Citrus Sinensis ID: 012084

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-

MSSLILNCSSCTSSSLPRLSPHKHSEQKAPIIQSNTNWAKKAVINVLTGALSFNLLLSSPLALESSSSVQSVPPSPSPSLTCHEGEDAAESEPRQVVAKTNEGIVEEAWQIVNDSFLDTGRHRWTPQNWQRKREDILSSSIQTRSKAHGIIKRMLASLGDPYTRFLSPAEFSKMARYDMSGIGINLREVPDANGVVTLKVLGLILDGPAHSAGVRQGDEVLAVNGVDVRGKSAFEVSSLLQGPSETFVTIEVKHGNCGPIESIQVQRQLVARTPVFYRLEHLDNGTTSVGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNLGGLVQAGIEIAKLFLNEGETITYTVGRDPQYQKTIVADNSPLVTAPVIVLVNNRTASASEIVASALHDNCRAVLVGEKTFGKGLIQSVYELHDGSGVVVTIGKYVTPNHMDINGNGIEPDYRNLPAWNDVTKHLSQCTMHPQG

ccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHccccHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHccccccccccHHHHcHHccccEEEEEEEEEEEcccccEEEEEEEEEccccHHHHcccccccEEEEEccEEcccccHHHHHHHccccccccEEEEEEEccccccEEEEEEEEEEEEccEEEEEEccccccccEEEEEEccccHHHHHHHHHHHHHHHHccccEEEEEccccccccHHHHHHHHHHHHcccccEEEEEcccccccEEEEccccccccccEEEEEccccccHHHHHHHHHcccccEEEEcccccccEEEEEEEEcccccEEEEEEEEEccccccccccccccccEEccccccHHHHHHHHccccccc

ccccEEEccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccHHHHcccccccccccccccHHHccccccccccccHHHHcccHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHccccccccccHHHHHHHccccccEEEEEEEEccccccccEEEEEEcccccHHHHcccccccEEEEEcccccccccHHHHHHHHccccccEEEEEEEEccccccEEEEEEEEEEEEccEEEEEEEcccccccEEEEEEHHccHHHHHHHHHHHHHHHHccccEEEEEcccccccHHHHHHHHHHHHHccccEEEEEEcccccEEEEEEccccccccccEEEEEccccccHHHHHHHHHHHccccEEEEcccccccEEEEEEEcccccEEEEEEEEEEcccccEcccccccccEEEccccHHHHHHHHHHcccccc

msslilncssctssslprlsphkhseqkapiiqsNTNWAKKAVINVLTGALSFNLllssplalessssvqsvppspspsltchegedaaeseprqvVAKTNEGIVEEAWQIVNDSFldtgrhrwtpqnwqrKREDILSSSIQTRSKAHGIIKRMLAslgdpytrflspaefSKMARYDMsgiginlrevpdangvVTLKVLGLIldgpahsagvrqgdevlavngvdvrgkSAFEVSsllqgpsetFVTIEVkhgncgpieSIQVQRQLVARTPVFYrlehldngttsvGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNLGGLVQAGIEIAKLFLNEGEtitytvgrdpqyqktivadnsplvtaPVIVLVNNRTASASEIVASALHDNCRAVLVGEKTFGKGLIQSVYelhdgsgvVVTIgkyvtpnhmdingngiepdyrnlpawnDVTKHlsqctmhpqg

msslilncssctssslprlsphkhsEQKAPIIQSNTNWAKKAVINVLTGALSFNLLLSSPLALESSSSVQSVPPSPSPSLTCHEGEDAAESEPRQVVAKTNEGIVEEAWQIVNDSfldtgrhrwtpqnwqrkredilsssiqtrsKAHGIIKRMlaslgdpytRFLSPAEFSKMARYDMSGIGINLREVPDANGVVTLKVLGLILDGPahsagvrqgdEVLAVNGVDVRGKSAFEvssllqgpseTFVTIEVKHGNCGPIESIQVQRQLVARTPVFYRLEHldngttsvgymrLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNLGGLVQAGIEIAKLFLNEGETITYTVGRDPQYQKTivadnsplvTAPVIVLVNNRTASASEIVASALHDNCRAVLVGEKTFGKGLIQSVyelhdgsgVVVTIGKYVTPNHMDINGNGIEPDYRNLPAWNDVTKHLSQCTMHPQG

