Citrus Sinensis ID: 030605

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170----
Protein Sequence
MLSSMALQSTVNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPESLTAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccHHHHHHcccEEccccccEEEEEEEEEcccEEEEEEEEEccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cccHcccccccccccccccccccccccccccccccccccccccccccccHHHcccHHHHcccccccccccccccccccccccEEEEcccccccEEEEEEEEcccEEEEEEEEEcccccccccccEEccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
mlssmalqstvngafttrssfpsqkltvkptkttilhqnrtkpisrnQRLValatpesltaeeatttstetipatpvetkkagvsvkqlekpRLVLKFIWMEKNIglaldqsipgygtiplsqyffwprkDAWEELKTTLESKPWISQKMMIILLNQATDIINLWqqsggnltt
Flexible Loop (DISEMBL)
MLSSMALQSTvngafttrssfpsqkltvkptkttilhqnrtkpisrnqrLVALATpesltaeeatttstetipatpvetkkagvsvkqlekprLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT
Low Complexity Region (SEG)
MLSSMALQSTVNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLValatpesltaeeatttstetipatPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT
Disordered region (IsUnstruct)
***************************************************************************************QLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQ********
Disordered Region (DISOPRED)
****************************************************************************************LEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLW**S******
Disordered Region (DISEMBL)
**********VNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPES************TIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT
Disordered Region (DISPRO)
*******************************************************************************KKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQS******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLSSMALQSTVNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPESLTAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT
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	174	2.2.26 [Sep-21-2011]
Q9SX22	166	30S ribosomal protein 3-1	yes	no	0.942	0.987	0.622	2e-51
P82412	179	30S ribosomal protein 3,	N/A	no	0.977	0.949	0.533	6e-45
Q9LFV0	183	30S ribosomal protein 3-2	no	no	0.965	0.918	0.5	3e-42
O48609	181	30S ribosomal protein 3,	N/A	no	0.563	0.541	0.714	4e-37
P59327	108	Probable 30S ribosomal pr	yes	no	0.5	0.805	0.534	4e-22
B8HTT7	109	Probable 30S ribosomal pr	yes	no	0.448	0.715	0.582	7e-22
P51351	99	Probable 30S ribosomal pr	N/A	no	0.436	0.767	0.584	1e-21
Q1XDD6	102	Probable 30S ribosomal pr	N/A	no	0.477	0.813	0.558	2e-21
Q9MUN2	123	Probable 30S ribosomal pr	N/A	no	0.431	0.609	0.565	3e-21
Q8YSC1	99	Probable 30S ribosomal pr	yes	no	0.448	0.787	0.556	3e-21

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

 Score =  201 bits (512), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 109/175 (62%), Positives = 128/175 (73%), Gaps = 11/175 (6%)

Query: 1   MLSSMALQST-VNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPESL 59
           M+SSMAL ST +  +F   S  P   +T  P    + H   TKPIS  ++++ LA PE+L
Sbjct: 1   MMSSMALSSTSLCSSFI--SQHPKLSITASPP---LFHTQTTKPISVKRKIITLAAPETL 55

Query: 60  TAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTI 119
           TAE  T T  +T   TP +T K    VK  EK R+VLKF+WMEKNIGL LDQ +PG+GTI
Sbjct: 56  TAE--TVTGIDTSDNTPQQTIKV---VKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTI 110

Query: 120 PLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT 174
           PLS YFFWPRKDAWEELK+TLE+KPWISQK MIILLNQATDIINLWQQSGGNLT+
Sbjct: 111 PLSPYFFWPRKDAWEELKSTLEAKPWISQKKMIILLNQATDIINLWQQSGGNLTS 165

Probably a ribosomal protein or a ribosome-associated protein.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  179 bits (455), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 95/178 (53%), Positives = 117/178 (65%), Gaps = 8/178 (4%)

Query: 4   SMALQSTVNGAFTTRSSFPSQKLTVKPTKTTILHQNR---TKP----ISRNQRLVALATP 56
           SMA+Q  +N A    S + S KL++KP KT      +   + P    + +         P
Sbjct: 3   SMAVQPNIN-AIAKPSIYQSPKLSLKPFKTPAFANPKPFFSSPSFSQLKKKNNWSLFVAP 61

