVGAGGGALAAGAAAAGGAAAAGGAAAAEEKKEEAKKEE  100 (114)
T ss_pred             eeehhhhhhHHHhcc-CcccccchhHHHHHhccCChHHHHHhcccCCccCCCccccccccccccccccchHHHHHhhhhh
Confidence            345566677777665 9999999999999999999999999999754443 2222222333333233 456666667778


Q ss_pred             ccccccccCcCCCC
Q 033353          108 KEESDEDMGFSLFD  121 (121)
Q Consensus       108 ~EEsddDmGF~LFD  121 (121)
                      .|||||||||+|||
T Consensus       101 seesddDmgfGLfd  114 (114)
T KOG1762|consen  101 SEESDDDMGFGLFD  114 (114)
T ss_pred             hcccccccccCCCC
Confidence            89999999999998

>cd05833 Ribosomal_P2 Ribosomal protein P2

Probab=99.76  E-value=2.3e-19  Score=130.16  Aligned_cols=88  Identities=33%  Similarity=0.389  Sum_probs=55.8

Q ss_pred             chHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCC--CCCcc-CCCCCCCCCCCCCCCCCCCchhhhhc-c
Q 033353           31 STYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAV--GSGFI-GGGAAASAPSGGGGAAAEAPAAEEKK-E  106 (121)
Q Consensus        31 ~~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~--g~~~~-gggaAa~aaagg~~aaa~~~k~Eekk-E  106 (121)
                      .|-+=-+++++++- ++|+++|+.+|++.|.+|||.+||.++..  +..++ +++++++  ++++++++.++++++|| |
T Consensus        18 pTa~dI~~IL~AaG-veVe~~~~~lf~~~L~GKdi~eLIa~g~~kl~s~~~~~~~aa~a--~~~~a~aa~~~~~e~kkee   94 (109)
T cd05833          18 PSAADVKKILGSVG-VEVDDEKLNKVISELEGKDVEELIAAGKEKLASVPAGAGGAAPA--AAAAAAAAAAAKKEEKKEE   94 (109)
T ss_pred             CCHHHHHHHHHHcC-CCccHHHHHHHHHHHcCCCHHHHHHHhHhhhcCCCccccccccc--cccccccccchhhhhhccC
Confidence            34444566777766 99999999999999999999999997665  22111 1112121  11111222223334444 4


Q ss_pred             cccccccccCcCCCC
Q 033353          107 EKEESDEDMGFSLFD  121 (121)
Q Consensus       107 E~EEsddDmGF~LFD  121 (121)
                      ++||+||||||+|||
T Consensus        95 ~eee~ddDmGf~LFd  109 (109)
T cd05833          95 SEEESDDDMGFGLFD  109 (109)
T ss_pred             CccccccccCCCCCC
Confidence            445679999999998

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=99.73  E-value=1.1e-18  Score=127.63  Aligned_cols=84  Identities=27%  Similarity=0.346  Sum_probs=53.9

Q ss_pred             HHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeee-------ccCCCCCccCCCCCCCCCCCCCCCCCCCchhhhhc
Q 033353           33 YELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVII-------GGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKK  105 (121)
Q Consensus        33 ~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~-------g~g~g~~~~gggaAa~aaagg~~aaa~~~k~Eekk  105 (121)
                      -+=-+++++++- ++|+++|+.+|.+.|.+|||.+||.       .+|++++++. ++++ +++++  ++++++++++|+
T Consensus        22 addI~kIL~AaG-veVd~~~~~l~~~~L~GKdI~ELIa~G~~kl~svgg~~~aa~-a~a~-~~~~~--~~~~~~~~e~k~   96 (112)
T PTZ00373         22 KKEVKNVLSAVN-ADVEDDVLDNFFKSLEGKTPHELIAAGMKKLQNIGGGVAAAA-APAA-GAATA--GAKAEAKKEEKK   96 (112)
T ss_pred             HHHHHHHHHHcC-CCccHHHHHHHHHHHcCCCHHHHHHHhHHHHhcccCcccccc-cccc-ccccc--ccchhhhhhhcc
Confidence            344456677666 9999999999999999999999996       2322111111 1111 11011  222334445556


