Citrus Sinensis ID: 029831

---

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
MASSSLTSALTSQSKSPFYPQQLSQLPSSPLFSFARSLKTFRTNAKSLLLHKKNSNSVSLTVKAQTLDFSGSFFEGGGFGSDDDPTSVPPGSVGTATAIEDKEEPQCPPGLRQYETMMVLRPDMSEDERLALTQNCLLLGVACMWRYSIEGLFHWPTASGRETKLGSPTLTWMVSISSSPTSLNQSQ
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccHHHHHHHHHHHHccccHHHHcccccccEEEEEEEEEcccccEEccccccccccccccccccccccccccccccccccccccccEEEEEEcccccHHHHHHHHHHHHHHHHcccccEEEEcccccccccccccccccccEEEEEEEEcccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccHHcccccccHcccccEEEcccccccEEEEEEEEEEccccEEcccccccccccccccccccccHHHHccccccccccccccEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccEEEEEEEccccccccccc
Coil and Loop (DISEMBL)
masssltsaltsqskspfypqqlsqlpssplfsFARSLKTFRTNAKSLLLHkknsnsvsLTVKaqtldfsgsffegggfgsdddptsvppgsvgtataiedkeepqcppglrqyetmmvlrpdmsedERLALTQNCLLLGVACMWRYSieglfhwptasgretklgsptltwmvsisssptslnqsq
Flexible Loop (DISEMBL)
masssltsALTSQSKSPFYPQQLSQLPSSPLFSFARSLKTFRTNAKSLLlhkknsnsvslTVKAQTLDFSGSFFEGGGFGSDDDPTSVPPGSVGTataiedkeepqcppglRQYETMMVLRPDMSEDERLALTQNCLLLGVACMWRYSIEGLFHWPTASGRETKLGSPTLTWmvsisssptslnqsq
Low Complexity Region (SEG)
MasssltsaltsqskspfypqqlsqlpssplfsfARSLKTFRTNAKSLLLHKKNSNSVSLTVKAQTLdfsgsffegggfgsdddPTSVPPGSVGTATAIEDKEEPQCPPGLRQYETMMVLRPDMSEDERLALTQNCLLLGVACMWRYSIEGLFHWPTASGRETKLGSPTLTWMVSISSSPTSLNQSQ
Disordered region (IsUnstruct)
*************************************LKTFRT****LLL*********LTVKAQTLDFSGSFF******************************************************RLALTQNCLLLGVACMWRYSIEGLFHWPTASGRETKLGSPTLTWMV*************
Disordered Region (DISOPRED)
*************SKSPFYPQQLSQLPSSPLFSFARSLKTFRTNAK*************LTVKAQTLDFSGSFFEGGG********************************LRQYETMMVLRPDMSEDERLALTQNCLLLGVACMWRYSIEGLFHWPTASGRETKLGSPTLTWMVSISS*********
Disordered Region (DISEMBL)
***********************SQLPSSPLFSFARSLKTFRTNAKSLLLHKKNSNSVSLTVKAQTLDFSGSFFEGGGFGSDDDPTSVPPGSVGTATAIEDKEEPQCPPGLRQYETMMVLRPDMSEDERLALTQNCLLLGVACMWRYSIEGLFHWPTASGRETKLGSPTLTWMVSIS**********
Disordered Region (DISPRO)
*****************FYPQQLSQLPSSPLFSFARSLKTFRTNAKSLLLHKKNSNSVSLTVKAQTLDFSGSFFEGGGFGS**********************EPQCPPGLRQYETMMVLRPDMSEDERLALTQNCLLLGVACMWRYSIEGLFHWPTASGRETKLGSPTLTWMVSIS**********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MASSSLTSALTSQSKSPFYPQQLSQLPSSPLFSFARSLKTFRTNAKSLLLHKKNSNSVSLTVKAQTLDFSGSFFEGGGFGSDDDPTSVPPGSVGTATAIEDKEEPQCPPGLRQYETMMVLRPDMSEDERLALTQNCLLLGVACMWRYSIEGLFHWPTASGRETKLGSPTLTWMVSISSSPTSLNQSQ
Positional Conservation
no confident homologs detected

---

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	187	2.2.26 [Sep-21-2011]
Q8VY91	207	30S ribosomal protein S6	yes	no	0.625	0.565	0.608	3e-31
P82403	168	30S ribosomal protein S6	N/A	no	0.427	0.476	0.639	5e-16

>sp|Q8VY91|RR6_ARATH 30S ribosomal protein S6 alpha, chloroplastic OS=Arabidopsis thaliana GN=RPS6 PE=1 SV=1

 Score =  134 bits (338), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 73/120 (60%), Positives = 85/120 (70%), Gaps = 3/120 (2%)

Query: 23  LSQLPSSPLFSFARSLKTFRTNAKSLLLHKKNSNSVSLTVKAQTLDFSGSFFEGGGFGSD 82
           L  + S PL SF+ SL+ F + +K +    +  +     VK+Q LDFSG+FFEGG FGSD
Sbjct: 15  LPNVSSQPLLSFSHSLRPFISKSKPMCASIQKRDGSQFVVKSQALDFSGTFFEGG-FGSD 73

Query: 83  DDPTSVPPGSVGTATAIEDKEEPQCPPGLRQYETMMVLRPDMSEDERLALTQNCLLLGVA 142
           DDPTS P GS G +TA+EDK EPQCPPGLRQYETM VLRPDMSEDERL LTQ    L VA
Sbjct: 74  DDPTS-PSGS-GVSTALEDKPEPQCPPGLRQYETMAVLRPDMSEDERLGLTQKYEELLVA 131

Binds together with S18 to 16S ribosomal RNA.
Arabidopsis thaliana (taxid: 3702)

>sp|P82403|RR6_SPIOL 30S ribosomal protein S6 alpha, chloroplastic (Fragment) OS=Spinacia oleracea GN=RPS6 PE=1 SV=2

 Score = 84.0 bits (206), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 55/86 (63%), Positives = 62/86 (72%), Gaps = 6/86 (6%)

Query: 62  VKAQTLDFSGSFFEGGGFGSDDDPTSVPPGSVGTATAIEDKEEPQCPPGLRQYETMMVLR 121
           VKA  LDFSGSFFEGG  G D+DP S PP  +    A+E+K EPQCPPGLRQYETM VLR
Sbjct: 17  VKAIALDFSGSFFEGGFGGLDEDPPSTPPAGL----AVEEKPEPQCPPGLRQYETMAVLR 72

Query: 122 PDMSEDERLALTQNC--LLLGVACMW 145
           PDM+EDERL LTQ    LL+    M+
Sbjct: 73  PDMTEDERLTLTQKYEELLVAGGAMY 98

Binds together with S18 to 16S ribosomal RNA.

