Citrus Sinensis ID: 039022

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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-------180-------190-------200-------210-------220--
Protein Sequence
MAFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKMDTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARRELRRQMYGGSSKQKQIEQGSADTQETAEEAAKILSEGIPNEYAPEDLVANS
Secondary Structure (PSIPRED)
ccccccccccccEEccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccEEEEccEEEEEEEEccccEEEEEEEEHHHHHHHHHHccHHHHHcccccccccHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHHHHccccccccccccccccccccccccccHcccccccccEEEEcccccccccccccccccccHHHHHHHHHHHcccEEEEEcHHHHHHHHHcccHHHHHHcccHHHHHHHccHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHcccccccccHcHEccc
Coil and Loop (DISEMBL)
MAFRGKEMMKKLVRKvggeknlapgvkeslkkcvpdsriVMNRAKrglfagkhiqfgnrvsedggnktrrnwkpnvqekRLFSYIMDRHIRVKVTTHALRCIdkaggideyllktpyhkmdtemGLYWKTKIEKLYEELGqtevafftpeeEAKLEQDFKDMKLAQRAARRELRRqmyggsskqkqieqgsADTQETAEEAAKILSegipneyapedlvans
Flexible Loop (DISEMBL)
mafrgkemMKKLVrkvggeknlapgvkeslkkcvpdsrIVMNRAKRglfagkhiqfgnrvsedggnktrrnwkpnvqekrlfsyimdRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKMDTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARRELRrqmyggsskqkqieqgsaDTQETAEEAAKILsegipneyapedlvans
Low Complexity Region (SEG)
MAFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKMDTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKlaqraarrelrrqMYGGSSKQKQIEQGSADTQETAEEAAKILSEGIPNEYAPEDLVANS
Disordered region (IsUnstruct)
********************************CVPDSRIVMNRAKRGLFAGKHIQFGNR************WKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKMDTEMGLYWKTKIEKLYEELGQTEVAFFT**************************************************************************
Disordered Region (DISOPRED)
***********LVRKVGGEKNL*PGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKMDTEMGLYWKTKIEKLY*******************EQDFKDMKLAQRAARRELRRQMYG*******************************************
Disordered Region (DISEMBL)
********MKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKMDTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARRELRRQ************************AAKILSEGIPNEYAPEDLVANS
Disordered Region (DISPRO)
*AFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKMDTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARRELRRQMYGGSSKQKQIEQG********************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKMDTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARRELRRQMYGGSSKQKQIEQGSADTQETAEEAAKILSEGIPNEYAPEDLVANS
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	222	2.2.26 [Sep-21-2011]
P36525	258	54S ribosomal protein L24	yes	no	0.454	0.391	0.369	2e-12
A0L5U1	95	50S ribosomal protein L28	yes	no	0.360	0.842	0.419	3e-12
A9HS05	100	50S ribosomal protein L28	yes	no	0.355	0.79	0.387	6e-11
Q5FUP5	100	50S ribosomal protein L28	yes	no	0.355	0.79	0.387	3e-10
B6IW31	99	50S ribosomal protein L28	yes	no	0.333	0.747	0.386	4e-10
O60091	176	54S ribosomal protein L24	yes	no	0.382	0.482	0.360	2e-09
Q9FDL9	95	50S ribosomal protein L28	yes	no	0.328	0.768	0.391	6e-09
Q2RXY0	99	50S ribosomal protein L28	yes	no	0.360	0.808	0.358	7e-09
A7HTU2	96	50S ribosomal protein L28	yes	no	0.405	0.937	0.347	4e-08
Q11DS9	98	50S ribosomal protein L28	yes	no	0.400	0.908	0.344	4e-08

>sp|P36525|RM24_YEAST 54S ribosomal protein L24, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=MRPL24 PE=1 SV=2

 Score = 72.8 bits (177), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 41/111 (36%), Positives = 61/111 (54%), Gaps = 10/111 (9%)

Query: 13  VRKVGGEKNLAPGVKESL-----KKCVPDSRI----VMNRAKRGLFAGKHIQFGNRVSED 63
            RK+  + N   G  + L     +K  PD +     +  ++ +GL+ G  +QFGN +SE 
Sbjct: 29  TRKIAKQPNYQVGDAKPLHMPKERKKFPDYKYGESNIFKQSNKGLYGGSFVQFGNNISES 88

Query: 64  GGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLK 114
              KTR+ W PNV +K L+S  ++R I +K+T   L+ I K GGID YL K
Sbjct: 89  KA-KTRKKWLPNVVKKGLWSETLNRKISIKMTAKVLKTISKEGGIDNYLTK 138

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|A0L5U1|RL28_MAGSM 50S ribosomal protein L28 OS=Magnetococcus sp. (strain MC-1) GN=rpmB PE=3 SV=1

 Score = 72.0 bits (175), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 34/81 (41%), Positives = 49/81 (60%), Gaps = 1/81 (1%)

Query: 44  AKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCID 103
           A++    GK  Q GN+VS     KTRR W PN+Q K L+S  + + ++V ++T ALR +D
Sbjct: 2   ARKRTLGGKAPQAGNKVSHSQ-RKTRRQWMPNIQTKALWSITLGQSVKVTISTSALRSVD 60

Query: 104 KAGGIDEYLLKTPYHKMDTEM 124
            AGG+D YLLK    ++   M
Sbjct: 61  NAGGLDNYLLKILPSELTPSM 81

Magnetococcus sp. (strain MC-1) (taxid: 156889)

>sp|A9HS05|RL28_GLUDA 50S ribosomal protein L28 OS=Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / PAl5) GN=rpmB PE=3 SV=1

 Score = 67.8 bits (164), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 31/80 (38%), Positives = 50/80 (62%), Gaps = 1/80 (1%)

Query: 44  AKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCID 103
           ++R    GK +  GN VS    NK+RR + PN+QE  L S I+   +R++++T+ +R ++
Sbjct: 2   SRRCQITGKGVLTGNNVSH-ANNKSRRRFLPNLQETSLLSDILGSAVRLRLSTNGIRTVE 60

Query: 104 KAGGIDEYLLKTPYHKMDTE 123
             GG+D +LL TP  K+ TE
Sbjct: 61  HNGGLDAFLLSTPNRKLPTE 80

Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / PAl5) (taxid: 272568)

>sp|Q5FUP5|RL28_GLUOX 50S ribosomal protein L28 OS=Gluconobacter oxydans (strain 621H) GN=rpmB PE=3 SV=1

 Score = 65.5 bits (158), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 31/80 (38%), Positives = 49/80 (61%), Gaps = 1/80 (1%)

Query: 44  AKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCID 103
           ++R    GK +  GN VS    NK+RR + PN+QE  L S I+   +R++++T  +R ++
Sbjct: 2   SRRCQITGKGVLTGNNVSH-ANNKSRRRFLPNLQETTLISDILGASVRMRLSTDGIRTVE 60

Query: 104 KAGGIDEYLLKTPYHKMDTE 123
             GG+D +LL TP  K+ TE
Sbjct: 61  HNGGLDSFLLGTPNRKLPTE 80

Gluconobacter oxydans (strain 621H) (taxid: 290633)

>sp|B6IW31|RL28_RHOCS 50S ribosomal protein L28 OS=Rhodospirillum centenum (strain ATCC 51521 / SW) GN=rpmB PE=3 SV=1

 Score = 65.1 bits (157), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 46/75 (61%), Gaps = 1/75 (1%)

Query: 49  FAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGI 108
             GK +Q GN VS    NK+RR W PN+QE  L S  + R +R++++T+ +R I+  GG+
Sbjct: 7   VTGKGVQTGNNVSH-ANNKSRRRWLPNLQETSLLSDTLGRMVRLRLSTNGIRTIEHKGGL 65

Query: 109 DEYLLKTPYHKMDTE 123
           D  LL  P  +++ +
Sbjct: 66  DAALLDIPDARLNQD 80

Rhodospirillum centenum (strain ATCC 51521 / SW) (taxid: 414684)

>sp|O60091|RM24_SCHPO 54S ribosomal protein L24, mitochondrial OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=mrpl24 PE=3 SV=1

 Score = 62.8 bits (151), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 31/86 (36%), Positives = 51/86 (59%), Gaps = 1/86 (1%)

Query: 41  MNRAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALR 100
            ++ ++ L+ G   + GN      G+KTRR W PN   K L+S +++    + VT+  LR
Sbjct: 24  FSKFQQNLYGGSKTEAGNNKIPKFGHKTRRVWIPNGHSKWLYSNVLEEKFHLYVTSRVLR 83

Query: 101 CIDKAGGIDEYLLKTPYHKMDTEMGL 126
            IDK GG+DEYL+K+   ++ + +GL
Sbjct: 84  TIDKEGGLDEYLVKSTPSRLKS-LGL 108

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

>sp|Q9FDL9|RL28_ZYMMO 50S ribosomal protein L28 OS=Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) GN=rpmB PE=3 SV=1

 Score = 61.2 bits (147), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 49  FAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGI 108
             GK  Q GN VS    N+T+R + PN+Q   L S  + + + ++V+TH LR ++  GG+
Sbjct: 7   LTGKGRQVGNNVSH-ANNRTKRTFLPNLQNVTLISDALGKGVTLRVSTHGLRSVEHVGGL 65

Query: 109 DEYLLKTPYHKMDT 122
           D +LLKT   K+ T
Sbjct: 66  DNWLLKTKNEKLST 79

Zymomonas mobilis (strain ATCC 31821 / ZM4 / CP4) (taxid: 264203)

>sp|Q2RXY0|RL28_RHORT 50S ribosomal protein L28 OS=Rhodospirillum rubrum (strain ATCC 11170 / NCIB 8255) GN=rpmB PE=3 SV=1

 Score = 60.8 bits (146), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)

Query: 44  AKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCID 103
           ++R    GK +Q GN VS     K+RR + PN+Q   L S ++   +R++++ H LR ++
Sbjct: 2   SRRCAVTGKGVQTGNNVSHSN-IKSRRRFLPNLQVNSLMSDLLREPVRMRLSAHGLRTVE 60

Query: 104 KAGGIDEYLLKTPYHKMDTEM 124
             GGID +LL TP  ++  E+
Sbjct: 61  HRGGIDAFLLSTPSVELTVEL 81

Rhodospirillum rubrum (strain ATCC 11170 / NCIB 8255) (taxid: 269796)

>sp|A7HTU2|RL28_PARL1 50S ribosomal protein L28 OS=Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966) GN=rpmB PE=3 SV=1

 Score = 58.5 bits (140), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 32/92 (34%), Positives = 51/92 (55%), Gaps = 2/92 (2%)

