Citrus Sinensis ID: 028492

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------21
Protein Sequence
MSLSSITGSRQSSTLPLSRLSWQTLNKLHSRTHVVLPPVEAASSRRHVISCSSTALVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL
Secondary Structure (PSIPRED)
ccccccccccccccccccccHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccccccEcccccccHHHHHHHccccccccccccccccccEEEEEccHHHHHEEHHcccccccccEcHHHHcccccccccEHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHcccHHHHHHHHccHHHHHHHHHHHHccccccHHccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
mslssitgsrqsstlplsrlSWQTLNKLhsrthvvlppveaassrrhviSCSSTALVAILTFncglaplpvqaedmsngqdekeEGVVGAIKslfdpnektksgkvlpKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWrgqktvageeSYVELEKAIRSLASFYskagpsaplpgevkSEILNDLDTAEKFL
Flexible Loop (DISEMBL)
mslssitgsrqsstlplSRLSWQTLNKLHSRTHVVLPPVEAASSRRHVISCSSTALVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVVGAIKslfdpnektksgkvlpkaylKSARELVKTLreslkedpkdianfrrnadsakeSIRDylsnwrgqktvageesYVELEKAIRSLASFYSKAgpsaplpgevkseILNDLDTAEKFL
Low Complexity Region (SEG)
MSLSSITGSRQSSTLPLSRLSWQTLNKLHSRTHVVLPPVEAASSRRHVISCSSTALVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL
Disordered region (IsUnstruct)
*******************LSWQTLNKLHSRTHVVLPPVEAASSRRHVISCSSTALVAILTFNCGLAPLPV******************************************************************************YLSNWRGQKTVAGEESYVELEKAIRSLASF*****************************
Disordered Region (DISOPRED)
************************************************ISCSSTALVAILTFNCGLAP******************VVGAIKSLF***********L*KAYLKSARELVKTLRESL******************ESIRDYL****************ELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL
Disordered Region (DISEMBL)
***************PLSRLSWQTLNKLHSRTHVVLPPVEAASSRRHVISCSSTALVAILTFNCGLAPLPVQAE***********GVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL
Disordered Region (DISPRO)
*************TLPLSRLSWQTLNKLHSRTHVVLP***AASSRRHVISCSSTALVAILTFNCGLAPLPVQAEDMSN******EGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSLSSITGSRQSSTLPLSRLSWQTLNKLHSRTHVVLPPVEAASSRRHVISCSSTALVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDxxxxxxxxxxxxxxxxxxxxxWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL
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	208	2.2.26 [Sep-21-2011]
P74367	134	Photosystem II 11 kDa pro	N/A	no	0.490	0.761	0.298	3e-07
Q9LR64	174	Thylakoid lumenal protein	no	no	0.451	0.540	0.277	3e-06

>sp|P74367|PS11_SYNY3 Photosystem II 11 kDa protein OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=slr1645 PE=1 SV=2

 Score = 55.1 bits (131), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 58/104 (55%), Gaps = 2/104 (1%)

Query: 103 SGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAG 162
           SG  L   Y +    ++ TLRE++ + P+D  N +   D+A+  I DY+S +R +    G
Sbjct: 27  SGTGLTGNYSQDTLTVIATLREAI-DLPQDAPNRQEVQDTARGQINDYISRYRRKGDAGG 85

Query: 163 EESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEK 206
            +S+  ++ A+ SLA +Y+  G + P+P ++K  +  +   AE+
Sbjct: 86  LKSFTTMQTALNSLAGYYTSYG-ARPIPEKLKKRLQLEFTQAER 128

Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)

>sp|Q9LR64|Y1360_ARATH Thylakoid lumenal protein At1g03610, chloroplastic OS=Arabidopsis thaliana GN=At1g03600 PE=1 SV=1

 Score = 51.6 bits (122), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 28/101 (27%), Positives = 56/101 (55%), Gaps = 7/101 (6%)

Query: 111 YLKSARELVKTLRESL---KEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYV 167
           Y+K    ++  +R +L   K DP    N        +E+   +++ +R +K + G+ S+ 
Sbjct: 74  YIKDTSAVISKVRSTLSMQKTDP----NVADAVAELREASNSWVAKYRKEKALLGKASFR 129

Query: 168 ELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL 208
           ++  A+ +++  Y   GP+AP+P + K+ IL +++TAEK L
Sbjct: 130 DIYSALNAVSGHYVSFGPTAPIPAKRKARILEEMETAEKAL 170

Arabidopsis thaliana (taxid: 3702)

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	208
225432660	209	PREDICTED: uncharacterized protein LOC10	0.927	0.923	0.740	3e-74
359477522	235	PREDICTED: uncharacterized protein LOC10	0.927	0.821	0.652	3e-70
147790522	230	hypothetical protein VITISV_022066 [Viti	0.927	0.839	0.668	3e-70
255552187	204	conserved hypothetical protein [Ricinus	0.865	0.882	0.697	2e-64
224102063	204	predicted protein [Populus trichocarpa]	0.889	0.906	0.64	2e-62
388498828	208	unknown [Lotus japonicus]	0.961	0.961	0.615	2e-61
356526109	207	PREDICTED: uncharacterized protein LOC10	0.865	0.869	0.661	2e-60
449444118	206	PREDICTED: uncharacterized protein LOC10	0.860	0.868	0.681	6e-58
18390518	199	LOW PSII accumulation 19 protein [Arabid	0.754	0.788	0.686	2e-54
26451618	199	unknown protein [Arabidopsis thaliana]	0.754	0.788	0.680	3e-54

>gi|225432660|ref|XP_002282406.1| PREDICTED: uncharacterized protein LOC100259756 isoform 1 [Vitis vinifera] gi|297737050|emb|CBI26251.3| unnamed protein product [Vitis vinifera]

 Score =  283 bits (724), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 143/193 (74%), Positives = 162/193 (83%)

Query: 16  PLSRLSWQTLNKLHSRTHVVLPPVEAASSRRHVISCSSTALVAILTFNCGLAPLPVQAED 75
           P+ + S+    KL SR H+VLP  E+ SSRRHV+  S  +LVAILTFN G  PLPV AED
Sbjct: 17  PIEKNSYIHEYKLKSRCHIVLPSQESPSSRRHVLVGSGASLVAILTFNGGFLPLPVWAED 76

Query: 76  MSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIAN 135
            SNGQ++ E+GVVGAIKSLFDPNEK KSGKVLPKAYL SARE+VKTLRESLKEDPKDIA 
Sbjct: 77  ESNGQEDDEKGVVGAIKSLFDPNEKIKSGKVLPKAYLNSAREVVKTLRESLKEDPKDIAK 136

Query: 136 FRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKS 195
           FRR AD+AKESIR+YLS+WRG++TV  EESY  LEKAIRSLASFYSKAGPSA LP EVKS
Sbjct: 137 FRRTADAAKESIREYLSSWRGKQTVVSEESYAMLEKAIRSLASFYSKAGPSAALPEEVKS 196

