Citrus Sinensis ID: 029878

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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------
Protein Sequence
MLSMSFHCHINAVLTPDTSSATAKWPSQNLPLKPFTKTSVMLRPQISYLKLRHGTRQVRVKHSSSSAAIDQTLDPEPPADDSDCDIILRKEKLGVVVKPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTSGGNLQQG
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccHHcccccccccccccccccHHHHHHHHcccEEccccccEEEEEEEEEcccEEEEEEEEEccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccEEEEcccccccEEEEEEEEcccEEEEEEEEccccccccccccEEccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
mlsmsfhchinavltpdtssatakwpsqnlplkpftktsvmlrpqisylklrhgtrqvrvkhssssaaidqtldpeppaddsdcdiilrkeklgvvvkpnekRRLVLKFIWMQNDigialdqvipghgtiplspyyfwprkDAWEELKVLLdskpwisqteRIHLLNQATDVINFWqtsggnlqqg
Flexible Loop (DISEMBL)
MLSMSFHCHINAVLTPDTSSATAKWPSqnlplkpftktsvmLRPQISYLklrhgtrqvrvkhssssaaidqtldpeppadDSDCDIILRkeklgvvvkpnekRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTSGGNLQQG
Low Complexity Region (SEG)
MLSMSFHCHINAVLTPDTSSATAKWPSQNLPLKPFTKTSVMLRPQISYLKLRHGTRQVRVKHSSSSAAIDQTLDPEPPADDSDCDIILRKEKLGVVVKPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTSGGNLQQG
Disordered region (IsUnstruct)
*****FHCHINAVLT******************PFTKTSVMLRPQISYLKLRH******************************CDIILRKEKLGVVVKPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQT********
Disordered Region (DISOPRED)
*********IN**LTPDT********************************************************************************PNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFW**********
Disordered Region (DISEMBL)
MLSMSFHCHINAVLTPDTSSATAKWPSQNLPLKPFTKTSVMLRPQISYLKLRH*************AAIDQTLDPEPPADDSDCDIILRKEKLGVVVKPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTSGGNLQQG
Disordered Region (DISPRO)
*LSMSFHCHINAVLTPDTSSATAKWPSQNLPLKPFTKTSVMLRP*********************************************KEKLGVVVKPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTSG******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLSMSFHCHINAVLTPDTSSATAKWPSQNLPLKPFTKTSVMLRPQISYLKLRHGTRQVRVKHSSSSAAIDQTLDPEPPADDSDCDIILRKEKLGVVVKPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTSGGNLQQG
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	186	2.2.26 [Sep-21-2011]
P82412	179	30S ribosomal protein 3,	N/A	no	0.913	0.949	0.526	2e-44
Q9LFV0	183	30S ribosomal protein 3-2	yes	no	0.822	0.836	0.529	1e-39
Q9SX22	166	30S ribosomal protein 3-1	no	no	0.473	0.530	0.738	5e-36
O48609	181	30S ribosomal protein 3,	N/A	no	0.591	0.607	0.581	6e-33
P51351	99	Probable 30S ribosomal pr	N/A	no	0.408	0.767	0.571	4e-23
Q1XDD6	102	Probable 30S ribosomal pr	N/A	no	0.408	0.745	0.571	6e-23
P59327	108	Probable 30S ribosomal pr	yes	no	0.435	0.75	0.524	5e-22
Q5N172	112	Probable 30S ribosomal pr	yes	no	0.408	0.678	0.558	7e-22
O05161	112	Probable 30S ribosomal pr	yes	no	0.408	0.678	0.558	7e-22
B8HTT7	109	Probable 30S ribosomal pr	yes	no	0.419	0.715	0.531	2e-21

>sp|P82412|RRP3_SPIOL 30S ribosomal protein 3, chloroplastic OS=Spinacia oleracea GN=PSRP3 PE=1 SV=1

 Score =  178 bits (451), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 100/190 (52%), Positives = 121/190 (63%), Gaps = 20/190 (10%)

Query: 1   MLSMSFHCHINAVLTPDTSSATAKWPSQNLPLKPFTKTSVMLRPQ-------ISYLKLRH 53
           MLSM+   +INA+  P        + S  L LKPF KT     P+        S LK ++
Sbjct: 1   MLSMAVQPNINAIAKPSI------YQSPKLSLKPF-KTPAFANPKPFFSSPSFSQLKKKN 53

Query: 54  GTRQVRVKHSSSSAAIDQTLDPEPPADDSDCDIILRKEKLGVVVKPNEKRRLVLKFIWMQ 113
                    + S  AI           D D D+++ KEKL V+VKP +K RLVLKFIWM+
Sbjct: 54  NWSLFVAPETISDVAIMGN------EVDIDDDLLVNKEKLKVLVKPMDKPRLVLKFIWME 107

Query: 114 NDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVI 173
            +IG+ALDQ IPGHGT+PLSPYYFWPRKDAWEELKVLL++KPWISQ + I LLNQATD+I
Sbjct: 108 KNIGLALDQTIPGHGTVPLSPYYFWPRKDAWEELKVLLENKPWISQKQMIILLNQATDII 167

Query: 174 NFWQTSGGNL 183
           N WQ SGGNL
Sbjct: 168 NLWQQSGGNL 177

One of the plastid-specific ribosomal proteins.
Spinacia oleracea (taxid: 3562)

>sp|Q9LFV0|RRP32_ARATH 30S ribosomal protein 3-2, chloroplastic OS=Arabidopsis thaliana GN=At5g15760 PE=2 SV=1

 Score =  162 bits (409), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 90/170 (52%), Positives = 110/170 (64%), Gaps = 17/170 (10%)