MsslilncssctssslprlsPHKHSEQKAPIIQSNTNWAKKAVINVLTGAlsfnlllssplalessssvqsvppspspslTCHEGEDAAESEPRQVVAKTNEGIVEEAWQIVNDSFLDTGRHRWTPQNWQRKREDILSSSIQTRSKAHGIIKRMLASLGDPYTRFLSPAEFSKMARYDMSGIGINLREVPDANGVVTLKVLGLILDGPAHSAGVRQGDEVLAVNGVDVRGKSAFEVSSLLQGPSETFVTIEVKHGNCGPIESIQVQRQLVARTPVFYRLEHLDNGTTSVGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNLGGLVQAGIEIAKLFLNEGETITYTVGRDPQYQKTIVADNSPLVTAPVIVLVNNRTASASEIVASALHDNCRAVLVGEKTFGKGLIQSVYELHDGSGVVVTIGKYVTPNHMDINGNGIEPDYRNLPAWNDVTKHLSQCTMHPQG

*******************************IQSNTNWAKKAVINVLTGALSFNLLL*******************************************NEGIVEEAWQIVNDSFLDTGRHRWTPQNWQR**************KAHGIIKRMLASLGDPYTRFLSPAEFSKMARYDMSGIGINLREVPDANGVVTLKVLGLILDGPAHSAGVRQGDEVLAVNGVDVRGKSAFEVSSLLQGPSETFVTIEVKHGNCGPIESIQVQRQLVARTPVFYRLEHLDNGTTSVGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNLGGLVQAGIEIAKLFLNEGETITYTVGRDPQYQKTIVADNSPLVTAPVIVLVNNRTASASEIVASALHDNCRAVLVGEKTFGKGLIQSVYELHDGSGVVVTIGKYVTPNHMDINGNGIEPDYRNLPAWNDVTKHL*********

***************************************KKAVINVLTGALSFNLLLSSPLALESSSSVQSVPPSPS**********************TNEGIVEEAWQIVNDSFLDTGRHRWTPQNWQRKREDILSSSIQTRSKAHGIIKRMLASLGDPYTRFLSPAEFSKMARYDMSGIGINLREVPDANGVVTLKVLGLILDGPAHSAGVRQGDEVLAVNGVDVRGKSAFEVSSLLQGPSETFVTIEVKHGNCGPIESIQVQRQLVARTPVFYRLEHLDNGTTSVGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNLGGLVQAGIEIAKLFLNEGETITYTVG***************LVTAPVIVLVNNRTASASEIVASALHDNCRAVLVGEKTFGKGLIQSVYELHDGSGVVVTIGKYVTPNHMDINGNGIEPDYRNLPA*****************

****************************APIIQSNTNWAKKAVINVLTGALSFNLLLSSPLA***********************************AKTNEGIVEEAWQIVNDSFLDTGRHRWTPQNWQRKREDILSSSIQTRSKAHGIIKRMLASLGDPYTRFLSPAEFSKMARYDMSGIGINLREVPDANGVVTLKVLGLILDGPAHSAGVRQGDEVLAVNGVDVRGKSAFEVSSLLQGPSETFVTIEVKHGNCGPIESIQVQRQLVARTPVFYRLEHLDNGTTSVGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNLGGLVQAGIEIAKLFLNEGETITYTVGRDPQYQKTIVADNSPLVTAPVIVLVNNRTASASEIVASALHDNCRAVLVGEKTFGKGLIQSVYELHDGSGVVVTIGKYVTPNHMDINGNGIEPDYRNLPAWNDVTKHL*********

*********SCTSSSLPRLSPHKHSEQKAPIIQSNTNWAKKAVINVLTGALSFNLLLSSPLALESSS**************************RQVVAKTNEGIVEEAWQIVNDSFLDTGRHRWTPQNWQRKREDILSSSIQTRSKAHGIIKRMLASLGDPYTRFLSPAEFSKMARYDMSGIGINLREVPDANGVVTLKVLGLILDGPAHSAGVRQGDEVLAVNGVDVRGKSAFEVSSLLQGPSETFVTIEVKHGNCGPIESIQVQRQLVARTPVFYRLEHLDNGTTSVGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNLGGLVQAGIEIAKLFLNEGETITYTVGRDPQYQKTIVADNSPLVTAPVIVLVNNRTASASEIVASALHDNCRAVLVGEKTFGKGLIQSVYELHDGSGVVVTIGKYVTPNHMDINGNGIEPDYRNLPAWNDVTKH*S********