Query: 196 EILNDLDTAEKFL 208
           EIL+DL+TAE+FL
Sbjct: 197 EILDDLNTAEEFL 209

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359477522|ref|XP_003631991.1| PREDICTED: uncharacterized protein LOC100259756 isoform 2 [Vitis vinifera]

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 143/219 (65%), Positives = 162/219 (73%), Gaps = 26/219 (11%)

Query: 16  PLSRLSWQTLNKLHSRTHVVLPPVEAASSRRHVISCSSTALVAILTFNCGLAPLPVQAED 75
           P+ + S+    KL SR H+VLP  E+ SSRRHV+  S  +LVAILTFN G  PLPV AED
Sbjct: 17  PIEKNSYIHEYKLKSRCHIVLPSQESPSSRRHVLVGSGASLVAILTFNGGFLPLPVWAED 76

Query: 76  MSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIAN 135
            SNGQ++ E+GVVGAIKSLFDPNEK KSGKVLPKAYL SARE+VKTLRESLKEDPKDIA 
Sbjct: 77  ESNGQEDDEKGVVGAIKSLFDPNEKIKSGKVLPKAYLNSAREVVKTLRESLKEDPKDIAK 136

Query: 136 FRRNADSAKESIRDYLSNWRGQKTV--------------------------AGEESYVEL 169
           FRR AD+AKESIR+YLS+WRG++TV                            EESY  L
Sbjct: 137 FRRTADAAKESIREYLSSWRGKQTVVSEYKGSLQLSSTAYHTRTEHFAERLGNEESYAML 196

Query: 170 EKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL 208
           EKAIRSLASFYSKAGPSA LP EVKSEIL+DL+TAE+FL
Sbjct: 197 EKAIRSLASFYSKAGPSAALPEEVKSEILDDLNTAEEFL 235

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147790522|emb|CAN69770.1| hypothetical protein VITISV_022066 [Vitis vinifera]

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 143/214 (66%), Positives = 162/214 (75%), Gaps = 21/214 (9%)

Query: 16  PLSRLSWQTLNKLHSRTHVVLPPVEAASSRRHVISCSSTALVAILTFNCGLAPLPVQAED 75
           P+ + S+    KL SR H+VLP  E+ SSRRHV+  S  +LVAILTFN G  PLPV AED
Sbjct: 17  PIEKNSYIHEYKLKSRCHIVLPSQESPSSRRHVLVGSGASLVAILTFNGGFLPLPVWAED 76

Query: 76  MSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIAN 135
            SNGQ++ E+GVVGAIKSLFDPNEK KSGKVLPKAYL SARE+VKTLRESLKEDPKDIA 
Sbjct: 77  ESNGQEDDEKGVVGAIKSLFDPNEKIKSGKVLPKAYLNSAREVVKTLRESLKEDPKDIAK 136

Query: 136 FRRNADSAKESIRDYLSNWRGQKTVAGE---------------------ESYVELEKAIR 174
           FRR AD+AKESIR+YLS+WRG++TV  E                     ESY  LEKAIR
Sbjct: 137 FRRTADAAKESIREYLSSWRGKQTVVSEVCILQKHFWFLRWIPVVTVXHESYAMLEKAIR 196

Query: 175 SLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL 208
           SLASFYSKAGPSA LP EVKSEIL+DL+TAE+FL
Sbjct: 197 SLASFYSKAGPSAALPEEVKSEILDDLNTAEEFL 230

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255552187|ref|XP_002517138.1| conserved hypothetical protein [Ricinus communis] gi|223543773|gb|EEF45301.1| conserved hypothetical protein [Ricinus communis]

 Score =  251 bits (640), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 127/182 (69%), Positives = 146/182 (80%), Gaps = 2/182 (1%)

Query: 27  KLHSRTHVVLPPVEAASSRRHVISCSSTALVAILTFNCGLAPLPVQAEDMSNGQDEKEEG 86
           KL  R   V        SRRH++ CS++ L  IL  NC   PLPV+AED SN Q+EK+ G
Sbjct: 25  KLQWRCDTVPSSPAVTLSRRHILLCSASFLT-ILNLNCISTPLPVRAEDESNAQEEKD-G 82

Query: 87  VVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKES 146
           V+G IKSLFDPNEKTKSGK+LPKAYLKSAR++VKTLR+SLKEDPKD+  FRR AD+AKES
Sbjct: 83  VIGTIKSLFDPNEKTKSGKLLPKAYLKSARDVVKTLRDSLKEDPKDVTQFRRTADAAKES 142

Query: 147 IRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEK 206
           IR+YL +WRGQ+ V  EESY+ELEKAIRSLASFYSKAGPSAPLP EVKSEILNDL  AE+
Sbjct: 143 IREYLGSWRGQEKVVREESYIELEKAIRSLASFYSKAGPSAPLPEEVKSEILNDLSAAEE 202

Query: 207 FL 208
           FL
Sbjct: 203 FL 204

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224102063|ref|XP_002312530.1| predicted protein [Populus trichocarpa] gi|118485936|gb|ABK94813.1| unknown [Populus trichocarpa] gi|222852350|gb|EEE89897.1| predicted protein [Populus trichocarpa]

 Score =  244 bits (623), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 128/200 (64%), Positives = 156/200 (78%), Gaps = 15/200 (7%)

Query: 18  SRLSWQTLN---------KLHSRTHVVLPPVEAASSRRHVISCSSTALVAILTFNCGLAP 68
           S ++++T+N         KL+SR + VL    A  SRRHV+  S++  V +LT NC L P
Sbjct: 11  SFVTFKTMNRTSKPDIDYKLNSRCNAVLSSQAALPSRRHVLVFSAS-FVTVLTLNCFLTP 69

Query: 69  LPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKE 128
           L  +A+     ++EK++GV GAIKSLFDPNEKTKSGK+LPKAYLK+ARE+VK LRESLKE
Sbjct: 70  LQARAK-----EEEKDDGVAGAIKSLFDPNEKTKSGKLLPKAYLKAAREVVKNLRESLKE 124

Query: 129 DPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAP 188
           D KDIA FRR AD+AKESIR+YL +WRGQ+ V  EESYVELEKAIRSLASFYS+AGPSA 
Sbjct: 125 DTKDIAKFRRTADAAKESIREYLGSWRGQEKVVREESYVELEKAIRSLASFYSRAGPSAQ 184

Query: 189 LPGEVKSEILNDLDTAEKFL 208
           LP EV+SEILNDL+TAE+FL
Sbjct: 185 LPEEVRSEILNDLNTAEEFL 204

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388498828|gb|AFK37480.1| unknown [Lotus japonicus]

 Score =  240 bits (613), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 128/208 (61%), Positives = 158/208 (75%), Gaps = 8/208 (3%)

Query: 2   SLSSITGSRQSSTLPLSRLSWQTLNKLHSRTHVVLPPVEAASSRRHVISCSSTALVAILT 61
           ++SSIT S+    +      +   +KL  R+++ LPP+EA+SSRRH++    T+LV   T
Sbjct: 8   NMSSITSSKTVERIK----RFDIHDKLQFRSNIALPPLEASSSRRHLLLSVGTSLV---T 60

