Citrus Sinensis ID: 032883

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-
Protein Sequence
MLSSMALQSTVNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPESLTAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGAVAILLLSWMKIPVSL
Secondary Structure (PSIPRED)
cccccccccccccccEEccccccccccccccccEEccccccccccccccEEEEEccccccccccccccccccccccccccccEEEEcccccccEEEEEEEEEccEEEEEcEEcccccccccccEEEccccc
Secondary Structure Prediction (SSPRO)
cccHEEEccccccccccccccccccccccccccEEEccccccccccccccEEEccccHccccccccccccccccccccccEEEEEEcccccccEHEHHHHHHHHHHHEHccccccccccccccccEccccc
Coil and Loop (DISEMBL)
mlssmalqstvngafttrssfpsqkltvkptkttilhqnrtkpisrnQRLValatpesltaeeatttstetipatpvetkkagvsvkqlekpRLVLKFIWMEKNIglaldqsiPGAVAILLLSWMKIPVSL
Flexible Loop (DISEMBL)
MLSSMALQSTvngafttrssfpsqkltvkptkttilhqnrtkpisrnqrLVALATpesltaeeatttstetipatpvetkkagvsvkqlekprLVLKFIWMEKNIGLALDQSIPGAVAILLLSWMKIPVSL
Low Complexity Region (SEG)
MLSSMALQSTVNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLValatpesltaeeatttstetipatPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGAVAILLLSWMKIPVSL
Disordered region (IsUnstruct)
***************************************************************************************QLEKPRLVLKFIWMEKNIGLALDQSIPGAVAILLLSWMKIP***
Disordered Region (DISOPRED)
*********T*******************************************************************************EKPRLVLKFIWMEKNIGLALDQSIPGAVAILLLSWMKIPVSL
Disordered Region (DISEMBL)
**********VNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPES************TIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGAVAILLLSWMKIPVSL
Disordered Region (DISPRO)
************GAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPESL*****************VETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGAVAILLLSWMKIPVSL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLSSMALQSTVNGAFTTRSSFPSQKLTVKPTKTTILHQNRTKPISRNQRLVALATPESLTAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGAVAILLLSWMKIPVSL
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	131	2.2.26 [Sep-21-2011]
Q9SX22	166	30S ribosomal protein 3-1	yes	no	0.847	0.668	0.475	2e-17
P82412	179	30S ribosomal protein 3,	N/A	no	0.847	0.620	0.386	1e-12
Q9LFV0	183	30S ribosomal protein 3-2	no	no	0.885	0.633	0.371	1e-12
O48609	181	30S ribosomal protein 3,	N/A	no	0.343	0.248	0.577	6e-08

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

 Score = 87.4 bits (215), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 58/122 (47%), Positives = 73/122 (59%), Gaps = 11/122 (9%)

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  TAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGAVAI 119
           TAE  T T  +T   TP +T K    VK  EK R+VLKF+WMEKNIGL LDQ +PG   I
Sbjct: 56  TAE--TVTGIDTSDNTPQQTIKV---VKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTI 110

Query: 120 LL 121
            L
Sbjct: 111 PL 112

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 = 72.0 bits (175), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 46/119 (38%), Positives = 63/119 (52%), Gaps = 8/119 (6%)

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

Query: 57  ESLTAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPG 115
           E+++         +      V  +K  V VK ++KPRLVLKFIWMEKNIGLALDQ+IPG
Sbjct: 62  ETISDVAIMGNEVDIDDDLLVNKEKLKVLVKPMDKPRLVLKFIWMEKNIGLALDQTIPG 120

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 = 71.6 bits (174), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 49/132 (37%), Positives = 70/132 (53%), Gaps = 16/132 (12%)

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 DQSIPGAVAILL 121
           D  IPG   I L
Sbjct: 120 DHMIPGFGTIPL 131

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 = 56.2 bits (134), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 26/45 (57%), Positives = 34/45 (75%)

Query: 77  VETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGAVAILL 121
           VE+++  V V + + P LVLKFIWMEKNIG+ALDQ +PG  +I L
Sbjct: 84  VESEEYKVEVPEKQDPMLVLKFIWMEKNIGIALDQMVPGVGSIPL 128

Probably a ribosomal protein or a ribosome-associated protein.

Hordeum vulgare (taxid: 4513)

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	131
255576477	180	Plastid-specific 30S ribosomal protein 3	0.870	0.633	0.469	9e-19
224099355	189	predicted protein [Populus trichocarpa]	0.938	0.650	0.429	2e-18
224111708	189	predicted protein [Populus trichocarpa]	0.946	0.656	0.460	2e-18
21554275	166	plastid-specific ribosomal protein 3 pre	0.847	0.668	0.475	1e-15
18409071	166	30S ribosomal protein 3-1 [Arabidopsis t	0.847	0.668	0.475	1e-15
225452011	176	PREDICTED: 30S ribosomal protein 3, chlo	0.854	0.636	0.429	2e-15
296087288	175	unnamed protein product [Vitis vinifera]	0.832	0.622	0.432	6e-15
145326692	163	30S ribosomal protein 3-1 [Arabidopsis t	0.824	0.662	0.459	6e-15
147784271	179	hypothetical protein VITISV_004015 [Viti	0.801	0.586	0.456	9e-15
297841583	162	plastid-specific ribosomal protein 3 pre	0.732	0.592	0.5	7e-13