Query: 26  PSQNLPLKPF------TKTSVMLRPQISYLKLRHGTRQVRVKHSSSSAAI------DQTL 73
           PSQ L  KP       TK     RP +S      G  Q+  +HS  +  I      + T 
Sbjct: 18  PSQKLSSKPIAHISLSTKLKPSSRPSLSCSTWNQG--QIPARHSCINPGIFAYPPSNLTF 75

Query: 74  DPEPPADDSDCDIILRKEKLGVVVKPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLS 133
             E P  +S     L K+K+ V+VKP EK ++VLKF+WMQ DIG+ALD +IPG GTIPLS
Sbjct: 76  SHELPESESPP---LGKKKMRVLVKPLEKPKVVLKFVWMQKDIGVALDHMIPGFGTIPLS 132

Query: 134 PYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTSGGNL 183
           PYYFWPRKDAWEELK LL+SKPWIS+  R+ LLNQATD+IN WQ+SGG+L
Sbjct: 133 PYYFWPRKDAWEELKTLLESKPWISELHRVFLLNQATDIINLWQSSGGDL 182

Probably a ribosomal protein or a ribosome-associated protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SX22|RRP31_ARATH 30S ribosomal protein 3-1, chloroplastic OS=Arabidopsis thaliana GN=At1g68590 PE=1 SV=1

 Score =  150 bits (378), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 65/88 (73%), Positives = 77/88 (87%)

Query: 96  VVKPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKP 155
           VVKP+EK R+VLKF+WM+ +IG+ LDQ +PGHGTIPLSPY+FWPRKDAWEELK  L++KP
Sbjct: 76  VVKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTIPLSPYFFWPRKDAWEELKSTLEAKP 135

Query: 156 WISQTERIHLLNQATDVINFWQTSGGNL 183
           WISQ + I LLNQATD+IN WQ SGGNL
Sbjct: 136 WISQKKMIILLNQATDIINLWQQSGGNL 163

Probably a ribosomal protein or a ribosome-associated protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O48609|RRP3_HORVU 30S ribosomal protein 3, chloroplastic OS=Hordeum vulgare GN=PSRP3 PE=2 SV=1

 Score =  140 bits (352), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 64/110 (58%), Positives = 80/110 (72%)

Query: 74  DPEPPADDSDCDIILRKEKLGVVVKPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLS 133
           D EP   + D + ++  E+  V V   +   LVLKFIWM+ +IGIALDQ++PG G+IPLS
Sbjct: 70  DDEPLGGEGDAEAVVESEEYKVEVPEKQDPMLVLKFIWMEKNIGIALDQMVPGVGSIPLS 129

Query: 134 PYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTSGGNL 183
           PYYFWPRKDAWEEL+  L+ K WISQ + I LLNQATD+IN WQ  GG+L
Sbjct: 130 PYYFWPRKDAWEELRAKLEEKEWISQKQMIILLNQATDIINLWQQGGGSL 179

Probably a ribosomal protein or a ribosome-associated protein.

Hordeum vulgare (taxid: 4513)

>sp|P51351|RRP3_PORPU Probable 30S ribosomal protein 3, chloroplastic OS=Porphyra purpurea GN=ycf65 PE=3 SV=1

 Score =  107 bits (267), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 44/77 (57%), Positives = 62/77 (80%), Gaps = 1/77 (1%)

Query: 104 RLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERI 163
           +  LK +W++N+I IA+DQ++ G+GT PL+ Y+FWPR DAWEELK  L+SKPWI++ +RI
Sbjct: 3   KFTLKVLWLENNIAIAIDQIV-GNGTSPLTSYFFWPRNDAWEELKAELESKPWIAERDRI 61

Query: 164 HLLNQATDVINFWQTSG 180
            LLN+ T+VIN+WQ  G
Sbjct: 62  ELLNKTTEVINYWQEEG 78

Probably a ribosomal protein or a ribosome-associated protein.

Porphyra purpurea (taxid: 2787)

>sp|Q1XDD6|RRP3_PORYE Probable 30S ribosomal protein 3, chloroplastic OS=Porphyra yezoensis GN=ycf65 PE=3 SV=1

 Score =  107 bits (266), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 44/77 (57%), Positives = 62/77 (80%), Gaps = 1/77 (1%)

Query: 104 RLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERI 163
           +  LK +W++N+I IA+DQ++ G+GT PL+ Y+FWPR DAWEELK  L+SKPWI++ +RI
Sbjct: 8   KFTLKVLWLENNIAIAIDQIV-GNGTSPLTSYFFWPRNDAWEELKAELESKPWIAERDRI 66

Query: 164 HLLNQATDVINFWQTSG 180
            LLN+ T+VIN+WQ  G
Sbjct: 67  ELLNKTTEVINYWQEEG 83

Probably a ribosomal protein or a ribosome-associated protein.

Porphyra yezoensis (taxid: 2788)

>sp|P59327|RRP3_THEEB Probable 30S ribosomal protein PSRP-3 OS=Thermosynechococcus elongatus (strain BP-1) GN=tlr0301 PE=3 SV=1

 Score =  103 bits (258), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 43/82 (52%), Positives = 60/82 (73%), Gaps = 1/82 (1%)

Query: 101 EKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQT 160
           E  R  L+ +W++ D+ IA+DQ++ G GT PL+ Y+FWPR DAWE LK  L+ K WI++ 
Sbjct: 9   ELSRFTLRVLWLEKDVAIAVDQIV-GKGTSPLTSYFFWPRTDAWELLKAELEKKSWITEA 67

Query: 161 ERIHLLNQATDVINFWQTSGGN 182
           ERI LLN+AT++IN+WQ  G N
Sbjct: 68  ERIELLNRATEIINYWQEEGKN 89

Probably a ribosomal protein or a ribosome-associated protein.