Query: 62  FNCG-LAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVK 120
             CG L+PL   AE+ S  +++ ++GVVGAIKSLFDPNEK+KSGKVLPKAYLKSARE+VK
Sbjct: 61  MTCGGLSPLMASAEENSADKEDDDKGVVGAIKSLFDPNEKSKSGKVLPKAYLKSAREVVK 120

Query: 121 TLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFY 180
           TLRESL E P D A FRR AD+AKESIRDYL  WRG + VA EESY  LEKAIRSLA FY
Sbjct: 121 TLRESLNEVPDDNAKFRRTADAAKESIRDYLGGWRGNQDVAQEESYDMLEKAIRSLAKFY 180

Query: 181 SKAGPSAPLPGEVKSEILNDLDTAEKFL 208
           S+AGPSAPLP EVK+EIL+ L+TAE+FL
Sbjct: 181 SRAGPSAPLPEEVKTEILDYLNTAEEFL 208

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356526109|ref|XP_003531662.1| PREDICTED: uncharacterized protein LOC100805317 [Glycine max]

 Score =  238 bits (606), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 121/183 (66%), Positives = 148/183 (80%), Gaps = 3/183 (1%)

Query: 26  NKLHSRTHVVLPPVEAASSRRHVISCSSTALVAILTFNCGLAPLPVQAEDMSNGQDEKEE 85
           +K+ SR+++ LPP EA+SSRRH++     +L   LT  CGL+P  V AE+ S  ++E+++
Sbjct: 28  DKMQSRSNIALPPSEASSSRRHLLIGVGPSL---LTLTCGLSPPTVWAEEKSGDKEEEDK 84

Query: 86  GVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKE 145
           GV+GAIKSLFDPNEKTKSGKVLPKAYL+SARE+VKTLRESL E   D A FRR ADSAKE
Sbjct: 85  GVIGAIKSLFDPNEKTKSGKVLPKAYLRSAREVVKTLRESLNEGTDDNAKFRRTADSAKE 144

Query: 146 SIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAE 205
           SIR+YL +WRG + VA EESYV LEK IRSLA++YSKAGPSAPL  EVKSEIL+ L+TAE
Sbjct: 145 SIREYLGSWRGNQIVAQEESYVILEKVIRSLANYYSKAGPSAPLSHEVKSEILDYLNTAE 204

Query: 206 KFL 208
           +FL
Sbjct: 205 EFL 207

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449444118|ref|XP_004139822.1| PREDICTED: uncharacterized protein LOC101211891 [Cucumis sativus] gi|449492573|ref|XP_004159036.1| PREDICTED: uncharacterized LOC101211891 [Cucumis sativus]

 Score =  229 bits (583), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 124/182 (68%), Positives = 145/182 (79%), Gaps = 3/182 (1%)

Query: 27  KLHSRTHVVLPPVEAASSRRHVISCSSTALVAILTFNCGLAPLPVQAEDMSNGQDEKEEG 86
           KL SR+ VVLP  E    RRH++  +  +LV  LTFN GL P   QAE+M N  +E++ G
Sbjct: 28  KLPSRSRVVLPYQEVC--RRHLV-WNGMSLVVFLTFNNGLTPSSAQAEEMPNNMEEEDNG 84

Query: 87  VVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKES 146
           V+G IKS+FDPNEKTKSGK+LPKAYLKSARE+VKTLRESL+EDPKD A FRR AD+AKES
Sbjct: 85  VIGTIKSIFDPNEKTKSGKILPKAYLKSAREVVKTLRESLQEDPKDGAKFRRTADAAKES 144

Query: 147 IRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEK 206
           IRDYLSNW G++TV  EESYV LEKAIRSLA FY+KAGPSAPLP  VKS+IL+DLD  E+
Sbjct: 145 IRDYLSNWLGKQTVVQEESYVVLEKAIRSLAGFYAKAGPSAPLPEAVKSDILDDLDKVEE 204

Query: 207 FL 208
            L
Sbjct: 205 SL 206

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18390518|ref|NP_563737.1| LOW PSII accumulation 19 protein [Arabidopsis thaliana] gi|8778732|gb|AAF79740.1|AC005106_21 T25N20.4 [Arabidopsis thaliana] gi|13877959|gb|AAK44057.1|AF370242_1 unknown protein [Arabidopsis thaliana] gi|23296694|gb|AAN13149.1| unknown protein [Arabidopsis thaliana] gi|332189712|gb|AEE27833.1| LOW PSII accumulation 19 protein [Arabidopsis thaliana]

 Score =  218 bits (554), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 114/166 (68%), Positives = 134/166 (80%), Gaps = 9/166 (5%)

Query: 45  RRHVISC--SSTALVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTK 102
           RR  + C   +++ +A + F+ GL     QA+      DE E GVVGA K+LFDPNE+TK
Sbjct: 41  RRGFLKCVVGASSFMATIEFS-GL-----QAQASEEKLDEGE-GVVGAFKTLFDPNERTK 93

Query: 103 SGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAG 162
           SGK LPKAYLKSARE+VKT+RESLKE+PKD A FRR+AD+AKESIRDYLSNWRGQKTVAG
Sbjct: 94  SGKELPKAYLKSAREVVKTMRESLKENPKDNAKFRRSADAAKESIRDYLSNWRGQKTVAG 153

Query: 163 EESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL 208
           EESYVELE  IR+LA FYSKAGPSAPLP EVK+EIL+DL+ AE+FL
Sbjct: 154 EESYVELENVIRALAKFYSKAGPSAPLPDEVKTEILDDLNKAEEFL 199

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|26451618|dbj|BAC42906.1| unknown protein [Arabidopsis thaliana]

 Score =  216 bits (551), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 113/166 (68%), Positives = 134/166 (80%), Gaps = 9/166 (5%)

Query: 45  RRHVISC--SSTALVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTK 102
           RR  + C   +++ +A + F+ GL     QA+      DE E GVVGA K+LFDPNE+TK
Sbjct: 41  RRGFLKCVVGASSFMATIEFS-GL-----QAQASEEKLDEGE-GVVGAFKTLFDPNERTK 93

Query: 103 SGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAG 162
           SGK LPKAYLKSARE+VKT+RESLKE+P+D A FRR+AD+AKESIRDYLSNWRGQKTVAG
Sbjct: 94  SGKELPKAYLKSAREVVKTMRESLKENPRDNAKFRRSADAAKESIRDYLSNWRGQKTVAG 153

Query: 163 EESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL 208
           EESYVELE  IR+LA FYSKAGPSAPLP EVK+EIL+DL+ AE+FL
Sbjct: 154 EESYVELENVIRALAKFYSKAGPSAPLPDEVKTEILDDLNKAEEFL 199

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	208
TAIR|locus:505006101	199	LPA19 "AT1G05385" [Arabidopsis	0.754	0.788	0.686	1.2e-51
UNIPROTKB|P74367	134	slr1645 "Photosystem II 11 kDa	0.490	0.761	0.298	2.2e-09
TAIR|locus:2020788	174	PSB27 "AT1G03600" [Arabidopsis	0.466	0.557	0.265	5.9e-09

TAIR|locus:505006101 LPA19 "AT1G05385" [Arabidopsis thaliana (taxid:3702)]