Q ss_pred             ccccccccccCcCCCC
Q 033353          106 EEKEESDEDMGFSLFD  121 (121)
Q Consensus       106 EE~EEsddDmGF~LFD  121 (121)
                      ||+|||||||||+|||
T Consensus        97 ee~ee~ddDmgf~LFd  112 (112)
T PTZ00373         97 EEEEEEEDDLGFSLFG  112 (112)
T ss_pred             cccccccccccccccC
Confidence            6667899999999998

>PLN00138 large subunit ribosomal protein LP2; Provisional

Probab=99.71  E-value=4.5e-18  Score=124.22  Aligned_cols=89  Identities=35%  Similarity=0.419  Sum_probs=55.3

Q ss_pred             chHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeee-------ccCCCCCccCCCCCCCCCCCCCCCCCCCchhhh
Q 033353           31 STYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVII-------GGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEE  103 (121)
Q Consensus        31 ~~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~-------g~g~g~~~~gggaAa~aaagg~~aaa~~~k~Ee  103 (121)
                      .|-+=-++|+.++- ++|+++|+.+|++.|++|+|.+||.       ++++|++++..++++++++++ +++++++++++
T Consensus        18 pta~dI~~IL~AaG-vevd~~~~~~f~~~L~gK~i~eLIa~G~~kl~sv~~gg~aa~a~a~a~~~~~~-~~~~~~~~~e~   95 (113)
T PLN00138         18 PSAEDLKDILGSVG-ADADDDRIELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAAAPAAGGA-AAPAAEAKKEE   95 (113)
T ss_pred             CCHHHHHHHHHHcC-CcccHHHHHHHHHHHcCCCHHHHHHhchhccccCCCCCccccccccccccccc-cccccchhhhh
Confidence            34455567777776 9999999999999999999999994       344333211111111111111 11122333344


Q ss_pred             hcccccccccccCcCCCC
Q 033353          104 KKEEKEESDEDMGFSLFD  121 (121)
Q Consensus       104 kkEE~EEsddDmGF~LFD  121 (121)
                      |+|++||+||||||+|||
T Consensus        96 k~e~eeE~ddDmGfgLFd  113 (113)
T PLN00138         96 KVEEKEESDDDMGFSLFD  113 (113)
T ss_pred             hccccccccccccccccC
Confidence            455557889999999998

>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p

Probab=99.69  E-value=8.6e-18  Score=121.13  Aligned_cols=87  Identities=29%  Similarity=0.319  Sum_probs=57.2

Q ss_pred             chHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCC--CCCccCCCCCCCCCCCCCCCCCCCchhhhhcccc
Q 033353           31 STYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAV--GSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEK  108 (121)
Q Consensus        31 ~~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~--g~~~~gggaAa~aaagg~~aaa~~~k~EekkEE~  108 (121)
                      -|-+=-++++..+. ++|+++|+.+|.+.|.+++|.+||.++..  ++.+.++++ +++++++ +++++++++|+|+||+
T Consensus        17 ~ta~~I~~IL~aaG-veVe~~~~~~~~~aLaGk~V~eli~~g~~kl~~~~~~~~a-~~~a~~~-~~~~~~~~~e~k~ee~   93 (105)
T cd04411          17 LTEDKIKELLSAAG-AEIEPERVKLFLSALNGKNIDEVISKGKELMSSQAAAAAA-PAATAAA-TAEPAEKAEEAKEEEE   93 (105)
T ss_pred             CCHHHHHHHHHHcC-CCcCHHHHHHHHHHHcCCCHHHHHHHHHhhccCCCCcccc-ccccccc-cccchhhhhhhhcccc
Confidence            34445567777776 99999999999999999999999987654  222222222 2111111 1222233444445566


Q ss_pred             cccccccCcCCC
Q 033353          109 EESDEDMGFSLF  120 (121)
Q Consensus       109 EEsddDmGF~LF  120 (121)
                      ||+||||||+||
T Consensus        94 eE~dddmgf~LF  105 (105)
T cd04411          94 EEEDEDFGFGLF  105 (105)
T ss_pred             cccccccCcccC
Confidence            788999999999

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

>cd05831 Ribosomal_P1 Ribosomal protein P1

Probab=99.63  E-value=1.2e-16  Score=114.61  Aligned_cols=85  Identities=33%  Similarity=0.374  Sum_probs=53.7