>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 = 98.2 bits (243), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 61/130 (46%), Positives = 77/130 (59%), Gaps = 16/130 (12%)

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 SIPGAVAILL 121
            IPG   I L
Sbjct: 118 VIPGHGTIPL 127

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

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 = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 61/142 (42%), Positives = 78/142 (54%), Gaps = 19/142 (13%)

Query: 4   SMALQSTVNGAFTTRS------SFPSQKLTV------KPTKTTILHQNRTKPISRNQRLV 51
           SMA QS VN  FT  S      S  + K T+       P +++       + +SRNQR  
Sbjct: 3   SMAFQSGVNNVFTYYSLPCRTPSCKTFKATISVNPKPNPIRSSTFFDRERRHVSRNQRYT 62

Query: 52  ALATPESLTAE-----EATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIG 106
             A PE+L AE       +  + E+IP    ET+KA + VKQ+EKPRLVLKF+WMEKNIG
Sbjct: 63  TFAVPEALAAETPADAPPSNAAGESIPIQ--ETEKAELVVKQVEKPRLVLKFVWMEKNIG 120

Query: 107 LALDQSIPGAVAILLLSWMKIP 128
           LALDQ IPG   + L  +   P
Sbjct: 121 LALDQVIPGHGTVPLSPYFFWP 142

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 = 96.7 bits (239), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 65/141 (46%), Positives = 79/141 (56%), Gaps = 17/141 (12%)

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 ALDQSIPGAVAILLLSWMKIP 128
           ALDQ IPG   + L  +   P
Sbjct: 122 ALDQVIPGHGTVPLSPYFFWP 142

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 = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 58/122 (47%), Positives = 73/122 (59%), Gaps = 11/122 (9%)

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  TAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGAVAI 119
           TAE  T T  +T   TP +T K    VK  EK R+VLKF+WMEKNIGL LDQ +PG   I
Sbjct: 56  TAE--TVTGIDTSDNTPQQTTKV---VKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTI 110

Query: 120 LL 121
            L
Sbjct: 111 PL 112

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 = 87.4 bits (215), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 58/122 (47%), Positives = 73/122 (59%), Gaps = 11/122 (9%)

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  TAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGAVAI 119
           TAE  T T  +T   TP +T K    VK  EK R+VLKF+WMEKNIGL LDQ +PG   I
Sbjct: 56  TAE--TVTGIDTSDNTPQQTIKV---VKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTI 110

Query: 120 LL 121
            L
Sbjct: 111 PL 112

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 = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 52/121 (42%), Positives = 74/121 (61%), Gaps = 9/121 (7%)

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 G 115
           G
Sbjct: 118 G 118

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 = 85.5 bits (210), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 51/118 (43%), Positives = 72/118 (61%), Gaps = 9/118 (7%)

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  SLTAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPG 115
           ++   E ++   E++ A+P++ +K GV VK +EKPRLVLKFIWMEKNIG+ALDQ+IPG
Sbjct: 60  AVAVSEQSSAPQESLSASPLDVEKLGVVVKPMEKPRLVLKFIWMEKNIGVALDQAIPG 117

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 = 85.5 bits (210), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 56/122 (45%), Positives = 72/122 (59%), Gaps = 14/122 (11%)

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  TAEEATTTSTETIPATPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGAVAI 119
           TAE  T T  +T   TP +T      +K  EK R+VLKF+WMEKNIGL LDQ +PG   I
Sbjct: 56  TAE--TVTGIDTSDNTPQQT------IKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTI 107

Query: 120 LL 121
            L
Sbjct: 108 PL 109

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 85.1 bits (209), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 58/127 (45%), Positives = 70/127 (55%), Gaps = 22/127 (17%)

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 LDQSIPG 115
           LDQ IPG
Sbjct: 115 LDQVIPG 121

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 = 79.0 bits (193), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 51/102 (50%), Positives = 64/102 (62%), Gaps = 6/102 (5%)

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  KKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPGAVAILL 121
            K    VK  EK R+VLKF+WMEKNIGL LDQ +PG   I L
Sbjct: 70  TKV---VKPDEKSRVVLKFVWMEKNIGLGLDQHVPGHGTIPL 108

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	131
TAIR|locus:2143211	183	PSRP3/2 "plastid-specifi	0.305	0.218	0.625	1.2e-14
TAIR|locus:2026940	166	PSRP3/1 "plastid-specifi	0.801	0.632	0.379	5e-12

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

 Score = 133 (51.9 bits), Expect = 1.2e-14, Sum P(2) = 1.2e-14
 Identities = 25/40 (62%), Positives = 32/40 (80%)

Query:    76 PVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPG 115
             P+  KK  V VK LEKP++VLKF+WM+K+IG+ALD  IPG
Sbjct:    86 PLGKKKMRVLVKPLEKPKVVLKFVWMQKDIGVALDHMIPG 125