 Score = 536 (193.7 bits), Expect = 1.2e-51, P = 1.2e-51
 Identities = 114/166 (68%), Positives = 134/166 (80%)

Query:    45 RRHVISC--SSTALVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTK 102
             RR  + C   +++ +A + F+ GL     QA+      DE E GVVGA K+LFDPNE+TK
Sbjct:    41 RRGFLKCVVGASSFMATIEFS-GL-----QAQASEEKLDEGE-GVVGAFKTLFDPNERTK 93

Query:   103 SGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAG 162
             SGK LPKAYLKSARE+VKT+RESLKE+PKD A FRR+AD+AKESIRDYLSNWRGQKTVAG
Sbjct:    94 SGKELPKAYLKSAREVVKTMRESLKENPKDNAKFRRSADAAKESIRDYLSNWRGQKTVAG 153

Query:   163 EESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL 208
             EESYVELE  IR+LA FYSKAGPSAPLP EVK+EIL+DL+ AE+FL
Sbjct:   154 EESYVELENVIRALAKFYSKAGPSAPLPDEVKTEILDDLNKAEEFL 199

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009543 "chloroplast thylakoid lumen" evidence=IDA

GO:0010207 "photosystem II assembly" evidence=IMP

GO:0006098 "pentose-phosphate shunt" evidence=RCA

UNIPROTKB|P74367 slr1645 "Photosystem II 11 kDa protein" [Synechocystis sp. PCC 6803 substr. Kazusa (taxid:1111708)]

 Score = 137 (53.3 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 31/104 (29%), Positives = 58/104 (55%)

Query:   103 SGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAG 162
             SG  L   Y +    ++ TLRE++ + P+D  N +   D+A+  I DY+S +R +    G
Sbjct:    27 SGTGLTGNYSQDTLTVIATLREAI-DLPQDAPNRQEVQDTARGQINDYISRYRRKGDAGG 85

Query:   163 EESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEK 206
              +S+  ++ A+ SLA +Y+  G + P+P ++K  +  +   AE+
Sbjct:    86 LKSFTTMQTALNSLAGYYTSYG-ARPIPEKLKKRLQLEFTQAER 128

GO:0030096 "plasma membrane-derived thylakoid photosystem II" evidence=IDA

TAIR|locus:2020788 PSB27 "AT1G03600" [Arabidopsis thaliana (taxid:3702)]

 Score = 133 (51.9 bits), Expect = 5.9e-09, P = 5.9e-09
 Identities = 26/98 (26%), Positives = 54/98 (55%)

Query:   111 YLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELE 170
             Y+K    ++  +R +L     D  N        +E+   +++ +R +K + G+ S+ ++ 
Sbjct:    74 YIKDTSAVISKVRSTLSMQKTD-PNVADAVAELREASNSWVAKYRKEKALLGKASFRDIY 132

Query:   171 KAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL 208
              A+ +++  Y   GP+AP+P + K+ IL +++TAEK L
Sbjct:   133 SALNAVSGHYVSFGPTAPIPAKRKARILEEMETAEKAL 170


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        0.310   0.126   0.347    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      208       208   0.00077  112 3  11 23  0.44    33
                                                     31  0.48    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  3
  No. of states in DFA:  595 (63 KB)
  Total size of DFA:  153 KB (2092 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:  23.18u 0.10s 23.28t   Elapsed:  00:00:01
  Total cpu time:  23.18u 0.10s 23.28t   Elapsed:  00:00:01
  Start:  Mon May 20 18:22:04 2013   End:  Mon May 20 18:22:05 2013

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0030095 "chloroplast photosystem II" evidence=ISS

GO:0009543 "chloroplast thylakoid lumen" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009534 "chloroplast thylakoid" evidence=IDA

GO:0010206 "photosystem II repair" evidence=IMP

GO:0006364 "rRNA processing" evidence=RCA

GO:0009657 "plastid organization" evidence=RCA

GO:0010207 "photosystem II assembly" evidence=RCA

GO:0019684 "photosynthesis, light reaction" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	208
PLN00061	150	PLN00061, PLN00061, photosystem II protein Psb27;	1e-83
pfam13326	110	pfam13326, PSII_Pbs27, Photosystem II Pbs27	1e-34
TIGR03044	135	TIGR03044, PS_II_psb27, photosystem II protein Psb	1e-09
PLN00064	166	PLN00064, PLN00064, photosystem II protein Psb27;	1e-07

>gnl|CDD|215043 PLN00061, PLN00061, photosystem II protein Psb27; Provisional

 Score =  244 bits (625), Expect = 1e-83
 Identities = 116/151 (76%), Positives = 128/151 (84%), Gaps = 2/151 (1%)

Query: 55  ALVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKS 114
           +  A LT N  + PL  +AE+    + E+ EGVVGAIKSLFDPNEKTKSGK LPKAYLKS
Sbjct: 2   SFAASLTLNGQMTPLQARAEE--EAKVEEGEGVVGAIKSLFDPNEKTKSGKKLPKAYLKS 59

Query: 115 ARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIR 174
           ARE+VKTLRESLKEDPKD A FRR AD+AKESIR+YL NWRGQKTVA EESYVELEKAIR
Sbjct: 60  AREVVKTLRESLKEDPKDEAKFRRTADAAKESIREYLGNWRGQKTVAEEESYVELEKAIR 119

Query: 175 SLASFYSKAGPSAPLPGEVKSEILNDLDTAE 205
           SLASFYSKAGPSAPLP +VKSEIL+DL+ AE
Sbjct: 120 SLASFYSKAGPSAPLPEDVKSEILDDLNKAE 150

Length = 150

>gnl|CDD|205506 pfam13326, PSII_Pbs27, Photosystem II Pbs27

 Score =  118 bits (298), Expect = 1e-34
 Identities = 45/116 (38%), Positives = 62/116 (53%), Gaps = 8/116 (6%)

Query: 93  SLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLS 152
           ++  P  K      L   Y+K    +V+TLRE+L E PKD  N    A  A+E I DY+S
Sbjct: 3   AVAAPAAK------LTGDYVKDTLAVVETLRETL-ELPKDDPNRAEAAAEARELINDYVS 55

Query: 153 NWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL 208
            +R   +VAG  S+  +  A+ SLA  YS  G   PLP ++K  +L +L  AEK L
Sbjct: 56  RYRRGPSVAGLASFTTMYTALNSLAGHYSSYGN-RPLPEKLKERLLKELKKAEKAL 110

This family of proteins contains Pbs27, a highly conserved component of photosystem II. Pbs27 is comprised of four helices arranged in a right handed up-down-up-down fold, with a less ordered region located at the N-terminus. Length = 110

>gnl|CDD|234098 TIGR03044, PS_II_psb27, photosystem II protein Psb27

 Score = 54.3 bits (131), Expect = 1e-09
 Identities = 31/91 (34%), Positives = 51/91 (56%), Gaps = 2/91 (2%)

Query: 118 LVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLA 177
           +++TLRE++   P D  N       A++ I DY+S +R +  V G  S+  ++ A+ SLA
Sbjct: 44  VIQTLREAIDL-PDDDPNKSEAQAEARQLINDYISRYRRRPRVNGLSSFTTMQTALNSLA 102

