Citrus Sinensis ID: 030457

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------
Protein Sequence
MASLSITTSIPPPWLTSKSTHHSRRIPSASLILRTGRSSVSVNVAGNNSSPSRPGLLHCSFVSSSLCSSAFHSAFSGLSLGLDFNSNAGVRKEKRQGLVVRAGKAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFDSLLGIFQRPSSGNKYVSTEKPPFQWM
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccEEEEEcccEEEEEEcccccccccccccEEEcccccccccccccccccccccEEEEcccccccccccEEEEEccccEEEEccccccHHHHHHHHHHcccccccHHHHHHHHHHHcccEEEEccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEcccccccEEccccccccccccEEEEEEcccccccEEEEcccccccccccEEEcEccccccccccccccccccccEEEccccccccccccEEEEEccccHHHHccccccHHHHHHHccHHHccccccHHHHHHHHHHcccEEEEHHHHHHcEccccccEEEEccccccccc
Coil and Loop (DISEMBL)
maslsittsipppwltsksthhsrripsaslilrtgrssvsvnvagnnsspsrpgllhcsfvssslcssafHSAFSglslgldfnsnagvrkekRQGLVVRAGKAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFDSLLGifqrpssgnkyvstekppfqwm
Flexible Loop (DISEMBL)
maslsittsipppwltsksthhsrriPSASLILRTGRSSVSVNVAGNNSSPSRPGLLHCSFVSSSLCSSAFHSAFSGLSLGLDFNSNAGVRKekrqglvvragkaalcqtkrnrsrkslarthgfrrrmrttsgrailkrrrakgrevvfdsllgifqrpssgnkyvstekppfqwm
Low Complexity Region (SEG)
MASLSITTSIPPPWLTSKSTHHSRRIPSASLILRTGRssvsvnvagnnsspsRPGllhcsfvssslcssafhsafsGLSLGLDFNSNAGVRKEKRQGLVVRAGKAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFDSLLGIFQRPSSGNKYVSTEKPPFQWM
Disordered region (IsUnstruct)
*******************************************************LLHCSFVSSSLCSSAFHSAFSGLSLGLDFNSNAGV*****QGLVVRAGKAALC************************************GREVVFDSLLGIF********************
Disordered Region (DISOPRED)
**********************************************************CSFVSS**********FSGLSLGLDFNSNAG********LVVRAGKAAL***********************************AKGREVVFD********************PPFQW*
Disordered Region (DISEMBL)
MASLSITTSIPPPWL**********IPSASLILRTGRSSVSVNVAGNNSSPSRPGLLHCSFVSSSLCSSAFHSAFSGLSLGLDFNSNAGVRKEKRQGLVVRAGKAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFDSLLGIFQRPSSGNKYVSTEKPPFQWM
Disordered Region (DISPRO)
**SLSITTSIPPPWLTSKSTHHSRRIPSASLILRTGRSSVSVN******SPSRPGLLHCSFVSS*****AFHSAFSGLSLGLDFNSNAGVRKEKRQGLVVRAGKAALCQTKR*************RRR***TSGRAILKRRRAKGREVVFDSLLGIFQRPSSGNKYVS*EKPPF***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASLSITTSIPPPWLTSKSTHHSRRIPSASLILRTGRSSVSVNVAGNNSSPSRPGLLHCSFVSSSLCSSAFHSAFSGLSLGLDFNSNAGVRKEKRQGLVVRAGKAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFDSLLGIFQRPSSGNKYVSTEKPPFQWM
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	177	2.2.26 [Sep-21-2011]
Q9LP37	157	50S ribosomal protein L34	yes	no	0.644	0.726	0.614	1e-26
P82244	152	50S ribosomal protein L34	N/A	no	0.841	0.980	0.521	6e-25
Q04CX6	44	50S ribosomal protein L34	yes	no	0.197	0.795	0.571	0.0008

>sp|Q9LP37|RK34_ARATH 50S ribosomal protein L34, chloroplastic OS=Arabidopsis thaliana GN=RPL34 PE=2 SV=1

 Score =  119 bits (298), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 75/122 (61%), Positives = 92/122 (75%), Gaps = 8/122 (6%)

Query: 26  IPSASLILRTGRSSVSVNVAGNNSSPSRPGLLHCSFVSSSLCSSAFHSAFSGLSLGLDFN 85
           +PSASL LRTG        + + +S +   LLHCSF+SS +   +  S FSGLS+  D +
Sbjct: 28  VPSASLSLRTG----CRRSSSSLTSSASSQLLHCSFLSSPV---SLASPFSGLSIAFDLS 80

Query: 86  SN-AGVRKEKRQGLVVRAGKAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAK 144
           S  +G+  ++R+GLVVRAGKAALCQTKR+RSRKSLARTHGFRRRMRTTSGRA +KRRRAK
Sbjct: 81  SQTSGLNGQRRRGLVVRAGKAALCQTKRSRSRKSLARTHGFRRRMRTTSGRATIKRRRAK 140

Query: 145 GR 146
           GR
Sbjct: 141 GR 142

This protein binds directly to 23S ribosomal RNA.
Arabidopsis thaliana (taxid: 3702)

>sp|P82244|RK34_SPIOL 50S ribosomal protein L34, chloroplastic OS=Spinacia oleracea GN=RPL34 PE=1 SV=1

 Score =  113 bits (283), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 86/165 (52%), Positives = 108/165 (65%), Gaps = 16/165 (9%)

Query: 1   MASLSITTSIPPPWLTSKSTHHSRRIPSASLILRTGRSSVSVNVAGNNSSPSRPGLLHCS 60
           MA+LS+ ++     +T+       R PSASL   TG  + +  V+ N  S +R G LHCS
Sbjct: 1   MATLSLLSTGVGAAITN-------RTPSASLTFITGSRTTNKRVSFNGGS-ARSGSLHCS 52

Query: 61  FVSSSLCSSAFHSAFSGLSLGLDFNSNAGVRKEKRQGLVVRAGKAALCQTKRNRSRKSLA 120
           F++ S   S+  S FSGLSLGLD  SN GV  ++ +  VVRAGKAALC TKR+RSRKSLA
Sbjct: 53  FLAPS---SSLSSNFSGLSLGLDLTSNTGVSTDRCRRFVVRAGKAALCLTKRSRSRKSLA 109

Query: 121 RTHGFRRRMRTTSGRAILKRRRAKGREVVFDSLLGIFQRPSSGNK 165
           RTHGFR RM TTSGRA+LKRRRAKGR+++          PSSG +
Sbjct: 110 RTHGFRLRMSTTSGRALLKRRRAKGRKILCTK-----TNPSSGKR 149

This protein binds directly to 23S ribosomal RNA.