Q ss_pred             hHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCCCCCccCCCCCCCCCCCCCCCCCCCchhhhhccccccc
Q 033353           32 TYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEES  111 (121)
Q Consensus        32 ~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~g~~~~gggaAa~aaagg~~aaa~~~k~EekkEE~EEs  111 (121)
                      |-+--+++++++. ++|+++|+.+|.+.|.+++|.+||.+++++++.+++ +++++++++  +..+++++++|+|++||+
T Consensus        19 Tae~I~~ilkAaG-veve~~~~~~f~~~L~gk~i~elIa~~~~~~~~aap-~a~~a~~~~--~~~~~~~~~kk~e~eee~   94 (103)
T cd05831          19 TADNINALLKAAG-VNVEPYWPGLFAKALEGKDIKDLLSNVGGGGGGAAP-AAAAAAAAA--AAAEAKKEEKKEEEEEES   94 (103)
T ss_pred             CHHHHHHHHHHcC-CcccHHHHHHHHHHHcCCCHHHHhhccccccccccc-ccccccccc--ccccchhhhccccccccc
Confidence            3334466666665 999999999999999999999999877643322111 111111111  112222334344555678


Q ss_pred             ccccCcCCC
Q 033353          112 DEDMGFSLF  120 (121)
Q Consensus       112 ddDmGF~LF  120 (121)
                      ||||||+||
T Consensus        95 d~dmgfglF  103 (103)
T cd05831          95 DDDMGFGLF  103 (103)
T ss_pred             ccccccccC
Confidence            999999999

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

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

Probab=99.48  E-value=1.2e-14  Score=106.60  Aligned_cols=85  Identities=38%  Similarity=0.481  Sum_probs=54.4

Q ss_pred             HHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCC--CCCccCCC--CCCCCCCCCCC-CCCCCchhhhhcccccc
Q 033353           36 QRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAV--GSGFIGGG--AAASAPSGGGG-AAAEAPAAEEKKEEKEE  110 (121)
Q Consensus        36 q~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~--g~~~~ggg--aAa~aaagg~~-aaa~~~k~EekkEE~EE  110 (121)
                      .++++..+- ++++.-+..+|-.-|.+|+|.+||..+=.  ...+.||+  +++++++++++ +++...++|+|+||+||
T Consensus        23 ikkIl~sVG-~E~d~e~i~~visel~GK~i~ElIA~G~eklAsvpsGGa~~aaa~~aaggaa~aa~~a~~~e~keEe~ee  101 (112)
T KOG3449|consen   23 IKKILESVG-AEIDDERINLVLSELKGKDIEELIAAGREKLASVPSGGAVAAAAAPAAGGAAGAAPAAAKEEEKEEEKEE  101 (112)
T ss_pred             HHHHHHHhC-cccCHHHHHHHHHHhcCCCHHHHHHHhHHHHhcCCCCCccccccCcCCCCCccCCccchhhhhhhhhccc
Confidence            356666665 89999999999999999999999873221  22222222  11111122222 22233344556666689


Q ss_pred             cccccCcCCCC
Q 033353          111 SDEDMGFSLFD  121 (121)
Q Consensus       111 sddDmGF~LFD  121 (121)
                      |||||||+|||
T Consensus       102 sddDmgf~lFd  112 (112)
T KOG3449|consen  102 SDDDMGFGLFD  112 (112)
T ss_pred             ccccccccccC
Confidence            99999999998

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

Probab=99.43  E-value=1.6e-16  Score=109.83  Aligned_cols=79  Identities=37%  Similarity=0.495  Sum_probs=47.5

Q ss_pred             HHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCCCCCccCCCCCCCCCCCCCCCCCCCchhhhhc-ccc-cccccc
Q 033353           37 RKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKK-EEK-EESDED  114 (121)
Q Consensus        37 ~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~g~~~~gggaAa~aaagg~~aaa~~~k~Eekk-EE~-EEsddD  114 (121)
                      ++|++++. ++|+++|+.+|++.|.+++|.+||.+++.+.+++++++++++++    .+++.++++++| +++ ||+|||
T Consensus         8 ~~vl~aag-~~v~~~~~~~~~~~l~~~~i~~li~~~~~~~~~~aaa~aaa~aa----~~~a~a~~e~kkEeeeeEEed~d   82 (88)
T PF00428_consen    8 KKVLKAAG-VEVEAIWLELFAKALEGKDIKELIANGSAGMAAAAAAAAAAAAA----AAAAAAAEEEKKEEEEEEEEDDD   82 (88)
T ss_dssp             HHHHHHHT-HHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHTTSSHHH----HHHHHHHSTTHHHHT--SS-SSS
T ss_pred             HHHHHHhC-CchhHHHHHHHHHHHcCCcHHHHHhccccccccccccccccccc----ccccccchhcccccccccccccc
Confidence            56677776 79999999999999999999999997664321111111110000    111112222222 222 588999