Spinacia oleracea (taxid: 3562)

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	187
297836915	211	ribosomal protein S6 family protein [Ara	0.652	0.578	0.593	4e-30
15217660	207	30S ribosomal protein S6 alpha [Arabidop	0.625	0.565	0.608	1e-29
6633831	231	F1N19.8 [Arabidopsis thaliana]	0.625	0.506	0.608	2e-29
351720783	214	uncharacterized protein LOC100500072 [Gl	0.748	0.654	0.556	7e-28
255555639	205	structural constituent of ribosome, puta	0.614	0.560	0.541	2e-27
351727673	214	uncharacterized protein LOC100305490 [Gl	0.582	0.509	0.608	2e-27
224053759	184	predicted protein [Populus trichocarpa]	0.609	0.619	0.608	4e-27
225426247	199	PREDICTED: 30S ribosomal protein S6 alph	0.582	0.547	0.591	3e-25
388511881	209	unknown [Lotus japonicus]	0.711	0.636	0.580	4e-25
449518755	222	PREDICTED: 30S ribosomal protein S6 alph	0.620	0.522	0.536	3e-24

>gi|297836915|ref|XP_002886339.1| ribosomal protein S6 family protein [Arabidopsis lyrata subsp. lyrata] gi|297332180|gb|EFH62598.1| ribosomal protein S6 family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 76/128 (59%), Positives = 89/128 (69%), Gaps = 6/128 (4%)

Query: 23  LSQLPSSPLFSFARSLKTFRTNAKSL---LLHKKNSNSVSLTVKAQTLDFSGSFFEGGGF 79
           L  + S PL SF+ SL+ F + +K +   L  ++  +     VK+Q LDFSG+FFEGG F
Sbjct: 16  LPNVSSQPLLSFSHSLRPFISKSKPICASLQQQQKRDGSQFVVKSQALDFSGTFFEGG-F 74

Query: 80  GSDDDPTSVPPGSVGTATAIEDKEEPQCPPGLRQYETMMVLRPDMSEDERLALTQNCLLL 139
           GSDDDPTS PPGS G +TA+EDK EPQCPPGLRQYETM VLRPDMSEDERL LTQ    L
Sbjct: 75  GSDDDPTS-PPGS-GVSTALEDKPEPQCPPGLRQYETMAVLRPDMSEDERLGLTQKYEEL 132

Query: 140 GVACMWRY 147
            VA    Y
Sbjct: 133 LVAGGGMY 140

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15217660|ref|NP_176632.1| 30S ribosomal protein S6 alpha [Arabidopsis thaliana] gi|75161441|sp|Q8VY91.1|RR6_ARATH RecName: Full=30S ribosomal protein S6 alpha, chloroplastic; Flags: Precursor gi|18252237|gb|AAL61951.1| plastid ribosomal protein S6, putative [Arabidopsis thaliana] gi|21386993|gb|AAM47900.1| plastid ribosomal protein S6, putative [Arabidopsis thaliana] gi|21553658|gb|AAM62751.1| plastid ribosomal protein S6, putative [Arabidopsis thaliana] gi|332196127|gb|AEE34248.1| 30S ribosomal protein S6 alpha [Arabidopsis thaliana]

 Score =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 73/120 (60%), Positives = 85/120 (70%), Gaps = 3/120 (2%)

Query: 23  LSQLPSSPLFSFARSLKTFRTNAKSLLLHKKNSNSVSLTVKAQTLDFSGSFFEGGGFGSD 82
           L  + S PL SF+ SL+ F + +K +    +  +     VK+Q LDFSG+FFEGG FGSD
Sbjct: 15  LPNVSSQPLLSFSHSLRPFISKSKPMCASIQKRDGSQFVVKSQALDFSGTFFEGG-FGSD 73

Query: 83  DDPTSVPPGSVGTATAIEDKEEPQCPPGLRQYETMMVLRPDMSEDERLALTQNCLLLGVA 142
           DDPTS P GS G +TA+EDK EPQCPPGLRQYETM VLRPDMSEDERL LTQ    L VA
Sbjct: 74  DDPTS-PSGS-GVSTALEDKPEPQCPPGLRQYETMAVLRPDMSEDERLGLTQKYEELLVA 131

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|6633831|gb|AAF19690.1|AC009519_24 F1N19.8 [Arabidopsis thaliana]

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 73/120 (60%), Positives = 85/120 (70%), Gaps = 3/120 (2%)

Query: 23  LSQLPSSPLFSFARSLKTFRTNAKSLLLHKKNSNSVSLTVKAQTLDFSGSFFEGGGFGSD 82
           L  + S PL SF+ SL+ F + +K +    +  +     VK+Q LDFSG+FFEGG FGSD
Sbjct: 39  LPNVSSQPLLSFSHSLRPFISKSKPMCASIQKRDGSQFVVKSQALDFSGTFFEGG-FGSD 97

Query: 83  DDPTSVPPGSVGTATAIEDKEEPQCPPGLRQYETMMVLRPDMSEDERLALTQNCLLLGVA 142
           DDPTS P GS G +TA+EDK EPQCPPGLRQYETM VLRPDMSEDERL LTQ    L VA
Sbjct: 98  DDPTS-PSGS-GVSTALEDKPEPQCPPGLRQYETMAVLRPDMSEDERLGLTQKYEELLVA 155

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351720783|ref|NP_001236420.1| uncharacterized protein LOC100500072 [Glycine max] gi|255628961|gb|ACU14825.1| unknown [Glycine max]

 Score =  129 bits (323), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 84/151 (55%), Positives = 99/151 (65%), Gaps = 11/151 (7%)

Query: 1   MASSSLTSALTSQSKSPFYPQQLSQ----LPSSPLFSFARSLKTFRTNAKSLLLHKKNSN 56
           MASSSLTS   S S S   P   S+      SSP+ +F+R+ KT    ++    H K  N
Sbjct: 1   MASSSLTSVPLSSS-SLNIPHSSSKASASFVSSPIGAFSRTPKTLFAESR-FHFHPKR-N 57

Query: 57  SVSLTVKAQTLDFSGSFFEGGGFGSDDDPTSVPPGSVGTATAIEDKEEPQCPPGLRQYET 116
               +++AQTLDFS SFFEGG FGS+D P+S  PG  G  TA+E+KEEPQCPPGLRQYET
Sbjct: 58  DYGFSIRAQTLDFSDSFFEGG-FGSEDVPSS--PGGPG-FTAVEEKEEPQCPPGLRQYET 113

Query: 117 MMVLRPDMSEDERLALTQNCLLLGVACMWRY 147
           MMVLRPDMSEDERLALTQ    + VA    Y
Sbjct: 114 MMVLRPDMSEDERLALTQKYEEVLVAGGGMY 144

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255555639|ref|XP_002518855.1| structural constituent of ribosome, putative [Ricinus communis] gi|223541842|gb|EEF43388.1| structural constituent of ribosome, putative [Ricinus communis]

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 72/133 (54%), Positives = 85/133 (63%), Gaps = 18/133 (13%)

Query: 11  TSQSKSPFYPQQLSQLPSSPLFSFARSLKTFRTNAKSLLLHKKNSNSVSLTVKAQTLDFS 70
           T  + SP  P+  S+ P  P  SFA ++K             K  +  SLT+K+Q LDFS
Sbjct: 15  TVINSSPLCPKLFSKFPCFPSLSFAHTIK-------------KRHSVRSLTIKSQALDFS 61

Query: 71  GSFFEGGGFGSDDDPTSVPPGSVGTA-TAIEDKEEPQCPPGLRQYETMMVLRPDMSEDER 129
           GSF+EG GFGS++DP    P   G+  TA+EDKE PQCPPGLRQYETM VLRPDMSEDER
Sbjct: 62  GSFYEGSGFGSEEDP----PTLTGSGMTAVEDKEPPQCPPGLRQYETMAVLRPDMSEDER 117