Spinacia oleracea (taxid: 3562)

>sp|Q04CX6|RL34_OENOB 50S ribosomal protein L34 OS=Oenococcus oeni (strain ATCC BAA-331 / PSU-1) GN=rpmH PE=3 SV=1

 Score = 43.5 bits (101), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 20/35 (57%), Positives = 27/35 (77%)

Query: 115 SRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVV 149
            ++ L R HGFR+RM T +GR +L RRRAKGR+V+
Sbjct: 8   KKRHLQRVHGFRKRMSTANGRKVLARRRAKGRKVL 42

Oenococcus oeni (strain ATCC BAA-331 / PSU-1) (taxid: 203123)

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	177
225443829	148	PREDICTED: 50S ribosomal protein L34, ch	0.802	0.959	0.625	1e-37
297740487	113	unnamed protein product [Vitis vinifera]	0.621	0.973	0.700	7e-34
255563108	161	50S ribosomal protein L34, chloroplast p	0.807	0.888	0.684	1e-32
449433766	155	PREDICTED: 50S ribosomal protein L34, ch	0.853	0.974	0.589	2e-27
147767567	148	hypothetical protein VITISV_036402 [Viti	0.491	0.587	0.728	2e-26
224116920	131	predicted protein [Populus trichocarpa]	0.666	0.900	0.704	3e-26
297845818	159	ribosomal protein L34 family protein [Ar	0.655	0.729	0.622	2e-25
15218810	157	50S ribosomal protein L34 [Arabidopsis t	0.644	0.726	0.614	5e-25
14285713	152	RecName: Full=50S ribosomal protein L34,	0.841	0.980	0.521	3e-23
351725279	146	uncharacterized protein LOC100526907 [Gl	0.700	0.849	0.546	2e-20

>gi|225443829|ref|XP_002274637.1| PREDICTED: 50S ribosomal protein L34, chloroplastic-like [Vitis vinifera]

 Score =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 100/160 (62%), Positives = 113/160 (70%), Gaps = 18/160 (11%)

Query: 9   SIPPPWLTSKSTHHSRRIPSASLILRTG---RSSVSVNVAGNNSSPSRPGLLHCSFVSSS 65
           SI   W+ S     SR +PSASL L  G   RS  S+N+  N   P+ P LLHCSF  + 
Sbjct: 3   SISVSWVCS-----SRAVPSASLSLLAGSKRRSLASLNMRNN---PTSPALLHCSFTPT- 53

Query: 66  LCSSAFHSAFSGLSLGLDFNSNAGVRKEKRQGLVVRAGKAALCQTKRNRSRKSLARTHGF 125
             S +F S+FSGLSLGLD NS+ GVRKE+  GLVVRAGKAALCQTKRNRSRKSLARTHGF
Sbjct: 54  -VSLSFPSSFSGLSLGLDLNSSVGVRKERGHGLVVRAGKAALCQTKRNRSRKSLARTHGF 112

Query: 126 RRRMRTTSGRAILKRRRAKGREVVFDSLLGIFQRPSSGNK 165
           RRRMRTTSGRA+LKRRRAKGR+V     L     PSSG +
Sbjct: 113 RRRMRTTSGRAVLKRRRAKGRKV-----LCTKSNPSSGKR 147

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297740487|emb|CBI30669.3| unnamed protein product [Vitis vinifera]

 Score =  148 bits (374), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 82/117 (70%), Positives = 93/117 (79%), Gaps = 7/117 (5%)

Query: 49  SSPSRPGLLHCSFVSSSLCSSAFHSAFSGLSLGLDFNSNAGVRKEKRQGLVVRAGKAALC 108
           ++P+ P LLHCSF  +   S +F S+FSGLSLGLD NS+ GVRKE+  GLVVRAGKAALC
Sbjct: 3   NNPTSPALLHCSFTPT--VSLSFPSSFSGLSLGLDLNSSVGVRKERGHGLVVRAGKAALC 60

Query: 109 QTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFDSLLGIFQRPSSGNK 165
           QTKRNRSRKSLARTHGFRRRMRTTSGRA+LKRRRAKGR+V     L     PSSG +
Sbjct: 61  QTKRNRSRKSLARTHGFRRRMRTTSGRAVLKRRRAKGRKV-----LCTKSNPSSGKR 112

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255563108|ref|XP_002522558.1| 50S ribosomal protein L34, chloroplast precursor, putative [Ricinus communis] gi|223538249|gb|EEF39858.1| 50S ribosomal protein L34, chloroplast precursor, putative [Ricinus communis]

 Score =  144 bits (363), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 104/152 (68%), Positives = 120/152 (78%), Gaps = 9/152 (5%)

Query: 2   ASLSITTSIPPP-WLTSKSTHHSRRIPSASLILRTG---RSSVSVNVAGNNSSPSRPGLL 57
           ASLS  +S PPP W++S+S   + R PSASL L TG   R+  S+NV  N  S SR GLL
Sbjct: 3   ASLSTISSAPPPQWMSSRS-QQTARCPSASLSLSTGTRPRNKFSMNVISN--STSRSGLL 59

Query: 58  HCSFVSSSLCSSAFHSAFSGLSLGLDFNSNAGVRKEKRQGLVVRAGKAALCQTKRNRSRK 117
           HCSF+S+S  S +  S+FSGLSLGLD NS+ GVRK +  GLVVRAGKAALCQTKRNRSRK
Sbjct: 60  HCSFLSTS--SLSLSSSFSGLSLGLDLNSSTGVRKGRGYGLVVRAGKAALCQTKRNRSRK 117

Query: 118 SLARTHGFRRRMRTTSGRAILKRRRAKGREVV 149
           SLARTHGFRRRMRTTSGRA+LKRRRAKGR+V+
Sbjct: 118 SLARTHGFRRRMRTTSGRAVLKRRRAKGRKVL 149

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449433766|ref|XP_004134668.1| PREDICTED: 50S ribosomal protein L34, chloroplastic-like [Cucumis sativus] gi|449479241|ref|XP_004155546.1| PREDICTED: 50S ribosomal protein L34, chloroplastic-like [Cucumis sativus]

 Score =  127 bits (318), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 99/168 (58%), Positives = 123/168 (73%), Gaps = 17/168 (10%)

Query: 1   MASLSITTSIPPPWLTSKSTHHSRRIPSASLILRTG---RSSVSVNVAGNNSSPSRPGLL 57
           MA++S+   +  PW+++ +   + R+PSASL+  TG     SVS+N   NNS+  R GLL
Sbjct: 1   MAAISV---LSTPWVSTGAI--AVRVPSASLVFSTGSRGYCSVSLNTVNNNSA--RSGLL 53