Thermosynechococcus elongatus (strain BP-1) (taxid: 197221)

>sp|Q5N172|RRP3_SYNP6 Probable 30S ribosomal protein PSRP-3 OS=Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) GN=syc1758_d PE=3 SV=1

 Score =  103 bits (257), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 43/77 (55%), Positives = 58/77 (75%), Gaps = 1/77 (1%)

Query: 104 RLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERI 163
           R  +K +W+  ++ IA+DQV+ G  T PL+ YYFWPR DAWE+LK  L+SK WI++ ER+
Sbjct: 16  RFTIKILWLNENVAIAVDQVV-GKATSPLTAYYFWPRHDAWEQLKTELESKSWITEAERV 74

Query: 164 HLLNQATDVINFWQTSG 180
            LLNQAT+VIN+WQ  G
Sbjct: 75  ELLNQATEVINYWQEEG 91

Probably a ribosomal protein or a ribosome-associated protein.

Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (taxid: 269084)

>sp|O05161|RRP3_SYNE7 Probable 30S ribosomal protein PSRP-3 OS=Synechococcus elongatus (strain PCC 7942) GN=mut3G PE=3 SV=1

 Score =  103 bits (257), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 43/77 (55%), Positives = 58/77 (75%), Gaps = 1/77 (1%)

Query: 104 RLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERI 163
           R  +K +W+  ++ IA+DQV+ G  T PL+ YYFWPR DAWE+LK  L+SK WI++ ER+
Sbjct: 16  RFTIKILWLNENVAIAVDQVV-GKATSPLTAYYFWPRHDAWEQLKTELESKSWITEAERV 74

Query: 164 HLLNQATDVINFWQTSG 180
            LLNQAT+VIN+WQ  G
Sbjct: 75  ELLNQATEVINYWQEEG 91

Probably a ribosomal protein or a ribosome-associated protein.

Synechococcus elongatus (strain PCC 7942) (taxid: 1140)

>sp|B8HTT7|RRP3_CYAP4 Probable 30S ribosomal protein PSRP-3 OS=Cyanothece sp. (strain PCC 7425 / ATCC 29141) GN=Cyan7425_0465 PE=3 SV=1

 Score =  101 bits (252), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 42/79 (53%), Positives = 61/79 (77%), Gaps = 1/79 (1%)

Query: 104 RLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERI 163
           + +LK +W+ +++ +A+DQV+ G GT PL+ Y+FWPR DAWE+LK  L+ K WIS+ +RI
Sbjct: 13  QFILKVLWLDSNVALAVDQVV-GKGTSPLTSYFFWPRADAWEQLKTELEKKTWISEADRI 71

Query: 164 HLLNQATDVINFWQTSGGN 182
            LLN+ATD+IN+WQ  G N
Sbjct: 72  ALLNRATDIINYWQEEGRN 90

Probably a ribosomal protein or a ribosome-associated protein.

Cyanothece sp. (strain PCC 7425 / ATCC 29141) (taxid: 395961)

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	186
449455804	192	PREDICTED: 30S ribosomal protein 3, chlo	0.978	0.947	0.549	2e-44
28380123	179	RecName: Full=30S ribosomal protein 3, c	0.913	0.949	0.526	1e-42
296087288	175	unnamed protein product [Vitis vinifera]	0.903	0.96	0.507	5e-42
225452011	176	PREDICTED: 30S ribosomal protein 3, chlo	0.903	0.954	0.507	6e-42
351723097	158	uncharacterized protein LOC100306266 [Gl	0.731	0.860	0.597	1e-40
255576477	180	Plastid-specific 30S ribosomal protein 3	0.758	0.783	0.588	5e-40
388517745	175	unknown [Lotus japonicus]	0.564	0.6	0.733	3e-39
388507154	175	unknown [Lotus japonicus]	0.564	0.6	0.733	3e-39
224099355	189	predicted protein [Populus trichocarpa]	0.946	0.931	0.476	5e-39
224111708	189	predicted protein [Populus trichocarpa]	0.951	0.936	0.484	2e-38

>gi|449455804|ref|XP_004145640.1| PREDICTED: 30S ribosomal protein 3, chloroplastic-like [Cucumis sativus] gi|449484535|ref|XP_004156909.1| PREDICTED: 30S ribosomal protein 3, chloroplastic-like [Cucumis sativus]

 Score =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 105/191 (54%), Positives = 125/191 (65%), Gaps = 9/191 (4%)

Query: 1   MLSMSFHCHINAVLTPDTSSATAKWPSQNLPLKPF-----TKTSVMLRPQISYLKLRHGT 55
           MLSM+     N     +TS+ TA+  S+   L PF     T  S  +    +   L+   
Sbjct: 2   MLSMAVQLQPNVNFCFNTSNFTAQTASKPFKL-PFAVRQRTTASSCIPNFHTVFGLQLRR 60

Query: 56  RQVRVKHSSSSAAIDQTLDPEPP---ADDSDCDIILRKEKLGVVVKPNEKRRLVLKFIWM 112
           +  R +  S+SAA  + ++       ADDSD      KEKLGVVVKP EK RLVLKFIWM
Sbjct: 61  QNFRTQEISASAAPIEAVEAASELLVADDSDSVSSPVKEKLGVVVKPMEKPRLVLKFIWM 120

Query: 113 QNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDV 172
           + +IGIALDQ+IPGHGTIPLSPYYFWPRKDAWEELKVLL+SKPWISQ + I LLNQATD+
Sbjct: 121 EKNIGIALDQMIPGHGTIPLSPYYFWPRKDAWEELKVLLESKPWISQKQMIILLNQATDI 180