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 = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 44/116 (37%), Positives = 57/116 (49%)

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

Query:    60 XXXXXXXXXXXXXXXXPVETKKAGVSVKQLEKPRLVLKFIWMEKNIGLALDQSIPG 115
                             P +T K    VK  EK R+VLKF+WMEKNIGL LDQ +PG
Sbjct:    56 TAETVTGIDTSDNT--PQQTIKV---VKPDEKSRVVLKFVWMEKNIGLGLDQHVPG 106


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        0.317   0.129   0.362    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      131       107   0.00091  102 3  11 22  0.42    30
                                                     29  0.40    32


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:  509 (54 KB)
  Total size of DFA:  101 KB (2071 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  8.61u 0.12s 8.73t   Elapsed:  00:00:00
  Total cpu time:  8.61u 0.12s 8.73t   Elapsed:  00:00:00
  Start:  Fri May 10 06:55:38 2013   End:  Fri May 10 06:55:38 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

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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!

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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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	131
PRK02724	104	hypothetical protein; Provisional	99.87
CHL00163	99	ycf65 putative ribosomal protein 3; Validated	99.87

>PRK02724 hypothetical protein; Provisional

Probab=99.87  E-value=6.9e-23  Score=151.48  Aligned_cols=41  Identities=29%  Similarity=0.617  Sum_probs=39.5

Q ss_pred             CCCCeEEEEEEeeeCceEEEeeeeecCCCcccceeeeecccC
Q 032883           89 LEKPRLVLKFIWMEKNIGLALDQSIPGAVAILLLSWMKIPVS  130 (131)
Q Consensus        89 ~~~~rfvLK~LWleknIgiAlDQvv~g~~t~PLT~YfFWPr~  130 (131)
                      .+++||+||||||||||||||||++ |+|++|||+||||||+
T Consensus         4 ~~~~rfvlKvlWle~~iaiAvDQ~v-g~~t~PLT~yfFWPr~   44 (104)
T PRK02724          4 ADEGRFILKVLWLDDNVALAVDQIV-GKGTSPLTAYFFWPRN   44 (104)
T ss_pred             cccceEEEEEEEeccceeEEeeeec-CCCCCcCcceeecCCc
Confidence            4689999999999999999999999 9999999999999997

>CHL00163 ycf65 putative ribosomal protein 3; Validated

Probab=99.87  E-value=8.7e-23  Score=149.81  Aligned_cols=39  Identities=36%  Similarity=0.657  Sum_probs=37.5

Q ss_pred             CCeEEEEEEeeeCceEEEeeeeecCCCcccceeeeecccC
Q 032883           91 KPRLVLKFIWMEKNIGLALDQSIPGAVAILLLSWMKIPVS  130 (131)
Q Consensus        91 ~~rfvLK~LWleknIgiAlDQvv~g~~t~PLT~YfFWPr~  130 (131)
                      ++||+||||||||||||||||++ |+|++|||+||||||+
T Consensus         1 m~kf~lKvlWl~~~iaiAvDq~v-~~~t~PlT~yfFWPr~   39 (99)
T CHL00163          1 MQKFTLKVLWLENNIGIAVDQIV-GNGTSPLTSYFFWPRT   39 (99)
T ss_pred             CCeEEEEEEEecCceEEEEeeee-CCCCccCcceeecCCc
Confidence            58999999999999999999999 7899999999999997

---

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	131
2kt9_A	116	Probable 30S ribosomal protein PSRP-3; structural	3e-07

>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 = 45.4 bits (107), Expect = 3e-07
 Identities = 7/27 (25%), Positives = 16/27 (59%)

Query: 87  KQLEKPRLVLKFIWMEKNIGLALDQSI 113
                   +LK +W+++N+ +A+DQ +
Sbjct: 3   ASTVHTSFILKVLWLDQNVAIAVDQIV 29

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	131
2kt9_A	116	Probable 30S ribosomal protein PSRP-3; structural	99.86

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

Probab=99.86  E-value=1.2e-22  Score=151.54  Aligned_cols=41  Identities=27%  Similarity=0.557  Sum_probs=38.9

Q ss_pred             CCCCeEEEEEEeeeCceEEEeeeeecCCCcccceeeeecccC
Q 032883           89 LEKPRLVLKFIWMEKNIGLALDQSIPGAVAILLLSWMKIPVS  130 (131)
Q Consensus        89 ~~~~rfvLK~LWleknIgiAlDQvv~g~~t~PLT~YfFWPr~  130 (131)
                      +-++||+||||||||||||||||++ |+|++|||+||||||+
T Consensus         5 ~~m~rf~LKvlWlek~IaiAvDQ~v-g~~t~PLT~YfFWPr~   45 (116)
T 2kt9_A            5 TVHTSFILKVLWLDQNVAIAVDQIV-GKGTSPLTSYFFWPRA   45 (116)
T ss_dssp             CCCCCEEEEEEECSSCEEEEEEEEE-TTEEEECSCCEEETTS
T ss_pred             hhhhhheeeEEEeccceeEEeeeee-cCCCCCCcceeeCCCc
Confidence            3478999999999999999999999 9999999999999997

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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