Q ss_pred             cCcCCC
Q 033353          115 MGFSLF  120 (121)
Q Consensus       115 mGF~LF  120 (121)
                      |||+||
T Consensus        83 mGf~LF   88 (88)
T PF00428_consen   83 MGFGLF   88 (88)
T ss_dssp             SSTTTT
T ss_pred             cCcCCC
Confidence            999999

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=99.37  E-value=1.5e-13  Score=100.39  Aligned_cols=86  Identities=28%  Similarity=0.352  Sum_probs=54.8

Q ss_pred             HHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCCCCCcc-CCCCCCCCCCCCCCCCCC-Cchhhhhc-cccccc
Q 033353           35 LQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAVGSGFI-GGGAAASAPSGGGGAAAE-APAAEEKK-EEKEES  111 (121)
Q Consensus        35 lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~g~~~~-gggaAa~aaagg~~aaa~-~~k~Eekk-EE~EEs  111 (121)
                      --+++++++. ++|++.|..+|...|+++||.++|.++....+++ .+++++++++++.++++. ++++|+++ +.+||+
T Consensus        21 ~l~~vl~aaG-veve~~r~k~lvaaLeg~~idE~i~~~~~~~~a~a~a~aaaa~~A~~~~a~~~~ea~eEe~eEe~~EE~   99 (109)
T COG2058          21 NLKSVLEAAG-VEVEEARAKALVAALEGVDIDEVIKNAAEAPAAAAAAGAAAAAAAGAEAAAEADEAEEEEKEEEAEEES   99 (109)
T ss_pred             HHHHHHHHcC-CCccHHHHHHHHHHhcCCCHHHHHHHhcccccccCCcccccccccccccccchhhHHHHHhhhchhhcc
Confidence            3456666554 9999999999999999999999999877642222 222222222333212222 33333333 344688


Q ss_pred             ccccCcCCCC
Q 033353          112 DEDMGFSLFD  121 (121)
Q Consensus       112 ddDmGF~LFD  121 (121)
                      ++||+|+|||
T Consensus       100 ~~~~lf~LF~  109 (109)
T COG2058         100 DDDMLFGLFG  109 (109)
T ss_pred             cccchhhccC
Confidence            9999999998

>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed

Probab=99.02  E-value=5.4e-11  Score=86.46  Aligned_cols=42  Identities=7%  Similarity=0.048  Sum_probs=35.2

Q ss_pred             hHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCC
Q 033353           32 TYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAV   74 (121)
Q Consensus        32 ~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~   74 (121)
                      |-+=-+++++++. ++|+++|+.+|.+.|.++||.++|.+.+.
T Consensus        18 t~e~I~~IL~AAG-veVee~~~k~~v~aL~GkdIeElI~~a~~   59 (106)
T PRK06402         18 NEDNLKKVLEAAG-VEVDEARVKALVAALEDVNIEEAIKKAAA   59 (106)
T ss_pred             CHHHHHHHHHHcC-CCccHHHHHHHHHHHcCCCHHHHHHhccc
Confidence            3444566677666 99999999999999999999999998775

>TIGR03685 L21P_arch 50S ribosomal protein L12P

Probab=98.46  E-value=5.7e-08  Score=70.22  Aligned_cols=43  Identities=7%  Similarity=0.003  Sum_probs=36.0

Q ss_pred             chHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCC
Q 033353           31 STYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAV   74 (121)
Q Consensus        31 ~~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~   74 (121)
                      .|-+--.+|+++|. ++|+++|+.+|++.|++++|.++|.+...
T Consensus        17 iT~e~I~~IL~AAG-v~ve~~~~~~la~~L~gk~i~eli~~~~~   59 (105)
T TIGR03685        17 INEENLKAVLEAAG-VEVDEARVKALVAALEGVNIEEAIKKAAA   59 (105)
T ss_pred             CCHHHHHHHHHHhC-CcccHHHHHHHHHHHcCCCHHHHHHhhhc
Confidence            34455667788777 99999999999999999999999987653

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

>PTZ00135 60S acidic ribosomal protein P0; Provisional

Probab=98.44  E-value=3.2e-08  Score=82.36  Aligned_cols=21  Identities=5%  Similarity=-0.088  Sum_probs=16.4

