Citrus Sinensis ID: 030735

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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
MSASIFTAPVAGSGYLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTTST
Secondary Structure (PSIPRED)
cccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccEEEEcccccEEcccccccccccccEEEEccccccccccHHHHHHHHHHHHHHccccEEEEEEEEccccEEEEEEEEEcccccccc
Secondary Structure Prediction (SSPRO)
cccHHHccHcccccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccHHHHHHHHHHHHHcccEEEEEEEcccccEccccccccccEccccEEEcccccccccHHHHHHHHHHHHHHccccEEEEEEEEccccEEEEEEEEEcccccccc
Coil and Loop (DISEMBL)
msasiftapvagsgylglkptskallpvkdsiawssktvsngsktrcmktwnpinnkkfealsylpslsddsIAKEIDYMLkkgwipclefdevgyvhrenskmpgyydgrywtmwklpmfgcndsSQILNEIQECKKAYPNAYIRCLAfnnqkqgqcmsfliqkpttttst
Flexible Loop (DISEMBL)
msasiftapvagsgylglkPTSKALLPVKDSiawssktvsngsktrcmktwnpinnkkFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFliqkpttttst
Low Complexity Region (SEG)
MSASIFTAPVAGSGYLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTTST
Disordered region (IsUnstruct)
******TAPVAGSGYLGLKPTSKALLPVKDSIAWSSKTVS*GSKTRCMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLI*********
Disordered Region (DISOPRED)
*******************************************KTRCMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFL***P******
Disordered Region (DISEMBL)
MSASIFTAPVAGSGYLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTTST
Disordered Region (DISPRO)
*****************************************GSKTRCMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPT*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSASIFTAPVAGSGYLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTTST
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	172	2.2.26 [Sep-21-2011]
O64416	180	Ribulose bisphosphate car	N/A	no	0.779	0.744	0.629	2e-50
P26574	181	Ribulose bisphosphate car	N/A	no	0.866	0.823	0.580	2e-50
P26577	180	Ribulose bisphosphate car	N/A	no	0.877	0.838	0.568	4e-50
P26576	180	Ribulose bisphosphate car	N/A	no	0.877	0.838	0.568	4e-50
P32764	181	Ribulose bisphosphate car	N/A	no	0.883	0.839	0.562	5e-50
O65349	187	Ribulose bisphosphate car	N/A	no	0.906	0.834	0.550	5e-50
P16031	189	Ribulose bisphosphate car	N/A	no	0.883	0.804	0.540	8e-50
P26575	180	Ribulose bisphosphate car	N/A	no	0.877	0.838	0.562	1e-49
P07089	173	Ribulose bisphosphate car	N/A	no	0.877	0.872	0.551	2e-49
P10053	171	Ribulose bisphosphate car	N/A	no	0.895	0.900	0.522	2e-49

>sp|O64416|RBS_MARPA Ribulose bisphosphate carboxylase small chain, chloroplastic OS=Marchantia paleacea GN=RBCS PE=2 SV=1

 Score =  197 bits (502), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 85/135 (62%), Positives = 103/135 (76%), Gaps = 1/135 (0%)

Query: 34  WSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDE 93
           W +KT +NGS+  CM+ W P NN KFE LSYLP LS D++AK+IDY++K GW PC+EFD 
Sbjct: 45  WQTKTQTNGSRVSCMQVWEPYNNLKFETLSYLPPLSQDALAKQIDYVIKSGWAPCIEFDV 104

Query: 94  VGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAY-PNAYIRCLAFNN 152
            G V RE S MPGYYDGRYWTMWKLPMFGC DS+ +L EI+ECKK Y    YIRCL F+N
Sbjct: 105 QGTVTREGSTMPGYYDGRYWTMWKLPMFGCTDSASVLREIEECKKLYGKKCYIRCLGFDN 164

Query: 153 QKQGQCMSFLIQKPT 167
            +Q QC SF++ +PT
Sbjct: 165 TRQVQCASFIVHQPT 179

RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.
Marchantia paleacea (taxid: 56867)
EC: 4EC: .EC: 1EC: .EC: 1EC: .EC: 3EC: 9

>sp|P26574|RBS1_SOLTU Ribulose bisphosphate carboxylase small chain 1, chloroplastic OS=Solanum tuberosum GN=RBCS-1 PE=3 SV=1

 Score =  197 bits (502), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 90/155 (58%), Positives = 118/155 (76%), Gaps = 6/155 (3%)

Query: 15  YLGLKPTSKALLPV--KDSIAWSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDS 72
           + GLK  S A  PV  K ++  +S   SNG + RCM+ W PIN KK+E LSYLP L+D+ 
Sbjct: 27  FTGLK--SAATFPVSRKQNLDITS-IASNGGRVRCMQVWPPINMKKYETLSYLPDLTDEQ 83

Query: 73  IAKEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILN 131
           + KE++Y+LK GW+PCLEF+ E G+V+REN K PGYYDGRYWTMWKLPMFGC D++Q+L 
Sbjct: 84  LLKEVEYLLKNGWVPCLEFETEHGFVYRENHKSPGYYDGRYWTMWKLPMFGCTDATQVLA 143

Query: 132 EIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           E+QECKK+YP A+IR + F+N +Q QC+SF+  KP
Sbjct: 144 EVQECKKSYPQAWIRIIGFDNVRQVQCISFIAYKP 178

RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.

Solanum tuberosum (taxid: 4113)

EC: 4

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 3

EC: 9

>sp|P26577|RBSC_SOLTU Ribulose bisphosphate carboxylase small chain 2C, chloroplastic OS=Solanum tuberosum GN=RBCS-2C PE=3 SV=1

 Score =  196 bits (499), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 87/153 (56%), Positives = 117/153 (76%), Gaps = 2/153 (1%)

Query: 15  YLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIA 74
           + GLK T+   +  K ++  +S   SNG + RCM+ W PIN KK+E LSYLP LSD+ + 
Sbjct: 26  FTGLKSTASFPVSRKQNLDITS-IASNGGRVRCMQVWPPINMKKYETLSYLPDLSDEQLL 84

Query: 75  KEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEI 133
           KE++Y+LK GW+PCLEF+ E G+V+REN+K PGYYDGRYWTMWKLPMFGC D++Q+L E+
Sbjct: 85  KEVEYLLKNGWVPCLEFETEHGFVYRENNKSPGYYDGRYWTMWKLPMFGCTDATQVLAEV 144

Query: 134 QECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           +E KKAYP A+IR + F+N +Q QC+SF+  KP
Sbjct: 145 EEAKKAYPQAWIRIIGFDNVRQVQCISFIAYKP 177

RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.

Solanum tuberosum (taxid: 4113)

EC: 4

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 3

EC: 9

>sp|P26576|RBSB_SOLTU Ribulose bisphosphate carboxylase small chain 2B, chloroplastic OS=Solanum tuberosum GN=RBCS-2B PE=3 SV=1

 Score =  196 bits (499), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 87/153 (56%), Positives = 117/153 (76%), Gaps = 2/153 (1%)

Query: 15  YLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIA 74
           + GLK T+   +  K ++  +S   SNG + RCM+ W PIN KK+E LSYLP LSD+ + 
Sbjct: 26  FTGLKSTASFPVSRKQNLDITS-IASNGGRVRCMQVWPPINMKKYETLSYLPDLSDEQLL 84

Query: 75  KEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEI 133
           KE++Y+LK GW+PCLEF+ E G+V+REN+K PGYYDGRYWTMWKLPMFGC D++Q+L E+
Sbjct: 85  KEVEYLLKNGWVPCLEFETEHGFVYRENNKSPGYYDGRYWTMWKLPMFGCTDATQVLAEV 144

Query: 134 QECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           +E KKAYP A+IR + F+N +Q QC+SF+  KP
Sbjct: 145 EEAKKAYPQAWIRIIGFDNVRQVQCISFIAYKP 177

RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.

Solanum tuberosum (taxid: 4113)

EC: 4

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 3

EC: 9

>sp|P32764|RBS3_SOLTU Ribulose bisphosphate carboxylase small chain 3, chloroplastic OS=Solanum tuberosum GN=RBCS-3 PE=3 SV=1

 Score =  196 bits (499), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 86/153 (56%), Positives = 114/153 (74%), Gaps = 1/153 (0%)

Query: 15  YLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIA 74
           + GLK  +   +  K++    +   SNG + RCM+ W PIN KK+E LSYLP LSD+ + 
Sbjct: 26  FTGLKSAASFPVTKKNNNVDITSLASNGGRVRCMQVWPPINMKKYETLSYLPDLSDEQLL 85

Query: 75  KEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEI 133
           KE++Y+LK GW+PCLEF+ E G+V+REN K PGYYDGRYWTMWKLPMFGC D++Q+L E+
Sbjct: 86  KEVEYLLKNGWVPCLEFETEHGFVYRENHKSPGYYDGRYWTMWKLPMFGCTDATQVLAEV 145

Query: 134 QECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           QE KKAYP A+IR + F+N +Q QC+SF+  KP
Sbjct: 146 QEAKKAYPQAWIRIIGFDNVRQVQCISFIAYKP 178

RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.

Solanum tuberosum (taxid: 4113)

EC: 4

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 3

EC: 9

>sp|O65349|RBS_CAPAN Ribulose bisphosphate carboxylase small chain, chloroplastic OS=Capsicum annuum GN=RBCS PE=2 SV=1

 Score =  196 bits (499), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 87/158 (55%), Positives = 116/158 (73%), Gaps = 2/158 (1%)

Query: 13  SGYLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDS 72
           + + GLK  +   +  K  +  +S   SNG +  CM  W PIN KK+E LSYLP LSD+ 
Sbjct: 24  ASFNGLKSAASFPVTRKQDLDITS-IASNGGRVECMLVWPPINKKKYETLSYLPDLSDEQ 82

Query: 73  IAKEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILN 131
           + KEI+Y+L+KGW+PCLEF+ E G+V+RE+ + PGYYDGRYWTMWKLPMFGC D++Q+LN
Sbjct: 83  LLKEIEYLLQKGWVPCLEFETEHGFVYREHHRSPGYYDGRYWTMWKLPMFGCTDATQVLN 142

Query: 132 EIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTT 169
           E+QE KKAYP A+IR + F+N +Q QC+SF+  KP  T
Sbjct: 143 EVQEAKKAYPQAWIRIIGFDNVRQVQCISFIAYKPEAT 180

RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.

Capsicum annuum (taxid: 4072)

EC: 4

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 3

EC: 9

>sp|P16031|RBS_LARLA Ribulose bisphosphate carboxylase small chain, chloroplastic OS=Larix laricina GN=RBCS PE=3 SV=1

 Score =  196 bits (497), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 86/159 (54%), Positives = 112/159 (70%), Gaps = 7/159 (4%)

Query: 13  SGYLGLKPTSKALLPVKDSIA-----WSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPS 67
           S + GLK  S A  P   +++     W  KT SNGS+ RCM+ W P  NKKFE LSYLP 
Sbjct: 30  SAFTGLK--SMAQFPSSKTMSNAGAEWEQKTTSNGSRVRCMQVWPPYANKKFETLSYLPR 87

Query: 68  LSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSS 127
           L+ + + KE++Y+LK  W+PCLEF+E G + R     PGYYDGRYW MWKLPMFGC ++S
Sbjct: 88  LTPEQLVKEVEYLLKNKWVPCLEFEEDGEIKRVYGNSPGYYDGRYWVMWKLPMFGCTEAS 147

Query: 128 QILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           Q+LNE+ EC KAYPNA+IR + F+N +Q QC+SF++ KP
Sbjct: 148 QVLNEVNECAKAYPNAFIRVIGFDNVRQVQCISFIVHKP 186

RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.

Larix laricina (taxid: 3326)

EC: 4

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 3

EC: 9

>sp|P26575|RBSA_SOLTU Ribulose bisphosphate carboxylase small chain 2A, chloroplastic OS=Solanum tuberosum GN=RBCS-2A PE=3 SV=1

 Score =  195 bits (495), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 86/153 (56%), Positives = 116/153 (75%), Gaps = 2/153 (1%)

Query: 15  YLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIA 74
           + GLK  +   +  K ++  +S   SNG + RCM+ W PIN KK+E LSYLP LSD+ + 
Sbjct: 26  FTGLKSAASFPVSRKQNLDITS-IASNGGRVRCMQVWPPINMKKYETLSYLPDLSDEQLL 84

Query: 75  KEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEI 133
           KE++Y+LK GW+PCLEF+ E G+V+REN+K PGYYDGRYWTMWKLPMFGC D++Q+L E+
Sbjct: 85  KEVEYLLKNGWVPCLEFETEHGFVYRENNKSPGYYDGRYWTMWKLPMFGCTDATQVLAEV 144

Query: 134 QECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           +E KKAYP A+IR + F+N +Q QC+SF+  KP
Sbjct: 145 EEAKKAYPQAWIRIIGFDNVRQVQCISFIAYKP 177

RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.

Solanum tuberosum (taxid: 4113)

EC: 4

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 3

EC: 9

>sp|P07089|RBS_FLATR Ribulose bisphosphate carboxylase small chain, chloroplastic OS=Flaveria trinervia GN=RBCS PE=2 SV=1

 Score =  194 bits (494), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 85/154 (55%), Positives = 113/154 (73%), Gaps = 3/154 (1%)

Query: 15  YLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIA 74
           + GLK  + A  PV   +   S   SNG + +CMK W P+  KK+E LSYLP L++  +A
Sbjct: 20  FTGLK--ANAAFPVTKKVNGFSTLPSNGGRVQCMKVWPPVGKKKYETLSYLPELTEAQLA 77

Query: 75  KEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEI 133
           KE+DY+L+  W+PCLEF+ E G+V+REN+  PGYYDGRYWTMWKLPMFGC DS+Q++ E+
Sbjct: 78  KEVDYLLRNKWVPCLEFELEHGFVYRENASSPGYYDGRYWTMWKLPMFGCTDSAQVMKEL 137

Query: 134 QECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPT 167
           QECKK YP A+IR + F+N +Q QC+SF+  KPT
Sbjct: 138 QECKKEYPQAWIRIIGFDNVRQVQCVSFIASKPT 171

RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.

Flaveria trinervia (taxid: 4227)

EC: 4

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 3

EC: 9

>sp|P10053|RBS_PINTH Ribulose bisphosphate carboxylase small chain, chloroplastic OS=Pinus thunbergii GN=RBCS PE=2 SV=1

 Score =  194 bits (494), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 82/157 (52%), Positives = 114/157 (72%), Gaps = 3/157 (1%)

Query: 13  SGYLGLKPTSKALLPVKDSIA---WSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLS 69
           S + GLK T++     K S A   W  KT SNG + RCM+ W P  N KFE LSYLP+L+
Sbjct: 14  SAFTGLKSTAQFPSSFKMSNAAAEWEQKTTSNGGRVRCMQVWPPFGNPKFETLSYLPTLT 73

Query: 70  DDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQI 129
           ++ + KE++Y+L+  W+PCLEFD  G + R+ ++ PGYYDGRYW MWKLPMFGC ++SQ+
Sbjct: 74  EEQLVKEVEYLLRNKWVPCLEFDLEGSISRKYNRSPGYYDGRYWVMWKLPMFGCTEASQV 133

Query: 130 LNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           +NE++EC KAYP A+IR + F+N +Q QC+SF++ KP
Sbjct: 134 INEVRECAKAYPKAFIRVIGFDNVRQVQCISFIVHKP 170

RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.

Pinus thunbergii (taxid: 3350)

EC: 4

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 3

EC: 9

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	172
225446032	169	PREDICTED: ribulose bisphosphate carboxy	0.982	1.0	0.786	4e-78
388492688	173	unknown [Lotus japonicus]	1.0	0.994	0.732	4e-74
388498620	173	unknown [Lotus japonicus]	1.0	0.994	0.726	3e-73
357479619	173	Ribulose bisphosphate carboxylase small	0.994	0.988	0.75	3e-72
224143693	170	predicted protein [Populus trichocarpa]	0.965	0.976	0.761	2e-70
351727062	172	uncharacterized protein LOC100527679 [Gl	1.0	1.0	0.703	1e-69
116789830	188	unknown [Picea sitchensis]	0.802	0.734	0.625	5e-54
302819794	178	hypothetical protein SELMODRAFT_186173 [	0.947	0.915	0.590	3e-53
302779908	178	hypothetical protein SELMODRAFT_147927 [	0.889	0.859	0.623	2e-52
115444275	183	Os02g0152400 [Oryza sativa Japonica Grou	0.784	0.737	0.570	4e-50

>gi|225446032|ref|XP_002270117.1| PREDICTED: ribulose bisphosphate carboxylase small chain, chloroplastic [Vitis vinifera] gi|297735404|emb|CBI17844.3| unnamed protein product [Vitis vinifera]

 Score =  295 bits (756), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 133/169 (78%), Positives = 148/169 (87%)

Query: 1   MSASIFTAPVAGSGYLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFE 60
           M+A I + PV   GY+GLKP    L P KDS+AWS KTVSNGSKT CMKTWNPINNKKFE
Sbjct: 1   MAAGILSGPVTSFGYVGLKPHQPKLFPAKDSVAWSRKTVSNGSKTHCMKTWNPINNKKFE 60

Query: 61  ALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPM 120
            LSYLP LSDDSIAKEIDYMLKKGWIPCLEFDEVGYV R+NS++PGYYDGRYWT+WKLPM
Sbjct: 61  TLSYLPPLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVFRKNSQIPGYYDGRYWTLWKLPM 120

Query: 121 FGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTT 169
           FGCND+SQ+LNEI ECKK YPNAYIRCLAF+N+ QGQCM+F+IQKPT +
Sbjct: 121 FGCNDASQVLNEIHECKKTYPNAYIRCLAFDNEHQGQCMAFVIQKPTCS 169

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388492688|gb|AFK34410.1| unknown [Lotus japonicus]

 Score =  282 bits (721), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 126/172 (73%), Positives = 146/172 (84%)

Query: 1   MSASIFTAPVAGSGYLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFE 60
           MSA  FTA VAG+G++GLK  S  L PV     W SKT SNGSKT CMKTWNPINN+KFE
Sbjct: 1   MSAGTFTALVAGAGFVGLKSNSSNLYPVTGFNEWRSKTTSNGSKTLCMKTWNPINNRKFE 60