Query: 44  AKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCID 103
           ++R   +GK +  GN VS     KTRR + PN+ +  L S  + R   ++V+ HALR ++
Sbjct: 2   SRRCELSGKAVMSGNNVSH-ANRKTRRRFLPNLCQVTLISDALGRQFSLRVSAHALRSVE 60

Query: 104 KAGGIDEYLLKTPYHKMDTEMGLYWKTKIEKL 135
             GG+D +LLK    ++ +   L  K  IEK+
Sbjct: 61  HNGGLDPFLLKASDAQLSSR-ALKLKRAIEKV 91

Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966) (taxid: 402881)

>sp|Q11DS9|RL28_MESSB 50S ribosomal protein L28 OS=Mesorhizobium sp. (strain BNC1) GN=rpmB PE=3 SV=1

 Score = 58.2 bits (139), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 31/90 (34%), Positives = 50/90 (55%), Gaps = 1/90 (1%)

Query: 49  FAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGI 108
             GK +  GN VS    NKTRR + PN+ +  L S  + +  R++V+ +ALR ++  GG+
Sbjct: 7   LTGKAVMSGNNVSH-ANNKTRRRFLPNLCDVTLMSEALGQSYRLRVSANALRSVEHRGGL 65

Query: 109 DEYLLKTPYHKMDTEMGLYWKTKIEKLYEE 138
           D +LLK   +++     L  K   +KL E+
Sbjct: 66  DAFLLKAKSNELSQRARLLKKQVAKKLTEQ 95

Mesorhizobium sp. (strain BNC1) (taxid: 266779)

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	222
225457937	216	PREDICTED: 60S ribosomal protein L24, mi	0.972	1.0	0.738	2e-85
224142087	177	predicted protein [Populus trichocarpa]	0.797	1.0	0.807	7e-85
388501160	235	unknown [Lotus japonicus]	0.981	0.927	0.659	5e-84
255646903	235	unknown [Glycine max]	0.927	0.876	0.734	9e-84
147865450	1084	hypothetical protein VITISV_028074 [Viti	0.945	0.193	0.736	1e-83
388514111	235	unknown [Lotus japonicus]	0.981	0.927	0.655	1e-83
356539112	235	PREDICTED: 39S ribosomal protein L28, mi	0.914	0.863	0.725	6e-83
255573228	211	60S ribosomal protein L24, mitochondrial	0.945	0.995	0.683	9e-83
449456779	221	PREDICTED: uncharacterized protein LOC10	0.851	0.855	0.794	2e-82
297798834	212	ribosomal protein L28 family protein [Ar	0.869	0.910	0.733	4e-81

>gi|225457937|ref|XP_002273919.1| PREDICTED: 60S ribosomal protein L24, mitochondrial [Vitis vinifera] gi|302142683|emb|CBI19886.3| unnamed protein product [Vitis vinifera]

 Score =  321 bits (822), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 164/222 (73%), Positives = 192/222 (86%), Gaps = 6/222 (2%)

Query: 1   MAFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRV 60
           MAFR +EMMKK+V+K+G  K     ++ESLKK VPDS++VM RAKRG++AG+HIQFGNRV
Sbjct: 1   MAFRSREMMKKIVKKMGDNK-----LEESLKKYVPDSKVVMGRAKRGIYAGRHIQFGNRV 55

Query: 61  SEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM 120
           SEDGGNKTRR+WKPNVQEKRLFSYI+DRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM
Sbjct: 56  SEDGGNKTRRSWKPNVQEKRLFSYILDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM 115

Query: 121 DTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARRELRRQMYGG 180
           DTEMGL+WK KIEK+YEELG+ +V FF+PE+E K EQ FK++KLA+RAARRE RR +YGG
Sbjct: 116 DTEMGLFWKAKIEKMYEELGEMDVVFFSPEDEVKFEQGFKELKLAERAARREARRHIYGG 175

Query: 181 SSKQKQIEQGSADTQETAEEAAKILSEGIPNEYAPEDLVANS 222
           S KQ Q+E+G AD QET E AA++L EG  +  APE LVANS
Sbjct: 176 SGKQVQLEEGGADIQETNEVAARVL-EGSSHVDAPERLVANS 216

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224142087|ref|XP_002324390.1| predicted protein [Populus trichocarpa] gi|222865824|gb|EEF02955.1| predicted protein [Populus trichocarpa]

 Score =  318 bits (816), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 143/177 (80%), Positives = 166/177 (93%)

Query: 1   MAFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRV 60
           MAFRGKEMMKK++ K+GGEKNLAPGVKE+LKK +P+S++VMNRAKRGLFAG+HIQFGN++
Sbjct: 1   MAFRGKEMMKKIMSKIGGEKNLAPGVKEALKKAIPNSKVVMNRAKRGLFAGRHIQFGNQI 60

Query: 61  SEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM 120
           SEDGGNK+RR+WKPNVQ+KRLFSYI+DRH+RVKVTTHA+RCIDKAGGIDEYLLKTPYHKM
Sbjct: 61  SEDGGNKSRRSWKPNVQDKRLFSYILDRHVRVKVTTHAIRCIDKAGGIDEYLLKTPYHKM 120

Query: 121 DTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARRELRRQM 177
           DTEMG+ WK KIEKLYEELG  EV FFTPE EA L+QDFKDM+L QR AR++LRRQ+
Sbjct: 121 DTEMGILWKAKIEKLYEELGNMEVVFFTPEAEADLDQDFKDMRLEQREARKQLRRQI 177

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388501160|gb|AFK38646.1| unknown [Lotus japonicus]

 Score =  316 bits (809), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 155/235 (65%), Positives = 185/235 (78%), Gaps = 17/235 (7%)

Query: 1   MAFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRV 60
           MAFRGKEMMKK+++KVG EKNL P  KESL+KC+P ++IVM RAKRGLFAG+HIQFGN V
Sbjct: 1   MAFRGKEMMKKVLKKVG-EKNLTPKAKESLQKCIPKTKIVMGRAKRGLFAGRHIQFGNTV 59

Query: 61  SEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM 120
           SEDGGNKTRRNWKPNVQ+KRLFSYI+DRHIR KVTTHALRCIDKAGGIDEYLLKTPYHKM
Sbjct: 60  SEDGGNKTRRNWKPNVQDKRLFSYILDRHIRAKVTTHALRCIDKAGGIDEYLLKTPYHKM 119

Query: 121 DTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARRELRRQMYGG 180
           DTE+G+ WK KIEKLYEELG+ EV FF+PE+EA  EQ FKD+KL++R AR+E+R+ MY G
Sbjct: 120 DTEIGVLWKAKIEKLYEELGKKEVVFFSPEDEANFEQSFKDLKLSEREARKEIRKIMYAG 179

Query: 181 SSKQKQI-----------EQGSADTQETAEEAAKILSEGIPNEY--APEDLVANS 222
             K K I           E G+ + +ET+ ++ K +   +P  Y  AP+ L   S
Sbjct: 180 MGKHKLIGVERKGDQSIEEGGTKNEEETSHDSTKRV---VPVSYVLAPDKLKIGS 231

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255646903|gb|ACU23921.1| unknown [Glycine max]

 Score =  315 bits (807), Expect = 9e-84,   Method: Compositional matrix adjust.
 Identities = 152/207 (73%), Positives = 174/207 (84%), Gaps = 1/207 (0%)

Query: 1   MAFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRV 60
           MAFRGKEMMKK+++ VG E  L+   KESL++C+P S+IVMNRAKRGLFAGKHIQFGNRV
Sbjct: 1   MAFRGKEMMKKVLKTVG-ENGLSRREKESLERCLPRSKIVMNRAKRGLFAGKHIQFGNRV 59

Query: 61  SEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM 120
           SEDGGNK+RR WKPNVQEKRLFSYI+DRH+RVKVTTHALRCIDKAGGIDEYLLKTPYHKM
Sbjct: 60  SEDGGNKSRRTWKPNVQEKRLFSYILDRHVRVKVTTHALRCIDKAGGIDEYLLKTPYHKM 119

Query: 121 DTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARRELRRQMYGG 180
           DTEMG+ WK KIEKLYEELG  EV FF+PE+E K EQ+F+D+KL++R AR+E+RR+MY G
Sbjct: 120 DTEMGILWKAKIEKLYEELGNKEVVFFSPEDEVKFEQEFEDLKLSEREARKEVRRKMYTG 179

Query: 181 SSKQKQIEQGSADTQETAEEAAKILSE 207
            SKQK IE    D Q   E   KI  E
Sbjct: 180 MSKQKLIEVERKDDQCIDEGGNKIEGE 206

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147865450|emb|CAN79404.1| hypothetical protein VITISV_028074 [Vitis vinifera]

 Score =  315 bits (807), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 159/216 (73%), Positives = 187/216 (86%), Gaps = 6/216 (2%)

Query: 1   MAFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRV 60
           MAFR +EMMKK+V+K+G  K     ++ESLKK VPDS++VM RAKRG++AG+HIQFGNRV
Sbjct: 1   MAFRSREMMKKIVKKMGDNK-----LEESLKKYVPDSKVVMGRAKRGIYAGRHIQFGNRV 55

Query: 61  SEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM 120
           SEDGGNKTRR+WKPNVQEKRLFSYI+DRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM
Sbjct: 56  SEDGGNKTRRSWKPNVQEKRLFSYILDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM 115

Query: 121 DTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARRELRRQMYGG 180
           DTEMGL+WK KIEK+YEELG+ +V FF+PE+E K EQ FK++KLA+RAARRE RR +YGG
Sbjct: 116 DTEMGLFWKAKIEKMYEELGEMDVVFFSPEDEVKFEQGFKELKLAERAARREARRHIYGG 175

Query: 181 SSKQKQIEQGSADTQETAEEAAKILSEGIPNEYAPE 216
           S KQ Q+E+G AD QET E AA++L EG  +  APE
Sbjct: 176 SGKQVQLEEGGADIQETNEVAARVL-EGSSHVDAPE 210

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388514111|gb|AFK45117.1| unknown [Lotus japonicus]

 Score =  315 bits (806), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 154/235 (65%), Positives = 187/235 (79%), Gaps = 17/235 (7%)

Query: 1   MAFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRV 60
           MAFRGKEMMKK+++KVG EKNL+P  KESL+KC+P ++IVM RAKRGLFAG+HIQFGN V
Sbjct: 1   MAFRGKEMMKKVLKKVG-EKNLSPKSKESLQKCIPKTKIVMGRAKRGLFAGRHIQFGNTV 59

Query: 61  SEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM 120
           SEDGGNKTRRNWKPNVQ+KRLFSYI+DRHIR KVTTHALRCIDKAGGIDEYLLKTPYHKM
Sbjct: 60  SEDGGNKTRRNWKPNVQDKRLFSYILDRHIRAKVTTHALRCIDKAGGIDEYLLKTPYHKM 119