Q ss_pred             HhhhccCCcchhhhhhccCCC
Q 033353           42 TSLSADSSGGVQSSFSLVTPT   62 (121)
Q Consensus        42 ~a~~~eVe~~w~slFA~~L~~   62 (121)
                      .+.+..++++||.+|++++.+
T Consensus       227 ~aag~pt~~s~p~~ia~a~k~  247 (310)
T PTZ00135        227 LAAGYPTEASAPHSILNAFKN  247 (310)
T ss_pred             HHhCCCcHHHHHHHHHHHHHH
Confidence            334678899999999987754

>cd05832 Ribosomal_L12p Ribosomal protein L12p

Probab=98.42  E-value=7.7e-08  Score=70.03  Aligned_cols=43  Identities=12%  Similarity=0.053  Sum_probs=36.5

Q ss_pred             chHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCC
Q 033353           31 STYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAV   74 (121)
Q Consensus        31 ~~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~   74 (121)
                      -|-+--++|+++|. ++|+++|+.+|+..|+++||.++|.+.+.
T Consensus        17 ITae~I~~IL~AAG-veVd~~~~~ala~aL~gkdIeElIa~~~~   59 (106)
T cd05832          17 INEENLKKVLEAAG-IEVDEARVKALVAALEEVNIDEAIKKAAV   59 (106)
T ss_pred             CCHHHHHHHHHHhC-CcccHHHHHHHHHHHcCCCHHHHHHhccc
Confidence            34455677788777 99999999999999999999999988774

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

>PTZ00240 60S ribosomal protein P0; Provisional

Probab=97.27  E-value=0.00015  Score=61.25  Aligned_cols=15  Identities=40%  Similarity=0.831  Sum_probs=11.0

Q ss_pred             hcccccccccccCcC
Q 033353          104 KKEEKEESDEDMGFS  118 (121)
Q Consensus       104 kkEE~EEsddDmGF~  118 (121)
                      ++||+||+||||||+
T Consensus       306 ~~~~~e~~~~d~~~~  320 (323)
T PTZ00240        306 KEEEEESDEDDFGMG  320 (323)
T ss_pred             ccCCccCcccccCcc
Confidence            345556788999995

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

Probab=92.92  E-value=0.09  Score=38.98  Aligned_cols=80  Identities=25%  Similarity=0.182  Sum_probs=37.1

Q ss_pred             cchHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCCCCCccCCCCCCCCCCCCCCCCCCCchhhhhccccc
Q 033353           30 ASTYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKE  109 (121)
Q Consensus        30 ~~~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~g~~~~gggaAa~aaagg~~aaa~~~k~EekkEE~E  109 (121)
                      +..-+--+.++....+-+++..++.--.+      +-.|-++++.  +.+..++++++ ++.+.+++.++++|+++||++
T Consensus        33 E~d~e~i~~visel~GK~i~ElIA~G~ek------lAsvpsGGa~--~aaa~~aagga-a~aa~~a~~~e~keEe~eesd  103 (112)
T KOG3449|consen   33 EIDDERINLVLSELKGKDIEELIAAGREK------LASVPSGGAV--AAAAAPAAGGA-AGAAPAAAKEEEKEEEKEESD  103 (112)
T ss_pred             ccCHHHHHHHHHHhcCCCHHHHHHHhHHH------HhcCCCCCcc--ccccCcCCCCC-ccCCccchhhhhhhhhccccc
Confidence            44556667788888877766544432222      1222222221  11111111111 112224444444444458888


Q ss_pred             ccccccCcC
Q 033353          110 ESDEDMGFS  118 (121)
Q Consensus       110 EsddDmGF~  118 (121)
                      ++..-+-|+
T Consensus       104 dDmgf~lFd  112 (112)
T KOG3449|consen  104 DDMGFGLFD  112 (112)
T ss_pred             ccccccccC
Confidence            887766553

>cd05833 Ribosomal_P2 Ribosomal protein P2

Probab=89.46  E-value=0.2  Score=36.52  Aligned_cols=19  Identities=26%  Similarity=0.349  Sum_probs=11.1

Q ss_pred             CCCCchhhhhccccccccc
Q 033353           95 AAEAPAAEEKKEEKEESDE  113 (121)
Q Consensus        95 aa~~~k~EekkEE~EEsdd  113 (121)
                      +..++++|+++||++++..
T Consensus        86 ~~~e~kkee~eee~ddDmG  104 (109)
T cd05833          86 AKKEEKKEESEEESDDDMG  104 (109)
T ss_pred             hhhhhhccCCccccccccC
Confidence            3455556666767666543