Query: 57  ESLTAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGY 116
           E+++         +      V  +K  V VK ++KPRLVLKFIWMEKNIGLALDQ+IPG+
Sbjct: 62  ETISDVAIMGNEVDIDDDLLVNKEKLKVLVKPMDKPRLVLKFIWMEKNIGLALDQTIPGH 121

Query: 117 GTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT 174
           GT+PLS Y+FWPRKDAWEELK  LE+KPWISQK MIILLNQATDIINLWQQSGGNL +
Sbjct: 122 GTVPLSPYYFWPRKDAWEELKVLLENKPWISQKQMIILLNQATDIINLWQQSGGNLAS 179

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 =  171 bits (432), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 92/184 (50%), Positives = 119/184 (64%), Gaps = 16/184 (8%)

Query: 5   MALQSTVNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISR--------NQRLV----A 52
           MA+Q+  + +F  R++ PSQKL+ KP     L   + KP SR        NQ  +    +
Sbjct: 1   MAVQANQSASFGFRTASPSQKLSSKPIAHISL-STKLKPSSRPSLSCSTWNQGQIPARHS 59

Query: 53  LATPESLTAEEATTTSTETIPAT---PVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLAL 109
              P       +  T +  +P +   P+  KK  V VK LEKP++VLKF+WM+K+IG+AL
Sbjct: 60  CINPGIFAYPPSNLTFSHELPESESPPLGKKKMRVLVKPLEKPKVVLKFVWMQKDIGVAL 119

Query: 110 DQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSG 169
           D  IPG+GTIPLS Y+FWPRKDAWEELKT LESKPWIS+   + LLNQATDIINLWQ SG
Sbjct: 120 DHMIPGFGTIPLSPYYFWPRKDAWEELKTLLESKPWISELHRVFLLNQATDIINLWQSSG 179

Query: 170 GNLT 173
           G+L+
Sbjct: 180 GDLS 183

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 =  154 bits (388), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 70/98 (71%), Positives = 82/98 (83%)

Query: 77  VETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEEL 136
           VE+++  V V + + P LVLKFIWMEKNIG+ALDQ +PG G+IPLS Y+FWPRKDAWEEL
Sbjct: 84  VESEEYKVEVPEKQDPMLVLKFIWMEKNIGIALDQMVPGVGSIPLSPYYFWPRKDAWEEL 143

Query: 137 KTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT 174
           +  LE K WISQK MIILLNQATDIINLWQQ GG+L+T
Sbjct: 144 RAKLEEKEWISQKQMIILLNQATDIINLWQQGGGSLST 181

Probably a ribosomal protein or a ribosome-associated protein.

Hordeum vulgare (taxid: 4513)

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

 Score =  104 bits (259), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 47/88 (53%), Positives = 63/88 (71%), Gaps = 1/88 (1%)

Query: 84  VSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESK 143
           +S ++LE  R  L+ +W+EK++ +A+DQ I G GT PL+ YFFWPR DAWE LK  LE K
Sbjct: 3   ISFRRLELSRFTLRVLWLEKDVAIAVDQ-IVGKGTSPLTSYFFWPRTDAWELLKAELEKK 61

Query: 144 PWISQKMMIILLNQATDIINLWQQSGGN 171
            WI++   I LLN+AT+IIN WQ+ G N
Sbjct: 62  SWITEAERIELLNRATEIINYWQEEGKN 89

Probably a ribosomal protein or a ribosome-associated protein.

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

>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 =  103 bits (256), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 46/79 (58%), Positives = 59/79 (74%), Gaps = 1/79 (1%)

Query: 93  RLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMI 152
           + +LK +W++ N+ LA+DQ + G GT PL+ YFFWPR DAWE+LKT LE K WIS+   I
Sbjct: 13  QFILKVLWLDSNVALAVDQVV-GKGTSPLTSYFFWPRADAWEQLKTELEKKTWISEADRI 71

Query: 153 ILLNQATDIINLWQQSGGN 171
            LLN+ATDIIN 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)

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

 Score =  102 bits (254), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 45/77 (58%), Positives = 58/77 (75%), Gaps = 1/77 (1%)

Query: 93  RLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMI 152
           +  LK +W+E NI +A+DQ I G GT PL+ YFFWPR DAWEELK  LESKPWI+++  I
Sbjct: 3   KFTLKVLWLENNIAIAIDQ-IVGNGTSPLTSYFFWPRNDAWEELKAELESKPWIAERDRI 61