Query: 58  HCSFVSSSLCSSAFHSAFSGLSLGLDFNSNAGVRKEKRQGLVVRAGKAALCQTKRNRSRK 117
           HCSF+ SS  S +  S+FSGLSLGLD++S  GV + K +GLVVRAGKAALCQTKRNRSRK
Sbjct: 54  HCSFLPSS--SLSCSSSFSGLSLGLDWSSKVGVGQGKGRGLVVRAGKAALCQTKRNRSRK 111

Query: 118 SLARTHGFRRRMRTTSGRAILKRRRAKGREVVFDSLLGIFQRPSSGNK 165
           SLARTHGFRRRMRTT+GRA+LKRRRAKGR+V     L     PSSG +
Sbjct: 112 SLARTHGFRRRMRTTNGRAVLKRRRAKGRKV-----LCTKSNPSSGKR 154

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147767567|emb|CAN60201.1| hypothetical protein VITISV_036402 [Vitis vinifera]

 Score =  124 bits (310), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 67/92 (72%), Positives = 74/92 (80%), Gaps = 5/92 (5%)

Query: 74  AFSGLSLGLDFNSNAGVRKEKRQGLVVRAGKAALCQTKRNRSRKSLARTHGFRRRMRTTS 133
            +  LSLGLD NS+ GVRKE+  GLVVRAGKAALCQTKRNRSRKSLARTHGFRRRMRTTS
Sbjct: 61  VWECLSLGLDLNSSVGVRKERGHGLVVRAGKAALCQTKRNRSRKSLARTHGFRRRMRTTS 120

Query: 134 GRAILKRRRAKGREVVFDSLLGIFQRPSSGNK 165
           GRA+LKRRRAKGR+V+          PSSG +
Sbjct: 121 GRAVLKRRRAKGRKVLCTK-----SNPSSGKR 147

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224116920|ref|XP_002317427.1| predicted protein [Populus trichocarpa] gi|222860492|gb|EEE98039.1| predicted protein [Populus trichocarpa]

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 88/125 (70%), Positives = 101/125 (80%), Gaps = 7/125 (5%)

Query: 28  SASLILRTG---RSSVSVNVAGNNSSPSRPGLLHCSFVSSSLCSSAFHSAFSGLSLGLDF 84
           SASL L +G   +   S+NVA N  S +R GLLHCSF+ SS  S +  S+FSGLSLGLD 
Sbjct: 1   SASLSLISGSRTKRGFSMNVATN--STTRSGLLHCSFLPSS--SLSLPSSFSGLSLGLDL 56

Query: 85  NSNAGVRKEKRQGLVVRAGKAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAK 144
           NSN GVRK+  +GLVVRAGKAALC TKR+RSRKSLARTHGFRRRMRTTSGRA+LKRRRAK
Sbjct: 57  NSNIGVRKDIGRGLVVRAGKAALCLTKRSRSRKSLARTHGFRRRMRTTSGRAVLKRRRAK 116

Query: 145 GREVV 149
           GR+V+
Sbjct: 117 GRKVL 121

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297845818|ref|XP_002890790.1| ribosomal protein L34 family protein [Arabidopsis lyrata subsp. lyrata] gi|297336632|gb|EFH67049.1| ribosomal protein L34 family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 76/122 (62%), Positives = 91/122 (74%), Gaps = 6/122 (4%)

Query: 26  IPSASLILRTGRSSVSVNVAGNNSSPSRPGLLHCSFVSSSLCSSAFHSAFSGLSLGLDFN 85
           +PSASL LRTG  S     +   +S +   LLHCSF+SS L   +  S FSGLS+  D +
Sbjct: 28  VPSASLSLRTG--SRQSPSSSLLTSSASSQLLHCSFLSSPL---SLASPFSGLSIAFDLS 82

Query: 86  SN-AGVRKEKRQGLVVRAGKAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAK 144
           S  +G+  ++ +GLVVRAGKAALCQTKR+RSRKSLARTHGFRRRMRTTSGRA +KRRRAK
Sbjct: 83  SQTSGLNSQRHRGLVVRAGKAALCQTKRSRSRKSLARTHGFRRRMRTTSGRATIKRRRAK 142

Query: 145 GR 146
           GR
Sbjct: 143 GR 144

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15218810|ref|NP_174202.1| 50S ribosomal protein L34 [Arabidopsis thaliana] gi|75311421|sp|Q9LP37.1|RK34_ARATH RecName: Full=50S ribosomal protein L34, chloroplastic; AltName: Full=CL34; Flags: Precursor gi|9502428|gb|AAF88127.1|AC021043_20 Putative ribosomal protein L34 [Arabidopsis thaliana] gi|17380840|gb|AAL36232.1| putative plastid ribosomal protein L34 precursor [Arabidopsis thaliana] gi|20259639|gb|AAM14176.1| putative plastid ribosomal protein L34 precursor [Arabidopsis thaliana] gi|21536900|gb|AAM61232.1| plastid ribosomal protein L34 precursor, putative [Arabidopsis thaliana] gi|332192918|gb|AEE31039.1| 50S ribosomal protein L34 [Arabidopsis thaliana]

 Score =  119 bits (298), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 75/122 (61%), Positives = 92/122 (75%), Gaps = 8/122 (6%)

Query: 26  IPSASLILRTGRSSVSVNVAGNNSSPSRPGLLHCSFVSSSLCSSAFHSAFSGLSLGLDFN 85
           +PSASL LRTG        + + +S +   LLHCSF+SS +   +  S FSGLS+  D +
Sbjct: 28  VPSASLSLRTG----CRRSSSSLTSSASSQLLHCSFLSSPV---SLASPFSGLSIAFDLS 80

Query: 86  SN-AGVRKEKRQGLVVRAGKAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAK 144
           S  +G+  ++R+GLVVRAGKAALCQTKR+RSRKSLARTHGFRRRMRTTSGRA +KRRRAK
Sbjct: 81  SQTSGLNGQRRRGLVVRAGKAALCQTKRSRSRKSLARTHGFRRRMRTTSGRATIKRRRAK 140

Query: 145 GR 146
           GR
Sbjct: 141 GR 142

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|14285713|sp|P82244.1|RK34_SPIOL RecName: Full=50S ribosomal protein L34, chloroplastic; AltName: Full=CL34; Flags: Precursor gi|189096152|pdb|3BBO|4 Chain 4, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome gi|7578860|gb|AAF64157.1|AF238221_1 plastid ribosomal protein L34 precursor [Spinacia oleracea]

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 86/165 (52%), Positives = 108/165 (65%), Gaps = 16/165 (9%)

Query: 1   MASLSITTSIPPPWLTSKSTHHSRRIPSASLILRTGRSSVSVNVAGNNSSPSRPGLLHCS 60
           MA+LS+ ++     +T+       R PSASL   TG  + +  V+ N  S +R G LHCS
Sbjct: 1   MATLSLLSTGVGAAITN-------RTPSASLTFITGSRTTNKRVSFNGGS-ARSGSLHCS 52