Query: 61  ALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPM 120
            LSYLP L+D+SIAKE+DYMLKKGWIPCLEFDE+G++ RENS+MPGYYDGRYWT+WKLPM
Sbjct: 61  TLSYLPPLTDESIAKEVDYMLKKGWIPCLEFDELGHIRRENSRMPGYYDGRYWTLWKLPM 120

Query: 121 FGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTTST 172
           FGCNDSSQ+LNEIQECK+AYPNAYIRC+AF+N +  Q M+F+IQKP   T+T
Sbjct: 121 FGCNDSSQVLNEIQECKRAYPNAYIRCIAFDNHRHMQSMAFIIQKPAANTTT 172

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388498620|gb|AFK37376.1| unknown [Lotus japonicus]

 Score =  279 bits (713), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 125/172 (72%), Positives = 145/172 (84%)

Query: 1   MSASIFTAPVAGSGYLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFE 60
           MSA  FTA VAG+G++GLK  S  L PV     W SKT SNGSKT CMKTWNPINN+KFE
Sbjct: 1   MSAGTFTALVAGAGFVGLKSNSSNLYPVTGFNEWKSKTTSNGSKTLCMKTWNPINNRKFE 60

Query: 61  ALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPM 120
            LSYLP L+D+SIAKE+DYMLKKGWIPCLEFDE+G++ RENS+MPGYYDGRYWT+WKLPM
Sbjct: 61  TLSYLPPLTDESIAKEVDYMLKKGWIPCLEFDELGHIRRENSRMPGYYDGRYWTLWKLPM 120

Query: 121 FGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTTST 172
           F CNDSSQ+LNEIQECK+AYPNAYIRC+AF+N +  Q M+F+IQKP   T+T
Sbjct: 121 FDCNDSSQVLNEIQECKRAYPNAYIRCIAFDNHRHMQSMAFIIQKPAANTTT 172

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357479619|ref|XP_003610095.1| Ribulose bisphosphate carboxylase small chain [Medicago truncatula] gi|355511150|gb|AES92292.1| Ribulose bisphosphate carboxylase small chain [Medicago truncatula] gi|388491552|gb|AFK33842.1| unknown [Medicago truncatula]

 Score =  276 bits (705), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 129/172 (75%), Positives = 142/172 (82%), Gaps = 1/172 (0%)

Query: 1   MSASIFTAPVAGSGYLGLKPTSKALLPVKD-SIAWSSKTVSNGSKTRCMKTWNPINNKKF 59
           MSA  F APVAG G++GLK  S +L P    SI W  KTVSNGSK  CMKTWNPINNKKF
Sbjct: 1   MSAGTFAAPVAGPGFVGLKSNSSSLWPSATYSIEWKKKTVSNGSKIHCMKTWNPINNKKF 60

Query: 60  EALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLP 119
           E LSYLP LSDDSIAKEIDYMLKK W PCLEFDE G +HR NS+MPGYYDGRYWT+WKLP
Sbjct: 61  ETLSYLPPLSDDSIAKEIDYMLKKRWTPCLEFDEFGCIHRANSQMPGYYDGRYWTLWKLP 120

Query: 120 MFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTTS 171
           MFGCNDSSQ+LNEI ECKK YPNAYIRCLAF+N++  Q M+F+I KPTTTT+
Sbjct: 121 MFGCNDSSQVLNEINECKKTYPNAYIRCLAFDNKRHMQAMAFVIHKPTTTTT 172

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224143693|ref|XP_002325043.1| predicted protein [Populus trichocarpa] gi|118488515|gb|ABK96070.1| unknown [Populus trichocarpa] gi|222866477|gb|EEF03608.1| predicted protein [Populus trichocarpa]

 Score =  270 bits (690), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 128/168 (76%), Positives = 144/168 (85%), Gaps = 2/168 (1%)

Query: 1   MSASIFTA-PVAGSGYLGLKPT-SKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKK 58
           MSA IF A  VA  GY GL+   +K     K+S+A SS+TVSNGSKT CMKTWNPINNKK
Sbjct: 1   MSAGIFAASAVAAPGYHGLRALPTKQPFATKNSVARSSRTVSNGSKTFCMKTWNPINNKK 60

Query: 59  FEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKL 118
           FEALSYLP LS+DSIAKEIDYM+KKGWIPCLEFDEVG V RE+S+MPGYYDGRYWT+WKL
Sbjct: 61  FEALSYLPPLSEDSIAKEIDYMMKKGWIPCLEFDEVGSVRREHSRMPGYYDGRYWTLWKL 120

Query: 119 PMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           PMFGC DSSQ+L EI ECKKAYP+AYIRCLAF+N+ QGQCM+F+IQKP
Sbjct: 121 PMFGCTDSSQVLEEIHECKKAYPDAYIRCLAFDNKHQGQCMAFVIQKP 168

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351727062|ref|NP_001235868.1| uncharacterized protein LOC100527679 [Glycine max] gi|255632934|gb|ACU16821.1| unknown [Glycine max]

 Score =  267 bits (682), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 121/172 (70%), Positives = 139/172 (80%)

Query: 1   MSASIFTAPVAGSGYLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFE 60
           MSA+ F A +AG+G++GLK  S  L P    I W  K VSNGSKT CMKTWNPINNKKFE
Sbjct: 1   MSAATFAAHIAGAGFVGLKSNSSNLCPSTGPIGWKRKIVSNGSKTYCMKTWNPINNKKFE 60

Query: 61  ALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPM 120
            LSYLP LSD+SIAKEIDYMLKKGWIPCLEFDE+G V RENS MP YYDGRYWT+WKLPM
Sbjct: 61  TLSYLPPLSDESIAKEIDYMLKKGWIPCLEFDELGCVRRENSHMPEYYDGRYWTLWKLPM 120

Query: 121 FGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTTST 172
           F C+DSSQ+L EI EC++ YPNAYIRCLAF+NQ+  Q M+F++ KP  TT+T
Sbjct: 121 FACSDSSQVLKEIHECRRVYPNAYIRCLAFDNQRHMQSMAFIVHKPDITTTT 172

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116789830|gb|ABK25403.1| unknown [Picea sitchensis]

 Score =  215 bits (547), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 87/139 (62%), Positives = 114/139 (82%), Gaps = 1/139 (0%)

Query: 32  IAWSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEF 91
           + W  KT +NGS+  CM+ W PINN+K+E LSYLP LS +S+ KEIDYM+ KGW+PCLEF
Sbjct: 49  LEWEEKTTTNGSRVHCMQVWPPINNRKYETLSYLPPLSQESLVKEIDYMISKGWVPCLEF 108

Query: 92  DEVGYVHRENSKM-PGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAF 150
           D VG + R N  M PGYYDGRYW++WKLPMFGC +S+Q+L+E++ECKKAYPNAYIRCL F
Sbjct: 109 DAVGQIQRTNGVMVPGYYDGRYWSLWKLPMFGCTNSAQVLSELEECKKAYPNAYIRCLGF 168

Query: 151 NNQKQGQCMSFLIQKPTTT 169
           +N++Q QC++F++ KP+ T
Sbjct: 169 DNKRQTQCIAFIVHKPSHT 187

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302819794|ref|XP_002991566.1| hypothetical protein SELMODRAFT_186173 [Selaginella moellendorffii] gi|300140599|gb|EFJ07320.1| hypothetical protein SELMODRAFT_186173 [Selaginella moellendorffii]

 Score =  212 bits (540), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 98/166 (59%), Positives = 120/166 (72%), Gaps = 3/166 (1%)

Query: 4   SIFTAPVAGS--GYLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFEA 61
           +  + PVA    G+ GLK T+ AL   K  + WS KTV+NGS+  CM TW P NN +FE 
Sbjct: 14  AALSTPVAPKVPGFTGLKATT-ALTANKGGLQWSQKTVANGSRVSCMLTWTPYNNPRFET 72

Query: 62  LSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMF 121
           LSYLP LS D IAKEIDYML+KGW PCLEF + GYV+RE  K PG YDGRYWTM+KLPMF
Sbjct: 73  LSYLPDLSADQIAKEIDYMLRKGWFPCLEFSDKGYVYRECHKSPGCYDGRYWTMYKLPMF 132

Query: 122 GCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPT 167
           GC DS+Q+L EIQEC++ +P +YIR L F+  +Q QC  F++ KPT
Sbjct: 133 GCQDSAQVLREIQECRREFPTSYIRVLGFDRVRQVQCAGFIVYKPT 178

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302779908|ref|XP_002971729.1| hypothetical protein SELMODRAFT_147927 [Selaginella moellendorffii] gi|300160861|gb|EFJ27478.1| hypothetical protein SELMODRAFT_147927 [Selaginella moellendorffii]

 Score =  210 bits (534), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 96/154 (62%), Positives = 115/154 (74%), Gaps = 1/154 (0%)

Query: 14  GYLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSI 73
           G+ GLK T+ AL   K  + WS KTV+NGS+  CM TW P NN +FE LSYLP LS D I
Sbjct: 26  GFTGLKATT-ALTANKGGLQWSQKTVANGSRVSCMLTWTPYNNPRFETLSYLPDLSPDQI 84

Query: 74  AKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEI 133
           AKEIDYMLKKGW PCLEF + GYV+RE  K PG YDGRYWTM+KLPMFGC DS+Q+L EI
Sbjct: 85  AKEIDYMLKKGWFPCLEFSDKGYVYRECHKSPGCYDGRYWTMYKLPMFGCQDSAQVLREI 144

Query: 134 QECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPT 167
           +ECKK +P ++IR L F+  +Q QC  F++ KPT
Sbjct: 145 EECKKDFPTSFIRVLGFDRVRQVQCAGFIVFKPT 178

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115444275|ref|NP_001045917.1| Os02g0152400 [Oryza sativa Japonica Group] gi|51535337|dbj|BAD38596.1| putative ribulose 1,5-bisphosphate carboxylase small subunit [Oryza sativa Japonica Group] gi|51535980|dbj|BAD38061.1| putative ribulose 1,5-bisphosphate carboxylase small subunit [Oryza sativa Japonica Group] gi|113535448|dbj|BAF07831.1| Os02g0152400 [Oryza sativa Japonica Group] gi|218190079|gb|EEC72506.1| hypothetical protein OsI_05882 [Oryza sativa Indica Group] gi|222622186|gb|EEE56318.1| hypothetical protein OsJ_05407 [Oryza sativa Japonica Group]

 Score =  202 bits (514), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 77/135 (57%), Positives = 112/135 (82%)

Query: 38  TVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYV 97
             SNG +T CM+TWNP  N+++EA+SYLP LS  SI+KEI++++ KGW+PCLEFD+ G +
Sbjct: 41  AASNGFRTYCMQTWNPFTNRRYEAMSYLPPLSAKSISKEIEFIMSKGWVPCLEFDKEGEI 100

Query: 98  HRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQ 157
           HR NS+MPGYYDGRYWT+WKLPMFGC+D++ +L E++EC++ YP+A+IR +AF++ +Q Q
Sbjct: 101 HRSNSRMPGYYDGRYWTLWKLPMFGCSDAAAVLREVEECRREYPDAFIRLIAFDSSRQCQ 160

Query: 158 CMSFLIQKPTTTTST 172
           CMSF++ KP +  ++
Sbjct: 161 CMSFVVHKPPSAAAS 175

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

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	172
TAIR|locus:2177406	181	RBCS1B "Rubisco small subunit	0.965	0.917	0.531	5.4e-47
TAIR|locus:2177416	181	RBCS2B "Rubisco small subunit	0.965	0.917	0.531	6.9e-47
UNIPROTKB|P69249	180	RBCS "Ribulose bisphosphate ca	0.866	0.827	0.561	1.4e-46
TAIR|locus:2177426	186	RBCS3B "Rubisco small subunit	0.970	0.897	0.513	2.3e-46
TAIR|locus:2033686	180	RBCS1A "ribulose bisphosphate	0.965	0.922	0.514	3.8e-46
UNIPROTKB|Q36688	169	rbcS "Ribulose bisphosphate ca	0.866	0.881	0.549	6.4e-44

TAIR|locus:2177406 RBCS1B "Rubisco small subunit 1B" [Arabidopsis thaliana (taxid:3702)]

 Score = 492 (178.3 bits), Expect = 5.4e-47, P = 5.4e-47
 Identities = 93/175 (53%), Positives = 123/175 (70%)

Query:     2 SASIFTAPVAGS---GYLGLKPTSKALLPV--KDSIAWSSKTVSNGSKTRCMKTWNPINN 56
             SA++ T+P   +    + GLK  S A  PV  K +   +S T SNG +  CMK W PI  
Sbjct:     8 SAAVVTSPAQATMVAPFTGLK--SSASFPVTRKANNDITSIT-SNGGRVSCMKVWPPIGK 64

Query:    57 KKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPGYYDGRYWTM 115
             KKFE LSYLP L+D  +AKE+DY+L+  WIPC+EF+ E G+V+RE+   PGYYDGRYWTM
Sbjct:    65 KKFETLSYLPDLTDVELAKEVDYLLRNKWIPCVEFELEHGFVYREHGNTPGYYDGRYWTM 124

Query:   116 WKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTT 170
             WKLP+FGC DS+Q+L E++ECKK YP A+IR + F+N +Q QC+SF+  KP + T
Sbjct:   125 WKLPLFGCTDSAQVLKEVEECKKEYPGAFIRIIGFDNTRQVQCISFIAYKPPSFT 179

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009573 "chloroplast ribulose bisphosphate carboxylase complex" evidence=ISS

GO:0015977 "carbon fixation" evidence=ISS

GO:0016984 "ribulose-bisphosphate carboxylase activity" evidence=ISS

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0048046 "apoplast" evidence=IDA

GO:0009637 "response to blue light" evidence=IEP

GO:0010114 "response to red light" evidence=IEP

GO:0010218 "response to far red light" evidence=IEP

TAIR|locus:2177416 RBCS2B "Rubisco small subunit 2B" [Arabidopsis thaliana (taxid:3702)]

 Score = 491 (177.9 bits), Expect = 6.9e-47, P = 6.9e-47
 Identities = 93/175 (53%), Positives = 122/175 (69%)

Query:     2 SASIFTAPVAGS---GYLGLKPTSKALLPV--KDSIAWSSKTVSNGSKTRCMKTWNPINN 56
             S ++ T+P   +    + GLK  S A  PV  K +   +S T SNG +  CMK W PI  
Sbjct:     8 STAVVTSPAQATMVAPFTGLK--SSASFPVTRKANNDITSIT-SNGGRVSCMKVWPPIGK 64

Query:    57 KKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPGYYDGRYWTM 115
             KKFE LSYLP LSD  +AKE+DY+L+  WIPC+EF+ E G+V+RE+   PGYYDGRYWTM
Sbjct:    65 KKFETLSYLPDLSDVELAKEVDYLLRNKWIPCVEFELEHGFVYREHGNTPGYYDGRYWTM 124

Query:   116 WKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTT 170
             WKLP+FGC DS+Q+L E++ECKK YP A+IR + F+N +Q QC+SF+  KP + T
Sbjct:   125 WKLPLFGCTDSAQVLKEVEECKKEYPGAFIRIIGFDNTRQVQCISFIAYKPPSFT 179

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009573 "chloroplast ribulose bisphosphate carboxylase complex" evidence=ISS

GO:0015977 "carbon fixation" evidence=ISS

GO:0016984 "ribulose-bisphosphate carboxylase activity" evidence=ISS

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0048046 "apoplast" evidence=IDA

GO:0009637 "response to blue light" evidence=IEP

GO:0010114 "response to red light" evidence=IEP

GO:0010218 "response to far red light" evidence=IEP

UNIPROTKB|P69249 RBCS "Ribulose bisphosphate carboxylase small chain, chloroplastic" [Nicotiana tabacum (taxid:4097)]

 Score = 488 (176.8 bits), Expect = 1.4e-46, P = 1.4e-46
 Identities = 87/155 (56%), Positives = 116/155 (74%)

Query:    15 YLGLKPTSKALLPV--KDSIAWSSKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDS 72
             + GLK  S A  PV  K ++  +S   SNG + +CM+ W PIN KK+E LSYLP LS + 
Sbjct:    26 FTGLK--SAASFPVSRKQNLDITS-IASNGGRVQCMQVWPPINKKKYETLSYLPDLSQEQ 82

Query:    73 IAKEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILN 131
             +  E++Y+LK GW+PCLEF+ E G+V+REN+K PGYYDGRYWTMWKLPMFGC D++Q+L 
Sbjct:    83 LLSEVEYLLKNGWVPCLEFETEHGFVYRENNKSPGYYDGRYWTMWKLPMFGCTDATQVLA 142

Query:   132 EIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
             E++E KKAYP A+IR + F+N +Q QC+SF+  KP
Sbjct:   143 EVEEAKKAYPQAWIRIIGFDNVRQVQCISFIAYKP 177

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2177426 RBCS3B "Rubisco small subunit 3B" [Arabidopsis thaliana (taxid:3702)]

 Score = 486 (176.1 bits), Expect = 2.3e-46, P = 2.3e-46
 Identities = 92/179 (51%), Positives = 121/179 (67%)

Query:     2 SASIFTAPVAGS---GYLGLKPTSKALLPVKDSIAWSSKTV-SNGSKTRCMKTWNPINNK 57
             SA++ T+P   +    + GLK  S A  PV         ++ SNG +  CMK W PI  K
Sbjct:     8 SAAVVTSPAQATMVAPFTGLK--SSAAFPVTRKTNKDITSIASNGGRVSCMKVWPPIGKK 65

Query:    58 KFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFD-EV-----GYVHRENSKMPGYYDGR 111
             KFE LSYLP LSD  +AKE+DY+L+  WIPC+EF+ EV     G+V+RE+   PGYYDGR
Sbjct:    66 KFETLSYLPDLSDVELAKEVDYLLRNKWIPCVEFELEVINTKHGFVYREHGNTPGYYDGR 125

Query:   112 YWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTT 170
             YWTMWKLP+FGC DS+Q+L E++ECKK YP A+IR + F+N +Q QC+SF+  KP + T
Sbjct:   126 YWTMWKLPLFGCTDSAQVLKEVEECKKEYPGAFIRIIGFDNTRQVQCISFIAYKPPSFT 184

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009573 "chloroplast ribulose bisphosphate carboxylase complex" evidence=ISS

GO:0015977 "carbon fixation" evidence=ISS

GO:0016984 "ribulose-bisphosphate carboxylase activity" evidence=ISS

GO:0005618 "cell wall" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0048046 "apoplast" evidence=IDA