Query: 130 LALTQNCLLLGVA 142
           LALTQ    L VA
Sbjct: 118 LALTQKYEELLVA 130

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351727673|ref|NP_001236145.1| uncharacterized protein LOC100305490 [Glycine max] gi|255625673|gb|ACU13181.1| unknown [Glycine max]

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 70/115 (60%), Positives = 83/115 (72%), Gaps = 6/115 (5%)

Query: 33  SFARSLKTFRTNAKSLLLHKKNSNSVSLTVKAQTLDFSGSFFEGGGFGSDDDPTSVPPGS 92
           +F+R+ KT    +KS    K+N +  S  ++AQTLDFS SFFEGG FGS+DDP+S  PG 
Sbjct: 36  AFSRTPKTLFAESKSHFYPKRNDHGFS--IRAQTLDFSDSFFEGG-FGSEDDPSS--PGG 90

Query: 93  VGTATAIEDKEEPQCPPGLRQYETMMVLRPDMSEDERLALTQNCLLLGVACMWRY 147
            G  T +E+KEEPQCPPGLRQYETMMVLRPDMSEDERLALTQ    + VA    Y
Sbjct: 91  PG-FTGVEEKEEPQCPPGLRQYETMMVLRPDMSEDERLALTQKYEEVLVAGGGMY 144

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224053759|ref|XP_002297965.1| predicted protein [Populus trichocarpa] gi|222845223|gb|EEE82770.1| predicted protein [Populus trichocarpa]

 Score =  126 bits (317), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 73/120 (60%), Positives = 88/120 (73%), Gaps = 6/120 (5%)

Query: 28  SSPLFSFARSLKTFRTNAKSLLLHKKNSNSVSLTVKAQTLDFSGSFFEGGGFGSDDDPTS 87
           S PL SF+++LK F   +K  L+++ +SN  +  VKAQT+DF+GSF+EGG  GSDD+P S
Sbjct: 1   SLPLLSFSQTLKPFPNTSK--LVYRAHSNPTT-AVKAQTVDFAGSFYEGG-IGSDDEPGS 56

Query: 88  VPPGSVGTATAIEDKEEPQCPPGLRQYETMMVLRPDMSEDERLALTQNCLLLGVACMWRY 147
            P GS GT TA+E+KE P CPPGLRQYETM VLRPDMSEDERLALTQ    L VA    Y
Sbjct: 57  -PIGS-GTMTAVEEKETPPCPPGLRQYETMAVLRPDMSEDERLALTQKYEELLVAGGGMY 114

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225426247|ref|XP_002264340.1| PREDICTED: 30S ribosomal protein S6 alpha, chloroplastic [Vitis vinifera]

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 71/120 (59%), Positives = 82/120 (68%), Gaps = 11/120 (9%)

Query: 28  SSPLFSFARSLKTFRTNAKSLLLHKKNSNSVSLTVKAQTLDFSGSFFEGGGFGSDDDPTS 87
           S P+ SF     T  +  +  + H + +    L+++A TLDFSGSFFEGG FGSDDDP S
Sbjct: 21  SPPITSF-----TVFSGKQRFIYHPRRAPG--LSIRALTLDFSGSFFEGG-FGSDDDPNS 72

Query: 88  VPPGSVGTATAIEDKEEPQCPPGLRQYETMMVLRPDMSEDERLALTQNCLLLGVACMWRY 147
            PPG  G A A+EDK+EPQCPPGLRQYETM VLRPDMSEDERLALTQ    L VA    Y
Sbjct: 73  -PPGP-GIA-AVEDKDEPQCPPGLRQYETMAVLRPDMSEDERLALTQKYEELLVAGGGMY 129

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388511881|gb|AFK44002.1| unknown [Lotus japonicus]

 Score =  119 bits (299), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 83/143 (58%), Positives = 93/143 (65%), Gaps = 10/143 (6%)

Query: 1   MASSSLTSA-LTSQSKSPFYPQQLSQLPSSPLFSFARSLKTFRTNAKSLLLHKKNSNSVS 59
           MAS+SL S  LTS S +   P   S  PS+   S  R+ K     +KS    KKN +SV 
Sbjct: 1   MASTSLNSIPLTSSSLN--IPHCYSIPPSTFFSSPIRAFKPLFAESKSHCYQKKN-DSV- 56

Query: 60  LTVKAQTLDFSGSFFEGGGFGSDDDPTSVPPGSVGTATAIEDKEEPQCPPGLRQYETMMV 119
           L+VKAQTLDF+ SFFEGG  GS+DD  S   G     TA E+KEEPQCPPGLRQYETM V
Sbjct: 57  LSVKAQTLDFTDSFFEGG-LGSEDDLNSSGTG----LTATEEKEEPQCPPGLRQYETMAV 111

Query: 120 LRPDMSEDERLALTQNCLLLGVA 142
           LRPDMSEDERLALTQ    L VA
Sbjct: 112 LRPDMSEDERLALTQKYEELLVA 134

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449518755|ref|XP_004166401.1| PREDICTED: 30S ribosomal protein S6 alpha, chloroplastic-like [Cucumis sativus]

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 66/123 (53%), Positives = 86/123 (69%), Gaps = 7/123 (5%)

Query: 58  VSLTVKAQTLDFSGSFFEGGGFGSDDDPTSVPPGSVGTATAIEDKEEPQCPPGLRQYETM 117
           + L+VKAQTL+FSGSFFEGG  GS D+P + PPG+ G ATA+E+KEEPQCPPGLR+YE+M
Sbjct: 54  LGLSVKAQTLEFSGSFFEGG-LGSQDEPPA-PPGT-GFATALEEKEEPQCPPGLRKYESM 110

Query: 118 MVLRPDMSEDERLALTQN---CLLLGVACMWRYSIEGLFHWPTASGRETKLGSPTLTWMV 174
           +VLRPDMSEDERLA T+     L+ G A       +GL     +  ++ K G  T T++ 
Sbjct: 111 VVLRPDMSEDERLAFTEKYEELLVAGGAMYVEVFNKGLIPLAYSIKKKNKAGE-TNTYLD 169

Query: 175 SIS 177
            I+
Sbjct: 170 GIN 172

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	187
TAIR|locus:2019489	207	AT1G64510 [Arabidopsis thalian	0.518	0.468	0.49	2e-17

TAIR|locus:2019489 AT1G64510 [Arabidopsis thaliana (taxid:3702)]

 Score = 213 (80.0 bits), Expect = 2.0e-17, P = 2.0e-17
 Identities = 49/100 (49%), Positives = 59/100 (59%)

Query:    35 ARSLKTFRTNAKSLLLHKKNSNSVSLTVKAQTLXXXXXXXXXXXXXXXXXPTSVPPGSVG 94
             + SL+ F + +K +    +  +     VK+Q L                 PTS P GS G
Sbjct:    27 SHSLRPFISKSKPMCASIQKRDGSQFVVKSQALDFSGTFFEGGFGSDDD-PTS-PSGS-G 83