Query: 153 ILLNQATDIINLWQQSG 169
            LLN+ T++IN 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 =  102 bits (253), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 48/86 (55%), Positives = 62/86 (72%), Gaps = 3/86 (3%)

Query: 84  VSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESK 143
           + +K L K    LK +W+E NI +A+DQ I G GT PL+ YFFWPR DAWEELK  LESK
Sbjct: 1   MEIKNLSK--FTLKVLWLENNIAIAIDQ-IVGNGTSPLTSYFFWPRNDAWEELKAELESK 57

Query: 144 PWISQKMMIILLNQATDIINLWQQSG 169
           PWI+++  I LLN+ T++IN WQ+ G
Sbjct: 58  PWIAERDRIELLNKTTEVINYWQEEG 83

Probably a ribosomal protein or a ribosome-associated protein.

Porphyra yezoensis (taxid: 2788)

>sp|Q9MUN2|RRP3_MESVI Probable 30S ribosomal protein 3, chloroplastic OS=Mesostigma viride GN=ycf65 PE=3 SV=1

 Score =  101 bits (251), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 43/76 (56%), Positives = 56/76 (73%), Gaps = 1/76 (1%)

Query: 93  RLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMI 152
           + VLKF+W+EKN+ + +DQ +   G  P+++YFFWPRKDAWEELK  L +KPWIS    I
Sbjct: 20  KFVLKFLWLEKNLAVTVDQ-VTNRGNSPITEYFFWPRKDAWEELKDALANKPWISYDESI 78

Query: 153 ILLNQATDIINLWQQS 168
            LLNQ TD+IN WQ+ 
Sbjct: 79  ALLNQTTDVINYWQED 94

Probably a ribosomal protein or a ribosome-associated protein.

Mesostigma viride (taxid: 41882)

>sp|Q8YSC1|RRP3_NOSS1 Probable 30S ribosomal protein PSRP-3 OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=asr3168 PE=3 SV=2

 Score =  101 bits (251), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 44/79 (55%), Positives = 60/79 (75%), Gaps = 1/79 (1%)

Query: 93  RLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMI 152
           + +LK +W+++N+ LA+DQ + G GT PL++YFFWPR DAWEELK  LESK WIS    +
Sbjct: 3   KFILKILWLDENVALAVDQVV-GKGTSPLTKYFFWPRNDAWEELKKELESKHWISDLDRV 61

Query: 153 ILLNQATDIINLWQQSGGN 171
            LLN+AT++IN WQ+ G N
Sbjct: 62  ELLNKATEVINYWQEEGRN 80

Probably a ribosomal protein or a ribosome-associated protein.

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

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	174
255576477	180	Plastid-specific 30S ribosomal protein 3	0.959	0.927	0.628	7e-54
224111708	189	predicted protein [Populus trichocarpa]	0.977	0.899	0.625	8e-53
224099355	189	predicted protein [Populus trichocarpa]	0.959	0.883	0.611	1e-52
21554275	166	plastid-specific ribosomal protein 3 pre	0.942	0.987	0.622	5e-50
18409071	166	30S ribosomal protein 3-1 [Arabidopsis t	0.942	0.987	0.622	8e-50
145326692	163	30S ribosomal protein 3-1 [Arabidopsis t	0.925	0.987	0.611	4e-49
225452011	176	PREDICTED: 30S ribosomal protein 3, chlo	0.977	0.965	0.569	1e-48
296087288	175	unnamed protein product [Vitis vinifera]	0.959	0.954	0.573	4e-48
297841583	162	plastid-specific ribosomal protein 3 pre	0.856	0.919	0.658	8e-47
147784271	179	hypothetical protein VITISV_004015 [Viti	0.925	0.899	0.584	2e-46

>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 =  214 bits (546), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 115/183 (62%), Positives = 132/183 (72%), Gaps = 16/183 (8%)

Query: 5   MALQSTVNGAFTTRSSFPSQKLTVKPTKTTILH-------------QNRTKPISRNQRLV 51
           MA+QS V+ +  T S  P +    K  KT+I                 + +PISRN+RL 
Sbjct: 1   MAIQSGVS-SILTYSPVPHRTPFCKSIKTSIFANPKISLLYSSTILDPKMRPISRNERLT 59