Query: 178 SFYSKAGPSAPLPGEVKSEILNDLDTAEKFL 208
             Y K+  + PLP ++K  +  +L  AEK L
Sbjct: 103 GHY-KSYANRPLPEKLKERLEKELKKAEKAL 132

Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single family models, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences from Arabidopsis are not, at this time, assigned as functionally equivalent photosystem II proteins [Energy metabolism, Photosynthesis]. Length = 135

>gnl|CDD|215045 PLN00064, PLN00064, photosystem II protein Psb27; Provisional

 Score = 49.6 bits (118), Expect = 1e-07
 Identities = 27/98 (27%), Positives = 56/98 (57%), Gaps = 1/98 (1%)

Query: 111 YLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELE 170
           Y+K  ++++  +R ++  D  D  N        +E+   +++ +R +K + G  S+ ++ 
Sbjct: 66  YVKETKDVIGKVRSTINMDKTD-PNVADAVAELRETSNSWVAKYRREKALLGRPSFRDMY 124

Query: 171 KAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL 208
            A+ +++  Y   GP+AP+P + K+ IL ++DTAEK L
Sbjct: 125 SALNAVSGHYISFGPTAPIPAKRKARILEEMDTAEKAL 162

Length = 166

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	208
PLN00061	150	photosystem II protein Psb27; Provisional	100.0
TIGR03044	135	PS_II_psb27 photosystem II protein Psb27. Members	100.0
PF13326	145	PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF	100.0
PLN00064	166	photosystem II protein Psb27; Provisional	100.0
TIGR02811	66	formate_TAT formate dehydrogenase region TAT targe	93.48
PF10518	26	TAT_signal: TAT (twin-arginine translocation) path	90.61
TIGR01409	29	TAT_signal_seq Tat (twin-arginine translocation) p	86.38
PF07240	85	Turandot: Stress-inducible humoral factor Turandot	84.37
PF10399	41	UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-	81.45

>PLN00061 photosystem II protein Psb27; Provisional

Probab=100.00  E-value=1.5e-64  Score=415.70  Aligned_cols=148  Identities=78%  Similarity=1.098  Sum_probs=143.5

Q ss_pred             HHHHHHhhcCCCCchhhhhcccCCCCccccccccchhcccCCCCcCcCCCCCcHHHHHHHHHHHHHHHHHhcCCCCCchH
Q 028492           56 LVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIAN  135 (208)
Q Consensus        56 ~~a~~~~~~~~~p~~~~A~~e~~~~~~~~~g~~~~~~~~fdp~~~~ksg~~LPk~Y~~dTr~VV~tLReaL~ldp~D~~~  135 (208)
                      ++++++++|...|++++|++|+  +.++++||||||||||||||+||||++||++|++||++||++||++|+++|+|+++
T Consensus         3 ~~~~~~~~~~~~~~~~~a~~e~--~~~~~~~~~~~~~~~fdp~e~tksg~~Lpg~Y~kdtr~VV~tLresl~l~p~D~~~   80 (150)
T PLN00061          3 FAASLTLNGQMTPLQARAEEEA--KVEEGEGVVGAIKSLFDPNEKTKSGKKLPKAYLKSAREVVKTLRESLKEDPKDEAK   80 (150)
T ss_pred             HHHHHHHhcCCCCCcchHHHHh--cccccccHHHHHHHhcCccccccccccCchHHHHHHHHHHHHHHHHHccCCcchHH
Confidence            3689999999999999999997  47777899999999999999999999999999999999999999999999999999


Q ss_pred             HHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHHHHHH
Q 028492          136 FRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAE  205 (208)
Q Consensus       136 ~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss~GpnrPLPeklK~RLlqEL~~AE  205 (208)
                      |++++++||++|||||++||+++.|+|++||+||+||||+|||||++|||||||||++|+||++||++||
T Consensus        81 ~~~aa~~Ake~IndYisryR~~~~V~gl~SfttMqtALnsLAghYssyGpnrPLPe~lK~Rll~EL~~AE  150 (150)
T PLN00061         81 FRRTADAAKESIREYLGNWRGQKTVAEEESYVELEKAIRSLASFYSKAGPSAPLPEDVKSEILDDLNKAE  150 (150)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCccccccchHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHhccC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999997

>TIGR03044 PS_II_psb27 photosystem II protein Psb27

Probab=100.00  E-value=5.2e-44  Score=290.46  Aligned_cols=104  Identities=31%  Similarity=0.520  Sum_probs=100.6

Q ss_pred             CCCCCcHHHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhh
Q 028492          103 SGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSK  182 (208)
Q Consensus       103 sg~~LPk~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss  182 (208)
                      +.+.|+++|.+||++||++||++|++ |+|++++++++++||++|||||+||||+++|+|++||+|||||||+|||||++
T Consensus        29 ~~~~Ltg~Y~~DT~~Vi~tlr~~i~l-pkd~p~~~~a~~~ar~~indyvsrYRr~~~v~g~~SFttm~TALNsLAGHY~s  107 (135)
T TIGR03044        29 AKTRLTGDYVEDTLAVIQTLREAIDL-PDDDPNKSEAQAEARQLINDYISRYRRRPRVNGLSSFTTMQTALNSLAGHYKS  107 (135)
T ss_pred             CcccccchHHHHHHHHHHHHHHHHcC-CCCCccHHHHHHHHHHHHHHHHHHhcCCCCcCCcccHHHHHHHHHHHHHHhcc
Confidence            34678999999999999999999999 99999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCChHHHHHHHHHHHHHHhcC
Q 028492          183 AGPSAPLPGEVKSEILNDLDTAEKFL  208 (208)
Q Consensus       183 ~GpnrPLPeklK~RLlqEL~~AE~aL  208 (208)
                      || |||||||+|+||+|||++||++|
T Consensus       108 y~-~rPlPeklk~Rl~~El~~AE~al  132 (135)
T TIGR03044       108 YA-NRPLPEKLKERLEKELKKAEKAL  132 (135)
T ss_pred             CC-CCCCCHHHHHHHHHHHHHHHHHH
Confidence            95 99999999999999999999986

Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single model families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins.