Query: 61  FVSSSLCSSAFHSAFSGLSLGLDFNSNAGVRKEKRQGLVVRAGKAALCQTKRNRSRKSLA 120
           F++ S   S+  S FSGLSLGLD  SN GV  ++ +  VVRAGKAALC TKR+RSRKSLA
Sbjct: 53  FLAPS---SSLSSNFSGLSLGLDLTSNTGVSTDRCRRFVVRAGKAALCLTKRSRSRKSLA 109

Query: 121 RTHGFRRRMRTTSGRAILKRRRAKGREVVFDSLLGIFQRPSSGNK 165
           RTHGFR RM TTSGRA+LKRRRAKGR+++          PSSG +
Sbjct: 110 RTHGFRLRMSTTSGRALLKRRRAKGRKILCTK-----TNPSSGKR 149

Source: Spinacia oleracea

Species: Spinacia oleracea

Genus: Spinacia

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725279|ref|NP_001235807.1| uncharacterized protein LOC100526907 [Glycine max] gi|255631125|gb|ACU15928.1| unknown [Glycine max]

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 76/139 (54%), Positives = 91/139 (65%), Gaps = 15/139 (10%)

Query: 1   MASLSITTSIPPPWLTSKSTHHSRRIPSASLILRTGR-SSVSVNVAGNNSSPSRPGLLHC 59
           MASLS+  ++  P             PSASLIL   + SS+S+N+    S+   P LLHC
Sbjct: 1   MASLSLCIAMTAP------------TPSASLILTAPKPSSLSLNLTRTCSTARSP-LLHC 47

Query: 60  SFVSSSLCSSAFHSAFSGLSLGLDFNSNAGVRKEKRQGLVVRAGKAALCQTKRNRSRKSL 119
           SF+SS     +  S+ SGLSLGLD  SN G R+ K  GLVVRAGKAALC TKR+RSRKSL
Sbjct: 48  SFLSSPS-LLSPPSSISGLSLGLDLTSNFGTRRGKGSGLVVRAGKAALCLTKRSRSRKSL 106

Query: 120 ARTHGFRRRMRTTSGRAIL 138
           ARTHGFR+RM T  GRA+L
Sbjct: 107 ARTHGFRKRMSTPGGRAVL 125

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	177
TAIR|locus:2029944	157	AT1G29070 [Arabidopsis thalian	0.785	0.885	0.463	8.7e-24
TIGR_CMR|CBU_1917	44	CBU_1917 "ribosomal protein L3	0.186	0.75	0.606	7e-06
TIGR_CMR|CHY_0001	44	CHY_0001 "ribosomal protein L3	0.186	0.75	0.583	9e-06
TIGR_CMR|CPS_5053	44	CPS_5053 "ribosomal protein L3	0.146	0.590	0.692	3.9e-05
UNIPROTKB|Q9KVY1	45	rpmH "50S ribosomal protein L3	0.152	0.6	0.666	5e-05
TIGR_CMR|SO_0007	45	SO_0007 "ribosomal protein L34	0.175	0.688	0.617	5e-05
TIGR_CMR|VC_0007	45	VC_0007 "ribosomal protein L34	0.152	0.6	0.666	5e-05
UNIPROTKB|P0A7P5	46	rpmH "50S ribosomal subunit pr	0.146	0.565	0.692	6.3e-05
TIGR_CMR|ECH_0440	44	ECH_0440 "ribosomal protein L3	0.197	0.795	0.6	6.3e-05
TIGR_CMR|CJE_1041	44	CJE_1041 "ribosomal protein L3	0.152	0.613	0.629	8.1e-05

TAIR|locus:2029944 AT1G29070 [Arabidopsis thaliana (taxid:3702)]

 Score = 273 (101.2 bits), Expect = 8.7e-24, P = 8.7e-24
 Identities = 69/149 (46%), Positives = 83/149 (55%)

Query:     1 MASLS--ITTSIPPPWLTSKSTHHSRRIPSASLILRTGRXXXXXXXXXXXXXXXRPGXXX 58
             MASLS  +  S         +++    +PSASL LRTG                      
Sbjct:     1 MASLSTSVVASASSRLWNPAASNGKICVPSASLSLRTGCRRSSSSLTSSASSQL------ 54

Query:    59 XXXXXXXXXXXXXXXXXXGLSLGLDFNSN-AGVRKEKRQGLVVRAGKAALCQTKRNRSRK 117
                               GLS+  D +S  +G+  ++R+GLVVRAGKAALCQTKR+RSRK
Sbjct:    55 -LHCSFLSSPVSLASPFSGLSIAFDLSSQTSGLNGQRRRGLVVRAGKAALCQTKRSRSRK 113

Query:   118 SLARTHGFRRRMRTTSGRAILKRRRAKGR 146
             SLARTHGFRRRMRTTSGRA +KRRRAKGR
Sbjct:   114 SLARTHGFRRRMRTTSGRATIKRRRAKGR 142

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

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM

GO:0042254 "ribosome biogenesis" evidence=ISS

TIGR_CMR|CBU_1917 CBU_1917 "ribosomal protein L34" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 104 (41.7 bits), Expect = 7.0e-06, P = 7.0e-06
 Identities = 20/33 (60%), Positives = 25/33 (75%)

Query:   115 SRKSLARTHGFRRRMRTTSGRAILKRRRAKGRE 147
             S++   RTHGFR RM T +GR +L RRRAKGR+
Sbjct:     8 SKQKRNRTHGFRARMATKNGRQVLNRRRAKGRK 40

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

TIGR_CMR|CHY_0001 CHY_0001 "ribosomal protein L34" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 103 (41.3 bits), Expect = 9.0e-06, P = 9.0e-06
 Identities = 21/36 (58%), Positives = 26/36 (72%)

Query:   112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGRE 147
             +NR RK   R HGF +RMRT  GR ++KRRR KGR+
Sbjct:     8 KNRRRK---RVHGFLKRMRTPGGRNVIKRRRLKGRK 40

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|CPS_5053 CPS_5053 "ribosomal protein L34" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 97 (39.2 bits), Expect = 3.9e-05, P = 3.9e-05
 Identities = 18/26 (69%), Positives = 21/26 (80%)

Query:   121 RTHGFRRRMRTTSGRAILKRRRAKGR 146
             R HGFR RM T +GRA++ RRRAKGR
Sbjct:    14 RNHGFRARMATKNGRAVIARRRAKGR 39

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

GO:0006412 "translation" evidence=ISS

GO:0015934 "large ribosomal subunit" evidence=ISS

UNIPROTKB|Q9KVY1 rpmH "50S ribosomal protein L34" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 96 (38.9 bits), Expect = 5.0e-05, P = 5.0e-05
 Identities = 18/27 (66%), Positives = 21/27 (77%)