Query: 173 INFWQTSGGNL 183
           IN WQ  GGNL
Sbjct: 181 INLWQQGGGNL 191

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|28380123|sp|P82412.1|RRP3_SPIOL RecName: Full=30S ribosomal protein 3, chloroplastic; AltName: Full=Plastid-specific 30S ribosomal protein 3; Short=PSRP-3; Flags: Precursor gi|7578871|gb|AAF64163.1|AF239218_1 plastid-specific ribosomal protein 3 precursor [Spinacia oleracea]

 Score =  178 bits (451), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 100/190 (52%), Positives = 121/190 (63%), Gaps = 20/190 (10%)

Query: 1   MLSMSFHCHINAVLTPDTSSATAKWPSQNLPLKPFTKTSVMLRPQ-------ISYLKLRH 53
           MLSM+   +INA+  P        + S  L LKPF KT     P+        S LK ++
Sbjct: 1   MLSMAVQPNINAIAKPSI------YQSPKLSLKPF-KTPAFANPKPFFSSPSFSQLKKKN 53

Query: 54  GTRQVRVKHSSSSAAIDQTLDPEPPADDSDCDIILRKEKLGVVVKPNEKRRLVLKFIWMQ 113
                    + S  AI           D D D+++ KEKL V+VKP +K RLVLKFIWM+
Sbjct: 54  NWSLFVAPETISDVAIMGN------EVDIDDDLLVNKEKLKVLVKPMDKPRLVLKFIWME 107

Query: 114 NDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVI 173
            +IG+ALDQ IPGHGT+PLSPYYFWPRKDAWEELKVLL++KPWISQ + I LLNQATD+I
Sbjct: 108 KNIGLALDQTIPGHGTVPLSPYYFWPRKDAWEELKVLLENKPWISQKQMIILLNQATDII 167

Query: 174 NFWQTSGGNL 183
           N WQ SGGNL
Sbjct: 168 NLWQQSGGNL 177

Source: Spinacia oleracea

Species: Spinacia oleracea

Genus: Spinacia

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296087288|emb|CBI33662.3| unnamed protein product [Vitis vinifera]

 Score =  176 bits (445), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 96/189 (50%), Positives = 118/189 (62%), Gaps = 21/189 (11%)

Query: 1   MLSMSFHCHINAVLTPDTSSATAKWPSQNLPLKPFTKTSVMLRPQ--ISYLKLRHGTRQV 58
           MLSM+   + NA L            S   P+       +M +    +S    R  +  +
Sbjct: 1   MLSMAVQPNPNAALK-----------SYTFPMSSNRNHRLMFKSSNALSLYSTRSASTNL 49

Query: 59  RVKHSSSS----AAIDQTLDPEPPADDSDCDIILRKEKLGVVVKPNEKRRLVLKFIWMQN 114
           R++ S +     A  +Q+  P+     S  D+    EKLGVVVKP EK RLVLKFIWM+ 
Sbjct: 50  RLRASPAPVVAVAVSEQSSAPQESLSASPLDV----EKLGVVVKPMEKPRLVLKFIWMEK 105

Query: 115 DIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVIN 174
           +IG+ALDQ IPGHGTIPLSPYYFWPRKDAWEE+KVLL+SKPWISQ + I LLNQATD+IN
Sbjct: 106 NIGVALDQAIPGHGTIPLSPYYFWPRKDAWEEIKVLLESKPWISQKQMIILLNQATDIIN 165

Query: 175 FWQTSGGNL 183
            WQ SGGNL
Sbjct: 166 LWQQSGGNL 174

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225452011|ref|XP_002283616.1| PREDICTED: 30S ribosomal protein 3, chloroplastic-like isoform 1 [Vitis vinifera] gi|359488272|ref|XP_003633730.1| PREDICTED: 30S ribosomal protein 3, chloroplastic-like isoform 2 [Vitis vinifera]

 Score =  175 bits (444), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 96/189 (50%), Positives = 118/189 (62%), Gaps = 21/189 (11%)

Query: 1   MLSMSFHCHINAVLTPDTSSATAKWPSQNLPLKPFTKTSVMLRPQ--ISYLKLRHGTRQV 58
           MLSM+   + NA L            S   P+       +M +    +S    R  +  +
Sbjct: 2   MLSMAVQPNPNAALK-----------SYTFPMSSNRNHRLMFKSSNALSLYSTRSASTNL 50

Query: 59  RVKHSSSS----AAIDQTLDPEPPADDSDCDIILRKEKLGVVVKPNEKRRLVLKFIWMQN 114
           R++ S +     A  +Q+  P+     S  D+    EKLGVVVKP EK RLVLKFIWM+ 
Sbjct: 51  RLRASPAPVVAVAVSEQSSAPQESLSASPLDV----EKLGVVVKPMEKPRLVLKFIWMEK 106

Query: 115 DIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVIN 174
           +IG+ALDQ IPGHGTIPLSPYYFWPRKDAWEE+KVLL+SKPWISQ + I LLNQATD+IN
Sbjct: 107 NIGVALDQAIPGHGTIPLSPYYFWPRKDAWEEIKVLLESKPWISQKQMIILLNQATDIIN 166

Query: 175 FWQTSGGNL 183
            WQ SGGNL
Sbjct: 167 LWQQSGGNL 175

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351723097|ref|NP_001236243.1| uncharacterized protein LOC100306266 [Glycine max] gi|255628049|gb|ACU14369.1| unknown [Glycine max]

 Score =  171 bits (433), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 89/149 (59%), Positives = 105/149 (70%), Gaps = 13/149 (8%)