Query: 121 DTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARRELRRQMYGG 180
           DTE+G+ W+ KIEKLYEELG+ EV FF+PE+EA  EQ FKD+KL++R AR+E+R+ MY G
Sbjct: 120 DTEIGVLWRAKIEKLYEELGKKEVVFFSPEDEANFEQSFKDLKLSEREARKEIRKIMYAG 179

Query: 181 SSKQKQI-----------EQGSADTQETAEEAAKILSEGIPNEY--APEDLVANS 222
             K K I           E G+ + +ET+ +++K +   +P  Y  AP+ L   S
Sbjct: 180 MGKHKLIGVDRKDDQSIEEGGTKNEEETSHDSSKRV---VPVSYVLAPDKLKIGS 231

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356539112|ref|XP_003538044.1| PREDICTED: 39S ribosomal protein L28, mitochondrial-like [Glycine max]

 Score =  312 bits (799), Expect = 6e-83,   Method: Compositional matrix adjust.
 Identities = 148/204 (72%), Positives = 171/204 (83%), Gaps = 1/204 (0%)

Query: 1   MAFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRV 60
           MAFRGKEM+KK+++ VG E  L+   KESL++C+P S+IVMNRAKRGLFAGKHIQFGNRV
Sbjct: 1   MAFRGKEMLKKVLKTVG-ENGLSRREKESLERCLPRSKIVMNRAKRGLFAGKHIQFGNRV 59

Query: 61  SEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM 120
           SEDGGNK+RR WKPNVQEKRLFSYI+DRH+RVK+TTHALRCIDKAGGIDEYL+KTPYHKM
Sbjct: 60  SEDGGNKSRRTWKPNVQEKRLFSYILDRHVRVKITTHALRCIDKAGGIDEYLMKTPYHKM 119

Query: 121 DTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARRELRRQMYGG 180
           DTEMG+ WK KIEKLYEELG  EV FF+PE+EAK EQ+F D+KL +R AR+E+RR+MY G
Sbjct: 120 DTEMGILWKAKIEKLYEELGNKEVVFFSPEDEAKFEQEFNDLKLTEREARKEVRRKMYTG 179

Query: 181 SSKQKQIEQGSADTQETAEEAAKI 204
            SK K IE    D Q   E   KI
Sbjct: 180 MSKHKLIEVERKDDQTIDEGGNKI 203

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255573228|ref|XP_002527543.1| 60S ribosomal protein L24, mitochondrial precursor, putative [Ricinus communis] gi|223533093|gb|EEF34852.1| 60S ribosomal protein L24, mitochondrial precursor, putative [Ricinus communis]

 Score =  311 bits (798), Expect = 9e-83,   Method: Compositional matrix adjust.
 Identities = 151/221 (68%), Positives = 182/221 (82%), Gaps = 11/221 (4%)

Query: 1   MAFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRV 60
           MAFRG+EMMK +++KVG + NL+P VKESLKKC+PDS++VM RAKRG+FAG+HIQFGNRV
Sbjct: 1   MAFRGREMMKNVLKKVG-DNNLSPEVKESLKKCMPDSKVVMGRAKRGIFAGRHIQFGNRV 59

Query: 61  SEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM 120
           SEDGGNKTRR WKPNVQEKRLFSYI+DRHI+VKVTTHALRCIDKAGGIDEYLLKTPY KM
Sbjct: 60  SEDGGNKTRRTWKPNVQEKRLFSYILDRHIQVKVTTHALRCIDKAGGIDEYLLKTPYQKM 119

Query: 121 DTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARRELRRQMYGG 180
           DT+MGL+WK KIEKLYE+LG+ E+ FF PE+EAK EQ  KD+KLA+R ARRE R+QMY  
Sbjct: 120 DTDMGLFWKAKIEKLYEDLGKREIVFFPPEDEAKFEQGLKDLKLAEREARREFRQQMYAR 179

Query: 181 SSKQKQIEQGSADTQETAEEAAKILSEGIPNEYAPEDLVAN 221
            +K+KQ       T E     + +L+    ++Y P+ +VAN
Sbjct: 180 LAKEKQ-------TDEERSYVSFVLASA--DDY-PDKMVAN 210

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449456779|ref|XP_004146126.1| PREDICTED: uncharacterized protein LOC101212331 [Cucumis sativus] gi|449528875|ref|XP_004171427.1| PREDICTED: uncharacterized LOC101212331 [Cucumis sativus]

 Score =  310 bits (795), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 151/190 (79%), Positives = 176/190 (92%), Gaps = 1/190 (0%)

Query: 1   MAFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRV 60
           MAFRGKEMMKK+++KVG E NLAPGVK+SLKKC+PDS+IVM RA RG++AG+HI+FGNRV
Sbjct: 1   MAFRGKEMMKKILKKVG-ENNLAPGVKDSLKKCIPDSKIVMGRANRGIYAGRHIRFGNRV 59

Query: 61  SEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM 120
           SEDGGNK+RRNWKPNVQEKRLFSYI+DRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM
Sbjct: 60  SEDGGNKSRRNWKPNVQEKRLFSYILDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM 119

Query: 121 DTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARRELRRQMYGG 180
           DTE+GL+WK+KIE LYEELG+ EV FF+PE+E K EQ FK++KL++RAARRE RRQMYG 
Sbjct: 120 DTELGLFWKSKIETLYEELGKMEVVFFSPEDEVKFEQRFKELKLSERAARREARRQMYGS 179

Query: 181 SSKQKQIEQG 190
           S+K  QI++G
Sbjct: 180 SAKLNQIKEG 189

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297798834|ref|XP_002867301.1| ribosomal protein L28 family protein [Arabidopsis lyrata subsp. lyrata] gi|297313137|gb|EFH43560.1| ribosomal protein L28 family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  306 bits (784), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 146/199 (73%), Positives = 170/199 (85%), Gaps = 6/199 (3%)

Query: 1   MAFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRV 60
           MAFRGKEMMKKLV++VG E N+ P +KE LK CVPD+++VM RAKRGL+AG+HIQ+GNRV
Sbjct: 1   MAFRGKEMMKKLVKRVGAE-NITPELKEKLKACVPDTKVVMGRAKRGLYAGRHIQYGNRV 59

Query: 61  SEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM 120
           SEDGGNK+RR WKPNVQEKRLFSYI DRHI+VKVTTHALRCIDKAGGIDEYLLKTPY KM
Sbjct: 60  SEDGGNKSRRCWKPNVQEKRLFSYIFDRHIKVKVTTHALRCIDKAGGIDEYLLKTPYQKM 119

Query: 121 DTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARRELRRQMYGG 180
           DTEMGLYWKTK+E+ Y ELGQ EVAFFTPE+EAK EQ FKD+ +A++ ARRE RR+MYG 
Sbjct: 120 DTEMGLYWKTKVEQRYAELGQMEVAFFTPEDEAKFEQGFKDLNIAKKDARREARRKMYG- 178

Query: 181 SSKQKQIEQGSADTQETAE 199
               K+  +G AD + + E
Sbjct: 179 ----KKGGEGKADEEASIE 193

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	222
TAIR|locus:2125234	212	AT4G31460 [Arabidopsis thalian	0.725	0.759	0.808	1.4e-69
DICTYBASE|DDB_G0281601	142	DDB_G0281601 [Dictyostelium di	0.531	0.830	0.411	2.8e-18
ASPGD|ASPL0000047744	203	AN1970 [Emericella nidulans (t	0.490	0.536	0.394	6e-16
SGD|S000004806	258	MRPL24 "Mitochondrial ribosoma	0.540	0.465	0.348	2.3e-14
POMBASE|SPBC14C8.10	176	mrpl24 "mitochondrial ribosoma	0.337	0.426	0.407	5.8e-11
ZFIN|ZDB-GENE-050522-113	252	mrpl28 "mitochondrial ribosoma	0.509	0.448	0.319	1.9e-09
TIGR_CMR|APH_0359	103	APH_0359 "ribosomal protein L2	0.364	0.786	0.409	2.2e-09
CGD|CAL0002685	265	orf19.828 [Candida albicans (t	0.558	0.467	0.343	2.3e-09
TIGR_CMR|SPO_0974	95	SPO_0974 "ribosomal protein L2	0.400	0.936	0.329	1.1e-07
UNIPROTKB|F1RGV8	256	MRPL28 "Uncharacterized protei	0.360	0.312	0.378	1.5e-07

TAIR|locus:2125234 AT4G31460 [Arabidopsis thaliana (taxid:3702)]

 Score = 705 (253.2 bits), Expect = 1.4e-69, P = 1.4e-69
 Identities = 131/162 (80%), Positives = 145/162 (89%)

Query:     1 MAFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRV 60
             MAFRGKEMMKKLV+KVG E N+ P +KE LK CVPD+++VM RAKRGL+AG+HIQ+GNRV
Sbjct:     1 MAFRGKEMMKKLVKKVGAE-NITPELKEKLKACVPDTKVVMGRAKRGLYAGRHIQYGNRV 59

Query:    61 SEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM 120
             SEDGGNK+RR WKPNVQEKRLFSYI D HI+VKVTTHALRCIDKAGGIDEYLLKTPY KM
Sbjct:    60 SEDGGNKSRRCWKPNVQEKRLFSYIFDSHIKVKVTTHALRCIDKAGGIDEYLLKTPYQKM 119

Query:   121 DTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDM 162
             DTEMGLYWKTK+E  Y ELGQ EVAFF PE+EAKLEQ FKD+
Sbjct:   120 DTEMGLYWKTKVEARYAELGQMEVAFFNPEDEAKLEQGFKDL 161

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

GO:0005622 "intracellular" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

DICTYBASE|DDB_G0281601 DDB_G0281601 [Dictyostelium discoideum (taxid:44689)]

 Score = 221 (82.9 bits), Expect = 2.8e-18, P = 2.8e-18
 Identities = 49/119 (41%), Positives = 70/119 (58%)

Query:    38 RIVMNRAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTH 97
             R VM RA+RGL+ GK I F ++ S     KTRR WKPNVQ K   S ++D +IRV +TT+
Sbjct:    14 RSVMKRAQRGLYGGKDIIFSDQ-SSFSTRKTRRTWKPNVQTKTYHSDVLDSNIRVSLTTY 72

Query:    98 ALRCIDKAGGIDEYLLKTPYHKMDTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLE 156
              +RCIDKAG  D Y++ T    + +E+G   K  ++   ++     +     EEE KL+
Sbjct:    73 TIRCIDKAGSFDNYIIHTKDKDLASELGSDLKVAMKHELQKKALLILENEKQEEELKLK 131