Query:   121 RTHGFRRRMRTTSGRAILKRRRAKGRE 147
             RTHGFR RM T +GR +L  RRAKGR+
Sbjct:    15 RTHGFRARMATANGRKVLNARRAKGRK 41

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|SO_0007 SO_0007 "ribosomal protein L34" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 96 (38.9 bits), Expect = 5.0e-05, P = 5.0e-05
 Identities = 21/34 (61%), Positives = 23/34 (67%)

Query:   113 NRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGR 146
             N  RK   R+HGFR RM T  GR +L RRRAKGR
Sbjct:    10 NLKRK---RSHGFRARMATAGGRKVLARRRAKGR 40

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|VC_0007 VC_0007 "ribosomal protein L34" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 96 (38.9 bits), Expect = 5.0e-05, P = 5.0e-05
 Identities = 18/27 (66%), Positives = 21/27 (77%)

Query:   121 RTHGFRRRMRTTSGRAILKRRRAKGRE 147
             RTHGFR RM T +GR +L  RRAKGR+
Sbjct:    15 RTHGFRARMATANGRKVLNARRAKGRK 41

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

GO:0006412 "translation" evidence=ISS

UNIPROTKB|P0A7P5 rpmH "50S ribosomal subunit protein L34" [Escherichia coli K-12 (taxid:83333)]

 Score = 95 (38.5 bits), Expect = 6.3e-05, P = 6.3e-05
 Identities = 18/26 (69%), Positives = 21/26 (80%)

Query:   121 RTHGFRRRMRTTSGRAILKRRRAKGR 146
             R+HGFR RM T +GR +L RRRAKGR
Sbjct:    14 RSHGFRARMATKNGRQVLARRRAKGR 39

GO:0006412 "translation" evidence=IEA

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

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

TIGR_CMR|ECH_0440 ECH_0440 "ribosomal protein L34" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 95 (38.5 bits), Expect = 6.3e-05, P = 6.3e-05
 Identities = 21/35 (60%), Positives = 23/35 (65%)

Query:   115 SRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVV 149
             SR    R HGFR RM T  GR IL RRRA+GR V+
Sbjct:     8 SRIVRKRRHGFRSRMSTKMGRRILNRRRAQGRRVL 42

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

GO:0006412 "translation" evidence=ISS

GO:0015934 "large ribosomal subunit" evidence=ISS

TIGR_CMR|CJE_1041 CJE_1041 "ribosomal protein L34" [Campylobacter jejuni RM1221 (taxid:195099)]

 Score = 94 (38.1 bits), Expect = 8.1e-05, P = 8.1e-05
 Identities = 17/27 (62%), Positives = 22/27 (81%)

Query:   121 RTHGFRRRMRTTSGRAILKRRRAKGRE 147
             RTHGFR RM+T +GR ++  RRAKGR+
Sbjct:    14 RTHGFRVRMKTKNGRKVINARRAKGRK 40

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

GO:0042254 "ribosome biogenesis" evidence=ISS

---

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)
Q9LP37	RK34_ARATH	No assigned EC number	0.6147	0.6440	0.7261	yes	no
P82244	RK34_SPIOL	No assigned EC number	0.5212	0.8418	0.9802	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

Your Input: gw1.XI.3354.1 hypothetical protein (131 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	177
pfam00468	44	pfam00468, Ribosomal_L34, Ribosomal protein L34	8e-10
PRK00399	44	PRK00399, rpmH, 50S ribosomal protein L34; Reviewe	2e-09
COG0230	44	COG0230, RpmH, Ribosomal protein L34 [Translation,	9e-08
TIGR01030	44	TIGR01030, rpmH_bact, ribosomal protein L34, bacte	4e-06
CHL00115	46	CHL00115, rpl34, ribosomal protein L34; Reviewed	0.001

>gnl|CDD|201247 pfam00468, Ribosomal_L34, Ribosomal protein L34

 Score = 51.3 bits (124), Expect = 8e-10
 Identities = 21/32 (65%), Positives = 24/32 (75%)

Query: 115 SRKSLARTHGFRRRMRTTSGRAILKRRRAKGR 146
           S +   RTHGFR RM T +GR +LKRRRAKGR
Sbjct: 8   SNRKRKRTHGFRARMATKNGRKVLKRRRAKGR 39

Length = 44

>gnl|CDD|179004 PRK00399, rpmH, 50S ribosomal protein L34; Reviewed

 Score = 50.5 bits (122), Expect = 2e-09
 Identities = 22/34 (64%), Positives = 24/34 (70%), Gaps = 3/34 (8%)

Query: 113 NRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGR 146
            R RK   RTHGFR RM T +GR +L RRRAKGR
Sbjct: 9   KRKRK---RTHGFRARMATKNGRKVLARRRAKGR 39

Length = 44

>gnl|CDD|223308 COG0230, RpmH, Ribosomal protein L34 [Translation, ribosomal structure and biogenesis]

 Score = 46.1 bits (110), Expect = 9e-08
 Identities = 20/32 (62%), Positives = 24/32 (75%)

Query: 115 SRKSLARTHGFRRRMRTTSGRAILKRRRAKGR 146
           S++   RTHGFR RM T +GR +L RRRAKGR
Sbjct: 8   SKRKRKRTHGFRARMATKNGRKVLARRRAKGR 39

Length = 44

>gnl|CDD|130102 TIGR01030, rpmH_bact, ribosomal protein L34, bacterial type

 Score = 41.7 bits (98), Expect = 4e-06
 Identities = 20/32 (62%), Positives = 23/32 (71%)

Query: 115 SRKSLARTHGFRRRMRTTSGRAILKRRRAKGR 146
           S     RTHGFR RM T +GR +L+RRRAKGR
Sbjct: 8   SNLKRKRTHGFRARMATKNGRKVLRRRRAKGR 39

This model describes the bacterial protein L34 and its equivalents in organelles [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 44

>gnl|CDD|177039 CHL00115, rpl34, ribosomal protein L34; Reviewed

 Score = 35.1 bits (81), Expect = 0.001
 Identities = 19/37 (51%), Positives = 20/37 (54%), Gaps = 1/37 (2%)

Query: 110 TKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGR 146
           T     RK   R  GFR RM T +GR IL  RR KGR
Sbjct: 5   TLSGTKRKK-VRKSGFRARMATAAGRKILNARRRKGR 40

Length = 46

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	177
COG0230	44	RpmH Ribosomal protein L34 [Translation, ribosomal	99.74
TIGR01030	44	rpmH_bact ribosomal protein L34, bacterial type. T	99.72
PRK00399	44	rpmH 50S ribosomal protein L34; Reviewed	99.71
CHL00115	46	rpl34 ribosomal protein L34; Reviewed	99.71
PF00468	44	Ribosomal_L34: Ribosomal protein L34; InterPro: IP	99.69
KOG4612	105	consensus Mitochondrial ribosomal protein L34 [Tra	99.42