GO:0009637 "response to blue light" evidence=IEP

GO:0010114 "response to red light" evidence=IEP

GO:0010218 "response to far red light" evidence=IEP

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0015979 "photosynthesis" evidence=IMP

GO:0080158 "chloroplast ribulose bisphosphate carboxylase complex biogenesis" evidence=IMP

TAIR|locus:2033686 RBCS1A "ribulose bisphosphate carboxylase small chain 1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 484 (175.4 bits), Expect = 3.8e-46, P = 3.8e-46
 Identities = 90/175 (51%), Positives = 122/175 (69%)

Query:     2 SASIFTAPVAGS---GYLGLKPTSKALLPV--KDSIAWSSKTVSNGSKTRCMKTWNPINN 56
             SA++  +P   +    + GLK  S A  P   K +   +S T SNG +  CM+ W PI  
Sbjct:     8 SATMVASPAQATMVAPFNGLK--SSAAFPATRKANNDITSIT-SNGGRVNCMQVWPPIGK 64

Query:    57 KKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPGYYDGRYWTM 115
             KKFE LSYLP L+D  +AKE+DY+++  WIPC+EF+ E G+V+RE+   PGYYDGRYWTM
Sbjct:    65 KKFETLSYLPDLTDSELAKEVDYLIRNKWIPCVEFELEHGFVYREHGNSPGYYDGRYWTM 124

Query:   116 WKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTT 170
             WKLP+FGC DS+Q+L E++ECKK YPNA+IR + F+N +Q QC+SF+  KP + T
Sbjct:   125 WKLPLFGCTDSAQVLKEVEECKKEYPNAFIRIIGFDNTRQVQCISFIAYKPPSFT 179

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009573 "chloroplast ribulose bisphosphate carboxylase complex" evidence=ISS

GO:0015977 "carbon fixation" evidence=ISS

GO:0016984 "ribulose-bisphosphate carboxylase activity" evidence=ISS

GO:0031977 "thylakoid lumen" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009409 "response to cold" evidence=IEP

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0005507 "copper ion binding" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0048046 "apoplast" evidence=IDA

GO:0009637 "response to blue light" evidence=IEP

GO:0010114 "response to red light" evidence=IEP

GO:0010218 "response to far red light" evidence=IEP

GO:0015979 "photosynthesis" evidence=IMP

GO:0080158 "chloroplast ribulose bisphosphate carboxylase complex biogenesis" evidence=IMP

UNIPROTKB|Q36688 rbcS "Ribulose bisphosphate carboxylase small chain" [Oryza sativa (taxid:4530)]

 Score = 463 (168.0 bits), Expect = 6.4e-44, P = 6.4e-44
 Identities = 84/153 (54%), Positives = 112/153 (73%)

Query:    15 YLGLKPTSKALLPVKDSIAWSSKTVSNGSKTRCMKTWNPINN-KKFEALSYLPSLSDDSI 73
             + GLK T  A +PV      S   VSNG + RCM+ W PI   KKFE LSYLP L+ + +
Sbjct:    11 FQGLKST--AGMPVARRSNSSFGNVSNGGRIRCMQVW-PIEGIKKFETLSYLPPLTVEDL 67

Query:    74 AKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEI 133
              K+I+Y+L+  W+PCLEF +VG+V+REN K PGYYDGRYWTMWKLPMFGC D++Q+L E+
Sbjct:    68 LKQIEYLLRSKWVPCLEFSKVGFVYRENHKSPGYYDGRYWTMWKLPMFGCTDATQVLKEL 127

Query:   134 QECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
             +E KKAYP+A++R + F+N +Q Q +SF+  KP
Sbjct:   128 EEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKP 160


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   0.131   0.414    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      172       172   0.00093  108 3  11 22  0.42    32
                                                     31  0.48    34


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:  6
  No. of states in DFA:  609 (65 KB)
  Total size of DFA:  183 KB (2105 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:  16.85u 0.09s 16.94t   Elapsed:  00:00:01
  Total cpu time:  16.86u 0.09s 16.95t   Elapsed:  00:00:01
  Start:  Thu May  9 18:34:32 2013   End:  Thu May  9 18:34:33 2013

GO:0009536 "plastid" evidence=IC;ISS

---

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)
O22645	RBS5_FRIAG	4, ., 1, ., 1, ., 3, 9	0.5294	0.8720	0.8379	N/A	no
P16031	RBS_LARLA	4, ., 1, ., 1, ., 3, 9	0.5408	0.8837	0.8042	N/A	no
P08706	RBS1_SOLLC	4, ., 1, ., 1, ., 3, 9	0.5490	0.8837	0.8397	N/A	no
P69249	RBS_TOBAC	4, ., 1, ., 1, ., 3, 9	0.5424	0.8779	0.8388	N/A	no
P00871	RBS1_WHEAT	4, ., 1, ., 1, ., 3, 9	0.5394	0.8720	0.8620	N/A	no
P32764	RBS3_SOLTU	4, ., 1, ., 1, ., 3, 9	0.5620	0.8837	0.8397	N/A	no
P05346	RBS1_BRANA	4, ., 1, ., 1, ., 3, 9	0.5028	0.9767	0.9281	N/A	no
O48550	RBS_ZANAE	4, ., 1, ., 1, ., 3, 9	0.5724	0.8430	0.8146	N/A	no
P10798	RBS3B_ARATH	4, ., 1, ., 1, ., 3, 9	0.5229	0.9709	0.9226	yes	no
P10797	RBS2B_ARATH	4, ., 1, ., 1, ., 3, 9	0.5172	0.9709	0.9226	yes	no
P10796	RBS1B_ARATH	4, ., 1, ., 1, ., 3, 9	0.5172	0.9709	0.9226	yes	no
P07089	RBS_FLATR	4, ., 1, ., 1, ., 3, 9	0.5519	0.8779	0.8728	N/A	no
P05348	RBS_MAIZE	4, ., 1, ., 1, ., 3, 9	0.5562	0.9186	0.9294	N/A	no
P05349	RBS3B_SOLLC	4, ., 1, ., 1, ., 3, 9	0.5620	0.8779	0.8388	N/A	no
Q39748	RBS6_FLAPR	4, ., 1, ., 1, ., 3, 9	0.5424	0.8720	0.8670	N/A	no
P26576	RBSB_SOLTU	4, ., 1, ., 1, ., 3, 9	0.5686	0.8779	0.8388	N/A	no
P26577	RBSC_SOLTU	4, ., 1, ., 1, ., 3, 9	0.5686	0.8779	0.8388	N/A	no
P26574	RBS1_SOLTU	4, ., 1, ., 1, ., 3, 9	0.5806	0.8662	0.8232	N/A	no
P26575	RBSA_SOLTU	4, ., 1, ., 1, ., 3, 9	0.5620	0.8779	0.8388	N/A	no
P26573	RBS8_NICPL	4, ., 1, ., 1, ., 3, 9	0.5294	0.8779	0.8388	N/A	no
Q42822	RBS_GLYTO	4, ., 1, ., 1, ., 3, 9	0.5084	0.9534	0.9213	N/A	no
O65349	RBS_CAPAN	4, ., 1, ., 1, ., 3, 9	0.5506	0.9069	0.8342	N/A	no
P27985	RBS2_BRANA	4, ., 1, ., 1, ., 3, 9	0.5057	0.9709	0.9226	N/A	no
Q42823	RBS_GLYTA	4, ., 1, ., 1, ., 3, 9	0.5141	0.9534	0.9213	N/A	no
P24007	RBS_PYRPY	4, ., 1, ., 1, ., 3, 9	0.5657	0.8662	0.8142	N/A	no
O24634	RBS1_FRIAG	4, ., 1, ., 1, ., 3, 9	0.5359	0.8720	0.8379	N/A	no
Q41351	RBS_STELP	4, ., 1, ., 1, ., 3, 9	0.5519	0.8720	0.8333	N/A	no
Q39747	RBS5_FLAPR	4, ., 1, ., 1, ., 3, 9	0.5490	0.8720	0.8670	N/A	no
Q39744	RBS2_FLAPR	4, ., 1, ., 1, ., 3, 9	0.5359	0.8720	0.8426	N/A	no
Q39745	RBS3_FLAPR	4, ., 1, ., 1, ., 3, 9	0.5490	0.8720	0.8670	N/A	no
P22433	RBS2_NICSY	4, ., 1, ., 1, ., 3, 9	0.5424	0.8779	0.8342	N/A	no
Q39743	RBS1_FLAPR	4, ., 1, ., 1, ., 3, 9	0.5490	0.8720	0.8670	N/A	no
Q02980	RBS_MALSP	4, ., 1, ., 1, ., 3, 9	0.5584	0.8779	0.8251	N/A	no
P10647	RBS0_SOLTU	4, ., 1, ., 1, ., 3, 9	0.5424	0.8837	0.8397	N/A	no
P08135	RBS_RAPSA	4, ., 1, ., 1, ., 3, 9	0.5287	0.9709	0.9226	N/A	no
P07180	RBS3A_SOLLC	4, ., 1, ., 1, ., 3, 9	0.5620	0.8779	0.8388	N/A	no
P07179	RBS2A_SOLLC	4, ., 1, ., 1, ., 3, 9	0.5741	0.8662	0.8277	N/A	no
Q39749	RBS7_FLAPR	4, ., 1, ., 1, ., 3, 9	0.5490	0.8720	0.8670	N/A	no
Q39746	RBS4_FLAPR	4, ., 1, ., 1, ., 3, 9	0.5490	0.8720	0.8426	N/A	no
P10053	RBS_PINTH	4, ., 1, ., 1, ., 3, 9	0.5222	0.8953	0.9005	N/A	no
O22573	RBS3_FRIAG	4, ., 1, ., 1, ., 3, 9	0.5359	0.8720	0.8379	N/A	no
O22572	RBS2_FRIAG	4, ., 1, ., 1, ., 3, 9	0.5294	0.8720	0.8379	N/A	no
P69250	RBS1_NICSY	4, ., 1, ., 1, ., 3, 9	0.5424	0.8779	0.8388	N/A	no
P18960	RBS_SILPR	4, ., 1, ., 1, ., 3, 9	0.5649	0.8720	0.8474	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

Prediction Level	EC number	Confidence of Prediction
3rd Layer	4.1.1.39	0.946
3rd Layer	4.1.1	0.963

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00031354001	RecName- Full=Ribulose bisphosphate carboxylase small chain; EC=4.1.1.39;; RuBisCO catalyzes two reactions- the carboxylation of D- ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site (By similarity) (169 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00035648001	RecName- Full=Ribulose bisphosphate carboxylase large chain; Short=RuBisCO large subunit; EC=4. [...] (327 aa)	•		•		•	•	•		0.993
	GSVIVG00035677001	RecName- Full=Phosphoglycerate kinase; EC=2.7.2.3; (401 aa)	•					•	•		0.945
	GSVIVG00014038001	RecName- Full=Phosphoribulokinase; EC=2.7.1.19; (404 aa)	•			•		•	•		0.945
	GSVIVG00035675001	RecName- Full=Phosphoglycerate kinase; EC=2.7.2.3; (405 aa)	•					•	•		0.943
	GSVIVG00036507001	SubName- Full=Chromosome chr3 scaffold_8, whole genome shotgun sequence; (66 aa)			•			•			0.894
	GSVIVG00017679001	RecName- Full=Ribulose bisphosphate carboxylase small chain; EC=4.1.1.39;; RuBisCO catalyzes tw [...] (180 aa)			•	•		•	•	•	0.829
	GSVIVG00019240001	SubName- Full=Chromosome chr7 scaffold_20, whole genome shotgun sequence; (189 aa)	•		•		•		•		0.768
	GSVIVG00016741001	SubName- Full=Chromosome chr11 scaffold_13, whole genome shotgun sequence; (484 aa)	•						•		0.597
	GSVIVG00015908001	SubName- Full=Chromosome chr17 scaffold_12, whole genome shotgun sequence; (324 aa)	•			•		•	•		0.597
	GSVIVG00027816001	SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (338 aa)				•			•		0.592

---

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	172
PLN02289	176	PLN02289, PLN02289, ribulose-bisphosphate carboxyl	8e-73
cd03527	99	cd03527, RuBisCO_small, Ribulose bisphosphate carb	2e-57
pfam00101	99	pfam00101, RuBisCO_small, Ribulose bisphosphate ca	1e-50
smart00961	96	smart00961, RuBisCO_small, Ribulose bisphosphate c	4e-37
CHL00130	138	CHL00130, rbcS, ribulose-1,5-bisphosphate carboxyl	1e-34
COG4451	127	COG4451, RbcS, Ribulose bisphosphate carboxylase s	5e-28
cd00307	84	cd00307, RuBisCO_small_like, Ribulose bisphosphate	6e-23

>gnl|CDD|215163 PLN02289, PLN02289, ribulose-bisphosphate carboxylase small chain

 Score =  216 bits (552), Expect = 8e-73
 Identities = 90/171 (52%), Positives = 120/171 (70%), Gaps = 7/171 (4%)

Query: 2   SASIFTAPVAGSG---YLGLKPTSKALLPVKDSIAWS-SKTVSNGSKTRCMKTWNPINNK 57
           SA++ T+P   +    + GLK  S A  PV        +   SNG +  CM+ W PI  K
Sbjct: 8   SAAVATSPAQATMVAPFTGLK--SSAAFPVTRKANNDITSIASNGGRVSCMQVWPPIGKK 65

Query: 58  KFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPGYYDGRYWTMW 116
           KFE LSYLP L+D+ +AKE+DY+L+  W+PCLEF+ E G+V+RE+ + PGYYDGRYWTMW
Sbjct: 66  KFETLSYLPDLTDEELAKEVDYLLRNKWVPCLEFELEHGFVYREHHRSPGYYDGRYWTMW 125

Query: 117 KLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPT 167
           KLPMFGC DS+Q+L E++E KKAYPNA+IR + F+N +Q QC+SF+  KP 
Sbjct: 126 KLPMFGCTDSAQVLKELEEAKKAYPNAFIRIIGFDNTRQVQCISFIAYKPP 176

Length = 176

>gnl|CDD|239603 cd03527, RuBisCO_small, Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit

 Score =  174 bits (444), Expect = 2e-57
 Identities = 60/110 (54%), Positives = 78/110 (70%), Gaps = 11/110 (10%)

Query: 57  KKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMW 116
           + FE  SYLP L+D+ IAK+IDY++  GW PCLEF E           P +YD RYWTMW
Sbjct: 1   RTFETFSYLPPLTDEQIAKQIDYIISNGWAPCLEFTE-----------PEHYDNRYWTMW 49

Query: 117 KLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           KLPMFGC D +Q+L EI+ C+KAYP+ Y+R + F+N KQ QCMSF++ +P
Sbjct: 50  KLPMFGCTDPAQVLREIEACRKAYPDHYVRVVGFDNYKQSQCMSFIVHRP 99

Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits. Length = 99

>gnl|CDD|201001 pfam00101, RuBisCO_small, Ribulose bisphosphate carboxylase, small chain

 Score =  157 bits (399), Expect = 1e-50
 Identities = 56/110 (50%), Positives = 78/110 (70%), Gaps = 13/110 (11%)

Query: 58  KFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEF-DEVGYVHRENSKMPGYYDGRYWTMW 116
           KFE  SYLP L+D+ IAK+I Y+L +GW PCLEF D+  +              RYWTMW
Sbjct: 1   KFETFSYLPPLTDEQIAKQIRYLLSQGWAPCLEFADDRRFR------------TRYWTMW 48

Query: 117 KLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           KLPMFGC D++Q+L E++EC+KAYP  Y+R + F+N++Q Q +SF++Q+P
Sbjct: 49  KLPMFGCTDAAQVLAELEECRKAYPGEYVRLIGFDNKRQSQVLSFIVQRP 98

Length = 99

>gnl|CDD|198029 smart00961, RuBisCO_small, Ribulose bisphosphate carboxylase, small chain

 Score =  123 bits (310), Expect = 4e-37
 Identities = 31/109 (28%), Positives = 56/109 (51%), Gaps = 13/109 (11%)

Query: 58  KFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWK 117
             E  SYLP L+D  I  ++ Y+L +G+   +E  +           P  +    W   K
Sbjct: 1   TQETFSYLPPLTDAEIVAQVRYLLAQGYAIGVEHAD-----------PRRFRTSSWQ--K 47

Query: 118 LPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           LPMFG  D++++L E++ C   +P  Y+R +  + + + + + F+IQ+P
Sbjct: 48  LPMFGATDAAEVLAELEACLAEHPGEYVRLIGIDPKAKRRVLEFIIQRP 96

RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP), thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome. which results in RuBisCO being more abundant during the day when it is required. Length = 96

>gnl|CDD|177052 CHL00130, rbcS, ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed

 Score =  117 bits (296), Expect = 1e-34
 Identities = 37/113 (32%), Positives = 58/113 (51%), Gaps = 13/113 (11%)

Query: 58  KFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWK 117
                S+LP L+D  I K+I Y + KGW   +E+ +    H  NS         YW +W 
Sbjct: 4   TQGTFSFLPDLTDQQIEKQIQYAISKGWALNVEWTDDP--HPRNS---------YWELWG 52

Query: 118 LPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQ--CMSFLIQKPTT 168
           LP+F   D + ++ EI EC+K  PN YI+  AF+  +  +   +SF++ +P  
Sbjct: 53  LPLFDVKDPAAVMFEINECRKQKPNGYIKVNAFDASRGVESCVLSFIVNRPAN 105

Length = 138

>gnl|CDD|226858 COG4451, RbcS, Ribulose bisphosphate carboxylase small subunit [Energy production and conversion]

 Score =  101 bits (252), Expect = 5e-28
 Identities = 33/112 (29%), Positives = 63/112 (56%), Gaps = 11/112 (9%)

Query: 55  NNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWT 114
            N +++ LS LP L+D+ IA+++ Y+L +G+   +E+ +                G  WT
Sbjct: 6   KNSRYKTLSSLPPLTDEQIAEQVRYLLSQGYKIGVEYVDD----------RRPRTG-SWT 54

Query: 115 MWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           MW  PMFG   + ++L E++ C+  +P  YIR + F+ + + + +SF++ +P
Sbjct: 55  MWGTPMFGAKTAGEVLAELEACRADHPGEYIRLIGFDPKGKRRVVSFIVHRP 106