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

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

GO:0044351 "macropinocytosis" evidence=RCA

ASPGD|ASPL0000047744 AN1970 [Emericella nidulans (taxid:162425)]

 Score = 199 (75.1 bits), Expect = 6.0e-16, P = 6.0e-16
 Identities = 47/119 (39%), Positives = 72/119 (60%)

Query:    40 VMNRAKRGLFAGKHIQFGNRVSEDGGN--KTRRNWKPNVQEKRLFSYIMDRHIRVKVTTH 97
             +  ++  GL+ G  IQFGN++S+ G N  KTRR WKPNV+ K+L+S  + + + +KVT  
Sbjct:    49 MFRQSNTGLYGGATIQFGNKISQ-GRNEGKTRRFWKPNVRRKKLWSEALQQFLFIKVTRK 107

Query:    98 ALRCIDKAGGIDEYLLKTPYHKMDTEMGLY-WKTK-----IEKLYEELGQTEVAFFTPE 150
             ALR I KAGG+D+YLL     ++  E+G++ WK +      +K+ E+  Q       PE
Sbjct:   108 ALRTIRKAGGLDQYLLDDRPARIK-ELGVFGWKLRWQVMQTDKIQEQFKQERKRLGLPE 165

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

SGD|S000004806 MRPL24 "Mitochondrial ribosomal protein of the large subunit" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 184 (69.8 bits), Expect = 2.3e-14, P = 2.3e-14
 Identities = 46/132 (34%), Positives = 70/132 (53%)

Query:    14 RKVGGEKNLAPGVKESL-----KKCVPDSRI----VMNRAKRGLFAGKHIQFGNRVSEDG 64
             RK+  + N   G  + L     +K  PD +     +  ++ +GL+ G  +QFGN +SE  
Sbjct:    30 RKIAKQPNYQVGDAKPLHMPKERKKFPDYKYGESNIFKQSNKGLYGGSFVQFGNNISESK 89

Query:    65 GNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKMDTEM 124
               KTR+ W PNV +K L+S  ++R I +K+T   L+ I K GGID YL K    ++  E+
Sbjct:    90 A-KTRKKWLPNVVKKGLWSETLNRKISIKMTAKVLKTISKEGGIDNYLTKEKSARIK-EL 147

Query:   125 G-LYWKTKIEKL 135
             G   WK +   L
Sbjct:   148 GPTGWKLRYRVL 159

GO:0005739 "mitochondrion" evidence=IEA;IDA

GO:0005840 "ribosome" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

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

GO:0005622 "intracellular" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0005762 "mitochondrial large ribosomal subunit" evidence=IDA

GO:0032543 "mitochondrial translation" evidence=IC

POMBASE|SPBC14C8.10 mrpl24 "mitochondrial ribosomal protein subunit L28 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 152 (58.6 bits), Expect = 5.8e-11, P = 5.8e-11
 Identities = 31/76 (40%), Positives = 46/76 (60%)

Query:    42 NRAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRC 101
             ++ ++ L+ G   + GN      G+KTRR W PN   K L+S +++    + VT+  LR 
Sbjct:    25 SKFQQNLYGGSKTEAGNNKIPKFGHKTRRVWIPNGHSKWLYSNVLEEKFHLYVTSRVLRT 84

Query:   102 IDKAGGIDEYLLK-TP 116
             IDK GG+DEYL+K TP
Sbjct:    85 IDKEGGLDEYLVKSTP 100

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

GO:0005737 "cytoplasm" evidence=IDA

GO:0005762 "mitochondrial large ribosomal subunit" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0032543 "mitochondrial translation" evidence=NAS

ZFIN|ZDB-GENE-050522-113 mrpl28 "mitochondrial ribosomal protein L28" [Danio rerio (taxid:7955)]

 Score = 148 (57.2 bits), Expect = 1.9e-09, P = 1.9e-09
 Identities = 38/119 (31%), Positives = 64/119 (53%)

Query:    47 GLFAGKHIQFGNRVSEDGGNKTR--RNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDK 104
             GL+ G+    G R ++D    TR  + WKP +  + L+S I+D+   V VT+ AL  ID 
Sbjct:    78 GLWGGEGWISGFRYAKDDKLSTRLPKTWKPQLFTRELYSEILDQKFSVTVTSRALDLIDA 137

Query:   105 AGGIDEYLLKTPYHKMDTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMK 163
             A G D Y+LKTP   ++++ G+  K     +   L + +   + PE++ + E+ +K  K
Sbjct:   138 AFGFDFYILKTPKQDLNSKFGMNLK---RAMLLRLARKDTDLY-PEDQQRKEKIYKRYK 192

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

GO:0005840 "ribosome" evidence=IEA

TIGR_CMR|APH_0359 APH_0359 "ribosomal protein L28" [Anaplasma phagocytophilum HZ (taxid:212042)]

 Score = 137 (53.3 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 34/83 (40%), Positives = 46/83 (55%)

Query:    51 GKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDE 110
             G    FGN+VS     KT+R++  N+    L S ++ R  RVKV +  LR ID  GG+D 
Sbjct:     9 GASKSFGNKVSHSN-RKTKRSYLVNLHNVTLVSEVLGRKFRVKVASRTLRTIDYKGGLDL 67

Query:   111 YLLKTPYHKMDTEMGLYWKTKIE 133
             YLL T   K+ TE+    K KI+
Sbjct:    68 YLLNTSSRKL-TEVARKIKRKIK 89

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

GO:0006412 "translation" evidence=ISS

CGD|CAL0002685 orf19.828 [Candida albicans (taxid:5476)]

 Score = 148 (57.2 bits), Expect = 2.3e-09, P = 2.3e-09
 Identities = 45/131 (34%), Positives = 69/131 (52%)

Query:    11 KLVRKVGGEK--NLA-PGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRVSEDGGNK 67
             K V ++G E+  N++ P       K   + R    R  RGL+ G   +     SE   NK
Sbjct:    52 KNVYEIGQERPDNISIPKDLPEFPKYEYEPRF-FKRQNRGLYGGLQRKRSKSCSEYL-NK 109

Query:    68 TRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKMDTEMGLY 127
             T R  +PN Q  +L+S  ++R +R++V T  L+ I K GG+D+YLLK+   ++ T MGL 
Sbjct:   110 TLRAHRPNAQWTKLWSETLNRRLRLRVATRVLKTISKEGGLDQYLLKSTPARVKT-MGLK 168

Query:   128 -WKTKIEKLYE 137
              W+ +   L E
Sbjct:   169 AWQLRYRILQE 179

GO:0005762 "mitochondrial large ribosomal subunit" evidence=IEA

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

TIGR_CMR|SPO_0974 SPO_0974 "ribosomal protein L28" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 122 (48.0 bits), Expect = 1.1e-07, P = 1.1e-07
 Identities = 30/91 (32%), Positives = 49/91 (53%)

Query:    44 AKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCID 103
             ++R    GK    GN VS    NKTRR + PN+ +  L S  + R ++++++  ALR +D
Sbjct:     2 SRRCELTGKGPMTGNNVSH-ANNKTRRRFLPNLNDVTLQSETLGRGVKLRISAAALRSVD 60

Query:   104 KAGGIDEYLLKTPYHKMDTEMGLYWKTKIEK 134
               GG+D +L K     + ++  L  K +I K
Sbjct:    61 HRGGLDAFLAKAKDEDL-SDAALKVKKEIAK 90

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

GO:0006412 "translation" evidence=ISS

GO:0042255 "ribosome assembly" evidence=ISS

UNIPROTKB|F1RGV8 MRPL28 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 136 (52.9 bits), Expect = 1.5e-07, P = 1.5e-07
 Identities = 31/82 (37%), Positives = 49/82 (59%)

Query:    47 GLFAGKHIQFGNR-VSEDGGNK-TRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDK 104
             GL+ G+    G+R V+ D  +K  R+ WKP + ++ L+S I+D+   V VT   L  ID+
Sbjct:    78 GLWGGEGWVLGHRYVNNDKLSKRVRKVWKPQLFQRELYSEILDKRFTVTVTMRTLDLIDQ 137

Query:   105 AGGIDEYLLKTPYHKMDTEMGL 126
             A G D Y+LKTP   + ++ G+
Sbjct:   138 ACGFDFYILKTPKEDLCSKFGM 159

GO:0005739 "mitochondrion" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00014400001 SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (216 aa) (Vitis vinifera)

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	222
pfam00830	61	pfam00830, Ribosomal_L28, Ribosomal L28 family	2e-22
COG0227	77	COG0227, RpmB, Ribosomal protein L28 [Translation,	3e-16
PRK00359	76	PRK00359, rpmB, 50S ribosomal protein L28; Reviewe	1e-14
TIGR00009	56	TIGR00009, L28, ribosomal protein L28	2e-07

>gnl|CDD|201462 pfam00830, Ribosomal_L28, Ribosomal L28 family

 Score = 86.0 bits (214), Expect = 2e-22
 Identities = 33/62 (53%), Positives = 42/62 (67%), Gaps = 1/62 (1%)

Query: 45  KRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDK 104
           +R    GK   FGN VS    NKT+R WKPN+Q+KRL+S  + R +R+KV+T ALR IDK
Sbjct: 1   RRCQLTGKGPMFGNNVSH-SNNKTKRRWKPNLQKKRLWSESLGRWVRLKVSTKALRTIDK 59

Query: 105 AG 106
            G
Sbjct: 60  KG 61

The ribosomal 28 family includes L28 proteins from bacteria and chloroplasts. The L24 protein from yeast also contains a region of similarity to prokaryotic L28 proteins. L24 from yeast is also found in the large ribosomal subunit. Length = 61

>gnl|CDD|223305 COG0227, RpmB, Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]

 Score = 70.4 bits (173), Expect = 3e-16
 Identities = 30/71 (42%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 44  AKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCID 103
           ++R    GK    GN VS    NKT+R + PN+Q+ R +S    R  R++V+  ALR ID
Sbjct: 2   SRRCQLTGKGPMSGNNVSH-SHNKTKRRFLPNLQKVRFWSLSDGRFKRLRVSAKALRTID 60

Query: 104 KAGGIDEYLLK 114
           K G ID  L K
Sbjct: 61  KKGKIDAVLAK 71

Length = 77

>gnl|CDD|234736 PRK00359, rpmB, 50S ribosomal protein L28; Reviewed

 Score = 66.0 bits (162), Expect = 1e-14
 Identities = 27/65 (41%), Positives = 37/65 (56%), Gaps = 2/65 (3%)

Query: 51  GKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDE 110
           GK    GN VS    NKT+R + PN+Q+ R +     R +R++V+  ALR IDK  G+D 
Sbjct: 9   GKGPMVGNNVSH-SNNKTKRRFLPNLQKVRFWVEEEGRFVRLRVSARALRTIDK-KGLDA 66