>PF13326 PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF_A 2Y6X_A

Probab=100.00  E-value=8.7e-45  Score=296.16  Aligned_cols=145  Identities=41%  Similarity=0.550  Sum_probs=93.0

Q ss_pred             hhHHHHHhhhhhHHHHHHhhcCCCCchhhhhcccCCCCccccccccchhcccCCCCcCcCCCCCcHHHHHHHHHHHHHHH
Q 028492           44 SRRHVISCSSTALVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLR  123 (208)
Q Consensus        44 sRr~~l~~~~~~~~a~~~~~~~~~p~~~~A~~e~~~~~~~~~g~~~~~~~~fdp~~~~ksg~~LPk~Y~~dTr~VV~tLR  123 (208)
                      +||+||.+.+.++ .++++.+..+++.+++.....+           ++|. +||+      .|+++|++||++||++||
T Consensus         1 ~rr~~l~~~~~~~-~al~l~~~~~~l~~~~l~~c~~-----------~~s~-~~~~------~l~~~Y~~dt~~vv~~lr   61 (145)
T PF13326_consen    1 SRRRLLLAASSAL-LALTLSARGAALAVIALTACRA-----------AKSG-DPNA------GLTGDYVKDTRAVVKTLR   61 (145)
T ss_dssp             ---------------------------------S------------------S--S------S--S-CHHHHHHHHHHHH
T ss_pred             CcchhhhHHHHHH-HHHHHhhhhHHHHhhcchhhhh-----------cccC-Cccc------cccchHHHHHHHHHHHHH
Confidence            6999998888874 4555555555655544222110           4455 6665      455679999999999999


Q ss_pred             HHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHHHH
Q 028492          124 ESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDT  203 (208)
Q Consensus       124 eaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss~GpnrPLPeklK~RLlqEL~~  203 (208)
                      ++|++ |+|++++++++++||++|||||++|||+++|+|++||++||+|||+|||||++|||++|||+|+|+||++||++
T Consensus        62 ~~l~l-~~d~~~~~~~~~~ar~~in~~vs~YRr~~~v~g~~Sf~~m~tAln~LaghY~s~g~raPlP~k~k~rll~el~~  140 (145)
T PF13326_consen   62 EALEL-DKDDPNRAEAAAEARELINDYVSRYRRGPSVSGLPSFTTMYTALNALAGHYSSYGNRAPLPEKLKERLLKELDQ  140 (145)
T ss_dssp             HHHCS--TT-TTHHHHHHHHHHHHHHHHCCCCCCHHCCTSHHHHHHHHHHHHHHHHCHHHTTS-S--HHHHHHHHHHHHH
T ss_pred             HHHcC-CCCCccHHHHHHHHHHHHHHHHHHhCCCCCcCCcchHHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHH
Confidence            99998 79999999999999999999999999999999999999999999999999999998889999999999999999


Q ss_pred             HHhcC
Q 028492          204 AEKFL  208 (208)
Q Consensus       204 AE~aL  208 (208)
                      ||++|
T Consensus       141 Ae~aL  145 (145)
T PF13326_consen  141 AEKAL  145 (145)
T ss_dssp             HHHHH
T ss_pred             HHhcC
Confidence            99986

>PLN00064 photosystem II protein Psb27; Provisional

Probab=100.00  E-value=1.9e-43  Score=294.52  Aligned_cols=98  Identities=27%  Similarity=0.555  Sum_probs=96.7

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhhcCCCCCC
Q 028492          110 AYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKAGPSAPL  189 (208)
Q Consensus       110 ~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss~GpnrPL  189 (208)
                      +|.+||.+||++||++|+| |+|+++++++++++|++|||||+||||+++|+|++||+|||||||+|||||++|||||||
T Consensus        65 ~Y~~DT~aVi~~lr~tI~L-~~ddp~~a~a~aeaR~~iNdyvSrYRr~~~v~Gl~SFttMyTALNaLAGHY~SfgpnrPl  143 (166)
T PLN00064         65 EYVKETKDVIGKVRSTINM-DKTDPNVADAVAELRETSNSWVAKYRREKALLGRPSFRDMYSALNAVSGHYISFGPTAPI  143 (166)
T ss_pred             ChHHHHHHHHHHHHHHHcC-CCCCccHHHHHHHHHHHHHHHHHHhcCCCcccCcccHHHHHHHHHHHHHHhhccCCCCCC
Confidence            7999999999999999999 999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChHHHHHHHHHHHHHHhcC
Q 028492          190 PGEVKSEILNDLDTAEKFL  208 (208)
Q Consensus       190 PeklK~RLlqEL~~AE~aL  208 (208)
                      |+|+|+||+|||++||++|
T Consensus       144 PeKlK~RL~qE~~~AEkal  162 (166)
T PLN00064        144 PAKRKARILEEMDTAEKAL  162 (166)
T ss_pred             cHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999986

>TIGR02811 formate_TAT formate dehydrogenase region TAT target

Probab=93.48  E-value=0.086  Score=38.57  Aligned_cols=15  Identities=27%  Similarity=0.357  Sum_probs=11.9

Q ss_pred             hhhhhHHHHHhhhhh
Q 028492           41 AASSRRHVISCSSTA   55 (208)
Q Consensus        41 ~~~sRr~~l~~~~~~   55 (208)
                      ...+||+||.+.+.+
T Consensus         7 ~~~sRR~Flk~lg~~   21 (66)
T TIGR02811         7 ADPSRRDLLKGLGVG   21 (66)
T ss_pred             CCccHHHHHHHHHHH
Confidence            356899999988765

Members of this uncharacterized protein family are all small, extending 70 or fewer residues from their respective likely start codons. All have the twin-arginine-dependent tranport (TAT) signal sequence at the N-terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal sequence suggests a bound cofactor. All members are encoded near genes for subunits of formate dehydrogenase, and may themselves be a subunit or accessory protein.

>PF10518 TAT_signal: TAT (twin-arginine translocation) pathway signal sequence; InterPro: IPR019546 The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []

Probab=90.61  E-value=0.24  Score=30.26  Aligned_cols=13  Identities=31%  Similarity=0.417  Sum_probs=11.0

Q ss_pred             hhhHHHHHhhhhh
Q 028492           43 SSRRHVISCSSTA   55 (208)
Q Consensus        43 ~sRr~~l~~~~~~   55 (208)
                      .+||+||.++++.
T Consensus         2 ~sRR~fLk~~~a~   14 (26)
T PF10518_consen    2 LSRRQFLKGGAAA   14 (26)
T ss_pred             CcHHHHHHHHHHH
Confidence            4899999999765

Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state []. It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases []. In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength []. The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].

>TIGR01409 TAT_signal_seq Tat (twin-arginine translocation) pathway signal sequence

Probab=86.38  E-value=0.6  Score=28.75  Aligned_cols=12  Identities=33%  Similarity=0.506  Sum_probs=10.3

Q ss_pred             hhHHHHHhhhhh
Q 028492           44 SRRHVISCSSTA   55 (208)
Q Consensus        44 sRr~~l~~~~~~   55 (208)
                      +||+||..++.+
T Consensus         2 sRR~Flk~~~~~   13 (29)
T TIGR01409         2 SRRDFLKGAAAA   13 (29)
T ss_pred             chhhhHHHHHHH
Confidence            799999999764

Members with small amino acid side chains at the -1 and -3 positions from the C-terminus of the model should be predicted to be cleaved as are Sec pathway signal sequences. Members are almost exclusively bacterial, although archaeal sequences are also found. A large fraction of the members of this family may have bound redox-active cofactors.