Length = 127

>gnl|CDD|238187 cd00307, RuBisCO_small_like, Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins

 Score = 86.6 bits (215), Expect = 6e-23
 Identities = 15/99 (15%), Positives = 39/99 (39%), Gaps = 17/99 (17%)

Query: 70  DDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGC--NDSS 127
            + + +++  +L +G+   LE  +                 R+ T              +
Sbjct: 1   SEDVVEQVRQLLAQGYKIGLEHAD---------------ARRFRTSSWQSCGPIEGRSEA 45

Query: 128 QILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           Q+L  ++ C   +P  Y+R +  + + + + +  +IQ+P
Sbjct: 46  QVLAALEACLAEHPGEYVRLIGIDPKAKRRVLEIIIQRP 84

Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits. This superfamily also contains specific proteins from cyanobacteria. CcmM plays a role in a CO2 concentrating mechanism, which cyanobacteria need to to overcome the low specificity of their Rubisco and fusions to Rubisco activase, a type of chaperone, which promotes and maintains the catalytic activity of Rubisco. CcmM contains an N-terminal carbonic anhydrase fused to four copies of the Rubisco-small subunit domain. Length = 84

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	172
PLN02289	176	ribulose-bisphosphate carboxylase small chain	100.0
CHL00130	138	rbcS ribulose-1,5-bisphosphate carboxylase/oxygena	100.0
cd03527	99	RuBisCO_small Ribulose bisphosphate carboxylase/ox	100.0
PF00101	99	RuBisCO_small: Ribulose bisphosphate carboxylase,	100.0
COG4451	127	RbcS Ribulose bisphosphate carboxylase small subun	100.0
cd00307	84	RuBisCO_small_like Ribulose bisphosphate carboxyla	100.0
PF12338	45	RbcS: Ribulose-1,5-bisphosphate carboxylase small	98.56

>PLN02289 ribulose-bisphosphate carboxylase small chain

Probab=100.00  E-value=1.2e-90  Score=566.12  Aligned_cols=157  Identities=53%  Similarity=1.089  Sum_probs=151.7

Q ss_pred             cccccccccccCCcccccccccccCCC-CccccCCcccceeeeeccCCccccccccCCCCCChHHHHHHHHHHHhCCCee
Q 030735            9 PVAGSGYLGLKPTSKALLPVKDSIAWS-SKTVSNGSKTRCMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIP   87 (172)
Q Consensus         9 ~~~va~f~glks~~~~~fp~~~~~~~~-~~~~sng~r~~cm~vw~p~~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p   87 (172)
                      ++||+||+||||+++  ||+++|.+++ ++.+|||+||+|||||||+|+|||||||||||||||||+|||+|||+|||+|
T Consensus        18 as~vapf~gLKs~~~--fp~~~k~~~~~~~~~sng~rv~cmqvw~~~~~kkfETfSYLPpLtdeqI~kQVeYli~~GW~p   95 (176)
T PLN02289         18 ATMVAPFTGLKSSAA--FPVTRKANNDITSIASNGGRVSCMQVWPPIGKKKFETLSYLPDLTDEELAKEVDYLLRNKWVP   95 (176)
T ss_pred             ccccccccccccccc--CcceeeccccccccccCCceeEEEEeecccCccceeeeecCCCCCHHHHHHHHHHHHhCCCee
Confidence            478999999999999  9999997655 7788999999999999999999999999999999999999999999999999


Q ss_pred             EEEeccC-CceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHHHHHCCCCeEEEEeeecCCCeEEEEEEEecC
Q 030735           88 CLEFDEV-GYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP  166 (172)
Q Consensus        88 ~lEfad~-~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C~k~~P~~YIRliGfDn~rqvq~~sfIV~RP  166 (172)
                      ||||+++ +++||||+++|||||||||+|||||||||+|++|||+||+||+|+|||+|||||||||++|+||++||||||
T Consensus        96 clEf~~~~~~~~r~~~~s~~yyD~rYWtMWKLPMFg~tD~~~Vl~Ei~eC~kayP~~yIRiigFDn~rqvq~~sFiv~rP  175 (176)
T PLN02289         96 CLEFELEHGFVYREHHRSPGYYDGRYWTMWKLPMFGCTDSAQVLKELEEAKKAYPNAFIRIIGFDNTRQVQCISFIAYKP  175 (176)
T ss_pred             eeeeccCCceeEecCCCCCCcccCceeEEeccccCCCCCHHHHHHHHHHHHHHCCcceEEEEEEECCCCEEEEEEEEecC
Confidence            9999966 899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             C
Q 030735          167 T  167 (172)
Q Consensus       167 ~  167 (172)
                      .
T Consensus       176 ~  176 (176)
T PLN02289        176 P  176 (176)
T ss_pred             C
Confidence            5

>CHL00130 rbcS ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed

Probab=100.00  E-value=1.3e-59  Score=371.95  Aligned_cols=103  Identities=34%  Similarity=0.776  Sum_probs=99.2

Q ss_pred             cccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHH
Q 030735           57 KKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQEC  136 (172)
Q Consensus        57 kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C  136 (172)
                      .||||||||||||||||++||+|||+|||+|||||++++++ |          |+||+|||||||||+|++|||+||+||
T Consensus         3 ~~~eTfSyLPpLTdeqI~kQI~Y~i~~GW~p~iEft~~~~~-~----------~~YW~MWkLPMFg~tD~~~Vl~Ei~~C   71 (138)
T CHL00130          3 LTQGTFSFLPDLTDQQIEKQIQYAISKGWALNVEWTDDPHP-R----------NSYWELWGLPLFDVKDPAAVMFEINEC   71 (138)
T ss_pred             eeeceeccCCCCCHHHHHHHHHHHHhcCCeEEEEecCCCCc-C----------ccEEeeeCCccCCCCCHHHHHHHHHHH
Confidence            58999999999999999999999999999999999999987 3          999999999999999999999999999


Q ss_pred             HHHCCCCeEEEEeeecCCCeEE--EEEEEecCCCCC
Q 030735          137 KKAYPNAYIRCLAFNNQKQGQC--MSFLIQKPTTTT  170 (172)
Q Consensus       137 ~k~~P~~YIRliGfDn~rqvq~--~sfIV~RP~~~~  170 (172)
                      +|+|||+|||||||||.+|+||  ++||||||.+..
T Consensus        72 rkayP~~yIRl~gFDn~rq~Q~~~~sFiV~rP~~ep  107 (138)
T CHL00130         72 RKQKPNGYIKVNAFDASRGVESCVLSFIVNRPANEP  107 (138)
T ss_pred             HHHCCCcEEEEEEeeCCCcEEEeEEEEEEeCCCCCC
Confidence            9999999999999999999999  999999997653

>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit

Probab=100.00  E-value=2.2e-59  Score=353.70  Aligned_cols=99  Identities=60%  Similarity=1.297  Sum_probs=96.6

Q ss_pred             cccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHH
Q 030735           57 KKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQEC  136 (172)
Q Consensus        57 kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C  136 (172)
                      +|||||||||||||+||++||+|||+|||+|||||+|+++           |+++||+|||||||||+|++|||+||++|
T Consensus         1 ~~~~t~sylp~lt~~~i~~QI~yll~qG~~~~lE~ad~~~-----------~~~~yW~mwklP~f~~~d~~~Vl~ei~~C   69 (99)
T cd03527           1 RTFETFSYLPPLTDEQIAKQIDYIISNGWAPCLEFTEPEH-----------YDNRYWTMWKLPMFGCTDPAQVLREIEAC   69 (99)
T ss_pred             CcccccccCCCCCHHHHHHHHHHHHhCCCEEEEEcccCCC-----------CCCCEEeeccCCCCCCCCHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999984           56999999999999999999999999999


Q ss_pred             HHHCCCCeEEEEeeecCCCeEEEEEEEecC
Q 030735          137 KKAYPNAYIRCLAFNNQKQGQCMSFLIQKP  166 (172)
Q Consensus       137 ~k~~P~~YIRliGfDn~rqvq~~sfIV~RP  166 (172)
                      +++|||+|||||||||++|+||++||||||
T Consensus        70 ~~~~p~~YVRliG~D~~~q~~~~~fIv~RP   99 (99)
T cd03527          70 RKAYPDHYVRVVGFDNYKQSQCMSFIVHRP   99 (99)
T ss_pred             HHHCCCCeEEEEEEeCCccEEEEEEEeeCc
Confidence            999999999999999999999999999999

Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.

>PF00101 RuBisCO_small: Ribulose bisphosphate carboxylase, small chain; InterPro: IPR000894 RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP) [], thus fixing carbon dioxide as the first step of the Calvin cycle

Probab=100.00  E-value=1.2e-56  Score=338.43  Aligned_cols=99  Identities=44%  Similarity=1.011  Sum_probs=89.8

Q ss_pred             ccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHHH
Q 030735           58 KFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECK  137 (172)
Q Consensus        58 kfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C~  137 (172)
                      |||||||||||||+||++||+|||+|||+|||||+|++++ |          ++||+|||||||||+|++|||+||++|+
T Consensus         1 k~et~S~lP~l~~~~i~~Qv~~ll~qG~~i~iE~ad~r~~-r----------~~~W~mW~~p~~~~~~~~~Vl~el~~c~   69 (99)
T PF00101_consen    1 KFETFSYLPPLTDEEIAKQVRYLLSQGWIIGIEHADPRRF-R----------TSYWQMWKLPMFGCTDPAQVLAELEACL   69 (99)
T ss_dssp             --STTTTSS---HHHHHHHHHHHHHTT-EEEEEEESCGGS-T----------SSS-EEESSEBTTBSSHHHHHHHHHHHH
T ss_pred             CCcccccCCCCCHHHHHHHHHhhhhcCceeeEEecCCCCC-C----------CCEeecCCCCCcCCCCHHHHHHHHHHHH
Confidence            7999999999999999999999999999999999999965 3          9999999999999999999999999999


Q ss_pred             HHCCCCeEEEEeeecCCCeEEEEEEEecCC
Q 030735          138 KAYPNAYIRCLAFNNQKQGQCMSFLIQKPT  167 (172)
Q Consensus       138 k~~P~~YIRliGfDn~rqvq~~sfIV~RP~  167 (172)
                      ++|||+|||||||||++|+||++||||||.
T Consensus        70 ~~~p~~yVRlig~D~~~q~r~~~~iVqRP~   99 (99)
T PF00101_consen   70 AEHPGEYVRLIGFDNKRQRRVLEFIVQRPN   99 (99)
T ss_dssp             HHSTTSEEEEEEEETTTTEEEEEEEEEGGT
T ss_pred             HhCCCceEEEEEEcCcccEEEEEEEEECCC
Confidence            999999999999999999999999999995

RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown []. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [], which results in RuBisCO being more abundant during the day when it is required. The RuBisCo small subunit consists of a central four-stranded beta-sheet, with two helices packed against it [].; PDB: 1BWV_W 1IWA_P 3AXM_X 1WDD_S 3AXK_T 1IR2_K 1RBL_N 1UZH_J 1RSC_P 1UW9_C ....

>COG4451 RbcS Ribulose bisphosphate carboxylase small subunit [Energy production and conversion]

Probab=100.00  E-value=1.9e-48  Score=303.87  Aligned_cols=104  Identities=32%  Similarity=0.749  Sum_probs=100.9

Q ss_pred             CccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHH
Q 030735           55 NNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQ  134 (172)
Q Consensus        55 ~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie  134 (172)
                      .+..++||||||+|||+||++||+|||.|||+|++||+|+++| |          +.||+|||+||||..++.+||+|||
T Consensus         6 ~~~~~~~~s~lp~Ltd~qi~~QVrylL~QGykigvE~~d~rrp-r----------tgsWt~wg~p~f~~~~~~evlaele   74 (127)
T COG4451           6 KNSRYKTLSSLPPLTDEQIAEQVRYLLSQGYKIGVEYVDDRRP-R----------TGSWTMWGTPMFGAKTAGEVLAELE   74 (127)
T ss_pred             CCCcccceecCCcCcHHHHHHHHHHHHhCCcccceeecccCCc-c----------cceeeecCCccccccchHHHHHHHH
Confidence            6889999999999999999999999999999999999999977 4          9999999999999999999999999


Q ss_pred             HHHHHCCCCeEEEEeeecCCCeEEEEEEEecCCCC
Q 030735          135 ECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTT  169 (172)
Q Consensus       135 ~C~k~~P~~YIRliGfDn~rqvq~~sfIV~RP~~~  169 (172)
                      +|+++||++|||||||||++|+|++|||||||.+.
T Consensus        75 ~Cr~dhp~eYIRliGfDp~gkrrv~sfIVhRPng~  109 (127)
T COG4451          75 ACRADHPGEYIRLIGFDPKGKRRVVSFIVHRPNGN  109 (127)
T ss_pred             HHHHhCCCCeEEEEEecCCCceEEEEEEEECCCCC
Confidence            99999999999999999999999999999999864

>cd00307 RuBisCO_small_like Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins

Probab=100.00  E-value=5.2e-46  Score=273.71  Aligned_cols=82  Identities=18%  Similarity=0.415  Sum_probs=80.1

Q ss_pred             hHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCC--CCHHHHHHHHHHHHHHCCCCeEEE
Q 030735           70 DDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGC--NDSSQILNEIQECKKAYPNAYIRC  147 (172)
Q Consensus        70 d~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~--td~sqVl~Eie~C~k~~P~~YIRl  147 (172)
                      |+||.+||+|||+|||+|||||+|+               +|||||||||||+|  +|++|||+||++|+++|||+||||
T Consensus         1 d~~i~~QI~yll~qG~~~~iE~~d~---------------~rywt~w~lp~f~~~~~~~~~Vl~el~~c~~~~p~~YVRl   65 (84)
T cd00307           1 SEDVVEQVRQLLAQGYKIGLEHADA---------------RRFRTSSWQSCGPIEGRSEAQVLAALEACLAEHPGEYVRL   65 (84)
T ss_pred             CHHHHHHHHHHHHCCCEeEEEECCC---------------CccHhhhcCCCCCCCCCCHHHHHHHHHHHHHHCCCCeEEE
Confidence            6899999999999999999999986               48999999999999  999999999999999999999999


Q ss_pred             EeeecCCCeEEEEEEEecC
Q 030735          148 LAFNNQKQGQCMSFLIQKP  166 (172)
Q Consensus       148 iGfDn~rqvq~~sfIV~RP  166 (172)
                      |||||++|+|++|||||||
T Consensus        66 ig~D~~~q~~~~~fIv~RP   84 (84)
T cd00307          66 IGIDPKAKRRVLEIIIQRP   84 (84)
T ss_pred             EEEeCCccEEEEEEEeeCc
Confidence            9999999999999999999

Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits. This superfamily also contains specific proteins from cyanobacteria. CcmM plays a role in a CO2 concentrating mechanism, which cyanobacteria need to to overcome t

>PF12338 RbcS: Ribulose-1,5-bisphosphate carboxylase small subunit; InterPro: IPR024680 This domain is found in the N-terminal region of the small subunit of ribulose-1,5-bisphosphate in plants

Probab=98.56  E-value=2.5e-08  Score=66.55  Aligned_cols=28  Identities=21%  Similarity=0.243  Sum_probs=24.4

Q ss_pred             ccCcccccccccccCCcccccccccccCCC
Q 030735            6 FTAPVAGSGYLGLKPTSKALLPVKDSIAWS   35 (172)
Q Consensus         6 ~a~~~~va~f~glks~~~~~fp~~~~~~~~   35 (172)
                      .++++|||||+||||+++  ||++||.++|
T Consensus        18 ~aqa~mVAPFtGLKS~a~--fPvtrK~~nd   45 (45)
T PF12338_consen   18 PAQASMVAPFTGLKSTAA--FPVTRKSNND   45 (45)
T ss_pred             ccccceeecccccccccc--CccccccCCC
Confidence            356689999999999999  9999998654

It contains a conserved APF sequence motif. There are also two completely conserved residues (L and P) that may be functionally important.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	172
1uzd_C	134	Chlamydomonas,Spinach Chimeric Rubisco Length = 134		7e-45
3rub_S	123	Crystal Structure Of The Unactivated Form Of Ribulo		2e-44
4rub_S	123	A Crystal Form Of Ribulose-1,5-Bisphosphate Carboxy		6e-44
4hhh_S	123	Structure Of Pisum Sativum Rubisco Length = 123		1e-42
3axk_S	129	Structure Of Rice Rubisco In Complex With Nadp(H) L		8e-42
1aus_S	123	Activated Unliganded Spinach Rubisco Length = 123		2e-41
1ir1_S	123	Crystal Structure Of Spinach Ribulose-1,5-Bisphosph		5e-41
3axm_S	129	Structure Of Rice Rubisco In Complex With 6pg Lengt		6e-41
1wdd_S	128	Crystal Structure Of Activated Rice Rubisco Complex		3e-40
1gk8_I	140	Rubisco From Chlamydomonas Reinhardtii Length = 140		1e-39
1uw9_C	140	L290f-a222t Chlamydomonas Rubisco Mutant Length = 1		1e-39
1ir2_I	140	Crystal Structure Of Activated Ribulose-1,5-Bisphos		3e-39
1uzh_C	122	A Chimeric Chlamydomonas, Synechococcus Rubisco Enz		1e-35
2ybv_B	118	Structure Of Rubisco From Thermosynechococcus Elong		6e-28
1rsc_M	111	Structure Of An Effector Induced Inactivated State		5e-23
1rbl_M	109	Structure Determination And Refinement Of Ribulose		1e-22
1svd_M	110	The Structure Of Halothiobacillus Neapolitanus Rubi		1e-15
1bxn_I	139	The Crystal Structure Of Rubisco From Alcaligenes E		8e-15
4f0h_B	138	Unactivated Rubisco With Oxygen Bound Length = 138		6e-14
1bwv_S	138	Activated Ribulose 1,5-Bisphosphate CarboxylaseOXYG		2e-13
1iwa_B	138	Rubisco From Galdieria Partita Length = 138		2e-13