Query: 111 YLLKT 115
            L K 
Sbjct: 67  VLKKA 71

Length = 76

>gnl|CDD|199985 TIGR00009, L28, ribosomal protein L28

 Score = 46.1 bits (110), Expect = 2e-07
 Identities = 20/50 (40%), Positives = 29/50 (58%), Gaps = 3/50 (6%)

Query: 51  GKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALR 100
           GK    GN VS     KT+R +KPN+Q+KR++     R  R++V+   LR
Sbjct: 9   GKGPLSGNNVSH-SHRKTKRRFKPNLQKKRVWVDG--RFKRLRVSAKCLR 55

This model describes bacterial and chloroplast forms of the 50S ribosomal protein L28, a polypeptide about 60 amino acids in length. Mitochondrial homologs differ substantially in architecture and are not included [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 56

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	222
KOG3278	215	consensus Mitochondrial/chloroplast ribosomal prot	100.0
PRK00359	76	rpmB 50S ribosomal protein L28; Reviewed	99.94
COG0227	77	RpmB Ribosomal protein L28 [Translation, ribosomal	99.94
PF00830	61	Ribosomal_L28: Ribosomal L28 family; InterPro: IPR	99.91
CHL00112	63	rpl28 ribosomal protein L28; Provisional	99.89
KOG3279	283	consensus Uncharacterized conserved protein (melan	99.89
TIGR00009	56	L28 ribosomal protein L28. This model describes ba	99.86

>KOG3278 consensus Mitochondrial/chloroplast ribosomal protein L28 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=3.9e-43  Score=300.91  Aligned_cols=187  Identities=63%  Similarity=0.963  Sum_probs=170.2

Q ss_pred             CccchHHHHHHHHHHhcCCCCCCchhhhhhhhcCCCchhhhhccccccccCceeeecccccCCCCCcccceeccceeEEE
Q 039022            1 MAFRGKEMMKKLVRKVGGEKNLAPGVKESLKKCVPDSRIVMNRAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKR   80 (222)
Q Consensus         1 ~~~~~~~~~~~~~~~vg~~~~~~~~~~~~~~~~~P~~~~v~krSr~Cl~~GK~~~~GN~VSh~S~~KTrR~WkPNLqkkr   80 (222)
                      ||||++|||+|++++++ ..+++|+..+.++-|+|+...+|+|+++|+|+|..+++|||++..+.+||||.|.||+|.++
T Consensus         1 ~~~r~~~m~~kl~~k~a-~p~~~P~~~~k~k~~vyd~~~vf~q~~~gLYgGs~iq~GNn~i~~~g~KTRr~W~PNv~~K~   79 (215)
T KOG3278|consen    1 MAFRGKEMMKKLVKKVA-APNITPELKEKLKACVYDTKVVFGQAKRGLYGGSHIQYGNNVIEDGGNKTRRCWKPNVQEKR   79 (215)
T ss_pred             CcchHHHHHHHHHHhhc-ccccCHHHHhhccccccChHHHHhhcccccccccceecCcccccccCcccceeecCcchhhH
Confidence            89999999999999998 44467888888888888888999999999999999999999766699999999999999999


Q ss_pred             EEEccCCeEEEEEeehhHHhhHhhcCChhHHhhcCCCCCCC--HHHhHHHHHHHHHHHH-HhcccccccCChHHHHHHHH
Q 039022           81 LFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKMD--TEMGLYWKTKIEKLYE-ELGQTEVAFFTPEEEAKLEQ  157 (222)
Q Consensus        81 l~SeiLgr~irVkVTTraLRTIdK~GGlD~YLLkt~~~~L~--selG~~lK~~I~~~y~-~l~~ke~~~~~pe~ea~~~e  157 (222)
                      |||++|++.|.|+|||++||||||.||||+||++++++++.  .++|.+||.+++..|+ +..+++..+++|+.+++.+|
T Consensus        80 L~S~il~~ki~vkvTt~vLrtIdKeGGiDeYL~K~~sar~K~lg~~G~~lr~~Vl~r~~ienp~~e~ap~~~~a~~k~~~  159 (215)
T KOG3278|consen   80 LFSYILDSKIKVKVTTHVLRTIDKEGGIDEYLLKTPSARQKMLGEMGLYLRTKVLARYAIENPQMEVAPFNPEAEAKLEQ  159 (215)
T ss_pred             HHHHHHhhheeeeeehHHHhhhccccChhHHHhcCcHHHHhhcccchHHHHHHHHHHhhccCCcccccCCCchhHHHHHH
Confidence            99999999999999999999999999999999999987764  3556689999999999 88999999999999999999


Q ss_pred             HHhhhcccHHHHHHHHHHHHhcCCcchhhhh
Q 039022          158 DFKDMKLAQRAARRELRRQMYGGSSKQKQIE  188 (222)
Q Consensus       158 ~~k~~~i~~~~a~~~~~~~~~~~~~~~~~~~  188 (222)
                      .|+++.|....++++.||++-...+..+..|
T Consensus       160 ~~kD~~i~~~~~k~~~rr~~~s~~g~~~~~e  190 (215)
T KOG3278|consen  160 GFKDLNIAKKDAKREARRTFRSKGGGNKGDE  190 (215)
T ss_pred             HHHHHHhccCHHHHHHHHHHHHHcCCcccch
Confidence            9999999999999999999866666554443

>PRK00359 rpmB 50S ribosomal protein L28; Reviewed

Probab=99.94  E-value=4.7e-28  Score=181.56  Aligned_cols=75  Identities=36%  Similarity=0.515  Sum_probs=70.9

Q ss_pred             ccccccccCceeeecccccCCCCCcccceeccceeEEEEEEccCCeEEEEEeehhHHhhHhhcCChhHHhhcCCCCC
Q 039022           43 RAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHK  119 (222)
Q Consensus        43 rSr~Cl~~GK~~~~GN~VSh~S~~KTrR~WkPNLqkkrl~SeiLgr~irVkVTTraLRTIdK~GGlD~YLLkt~~~~  119 (222)
                      ||++|++|||++++||+||| |+++|+|+|+||||++++||+++|++++|+|||+|||||+|.| +|+||+.+....
T Consensus         1 Msr~C~i~GK~~~~Gn~vSh-s~~kTkR~~~pNlq~~~~~~~~~g~~v~~~vst~~Lrti~k~G-l~~~~~~~~~~~   75 (76)
T PRK00359          1 MSRVCEITGKGPMVGNNVSH-SNNKTKRRFLPNLQKVRFWVEEEGRFVRLRVSARALRTIDKKG-LDAVLKKARARG   75 (76)
T ss_pred             CCCccccCCCCCccCCeeee-cCCccCceecccceEEEEEEccCCEEEEEEEEchheeeehhhh-HHHHHHhhhhcc
Confidence            57899999999999999999 8999999999999999999999999999999999999999995 999999876543

>COG0227 RpmB Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]

Probab=99.94  E-value=7.7e-28  Score=181.37  Aligned_cols=73  Identities=41%  Similarity=0.567  Sum_probs=70.7

Q ss_pred             ccccccccCceeeecccccCCCCCcccceeccceeEEEEEEccCCeEEEEEeehhHHhhHhhcCChhHHhhcCC
Q 039022           43 RAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTP  116 (222)
Q Consensus        43 rSr~Cl~~GK~~~~GN~VSh~S~~KTrR~WkPNLqkkrl~SeiLgr~irVkVTTraLRTIdK~GGlD~YLLkt~  116 (222)
                      ||++|++||+++++||+||| |+++|+|+|.||||++++|++.+|++++|+|||+|||+||+.||+|+|+.+..
T Consensus         1 Msr~C~lTGk~~~~GnnvSh-s~~kTkRr~~pNlq~~~~~~~~~g~~~~l~Vsa~~Lrtidk~G~~~~~~~~~~   73 (77)
T COG0227           1 MSRRCQLTGKGPMSGNNVSH-SHNKTKRRFLPNLQKVRFWSLSDGRFKRLRVSAKALRTIDKKGKIDAVLAKAR   73 (77)
T ss_pred             CCceeeeccccccccccccc-cccccceeecCccEEEEEEEccCCcEEEEEEEhHHhhccccccchhhhhhhhc
Confidence            57899999999999999999 89999999999999999999999999999999999999999999999998865

>PF00830 Ribosomal_L28: Ribosomal L28 family; InterPro: IPR001383 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.91  E-value=5e-25  Score=158.70  Aligned_cols=61  Identities=57%  Similarity=0.932  Sum_probs=57.0

Q ss_pred             ccccccCceeeecccccCCCCCcccceeccceeEEEEEEccCCeEEEEEeehhHHhhHhhcC
Q 039022           45 KRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAG  106 (222)
Q Consensus        45 r~Cl~~GK~~~~GN~VSh~S~~KTrR~WkPNLqkkrl~SeiLgr~irVkVTTraLRTIdK~G  106 (222)
                      ++|+||||++++||+||| |+++|+|+|+||||++++||++||++++|+|||+|||+|+|.|
T Consensus         1 r~c~~~GK~~~~Gn~vsh-s~~ktkR~~~pNlq~~~~~~~~lg~~~~v~vst~~Lrti~k~G   61 (61)
T PF00830_consen    1 RRCLITGKKPMFGNNVSH-SNNKTKRRWKPNLQKKRLWSEILGKKIRVRVSTRALRTIDKKG   61 (61)
T ss_dssp             -S-TTT-CTTCEECEEEE-ECEEEEEEEBTTEEEEEEEESTTSSEEEEEEEHCHHHHHHCHT
T ss_pred             CEeecCCCeecccceEee-cCCcCCcEEcCcCEEEEEEEcCCCeEEEEEEEhHHeeeeccCC
Confidence            489999999999999999 8999999999999999999999999999999999999999986

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 ribosomal L28 protein family include proteins from bacteria and chloroplasts. The L24 protein from yeast, found in the large subunit of the mitochodrial ribosome, contains a region similar to the bacterial L28 protein.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZJP_U 3CF5_U 2ZJR_U 3PIP_U 3PIO_U 2ZJQ_U 3DLL_U 2Y15_1 3KIY_1 3V2D_1 ....