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=88.25  E-value=0.29  Score=35.37  Aligned_cols=28  Identities=7%  Similarity=-0.039  Sum_probs=15.2

Q ss_pred             chHHHHHHHHHHhhhccCCcchhhhhhc
Q 033353           31 STYELQRKLVQTSLSADSSGGVQSSFSL   58 (121)
Q Consensus        31 ~~~~lq~~lv~~a~~~eVe~~w~slFA~   58 (121)
                      .+=+.-..+++...+.+++..+...-++
T Consensus        33 Ve~~~~~~~~~aLaGk~V~eli~~g~~k   60 (105)
T cd04411          33 IEPERVKLFLSALNGKNIDEVISKGKEL   60 (105)
T ss_pred             cCHHHHHHHHHHHcCCCHHHHHHHHHhh
Confidence            3334445566665677776655444333

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

>cd05831 Ribosomal_P1 Ribosomal protein P1

Probab=83.55  E-value=0.82  Score=32.84  Aligned_cols=18  Identities=6%  Similarity=-0.158  Sum_probs=9.6

Q ss_pred             HHHHHHHHHhhhccCCcc
Q 033353           34 ELQRKLVQTSLSADSSGG   51 (121)
Q Consensus        34 ~lq~~lv~~a~~~eVe~~   51 (121)
                      .+-..+++...+.++...
T Consensus        37 ~~~~~f~~~L~gk~i~el   54 (103)
T cd05831          37 YWPGLFAKALEGKDIKDL   54 (103)
T ss_pred             HHHHHHHHHHcCCCHHHH
Confidence            344455666666565543

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=82.20  E-value=0.92  Score=33.29  Aligned_cols=15  Identities=27%  Similarity=0.415  Sum_probs=7.1

Q ss_pred             CCchhhhhcccccccc
Q 033353           97 EAPAAEEKKEEKEESD  112 (121)
Q Consensus        97 ~~~k~EekkEE~EEsd  112 (121)
                      .++++ +++||+|++.
T Consensus        93 ~e~k~-e~eeE~ddDm  107 (113)
T PLN00138         93 KEEKV-EEKEESDDDM  107 (113)
T ss_pred             hhhhc-cccccccccc
Confidence            34333 4445556554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	121
3iz5_t	110	60S acidic ribosomal protein P11 - P1 (L12P); euka	99.87
3izc_t	106	60S acidic ribosomal protein RPP11 (P1); eukaryoti	99.84
3iz5_v	113	60S acidic ribosomal protein P21 - P2 (L12P); euka	99.83
3izc_v	106	60S acidic ribosomal protein (P2); eukaryotic ribo	99.79
3iz5_s	319	60S acidic ribosomal protein P0 (L10P); eukaryotic	98.76
3u5i_q	312	A0, L10E, 60S acidic ribosomal protein P0; transla	98.64
2lbf_A	69	60S acidic ribosomal protein P1; ribosome, stalk,	98.49
2zkr_g	317	60S acidic ribosomal protein P0; protein-RNA compl	98.48
3a1y_A	58	50S ribosomal protein P1 (L12P); stalk, helix SPIN	97.48
2lbf_B	70	60S acidic ribosomal protein P2; ribosome, stalk,	97.3
3izc_v	106	60S acidic ribosomal protein (P2); eukaryotic ribo	89.83
3iz5_t	110	60S acidic ribosomal protein P11 - P1 (L12P); euka	87.59
3izc_t	106	60S acidic ribosomal protein RPP11 (P1); eukaryoti	86.17
3iz5_v	113	60S acidic ribosomal protein P21 - P2 (L12P); euka	84.59

>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=98.64  E-value=3.1e-09  Score=87.17  Aligned_cols=22  Identities=68%  Similarity=1.046  Sum_probs=0.0

Q ss_pred             hhhhhcccccccccccCcCCCC
Q 033353          100 AAEEKKEEKEESDEDMGFSLFD  121 (121)
Q Consensus       100 k~EekkEE~EEsddDmGF~LFD  121 (121)
                      ++++++||+|||||||||+|||
T Consensus       291 ~~~~~~e~~ee~d~d~gf~lfd  312 (312)
T 3u5i_q          291 AEEAAAEEEEESDDDMGFGLFD  312 (312)
T ss_dssp             ----------------------
T ss_pred             cccccccccccccccCCCCCCC
Confidence            3344555667899999999998