Query: 52  ALATPESLTAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQ 111
             A+PE+LT E+ T+ + E I    +E  K  V+VKQ+EKPRLVLKFIWMEKNIGLALDQ
Sbjct: 60  TFASPEALTVEDKTSETEEPISDDIIE--KVEVAVKQVEKPRLVLKFIWMEKNIGLALDQ 117

Query: 112 SIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGN 171
            IPG+GTIPLS YFFWPRKDAWEELKTTLESKPWISQK MIILLNQATDIINLWQQSGGN
Sbjct: 118 VIPGHGTIPLSPYFFWPRKDAWEELKTTLESKPWISQKKMIILLNQATDIINLWQQSGGN 177

Query: 172 LTT 174
           LTT
Sbjct: 178 LTT 180

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

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 =  211 bits (537), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 117/187 (62%), Positives = 131/187 (70%), Gaps = 17/187 (9%)

Query: 4   SMALQSTVNGAFTTRSSFPSQKLTVKPTKTT--------ILH-----QNRTKPISRNQRL 50
           S+A Q   +  FT  SS P Q  + K  K T        ++H       + K +SRNQR 
Sbjct: 3   SVAFQCGFSNVFTN-SSLPCQTPSCKTFKATFSTNPKPNLIHSSTFLDRKRKRVSRNQRY 61

Query: 51  VALATPESLTAEEATTT--STETIPATPVE-TKKAGVSVKQLEKPRLVLKFIWMEKNIGL 107
              A PE+LT E    T  STET  + P + T+KA V VKQ+EKPRLVLKFIWMEKNIGL
Sbjct: 62  TTFAAPEALTVETPIDTPPSTETEESIPAQGTEKAEVLVKQVEKPRLVLKFIWMEKNIGL 121

Query: 108 ALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQ 167
           ALDQ IPG+GT+PLS YFFWPRKDAWEELK TLESKPWISQK MIILLNQATDIINLWQQ
Sbjct: 122 ALDQVIPGHGTVPLSPYFFWPRKDAWEELKATLESKPWISQKKMIILLNQATDIINLWQQ 181

Query: 168 SGGNLTT 174
           SGGNLTT
Sbjct: 182 SGGNLTT 188

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  211 bits (536), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 115/188 (61%), Positives = 128/188 (68%), Gaps = 21/188 (11%)

Query: 4   SMALQSTVNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPI-------------SRNQRL 50
           SMA QS VN  FT  S  P +  + K  K TI    +  PI             SRNQR 
Sbjct: 3   SMAFQSGVNNVFTYYS-LPCRTPSCKTFKATISVNPKPNPIRSSTFFDRERRHVSRNQRY 61

Query: 51  VALATPESLTAE-----EATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNI 105
              A PE+L AE       +  + E+IP    ET+KA + VKQ+EKPRLVLKF+WMEKNI
Sbjct: 62  TTFAVPEALAAETPADAPPSNAAGESIPIQ--ETEKAELVVKQVEKPRLVLKFVWMEKNI 119

Query: 106 GLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLW 165
           GLALDQ IPG+GT+PLS YFFWPRKDAWEELK TLESKPWISQK MIILLNQATDIINLW
Sbjct: 120 GLALDQVIPGHGTVPLSPYFFWPRKDAWEELKATLESKPWISQKKMIILLNQATDIINLW 179

Query: 166 QQSGGNLT 173
           QQSGGNLT
Sbjct: 180 QQSGGNLT 187

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21554275|gb|AAM63350.1| plastid-specific ribosomal protein 3 precursor [Arabidopsis thaliana]

 Score =  202 bits (513), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 109/175 (62%), Positives = 128/175 (73%), Gaps = 11/175 (6%)

Query: 1   MLSSMALQST-VNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPESL 59
           M+SSMAL ST +  +F   S  P   +T  P    + H   TKPIS  ++++ LA PE+L
Sbjct: 1   MMSSMALSSTSLCSSFI--SQHPKLSITASPP---LFHTQTTKPISVKRKIITLAAPETL 55

Query: 60  TAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTI 119
           TAE  T T  +T   TP +T K    VK  EK R+VLKF+WMEKNIGL LDQ +PG+GTI
Sbjct: 56  TAE--TVTGIDTSDNTPQQTTKV---VKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTI 110