>PF07240 Turandot: Stress-inducible humoral factor Turandot; InterPro: IPR010825 This family consists of several Drosophila species specific Turandot proteins

Probab=84.37  E-value=2.3  Score=32.99  Aligned_cols=34  Identities=26%  Similarity=0.419  Sum_probs=29.4

Q ss_pred             HHHHHHHHhhhhhcCCCCCCChHHHHHHHHHHHH
Q 028492          170 EKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDT  203 (208)
Q Consensus       170 ~TALNsLAGhYss~GpnrPLPeklK~RLlqEL~~  203 (208)
                      ..=+.+|-+||..|.|.-||++..|+++...+++
T Consensus         9 ~rni~eLi~fY~ky~~~~~L~~~~r~~~d~~i~~   42 (85)
T PF07240_consen    9 IRNIQELIAFYEKYSPRLPLTPQDRQRIDRFIRR   42 (85)
T ss_pred             HhhHHHHHHHHHHcCccCCCCHHHHHHHHHHHHH
Confidence            3447789999999999999999999999887765

The Turandot A (TotA) gene encodes a humoral factor, which is secreted from the fat body and accumulates in the body fluids. TotA is strongly induced upon bacterial challenge, as well as by other types of stress such as high temperature, mechanical pressure, dehydration, UV irradiation, and oxidative agents. It is also upregulated during metamorphosis and at high age. Flies that overexpress TotA show prolonged survival and retain normal activity at otherwise lethal temperatures. Although TotA is only induced by severe stress, it responds to a much wider range of stimuli than heat shock genes such as hsp70 or immune genes such as Cecropin A1 [].

>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex)

Probab=81.45  E-value=0.57  Score=31.64  Aligned_cols=29  Identities=17%  Similarity=0.276  Sum_probs=16.1

Q ss_pred             hhhhhhhHHHHHhhhhhHHHHHHhhcCCCC
Q 028492           39 VEAASSRRHVISCSSTALVAILTFNCGLAP   68 (208)
Q Consensus        39 ~~~~~sRr~~l~~~~~~~~a~~~~~~~~~p   68 (208)
                      .....+||+||..+.++ ++++-.+++.+|
T Consensus         5 ~~~~~~RRdFL~~at~~-~gavG~~~~a~P   33 (41)
T PF10399_consen    5 EPVDPTRRDFLTIATSA-VGAVGAAAAAWP   33 (41)
T ss_dssp             -----HHHHHHHHHHHH-HHHHHHHHHHHH
T ss_pred             CCCCchHHHHHHHHHHH-HHHHHHHHHHHH
Confidence            34567999999555443 566666666666

This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	208
2kmf_A	115	Solution Structure Of Psb27 From Cyanobacterial Pho		3e-08
2knd_A	110	Psb27 Structure From Synechocystis Length = 110		4e-08

>pdb|2KMF|A Chain A, Solution Structure Of Psb27 From Cyanobacterial Photosystem Ii Length = 115

Iteration: 1
 Score = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 58/104 (55%), Gaps = 2/104 (1%)
Query: 103 SGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAG 162
           SG  L   Y +    ++ TLRE++ + P+D  N +   D+A+  I DY+S +R +    G
Sbjct: 8   SGTGLTGNYSQDTLTVIATLREAI-DLPQDAPNRQEVQDTARGQINDYISRYRRKGDAGG 66
Query: 163 EESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEK 206
            +S+  ++ A+ SLA +Y+  G + P+P ++K  +  +   AE+
Sbjct: 67  LKSFTTMQTALNSLAGYYTSYG-ARPIPEKLKKRLQLEFTQAER 109

>pdb|2KND|A Chain A, Psb27 Structure From Synechocystis Length = 110

Iteration: 1
 Score = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 58/104 (55%), Gaps = 2/104 (1%)
Query: 103 SGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAG 162
           SG  L   Y +    ++ TLRE++ + P+D  N +   D+A+  I DY+S +R +    G
Sbjct: 3   SGTGLTGNYSQDTLTVIATLREAI-DLPQDAPNRQEVQDTARGQINDYISRYRRKGDAGG 61
Query: 163 EESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEK 206
            +S+  ++ A+ SLA +Y+  G + P+P ++K  +  +   AE+
Sbjct: 62  LKSFTTMQTALNSLAGYYTSYG-ARPIPEKLKKRLQLEFTQAER 104

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	208
2kmf_A	115	Photosystem II 11 kDa protein; PSB27, structure, h	1e-32
2y6x_A	113	PSB27, photosystem II 11 KD protein; photosynthesi	3e-25
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07

>2kmf_A Photosystem II 11 kDa protein; PSB27, structure, helical bundle, cyanobacteria, photosynthesis; NMR {Synechocystis SP} PDB: 2knd_A Length = 115

 Score =  112 bits (282), Expect = 1e-32
 Identities = 32/112 (28%), Positives = 59/112 (52%), Gaps = 2/112 (1%)

Query: 97  PNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRG 156
           P     SG  L   Y +    ++ TLRE++ + P+D  N +   D+A+  I DY+S +R 
Sbjct: 2   PLGSCDSGTGLTGNYSQDTLTVIATLREAI-DLPQDAPNRQEVQDTARGQINDYISRYRR 60

Query: 157 QKTVAGEESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL 208
           +    G +S+  ++ A+ SLA +Y+  G   P+P ++K  +  +   AE+ +
Sbjct: 61  KGDAGGLKSFTTMQTALNSLAGYYTSYGA-RPIPEKLKKRLQLEFTQAERSI 111

>2y6x_A PSB27, photosystem II 11 KD protein; photosynthesis; 1.60A {Thermosynechococcus elongatus} Length = 113

 Score = 93.9 bits (233), Expect = 3e-25
 Identities = 24/102 (23%), Positives = 53/102 (51%), Gaps = 2/102 (1%)

Query: 107 LPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESY 166
           L   + +    L+ +LRE++   P++  N +     A++ + D+ + +R   ++    S+
Sbjct: 8   LTGNFREDTLALISSLREAI-ALPENDPNKKAAQAEARKKLNDFFALYRRDDSLRSLSSF 66

Query: 167 VELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEKFL 208
           + ++ A+ SLA  YS + P+ PLP ++K+ +  +    E  L
Sbjct: 67  MTMQTALNSLAGHYS-SYPNRPLPEKLKARLEQEFKQVELAL 107

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 49.5 bits (117), Expect = 2e-07
 Identities = 39/220 (17%), Positives = 74/220 (33%), Gaps = 40/220 (18%)

Query: 1   MSLSSITGSRQSSTLPL------SRLSWQTLNKLHSRTHVVLPPVEAASSRRHV----IS 50
           +  +  + S  SS + L      + L     +K +    +VL  V    + +      +S
Sbjct: 209 IDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV---QNAKAWNAFNLS 265

Query: 51  CS---STALVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVVGAIKSLFDPNEKTKSGKVL 107
           C    +T    +  F        +  +  S      E      +KSL       +    L
Sbjct: 266 CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDE------VKSLLLKYLDCRPQD-L 318

Query: 108 PKAYLKSARELVKTLRESLKEDPKDIANFRR-NADSAKESIRDYLSNWRGQKTVAGEESY 166
           P+  L +    +  + ES+++      N++  N D     I         + ++   E  
Sbjct: 319 PREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTII---------ESSLNVLEPA 369

Query: 167 VELEKAIRSLASFYSKAGP-SAPLPGEVKSEILNDLDTAE 205
            E  K    L+ F     P SA +P  + S I  D+  ++
Sbjct: 370 -EYRKMFDRLSVF-----PPSAHIPTILLSLIWFDVIKSD 403