>pdb|1UZD|C Chain C, Chlamydomonas,Spinach Chimeric Rubisco Length = 134

Iteration: 1
 Score =  176 bits (445), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 74/123 (60%), Positives = 93/123 (75%), Gaps = 1/123 (0%)
Query: 48  MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEF-DEVGYVHRENSKMPG 106
           M  W P+NNK FE  SYLP L+D+ IA ++DY++  GWIPCLEF  + G+V+RE+   PG
Sbjct: 1   MMVWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLEFATDHGFVYREHHNSPG 60
Query: 107 YYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           YYDGRYWTMWKLPMFGC D  Q+L EI  C KA+P+AY+R +AF+NQKQ Q M FL+Q+P
Sbjct: 61  YYDGRYWTMWKLPMFGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMGFLVQRP 120
Query: 167 TTT 169
            T 
Sbjct: 121 KTA 123

>pdb|3RUB|S Chain S, Crystal Structure Of The Unactivated Form Of Ribulose-1,5-Bisphosphate Carboxylase(Slash)oxygenase From Tobacco Refined At 2.0-Angstroms Resolution Length = 123

Iteration: 1
 Score =  174 bits (442), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 74/120 (61%), Positives = 97/120 (80%), Gaps = 1/120 (0%)
Query: 48  MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPG 106
           M+ W PIN KK+E LSYLP LS + +  E++Y+LK GW+PCLEF+ E G+V+REN+K PG
Sbjct: 1   MQVWPPINKKKYETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEFETEHGFVYRENNKSPG 60
Query: 107 YYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           YYDGRYWTMWKLPMFGC D++Q+L E++E KKAYP A+IR + F+N +Q QC+SF+  KP
Sbjct: 61  YYDGRYWTMWKLPMFGCTDATQVLAEVEEAKKAYPQAWIRIIGFDNVRQVQCISFIAYKP 120

>pdb|4RUB|S Chain S, A Crystal Form Of Ribulose-1,5-Bisphosphate Carboxylase(Slash) Oxygenase From Nicotiana Tabacum In The Activated State Length = 123

Iteration: 1
 Score =  172 bits (437), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 74/120 (61%), Positives = 96/120 (80%), Gaps = 1/120 (0%)
Query: 48  MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPG 106
           M+ W PIN KK+E LSYLP LS + +  E++Y+LK GW+PCLEF+ E G+V+REN+K PG
Sbjct: 1   MQVWPPINKKKYETLSYLPDLSQEQLLSEVEYLLKNGWVPCLEFETEHGFVYRENNKSPG 60
Query: 107 YYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           YYDGRYWTMWKLPMFGC D++Q+L E+ E KKAYP A+IR + F+N +Q QC+SF+  KP
Sbjct: 61  YYDGRYWTMWKLPMFGCTDATQVLAEVGEAKKAYPQAWIRIIGFDNVRQVQCISFIAYKP 120

>pdb|4HHH|S Chain S, Structure Of Pisum Sativum Rubisco Length = 123

Iteration: 1
 Score =  169 bits (427), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 70/122 (57%), Positives = 94/122 (77%), Gaps = 1/122 (0%)
Query: 48  MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPG 106
           M+ W PI  KKFE LSYLP L+ D + KE++Y+L+KGW+PCLEF+ + G+V+RE++K PG
Sbjct: 1   MQVWPPIGKKKFETLSYLPPLTRDQLLKEVEYLLRKGWVPCLEFELKKGFVYREHNKSPG 60
Query: 107 YYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           YYDGRYWTMWKLPMFG  D +Q+L E+ E KK YP A++R + FNN +Q QC+SF+   P
Sbjct: 61  YYDGRYWTMWKLPMFGTTDPAQVLKELDEVKKEYPRAFVRVIGFNNVRQVQCISFIAHTP 120
Query: 167 TT 168
            +
Sbjct: 121 ES 122

>pdb|3AXK|S Chain S, Structure Of Rice Rubisco In Complex With Nadp(H) Length = 129

Iteration: 1
 Score =  166 bits (419), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 68/119 (57%), Positives = 94/119 (78%)
Query: 48  MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGY 107
           M+ W     KKFE LSYLP L+ + + K+I+Y+L+  W+PCLEF +VG+V+REN + PGY
Sbjct: 2   MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGY 61
Query: 108 YDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           YDGRYWTMWKLPMFGC D++Q+L E++E KKAYP+A++R + F+N +Q QC+SF+  KP
Sbjct: 62  YDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQCISFIAYKP 120

>pdb|1AUS|S Chain S, Activated Unliganded Spinach Rubisco Length = 123

Iteration: 1
 Score =  164 bits (416), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 68/121 (56%), Positives = 95/121 (78%), Gaps = 1/121 (0%)
Query: 48  MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPG 106
           M+ W  +N KK+E LSYLP L+ D +A+++DY+L   W+PCLEF+ + G+V+RE+   PG
Sbjct: 1   MQVWPILNLKKYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPG 60
Query: 107 YYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           YYDGRYWTMWKLPMFGC D +Q+LNE++ECKK YPNA+IR + F++ ++ QC+SF+  KP
Sbjct: 61  YYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNREVQCISFIAYKP 120
Query: 167 T 167
Sbjct: 121 A 121

>pdb|1IR1|S Chain S, Crystal Structure Of Spinach Ribulose-1,5-Bisphosphate CarboxylaseOXYGENASE (RUBISCO) COMPLEXED WITH CO2, MG2+ AND 2- Carboxyarabinitol-1,5-Bisphosphate Length = 123

Iteration: 1
 Score =  163 bits (412), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 68/119 (57%), Positives = 93/119 (78%), Gaps = 1/119 (0%)
Query: 49  KTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFD-EVGYVHRENSKMPGY 107
           K W   N K++E LSYLP L+ D +A+++DY+L   W+PCLEF+ + G+V+RE+   PGY
Sbjct: 2   KVWPTQNMKRYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPGY 61
Query: 108 YDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           YDGRYWTMWKLPMFGC D +Q+LNE++ECKK YPNA+IR + F++ +Q QC+SF+  KP
Sbjct: 62  YDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNRQVQCVSFIAYKP 120

>pdb|3AXM|S Chain S, Structure Of Rice Rubisco In Complex With 6pg Length = 129

Iteration: 1
 Score =  163 bits (412), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 67/119 (56%), Positives = 93/119 (78%)
Query: 48  MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGY 107
           M+ W     KKFE LSYLP L+ + + K+I+Y+L+  W+PCLEF +VG+V+REN + PGY
Sbjct: 2   MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGY 61
Query: 108 YDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           YDGRYWTMWKLPMFGC D++Q+L E++E KKAYP+A++R + F+N +Q Q +SF+  KP
Sbjct: 62  YDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKP 120

>pdb|1WDD|S Chain S, Crystal Structure Of Activated Rice Rubisco Complexed With 2- Carboxyarabinitol-1,5-Bisphosphate Length = 128

Iteration: 1
 Score =  160 bits (405), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 66/118 (55%), Positives = 92/118 (77%)
Query: 49  KTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYY 108
           + W     KKFE LSYLP L+ + + K+I+Y+L+  W+PCLEF +VG+V+REN + PGYY
Sbjct: 2   QVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYY 61
Query: 109 DGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           DGRYWTMWKLPMFGC D++Q+L E++E KKAYP+A++R + F+N +Q Q +SF+  KP
Sbjct: 62  DGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKP 119

>pdb|1GK8|I Chain I, Rubisco From Chlamydomonas Reinhardtii Length = 140

Iteration: 1
 Score =  159 bits (401), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 71/127 (55%), Positives = 88/127 (69%), Gaps = 7/127 (5%)
Query: 50  TWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEV--GYVHRENSKMPG- 106
            W P+NNK FE  SYLP L+D+ IA ++DY++  GWIPCLEF E    YV  E++   G 
Sbjct: 3   VWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLEFAEADKAYVSNESAIRFGS 62
Query: 107 ----YYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFL 162
               YYD RYWTMWKLPMFGC D  Q+L EI  C KA+P+AY+R +AF+NQKQ Q M FL
Sbjct: 63  VSCLYYDNRYWTMWKLPMFGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMGFL 122
Query: 163 IQKPTTT 169
           +Q+P T 
Sbjct: 123 VQRPKTA 129

>pdb|1UW9|C Chain C, L290f-a222t Chlamydomonas Rubisco Mutant Length = 140

Iteration: 1
 Score =  158 bits (400), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 71/129 (55%), Positives = 89/129 (68%), Gaps = 7/129 (5%)
Query: 48  MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEV--GYVHRENSKMP 105
           M  W P+NNK FE  SYLP L+D+ IA ++DY++  GWIPCLEF E    YV  E++   
Sbjct: 1   MMVWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLEFAEADKAYVSNESAIRF 60
Query: 106 G-----YYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMS 160
           G     YYD RYWTMWKLPMFGC D  Q+L EI  C KA+P+AY+R +AF+NQKQ Q M 
Sbjct: 61  GSVSCLYYDNRYWTMWKLPMFGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMG 120
Query: 161 FLIQKPTTT 169
           FL+Q+P + 
Sbjct: 121 FLVQRPKSA 129

>pdb|1IR2|I Chain I, Crystal Structure Of Activated Ribulose-1,5-Bisphosphate CarboxylaseOXYGENASE (RUBISCO) FROM GREEN ALGA, CHLAMYDOMONAS Reinhardtii Complexed With 2-Carboxyarabinitol-1,5-Bisphosphate (2- Cabp) Length = 140

Iteration: 1
 Score =  157 bits (397), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 71/127 (55%), Positives = 88/127 (69%), Gaps = 7/127 (5%)
Query: 50  TWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEV--GYVHRENSKMPG- 106
            W P+NNK FE  SYLP LSD+ IA ++DY++  GWIPCLEF E    YV  E++   G 
Sbjct: 3   VWTPVNNKMFETFSYLPPLSDEQIAAQVDYIVANGWIPCLEFAESDKAYVSNESAIRFGS 62
Query: 107 ----YYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFL 162
               YYD RYWTMWKLPMFGC D  Q+L EI  C KA+P+AY+R +AF+NQKQ Q M FL
Sbjct: 63  VSCLYYDNRYWTMWKLPMFGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMGFL 122
Query: 163 IQKPTTT 169
           +Q+P + 
Sbjct: 123 VQRPKSA 129

>pdb|1UZH|C Chain C, A Chimeric Chlamydomonas, Synechococcus Rubisco Enzyme Length = 122

Iteration: 1
 Score =  145 bits (365), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 65/122 (53%), Positives = 81/122 (66%), Gaps = 11/122 (9%)
Query: 48  MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGY 107
           M  W P+NNK FE  SYLP L+D+ IA ++DY++  GWIPCLEF E    H    +    
Sbjct: 1   MMVWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLEFAE----HSNPEEF--- 53
Query: 108 YDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPT 167
               YWTMWKLPMFGC D  Q+L EI  C KA+P+AY+R +AF+NQKQ Q M FL+Q+P 
Sbjct: 54  ----YWTMWKLPMFGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMGFLVQRPK 109
Query: 168 TT 169
           T 
Sbjct: 110 TA 111

>pdb|2YBV|B Chain B, Structure Of Rubisco From Thermosynechococcus Elongatus Length = 118

Iteration: 1
 Score =  119 bits (299), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 52/115 (45%), Positives = 77/115 (66%), Gaps = 11/115 (9%)
Query: 57  KKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMW 116
           +++E  SYLP LSD  IA++I Y + +G+ PC+EF+E       N+++      RYWTMW
Sbjct: 8   RRYETFSYLPPLSDAQIARQIQYAIDQGYHPCVEFNETS-----NAEI------RYWTMW 56
Query: 117 KLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTTS 171
           KLP+F C ++  +LNE+Q+C+  YPN +IR +AF+N KQ Q MSF++ KP    S
Sbjct: 57  KLPLFNCTNAQDVLNEVQQCRSEYPNCFIRVVAFDNIKQCQVMSFIVYKPNQANS 111

>pdb|1RSC|M Chain M, Structure Of An Effector Induced Inactivated State Of Ribulose Bisphosphate Carboxylase(Slash)oxygenase: The Binary Complex Between Enzyme And Xylulose Bisphosphate Length = 111

Iteration: 1
 Score =  103 bits (257), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 46/111 (41%), Positives = 70/111 (63%), Gaps = 11/111 (9%)
Query: 56  NKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTM 115
            ++FE  SYLP LSD  IA +I+YM+++G+ P +EF+E    H    +        YWTM
Sbjct: 9   ERRFETFSYLPPLSDRQIAAQIEYMIEQGFHPLIEFNE----HSNPEEF-------YWTM 57
Query: 116 WKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           WKLP+F C    Q+L+E++EC+  Y + YIR   F+N K+ Q +SF++ +P
Sbjct: 58  WKLPLFDCKSPQQVLDEVRECRSEYGDCYIRVAGFDNIKECQTVSFIVHRP 108

>pdb|1RBL|M Chain M, Structure Determination And Refinement Of Ribulose 1,5 Bisphosphate Carboxylase(Slash)oxygenase From Synechococcus Pcc6301 Length = 109

Iteration: 1
 Score =  102 bits (254), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 46/111 (41%), Positives = 69/111 (62%), Gaps = 11/111 (9%)
Query: 56  NKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTM 115
            ++FE  SYLP LSD  IA +I+YM+++G+ P +EF+E    H    +        YWTM
Sbjct: 8   ERRFETFSYLPPLSDRQIAAQIEYMIEQGFHPLIEFNE----HSNPEEF-------YWTM 56
Query: 116 WKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           WKLP+F C    Q+L+E++EC+  Y + YIR   F+N K+ Q  SF++ +P
Sbjct: 57  WKLPLFACAAPQQVLDEVRECRSEYGDCYIRVAGFDNIKECQTSSFIVHRP 107

>pdb|1SVD|M Chain M, The Structure Of Halothiobacillus Neapolitanus Rubisco Length = 110

Iteration: 1
 Score = 79.0 bits (193), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 37/108 (34%), Positives = 61/108 (56%), Gaps = 11/108 (10%)
Query: 58  KFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWK 117
           K+E  SYLP ++ + I  +I Y + +GW P +E  EV     +NS        +YW MWK
Sbjct: 12  KYETFSYLPPMNAERIRAQIKYAIAQGWSPGIEHVEV-----KNSM------NQYWYMWK 60
Query: 118 LPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQK 165
           LP FG  +   +L EI+ C+ AYP   ++ +A++N  Q   ++F++ +
Sbjct: 61  LPFFGEQNVDNVLAEIEACRSAYPTHQVKLVAYDNYAQSLGLAFVVYR 108

>pdb|1BXN|I Chain I, The Crystal Structure Of Rubisco From Alcaligenes Eutrophus To 2.7 Angstroms. Length = 139

Iteration: 1
 Score = 76.3 bits (186), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 38/107 (35%), Positives = 59/107 (55%), Gaps = 13/107 (12%)
Query: 62  LSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMF 121
            S+LP L+D+ I K+++Y L +GW   LE+ +    H  N+         YW M+ LPMF
Sbjct: 8   FSFLPELTDEQITKQLEYCLNQGWAVGLEYTDDP--HPRNT---------YWEMFGLPMF 56
Query: 122 GCNDSSQILNEIQECKKAYPNAYIRCLAFNNQK--QGQCMSFLIQKP 166
              D++ IL EI   +  +PN YIR  AF++    +   MSF++ +P
Sbjct: 57  DLRDAAGILMEINNARNTFPNHYIRVTAFDSTHTVESVVMSFIVNRP 103

>pdb|4F0H|B Chain B, Unactivated Rubisco With Oxygen Bound Length = 138

Iteration: 1
 Score = 73.6 bits (179), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 36/108 (33%), Positives = 60/108 (55%), Gaps = 13/108 (12%)
Query: 61  ALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPM 120
             S+LP L+D+ I K+IDYM+ K     +E+     +H  NS         +W MW LP+
Sbjct: 7   TFSFLPDLTDEQIKKQIDYMISKKLAIGIEY--TNDIHPRNS---------FWEMWGLPL 55
Query: 121 FGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQK--QGQCMSFLIQKP 166
           F   D + +L EI  C+KA  N YI+ + F++++  +   +SF++ +P
Sbjct: 56  FEVTDPAPVLFEINACRKAKSNFYIKVVGFSSERGIESTIISFIVNRP 103

>pdb|1BWV|S Chain S, Activated Ribulose 1,5-Bisphosphate CarboxylaseOXYGENASE (RUBISCO) Complexed With The Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate Length = 138

Iteration: 1
 Score = 72.0 bits (175), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/107 (32%), Positives = 59/107 (55%), Gaps = 13/107 (12%)
Query: 62  LSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMF 121
            S+LP L+D+ I K+IDYM+ K     +E+     +H  N+         YW +W LP+F
Sbjct: 8   FSFLPDLTDEQIKKQIDYMISKKLAIGIEY--TNDIHPRNA---------YWEIWGLPLF 56
Query: 122 GCNDSSQILNEIQECKKAYPNAYIRCLAFNNQK--QGQCMSFLIQKP 166
              D + +L EI  C+KA  N YI+ + F++ +  +   +SF++ +P
Sbjct: 57  DVTDPAAVLFEINACRKARSNFYIKVVGFSSVRGIESTIISFIVNRP 103

>pdb|1IWA|B Chain B, Rubisco From Galdieria Partita Length = 138

Iteration: 1
 Score = 71.6 bits (174), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/107 (32%), Positives = 59/107 (55%), Gaps = 13/107 (12%)
Query: 62  LSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMF 121
            S+LP L+D+ I K+IDYM+ K     +E+     +H  N+         YW +W LP+F
Sbjct: 8   FSFLPDLTDEQIKKQIDYMISKKLAIGIEY--TNDIHPRNA---------YWEIWGLPLF 56
Query: 122 GCNDSSQILNEIQECKKAYPNAYIRCLAFNNQK--QGQCMSFLIQKP 166
              D + +L EI  C+KA  N YI+ + F++ +  +   +SF++ +P
Sbjct: 57  DVTDPAAVLFEINACRKARSNFYIKVVGFSSVRGIESTIISFIVNRP 103

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	172
1wdd_S	128	Ribulose bisphosphate carboxylase small chain C; r	7e-61
1gk8_I	140	Ribulose bisphosphate carboxylase small chain 1; l	3e-56
1svd_M	110	Ribulose bisphosphate carboxylase small chain; bet	6e-45
2ybv_B	118	Ribulose bisphosphate carboxylase small subunit; C	1e-44
1rbl_M	109	Ribulose 1,5 bisphosphate carboxylase/oxygenase (	2e-41
1bwv_S	138	Rubisco, protein (ribulose bisphosphate carboxylas	1e-39
1bxn_I	139	Rubisco, protein (ribulose bisphosphate carboxylas	2e-38