Query: 120 PLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT 174
           PLS YFFWPRKDAWEELK+TLE+KPWISQK MIILLNQATDIINLWQQSGGNLT+
Sbjct: 111 PLSPYFFWPRKDAWEELKSTLEAKPWISQKKMIILLNQATDIINLWQQSGGNLTS 165

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18409071|ref|NP_564934.1| 30S ribosomal protein 3-1 [Arabidopsis thaliana] gi|28380141|sp|Q9SX22.1|RRP31_ARATH RecName: Full=30S ribosomal protein 3-1, chloroplastic; AltName: Full=Plastid-specific 30S ribosomal protein 3-1; Short=PSRP-3 1; Flags: Precursor gi|5734719|gb|AAD49984.1|AC008075_17 ESTs gb|H37416, gb|T21163, gb|T76138 and gb|AA651329 come from this gene [Arabidopsis thaliana] gi|28393198|gb|AAO42029.1| unknown protein [Arabidopsis thaliana] gi|28827558|gb|AAO50623.1| unknown protein [Arabidopsis thaliana] gi|332196695|gb|AEE34816.1| 30S ribosomal protein 3-1 [Arabidopsis thaliana]

 Score =  201 bits (512), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 109/175 (62%), Positives = 128/175 (73%), Gaps = 11/175 (6%)

Query: 1   MLSSMALQST-VNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPESL 59
           M+SSMAL ST +  +F   S  P   +T  P    + H   TKPIS  ++++ LA PE+L
Sbjct: 1   MMSSMALSSTSLCSSFI--SQHPKLSITASPP---LFHTQTTKPISVKRKIITLAAPETL 55

Query: 60  TAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTI 119
           TAE  T T  +T   TP +T K    VK  EK R+VLKF+WMEKNIGL LDQ +PG+GTI
Sbjct: 56  TAE--TVTGIDTSDNTPQQTIKV---VKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTI 110

Query: 120 PLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT 174
           PLS YFFWPRKDAWEELK+TLE+KPWISQK MIILLNQATDIINLWQQSGGNLT+
Sbjct: 111 PLSPYFFWPRKDAWEELKSTLEAKPWISQKKMIILLNQATDIINLWQQSGGNLTS 165

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145326692|ref|NP_001077793.1| 30S ribosomal protein 3-1 [Arabidopsis thaliana] gi|332196696|gb|AEE34817.1| 30S ribosomal protein 3-1 [Arabidopsis thaliana]

 Score =  199 bits (505), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 107/175 (61%), Positives = 127/175 (72%), Gaps = 14/175 (8%)

Query: 1   MLSSMALQST-VNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPESL 59
           M+SSMAL ST +  +F   S  P   +T  P    + H   TKPIS  ++++ LA PE+L
Sbjct: 1   MMSSMALSSTSLCSSFI--SQHPKLSITASPP---LFHTQTTKPISVKRKIITLAAPETL 55

Query: 60  TAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTI 119
           TAE  T T  +T   TP +T      +K  EK R+VLKF+WMEKNIGL LDQ +PG+GTI
Sbjct: 56  TAE--TVTGIDTSDNTPQQT------IKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTI 107

Query: 120 PLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT 174
           PLS YFFWPRKDAWEELK+TLE+KPWISQK MIILLNQATDIINLWQQSGGNLT+
Sbjct: 108 PLSPYFFWPRKDAWEELKSTLEAKPWISQKKMIILLNQATDIINLWQQSGGNLTS 162

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  197 bits (502), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 102/179 (56%), Positives = 127/179 (70%), Gaps = 9/179 (5%)

Query: 1   MLSSMALQSTVNGAFTTRSSFP-----SQKLTVKPTKTTILHQNRTKPISRNQRLVALAT 55
           M+ SMA+Q   N A  + + FP     + +L  K +    L+  R+   S N RL A   
Sbjct: 1   MMLSMAVQPNPNAALKSYT-FPMSSNRNHRLMFKSSNALSLYSTRSA--STNLRLRASPA 57

Query: 56  PE-SLTAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIP 114
           P  ++   E ++   E++ A+P++ +K GV VK +EKPRLVLKFIWMEKNIG+ALDQ+IP
Sbjct: 58  PVVAVAVSEQSSAPQESLSASPLDVEKLGVVVKPMEKPRLVLKFIWMEKNIGVALDQAIP 117