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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		471	2.2.26 [Sep-21-2011]
P42784		414	Carboxyl-terminal-process	yes	no	0.732	0.833	0.405	7e-71
Q55669		427	Carboxyl-terminal-process	N/A	no	0.736	0.812	0.401	1e-69
O04073		464	C-terminal processing pep	N/A	no	0.721	0.732	0.354	9e-52
O34666		466	Carboxy-terminal processi	yes	no	0.622	0.628	0.326	9e-35
Q5HPB7		491	Probable CtpA-like serine	yes	no	0.598	0.574	0.314	3e-33
Q8CSK8		491	Probable CtpA-like serine	yes	no	0.598	0.574	0.314	6e-33
Q44879		434	Carboxy-terminal-processi	yes	no	0.651	0.707	0.333	1e-32
Q6GGY8		496	Probable CtpA-like serine	yes	no	0.651	0.618	0.284	9e-32
Q2YXZ9		496	Probable CtpA-like serine	yes	no	0.651	0.618	0.284	1e-31
Q5HG01		496	Probable CtpA-like serine	yes	no	0.598	0.568	0.308	1e-31

>sp\|P42784\|CTPA_SYNP2 Carboxyl-terminal-processing protease OS=Synechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6) GN=ctpA PE=3 SV=2	Back alignment and function desciption

 Score =  268 bits (685), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 145/358 (40%), Positives = 227/358 (63%), Gaps = 13/358 (3%)

Query: 94  RQVVAKTNEGIVEEAWQIVNDSFLDTGRHRWTPQNWQRKREDILSSSIQTRSKAHGIIKR 153
           R +     + ++ +AW+ V+ +++D     +  QNW   R+  L   ++TR +A+  +  
Sbjct: 26  RAIAFTDEQDLLLQAWRYVSQAYVD---ETFNHQNWWLIRQKFLKRPLKTRDEAYEAVGE 82

Query: 154 MLASLGDPYTRFLSPAEFSKM---ARYDMSGIGINLREVPDANGVVTLKVLGLILDGPAH 210
           MLA L DPYTR L P ++  +      ++SG+G+ +   P+ +    L+V+  +   PA 
Sbjct: 83  MLALLDDPYTRLLRPEQYRSLKVSTSGELSGVGLQINVNPEVD---VLEVILPLPGSPAE 139

Query: 211 SAGVRQGDEVLAVNGVDVRGKSAFEVSSLLQGPSETFVTIEVKHGNCGPIESIQVQRQLV 270
           +AG+   D++LA++G+D R     E ++ ++G   + V++ VK      + +++V R  +
Sbjct: 140 AAGIEAKDQILAIDGIDTRNIGLEEAAARMRGKKGSTVSLTVKSPKTDTVRTVKVTRDTI 199

Query: 271 ARTPVFYRLEHLDNGTTSVGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNLGG 330
           A  PV+ +L+   NG   VGY+RL +F+A A+ +++ ++ +LQ  GA  ++LDLR+N GG
Sbjct: 200 ALNPVYDKLDE-KNGE-KVGYIRLNQFSANAKTEIIKSLNQLQKQGADRYVLDLRNNPGG 257

Query: 331 LVQAGIEIAKLFLNEGETITYTVGRDPQYQKTIVADNSPLVTAPVIVLVNNRTASASEIV 390
           L+QAGIEIA+L+L++ ETI YTV R   ++ +  A   PL  AP++VLVN  TASASEI+
Sbjct: 258 LLQAGIEIARLWLDQ-ETIVYTVNRQGIFE-SYSAVGQPLTDAPLVVLVNQATASASEIL 315

Query: 391 ASALHDNCRAVLVGEKTFGKGLIQSVYELHDGSGVVVTIGKYVTPNHMDINGNGIEPD 448
           A AL DN RA+LVGEKTFGKGLIQS++EL DG+G+ VT+ KY TP H DIN  GI PD
Sbjct: 316 AGALQDNGRAMLVGEKTFGKGLIQSLFELPDGAGMAVTVAKYETPLHHDINKLGIMPD 373

Cleavage of the 16 C-terminal residues from the D1 precursor of photosystem II. May be involved in protection of the bacterium from thermal and osmotic stresses.
Synechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6) (taxid: 32049)
EC: 3EC: .EC: 4EC: .EC: 2EC: 1EC: .EC: 1EC: 0EC: 2

>sp\|Q55669\|CTPA_SYNY3 Carboxyl-terminal-processing protease OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=ctpA PE=3 SV=1	Back alignment and function description

>sp\|O04073\|CTPA_SCEOB C-terminal processing peptidase, chloroplastic OS=Scenedesmus obliquus GN=ctpA PE=1 SV=1	Back alignment and function description

>sp\|O34666\|CTPA_BACSU Carboxy-terminal processing protease CtpA OS=Bacillus subtilis (strain 168) GN=ctpA PE=2 SV=1	Back alignment and function description