Query:    95 TATAIEDKEEPQCPPGLRQYETMMVLRPDMSEDERLALTQ 134
              +TA+EDK EPQCPPGLRQYETM VLRPDMSEDERL LTQ
Sbjct:    84 VSTALEDKPEPQCPPGLRQYETMAVLRPDMSEDERLGLTQ 123


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        0.313   0.126   0.372    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      187       137   0.00091  102 3  11 23  0.46    31
                                                     30  0.45    33


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:  1
  No. of states in DFA:  585 (62 KB)
  Total size of DFA:  134 KB (2083 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:  13.67u 0.09s 13.76t   Elapsed:  00:00:02
  Total cpu time:  13.67u 0.09s 13.76t   Elapsed:  00:00:02
  Start:  Thu May  9 20:06:29 2013   End:  Thu May  9 20:06:31 2013

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

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0019843 "rRNA binding" evidence=IEA

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0010027 "thylakoid membrane organization" 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

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	fgenesh2_kg.2__26__AT1G64510.1	annotation not avaliable (211 aa)
		(Arabidopsis lyrata)
Predicted Functional Partners:
	fgenesh2_kg.4__1881__AT2G38140.1	annotation not avaliable (114 aa)				•			•		0.712
	fgenesh2_kg.2__2411__AT1G79850.1	annotation not avaliable (148 aa)				•			•		0.563
	fgenesh2_kg.5__880__AT3G44890.1	annotation not avaliable (197 aa)	•			•			•		0.553
	fgenesh2_kg.4__326__AT2G24090.1	annotation not avaliable (140 aa)				•			•		0.503
	scaffold_202477.1	annotation not avaliable (145 aa)				•			•		0.484
	fgenesh2_kg.1__3067__AT1G29070.1	annotation not avaliable (159 aa)				•					0.478
	scaffold_301763.1	annotation not avaliable (197 aa)				•					0.470
	fgenesh2_kg.6__1467__AT5G14910.1	annotation not avaliable (178 aa)				•					0.468
	fgenesh2_kg.7__1761__AT4G25080.3	annotation not avaliable (312 aa)				•					0.461
	fgenesh2_kg.4__2681__AT2G44920.2	annotation not avaliable (226 aa)				•					0.461

---

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	187
pfam01250	92	pfam01250, Ribosomal_S6, Ribosomal protein S6	5e-06
PRK00453	108	PRK00453, rpsF, 30S ribosomal protein S6; Reviewed	6e-04

>gnl|CDD|216388 pfam01250, Ribosomal_S6, Ribosomal protein S6

 Score = 42.9 bits (102), Expect = 5e-06
 Identities = 14/24 (58%), Positives = 19/24 (79%)

Query: 112 RQYETMMVLRPDMSEDERLALTQN 135
           R+YETM +LRPD+SE+E  AL + 
Sbjct: 1   RKYETMFILRPDLSEEEVKALIEK 24

Length = 92

>gnl|CDD|179034 PRK00453, rpsF, 30S ribosomal protein S6; Reviewed

 Score = 37.5 bits (88), Expect = 6e-04
 Identities = 11/21 (52%), Positives = 17/21 (80%)

Query: 112 RQYETMMVLRPDMSEDERLAL 132
           R+YE + +LRPD+SE++  AL
Sbjct: 2   RKYEIVFILRPDLSEEQVKAL 22

Length = 108

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	187
CHL00123	97	rps6 ribosomal protein S6; Validated	98.98
COG0360	112	RpsF Ribosomal protein S6 [Translation, ribosomal	98.71
PRK00453	108	rpsF 30S ribosomal protein S6; Reviewed	98.69
PF01250	92	Ribosomal_S6: Ribosomal protein S6; InterPro: IPR0	98.48
TIGR00166	93	S6 ribosomal protein S6. MRP17 protein is a compon	98.46
PRK14074	257	rpsF 30S ribosomal protein S6; Provisional	94.69

>CHL00123 rps6 ribosomal protein S6; Validated

Probab=98.98  E-value=1.6e-10  Score=85.24  Aligned_cols=38  Identities=37%  Similarity=0.497  Sum_probs=36.0

Q ss_pred             cccceeEEEEecCCCCHHHHHhhhccE--EEEeCCeEEEE
Q 029831          110 GLRQYETMMVLRPDMSEDERLALTQNC--LLLGVACMWRY  147 (187)
Q Consensus       110 GMRKYETMfILRPDLEEEAr~AlVEKF--IIe~nGGEIv~  147 (187)
                      .||+||+|||++|+++||+++++++++  +|+++||+|+.
T Consensus         4 ~mr~YE~~~Il~p~l~e~~~~~~~~~~~~~i~~~gg~i~~   43 (97)
T CHL00123          4 KLNKYETMYLLKPDLNEEELLKWIENYKKLLRKRGAKNIS   43 (97)
T ss_pred             cccceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEE
Confidence            599999999999999999999999999  99999998865

>COG0360 RpsF Ribosomal protein S6 [Translation, ribosomal structure and biogenesis]

Probab=98.71  E-value=5.2e-09  Score=80.81  Aligned_cols=36  Identities=31%  Similarity=0.521  Sum_probs=33.7

Q ss_pred             cceeEEEEecCCCCHHHHHhhhccE--EEEeCCeEEEE
Q 029831          112 RQYETMMVLRPDMSEDERLALTQNC--LLLGVACMWRY  147 (187)
Q Consensus       112 RKYETMfILRPDLEEEAr~AlVEKF--IIe~nGGEIv~  147 (187)
                      |+||+|||++||++||++++++|||  +|+++||+|+.
T Consensus         1 ~~YEi~~iv~p~~see~~~~~ve~~~~~l~~~gg~i~~   38 (112)
T COG0360           1 RKYEIVFIVRPDLSEEQVAALVEKYKGVLTNNGGEIHK   38 (112)
T ss_pred             CceEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEE
Confidence            6899999999999999999999999  99999998864

>PRK00453 rpsF 30S ribosomal protein S6; Reviewed

Probab=98.69  E-value=6.6e-09  Score=76.55  Aligned_cols=37  Identities=30%  Similarity=0.528  Sum_probs=34.8

Q ss_pred             ccceeEEEEecCCCCHHHHHhhhccE--EEEeCCeEEEE
Q 029831          111 LRQYETMMVLRPDMSEDERLALTQNC--LLLGVACMWRY  147 (187)
Q Consensus       111 MRKYETMfILRPDLEEEAr~AlVEKF--IIe~nGGEIv~  147 (187)
                      ||+||+|||++|+++||+++++++++  +|.++||+|..
T Consensus         1 M~~YE~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~i~~   39 (108)
T PRK00453          1 MRKYEIVFILRPDLSEEQVKALVERFKGVITENGGTIHK   39 (108)
T ss_pred             CCceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEE
Confidence            89999999999999999999999999  99999998754

>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.48  E-value=4.4e-08  Score=69.49  Aligned_cols=68  Identities=26%  Similarity=0.464  Sum_probs=44.8

Q ss_pred             cceeEEEEecCCCCHHHHHhhhccE--EEEeCCeEEEEeee--ceeeccCCCCcccccCCCceEEEEEeecCCCCcC
Q 029831          112 RQYETMMVLRPDMSEDERLALTQNC--LLLGVACMWRYSIE--GLFHWPTASGRETKLGSPTLTWMVSISSSPTSLN  184 (187)
Q Consensus       112 RKYETMfILRPDLEEEAr~AlVEKF--IIe~nGGEIv~~ie--g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  184 (187)
                      |+||+|+|++|+++||+.+++++++  +|.++||+|. .+|  |.=.-|..-.+-    .--.-+++.+..+|..++
T Consensus         1 r~YE~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~v~-~~~~~G~r~LaY~i~k~----~~G~Y~~~~f~~~~~~i~   72 (92)
T PF01250_consen    1 RKYELMFILRPDLSEEEIKKLIERVKKIIEKNGGVVR-SVENWGKRRLAYPIKKQ----KEGHYFLFNFDASPSAIK   72 (92)
T ss_dssp             EEEEEEEEE-TTSCHHHHHHHHHHHHHHHHHTTEEEE-EEEEEEEEEESSEETTE----CEEEEEEEEEEESTTHHH
T ss_pred             CceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEE-EEEEEeecccccCCCCC----CEEEEEEEEEEeCHHHHH
Confidence            7999999999999999999999999  9999999664 343  222222111111    222345666677666543

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....