>1wdd_S Ribulose bisphosphate carboxylase small chain C; rubisco, photosynthesis, alpha/beta barrel, N-methylmethioni translational modification, lyase; HET: KCX CAP; 1.35A {Oryza sativa} SCOP: d.73.1.1 PDB: 3axm_S* 3axk_S* 8ruc_I* 1aus_S 1rbo_S* 1rco_S* 1rcx_S* 1rxo_S* 1upm_C* 1upp_I* 1aa1_S* 3rub_S 1rlc_S* 1rld_S 1ej7_S 1ir1_S* 4rub_S* Length = 128

 Score =  184 bits (467), Expect = 7e-61
 Identities = 66/123 (53%), Positives = 92/123 (74%)

Query: 49  KTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYY 108
           + W     KKFE LSYLP L+ + + K+I+Y+L+  W+PCLEF +VG+V+REN + PGYY
Sbjct: 2   QVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYY 61

Query: 109 DGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTT 168
           DGRYWTMWKLPMFGC D++Q+L E++E KKAYP+A++R + F+N +Q Q +SF+  KP  
Sbjct: 62  DGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPPG 121

Query: 169 TTS 171
              
Sbjct: 122 CEE 124

>1gk8_I Ribulose bisphosphate carboxylase small chain 1; lyase, rubisco, photosynthesis; HET: KCX CAP; 1.4A {Chlamydomonas reinhardtii} SCOP: d.73.1.1 PDB: 2v63_I* 2v67_I* 2v68_I* 2v69_I* 2v6a_I* 2vdh_I* 2vdi_I* 1uw9_C* 1uwa_C* 1ir2_I* 1uzd_C* 1uzh_C* Length = 140

 Score =  173 bits (438), Expect = 3e-56
 Identities = 69/127 (54%), Positives = 85/127 (66%), Gaps = 7/127 (5%)

Query: 51  WNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVH-------RENSK 103
           W P+NNK FE  SYLP L+D+ IA ++DY++  GWIPCLEF E    +       R  S 
Sbjct: 4   WTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLEFAEADKAYVSNESAIRFGSV 63

Query: 104 MPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLI 163
              YYD RYWTMWKLPMFGC D  Q+L EI  C KA+P+AY+R +AF+NQKQ Q M FL+
Sbjct: 64  SCLYYDNRYWTMWKLPMFGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMGFLV 123

Query: 164 QKPTTTT 170
           Q+P T  
Sbjct: 124 QRPKTAR 130

>1svd_M Ribulose bisphosphate carboxylase small chain; beta-alpha-barrel, lyase; 1.80A {Halothiobacillus neapolitanus} SCOP: d.73.1.1 Length = 110

 Score =  142 bits (360), Expect = 6e-45
 Identities = 33/116 (28%), Positives = 58/116 (50%), Gaps = 11/116 (9%)

Query: 51  WNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDG 110
            +   + K+E  SYLP ++ + I  +I Y + +GW P +E                    
Sbjct: 5   QDYKQSLKYETFSYLPPMNAERIRAQIKYAIAQGWSPGIEHV-----------EVKNSMN 53

Query: 111 RYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           +YW MWKLP FG  +   +L EI+ C+ AYP   ++ +A++N  Q   ++F++ + 
Sbjct: 54  QYWYMWKLPFFGEQNVDNVLAEIEACRSAYPTHQVKLVAYDNYAQSLGLAFVVYRG 109

>2ybv_B Ribulose bisphosphate carboxylase small subunit; CO2/O2 specificity, carbon dioxide fixation, photosynthesis, thermostability; 2.30A {Thermosynechococcus elongatus} Length = 118

 Score =  142 bits (358), Expect = 1e-44
 Identities = 53/124 (42%), Positives = 76/124 (61%), Gaps = 13/124 (10%)

Query: 48  MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGY 107
           MKT      +++E  SYLP LSD  IA++I Y + +G+ PC+EF+               
Sbjct: 1   MKTLPK--ERRYETFSYLPPLSDAQIARQIQYAIDQGYHPCVEFN-----------ETSN 47

Query: 108 YDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPT 167
            + RYWTMWKLP+F C ++  +LNE+Q+C+  YPN +IR +AF+N KQ Q MSF++ KP 
Sbjct: 48  AEIRYWTMWKLPLFNCTNAQDVLNEVQQCRSEYPNCFIRVVAFDNIKQCQVMSFIVYKPN 107

Query: 168 TTTS 171
              S
Sbjct: 108 QANS 111

>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* Length = 109

 Score =  134 bits (337), Expect = 2e-41
 Identities = 48/120 (40%), Positives = 71/120 (59%), Gaps = 13/120 (10%)

Query: 48  MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGY 107
           MKT      ++FE  SYLP LSD  IA +I+YM+++G+ P +EF+E              
Sbjct: 2   MKTLPK--ERRFETFSYLPPLSDRQIAAQIEYMIEQGFHPLIEFNE-----------HSN 48

Query: 108 YDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPT 167
            +  YWTMWKLP+F C    Q+L+E++EC+  Y + YIR   F+N K+ Q  SF++ +P 
Sbjct: 49  PEEFYWTMWKLPLFACAAPQQVLDEVRECRSEYGDCYIRVAGFDNIKECQTSSFIVHRPG 108

>1bwv_S Rubisco, protein (ribulose bisphosphate carboxylase); carbon dioxide fixation, complex (rubisco-reaction intermedi high specificity factor; HET: KCX CAP; 2.40A {Galdieria partita} SCOP: d.73.1.1 PDB: 1iwa_B Length = 138

 Score =  130 bits (327), Expect = 1e-39
 Identities = 33/117 (28%), Positives = 56/117 (47%), Gaps = 13/117 (11%)

Query: 57  KKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMW 116
                 S+LP L+D+ I K+IDYM+ K     +E+               +    YW +W
Sbjct: 3   ITQGTFSFLPDLTDEQIKKQIDYMISKKLAIGIEYT-----------NDIHPRNAYWEIW 51

Query: 117 KLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQC--MSFLIQKPTTTTS 171
            LP+F   D + +L EI  C+KA  N YI+ + F++ +  +   +SF++ +P     
Sbjct: 52  GLPLFDVTDPAAVLFEINACRKARSNFYIKVVGFSSVRGIESTIISFIVNRPKHEPG 108

>1bxn_I Rubisco, protein (ribulose bisphosphate carboxylase small; lyase (carbon-carbon), lyase; 2.70A {Cupriavidus necator} SCOP: d.73.1.1 Length = 139

 Score =  127 bits (320), Expect = 2e-38
 Identities = 36/115 (31%), Positives = 56/115 (48%), Gaps = 13/115 (11%)

Query: 58  KFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWK 117
                S+LP L+D+ I K+++Y L +GW   LE+               +    YW M+ 
Sbjct: 4   TQGTFSFLPELTDEQITKQLEYCLNQGWAVGLEYT-----------DDPHPRNTYWEMFG 52

Query: 118 LPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQC--MSFLIQKPTTTT 170
           LPMF   D++ IL EI   +  +PN YIR  AF++    +   MSF++ +P    
Sbjct: 53  LPMFDLRDAAGILMEINNARNTFPNHYIRVTAFDSTHTVESVVMSFIVNRPADEP 107

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	172
1wdd_S	128	Ribulose bisphosphate carboxylase small chain C; r	100.0
1gk8_I	140	Ribulose bisphosphate carboxylase small chain 1; l	100.0
3zxw_B	118	Ribulose bisphosphate carboxylase small chain; CO2	100.0
1rbl_M	109	Ribulose 1,5 bisphosphate carboxylase/oxygenase (	100.0
1svd_M	110	Ribulose bisphosphate carboxylase small chain; bet	100.0
1bwv_S	138	Rubisco, protein (ribulose bisphosphate carboxylas	100.0
1bxn_I	139	Rubisco, protein (ribulose bisphosphate carboxylas	100.0
4f0h_B	138	Ribulose bisphosphate carboxylase small chain; alp	100.0
3frm_A	254	Uncharacterized conserved protein; APC61048, staph	88.07

>1wdd_S Ribulose bisphosphate carboxylase small chain C; rubisco, photosynthesis, alpha/beta barrel, N-methylmethioni translational modification, lyase; HET: KCX CAP; 1.35A {Oryza sativa} SCOP: d.73.1.1 PDB: 3axm_S* 3axk_S* 8ruc_I* 1aus_S 1rbo_S* 1rco_S* 1rcx_S* 1rxo_S* 1upm_C* 1upp_I* 1aa1_S* 3rub_S 1rlc_S* 1rld_S 1ej7_S 1ir1_S* 4rub_S*

Probab=100.00  E-value=5.5e-76  Score=460.32  Aligned_cols=124  Identities=53%  Similarity=1.100  Sum_probs=121.1

Q ss_pred             eeeeccCCccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHH
Q 030735           48 MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSS  127 (172)
Q Consensus        48 m~vw~p~~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~s  127 (172)
                      ||||||+|+||||||||||||||+||++||+|||+|||+|||||+|++|+||+|++||||||++||+|||||||||+|++
T Consensus         1 m~vw~p~~~~~~~tfSyLP~lt~eqI~kQI~Yll~qGw~p~lEf~d~~~~~R~~~~~~~~~~~~yW~mWkLPmFg~td~~   80 (128)
T 1wdd_S            1 XQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLPMFGCTDAT   80 (128)
T ss_dssp             CCCCCSSSCCCCSTTTTSSCCCHHHHHHHHHHHHHTTCEEEEEEESCCSCBCSSCCSTTCCBSCCCEEESCCCTTCCCHH
T ss_pred             CcccCCCCCccccccccCCCCCHHHHHHHHHHHHHCCCeeeEEecCCCceeeccCCCCCcccCCcccccCccCccCCCHH
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHCCCCeEEEEeeecCCCeEEEEEEEecCCCCCC
Q 030735          128 QILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTTS  171 (172)
Q Consensus       128 qVl~Eie~C~k~~P~~YIRliGfDn~rqvq~~sfIV~RP~~~~~  171 (172)
                      |||+||++|+++|||+|||||||||++|+||+|||||||.+.+.
T Consensus        81 ~Vl~El~~C~k~~P~~YVRligfDn~~q~q~~sfIv~RP~~~~~  124 (128)
T 1wdd_S           81 QVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPPGCEE  124 (128)
T ss_dssp             HHHHHHHHHHHHCTTSEEEEEEEETTTTEEEEEEEEECCTTC--
T ss_pred             HHHHHHHHHHHHCCCCeEEEEEEeCCCCEEEEEEEEECCCCccc
Confidence            99999999999999999999999999999999999999998764

>1gk8_I Ribulose bisphosphate carboxylase small chain 1; lyase, rubisco, photosynthesis; HET: KCX CAP; 1.4A {Chlamydomonas reinhardtii} SCOP: d.73.1.1 PDB: 2v63_I* 2v67_I* 2v68_I* 2v69_I* 2v6a_I* 2vdh_I* 2vdi_I* 1uw9_C* 1uwa_C* 1ir2_I* 1uzd_C* 1uzh_C*

Probab=100.00  E-value=1.6e-74  Score=457.68  Aligned_cols=123  Identities=56%  Similarity=1.080  Sum_probs=118.3

Q ss_pred             eeeeccCCccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecC-------CCCCCccCCcceeeccCCC
Q 030735           48 MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHREN-------SKMPGYYDGRYWTMWKLPM  120 (172)
Q Consensus        48 m~vw~p~~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~-------~~sp~yyd~ryWtmWkLPm  120 (172)
                      ||||+|+|+||||||||||||||+||++||+|||+|||+|||||+|++++||++       ++|||||||+||+||||||
T Consensus         1 m~vw~p~~~~~~etfSyLP~lt~eqI~kQI~YlL~qGw~p~lEf~d~~~~~r~~~~~~~~~~~~~~yyd~~YW~mWkLPm   80 (140)
T 1gk8_I            1 XMVWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLEFAEADKAYVSNESAIRFGSVSCLYYDNRYWTMWKLPM   80 (140)
T ss_dssp             CCCCCCSSCCCCSTTTTSSCCCHHHHHHHHHHHHHTTCEEEEEEECGGGTSCBCGGGGGCSSCCTTCCBTSSCEEESCCC
T ss_pred             CcccCCcCCceecccccCCCCCHHHHHHHHHHHHHCCCEeeEEeccCCcceecccccccccccCCCcCcCCeeeeCCcCC
Confidence            899999999999999999999999999999999999999999999999999999       9999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCeEEEEeeecCCCeEEEEEEEecCCCCC
Q 030735          121 FGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTT  170 (172)
Q Consensus       121 fg~td~sqVl~Eie~C~k~~P~~YIRliGfDn~rqvq~~sfIV~RP~~~~  170 (172)
                      |||+|++|||+||++|+|+|||+|||||||||++|+||+|||||||.+..
T Consensus        81 Fg~td~~qVl~El~~C~k~~P~~YVRligfDn~~q~q~~sfIV~RP~~~~  130 (140)
T 1gk8_I           81 FGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMGFLVQRPKTAR  130 (140)
T ss_dssp             TTCCCHHHHHHHHHHHHHHCTTSEEEEEEEETTTTEEEEEEEEECC----
T ss_pred             cCCCCHHHHHHHHHHHHHHCCCCeEEEEEEeCCCCEEEEEEEeECCCCCC
Confidence            99999999999999999999999999999999999999999999998754

>3zxw_B Ribulose bisphosphate carboxylase small chain; CO2/O2 specificity, carbon dioxide fixation, photosynthesis, thermostability; HET: KCX CAP; 2.10A {Thermosynechococcus elongatus} PDB: 2ybv_B*

Probab=100.00  E-value=6.6e-66  Score=398.60  Aligned_cols=111  Identities=49%  Similarity=1.019  Sum_probs=91.1

Q ss_pred             eeeeccCCccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHH
Q 030735           48 MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSS  127 (172)
Q Consensus        48 m~vw~p~~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~s  127 (172)
                      |||||+  +|||||||||||||||||++||+|||+|||+|||||+|+++           |+++||+|||||||||+|++
T Consensus         1 m~~~p~--~kkfeTfSyLP~Lt~eqI~kQV~yll~qGw~~~lE~~d~~~-----------~~~~yW~mWklPmf~~~d~~   67 (118)
T 3zxw_B            1 MKTLPK--ERRYETFSYLPPLSDAQIARQIQYAIDQGYHPCVEFNETSN-----------AEIRYWTMWKLPLFNCTNAQ   67 (118)
T ss_dssp             ---------------CCSCCCCHHHHHHHHHHHHHHTCEEEEEEESCCC-----------TTCCCCEEESSCCTTCCCHH
T ss_pred             CCcCCC--CccccccccCCCCCHHHHHHHHHHHHhCCCeeEEEeccCCC-----------cccCEEeecccCCcCCCCHH
Confidence            899996  79999999999999999999999999999999999999885           45999999999999999999


Q ss_pred             HHHHHHHHHHHHCCCCeEEEEeeecCCCeEEEEEEEecCCCCCC
Q 030735          128 QILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTTTS  171 (172)
Q Consensus       128 qVl~Eie~C~k~~P~~YIRliGfDn~rqvq~~sfIV~RP~~~~~  171 (172)
                      |||+||++|+++|||+|||||||||++|+||+|||||||+++.+
T Consensus        68 ~Vl~Ele~C~k~~p~~yVRliGfD~~~q~q~~sfIv~RP~~~~p  111 (118)
T 3zxw_B           68 DVLNEVQQCRSEYPNCFIRVVAFDNIKQCQVMSFIVYKPNQANS  111 (118)
T ss_dssp             HHHHHHHHHHHHCTTSEEEEEEEETTTTEEEEEEEEECC-----
T ss_pred             HHHHHHHHHHHHCCCceEEEEEEeCCcCEEEEEEEEECCCCCCC
Confidence            99999999999999999999999999999999999999987654

>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=100.00  E-value=1.7e-64  Score=386.07  Aligned_cols=107  Identities=45%  Similarity=0.944  Sum_probs=103.8

Q ss_pred             eeeeccCCccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHH
Q 030735           48 MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSS  127 (172)
Q Consensus        48 m~vw~p~~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~s  127 (172)
                      ||+|+  |+||||||||||||||+||++||+|||+|||+|||||+|++++           +|+||+|||||||||+|++
T Consensus         2 ~~~~~--~~~~~etfSyLP~lt~eqI~kQI~Yll~qGw~p~lEf~d~~~~-----------~~~yW~mwklPmf~~~d~~   68 (109)
T 1rbl_M            2 MKTLP--KERRFETFSYLPPLSDRQIAAQIEYMIEQGFHPLIEFNEHSNP-----------EEFYWTMWKLPLFACAAPQ   68 (109)
T ss_dssp             CCCCC--CCCCCSTTTTSSCCCHHHHHHHHHHHHHHTCEEEEEEESCCCT-----------TCCCCEECSSCCTTCCCHH
T ss_pred             CccCC--CcccccccccCCCCCHHHHHHHHHHHHHCCCEEEEEeccCccc-----------cccEEeecccCCcCCCCHH
Confidence            89998  7899999999999999999999999999999999999998865           4999999999999999999


Q ss_pred             HHHHHHHHHHHHCCCCeEEEEeeecCCCeEEEEEEEecCC
Q 030735          128 QILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPT  167 (172)
Q Consensus       128 qVl~Eie~C~k~~P~~YIRliGfDn~rqvq~~sfIV~RP~  167 (172)
                      |||+||++|+++|||+|||||||||++|+||+|||||||+
T Consensus        69 ~Vl~Ele~C~k~~p~~yVRligfD~~~q~q~~sfIv~RP~  108 (109)
T 1rbl_M           69 QVLDEVRECRSEYGDCYIRVAGFDNIKECQTSSFIVHRPG  108 (109)
T ss_dssp             HHHHHHHHHHHHCTTSEEEEEEEETTTTEEEEEEEEECCC
T ss_pred             HHHHHHHHHHHHCCCCeEEEEEEeCCCcEEEEEEEeeCCC
Confidence            9999999999999999999999999999999999999996

>1svd_M Ribulose bisphosphate carboxylase small chain; beta-alpha-barrel, lyase; 1.80A {Halothiobacillus neapolitanus} SCOP: d.73.1.1

Probab=100.00  E-value=4.3e-63  Score=378.82  Aligned_cols=107  Identities=34%  Similarity=0.781  Sum_probs=102.1