Query: 35  FTKTSVMLRPQISYLKLRHGTRQVRVKHSSSSAAIDQTLDPEPPADDSDCDIILRKEKLG 94
            T  S+ L+P +S++     TR      S S +A + T    PP          + EKLG
Sbjct: 22  LTFPSIKLKPSLSHVPSPTPTR-----FSLSVSAAETTAFAAPPTP--------QPEKLG 68

Query: 95  VVVKPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSK 154
           VVVKP EK RLVLKFIWM+ +IGIALDQ++PGHGTIPLSPYYFWPRKDAWEELK LL++K
Sbjct: 69  VVVKPTEKPRLVLKFIWMEKNIGIALDQMVPGHGTIPLSPYYFWPRKDAWEELKELLENK 128

Query: 155 PWISQTERIHLLNQATDVINFWQTSGGNL 183
           PWISQ + I LLNQATD+IN WQ SGGNL
Sbjct: 129 PWISQKQMIILLNQATDIINLWQQSGGNL 157

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255576477|ref|XP_002529130.1| Plastid-specific 30S ribosomal protein 3, chloroplast precursor, putative [Ricinus communis] gi|223531409|gb|EEF33243.1| Plastid-specific 30S ribosomal protein 3, chloroplast precursor, putative [Ricinus communis]

 Score =  169 bits (428), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 93/158 (58%), Positives = 110/158 (69%), Gaps = 17/158 (10%)

Query: 37  KTSVMLRPQISYL--------KLRHGTRQVRVKHSSSSAAI---DQTLDPEPPADDSDCD 85
           KTS+   P+IS L        K+R  +R  R+   +S  A+   D+T + E P  D   D
Sbjct: 27  KTSIFANPKISLLYSSTILDPKMRPISRNERLTTFASPEALTVEDKTSETEEPISD---D 83

Query: 86  IILRKEKLGVVVKPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWE 145
           II   EK+ V VK  EK RLVLKFIWM+ +IG+ALDQVIPGHGTIPLSPY+FWPRKDAWE
Sbjct: 84  II---EKVEVAVKQVEKPRLVLKFIWMEKNIGLALDQVIPGHGTIPLSPYFFWPRKDAWE 140

Query: 146 ELKVLLDSKPWISQTERIHLLNQATDVINFWQTSGGNL 183
           ELK  L+SKPWISQ + I LLNQATD+IN WQ SGGNL
Sbjct: 141 ELKTTLESKPWISQKKMIILLNQATDIINLWQQSGGNL 178

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388517745|gb|AFK46934.1| unknown [Lotus japonicus]

 Score =  167 bits (422), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 77/105 (73%), Positives = 87/105 (82%)

Query: 79  ADDSDCDIILRKEKLGVVVKPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFW 138
           A+  D  +    +KLGVVVKP +K RLVLKFIWM+ +IGIALDQ +PGHGTIPLSPYYFW
Sbjct: 70  AEQDDTSLSPPPQKLGVVVKPTDKPRLVLKFIWMEKNIGIALDQAVPGHGTIPLSPYYFW 129

Query: 139 PRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTSGGNL 183
           PRKDAWEELK LL+SKPWISQ + I LLNQATD+IN WQ SGGNL
Sbjct: 130 PRKDAWEELKELLESKPWISQKQMIILLNQATDIINLWQQSGGNL 174

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388507154|gb|AFK41643.1| unknown [Lotus japonicus]

 Score =  166 bits (421), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 77/105 (73%), Positives = 87/105 (82%)

Query: 79  ADDSDCDIILRKEKLGVVVKPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFW 138
           A+  D  +    +KLGVVVKP +K RLVLKFIWM+ +IGIALDQ +PGHGTIPLSPYYFW
Sbjct: 70  AEQDDTSLSPPPQKLGVVVKPTDKPRLVLKFIWMEKNIGIALDQAVPGHGTIPLSPYYFW 129

Query: 139 PRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTSGGNL 183
           PRKDAWEELK LL+SKPWISQ + I LLNQATD+IN WQ SGGNL
Sbjct: 130 PRKDAWEELKELLESKPWISQKQMIILLNQATDIINLWQQSGGNL 174

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224099355|ref|XP_002311451.1| predicted protein [Populus trichocarpa] gi|222851271|gb|EEE88818.1| predicted protein [Populus trichocarpa]

 Score =  166 bits (419), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 92/193 (47%), Positives = 117/193 (60%), Gaps = 17/193 (8%)

Query: 1   MLSMSFHCHINAVLTPDTSSATAKWPSQNLPLKPFTKTSVMLRPQISYLK----LRHGTR 56
           MLSM+F   +N V T          P +    K F K ++ + P+ + ++         R
Sbjct: 1   MLSMAFQSGVNNVFT------YYSLPCRTPSCKTF-KATISVNPKPNPIRSSTFFDRERR 53

Query: 57  QVRVKHSSSSAAIDQTLDPEPPADDSDCDI------ILRKEKLGVVVKPNEKRRLVLKFI 110
            V      ++ A+ + L  E PAD    +       I   EK  +VVK  EK RLVLKF+
Sbjct: 54  HVSRNQRYTTFAVPEALAAETPADAPPSNAAGESIPIQETEKAELVVKQVEKPRLVLKFV 113

Query: 111 WMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQAT 170
           WM+ +IG+ALDQVIPGHGT+PLSPY+FWPRKDAWEELK  L+SKPWISQ + I LLNQAT
Sbjct: 114 WMEKNIGLALDQVIPGHGTVPLSPYFFWPRKDAWEELKATLESKPWISQKKMIILLNQAT 173

Query: 171 DVINFWQTSGGNL 183
           D+IN WQ SGGNL
Sbjct: 174 DIINLWQQSGGNL 186

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224111708|ref|XP_002315948.1| predicted protein [Populus trichocarpa] gi|222864988|gb|EEF02119.1| predicted protein [Populus trichocarpa]