>TIGR00166 S6 ribosomal protein S6

Probab=98.46  E-value=5.4e-08  Score=70.07  Aligned_cols=35  Identities=20%  Similarity=0.323  Sum_probs=32.0

Q ss_pred             cceeEEEEecCCCCHHHHHhhhccE--EEEeCCeEEEE
Q 029831          112 RQYETMMVLRPDMSEDERLALTQNC--LLLGVACMWRY  147 (187)
Q Consensus       112 RKYETMfILRPDLEEEAr~AlVEKF--IIe~nGGEIv~  147 (187)
                      |+||+|||++|+++|| ++++++++  +|.++||+|..
T Consensus         1 ~~YE~~~Il~p~~~~~-~~~~~~~~~~~i~~~gg~i~~   37 (93)
T TIGR00166         1 RHYEIIFLVRPTLSEE-VKGQIERYKKVITLNGAEIVR   37 (93)
T ss_pred             CceeEEEEECCCCcHH-HHHHHHHHHHHHHhCCCEEEE
Confidence            6899999999999999 99999999  89999997754

MRP17 protein is a component of the small ribosomal subunit in mitochondria, and is shown here to be an ortholog of S6.

>PRK14074 rpsF 30S ribosomal protein S6; Provisional

Probab=94.69  E-value=0.011  Score=52.29  Aligned_cols=38  Identities=16%  Similarity=0.260  Sum_probs=35.5

Q ss_pred             ccceeEEEEecCCCCHHHHHhhhccE--EEEeCCeEEEEe
Q 029831          111 LRQYETMMVLRPDMSEDERLALTQNC--LLLGVACMWRYS  148 (187)
Q Consensus       111 MRKYETMfILRPDLEEEAr~AlVEKF--IIe~nGGEIv~~  148 (187)
                      |..||-+||.|+||..-+..+++|.|  +|.++||.++..
T Consensus         1 m~lYE~~fIa~q~ls~~q~e~l~e~~~~~l~~~~~~v~~~   40 (257)
T PRK14074          1 MNLYEFTFIAQQGLLQQEVEEMVQELAVLLKNIKADVMFQ   40 (257)
T ss_pred             CCccceeeeecccccHHHHHHHHHHHHHHHHhcCCeeehh
Confidence            78999999999999999999999999  999999988753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	187
3bbn_F	168	Homology Model For The Spinach Chloroplast 30s Subu		6e-15

>pdb|3BBN|F Chain F, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 168

Iteration: 1
 Score = 77.0 bits (188), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 38/63 (60%), Positives = 44/63 (69%), Gaps = 6/63 (9%)
Query: 85  PTSVPPGSVGTATAIEDKEEPQCPPGLRQYETMMVLRPDMSEDERLALTQNC--LLLGVA 142
           P S PP  +    A+E+K EPQCPPGLRQYETM VLRPDM+EDERL LTQ    LL+   
Sbjct: 40  PPSTPPAGL----AVEEKPEPQCPPGLRQYETMAVLRPDMTEDERLTLTQKYEELLVAGG 95
Query: 143 CMW 145
            M+
Sbjct: 96  AMY 98
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	187
3bbn_F	168	Ribosomal protein S6; small ribosomal subunit, spi	3e-21
3r3t_A	99	30S ribosomal protein S6; structural genomics, cen	3e-04
1cqm_A	101	Ribosomal protein S6; alzheimer disease, oligomeri	3e-04
1vmb_A	140	30S ribosomal protein S6; TM0603, structural genom	3e-04
2j5a_A	110	30S ribosomal protein S6; ribonucleoprotein, RIBO	5e-04

>3bbn_F Ribosomal protein S6; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 168

 Score = 84.6 bits (209), Expect = 3e-21
 Identities = 55/84 (65%), Positives = 60/84 (71%), Gaps = 5/84 (5%)

Query: 51  HKKNSNSVSLTVKAQTLDFSGSFFEGGGFGSDDDPTSVPPGSVGTATAIEDKEEPQCPPG 110
           H   SN     VKA  LDFSGSFFEGG  G D+DP S PP  +    A+E+K EPQCPPG
Sbjct: 7   HHYLSNY-GPYVKAIALDFSGSFFEGGFGGLDEDPPSTPPAGL----AVEEKPEPQCPPG 61

Query: 111 LRQYETMMVLRPDMSEDERLALTQ 134
           LRQYETM VLRPDM+EDERL LTQ
Sbjct: 62  LRQYETMAVLRPDMTEDERLTLTQ 85

>3r3t_A 30S ribosomal protein S6; structural genomics, center for structural genomics of infec diseases, csgid, beta-barrel, cytosol; 2.30A {Bacillus anthracis} Length = 99

 Score = 37.6 bits (88), Expect = 3e-04
 Identities = 9/21 (42%), Positives = 15/21 (71%)

Query: 112 RQYETMMVLRPDMSEDERLAL 132
           R+YE M ++RP + E+ + AL
Sbjct: 5   RKYEIMYIIRPGVEEEAQKAL 25

>1cqm_A Ribosomal protein S6; alzheimer disease, oligomerization; 1.65A {Thermus thermophilus} SCOP: d.58.14.1 PDB: 1cqn_A 1qjh_A 1ris_A 1fka_F 1gix_I* 1hnw_F* 1hnx_F* 1hnz_F* 1hr0_F 1i94_F* 1i95_F* 1i96_F* 1i97_F* 1ibk_F* 1ibl_F* 1ibm_F 1j5e_F 1jgo_I* 1jgp_I* 1jgq_I* ... Length = 101

 Score = 37.6 bits (88), Expect = 3e-04
 Identities = 6/21 (28%), Positives = 12/21 (57%)

Query: 112 RQYETMMVLRPDMSEDERLAL 132
           R+YE  +VL P++ + +    
Sbjct: 2   RRYEVNIVLNPNLDQSQLALE 22

>1vmb_A 30S ribosomal protein S6; TM0603, structural genomics, JCSG, structure initiative, PSI, joint center for structural GENO translation; 1.70A {Thermotoga maritima} SCOP: d.58.14.1 Length = 140

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 9/21 (42%), Positives = 15/21 (71%)