>CHL00112 rpl28 ribosomal protein L28; Provisional

Probab=99.89  E-value=6.4e-24  Score=154.61  Aligned_cols=62  Identities=27%  Similarity=0.466  Sum_probs=59.7

Q ss_pred             ccccccccCceeeecccccCCCCCcccceeccceeEEEEEEccCCeEEEEEeehhHHhhHhhc
Q 039022           43 RAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKA  105 (222)
Q Consensus        43 rSr~Cl~~GK~~~~GN~VSh~S~~KTrR~WkPNLqkkrl~SeiLgr~irVkVTTraLRTIdK~  105 (222)
                      ||++|++|||++++||+||| |+++|+|+|+||||++++|++.++++++|+|||+|||+|+|.
T Consensus         1 Msr~C~i~GK~~~~Gn~vSH-s~~kTkR~f~pNLq~vr~~~~~~~~~~kl~Vstr~Lrt~~k~   62 (63)
T CHL00112          1 MSKKCQLTGKKANNGYTVSH-SHKRTKKLQKVNLQTKKIWSNTQNRWVKLKISTKAIKTLKKK   62 (63)
T ss_pred             CCCeeccCCCcCccCceeEc-cCcccCceecccccEEEEEECCCCeEEEEEEEHHHhhhcccc
Confidence            57899999999999999999 899999999999999999999999999999999999999985

>KOG3279 consensus Uncharacterized conserved protein (melanoma antigen P15) [Function unknown]

Probab=99.89  E-value=4e-24  Score=188.45  Aligned_cols=155  Identities=23%  Similarity=0.370  Sum_probs=131.5

Q ss_pred             hhcCCCchhhhhccccccccCceeeecccccCCCCCcccceeccceeEEEEEEccCCeEEEEEeehhHHhhHhhcCChhH
Q 039022           31 KKCVPDSRIVMNRAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDE  110 (222)
Q Consensus        31 ~~~~P~~~~v~krSr~Cl~~GK~~~~GN~VSh~S~~KTrR~WkPNLqkkrl~SeiLgr~irVkVTTraLRTIdK~GGlD~  110 (222)
                      ..++|..-|..+++++|+|+|+.++.|..-|...++|..|.|.|||.++.++|++|+.+++|.||.|+|+.||.+.|||.
T Consensus        69 ~~~~p~~~i~tpe~~~g~wgge~vikg~~~~~~tk~~~p~~wvp~l~~~v~~s~ild~y~~v~vteRtl~LIDE~~GLD~  148 (283)
T KOG3279|consen   69 VQNIPLPLIDTPESHRGIWGGEAVIKGFQKREQTKRRVPHFWVPNLRRSVVHSHVLDCYMSVVVTERTLELIDECHGLDH  148 (283)
T ss_pred             hhcCCcccccCCcccccccccHHHHHHHHHHHHHhhcCCcccccchhhHHHHHHHHhhhheeeehHHHHHHHHHhcCcce
Confidence            45678888999999999999999999999888556789999999999999999999999999999999999999999999


Q ss_pred             HhhcCCCCCCCHHHhHHHHHHHHHHHHHhcccccccCChHHHHHHHHHHhhhcccHHHHHH---HHHHHHhcCCcchhhh
Q 039022          111 YLLKTPYHKMDTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLEQDFKDMKLAQRAARR---ELRRQMYGGSSKQKQI  187 (222)
Q Consensus       111 YLLkt~~~~L~selG~~lK~~I~~~y~~l~~ke~~~~~pe~ea~~~e~~k~~~i~~~~a~~---~~~~~~~~~~~~~~~~  187 (222)
                      |||+++..+|+|++|+.|||.|+.....-..  .....||.+|.+.+.|++|.|+++||+=   ++-.++    -||+++
T Consensus       149 YILk~~~~DL~SKFa~~LKReMLL~L~~~~p--~~~E~pEr~A~I~~KY~~F~IPEeEAEW~GLtL~EAi----rKQ~~l  222 (283)
T KOG3279|consen  149 YILKNRACDLRSKFALKLKREMLLALQNGVP--ALAEEPERQAEILKKYRRFLIPEEEAEWYGLTLLEAI----RKQKQL  222 (283)
T ss_pred             eeecCcchhHHHHHHHHHHHHHHHHHhcCCC--cccCChHHHHHHHHHHHHhcCCHHHhhHhhhHHHHHH----HHHHHH
Confidence            9999999999999999999999876654433  2335588888888999999999888862   222233    566677


Q ss_pred             hcCC
Q 039022          188 EQGS  191 (222)
Q Consensus       188 ~~~~  191 (222)
                      |+..
T Consensus       223 Ee~~  226 (283)
T KOG3279|consen  223 EEAE  226 (283)
T ss_pred             Hhcc
Confidence            6543

>TIGR00009 L28 ribosomal protein L28

Probab=99.86  E-value=3.1e-22  Score=142.31  Aligned_cols=56  Identities=36%  Similarity=0.564  Sum_probs=53.7

Q ss_pred             ccccccccCceeeecccccCCCCCcccceeccceeEEEEEEccCCeEEEEEeehhHHhh
Q 039022           43 RAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRC  101 (222)
Q Consensus        43 rSr~Cl~~GK~~~~GN~VSh~S~~KTrR~WkPNLqkkrl~SeiLgr~irVkVTTraLRT  101 (222)
                      ||++|++|||++++||+||| |+++|+|+|+||||++++|++  |++++|+|||+|||+
T Consensus         1 Ms~~C~i~GK~~~~Gn~vsh-s~~ktkR~~~pNlq~~ri~~~--~~~~~~~vst~~Lkt   56 (56)
T TIGR00009         1 MSRKCQLTGKGPLSGNNVSH-SHRKTKRRFKPNLQKKRVWVD--GRFKRLRVSAKCLRT   56 (56)
T ss_pred             CCCEeeeCCCcCccCCeeee-cCCccCceecccceEEEEEEC--CEEEEEEEEcHHhcC
Confidence            57899999999999999999 899999999999999999998  799999999999986

This model describes bacterial and chloroplast forms of the 50S ribosomal protein L28, a polypeptide about 60 amino acids in length. Mitochondrial homologs differ substantially in architecture and are not included.

---

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 RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	222
3bbo_Y	151	Ribosomal protein L28; large ribosomal subunit, sp	5e-16
3r8s_X	77	50S ribosomal protein L28; protein biosynthesis, R	1e-15
2jz6_A	77	50S ribosomal protein L28; structure, NESG, ribonu	3e-10
2jl6_1	89	50S ribosomal protein L28, 50S ribosomal protein L	6e-08
3v2d_1	98	50S ribosomal protein L28; ribosome associated inh	3e-07
2zjr_U	81	50S ribosomal protein L28; ribosome, large ribosom	2e-06

>3bbo_Y Ribosomal protein L28; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 151

 Score = 71.5 bits (175), Expect = 5e-16
 Identities = 19/64 (29%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 51  GKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDE 110
           GK     N+VS    +KT++    N+Q KR++     R+++++++T A++ I+K  G+D 
Sbjct: 82  GKKSNRANKVS-HSNHKTKKLQFVNLQYKRIWWEAGKRYVKLRLSTKAIKTIEK-NGLDA 139

Query: 111 YLLK 114
              K
Sbjct: 140 VAKK 143

>3r8s_X 50S ribosomal protein L28; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 2i2v_X 2wwq_0* 3fik_X 3j01_X 3j0t_Z* 3j0w_Z* 3j0y_Z* 3j11_Z* 3j12_Z* 3j14_Z* 3oas_X 3oat_X* 2i2t_X* 3ofd_X 3ofc_X 3ofr_X* 3ofz_X* 3og0_X 3ofq_X 3r8t_X ... Length = 77

 Score = 68.4 bits (168), Expect = 1e-15
 Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 51  GKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDE 110
           GK    GN  S    N T+R + PN+   R +     R + ++V+   +R IDK  GID 
Sbjct: 8   GKRPVTGNNRS-HALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDK-KGIDT 65

Query: 111 YLLK 114
            L +
Sbjct: 66  VLAE 69

>2jz6_A 50S ribosomal protein L28; structure, NESG, ribonucleoprotein, structural genomics, PSI-2, protein structure initiative; NMR {Thermotoga maritima MSB8} SCOP: d.325.1.1 Length = 77

 Score = 53.9 bits (130), Expect = 3e-10
 Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 2/56 (3%)

Query: 51  GKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAG 106
           GK  + GN VS     K+ R ++PN+Q+ R+         R++V T  L+      
Sbjct: 14  GKAPRSGNTVSH-SDKKSERWFRPNLQKVRVVLPD-GTIKRMRVCTSCLKSGKVKK 67

>3v2d_1 50S ribosomal protein L28; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2j03_1 2v47_1 2v49_1 2wdi_1 2wdj_1 2wdl_1 2wdn_1 2wh2_1 2wh4_1 2wrj_1 2wrl_1 2wro_1 2wrr_1 2x9s_1 2x9u_1 2xqe_1 2xtg_1 2xux_1 2y0v_1 2y0x_1 ... Length = 98

 Score = 46.5 bits (110), Expect = 3e-07
 Identities = 12/74 (16%), Positives = 25/74 (33%), Gaps = 14/74 (18%)

Query: 51  GKHIQFGNRVSEDG------------GNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHA 98
           GK     N +   G               ++R   PN+Q+ R+   +  + I  +V    
Sbjct: 9   GKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRVR--VAGQEITFRVAASH 66

Query: 99  LRCIDKAGGIDEYL 112
           +  + +     + L
Sbjct: 67  IPKVYELVERAKGL 80

>2zjr_U 50S ribosomal protein L28; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.325.1.1 PDB: 2zjp_U 2zjq_U 3cf5_U* 3dll_U* 3pio_U* 3pip_U* Length = 81

 Score = 43.4 bits (102), Expect = 2e-06
 Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 14/68 (20%)

Query: 51  GKHIQFGNRVSEDG------------GNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHA 98
           GK     N V   G               T+R  + N+ +K +      +   V ++ +A
Sbjct: 9   GKKNLVVNSVIRRGKARADGGVGRKTTGITKRVQRANLHKKAI--RENGQVKTVWLSANA 66

Query: 99  LRCIDKAG 106
           LR + K  
Sbjct: 67  LRTLSKGP 74

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	222
3r8s_X	77	50S ribosomal protein L28; protein biosynthesis, R	99.95
3bbo_Y	151	Ribosomal protein L28; large ribosomal subunit, sp	99.92
2jz6_A	77	50S ribosomal protein L28; structure, NESG, ribonu	99.88
2zjr_U	81	50S ribosomal protein L28; ribosome, large ribosom	99.88
2jl6_1	89	50S ribosomal protein L28, 50S ribosomal protein L	99.86
3v2d_1	98	50S ribosomal protein L28; ribosome associated inh	99.83

>3r8s_X 50S ribosomal protein L28; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 2i2v_X 2wwq_0* 3fik_X 3j01_X 3j0t_Z* 3j0w_Z* 3j0y_Z* 3j11_Z* 3j12_Z* 3j14_Z* 3j19_X 3oas_X 3oat_X* 2i2t_X* 3ofd_X 3ofc_X 3ofr_X* 3ofz_X* 3og0_X 3ofq_X ...