>COG0230 RpmH Ribosomal protein L34 [Translation, ribosomal structure and biogenesis]

Probab=99.74  E-value=8.3e-19  Score=118.05  Aligned_cols=40  Identities=50%  Similarity=0.748  Sum_probs=37.8

Q ss_pred             CCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceEec
Q 030457          112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFD  151 (177)
Q Consensus       112 r~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~Ls~  151 (177)
                      ||||++||||+|||++||+|++||+||++||+|||++|++
T Consensus         5 yQPs~~kRkr~hGFraRM~Tk~GR~vl~~RR~KGR~~Ls~   44 (44)
T COG0230           5 YQPSKRKRKRTHGFRARMATKNGRKVLARRRAKGRKRLSV   44 (44)
T ss_pred             cCCcchhhhhhhhHHHHhcccchHHHHHHHHHcCCcccCC
Confidence            4788889999999999999999999999999999999985

>TIGR01030 rpmH_bact ribosomal protein L34, bacterial type

Probab=99.72  E-value=1.9e-18  Score=116.00  Aligned_cols=40  Identities=50%  Similarity=0.715  Sum_probs=37.8

Q ss_pred             CCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceEec
Q 030457          112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFD  151 (177)
Q Consensus       112 r~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~Ls~  151 (177)
                      +||++++|+|+|||++||+|++||+||++||+|||++|++
T Consensus         5 ~qps~~kRkr~hGFraRm~T~~GR~vl~rRr~KGRk~Ls~   44 (44)
T TIGR01030         5 YQPSNLKRKRTHGFRARMATKNGRKVLRRRRAKGRHKLTV   44 (44)
T ss_pred             CCCcceeechhhcHHHHccChhhHHHHHHHHHcCCccccC
Confidence            4688889999999999999999999999999999999985

This model describes the bacterial protein L34 and its equivalents in organelles.

>PRK00399 rpmH 50S ribosomal protein L34; Reviewed

Probab=99.71  E-value=2.7e-18  Score=115.24  Aligned_cols=40  Identities=50%  Similarity=0.770  Sum_probs=37.7

Q ss_pred             CCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceEec
Q 030457          112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFD  151 (177)
Q Consensus       112 r~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~Ls~  151 (177)
                      +||++++|+|+|||++||+|++||+||++||+|||++|++
T Consensus         5 ~qps~~kr~r~hGFraRm~T~~GRkvl~rRR~KGR~~Lt~   44 (44)
T PRK00399          5 YQPSKRKRKRTHGFRARMATKNGRKVLARRRAKGRKRLSA   44 (44)
T ss_pred             CCCcceeechhhhHHHHccCcccHHHHHHHHHcCCccccC
Confidence            4677889999999999999999999999999999999985

>CHL00115 rpl34 ribosomal protein L34; Reviewed

Probab=99.71  E-value=3.7e-18  Score=115.63  Aligned_cols=40  Identities=40%  Similarity=0.625  Sum_probs=37.9

Q ss_pred             CCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceEec
Q 030457          112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFD  151 (177)
Q Consensus       112 r~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~Ls~  151 (177)
                      +||++++|+|+|||++||+|++||+||++||+|||++|++
T Consensus         6 ~qps~~krkr~hGFraRm~T~~GRkvl~rRR~KGRk~L~v   45 (46)
T CHL00115          6 LSGTKRKKVRKSGFRARMATAAGRKILNARRRKGRKKLAL   45 (46)
T ss_pred             cCCcceeecccccHHHHcCCcchHHHHHHHHHcCCceeec
Confidence            4677889999999999999999999999999999999997

>PF00468 Ribosomal_L34: Ribosomal protein L34; InterPro: IPR000271 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.69  E-value=4.4e-18  Score=114.10  Aligned_cols=40  Identities=50%  Similarity=0.742  Sum_probs=36.4

Q ss_pred             CCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceEec
Q 030457          112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFD  151 (177)
Q Consensus       112 r~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~Ls~  151 (177)
                      +||++++|+|+|||++||+|++||+||++||+|||++|++
T Consensus         5 ~qps~~kr~r~hGFr~Rm~T~~GRkvl~rRr~KGR~~Ls~   44 (44)
T PF00468_consen    5 YQPSNRKRKRKHGFRARMSTKNGRKVLKRRRAKGRKRLSV   44 (44)
T ss_dssp             S-S-HHHHHHHCSHHHHHCSHHHHHHHHHHHCHTSSTSSC
T ss_pred             CCCceeeeeccccchhhhcchhHHHHHHHHHHcCCeeccC
Confidence            5788899999999999999999999999999999999985

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 [, ]. Ribosomal protein L34 is one of the proteins from the large subunit of the prokaryotic ribosome. It is a small basic protein of 44 to 51 amino-acid residues []. L34 belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Eubacterial L34, Red algal chloroplast L34 and Cyanelle L34.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBO_4 3PIO_2 3PIP_2 3SGF_6 2AW4_2 2AWB_2 2VHM_2 3OFZ_2 3UOS_6 2QOX_2 ....

>KOG4612 consensus Mitochondrial ribosomal protein L34 [Translation, ribosomal structure and biogenesis]

Probab=99.42  E-value=6e-14  Score=108.13  Aligned_cols=43  Identities=33%  Similarity=0.474  Sum_probs=40.9

Q ss_pred             ccccCCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceEe
Q 030457          108 CQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVF  150 (177)
Q Consensus       108 ~~Tkr~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~Ls  150 (177)
                      .+.+||||++||||+|||++|.+|++|++||+||+.|||+.|+
T Consensus        62 rGNeYQPSn~KRKrkhGfl~R~~s~~G~~vl~rR~lKGR~~LS  104 (105)
T KOG4612|consen   62 RGNEYQPSNLKRKRKHGFLARAKSKQGSKVLKRRKLKGRWFLS  104 (105)
T ss_pred             cCCccCchhhhhhhhhhhhhhhcccchhHHHHHHHhccccccc
Confidence            3578999999999999999999999999999999999999986

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	177
3bbo_4	152	Homology Model For The Spinach Chloroplast 50s Subu		2e-21
1nkw_2	47	Crystal Structure Of The Large Ribosomal Subunit Fr		1e-04
1pnu_2	46	Crystal Structure Of A Streptomycin Dependent Ribos		2e-04
3mrz_4	48	Recognition Of The Amber Stop Codon By Release Fact		3e-04
2j01_7	49	Structure Of The Thermus Thermophilus 70s Ribosome		4e-04