Query: 115 GYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLT 173
           G+GTIPLS Y+FWPRKDAWEE+K  LESKPWISQK MIILLNQATDIINLWQQSGGNL 
Sbjct: 118 GHGTIPLSPYYFWPRKDAWEEIKVLLESKPWISQKQMIILLNQATDIINLWQQSGGNLA 176

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  196 bits (497), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 101/176 (57%), Positives = 125/176 (71%), Gaps = 9/176 (5%)

Query: 4   SMALQSTVNGAFTTRSSFP-----SQKLTVKPTKTTILHQNRTKPISRNQRLVALATPE- 57
           SMA+Q   N A  + + FP     + +L  K +    L+  R+   S N RL A   P  
Sbjct: 3   SMAVQPNPNAALKSYT-FPMSSNRNHRLMFKSSNALSLYSTRSA--STNLRLRASPAPVV 59

Query: 58  SLTAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYG 117
           ++   E ++   E++ A+P++ +K GV VK +EKPRLVLKFIWMEKNIG+ALDQ+IPG+G
Sbjct: 60  AVAVSEQSSAPQESLSASPLDVEKLGVVVKPMEKPRLVLKFIWMEKNIGVALDQAIPGHG 119

Query: 118 TIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLT 173
           TIPLS Y+FWPRKDAWEE+K  LESKPWISQK MIILLNQATDIINLWQQSGGNL 
Sbjct: 120 TIPLSPYYFWPRKDAWEEIKVLLESKPWISQKQMIILLNQATDIINLWQQSGGNLA 175

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297841583|ref|XP_002888673.1| plastid-specific ribosomal protein 3 precursor [Arabidopsis lyrata subsp. lyrata] gi|297334514|gb|EFH64932.1| plastid-specific ribosomal protein 3 precursor [Arabidopsis lyrata subsp. lyrata]

 Score =  191 bits (486), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 102/155 (65%), Positives = 119/155 (76%), Gaps = 6/155 (3%)

Query: 21  FPSQKLTVKPTKTTILHQNRT-KPISRNQRLVALATPESLTAEEATTTSTETIPATPVET 79
           F SQ   +  T +T L  N+T KPIS  ++++ LA PE+LTAE  T T  +T   TP +T
Sbjct: 12  FISQHPKLSITASTPLFLNQTTKPISVKRKIITLAAPETLTAE--TVTGIDTSDNTPQQT 69

Query: 80  KKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTT 139
            K    VK  EK R+VLKF+WMEKNIGL LDQ +PG+GTIPLS YFFWPRKDAWEELK+T
Sbjct: 70  TKV---VKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTIPLSPYFFWPRKDAWEELKST 126

Query: 140 LESKPWISQKMMIILLNQATDIINLWQQSGGNLTT 174
           LE+KPWISQK MIILLNQATDIINLWQQSGGNLT+
Sbjct: 127 LEAKPWISQKKMIILLNQATDIINLWQQSGGNLTS 161

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147784271|emb|CAN68341.1| hypothetical protein VITISV_004015 [Vitis vinifera]

 Score =  190 bits (483), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 107/183 (58%), Positives = 122/183 (66%), Gaps = 22/183 (12%)

Query: 5   MALQSTVNGAFTTRSSFPSQKLTVKPTKTTI--------LHQN--------RTKPISRNQ 48
           MA QS++N  F   SSFPSQ  + K +KT          L Q         RTKP  + Q
Sbjct: 1   MAAQSSINSTFIC-SSFPSQNPSFKISKTPFPIPLNPKPLFQRSSTXTPGIRTKPSMKLQ 59

Query: 49  RLVALATPESLTAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLA 108
           RL   A  E+ TAE +T       P +  E +K  V VK +E PRLVLKF+WMEKNIG+A
Sbjct: 60  RLAVSAASEARTAEPSTAN-----PISSEENEKVEVIVKVMETPRLVLKFVWMEKNIGVA 114

Query: 109 LDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQS 168
           LDQ IPGYGT PLS Y+FWP KDAWEELK+TLESKPWISQK MIILLN+ATDIINLWQQS
Sbjct: 115 LDQVIPGYGTNPLSPYYFWPGKDAWEELKSTLESKPWISQKKMIILLNEATDIINLWQQS 174

Query: 169 GGN 171
           GGN
Sbjct: 175 GGN 177

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	174
TAIR|locus:2026940	166	PSRP3/1 "plastid-specifi	0.942	0.987	0.554	5.7e-43
TAIR|locus:2143211	183	PSRP3/2 "plastid-specifi	0.563	0.535	0.714	3.2e-41