 Score =  164 bits (415), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 93/192 (48%), Positives = 116/192 (60%), Gaps = 15/192 (7%)

Query: 1   MLSMSFHCHINAVLTPDTSSATAKWPSQNLPLKPFTKT-SVMLRPQI---SYLKLRHGTR 56
           MLS++F C  + V T       +  P Q    K F  T S   +P +   S    R   R
Sbjct: 1   MLSVAFQCGFSNVFT------NSSLPCQTPSCKTFKATFSTNPKPNLIHSSTFLDRKRKR 54

Query: 57  QVRVKHSSSSAA-----IDQTLDPEPPADDSDCDIILRKEKLGVVVKPNEKRRLVLKFIW 111
             R +  ++ AA     ++  +D  P  +  +       EK  V+VK  EK RLVLKFIW
Sbjct: 55  VSRNQRYTTFAAPEALTVETPIDTPPSTETEESIPAQGTEKAEVLVKQVEKPRLVLKFIW 114

Query: 112 MQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATD 171
           M+ +IG+ALDQVIPGHGT+PLSPY+FWPRKDAWEELK  L+SKPWISQ + I LLNQATD
Sbjct: 115 MEKNIGLALDQVIPGHGTVPLSPYFFWPRKDAWEELKATLESKPWISQKKMIILLNQATD 174

Query: 172 VINFWQTSGGNL 183
           +IN WQ SGGNL
Sbjct: 175 IINLWQQSGGNL 186

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	186
TAIR|locus:2143211	183	PSRP3/2 "plastid-specifi	0.822	0.836	0.529	2.9e-39
TAIR|locus:2026940	166	PSRP3/1 "plastid-specifi	0.763	0.855	0.517	2.4e-35

TAIR|locus:2143211 PSRP3/2 "plastid-specific ribosomal protein 3/2" [Arabidopsis thaliana (taxid:3702)]

 Score = 419 (152.6 bits), Expect = 2.9e-39, P = 2.9e-39
 Identities = 90/170 (52%), Positives = 110/170 (64%)

Query:    26 PSQNLPLKPF------TKTSVMLRPQISYLKLRHGTRQVRVKHSSSSAAI------DQTL 73
             PSQ L  KP       TK     RP +S      G  Q+  +HS  +  I      + T 
Sbjct:    18 PSQKLSSKPIAHISLSTKLKPSSRPSLSCSTWNQG--QIPARHSCINPGIFAYPPSNLTF 75

Query:    74 DPEPPADDSDCDIILRKEKLGVVVKPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLS 133
               E P  +S     L K+K+ V+VKP EK ++VLKF+WMQ DIG+ALD +IPG GTIPLS
Sbjct:    76 SHELPESESPP---LGKKKMRVLVKPLEKPKVVLKFVWMQKDIGVALDHMIPGFGTIPLS 132

Query:   134 PYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTSGGNL 183
             PYYFWPRKDAWEELK LL+SKPWIS+  R+ LLNQATD+IN WQ+SGG+L
Sbjct:   133 PYYFWPRKDAWEELKTLLESKPWISELHRVFLLNQATDIINLWQSSGGDL 182

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

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0009536 "plastid" evidence=IEA

TAIR|locus:2026940 PSRP3/1 "plastid-specific ribosomal protein 3/1" [Arabidopsis thaliana (taxid:3702)]

 Score = 382 (139.5 bits), Expect = 2.4e-35, P = 2.4e-35
 Identities = 76/147 (51%), Positives = 98/147 (66%)

Query:    37 KTSVMLRPQISYLKLRHGTRQVRVKHSSSSAAIDQTLDPEPPADDSDCDIILRKEKLGVV 96
             K S+   P + + +    T+ + VK    + A  +TL  E        D     ++   V
Sbjct:    22 KLSITASPPLFHTQT---TKPISVKRKIITLAAPETLTAETVTGIDTSDNT--PQQTIKV 76

Query:    97 VKPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPW 156
             VKP+EK R+VLKF+WM+ +IG+ LDQ +PGHGTIPLSPY+FWPRKDAWEELK  L++KPW
Sbjct:    77 VKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTIPLSPYFFWPRKDAWEELKSTLEAKPW 136

Query:   157 ISQTERIHLLNQATDVINFWQTSGGNL 183
             ISQ + I LLNQATD+IN WQ SGGNL
Sbjct:   137 ISQKKMIILLNQATDIINLWQQSGGNL 163


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.319   0.134   0.418    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      186       186   0.00083  110 3  11 22  0.45    32
                                                     31  0.41    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  2
  No. of states in DFA:  617 (66 KB)
  Total size of DFA:  181 KB (2103 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  18.68u 0.14s 18.82t   Elapsed:  00:00:01
  Total cpu time:  18.68u 0.14s 18.82t   Elapsed:  00:00:01
  Start:  Tue May 21 01:17:52 2013   End:  Tue May 21 01:17:53 2013

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

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0032544 "plastid translation" evidence=IMP

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9LFV0	RRP32_ARATH	No assigned EC number	0.5294	0.8225	0.8360	yes	no
P82412	RRP3_SPIOL	No assigned EC number	0.5263	0.9139	0.9497	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	186
CHL00163	99	CHL00163, ycf65, putative ribosomal protein 3; Val	1e-34
PRK02724	104	PRK02724, PRK02724, hypothetical protein; Provisio	2e-33
pfam04839	47	pfam04839, PSRP-3_Ycf65, Plastid and cyanobacteria	8e-26