>pdb|3BBO|4 Chain 4, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 152

Iteration: 1
 Score = 98.6 bits (244), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 55/85 (64%), Positives = 63/85 (74%), Gaps = 5/85 (5%)
Query: 81  GLDFNSNAGVRKEKRQGLVVRAGKAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKR 140
           GLD  SN GV  ++ +  VVRAGKAALC TKR+RSRKSLARTHGFR RM TTSGRA+LKR
Sbjct: 70  GLDLTSNTGVSTDRCRRFVVRAGKAALCLTKRSRSRKSLARTHGFRLRMSTTSGRALLKR 129
Query: 141 RRAKGREVVFDSLLGIFQRPSSGNK 165
           RRAKGR++     L     PSSG +
Sbjct: 130 RRAKGRKI-----LCTKTNPSSGKR 149

>pdb|1NKW|2 Chain 2, Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Length = 47

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/28 (75%), Positives = 23/28 (82%)
Query: 120 ARTHGFRRRMRTTSGRAILKRRRAKGRE 147
           A+THGFR RM+T SGR IL RRRAKGR 
Sbjct: 13  AKTHGFRARMKTKSGRNILARRRAKGRH 40

>pdb|1PNU|2 Chain 2, Crystal Structure Of A Streptomycin Dependent Ribosome From Escherichia Coli, 50s Subunit Of 70s Ribosome. This File, 1pnu, Contains Only Molecules Of The 50s Ribosomal Subunit. The 30s Subunit, Mrna, P-Site Trna, And A-Site Trna Are In The Pdb File 1pns. Length = 46

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/28 (75%), Positives = 23/28 (82%)
Query: 120 ARTHGFRRRMRTTSGRAILKRRRAKGRE 147
           A+THGFR RM+T SGR IL RRRAKGR 
Sbjct: 13  AKTHGFRARMKTKSGRNILARRRAKGRH 40

>pdb|3MRZ|4 Chain 4, Recognition Of The Amber Stop Codon By Release Factor Rf1. This Entry 3mrz Contains 50s Ribosomal Subunit. The 30s Ribosomal Subunit Can Be Found In Pdb Entry 3ms0. Molecule A In The Same Asymmetric Unit Is Deposited As 3mr8 (50s) And 3ms1 (30s). Length = 48

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/32 (65%), Positives = 25/32 (78%)
Query: 115 SRKSLARTHGFRRRMRTTSGRAILKRRRAKGR 146
           +R+  A+THGFR RMRT  GR +LKRRR KGR
Sbjct: 8   NRRKRAKTHGFRARMRTPGGRKVLKRRRQKGR 39

>pdb|2J01|7 Chain 7, Structure Of The Thermus Thermophilus 70s Ribosome Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4). This File Contains The 50s Subunit From Molecule I. Length = 49

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/32 (65%), Positives = 25/32 (78%)
Query: 115 SRKSLARTHGFRRRMRTTSGRAILKRRRAKGR 146
           +R+  A+THGFR RMRT  GR +LKRRR KGR
Sbjct: 8   NRRKRAKTHGFRARMRTPGGRKVLKRRRQKGR 39

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	177
3bbo_4	152	Ribosomal protein L34; large ribosomal subunit, sp	2e-20
3r8s_2	46	50S ribosomal protein L34; protein biosynthesis, R	8e-07
3v2d_7	49	50S ribosomal protein L34; ribosome associated inh	1e-04

>3bbo_4 Ribosomal protein L34; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 152

 Score = 82.1 bits (201), Expect = 2e-20
 Identities = 80/149 (53%), Positives = 101/149 (67%), Gaps = 11/149 (7%)

Query: 1   MASLSITTSIPPPWLTSKSTHHSRRIPSASLILRTGRSSVSVNVAGNNSSPSRPGLLHCS 60
           MA+LS+ ++     +T+++       PSASL   TG S  +      N   +R G LHCS
Sbjct: 1   MATLSLLSTGVGAAITNRT-------PSASLTFITG-SRTTNKRVSFNGGSARSGSLHCS 52

Query: 61  FVSSSLCSSAFHSAFSGLSLGLDFNSNAGVRKEKRQGLVVRAGKAALCQTKRNRSRKSLA 120
           F++ S   S+  S FSGLSLGLD  SN GV  ++ +  VVRAGKAALC TKR+RSRKSLA
Sbjct: 53  FLAPS---SSLSSNFSGLSLGLDLTSNTGVSTDRCRRFVVRAGKAALCLTKRSRSRKSLA 109

Query: 121 RTHGFRRRMRTTSGRAILKRRRAKGREVV 149
           RTHGFR RM TTSGRA+LKRRRAKGR+++
Sbjct: 110 RTHGFRLRMSTTSGRALLKRRRAKGRKIL 138

>3r8s_2 50S ribosomal protein L34; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1vs8_2 1vs6_2 2aw4_2 2awb_2 1vt2_2 2i2v_2 2j28_2 2i2t_2* 2qao_2* 2qba_2* 2qbc_2* 2qbe_2 2qbg_2 2qbi_2* 2qbk_2* 2qov_2 2qox_2 2qoz_2* 2qp1_2* 2rdo_2 ... Length = 46

 Score = 43.3 bits (102), Expect = 8e-07
 Identities = 19/32 (59%), Positives = 22/32 (68%)

Query: 115 SRKSLARTHGFRRRMRTTSGRAILKRRRAKGR 146
           S     R+HGFR RM T +GR +L RRRAKGR
Sbjct: 8   SVLKRNRSHGFRARMATKNGRQVLARRRAKGR 39

>3v2d_7 50S ribosomal protein L34; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_Z 2hgj_6 2hgq_6 2hgu_6 1vsa_Z 2j03_7 2jl6_7 2jl8_7 2v47_7 2v49_7 2wdi_7 2wdj_7 2wdl_7 2wdn_7 2wh2_7 2wh4_7 2wrj_7 2wrl_7 2wro_7 2wrr_7 ... Length = 49

 Score = 37.3 bits (86), Expect = 1e-04
 Identities = 21/32 (65%), Positives = 25/32 (78%)

Query: 115 SRKSLARTHGFRRRMRTTSGRAILKRRRAKGR 146
           +R+  A+THGFR RMRT  GR +LKRRR KGR
Sbjct: 8   NRRKRAKTHGFRARMRTPGGRKVLKRRRQKGR 39

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	177
3bbo_4	152	Ribosomal protein L34; large ribosomal subunit, sp	100.0
3r8s_2	46	50S ribosomal protein L34; protein biosynthesis, R	99.75
2ftc_Q	38	L34MT, MRP-L34, 39S ribosomal protein L34, mitocho	99.73
3v2d_7	49	50S ribosomal protein L34; ribosome associated inh	99.73