Q ss_pred             eeeeccCCccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHH
Q 030735           48 MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSS  127 (172)
Q Consensus        48 m~vw~p~~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~s  127 (172)
                      ||.|+  |+||||||||||||||+||++||+|||+|||+|||||+|++++           +|+||+|||||||||+|++
T Consensus         4 ~~~~~--~~~~~etfSyLP~lt~eqI~kQV~Yll~qGw~p~iEf~d~~~~-----------~~~yW~mwklPmf~~~d~~   70 (110)
T 1svd_M            4 MQDYK--QSLKYETFSYLPPMNAERIRAQIKYAIAQGWSPGIEHVEVKNS-----------MNQYWYMWKLPFFGEQNVD   70 (110)
T ss_dssp             CCCCC--CCCCCSTTTTSCCCCHHHHHHHHHHHHHTTCEEEEEEECGGGT-----------TCSCCEEESCCCTTCCCHH
T ss_pred             ccccC--CCccccccccCCCCCHHHHHHHHHHHHHCCCeeEEEeccCCcc-----------CCcEEeecccCCcCCCCHH
Confidence            45664  8999999999999999999999999999999999999998854           4999999999999999999


Q ss_pred             HHHHHHHHHHHHCCCCeEEEEeeecCCCeEEEEEEEecCC
Q 030735          128 QILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPT  167 (172)
Q Consensus       128 qVl~Eie~C~k~~P~~YIRliGfDn~rqvq~~sfIV~RP~  167 (172)
                      |||+||++|+++|||+|||||||||++|+||+|||||||+
T Consensus        71 ~Vl~El~~C~k~~p~~yVRligfD~~~q~q~~sfIv~RP~  110 (110)
T 1svd_M           71 NVLAEIEACRSAYPTHQVKLVAYDNYAQSLGLAFVVYRGN  110 (110)
T ss_dssp             HHHHHHHHHHHHSTTSEEEEEEEETTTTEEEEEEEEECCC
T ss_pred             HHHHHHHHHHHHCCCCeEEEEEEeCCCCEEEEEEEeeCCC
Confidence            9999999999999999999999999999999999999995

>1bwv_S Rubisco, protein (ribulose bisphosphate carboxylase); carbon dioxide fixation, complex (rubisco-reaction intermedi high specificity factor; HET: KCX CAP; 2.40A {Galdieria partita} SCOP: d.73.1.1 PDB: 1iwa_B

Probab=100.00  E-value=3.1e-58  Score=363.75  Aligned_cols=102  Identities=33%  Similarity=0.691  Sum_probs=97.2

Q ss_pred             cccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHH
Q 030735           57 KKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQEC  136 (172)
Q Consensus        57 kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C  136 (172)
                      .+||||||||||||+||++||+|||+|||+|||||+|++|+ |          |+||+|||||||||+|++|||+||++|
T Consensus         3 ~~~etfSyLP~ltdeqI~kQI~Yll~qGw~p~iEf~d~~~~-r----------~~yW~mWkLPmF~~td~~~Vl~Ele~C   71 (138)
T 1bwv_S            3 ITQGTFSFLPDLTDEQIKKQIDYMISKKLAIGIEYTNDIHP-R----------NAYWEIWGLPLFDVTDPAAVLFEINAC   71 (138)
T ss_dssp             CCCSTTTTSCCCCHHHHHHHHHHHHHTTCEEEEEEESCCCT-T----------CCCCEECSSCBCSCCCHHHHHHHHHHH
T ss_pred             eecceeccCCCCCHHHHHHHHHHHHHCCCeeeEEecCCCCC-c----------cCEEeccCCCCcCCCCHHHHHHHHHHH
Confidence            58999999999999999999999999999999999999876 4          999999999999999999999999999


Q ss_pred             HHHCCCCeEEEEeeecCCCeE--EEEEEEecCCCC
Q 030735          137 KKAYPNAYIRCLAFNNQKQGQ--CMSFLIQKPTTT  169 (172)
Q Consensus       137 ~k~~P~~YIRliGfDn~rqvq--~~sfIV~RP~~~  169 (172)
                      +++|||+|||||||||++|+|  |+|||||||.+.
T Consensus        72 ~k~~p~~YVRliGfD~~~~~qs~~~sfIV~RP~~~  106 (138)
T 1bwv_S           72 RKARSNFYIKVVGFSSVRGIESTIISFIVNRPKHE  106 (138)
T ss_dssp             HHHCTTSEEEEEEEECCTTTCEEEEEEEEECCSCC
T ss_pred             HHHCCCCeEEEEEEeCCCceEEEEEEEEEECCCCC
Confidence            999999999999999999654  999999999764

>1bxn_I Rubisco, protein (ribulose bisphosphate carboxylase small; lyase (carbon-carbon), lyase; 2.70A {Cupriavidus necator} SCOP: d.73.1.1

Probab=100.00  E-value=3.7e-58  Score=363.71  Aligned_cols=102  Identities=36%  Similarity=0.768  Sum_probs=97.5

Q ss_pred             cccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHH
Q 030735           57 KKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQEC  136 (172)
Q Consensus        57 kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C  136 (172)
                      .+||||||||||||+||++||+|||+|||+|||||+|++|+ |          |+||+|||||||||+|++|||+||++|
T Consensus         3 ~~~etfSyLP~ltdeqI~kQI~YlL~qGw~p~lE~~d~~~~-r----------~~yW~mWkLPmF~~td~~~Vl~Ele~C   71 (139)
T 1bxn_I            3 ITQGTFSFLPELTDEQITKQLEYCLNQGWAVGLEYTDDPHP-R----------NTYWEMFGLPMFDLRDAAGILMEINNA   71 (139)
T ss_dssp             CCCSBTTTSSCCCHHHHHHHHHHHHHHTCEEEEEEESCCCT-T----------CCCCEESSSCBTTCCCHHHHHHHHHHH
T ss_pred             eecceeccCCCCCHHHHHHHHHHHHHCCCeEEEEeccCCcc-c----------cCEEeecCCCCcCCCCHHHHHHHHHHH
Confidence            58999999999999999999999999999999999999876 4          999999999999999999999999999


Q ss_pred             HHHCCCCeEEEEeeecCCCeE--EEEEEEecCCCC
Q 030735          137 KKAYPNAYIRCLAFNNQKQGQ--CMSFLIQKPTTT  169 (172)
Q Consensus       137 ~k~~P~~YIRliGfDn~rqvq--~~sfIV~RP~~~  169 (172)
                      +++|||+|||||||||++|+|  |+|||||||.+.
T Consensus        72 ~k~~p~~YVRliGfD~~~~~qs~~~sfIV~RP~~~  106 (139)
T 1bxn_I           72 RNTFPNHYIRVTAFDSTHTVESVVMSFIVNRPADE  106 (139)
T ss_dssp             HHHCSSSEEEEEEECTTTCCEEEEEECCCCGGGSC
T ss_pred             HHHCCCCeEEEEEEeCCCceEEEEEEEEEECCCCC
Confidence            999999999999999999766  999999999754

>4f0h_B Ribulose bisphosphate carboxylase small chain; alpha beta domain, catalytic domain TIM barrel, carboxylase/oxygenase, nitrosylation; 1.96A {Galdieria sulphuraria} PDB: 4f0k_B 4f0m_B 1iwa_B 1bwv_S*

Probab=100.00  E-value=8e-57  Score=355.71  Aligned_cols=101  Identities=34%  Similarity=0.704  Sum_probs=96.1

Q ss_pred             ccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHHH
Q 030735           58 KFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECK  137 (172)
Q Consensus        58 kfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C~  137 (172)
                      ..|||||||||||+||.+||+|||+|||+|||||+|++|+ |          |+||+|||||||||+|++|||+||++|+
T Consensus         4 t~~tfSyLP~ltd~qI~kQI~YlL~qGw~~~iEf~d~~~~-r----------~~yW~mWkLPmFg~~d~~~Vl~Ele~C~   72 (138)
T 4f0h_B            4 TQGTFSFLPDLTDEQIKKQIDYMISKKLAIGIEYTNDIHP-R----------NSFWEMWGLPLFEVTDPAPVLFEINACR   72 (138)
T ss_dssp             CCSTTTTSCCCCHHHHHHHHHHHHHTTCEEEEEEESCCCT-T----------CCCCEESSCCBCSCCSHHHHHHHHHHHH
T ss_pred             cccccccCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCCCC-c----------CCEEeecCCCCcCCCCHHHHHHHHHHHH
Confidence            4699999999999999999999999999999999999865 3          9999999999999999999999999999


Q ss_pred             HHCCCCeEEEEeeecCCCe--EEEEEEEecCCCC
Q 030735          138 KAYPNAYIRCLAFNNQKQG--QCMSFLIQKPTTT  169 (172)
Q Consensus       138 k~~P~~YIRliGfDn~rqv--q~~sfIV~RP~~~  169 (172)
                      ++|||+|||||||||++|+  ||+|||||||++.
T Consensus        73 k~~p~~YVRliGfDn~~~~qs~~~sfIV~RP~~e  106 (138)
T 4f0h_B           73 KAKSNFYIKVVGFSSERGIESTIISFIVNRPKHE  106 (138)
T ss_dssp             HHTTTSEEEEEEEECCTTTCEEEEEEEEECCSCC
T ss_pred             HHCCCCeEEEEEEeCCCceEEEEEEEEEeCCCCC
Confidence            9999999999999999976  6999999999864

>3frm_A Uncharacterized conserved protein; APC61048, staphylococcus epidermidis ATCC structural genomics, PSI-2, protein structure initiative; HET: MES; 2.32A {Staphylococcus epidermidis}

Probab=88.07  E-value=0.72  Score=36.54  Aligned_cols=60  Identities=18%  Similarity=0.169  Sum_probs=42.5

Q ss_pred             HhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHHHH---HCCCCeEEEE
Q 030735           81 LKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKK---AYPNAYIRCL  148 (172)
Q Consensus        81 L~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C~k---~~P~~YIRli  148 (172)
                      +..| .+-.|.++.- +|| +...|.||++.||.+.+.|-     ..+...+|+.|.+   +++..++++.
T Consensus        13 ~~~~-~~~~~~~~~~-~~~-~~~~p~~y~~N~~~~~~~p~-----~~~~~~~i~~~~~~~~~~~~~~~~~~   75 (254)
T 3frm_A           13 YIDG-NKITEDSRKA-IYL-LPPQPLKYASNTWIYKTMPT-----MNQWLKDIEVQKKMHLNQSSYHLSFS   75 (254)
T ss_dssp             CCCS-EEEEECSSEE-EEE-CTTCTTCGGGSEEEESSCCC-----HHHHHHHHHHHHHHHHHTTCCCEEEE
T ss_pred             hccC-ceEEecCcEE-Eec-CCccccccccceEEEecCCC-----HHHHHHHHHHHHHHHHHcCCCeEEEE
Confidence            3445 4444544432 335 67899999999999998886     7788777777755   4577788886

---

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	172
d1gk8i_	126	d.73.1.1 (I:) Ribulose 1,5-bisphosphate carboxylas	5e-67
d1wdds_	122	d.73.1.1 (S:) Ribulose 1,5-bisphosphate carboxylas	7e-64
d1svdm1	108	d.73.1.1 (M:3-110) Ribulose 1,5-bisphosphate carbo	2e-50
d1rbli_	109	d.73.1.1 (I:) Ribulose 1,5-bisphosphate carboxylas	3e-47
d1bxni_	129	d.73.1.1 (I:) Ribulose 1,5-bisphosphate carboxylas	2e-42
d1bwvs_	138	d.73.1.1 (S:) Ribulose 1,5-bisphosphate carboxylas	2e-41

>d1gk8i_ d.73.1.1 (I:) Ribulose 1,5-bisphosphate carboxylase-oxygenase {Chlamydomonas reinhardtii [TaxId: 3055]} Length = 126

class: Alpha and beta proteins (a+b)
fold: RuBisCO, small subunit
superfamily: RuBisCO, small subunit
family: RuBisCO, small subunit
domain: Ribulose 1,5-bisphosphate carboxylase-oxygenase
species: Chlamydomonas reinhardtii [TaxId: 3055]

 Score =  198 bits (504), Expect = 5e-67
 Identities = 69/126 (54%), Positives = 85/126 (67%), Gaps = 7/126 (5%)

Query: 48  MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVH-------RE 100
           M  W P+NNK FE  SYLP L+D+ IA ++DY++  GWIPCLEF E    +       R 
Sbjct: 1   MMVWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLEFAEADKAYVSNESAIRF 60

Query: 101 NSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMS 160
            S    YYD RYWTMWKLPMFGC D  Q+L EI  C KA+P+AY+R +AF+NQKQ Q M 
Sbjct: 61  GSVSCLYYDNRYWTMWKLPMFGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMG 120

Query: 161 FLIQKP 166
           FL+Q+P
Sbjct: 121 FLVQRP 126

>d1wdds_ d.73.1.1 (S:) Ribulose 1,5-bisphosphate carboxylase-oxygenase {Rice (Oryza sativa) [TaxId: 4530]} Length = 122

class: Alpha and beta proteins (a+b)
fold: RuBisCO, small subunit
superfamily: RuBisCO, small subunit
family: RuBisCO, small subunit
domain: Ribulose 1,5-bisphosphate carboxylase-oxygenase
species: Rice (Oryza sativa) [TaxId: 4530]

 Score =  190 bits (483), Expect = 7e-64
 Identities = 67/119 (56%), Positives = 93/119 (78%)

Query: 48  MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGY 107
           M+ W     KKFE LSYLP L+ + + K+I+Y+L+  W+PCLEF +VG+V+REN + PGY
Sbjct: 1   MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGY 60

Query: 108 YDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           YDGRYWTMWKLPMFGC D++Q+L E++E KKAYP+A++R + F+N +Q Q +SF+  KP
Sbjct: 61  YDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKP 119

>d1svdm1 d.73.1.1 (M:3-110) Ribulose 1,5-bisphosphate carboxylase-oxygenase {Halothiobacillus neapolitanus [TaxId: 927]} Length = 108

class: Alpha and beta proteins (a+b)
fold: RuBisCO, small subunit
superfamily: RuBisCO, small subunit
family: RuBisCO, small subunit
domain: Ribulose 1,5-bisphosphate carboxylase-oxygenase
species: Halothiobacillus neapolitanus [TaxId: 927]

 Score =  155 bits (394), Expect = 2e-50
 Identities = 34/115 (29%), Positives = 59/115 (51%), Gaps = 11/115 (9%)

Query: 52  NPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGR 111
           +   + K+E  SYLP ++ + I  +I Y + +GW P +E  E                 +
Sbjct: 4   DYKQSLKYETFSYLPPMNAERIRAQIKYAIAQGWSPGIEHVE-----------VKNSMNQ 52

Query: 112 YWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
           YW MWKLP FG  +   +L EI+ C+ AYP   ++ +A++N  Q   ++F++ + 
Sbjct: 53  YWYMWKLPFFGEQNVDNVLAEIEACRSAYPTHQVKLVAYDNYAQSLGLAFVVYRG 107

>d1rbli_ d.73.1.1 (I:) Ribulose 1,5-bisphosphate carboxylase-oxygenase {Synechococcus sp., strain pcc 6301 [TaxId: 1131]} Length = 109

class: Alpha and beta proteins (a+b)
fold: RuBisCO, small subunit
superfamily: RuBisCO, small subunit
family: RuBisCO, small subunit
domain: Ribulose 1,5-bisphosphate carboxylase-oxygenase
species: Synechococcus sp., strain pcc 6301 [TaxId: 1131]

 Score =  147 bits (373), Expect = 3e-47
 Identities = 48/119 (40%), Positives = 71/119 (59%), Gaps = 13/119 (10%)

Query: 48  MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGY 107
           MKT      ++FE  SYLP LSD  IA +I+YM+++G+ P +EF+E              
Sbjct: 2   MKTLP--KERRFETFSYLPPLSDRQIAAQIEYMIEQGFHPLIEFNE-----------HSN 48

Query: 108 YDGRYWTMWKLPMFGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP 166
            +  YWTMWKLP+F C    Q+L+E++EC+  Y + YIR   F+N K+ Q  SF++ +P
Sbjct: 49  PEEFYWTMWKLPLFACAAPQQVLDEVRECRSEYGDCYIRVAGFDNIKECQTSSFIVHRP 107

>d1bxni_ d.73.1.1 (I:) Ribulose 1,5-bisphosphate carboxylase-oxygenase {Alcaligenes eutrophus [TaxId: 106590]} Length = 129

class: Alpha and beta proteins (a+b)
fold: RuBisCO, small subunit
superfamily: RuBisCO, small subunit
family: RuBisCO, small subunit
domain: Ribulose 1,5-bisphosphate carboxylase-oxygenase
species: Alcaligenes eutrophus [TaxId: 106590]

 Score =  136 bits (343), Expect = 2e-42
 Identities = 36/107 (33%), Positives = 57/107 (53%), Gaps = 13/107 (12%)

Query: 62  LSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMF 121
            S+LP L+D+ I K+++Y L +GW   LE+ +             +    YW M+ LPMF
Sbjct: 8   FSFLPELTDEQITKQLEYCLNQGWAVGLEYTD-----------DPHPRNTYWEMFGLPMF 56

Query: 122 GCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQC--MSFLIQKP 166
              D++ IL EI   +  +PN YIR  AF++    +   MSF++ +P
Sbjct: 57  DLRDAAGILMEINNARNTFPNHYIRVTAFDSTHTVESVVMSFIVNRP 103

>d1bwvs_ d.73.1.1 (S:) Ribulose 1,5-bisphosphate carboxylase-oxygenase {Galdieria partita [TaxId: 83374]} Length = 138

class: Alpha and beta proteins (a+b)
fold: RuBisCO, small subunit
superfamily: RuBisCO, small subunit
family: RuBisCO, small subunit
domain: Ribulose 1,5-bisphosphate carboxylase-oxygenase
species: Galdieria partita [TaxId: 83374]

 Score =  133 bits (337), Expect = 2e-41
 Identities = 33/107 (30%), Positives = 55/107 (51%), Gaps = 13/107 (12%)

Query: 62  LSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMF 121
            S+LP L+D+ I K+IDYM+ K     +E+               +    YW +W LP+F
Sbjct: 8   FSFLPDLTDEQIKKQIDYMISKKLAIGIEYTN-----------DIHPRNAYWEIWGLPLF 56