Query: 112 RQYETMMVLRPDMSEDERLAL 132
           R YE+M ++ P++ E+ER  L
Sbjct: 19  RIYESMFIIAPNVPEEERENL 39

>2j5a_A 30S ribosomal protein S6; ribonucleoprotein, RIBO protein S6, RNA-binding, rRNA-binding, protein folding; 2.3A {Aquifex aeolicus} SCOP: d.58.14.1 Length = 110

 Score = 36.8 bits (86), Expect = 5e-04
 Identities = 8/23 (34%), Positives = 14/23 (60%)

Query: 112 RQYETMMVLRPDMSEDERLALTQ 134
           R YET+  ++P +SE+E     +
Sbjct: 8   RYYETVFAVKPTLSEEEMKKKFE 30

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	187
3bbn_F	168	Ribosomal protein S6; small ribosomal subunit, spi	99.97
3zzp_A	77	TS9, ribosomal protein S6; protein folding, RNA-bi	99.09
1vmb_A	140	30S ribosomal protein S6; TM0603, structural genom	99.05
1cqm_A	101	Ribosomal protein S6; alzheimer disease, oligomeri	99.04
2kjw_A	96	TS9, 30S ribosomal protein S6; S6 permutant, solut	99.02
2j5a_A	110	30S ribosomal protein S6; ribonucleoprotein, RIBO	99.0
3r3t_A	99	30S ribosomal protein S6; structural genomics, cen	98.94
3r8n_F	100	30S ribosomal protein S6; protein biosynthesis, RN	98.78
3i1m_F	135	30S ribosomal protein S6; ribosome structure, prot	98.69
1rbl_M	109	Ribulose 1,5 bisphosphate carboxylase/oxygenase (	87.49

>3bbn_F Ribosomal protein S6; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=99.97  E-value=8.8e-33  Score=223.14  Aligned_cols=87  Identities=64%  Similarity=1.051  Sum_probs=35.1

Q ss_pred             CceeeeEeeeeeecccceeccCCCCC-CCCCCCCCCCCCcccccccccCCCCCCccccceeEEEEecCCCCHHHHHhhhc
Q 029831           56 NSVSLTVKAQTLDFSGSFFEGGGFGS-DDDPTSVPPGSVGTATAIEDKEEPQCPPGLRQYETMMVLRPDMSEDERLALTQ  134 (187)
Q Consensus        56 ~~~~~~vk~~~ldf~gsffeg~g~gs-~~d~~s~~p~g~g~~~~~~~~~~~~~P~GMRKYETMfILRPDLEEEAr~AlVE  134 (187)
                      +..+++||+|+|||+|+|||| |||+ ||||++++  |+|  +|++++|.+|||+|||+||+||||+|+++||+++++++
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~--~~~--~~~~~~~~~~~~~~Mr~YE~m~IlrPdl~eeev~alve   85 (168)
T 3bbn_F           11 SNYGPYVKAIALDFSGSFFEG-GFGGLDEDPPSTP--PAG--LAVEEKPEPQCPPGLRQYETMAVLRPDMTEDERLTLTQ   85 (168)
T ss_dssp             --------------------------------------------------------CEEEEEEEEECTTSCHHHHHSTTH
T ss_pred             ccCcceeeeeeeccccceeec-cCCCcccCCCCCC--CCC--ccccccccccCCCCCCceeEEEEECCCCCHHHHHHHHH
Confidence            456899999999999999999 9999 99999988  666  89999999999999999999999999999999999999


Q ss_pred             cE--EEEeCCeEEEE
Q 029831          135 NC--LLLGVACMWRY  147 (187)
Q Consensus       135 KF--IIe~nGGEIv~  147 (187)
                      ||  +|+++||+|+.
T Consensus        86 r~~~iI~~~GG~I~~  100 (168)
T 3bbn_F           86 KYEELLVAGGAMYVE  100 (168)
T ss_dssp             HHHHHHTTTSCEEEE
T ss_pred             HHHHHHHHCCCEEEE
Confidence            99  99999997764

>3zzp_A TS9, ribosomal protein S6; protein folding, RNA-binding; 0.96A {Thermus thermophilus}

Probab=99.09  E-value=1.1e-11  Score=88.26  Aligned_cols=35  Identities=17%  Similarity=0.239  Sum_probs=32.7

Q ss_pred             ccccceeEEEEecCCCCHHHHHhhhccE--EEEeCCe
Q 029831          109 PGLRQYETMMVLRPDMSEDERLALTQNC--LLLGVAC  143 (187)
Q Consensus       109 ~GMRKYETMfILRPDLEEEAr~AlVEKF--IIe~nGG  143 (187)
                      ..+|+||+||||+|+|+||++++++|||  +|+++||
T Consensus        41 d~~r~YE~m~Il~P~l~ee~~~~~vek~~~~i~~~Gg   77 (77)
T 3zzp_A           41 TTPGRYEVNIVLNPNLDQSQLQNEKEIIQRALENYGA   77 (77)
T ss_dssp             SSTTEEEEEEEECTTCCHHHHHHHHHHHHHHHHHHTC
T ss_pred             cCCCceEEEEEECCCCCHHHHHHHHHHHHHHHHhcCC
Confidence            4579999999999999999999999999  9998887

>1vmb_A 30S ribosomal protein S6; TM0603, structural genomics, JCSG, structure initiative, PSI, joint center for structural GENO translation; 1.70A {Thermotoga maritima} SCOP: d.58.14.1

Probab=99.05  E-value=3.1e-11  Score=94.04  Aligned_cols=41  Identities=22%  Similarity=0.335  Sum_probs=35.4

Q ss_pred             CCCccccceeEEEEecCCCCHHHHHhhhccE--EEEeC-CeEEE
Q 029831          106 QCPPGLRQYETMMVLRPDMSEDERLALTQNC--LLLGV-ACMWR  146 (187)
Q Consensus       106 ~~P~GMRKYETMfILRPDLEEEAr~AlVEKF--IIe~n-GGEIv  146 (187)
                      --|.+||+||+||||+|+|++|+++++++||  +|+++ ||+|.
T Consensus        13 ~~~~~Mr~YE~~~Il~P~l~ee~v~~~ve~~~~~I~~~~GG~I~   56 (140)
T 1vmb_A           13 MAYVKERIYESMFIIAPNVPEEERENLVERVKKIIEERVKGKID   56 (140)
T ss_dssp             ----CCEEEEEEEEECTTSCHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             ccccccccceEEEEECCCCCHHHHHHHHHHHHHHHHhcCCCEEE
Confidence            3578899999999999999999999999999  99999 99775

>1cqm_A Ribosomal protein S6; alzheimer disease, oligomerization; 1.65A {Thermus thermophilus} SCOP: d.58.14.1 PDB: 1cqn_A 1qjh_A 1ris_A 1fka_F 1gix_I* 1hnw_F* 1hnx_F* 1hnz_F* 1hr0_F 1i94_F* 1i95_F* 1i96_F* 1i97_F* 1ibk_F* 1ibl_F* 1ibm_F 1j5e_F 1jgo_I* 1jgp_I* 1jgq_I* ...