Probab=99.95  E-value=9e-29  Score=184.93  Aligned_cols=70  Identities=30%  Similarity=0.470  Sum_probs=67.4

Q ss_pred             cccccccCceeeecccccCCCCCcccceeccceeEEEEEEccCCeEEEEEeehhHHhhHhhcCChhHHhhcC
Q 039022           44 AKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKT  115 (222)
Q Consensus        44 Sr~Cl~~GK~~~~GN~VSh~S~~KTrR~WkPNLqkkrl~SeiLgr~irVkVTTraLRTIdK~GGlD~YLLkt  115 (222)
                      |++|++|||++++||+||| |+++|+|+|+||||++++|++.++++++|+|||+|||||||. |||+||+..
T Consensus         1 sr~C~itGK~~~~Gn~VSh-s~~kTkR~~~PNlq~~r~~~~~~~r~~rlrVst~~LRti~k~-Gld~~l~~~   70 (77)
T 3r8s_X            1 SRVCQVTGKRPVTGNNRSH-ALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKK-GIDTVLAEL   70 (77)
T ss_dssp             CCCCTTTCCCCEEEEEECS-SCCEEEEEECCCEEEEEEEEGGGTEEEEEEEEHHHHHHHHHH-CHHHHHHHH
T ss_pred             CCEeeeCCCccccCceEec-cCCccCceecCccEEEEEEECCCCEEEEEEEEcceEeeeccc-CHHHHHHHH
Confidence            5799999999999999999 899999999999999999999999999999999999999999 899999764

>3bbo_Y Ribosomal protein L28; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=99.92  E-value=1.4e-27  Score=197.81  Aligned_cols=101  Identities=25%  Similarity=0.289  Sum_probs=66.9

Q ss_pred             HHhcCCCCCCchhhhhhh-hcCCCchhhhh-ccccccccCceeeecccccCCCCCcccceeccceeEEEEEEccCCeEEE
Q 039022           14 RKVGGEKNLAPGVKESLK-KCVPDSRIVMN-RAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIR   91 (222)
Q Consensus        14 ~~vg~~~~~~~~~~~~~~-~~~P~~~~v~k-rSr~Cl~~GK~~~~GN~VSh~S~~KTrR~WkPNLqkkrl~SeiLgr~ir   91 (222)
                      .++||++-.+++.++..+ ..+|....+.. ++++|+||||++++||+||| +++||+|+|+||||++++|++.++++++
T Consensus        43 s~~~g~~~~~~~~~~~~~~~~~p~~~~~~~mMsR~C~itGK~p~~GNnVSH-S~~KTKRrw~PNLQkvri~~~~g~r~vr  121 (151)
T 3bbo_Y           43 SQLSGLKISSTHFISSSAPLSVPFKPSLQPVARRICPFTGKKSNRANKVSH-SNHKTKKLQFVNLQYKRIWWEAGKRYVK  121 (151)
T ss_dssp             ---------------------------------CCCCCSCCTTCCCCCCEE-CCSSSCCEECCCCCCCCBCCCTTSSCCC
T ss_pred             hhccCcccccccccccccccccCCCCccccchhceeeccCcccccCCeeee-cCCccCceeccccEEEEEEECCCCEEEE
Confidence            467777766556655554 46677654333 77889999999999999999 8999999999999999999998899999


Q ss_pred             EEeehhHHhhHhhcCChhHHhhcCC
Q 039022           92 VKVTTHALRCIDKAGGIDEYLLKTP  116 (222)
Q Consensus        92 VkVTTraLRTIdK~GGlD~YLLkt~  116 (222)
                      |+|||+|||+|++. |||+||++..
T Consensus       122 lrVsTr~LRTikk~-GlD~~l~~~g  145 (151)
T 3bbo_Y          122 LRLSTKAIKTIEKN-GLDAVAKKAG  145 (151)
T ss_dssp             BCCCSSSTTTTTTS-TTTCSCCSSS
T ss_pred             EEEEchheeehhhh-hHHHHHHHhc
Confidence            99999999999999 8999997643

>2jz6_A 50S ribosomal protein L28; structure, NESG, ribonucleoprotein, structural genomics, PSI-2, protein structure initiative; NMR {Thermotoga maritima MSB8} SCOP: d.325.1.1

Probab=99.88  E-value=2e-23  Score=156.29  Aligned_cols=60  Identities=32%  Similarity=0.356  Sum_probs=57.1

Q ss_pred             ccccccccCceeeecccccCCCCCcccceeccceeEEEEEEccCCeEEEEEeehhHHhhHhh
Q 039022           43 RAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDK  104 (222)
Q Consensus        43 rSr~Cl~~GK~~~~GN~VSh~S~~KTrR~WkPNLqkkrl~SeiLgr~irVkVTTraLRTIdK  104 (222)
                      ||++|++|||++++||+||| |+++|+|+|+||||++++|++. |++++|+|||+|||+++.
T Consensus         6 Msr~C~itGK~~~~Gn~VSH-S~~kTkR~~~PNLq~vr~~~~~-g~~~rl~Vst~~LRtgkv   65 (77)
T 2jz6_A            6 MAKRCEVCGKAPRSGNTVSH-SDKKSERWFRPNLQKVRVVLPD-GTIKRMRVCTSCLKSGKV   65 (77)
T ss_dssp             CCCCCTTTCCCCCCCCCCCC-SCCCCSSSCBTTEEEEEEEETT-TEEEEEEEEHHHHHHCCS
T ss_pred             eeeeeeecCCccccCCeEee-cCCccCcccccceEEEEEEecC-CcEEEEEEEhHHeeeccE
Confidence            68899999999999999999 8999999999999999999965 999999999999999873

>2zjr_U 50S ribosomal protein L28; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.325.1.1 PDB: 2zjp_U 2zjq_U 3cf5_U* 3dll_U* 3pio_U* 3pip_U*

Probab=99.88  E-value=1.1e-24  Score=164.45  Aligned_cols=67  Identities=21%  Similarity=0.207  Sum_probs=56.0

Q ss_pred             ccccccccCceeeecccccCC------------CCCcccceeccceeEEEEEEccCCeEEEEEeehhHHhhHhhcCChhH
Q 039022           43 RAKRGLFAGKHIQFGNRVSED------------GGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDE  110 (222)
Q Consensus        43 rSr~Cl~~GK~~~~GN~VSh~------------S~~KTrR~WkPNLqkkrl~SeiLgr~irVkVTTraLRTIdK~GGlD~  110 (222)
                      ||++|++|||++++||+|||+            |+++|+|+|+||||++++|.  +|++++|+|||+|||+|||  |||+
T Consensus         1 Msr~C~itGK~~~~Gn~vshrGkak~~Gg~~s~s~~kTkR~~~PNlq~vr~~~--~g~~~~l~Vst~~LRti~k--Gld~   76 (81)
T 2zjr_U            1 MSRECYLTGKKNLVVNSVIRRGKARADGGVGRKTTGITKRVQRANLHKKAIRE--NGQVKTVWLSANALRTLSK--GPYK   76 (81)
T ss_dssp             -------CCSSSCCCCCCCCCCEESCCCTTTCSCCEECCCCCCCCCCCCCCCC--SSSCCCCCCCHHHHHHHHS--SCCS
T ss_pred             CCCEeecCCCccccCCeeeeccccccccccchhhCCccCceecccceEEEEEE--CCEEEEEEEEcceeeeech--hHHH
Confidence            578999999999999999993            48999999999999999994  6999999999999999999  8999


Q ss_pred             Hhh
Q 039022          111 YLL  113 (222)
Q Consensus       111 YLL  113 (222)
                      ++.
T Consensus        77 ~~~   79 (81)
T 2zjr_U           77 GIE   79 (81)
T ss_dssp             SCC
T ss_pred             HHh
Confidence            864

>3v2d_1 50S ribosomal protein L28; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2j03_1 2v47_1 2v49_1 2wdi_1 2wdj_1 2wdl_1 2wdn_1 2wh2_1 2wh4_1 2wrj_1 2wrl_1 2wro_1 2wrr_1 2x9s_1 2x9u_1 2xqe_1 2xtg_1 2xux_1 2y0v_1 2y0x_1 ...

Probab=99.83  E-value=9.9e-22  Score=152.95  Aligned_cols=60  Identities=20%  Similarity=0.266  Sum_probs=55.5

Q ss_pred             ccccccccCceeeecccccCCCCC-------------cccceeccceeEEEEEEccCCeEEEEEeehhHHhhHhhc
Q 039022           43 RAKRGLFAGKHIQFGNRVSEDGGN-------------KTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKA  105 (222)
Q Consensus        43 rSr~Cl~~GK~~~~GN~VSh~S~~-------------KTrR~WkPNLqkkrl~SeiLgr~irVkVTTraLRTIdK~  105 (222)
                      ||++|++|||++++||+||| |++             +|+|+|+||||++++|++  |++++|+|||+|||||++.
T Consensus         1 Msr~C~itGK~p~~Gn~VSh-s~~Ak~~GGvG~k~t~kTkR~f~PNLqkvr~~~~--G~~~rlrVst~~LRtI~~~   73 (98)
T 3v2d_1            1 MSKVCEISGKRPIVANSIQR-RGKAKREGGVGKKTTGISKRRQYPNLQKVRVRVA--GQEITFRVAASHIPKVYEL   73 (98)
T ss_dssp             -CCCCTTTCCCCEEEEEEEE-EEECGGGTSSEEEEEEEEEEEECCCEEEEEEEET--TEEEEEEEEGGGHHHHHHH
T ss_pred             CCCeeecCCCccccCccEec-cCccccccccccccCCcccceeccceEEEEEEEC--CEEEEEEEEchhheehhhh
Confidence            57899999999999999999 674             999999999999999995  9999999999999999853

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	222
d2qamz1	77	d.325.1.1 (Z:2-78) Ribosomal protein L28 (L28p) {E	9e-20
d2jz6a1	70	d.325.1.1 (A:6-75) Ribosomal protein L28 (L28p) {T	8e-17
d2zjru1	72	d.325.1.1 (U:8-79) Ribosomal protein L28 (L28p) {D	1e-12
d2j0111	89	d.325.1.1 (1:8-96) Ribosomal protein L28 (L28p) {T	6e-11

>d2qamz1 d.325.1.1 (Z:2-78) Ribosomal protein L28 (L28p) {Escherichia coli [TaxId: 562]} Length = 77

class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L28
domain: Ribosomal protein L28 (L28p)
species: Escherichia coli [TaxId: 562]

 Score = 77.8 bits (192), Expect = 9e-20
 Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 2/65 (3%)