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

 Score = 454 (164.9 bits), Expect = 5.7e-43, P = 5.7e-43
 Identities = 97/175 (55%), Positives = 114/175 (65%)

Query:     1 MLSSMALQST-VNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVXXXXXXXX 59
             M+SSMAL ST +  +F   S  P   +T  P    + H   TKPIS  ++++        
Sbjct:     1 MMSSMALSSTSLCSSFI--SQHPKLSITASPP---LFHTQTTKPISVKRKIITLAAPETL 55

Query:    60 XXXXXXXXXXXXXXXXPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTI 119
                             P +T K    VK  EK R+VLKF+WMEKNIGL LDQ +PG+GTI
Sbjct:    56 TAETVTGIDTSDNT--PQQTIKV---VKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTI 110

Query:   120 PLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLTT 174
             PLS YFFWPRKDAWEELK+TLE+KPWISQK MIILLNQATDIINLWQQSGGNLT+
Sbjct:   111 PLSPYFFWPRKDAWEELKSTLEAKPWISQKKMIILLNQATDIINLWQQSGGNLTS 165

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

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

 Score = 387 (141.3 bits), Expect = 3.2e-41, Sum P(2) = 3.2e-41
 Identities = 70/98 (71%), Positives = 83/98 (84%)

Query:    76 PVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEE 135
             P+  KK  V VK LEKP++VLKF+WM+K+IG+ALD  IPG+GTIPLS Y+FWPRKDAWEE
Sbjct:    86 PLGKKKMRVLVKPLEKPKVVLKFVWMQKDIGVALDHMIPGFGTIPLSPYYFWPRKDAWEE 145

Query:   136 LKTTLESKPWISQKMMIILLNQATDIINLWQQSGGNLT 173
             LKT LESKPWIS+   + LLNQATDIINLWQ SGG+L+
Sbjct:   146 LKTLLESKPWISELHRVFLLNQATDIINLWQSSGGDLS 183

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

---

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)
Q9SX22	RRP31_ARATH	No assigned EC number	0.6228	0.9425	0.9879	yes	no
P82412	RRP3_SPIOL	No assigned EC number	0.5337	0.9770	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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	174
CHL00163	99	CHL00163, ycf65, putative ribosomal protein 3; Val	4e-33
PRK02724	104	PRK02724, PRK02724, hypothetical protein; Provisio	3e-31
pfam04839	47	pfam04839, PSRP-3_Ycf65, Plastid and cyanobacteria	1e-23

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

 Score =  113 bits (284), Expect = 4e-33
 Identities = 44/81 (54%), Positives = 57/81 (70%), Gaps = 1/81 (1%)

Query: 92  PRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMM 151
            +  LK +W+E NIG+A+DQ + G GT PL+ YFFWPR DAWE LK  LESKPWIS+   
Sbjct: 2   QKFTLKVLWLENNIGIAVDQIV-GNGTSPLTSYFFWPRTDAWELLKLELESKPWISEDER 60

Query: 152 IILLNQATDIINLWQQSGGNL 172
           I +LN+ T+IIN WQ++    
Sbjct: 61  IEILNKTTEIINYWQENKKKY 81

Length = 99

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

 Score =  108 bits (271), Expect = 3e-31
 Identities = 43/84 (51%), Positives = 62/84 (73%), Gaps = 1/84 (1%)

Query: 88  QLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWIS 147
           + ++ R +LK +W++ N+ LA+DQ I G GT PL+ YFFWPR DAWE+LKT LESK WI+
Sbjct: 3   KADEGRFILKVLWLDDNVALAVDQ-IVGKGTSPLTAYFFWPRNDAWEQLKTELESKHWIT 61

Query: 148 QKMMIILLNQATDIINLWQQSGGN 171
           +   + +LN+AT++IN WQ+ G  
Sbjct: 62  ENERVEVLNKATEVINYWQEEGKG 85

Length = 104

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

 Score = 87.4 bits (217), Expect = 1e-23
 Identities = 32/47 (68%), Positives = 39/47 (82%)

Query: 121 LSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQ 167
           L++YFFWPR DAWE+LK  LESKPWIS+   + LLNQAT+IIN WQ+
Sbjct: 1   LTEYFFWPRTDAWEQLKAELESKPWISEAERVNLLNQATEIINYWQE 47