>sp\|Q5HPB7\|CTPAL_STAEQ Probable CtpA-like serine protease OS=Staphylococcus epidermidis (strain ATCC 35984 / RP62A) GN=SERP0996 PE=3 SV=1	Back alignment and function description

>sp\|Q8CSK8\|CTPAL_STAES Probable CtpA-like serine protease OS=Staphylococcus epidermidis (strain ATCC 12228) GN=SE_1113 PE=3 SV=1	Back alignment and function description

>sp\|Q44879\|CTPA_BARBK Carboxy-terminal-processing protease OS=Bartonella bacilliformis (strain ATCC 35685 / KC583) GN=ctpA PE=3 SV=1	Back alignment and function description

>sp\|Q6GGY8\|CTPAL_STAAR Probable CtpA-like serine protease OS=Staphylococcus aureus (strain MRSA252) GN=SAR1432 PE=3 SV=1	Back alignment and function description

>sp\|Q2YXZ9\|CTPAL_STAAB Probable CtpA-like serine protease OS=Staphylococcus aureus (strain bovine RF122 / ET3-1) GN=SAB1275c PE=3 SV=1	Back alignment and function description

>sp\|Q5HG01\|CTPAL_STAAC Probable CtpA-like serine protease OS=Staphylococcus aureus (strain COL) GN=SACOL1455 PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		471
255557425		491	Carboxyl-terminal-processing protease pr	0.987	0.947	0.735	0.0
297740636		500	unnamed protein product [Vitis vinifera]	0.936	0.882	0.741	0.0
225463392		462	PREDICTED: carboxyl-terminal-processing	0.936	0.954	0.741	0.0
356512566		442	PREDICTED: carboxyl-terminal-processing	0.927	0.988	0.696	0.0
224114365		468	predicted protein [Populus trichocarpa]	0.978	0.985	0.742	0.0
449459336		489	PREDICTED: carboxyl-terminal-processing	0.959	0.924	0.683	0.0
357519225		465	Carboxyl-terminal-processing protease [M	0.970	0.982	0.671	1e-180
388502616		465	unknown [Medicago truncatula]	0.970	0.982	0.669	1e-180
19774137		467	D1 protease-like protein precursor [Nico	0.861	0.869	0.730	1e-176
42573594		489	Peptidase S41 family protein [Arabidopsi	0.985	0.948	0.630	1e-175

>gi\|255557425\|ref\|XP_002519743.1\| Carboxyl-terminal-processing protease precursor, putative [Ricinus communis] gi\|223541160\|gb\|EEF42716.1\| Carboxyl-terminal-processing protease precursor, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  693 bits (1788), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/492 (73%), Positives = 401/492 (81%), Gaps = 27/492 (5%)

Query: 6   LNCSSCTSSSLPRLSPHKHSEQKAP---------IIQSNTNWAKKAVINVLTGALSFNLL 56
           +N   C SS+   LS    S  KAP         +    T WA+K  +  LTG LSFNLL
Sbjct: 1   MNVLLCNSSATLPLSQSSLSSPKAPPTKFSFSLNLNNHTTTWARKTFLGALTGVLSFNLL 60

Query: 57  LSSPLALESSSSVQSVP-PSPSPSLTCHEGEDAAESEPRQVVAKTNEGIVEEAWQIVNDS 115
           LSSP +L S S    +  PSP P+ +  E     E   +   + TNEGIVEEAWQIVNDS
Sbjct: 61  LSSPFSLASQSPYPQLQLPSP-PNNSSIEQCQEQEQVEQNQESVTNEGIVEEAWQIVNDS 119

Query: 116 FLDTGRHRWTPQNWQRKREDILSSSIQTRSKAHGIIKRMLASLGDPYTRFLSPAEFSKMA 175
           FLD GRHRWTPQ+WQ+K+EDILS+SIQ+RSKAH +IKRMLASLGDPYTRFLSPAEFSKMA
Sbjct: 120 FLDAGRHRWTPQSWQQKKEDILSTSIQSRSKAHDLIKRMLASLGDPYTRFLSPAEFSKMA 179

Query: 176 RYDMSGIGINLREVPDANGVVTLKVLGLILDGPAHSAGVRQGDEVLAVNGVDVRGKSAFE 235
           RYDMSGIGINLREVP+ NG V LKVLGL+LDGPA++AGV+QGDE+LAVNG DVRGKSAFE
Sbjct: 180 RYDMSGIGINLREVPEENGEVKLKVLGLLLDGPAYTAGVKQGDEILAVNGEDVRGKSAFE 239