>gnl|CDD|214381 CHL00163, ycf65, putative ribosomal protein 3; Validated

 Score =  117 bits (295), Expect = 1e-34
 Identities = 43/74 (58%), Positives = 62/74 (83%), Gaps = 1/74 (1%)

Query: 104 RLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERI 163
           +  LK +W++N+IGIA+DQ++ G+GT PL+ Y+FWPR DAWE LK+ L+SKPWIS+ ERI
Sbjct: 3   KFTLKVLWLENNIGIAVDQIV-GNGTSPLTSYFFWPRTDAWELLKLELESKPWISEDERI 61

Query: 164 HLLNQATDVINFWQ 177
            +LN+ T++IN+WQ
Sbjct: 62  EILNKTTEIINYWQ 75

Length = 99

>gnl|CDD|235062 PRK02724, PRK02724, hypothetical protein; Provisional

 Score =  114 bits (287), Expect = 2e-33
 Identities = 40/79 (50%), Positives = 61/79 (77%), Gaps = 1/79 (1%)

Query: 104 RLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERI 163
           R +LK +W+ +++ +A+DQ++ G GT PL+ Y+FWPR DAWE+LK  L+SK WI++ ER+
Sbjct: 8   RFILKVLWLDDNVALAVDQIV-GKGTSPLTAYFFWPRNDAWEQLKTELESKHWITENERV 66

Query: 164 HLLNQATDVINFWQTSGGN 182
            +LN+AT+VIN+WQ  G  
Sbjct: 67  EVLNKATEVINYWQEEGKG 85

Length = 104

>gnl|CDD|203104 pfam04839, PSRP-3_Ycf65, Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65)

 Score = 93.2 bits (232), Expect = 8e-26
 Identities = 31/46 (67%), Positives = 41/46 (89%)

Query: 132 LSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQ 177
           L+ Y+FWPR DAWE+LK  L+SKPWIS+ ER++LLNQAT++IN+WQ
Sbjct: 1   LTEYFFWPRTDAWEQLKAELESKPWISEAERVNLLNQATEIINYWQ 46

This small acidic protein is found in 30S ribosomal subunit of cyanobacteria and plant plastids. In plants it has been named plastid-specific ribosomal protein 3 (PSRP-3), and in cyanobacteria it is named Ycf65. Plastid-specific ribosomal proteins may mediate the effects of nuclear factors on plastid translation. The acidic PSRPs are thought to contribute to protein-protein interactions in the 30S subunit, and are not thought to bind RNA. Length = 47

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	186
PRK02724	104	hypothetical protein; Provisional	100.0
CHL00163	99	ycf65 putative ribosomal protein 3; Validated	100.0
PF04839	49	PSRP-3_Ycf65: Plastid and cyanobacterial ribosomal	99.98

>PRK02724 hypothetical protein; Provisional

Probab=100.00  E-value=1.1e-49  Score=307.20  Aligned_cols=83  Identities=48%  Similarity=1.106  Sum_probs=79.6

Q ss_pred             CCCceEEEEEEeecCcEEEEeeeeecCCCcccCcccccccCCchHHHHHhhhcCCCCCChhhHHHHhhhhHHHHHHHHhc
Q 029878          100 NEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTS  179 (186)
Q Consensus       100 ~~~~rfvLK~LWlek~IgiAvDQ~v~g~~t~PLT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIINyWQe~  179 (186)
                      .+++||+||||||+|||||||||+| |+|++|||+||||||+||||+||.+||+|+||+++|||+|||++||||||||++
T Consensus         4 ~~~~rfvlKvlWle~~iaiAvDQ~v-g~~t~PLT~yfFWPr~DAWe~LK~~LesK~WIs~~~~i~lLN~~TeiIN~WQe~   82 (104)
T PRK02724          4 ADEGRFILKVLWLDDNVALAVDQIV-GKGTSPLTAYFFWPRNDAWEQLKTELESKHWITENERVEVLNKATEVINYWQEE   82 (104)
T ss_pred             cccceEEEEEEEeccceeEEeeeec-CCCCCcCcceeecCCccHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHc
Confidence            4678999999999999999999999 999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 029878          180 GGNL  183 (186)
Q Consensus       180 ~~~l  183 (186)
                      |++-
T Consensus        83 ~~~~   86 (104)
T PRK02724         83 GKGK   86 (104)
T ss_pred             cCCC
Confidence            7653

>CHL00163 ycf65 putative ribosomal protein 3; Validated

Probab=100.00  E-value=1.4e-49  Score=304.52  Aligned_cols=80  Identities=54%  Similarity=1.166  Sum_probs=77.6

Q ss_pred             CceEEEEEEeecCcEEEEeeeeecCCCcccCcccccccCCchHHHHHhhhcCCCCCChhhHHHHhhhhHHHHHHHHhcCC
Q 029878          102 KRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTSGG  181 (186)
Q Consensus       102 ~~rfvLK~LWlek~IgiAvDQ~v~g~~t~PLT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIINyWQe~~~  181 (186)
                      ++||+|||||||++|||||||+| |+|++|||+||||||+||||+||.+||+|+||+++|||+||||+||||||||++++
T Consensus         1 m~kf~lKvlWl~~~iaiAvDq~v-~~~t~PlT~yfFWPr~DAWe~LK~~LesK~WIs~~~~i~lLN~~TeiIN~Wqe~~~   79 (99)
T CHL00163          1 MQKFTLKVLWLENNIGIAVDQIV-GNGTSPLTSYFFWPRTDAWELLKLELESKPWISEDERIEILNKTTEIINYWQENKK   79 (99)
T ss_pred             CCeEEEEEEEecCceEEEEeeee-CCCCccCcceeecCCccHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHccC
Confidence            57999999999999999999999 88999999999999999999999999999999999999999999999999999876