Probab=99.04  E-value=3.3e-11  Score=87.58  Aligned_cols=36  Identities=19%  Similarity=0.301  Sum_probs=34.4

Q ss_pred             ccceeEEEEecCCCCHHHHHhhhccE--EEEeCCeEEE
Q 029831          111 LRQYETMMVLRPDMSEDERLALTQNC--LLLGVACMWR  146 (187)
Q Consensus       111 MRKYETMfILRPDLEEEAr~AlVEKF--IIe~nGGEIv  146 (187)
                      ||+||+|||++|++++|++++++++|  +|+++||+|.
T Consensus         1 M~~YE~~~Il~p~l~~e~~~~~~~~~~~~i~~~gg~i~   38 (101)
T 1cqm_A            1 MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVE   38 (101)
T ss_dssp             CEEEEEEEEECTTCCHHHHHHHHHHHHHHHHHTTCEEE
T ss_pred             CCceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEE
Confidence            99999999999999999999999999  9999999775

>2kjw_A TS9, 30S ribosomal protein S6; S6 permutant, solution structure, backbone dynamics, folding, ribonucleoprotein, RNA-binding, rRNA-binding; NMR {Thermus thermophilus}

Probab=99.02  E-value=2.3e-11  Score=89.98  Aligned_cols=36  Identities=17%  Similarity=0.201  Sum_probs=34.6

Q ss_pred             ccceeEEEEecCCCCHHHHHhhhccE--EEEeCCeEEE
Q 029831          111 LRQYETMMVLRPDMSEDERLALTQNC--LLLGVACMWR  146 (187)
Q Consensus       111 MRKYETMfILRPDLEEEAr~AlVEKF--IIe~nGGEIv  146 (187)
                      ||+||+|||++||++||+++++++||  +|+++||+|.
T Consensus        43 Mr~YE~m~Il~P~l~ee~~~~~ve~~~~iI~~~gG~i~   80 (96)
T 2kjw_A           43 PGRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVE   80 (96)
T ss_dssp             SSCEEEEEECCSSCCHHHHHHHHHHHHHHHHHHTCCCS
T ss_pred             hhhhheeeeeCCCCCHHHHHHHHHHHHHHHHhCCCEEE
Confidence            99999999999999999999999999  9999999865

>2j5a_A 30S ribosomal protein S6; ribonucleoprotein, RIBO protein S6, RNA-binding, rRNA-binding, protein folding; 2.3A {Aquifex aeolicus} SCOP: d.58.14.1

Probab=99.00  E-value=7.8e-11  Score=87.11  Aligned_cols=37  Identities=27%  Similarity=0.410  Sum_probs=34.9

Q ss_pred             ccceeEEEEecCCCCHHHHHhhhccE--EEEeCCeEEEE
Q 029831          111 LRQYETMMVLRPDMSEDERLALTQNC--LLLGVACMWRY  147 (187)
Q Consensus       111 MRKYETMfILRPDLEEEAr~AlVEKF--IIe~nGGEIv~  147 (187)
                      ||+||+|||++|+++||++++++++|  +|+++||+|..
T Consensus         7 M~~YE~~~Il~p~l~~e~~~~~v~~~~~~i~~~Gg~i~~   45 (110)
T 2j5a_A            7 LRYYETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILY   45 (110)
T ss_dssp             CEEEEEEEEECTTSCHHHHHHHHHHHHHHHHHTTEEEEE
T ss_pred             CCcceEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEE
Confidence            99999999999999999999999999  99999997754

>3r3t_A 30S ribosomal protein S6; structural genomics, center for structural genomics of infec diseases, csgid, beta-barrel, cytosol; 2.30A {Bacillus anthracis}

Probab=98.94  E-value=2.9e-11  Score=87.82  Aligned_cols=36  Identities=28%  Similarity=0.508  Sum_probs=34.4

Q ss_pred             ccceeEEEEecCCCCHHHHHhhhccE--EEEeCCeEEE
Q 029831          111 LRQYETMMVLRPDMSEDERLALTQNC--LLLGVACMWR  146 (187)
Q Consensus       111 MRKYETMfILRPDLEEEAr~AlVEKF--IIe~nGGEIv  146 (187)
                      ||+||+|||++|+++||++++++++|  +|+++||+|.
T Consensus         4 M~~YE~~~Il~p~~~~e~~~~~~~~~~~~i~~~gg~i~   41 (99)
T 3r3t_A            4 MRKYEIMYIIRPGVEEEAQKALVERFAGVLTNNGAEII   41 (99)
T ss_dssp             CCCCCCCCCCCTTSCHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             CcceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEE
Confidence            99999999999999999999999999  9999999765

>3i1m_F 30S ribosomal protein S6; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1p6g_F 1p87_F* 1vs7_F* 2avy_F 2aw7_F 1vs5_F 2i2u_F 2i2p_F* 2qan_F* 2qb9_F* 2qbb_F* 2qbd_F 2qbf_F 2qbh_F* 2qbj_F* 2qou_F* 2qow_F* 2qoy_F* 2qp0_F* 2vho_F ...

Probab=98.69  E-value=1.1e-09  Score=84.63  Aligned_cols=35  Identities=20%  Similarity=0.448  Sum_probs=33.0

Q ss_pred             ccceeEEEEecCCCCHHHHHhhhccE--EEEeCCeEEE
Q 029831          111 LRQYETMMVLRPDMSEDERLALTQNC--LLLGVACMWR  146 (187)
Q Consensus       111 MRKYETMfILRPDLEEEAr~AlVEKF--IIe~nGGEIv  146 (187)
                      ||+||+||||+|+++ |++++++++|  +|+++||+|.
T Consensus         1 Mr~YE~~~Il~P~~~-e~v~~~ve~~~~~I~~~GG~I~   37 (135)
T 3i1m_F            1 MRHYEIVFMVHPDQS-EQVPGMIERYTAAITGAEGKIH   37 (135)
T ss_dssp             CCEECBEEEECSTTT-TSHHHHHHHHHHHHHHTTCEEC
T ss_pred             CCceEEEEEECCCch-HHHHHHHHHHHHHHHHCCCEEE
Confidence            999999999999998 8999999999  9999999775

>1rbl_M Ribulose 1,5 bisphosphate carboxylase/oxygenase ( chain); lyase(carbon-carbon), lyase; HET: CAP; 2.20A {Synechococcus elongatus} SCOP: d.73.1.1 PDB: 1rsc_M*

Probab=87.49  E-value=0.12  Score=39.33  Aligned_cols=31  Identities=23%  Similarity=0.296  Sum_probs=24.7

Q ss_pred             CCCCccccceeEEEEecCCCCHHHHHhhhccE
Q 029831          105 PQCPPGLRQYETMMVLRPDMSEDERLALTQNC  136 (187)
Q Consensus       105 ~~~P~GMRKYETMfILRPDLEEEAr~AlVEKF  136 (187)
                      -|-|+|||+|||.- -=|+|+||+..+-|+-.
T Consensus         2 ~~~~~~~~~~etfS-yLP~lt~eqI~kQI~Yl   32 (109)
T 1rbl_M            2 MKTLPKERRFETFS-YLPPLSDRQIAAQIEYM   32 (109)
T ss_dssp             CCCCCCCCCCSTTT-TSSCCCHHHHHHHHHHH
T ss_pred             CccCCCcccccccc-cCCCCCHHHHHHHHHHH
Confidence            36789999999954 44779999998877765