>3bbo_4 Ribosomal protein L34; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=100.00  E-value=9.1e-44  Score=284.98  Aligned_cols=146  Identities=57%  Similarity=0.810  Sum_probs=36.9

Q ss_pred             CCccc--ccccCCCCCcCCCcCCCcccCCcceeeeecc-cccceeecccCCCCCCCCCceeecccccccccccccccccc
Q 030457            1 MASLS--ITTSIPPPWLTSKSTHHSRRIPSASLILRTG-RSSVSVNVAGNNSSPSRPGLLHCSFVSSSLCSSAFHSAFSG   77 (177)
Q Consensus         1 ~~s~~--~~~~~~~~w~~~~s~~~~~~~p~asl~~~s~-r~~~~~~~~~~~~~~sr~~~L~~sFlss~~sssf~~ssfsg   77 (177)
                      ||+++  .++++..+         +..+|+++|+|++| |.....|++.+  +.+++++|||+||+|+.+   ++++|+|
T Consensus         1 ma~~~~~~~~~~~~~---------~~~~p~~s~s~~~~~r~~~~~~~~~~--~~a~s~~l~~sf~ss~~s---~~ssf~G   66 (152)
T 3bbo_4            1 MATLSLLSTGVGAAI---------TNRTPSASLTFITGSRTTNKRVSFNG--GSARSGSLHCSFLAPSSS---LSSNFSG   66 (152)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             Cccccccccccccee---------eccCCCcccccccccccccccccccc--ccccCcceeeeecccccc---CCCcccc
Confidence            45444  35666555         67789999999999 76666666666  889999999999999966   7899999


Q ss_pred             cccccccccccccccCCCceeEEEecCcccccccCCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceEeccccccc
Q 030457           78 LSLGLDFNSNAGVRKEKRQGLVVRAGKAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFDSLLGIF  157 (177)
Q Consensus        78 ~SlgLdl~~~~~v~~~r~~~~~VraGkRtl~~Tkr~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~Ls~sl~~~~  157 (177)
                      +++++||++++++..++++++||+|||+++++|+|+|+++||||+||||+||+|++||+||+|||+||||+|++     .
T Consensus        67 ~sl~~~l~~~i~~~~~r~~gl~Vr~Gkr~~~~T~r~pS~~kRkR~HGFraRM~Tk~GRkVL~rRRaKGRk~Ls~-----s  141 (152)
T 3bbo_4           67 LSLGLDLTSNTGVSTDRCRRFVVRAGKAALCLTKRSRSRKSLARTHGFRLRMSTTSGRALLKRRRAKGRKILCT-----K  141 (152)
T ss_dssp             -------------------------------------CTTHHHHTSCHHHHHHSGGGTTTTHHHHTTTCSCSCC------
T ss_pred             cccccccccceeeccCCCcceEEEccCccccccCCCCccceeehhhcHHHHhcChhhHHHHHHHHHhCCcEEee-----c
Confidence            99999999999998899999999999999999999999999999999999999999999999999999999999     8


Q ss_pred             cCCCCCCc
Q 030457          158 QRPSSGNK  165 (177)
Q Consensus       158 ~~~~sgk~  165 (177)
                      .++++||+
T Consensus       142 ~~~~sGk~  149 (152)
T 3bbo_4          142 TNPSSGKR  149 (152)
T ss_dssp             --------
T ss_pred             cCCCCCCc
Confidence            99999994

>3r8s_2 50S ribosomal protein L34; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 1vs8_2 1vs6_2 2aw4_2 2awb_2 1vt2_2 2i2v_2 2j28_2 2i2t_2* 2qao_2* 2qba_2* 2qbc_2* 2qbe_2 2qbg_2 2qbi_2* 2qbk_2* 2qov_2 2qox_2 2qoz_2* 2qp1_2* 2rdo_2 ...

Probab=99.75  E-value=2.8e-19  Score=120.05  Aligned_cols=41  Identities=49%  Similarity=0.649  Sum_probs=38.8

Q ss_pred             CCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceEecc
Q 030457          112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFDS  152 (177)
Q Consensus       112 r~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~Ls~s  152 (177)
                      |||++++|+|+|||++||+|++||+||++||+|||++|++|
T Consensus         5 yQPs~~kRkr~hGFraRm~T~~GRkvL~rRR~KGRk~Ls~s   45 (46)
T 3r8s_2            5 FQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVS   45 (46)
T ss_dssp             CCCCHHHHHHHHSHHHHHTSHHHHHHHHHHHHHTCSCSSCC
T ss_pred             CCCCceeechhhcHHHHccCcchhHHHHHHHHcCCceeccc
Confidence            47888899999999999999999999999999999999984

>2ftc_Q L34MT, MRP-L34, 39S ribosomal protein L34, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus}

Probab=99.73  E-value=7.4e-19  Score=114.07  Aligned_cols=38  Identities=32%  Similarity=0.504  Sum_probs=36.5

Q ss_pred             CCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceE
Q 030457          112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVV  149 (177)
Q Consensus       112 r~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~L  149 (177)
                      +||++++|+|+|||++||+|++||+||++||+|||++|
T Consensus         1 yqPs~~kRkr~hGFraRm~T~~GRkvl~rRR~KGR~~L   38 (38)
T 2ftc_Q            1 YQPSNIKRKNKHGWVRRLSTPAGVQVILRRMLKGRKSL   38 (38)
T ss_pred             CCCccccchhhhcHHHHccChhhHHHHHHHHHcCcccC
Confidence            58999999999999999999999999999999999986

>3v2d_7 50S ribosomal protein L34; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_Z 2hgj_6 2hgq_6 2hgu_6 1vsa_Z 2j03_7 2jl6_7 2jl8_7 2v47_7 2v49_7 2wdi_7 2wdj_7 2wdl_7 2wdn_7 2wh2_7 2wh4_7 2wrj_7 2wrl_7 2wro_7 2wrr_7 ...

Probab=99.73  E-value=5.7e-19  Score=119.94  Aligned_cols=40  Identities=53%  Similarity=0.788  Sum_probs=38.4

Q ss_pred             CCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceEec
Q 030457          112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFD  151 (177)
Q Consensus       112 r~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~Ls~  151 (177)
                      |||++++|+|+|||++||+|++||+||++||+|||++|++
T Consensus         5 yQPs~~kRkr~hGFraRm~T~~GRkVL~rRR~KGRk~Ls~   44 (49)
T 3v2d_7            5 WQPNRRKRAKTHGFRARMRTPGGRKVLKRRRQKGRWRLTP   44 (49)
T ss_dssp             CCCCHHHHHHHHSHHHHHHSHHHHHHHHHHHHHTCSCSSC
T ss_pred             CCCCceeechhhcHHHHccCcchhHHHHHHHHcCCcEeee
Confidence            4788889999999999999999999999999999999999

---

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