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	174
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=6.7e-50  Score=305.78  Aligned_cols=83  Identities=51%  Similarity=1.037  Sum_probs=79.8

Q ss_pred             CCCCcEEEEEEeecCceeEEeeeeecCCCCccccccccccCCchHHHHHHhhccCCCCChhhHHHHHHhHHHHHHHHHhc
Q 030605           89 LEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQS  168 (174)
Q Consensus        89 ~e~~rfvLK~LWleknIgiAvDQ~v~g~~t~PLT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIINyWQe~  168 (174)
                      .+++||+||||||++||||||||++ |+|++|||+||||||+||||+||.+||+||||+++|||+|||++||||||||++
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            4679999999999999999999999 999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 030605          169 GGNL  172 (174)
Q Consensus       169 ~~~~  172 (174)
                      |++-
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=8.6e-50  Score=302.95  Aligned_cols=80  Identities=55%  Similarity=1.063  Sum_probs=77.7

Q ss_pred             CCcEEEEEEeecCceeEEeeeeecCCCCccccccccccCCchHHHHHHhhccCCCCChhhHHHHHHhHHHHHHHHHhcCC
Q 030605           91 KPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGG  170 (174)
Q Consensus        91 ~~rfvLK~LWleknIgiAvDQ~v~g~~t~PLT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIINyWQe~~~  170 (174)
                      ++||+||||||+++|||||||++ |+|++|||+||||||+||||+||.+||+||||+++|||+|||++|||||||||+++
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            58999999999999999999999 88999999999999999999999999999999999999999999999999999876


Q ss_pred             C
Q 030605          171 N  171 (174)
Q Consensus       171 ~  171 (174)
                      +
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=2.5e-33  Score=190.97  Aligned_cols=48  Identities=71%  Similarity=1.297  Sum_probs=41.8

Q ss_pred             ccccccccCCchHHHHHHhhccCCCCChhhHHHHHHhHHHHHHHHHhc
Q 030605          121 LSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQS  168 (174)
Q Consensus       121 LT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIINyWQe~  168 (174)
                      ||+||||||+||||+||.+||+||||+++|||.|||++||||||||++
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	174
2kt9_A	116	Solution Nmr Structure Of Probable 30s Ribosomal Pr		9e-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 = 92.8 bits (229), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 39/73 (53%), Positives = 56/73 (76%), Gaps = 1/73 (1%)
Query: 94  LVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMII 153
            +LK +W+++N+ +A+DQ I G GT PL+ YFFWPR DAW++LK  LE+K WI++   I 
Sbjct: 10  FILKVLWLDQNVAIAVDQ-IVGKGTSPLTSYFFWPRADAWQQLKDELEAKHWIAEADRIN 68
Query: 154 LLNQATDIINLWQ 166
           +LNQAT++IN WQ
Sbjct: 69  VLNQATEVINFWQ 81
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	174
2kt9_A	116	Probable 30S ribosomal protein PSRP-3; structural	4e-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 =  133 bits (336), Expect = 4e-41
 Identities = 38/82 (46%), Positives = 56/82 (68%), Gaps = 1/82 (1%)

Query: 87  KQLEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWI 146
                   +LK +W+++N+ +A+DQ + G GT PL+ YFFWPR DAW++LK  LE+K WI
Sbjct: 3   ASTVHTSFILKVLWLDQNVAIAVDQIV-GKGTSPLTSYFFWPRADAWQQLKDELEAKHWI 61

Query: 147 SQKMMIILLNQATDIINLWQQS 168
           ++   I +LNQAT++IN WQ  
Sbjct: 62  AEADRINVLNQATEVINFWQDL 83

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	174
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=1.1e-48  Score=302.56  Aligned_cols=77  Identities=49%  Similarity=1.044  Sum_probs=75.5

Q ss_pred             CCCcEEEEEEeecCceeEEeeeeecCCCCccccccccccCCchHHHHHHhhccCCCCChhhHHHHHHhHHHHHHHHHh
Q 030605           90 EKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQ  167 (174)
Q Consensus        90 e~~rfvLK~LWleknIgiAvDQ~v~g~~t~PLT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIINyWQe  167 (174)
                      -++||+|||||||++|||||||+| |+|++|||+||||||+||||+||.+||+||||+++|||+|||++|||||||||
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