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	187
d1vmba_	107	d.58.14.1 (A:) Ribosomal protein S6 {Thermotoga ma	2e-04
d2j5aa1	106	d.58.14.1 (A:3-108) Ribosomal protein S6 {Aquifex	6e-04
d1loua_	97	d.58.14.1 (A:) Ribosomal protein S6 {Thermus therm	7e-04

>d1vmba_ d.58.14.1 (A:) Ribosomal protein S6 {Thermotoga maritima [TaxId: 2336]} Length = 107

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Thermotoga maritima [TaxId: 2336]

 Score = 37.1 bits (86), Expect = 2e-04
 Identities = 9/24 (37%), Positives = 16/24 (66%)

Query: 112 RQYETMMVLRPDMSEDERLALTQN 135
           R YE+M ++ P++ E+ER  L + 
Sbjct: 3   RIYESMFIIAPNVPEEERENLVER 26

>d2j5aa1 d.58.14.1 (A:3-108) Ribosomal protein S6 {Aquifex aeolicus [TaxId: 63363]} Length = 106

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Aquifex aeolicus [TaxId: 63363]

 Score = 35.5 bits (82), Expect = 6e-04
 Identities = 9/25 (36%), Positives = 15/25 (60%)

Query: 111 LRQYETMMVLRPDMSEDERLALTQN 135
           LR YET+  ++P +SE+E     + 
Sbjct: 5   LRYYETVFAVKPTLSEEEMKKKFEQ 29

>d1loua_ d.58.14.1 (A:) Ribosomal protein S6 {Thermus thermophilus [TaxId: 274]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Thermus thermophilus [TaxId: 274]

 Score = 35.2 bits (81), Expect = 7e-04
 Identities = 6/24 (25%), Positives = 13/24 (54%)

Query: 112 RQYETMMVLRPDMSEDERLALTQN 135
           R+YE  +VL P++ + +     + 
Sbjct: 2   RRYEVNIVLNPNLDQSQLALEKEI 25

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	187
d1loua_	97	Ribosomal protein S6 {Thermus thermophilus [TaxId:	98.87
d2j5aa1	106	Ribosomal protein S6 {Aquifex aeolicus [TaxId: 633	98.79
d2qalf1	100	Ribosomal protein S6 {Escherichia coli [TaxId: 562	98.62
d1vmba_	107	Ribosomal protein S6 {Thermotoga maritima [TaxId:	98.6

>d1loua_ d.58.14.1 (A:) Ribosomal protein S6 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Thermus thermophilus [TaxId: 274]

Probab=98.87  E-value=1.9e-10  Score=80.53  Aligned_cols=37  Identities=16%  Similarity=0.227  Sum_probs=35.4

Q ss_pred             ccceeEEEEecCCCCHHHHHhhhccE--EEEeCCeEEEE
Q 029831          111 LRQYETMMVLRPDMSEDERLALTQNC--LLLGVACMWRY  147 (187)
Q Consensus       111 MRKYETMfILRPDLEEEAr~AlVEKF--IIe~nGGEIv~  147 (187)
                      ||+||+|||++|+++|++.+++++++  +|+++||+|+.
T Consensus         1 M~~YE~~~i~~p~l~~~~~~~~~~~~~~~i~~~gg~i~~   39 (97)
T d1loua_           1 MRRYEVNIVLNPNLDQSQLALEKEIIQRAAENYGARVEK   39 (97)
T ss_dssp             CEEEEEEEEECTTCCHHHHHHHHHHHHHHHHHTTCEEEE
T ss_pred             CCcceEEEEECCCCCHHHHHHHHHHHHHHHHhCCCEEEE
Confidence            99999999999999999999999999  99999998874

>d2j5aa1 d.58.14.1 (A:3-108) Ribosomal protein S6 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.79  E-value=5.5e-10  Score=79.63  Aligned_cols=38  Identities=26%  Similarity=0.401  Sum_probs=36.2

Q ss_pred             ccceeEEEEecCCCCHHHHHhhhccE--EEEeCCeEEEEe
Q 029831          111 LRQYETMMVLRPDMSEDERLALTQNC--LLLGVACMWRYS  148 (187)
Q Consensus       111 MRKYETMfILRPDLEEEAr~AlVEKF--IIe~nGGEIv~~  148 (187)
                      ||.||+|||++|+++|++++++++++  +|+++||+|+.-
T Consensus         5 Mr~YE~~~Il~p~l~~~~~~~~~~~~~~~i~~~gg~i~~~   44 (106)
T d2j5aa1           5 LRYYETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILYE   44 (106)
T ss_dssp             CEEEEEEEEECTTSCHHHHHHHHHHHHHHHHHTTEEEEEE
T ss_pred             cccccEEEEECCCCCHHHHHHHHHHHHHHHHHCCCeEEEE
Confidence            99999999999999999999999999  999999998863

>d2qalf1 d.58.14.1 (F:1-100) Ribosomal protein S6 {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Escherichia coli [TaxId: 562]

Probab=98.62  E-value=8.4e-10  Score=77.77  Aligned_cols=35  Identities=23%  Similarity=0.456  Sum_probs=32.5

Q ss_pred             ccceeEEEEecCCCCHHHHHhhhccE--EEEeCCeEEE
Q 029831          111 LRQYETMMVLRPDMSEDERLALTQNC--LLLGVACMWR  146 (187)
Q Consensus       111 MRKYETMfILRPDLEEEAr~AlVEKF--IIe~nGGEIv  146 (187)
                      ||+||+|||++|+++| +.+++++++  +|+++||+|+
T Consensus         1 M~~YE~~~Il~p~~~e-~~~~~~~~~~~~i~~~gg~v~   37 (100)
T d2qalf1           1 MRHYEIVFMVHPDQSE-QVPGMIERYTAAITGAEGKIH   37 (100)
T ss_dssp             CCEECEEEEECGGGTT-HHHHHHHHHHHHHHHTTCCCC
T ss_pred             CCcceEEEEECCCcHH-HHHHHHHHHHHHHHhCCCEEE
Confidence            9999999999999986 679999999  9999999876

>d1vmba_ d.58.14.1 (A:) Ribosomal protein S6 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Thermotoga maritima [TaxId: 2336]

Probab=98.60  E-value=3.9e-09  Score=75.40  Aligned_cols=37  Identities=24%  Similarity=0.410  Sum_probs=33.9

Q ss_pred             ccceeEEEEecCCCCHHHHHhhhccE--EEEeC-CeEEEE
Q 029831          111 LRQYETMMVLRPDMSEDERLALTQNC--LLLGV-ACMWRY  147 (187)
Q Consensus       111 MRKYETMfILRPDLEEEAr~AlVEKF--IIe~n-GGEIv~  147 (187)
                      ||.||+|||++|+++|++.+++++++  +|+++ ||+|..
T Consensus         2 ~R~YE~~~Il~p~l~~~~~~~~~~~~~~~i~~~~gg~i~~   41 (107)
T d1vmba_           2 ERIYESMFIIAPNVPEEERENLVERVKKIIEERVKGKIDK   41 (107)
T ss_dssp             CEEEEEEEEECTTSCHHHHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CceeEEEEEECCCCCHHHHHHHHHHHHHHHHhcCCCEEEE
Confidence            89999999999999999999999999  88775 888853