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	208
2kmf_A	115	Photosystem II 11 kDa protein; PSB27, structure, h	100.0
2y6x_A	113	PSB27, photosystem II 11 KD protein; photosynthesi	100.0
2pq4_B	35	Periplasmic nitrate reductase precursor; NAPD/NAPA	88.84

>2kmf_A Photosystem II 11 kDa protein; PSB27, structure, helical bundle, cyanobacteria, photosynthesis; NMR {Synechocystis SP} PDB: 2knd_A

Probab=100.00  E-value=1.2e-43  Score=280.50  Aligned_cols=103  Identities=29%  Similarity=0.564  Sum_probs=100.6

Q ss_pred             CCCCcHHHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhhc
Q 028492          104 GKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKA  183 (208)
Q Consensus       104 g~~LPk~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss~  183 (208)
                      .+.||++|.+||++||++||++|++ |+|++++++++++||++|||||++|||++.|+|++||+|||||||+|||||++|
T Consensus         9 ~~~L~~~Y~~dT~~Vv~~lr~~l~l-~~d~~~~~~a~~~ar~~ind~vsrYRr~~~v~g~~Sf~tm~tAlNaLAGHY~s~   87 (115)
T 2kmf_A            9 GTGLTGNYSQDTLTVIATLREAIDL-PQDAPNRQEVQDTARGQINDYISRYRRKGDAGGLKSFTTMQTALNSLAGYYTSY   87 (115)
T ss_dssp             CSSCCSCHHHHHHHHHHHHHHHHHS-CTTCTTHHHHHHHHHHHHHHHHHHTHHHHCSSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCccHHHHHHHHHHHHHHHHcC-CCCCccHHHHHHHHHHHHHHHHHHhcCCCCccccchHHHHHHHHHHHHHHHhhc
Confidence            5779999999999999999999998 899999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhcC
Q 028492          184 GPSAPLPGEVKSEILNDLDTAEKFL  208 (208)
Q Consensus       184 GpnrPLPeklK~RLlqEL~~AE~aL  208 (208)
                      | ++|||+|+|+||++||++||++|
T Consensus        88 g-~~PlPek~k~Rl~~el~~AE~al  111 (115)
T 2kmf_A           88 G-ARPIPEKLKKRLQLEFTQAERSI  111 (115)
T ss_dssp             S-SCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             C-CCCCCHHHHHHHHHHHHHHHHHH
Confidence            8 99999999999999999999986

>2y6x_A PSB27, photosystem II 11 KD protein; photosynthesis; 1.60A {Thermosynechococcus elongatus}

Probab=100.00  E-value=2.8e-43  Score=277.74  Aligned_cols=103  Identities=22%  Similarity=0.425  Sum_probs=100.0

Q ss_pred             CCCCcHHHHHHHHHHHHHHHHHhcCCCCCchHHHhhHHHHHHHHHHHHhhccCCCCCCCcchHHHHHHHHHHHHhhhhhc
Q 028492          104 GKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLASFYSKA  183 (208)
Q Consensus       104 g~~LPk~Y~~dTr~VV~tLReaL~ldp~D~~~~r~aa~~AKe~IndyvsrYRr~~~V~G~~SFttM~TALNsLAGhYss~  183 (208)
                      .+.||++|.+||++||++||++|+| |+|++++++++++||++|||||++|||++.|+|++||+|||||||+|||||++|
T Consensus         5 ~~~L~~~Y~~dT~~Vv~~lr~~l~l-~~d~~~~~~a~~~ar~~ind~vsrYRr~~~v~g~~Sfttm~tAlNaLAGHY~s~   83 (113)
T 2y6x_A            5 PTGLTGNFREDTLALISSLREAIAL-PENDPNKKAAQAEARKKLNDFFALYRRDDSLRSLSSFMTMQTALNSLAGHYSSY   83 (113)
T ss_dssp             CCCCCSCHHHHHHHHHHHHHHHHHS-CTTCTTHHHHHHHHHHHHHHHHHHHTTCHHHHTSHHHHHHHHHHHHHHHHHHHC
T ss_pred             ccCCCccHHHHHHHHHHHHHHHHcC-CCCCccHHHHHHHHHHHHHHHHHHhcCCCCccccchHHHHHHHHHHHHHHHhhc
Confidence            3569999999999999999999999 789999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCChHHHHHHHHHHHHHHhcC
Q 028492          184 GPSAPLPGEVKSEILNDLDTAEKFL  208 (208)
Q Consensus       184 GpnrPLPeklK~RLlqEL~~AE~aL  208 (208)
                      | ++|||+|+|+||++||++||++|
T Consensus        84 g-~~PlPek~k~Rl~~el~~AE~al  107 (113)
T 2y6x_A           84 P-NRPLPEKLKARLEQEFKQVELAL  107 (113)
T ss_dssp             T-TSCCCHHHHHHHHHHHHHHHHHH
T ss_pred             C-CCCCCHHHHHHHHHHHHHHHHHH
Confidence            8 99999999999999999999986

>2pq4_B Periplasmic nitrate reductase precursor; NAPD/NAPA1-35, mixed beta-alpha sandwich structure, protein- peptide complex, alpha-helix; NMR {Escherichia coli}

Probab=88.84  E-value=0.22  Score=31.56  Aligned_cols=24  Identities=25%  Similarity=0.203  Sum_probs=15.3

Q ss_pred             hhhHHHHHhhhhhHHHHHHhhcCCCC
Q 028492           43 SSRRHVISCSSTALVAILTFNCGLAP   68 (208)
Q Consensus        43 ~sRr~~l~~~~~~~~a~~~~~~~~~p   68 (208)
                      .+||+||.+++++  ++....+..+|
T Consensus         3 lsRR~FLK~~aaa--~Aaaaag~~~~   26 (35)
T 2pq4_B            3 LSRRSFMKANAVA--AAAAAAGLSVP   26 (35)
T ss_dssp             CCSHHHHHHHHHH--HHHHHHCCCCS
T ss_pred             CcHHHHHHHHHHH--HHHHHhcccch
Confidence            4799999988765  33333345555

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	208
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	82.07

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.07  E-value=0.089  Score=35.64  Aligned_cols=26  Identities=27%  Similarity=0.579  Sum_probs=22.1

Q ss_pred             HHHHHhhhhhcCCCCCCChHHHHHHHHHH
Q 028492          173 IRSLASFYSKAGPSAPLPGEVKSEILNDL  201 (208)
Q Consensus       173 LNsLAGhYss~GpnrPLPeklK~RLlqEL  201 (208)
                      +|.|+|-|.+ |  +|||-++|+||.+-.
T Consensus         2 ~n~~gg~~~~-G--rPls~DLR~Riv~~~   27 (63)
T d1k78a1           2 VNQLGGVFVN-G--RPLPDVVRQRIVELA   27 (63)
T ss_dssp             BCTTSCBCCT-T--SCCCHHHHHHHHHHH
T ss_pred             cCCCCccccC-C--CcCCHHHHHHHHHHH
Confidence            4778999988 5  999999999999643