Q ss_pred             C
Q 029878          182 N  182 (186)
Q Consensus       182 ~  182 (186)
                      +
T Consensus        80 ~   80 (99)
T CHL00163         80 K   80 (99)
T ss_pred             C
Confidence            5

>PF04839 PSRP-3_Ycf65: Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65); InterPro: IPR006924 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.98  E-value=3.1e-33  Score=191.98  Aligned_cols=48  Identities=67%  Similarity=1.325  Sum_probs=41.8

Q ss_pred             CcccccccCCchHHHHHhhhcCCCCCChhhHHHHhhhhHHHHHHHHhc
Q 029878          132 LSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTS  179 (186)
Q Consensus       132 LT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIINyWQe~  179 (186)
                      ||+||||||+||||+||.+||+|+||+++|||.|||++||||||||++
T Consensus         1 lT~yfFWPr~DAWe~lk~eLe~K~WIs~~e~i~lLN~~TeiIN~Wqe~   48 (49)
T PF04839_consen    1 LTEYFFWPREDAWEQLKNELESKPWISEKERIELLNQATEIINYWQEE   48 (49)
T ss_dssp             -S--EEETTS-HHHHHHHHHHHSTTS-HHHHHHHHHHHHHHHHHHHH-
T ss_pred             CCCcccCCCCcHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhhc
Confidence            799999999999999999999999999999999999999999999996

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 [, ]. This small acidic protein is found in 30S ribosomal subunit of cyanobacteria and plant plastids. In plants it has been named plastid-specific ribosomal protein 3 (PSRP-3), and in cyanobacteria it is named Ycf65. Plastid-specific ribosomal proteins may mediate the effects of nuclear factors on plastid translation. The acidic PSRPs are thought to contribute to protein-protein interactions in the 30S subunit, and are not thought to bind RNA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome, 0009536 plastid; PDB: 2KT9_A.

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	186
2kt9_A	116	Solution Nmr Structure Of Probable 30s Ribosomal Pr		1e-20

>pdb|2KT9|A Chain A, Solution Nmr Structure Of Probable 30s Ribosomal Protein Psrp-3 (Ycf65-Like Protein) From Synechocystis Sp. (Strain Pcc 6803), Northeast Structural Genomics Consortium Target Target Sgr46 Length = 116

Iteration: 1
 Score = 96.3 bits (238), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 39/73 (53%), Positives = 59/73 (80%), Gaps = 1/73 (1%)
Query: 105 LVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIH 164
            +LK +W+  ++ IA+DQ++ G GT PL+ Y+FWPR DAW++LK  L++K WI++ +RI+
Sbjct: 10  FILKVLWLDQNVAIAVDQIV-GKGTSPLTSYFFWPRADAWQQLKDELEAKHWIAEADRIN 68
Query: 165 LLNQATDVINFWQ 177
           +LNQAT+VINFWQ
Sbjct: 69  VLNQATEVINFWQ 81

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	186
2kt9_A	116	Probable 30S ribosomal protein PSRP-3; structural	2e-41

>2kt9_A Probable 30S ribosomal protein PSRP-3; structural genomics, northeast structural genomics consortium (NESG), target SGR46, PSI-2; NMR {Synechocystis SP} Length = 116

 Score =  134 bits (338), Expect = 2e-41
 Identities = 40/88 (45%), Positives = 61/88 (69%), Gaps = 1/88 (1%)

Query: 98  KPNEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWI 157
                   +LK +W+  ++ IA+DQ++ G GT PL+ Y+FWPR DAW++LK  L++K WI
Sbjct: 3   ASTVHTSFILKVLWLDQNVAIAVDQIV-GKGTSPLTSYFFWPRADAWQQLKDELEAKHWI 61

Query: 158 SQTERIHLLNQATDVINFWQTSGGNLQQ 185
           ++ +RI++LNQAT+VINFWQ      +Q
Sbjct: 62  AEADRINVLNQATEVINFWQDLKNQNKQ 89

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	186
2kt9_A	116	Probable 30S ribosomal protein PSRP-3; structural	100.0

>2kt9_A Probable 30S ribosomal protein PSRP-3; structural genomics, northeast structural genomics consortium (NESG), target SGR46, PSI-2; NMR {Synechocystis SP}

Probab=100.00  E-value=1.5e-48  Score=304.32  Aligned_cols=77  Identities=51%  Similarity=1.120  Sum_probs=75.4

Q ss_pred             CCceEEEEEEeecCcEEEEeeeeecCCCcccCcccccccCCchHHHHHhhhcCCCCCChhhHHHHhhhhHHHHHHHHh
Q 029878          101 EKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQT  178 (186)
Q Consensus       101 ~~~rfvLK~LWlek~IgiAvDQ~v~g~~t~PLT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIINyWQe  178 (186)
                      -++||+||||||||||||||||+| |+|++|||+||||||+||||+||.+||+|+||+++|||+||||+||||||||+
T Consensus         6 ~m~rf~LKvlWlek~IaiAvDQ~v-g~~t~PLT~YfFWPr~DAWe~LK~eLEsK~WIse~e~i~lLN~~TeiIN~WQe   82 (116)
T 2kt9_A            6 VHTSFILKVLWLDQNVAIAVDQIV-GKGTSPLTSYFFWPRADAWQQLKDELEAKHWIAEADRINVLNQATEVINFWQD   82 (116)
T ss_dssp             CCCCEEEEEEECSSCEEEEEEEEE-TTEEEECSCCEEETTSCHHHHHHHHHHHSTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhheeeEEEeccceeEEeeeee-cCCCCCCcceeeCCCccHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            358999999999999999999999 99999999999999999999999999999999999999999999999999998

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Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00