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

Probab=98.49  E-value=4.3e-08  Score=65.24  Aligned_cols=44  Identities=11%  Similarity=0.050  Sum_probs=36.9

Q ss_pred             hHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCCCC
Q 033353           32 TYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAVGS   76 (121)
Q Consensus        32 ~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~g~   76 (121)
                      |-+=-++++++|. ++|+++|+.+|++.|+++||.++|.+.|+|+
T Consensus        24 ta~~I~~il~AaG-veve~~~~~lf~~aL~gk~I~elI~~~g~g~   67 (69)
T 2lbf_A           24 TEDKINALIKAAG-VNVEPFWPGLFAKALANVNIGSLICNVGAGG   67 (69)
T ss_dssp             CHHHHHHHHHHHT-CCCCTHHHHHHHHHTTTSCGGGGGTTTTCCC
T ss_pred             CHHHHHHHHHHcC-CCccHHHHHHHHHHHCCCCHHHHHHhccCCC
Confidence            3444567777776 9999999999999999999999999887654

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

Probab=98.48  E-value=4.1e-10  Score=92.59  Aligned_cols=57  Identities=42%  Similarity=0.483  Sum_probs=21.5

Q ss_pred             CCcceeeeeeccCCCCCccCCCCCCCCCCCCCCCCCCCchhhhhcccccccccccCcCCCC
Q 033353           61 PTSAVFQVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEESDEDMGFSLFD  121 (121)
Q Consensus        61 ~~k~V~~~i~g~g~g~~~~gggaAa~aaagg~~aaa~~~k~EekkEE~EEsddDmGF~LFD  121 (121)
                      +.++|+++|.+.+.+++++    |+++++++++++++++++++++||+|||||||||+|||
T Consensus       261 ea~~vk~~l~~~~~~~~a~----a~~a~~~~~~~~~~~~~~~~~~ee~ee~d~d~gf~lfd  317 (317)
T 2zkr_g          261 LAEKVKAFLADPSAFVAAA----PVAAATTAAPAAAAAPAKVEAKEESEESDEDMGFGLFD  317 (317)
T ss_dssp             CHHHHHTTTHHHHHHHHHH----HHHTTSSHHHHHHHHHHSTTHHHHTSSCC---------
T ss_pred             hhhhHHHHHhccCcccccc----ccccccccccccccccccccccCCccccccccCcCCCC
Confidence            3567788887665432211    11111111001112233444556667899999999998

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

Probab=97.48  E-value=1e-05  Score=51.90  Aligned_cols=38  Identities=11%  Similarity=0.022  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeec
Q 033353           33 YELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIG   71 (121)
Q Consensus        33 ~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g   71 (121)
                      -+=-++++++|. ++|+++|+.+|++.|+++||.++|.+
T Consensus        19 ~~~I~~il~aaG-veve~~~~~~~~~~L~gk~i~elI~~   56 (58)
T 3a1y_A           19 EENLKAVLQAAG-VEPEEARIKALVAALEGVNIDEVIEK   56 (58)
T ss_dssp             HHHHHHHHHHTT-CCCCHHHHHHHHHHHSSCCHHHHHHH
T ss_pred             HHHHHHHHHHcC-CCccHHHHHHHHHHHCCCCHHHHHHc
Confidence            344466777666 99999999999999999999999865

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

Probab=97.30  E-value=5.4e-05  Score=50.44  Aligned_cols=39  Identities=10%  Similarity=0.055  Sum_probs=32.4

Q ss_pred             HHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccC
Q 033353           34 ELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGA   73 (121)
Q Consensus        34 ~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g   73 (121)
                      +=-++++++|. ++|+++|+.+|++.|++|||.+||.++-
T Consensus        22 ~~I~~il~aaG-vevd~~~~~~~~~aL~gk~i~elIa~g~   60 (70)
T 2lbf_B           22 KDIKKILDSVG-IEADDDRLNKVISELNGKNIEDVIAQGI   60 (70)
T ss_dssp             HHHHHHHHTTT-CCCCTTHHHHHHHHHSSCCHHHHHTTCS
T ss_pred             HHHHHHHHHcC-CCccHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            33456677665 9999999999999999999999997643

---

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