Query: 122 GCNDSSQILNEIQECKKAYPNAYIRCLAFNN--QKQGQCMSFLIQKP 166
              D + +L EI  C+KA  N YI+ + F++    +   +SF++ +P
Sbjct: 57  DVTDPAAVLFEINACRKARSNFYIKVVGFSSVRGIESTIISFIVNRP 103

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	172
d1gk8i_	126	Ribulose 1,5-bisphosphate carboxylase-oxygenase {C	100.0
d1wdds_	122	Ribulose 1,5-bisphosphate carboxylase-oxygenase {R	100.0
d1rbli_	109	Ribulose 1,5-bisphosphate carboxylase-oxygenase {S	100.0
d1svdm1	108	Ribulose 1,5-bisphosphate carboxylase-oxygenase {H	100.0
d1bwvs_	138	Ribulose 1,5-bisphosphate carboxylase-oxygenase {G	100.0
d1bxni_	129	Ribulose 1,5-bisphosphate carboxylase-oxygenase {A	100.0
d2hgca1	78	Uncharacterized protein YjcQ {Bacillus subtilis [T	82.14

>d1gk8i_ d.73.1.1 (I:) Ribulose 1,5-bisphosphate carboxylase-oxygenase {Chlamydomonas reinhardtii [TaxId: 3055]}

class: Alpha and beta proteins (a+b)
fold: RuBisCO, small subunit
superfamily: RuBisCO, small subunit
family: RuBisCO, small subunit
domain: Ribulose 1,5-bisphosphate carboxylase-oxygenase
species: Chlamydomonas reinhardtii [TaxId: 3055]

Probab=100.00  E-value=1.4e-76  Score=460.14  Aligned_cols=119  Identities=58%  Similarity=1.124  Sum_probs=115.3

Q ss_pred             eeeeccCCccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCcee-------ecCCCCCCccCCcceeeccCCC
Q 030735           48 MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVH-------RENSKMPGYYDGRYWTMWKLPM  120 (172)
Q Consensus        48 m~vw~p~~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~-------R~~~~sp~yyd~ryWtmWkLPm  120 (172)
                      ||||+|+|+|||||||||||||||||+|||+|||+|||+|||||+|++++|       |.++++|||||||||+||||||
T Consensus         1 m~vw~p~~~kkfETfSyLPpLtdeqI~kQI~Y~i~~GW~p~iEft~~~~~~~~~~~~~~~~~~~~~yyd~rYWtMWKLPM   80 (126)
T d1gk8i_           1 MMVWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLEFAEADKAYVSNESAIRFGSVSCLYYDNRYWTMWKLPM   80 (126)
T ss_dssp             CCCCCCSSCCCCSTTTTSSCCCHHHHHHHHHHHHHTTCEEEEEEECGGGTSCBCGGGGGCSSCCTTCCBTSSCEEESCCC
T ss_pred             CcccCCCCCcceeecccCCCCCHHHHHHHHHHHHhcCCceeeEeccCCcceecccccccccCCCCCcccccceeeeCccc
Confidence            899999999999999999999999999999999999999999999988776       3457899999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCeEEEEeeecCCCeEEEEEEEecC
Q 030735          121 FGCNDSSQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKP  166 (172)
Q Consensus       121 fg~td~sqVl~Eie~C~k~~P~~YIRliGfDn~rqvq~~sfIV~RP  166 (172)
                      |||||++|||+||+||+|+|||+|||||||||+||+||+|||||||
T Consensus        81 Fg~tD~~~Vl~Ei~~Crka~P~~yIRiigFDn~rQvQ~~sFiv~rP  126 (126)
T d1gk8i_          81 FGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMGFLVQRP  126 (126)
T ss_dssp             TTCCCHHHHHHHHHHHHHHCTTSEEEEEEEETTTTEEEEEEEEECC
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCceEEEEEEeCCccEEEEEEEEeCc
Confidence            9999999999999999999999999999999999999999999999

>d1wdds_ d.73.1.1 (S:) Ribulose 1,5-bisphosphate carboxylase-oxygenase {Rice (Oryza sativa) [TaxId: 4530]}

class: Alpha and beta proteins (a+b)
fold: RuBisCO, small subunit
superfamily: RuBisCO, small subunit
family: RuBisCO, small subunit
domain: Ribulose 1,5-bisphosphate carboxylase-oxygenase
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=100.00  E-value=3.7e-74  Score=445.09  Aligned_cols=122  Identities=55%  Similarity=1.136  Sum_probs=120.8

Q ss_pred             eeeeccCCccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHH
Q 030735           48 MKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSS  127 (172)
Q Consensus        48 m~vw~p~~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~s  127 (172)
                      ||||||+|+||||||||||||||+||++||+|||+|||+|||||+|++++||++|++|+||||+||+|||||||||+|++
T Consensus         1 m~~~~~~~~~k~ETfSyLP~ltd~qI~~QI~yll~qGw~p~lEf~d~~~~~~~~h~~p~~~~~~yW~mWkLPmFg~~d~~   80 (122)
T d1wdds_           1 MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLPMFGCTDAT   80 (122)
T ss_dssp             CCCCCSSSCCCCSTTTTSSCCCHHHHHHHHHHHHHTTCEEEEEEESCCSCBCSSCCSTTCCBSCCCEEESCCCTTCCCHH
T ss_pred             CcccCCCCCccceeeccCCCCCHHHHHHHHHHHHHCCCeeeEEecCCCcccccCCCCccccccCeeeecCcCCcCCCCHH
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHCCCCeEEEEeeecCCCeEEEEEEEecCCCC
Q 030735          128 QILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPTTT  169 (172)
Q Consensus       128 qVl~Eie~C~k~~P~~YIRliGfDn~rqvq~~sfIV~RP~~~  169 (172)
                      |||+||++|+++|||+|||||||||++|+||+|||||||+|.
T Consensus        81 ~Vl~Ele~C~k~~p~~YVRligfD~~~q~q~~sfIV~RP~G~  122 (122)
T d1wdds_          81 QVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPPGC  122 (122)
T ss_dssp             HHHHHHHHHHHHCTTSEEEEEEEETTTTEEEEEEEEECCTTC
T ss_pred             HHHHHHHHHHHHCCCceEEEEEEeCccCEEEEEEEEECCCCC
Confidence            999999999999999999999999999999999999999984

>d1rbli_ d.73.1.1 (I:) Ribulose 1,5-bisphosphate carboxylase-oxygenase {Synechococcus sp., strain pcc 6301 [TaxId: 1131]}

class: Alpha and beta proteins (a+b)
fold: RuBisCO, small subunit
superfamily: RuBisCO, small subunit
family: RuBisCO, small subunit
domain: Ribulose 1,5-bisphosphate carboxylase-oxygenase
species: Synechococcus sp., strain pcc 6301 [TaxId: 1131]

Probab=100.00  E-value=1.1e-63  Score=379.79  Aligned_cols=108  Identities=44%  Similarity=0.932  Sum_probs=104.2

Q ss_pred             eeeeeccCCccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCH
Q 030735           47 CMKTWNPINNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDS  126 (172)
Q Consensus        47 cm~vw~p~~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~  126 (172)
                      .|||||+  +||||||||||||||+||++||+|||+|||+|||||+|++++           +++||+|||||||||+|+
T Consensus         1 ~m~~~p~--~~~~eTfSyLP~Ltd~~I~~QV~yll~qGw~i~iE~ad~~~~-----------~~~yW~mwklPmf~~~d~   67 (109)
T d1rbli_           1 SMKTLPK--ERRFETFSYLPPLSDRQIAAQIEYMIEQGFHPLIEFNEHSNP-----------EEFYWTMWKLPLFACAAP   67 (109)
T ss_dssp             CCCCCCC--CCCCSTTTTSSCCCHHHHHHHHHHHHHHTCEEEEEEESCCCT-----------TCCCCEECSSCCTTCCCH
T ss_pred             CccccCC--CccccccccCCCCCHHHHHHHHHHHHhCCCceeEEEccCCCc-----------cceeeeecccCcccCCCH
Confidence            3999994  799999999999999999999999999999999999999865           499999999999999999


Q ss_pred             HHHHHHHHHHHHHCCCCeEEEEeeecCCCeEEEEEEEecCC
Q 030735          127 SQILNEIQECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPT  167 (172)
Q Consensus       127 sqVl~Eie~C~k~~P~~YIRliGfDn~rqvq~~sfIV~RP~  167 (172)
                      +|||+||++|+++|||+|||||||||++|+||+|||||||+
T Consensus        68 ~~Vl~ele~c~~~~p~~YVRliG~D~~~q~r~~~fIV~RP~  108 (109)
T d1rbli_          68 QQVLDEVRECRSEYGDCYIRVAGFDNIKECQTSSFIVHRPG  108 (109)
T ss_dssp             HHHHHHHHHHHHHCTTSEEEEEEEETTTTEEEEEEEEECCC
T ss_pred             HHHHHHHHHHHHhCCcCEEEEEEEeCCCCEEEEEEEEeCCC
Confidence            99999999999999999999999999999999999999997

>d1svdm1 d.73.1.1 (M:3-110) Ribulose 1,5-bisphosphate carboxylase-oxygenase {Halothiobacillus neapolitanus [TaxId: 927]}

class: Alpha and beta proteins (a+b)
fold: RuBisCO, small subunit
superfamily: RuBisCO, small subunit
family: RuBisCO, small subunit
domain: Ribulose 1,5-bisphosphate carboxylase-oxygenase
species: Halothiobacillus neapolitanus [TaxId: 927]

Probab=100.00  E-value=6.1e-61  Score=364.28  Aligned_cols=102  Identities=34%  Similarity=0.782  Sum_probs=98.8

Q ss_pred             CccccccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHH
Q 030735           55 NNKKFEALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQ  134 (172)
Q Consensus        55 ~~kkfeT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie  134 (172)
                      .++|||||||||||||+||++||+|||+|||+|||||+|++|           |+++||+|||||||||+|++|||+||+
T Consensus         7 ~~~~~eTfSyLP~Ltde~I~~QV~yll~qGw~~~~E~~d~~~-----------~r~~yW~mwklPmf~~~d~~~Vl~Ele   75 (108)
T d1svdm1           7 QSLKYETFSYLPPMNAERIRAQIKYAIAQGWSPGIEHVEVKN-----------SMNQYWYMWKLPFFGEQNVDNVLAEIE   75 (108)
T ss_dssp             CCCCCSTTTTSCCCCHHHHHHHHHHHHHTTCEEEEEEECGGG-----------TTCSCCEEESCCCTTCCCHHHHHHHHH
T ss_pred             ccccccccccCCCCCHHHHHHHHHHHHHCCCEeeEeecccCC-----------CcCceeeecCCCCcCCCcHHHHHHHHH
Confidence            579999999999999999999999999999999999999885           459999999999999999999999999


Q ss_pred             HHHHHCCCCeEEEEeeecCCCeEEEEEEEecCC
Q 030735          135 ECKKAYPNAYIRCLAFNNQKQGQCMSFLIQKPT  167 (172)
Q Consensus       135 ~C~k~~P~~YIRliGfDn~rqvq~~sfIV~RP~  167 (172)
                      +|+++|||+|||||||||++|+||+|||||||+
T Consensus        76 ~c~~~~p~~YVRliG~D~~~q~q~~~fIV~RPn  108 (108)
T d1svdm1          76 ACRSAYPTHQVKLVAYDNYAQSLGLAFVVYRGN  108 (108)
T ss_dssp             HHHHHSTTSEEEEEEEETTTTEEEEEEEEECCC
T ss_pred             HHHHHCCCCEEEEEEEcCCccEEEEEEEEECCC
Confidence            999999999999999999999999999999995

>d1bwvs_ d.73.1.1 (S:) Ribulose 1,5-bisphosphate carboxylase-oxygenase {Galdieria partita [TaxId: 83374]}

class: Alpha and beta proteins (a+b)
fold: RuBisCO, small subunit
superfamily: RuBisCO, small subunit
family: RuBisCO, small subunit
domain: Ribulose 1,5-bisphosphate carboxylase-oxygenase
species: Galdieria partita [TaxId: 83374]

Probab=100.00  E-value=3e-56  Score=350.52  Aligned_cols=99  Identities=33%  Similarity=0.700  Sum_probs=93.4

Q ss_pred             ccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHHHHH
Q 030735           60 EALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKA  139 (172)
Q Consensus        60 eT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C~k~  139 (172)
                      +|||||||||||||++||+|||+|||+|||||+|+++           |+++||+|||||||||+|++|||+||++|+++
T Consensus         6 gtfSyLP~LtdeqI~~QV~yll~qGw~~~iE~~d~~~-----------~r~~yW~mwklPmf~~~d~~~Vl~Ele~C~k~   74 (138)
T d1bwvs_           6 GTFSFLPDLTDEQIKKQIDYMISKKLAIGIEYTNDIH-----------PRNAYWEIWGLPLFDVTDPAAVLFEINACRKA   74 (138)
T ss_dssp             STTTTSCCCCHHHHHHHHHHHHHTTCEEEEEEESCCC-----------TTCCCCEECSSCBCSCCCHHHHHHHHHHHHHH
T ss_pred             ceeccCCCCCHHHHHHHHHHHHcCCCEeeeEeccccc-----------cccchhhccccccccCCCHHHHHHHHHHHHHH
Confidence            7999999999999999999999999999999999874           45999999999999999999999999999999


Q ss_pred             CCCCeEEEEeeecCCCe--EEEEEEEecCCCC
Q 030735          140 YPNAYIRCLAFNNQKQG--QCMSFLIQKPTTT  169 (172)
Q Consensus       140 ~P~~YIRliGfDn~rqv--q~~sfIV~RP~~~  169 (172)
                      |||+|||||||||++|+  ||++||||||.+.
T Consensus        75 ~p~~YVRliGfDn~rq~Q~~~~sfIV~RP~~~  106 (138)
T d1bwvs_          75 RSNFYIKVVGFSSVRGIESTIISFIVNRPKHE  106 (138)
T ss_dssp             CTTSEEEEEEEECCTTTCEEEEEEEEECCSCC
T ss_pred             CCcceEEEEEEeCccceeEEEEEEEEeCCCCC
Confidence            99999999999999754  5999999999753

>d1bxni_ d.73.1.1 (I:) Ribulose 1,5-bisphosphate carboxylase-oxygenase {Alcaligenes eutrophus [TaxId: 106590]}

class: Alpha and beta proteins (a+b)
fold: RuBisCO, small subunit
superfamily: RuBisCO, small subunit
family: RuBisCO, small subunit
domain: Ribulose 1,5-bisphosphate carboxylase-oxygenase
species: Alcaligenes eutrophus [TaxId: 106590]

Probab=100.00  E-value=2.9e-54  Score=336.01  Aligned_cols=99  Identities=36%  Similarity=0.785  Sum_probs=94.0

Q ss_pred             ccccCCCCCChHHHHHHHHHHHhCCCeeEEEeccCCceeecCCCCCCccCCcceeeccCCCCCCCCHHHHHHHHHHHHHH
Q 030735           60 EALSYLPSLSDDSIAKEIDYMLKKGWIPCLEFDEVGYVHRENSKMPGYYDGRYWTMWKLPMFGCNDSSQILNEIQECKKA  139 (172)
Q Consensus        60 eT~SyLP~ltd~qi~kQV~ylL~qGw~p~lEfad~~~~~R~~~~sp~yyd~ryWtmWkLPmfg~td~sqVl~Eie~C~k~  139 (172)
                      +||||||||||+||++||+|||+|||+|||||+|+++           |+++||+|||||||||+|+++||+||++|+++
T Consensus         6 gtfSyLP~Ltd~~I~~QV~yll~qG~~i~iE~ad~r~-----------~r~~yW~mw~lPmf~~~d~~~Vl~ele~c~~e   74 (129)
T d1bxni_           6 GTFSFLPELTDEQITKQLEYCLNQGWAVGLEYTDDPH-----------PRNTYWEMFGLPMFDLRDAAGILMEINNARNT   74 (129)
T ss_dssp             SBTTTSSCCCHHHHHHHHHHHHHHTCEEEEEEESCCC-----------TTCCCCEESSSCBTTCCCHHHHHHHHHHHHHH
T ss_pred             ceeccCCCCCHHHHHHHHHHHHHCCCEeeEEEecCcC-----------cccchhhccccccccCCCHHHHHHHHHHHHHH
Confidence            7999999999999999999999999999999999985           45999999999999999999999999999999


Q ss_pred             CCCCeEEEEeeecCCCeE--EEEEEEecCCCC
Q 030735          140 YPNAYIRCLAFNNQKQGQ--CMSFLIQKPTTT  169 (172)
Q Consensus       140 ~P~~YIRliGfDn~rqvq--~~sfIV~RP~~~  169 (172)
                      |||+|||||||||++|+|  +++||||||++.
T Consensus        75 ~p~~YVRliG~D~~r~~q~~~~sfIV~RP~~~  106 (129)
T d1bxni_          75 FPNHYIRVTAFDSTHTVESVVMSFIVNRPADE  106 (129)
T ss_dssp             CSSSEEEEEEECTTTCCEEEEEECCCCGGGSC
T ss_pred             CCcCEEEEEEEeCCCceEEeEEEEEEECCCCC
Confidence            999999999999997777  789999999754

>d2hgca1 a.4.5.77 (A:5-82) Uncharacterized protein YjcQ {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: YjcQ-like
domain: Uncharacterized protein YjcQ
species: Bacillus subtilis [TaxId: 1423]

Probab=82.14  E-value=0.48  Score=31.70  Aligned_cols=28  Identities=11%  Similarity=0.522  Sum_probs=25.2

Q ss_pred             CChHHHHHHHHHHHhCCCeeEEEeccCC
Q 030735           68 LSDDSIAKEIDYMLKKGWIPCLEFDEVG   95 (172)
Q Consensus        68 ltd~qi~kQV~ylL~qGw~p~lEfad~~   95 (172)
                      .|++|...-|.+|-+.||++++-|+|++
T Consensus        24 vtedqfddavnflkregyiigvhysddr   51 (78)
T d2hgca1          24 VTEDQFDDAVNFLKREGYIIGVHYSDDR   51 (78)
T ss_dssp             SCHHHHHHHHHHHHHHTSEECCEESSSS
T ss_pred             cchhHhhHHHHHHHhcCeEEEEeccCCC
Confidence            4678888999999999999999999875