Query: 51  GKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDE 110
           GK    GN  S    N T+R + PN+   R +     R + ++V+   +R IDK  GID 
Sbjct: 8   GKRPVTGNNRSH-ALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDK-KGIDT 65

Query: 111 YLLKT 115
            L + 
Sbjct: 66  VLAEL 70

>d2jz6a1 d.325.1.1 (A:6-75) Ribosomal protein L28 (L28p) {Thermotoga maritima [TaxId: 2336]} Length = 70

class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L28
domain: Ribosomal protein L28 (L28p)
species: Thermotoga maritima [TaxId: 2336]

 Score = 70.0 bits (172), Expect = 8e-17
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 44  AKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCID 103
           AKR    GK  + GN VS     K+ R ++PN+Q+ R+         R++V T  L+   
Sbjct: 2   AKRCEVCGKAPRSGNTVSH-SDKKSERWFRPNLQKVRVVLPD-GTIKRMRVCTSCLK--- 56

Query: 104 KAGGIDEYLLKT 115
            +G + +Y+ + 
Sbjct: 57  -SGKVKKYVGQV 67

>d2zjru1 d.325.1.1 (U:8-79) Ribosomal protein L28 (L28p) {Deinococcus radiodurans [TaxId: 1299]} Length = 72

class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L28
domain: Ribosomal protein L28 (L28p)
species: Deinococcus radiodurans [TaxId: 1299]

 Score = 58.9 bits (143), Expect = 1e-12
 Identities = 12/56 (21%), Positives = 23/56 (41%), Gaps = 3/56 (5%)

Query: 51  GKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAG 106
           GK    G    +     T+R  + N+ +K +      +   V ++ +ALR + K  
Sbjct: 15  GKARADGGVGRK-TTGITKRVQRANLHKKAIRE--NGQVKTVWLSANALRTLSKGP 67

>d2j0111 d.325.1.1 (1:8-96) Ribosomal protein L28 (L28p) {Thermus thermophilus [TaxId: 274]} Length = 89

class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L28
domain: Ribosomal protein L28 (L28p)
species: Thermus thermophilus [TaxId: 274]

 Score = 54.8 bits (132), Expect = 6e-11
 Identities = 11/63 (17%), Positives = 25/63 (39%), Gaps = 3/63 (4%)

Query: 50  AGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGID 109
            GK  + G    +     ++R   PN+Q+ R+   +  + I  +V    +  + +     
Sbjct: 14  RGKAKREGGVGKK-TTGISKRRQYPNLQKVRV--RVAGQEITFRVAASHIPKVYELVERA 70

Query: 110 EYL 112
           + L
Sbjct: 71  KGL 73

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	222
d2qamz1	77	Ribosomal protein L28 (L28p) {Escherichia coli [Ta	99.95
d2jz6a1	70	Ribosomal protein L28 (L28p) {Thermotoga maritima	99.92
d2j0111	89	Ribosomal protein L28 (L28p) {Thermus thermophilus	99.82
d2zjru1	72	Ribosomal protein L28 (L28p) {Deinococcus radiodur	99.8

>d2qamz1 d.325.1.1 (Z:2-78) Ribosomal protein L28 (L28p) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L28
domain: Ribosomal protein L28 (L28p)
species: Escherichia coli [TaxId: 562]

Probab=99.95  E-value=4.3e-30  Score=190.45  Aligned_cols=75  Identities=28%  Similarity=0.411  Sum_probs=72.0

Q ss_pred             cccccccCceeeecccccCCCCCcccceeccceeEEEEEEccCCeEEEEEeehhHHhhHhhcCChhHHhhcCCCCCC
Q 039022           44 AKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKM  120 (222)
Q Consensus        44 Sr~Cl~~GK~~~~GN~VSh~S~~KTrR~WkPNLqkkrl~SeiLgr~irVkVTTraLRTIdK~GGlD~YLLkt~~~~L  120 (222)
                      |++|++||+++++||+||| |+++|+|+|.||||++++||+++|++++|+|||+|||||+| ||||+||+++++..+
T Consensus         1 Sr~C~itGK~~~~Gn~vSh-s~~kTkR~~~pNlq~kr~~~~~~~~~v~lkvstk~LRtI~K-~Gld~~l~k~~~~g~   75 (77)
T d2qamz1           1 SRVCQVTGKRPVTGNNRSH-ALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDK-KGIDTVLAELRARGE   75 (77)
T ss_dssp             CCCCSSSCCCCCCCBCCBG-GGBCCBCCCCCCCCCEECCCSTTCCCCEECCCTTHHHHHTT-SCHHHHHHTTTTTTC
T ss_pred             CCCcccCCCccccCceeee-cccccCceeccceEEEEEEEcCCCEEEEEEEEhhheeeehh-CCHHHHHHHHHHccC
Confidence            6799999999999999999 89999999999999999999999999999999999999999 799999999987764

>d2jz6a1 d.325.1.1 (A:6-75) Ribosomal protein L28 (L28p) {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L28
domain: Ribosomal protein L28 (L28p)
species: Thermotoga maritima [TaxId: 2336]

Probab=99.92  E-value=1.6e-26  Score=168.29  Aligned_cols=69  Identities=30%  Similarity=0.408  Sum_probs=65.7

Q ss_pred             ccccccccCceeeecccccCCCCCcccceeccceeEEEEEEccCCeEEEEEeehhHHhhHhhcCChhHHhhcCCC
Q 039022           43 RAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPY  117 (222)
Q Consensus        43 rSr~Cl~~GK~~~~GN~VSh~S~~KTrR~WkPNLqkkrl~SeiLgr~irVkVTTraLRTIdK~GGlD~YLLkt~~  117 (222)
                      ||++|++|||++++||+||| |+++|+|+|+||||++++|++. |++++|+|||+||||    ||+|.|++++++
T Consensus         1 Mar~C~itGK~~~~Gn~vSh-s~~kTkR~f~PNlq~~r~~~~~-g~~v~~kvst~~lrt----g~v~k~~~~~~~   69 (70)
T d2jz6a1           1 MAKRCEVCGKAPRSGNTVSH-SDKKSERWFRPNLQKVRVVLPD-GTIKRMRVCTSCLKS----GKVKKYVGQVSE   69 (70)
T ss_dssp             CCCCCTTTCCCCCCCCCCCC-SCCCCSSSCBTTEEEEEEEETT-TEEEEEEEEHHHHHH----CCSCCCCCCCCS
T ss_pred             CCcEeeecCCccccCCeEEe-cCcccCceecCCeEEEEEEecC-CCEEEEEEEHHHhhh----cCHHHHhHhhcc
Confidence            57899999999999999999 8999999999999999999985 999999999999999    999999998865

>d2j0111 d.325.1.1 (1:8-96) Ribosomal protein L28 (L28p) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L28
domain: Ribosomal protein L28 (L28p)
species: Thermus thermophilus [TaxId: 274]

Probab=99.82  E-value=3.1e-22  Score=151.67  Aligned_cols=82  Identities=16%  Similarity=0.099  Sum_probs=72.0

Q ss_pred             ccccccccCceeeecccccCCCCCcccceeccceeEEEEEEccCCeEEEEEeehhHHhhHhhcCChhHHhhcCCCCCCCH
Q 039022           43 RAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYLLKTPYHKMDT  122 (222)
Q Consensus        43 rSr~Cl~~GK~~~~GN~VSh~S~~KTrR~WkPNLqkkrl~SeiLgr~irVkVTTraLRTIdK~GGlD~YLLkt~~~~L~s  122 (222)
                      .++.|...|+++++||++|| ++++|+|+|+||||++++|++  |++++|+|||+|||||+|.||+|+||   +.+.|+.
T Consensus         7 ~Gn~v~~~Gk~~~~G~~vsh-s~~kTkRrf~PNLq~vr~~v~--g~~~~lrVst~alRti~k~~g~~~~l---k~~~l~~   80 (89)
T d2j0111           7 VANSIQRRGKAKREGGVGKK-TTGISKRRQYPNLQKVRVRVA--GQEITFRVAASHIPKVYELVERAKGL---KLEGLSP   80 (89)
T ss_dssp             CCCCCCCCCEECSCCSSSSC-CCEEECCCCCCCCCCCCEEET--TTTEEECCCSSSHHHHHHHHSCCCCC---CCCSCCH
T ss_pred             cCceEEecCcccccCCceee-ccccccceecCCceEEEEEEC--CEEEEEEEEHHHHHhHHhhhhHHHHH---HHcCCCH
Confidence            35678889999999999999 899999999999999999988  89999999999999999999999999   5556653


Q ss_pred             HHhHHHHHHHH
Q 039022          123 EMGLYWKTKIE  133 (222)
Q Consensus       123 elG~~lK~~I~  133 (222)
                      .   .+|++|+
T Consensus        81 ~---~~k~~~~   88 (89)
T d2j0111          81 K---EIKKELL   88 (89)
T ss_dssp             H---HHHHHCC
T ss_pred             H---HHHHHhh
Confidence            2   6677654

>d2zjru1 d.325.1.1 (U:8-79) Ribosomal protein L28 (L28p) {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a+b)
fold: L28p-like
superfamily: L28p-like
family: Ribosomal protein L28
domain: Ribosomal protein L28 (L28p)
species: Deinococcus radiodurans [TaxId: 1299]

Probab=99.80  E-value=8.5e-22  Score=144.07  Aligned_cols=64  Identities=22%  Similarity=0.218  Sum_probs=59.6

Q ss_pred             ccccccccCceeeecccccCCCCCcccceeccceeEEEEEEccCCeEEEEEeehhHHhhHhh--cCChh
Q 039022           43 RAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDK--AGGID  109 (222)
Q Consensus        43 rSr~Cl~~GK~~~~GN~VSh~S~~KTrR~WkPNLqkkrl~SeiLgr~irVkVTTraLRTIdK--~GGlD  109 (222)
                      +++.|.+.|+++++||++|| ++++|+|+|+||||++++||+  +++++|+|||+|||||+|  .+|+|
T Consensus         7 ~~~~~~~~GK~~~~Gn~vsh-~~~~TkR~f~PNLq~~ri~~~--g~~~klkVst~~lRtI~K~~~~~~~   72 (72)
T d2zjru1           7 VVNSVIRRGKARADGGVGRK-TTGITKRVQRANLHKKAIREN--GQVKTVWLSANALRTLSKGPYKGIE   72 (72)
T ss_dssp             CCCCCCCCCEESCCCTTTCS-CCEECCCCCCCCCCCCCCCCS--SSCCCCCCCHHHHHHHHSSCCSSCC
T ss_pred             ecCEEEEeccccccCCceee-cCCccCceeccccEEEEEEEC--CEeEEEEEEhHheeeecccccccCC
Confidence            56899999999999999999 899999999999999999998  889999999999999999  55554