Query: 236 VSSLLQGPSETFVTIEVKHGNCGPIESIQVQRQLVARTPVFYRLEHLDNGTTSVGYMRLK 295
           VSS LQGP+ETFVTI+VKHGNCGPI+S++VQRQLVARTPVFYRLE +D GTTSVGYMRLK
Sbjct: 240 VSSSLQGPNETFVTIKVKHGNCGPIQSLEVQRQLVARTPVFYRLEQVDKGTTSVGYMRLK 299

Query: 296 EFNALARKDLVTAMKRLQDMGASYFILDLRDNLGGLVQAGIEIAKLFLNEGETITYTVGR 355
           EFNALARKDLV AMKRL+DMGASYFILDLRDNLGGLVQAGIEI+KLFLNEGE + YTVGR
Sbjct: 300 EFNALARKDLVIAMKRLKDMGASYFILDLRDNLGGLVQAGIEISKLFLNEGEKVIYTVGR 359

Query: 356 DPQYQKTIVADNSPLVTAPVIVLVNNRTASASEIVASALHDNCRAVLVGEKTFGKGLIQS 415
           DPQYQ TIVAD +PLVTAPVIVLVNN TASASEIVASALHDNCRAVLVGE+TFGKGLIQS
Sbjct: 360 DPQYQNTIVADTAPLVTAPVIVLVNNNTASASEIVASALHDNCRAVLVGERTFGKGLIQS 419

Query: 416 VYELHDGSGVVVTIGKYVTPNHMDINGNGIEPDYRNLP----------------AWNDVT 459
           V+ELHDGSGVVVT+GKYVTPNHMDINGNGIEPDYRN P                AW+DVT
Sbjct: 420 VFELHDGSGVVVTVGKYVTPNHMDINGNGIEPDYRNFPVKWQEPLIVEEPSLYAAWSDVT 479

Query: 460 KHLSQCTMHPQG 471
           +HLSQC M+ QG
Sbjct: 480 RHLSQCNMNRQG 491

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|297740636\|emb\|CBI30818.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|225463392\|ref\|XP_002271932.1\| PREDICTED: carboxyl-terminal-processing protease [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356512566\|ref\|XP_003524989.1\| PREDICTED: carboxyl-terminal-processing protease-like [Glycine max]	Back alignment and taxonomy information

>gi\|224114365\|ref\|XP_002316739.1\| predicted protein [Populus trichocarpa] gi\|222859804\|gb\|EEE97351.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449459336\|ref\|XP_004147402.1\| PREDICTED: carboxyl-terminal-processing protease-like [Cucumis sativus] gi\|449529666\|ref\|XP_004171819.1\| PREDICTED: carboxyl-terminal-processing protease-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|357519225\|ref\|XP_003629901.1\| Carboxyl-terminal-processing protease [Medicago truncatula] gi\|355523923\|gb\|AET04377.1\| Carboxyl-terminal-processing protease [Medicago truncatula]	Back alignment and taxonomy information

>gi\|388502616\|gb\|AFK39374.1\| unknown [Medicago truncatula]	Back alignment and taxonomy information

>gi\|19774137\|gb\|AAL99045.1\|AF487527_1 D1 protease-like protein precursor [Nicotiana plumbaginifolia]	Back alignment and taxonomy information

>gi\|42573594\|ref\|NP_974893.1\| Peptidase S41 family protein [Arabidopsis thaliana] gi\|332007995\|gb\|AED95378.1\| Peptidase S41 family protein [Arabidopsis thaliana]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		471
TAIR\|locus:2170443		489	AT5G46390 [Arabidopsis thalian	0.798	0.768	0.736	4.1e-152
UNIPROTKB\|P73458		423	prc "Carboxyl-terminal proteas	0.704	0.784	0.395	1.7e-57
UNIPROTKB\|P75023		462	ctpB "Carboxyl-terminal protea	0.768	0.783	0.365	3.7e-55
TAIR\|locus:2129411		515	AT4G17740 [Arabidopsis thalian	0.732	0.669	0.353	3.1e-51
TIGR_CMR\|CHY_0170		377	CHY_0170 "carboxyl-terminal pr	0.630	0.787	0.361	5.9e-41
TIGR_CMR\|GSU_1772		443	GSU_1772 "carboxy-terminal pro	0.628	0.668	0.336	7.8e-39
TIGR_CMR\|GSU_0969		450	GSU_0969 "carboxy-terminal pro	0.607	0.635	0.351	3e-37
TIGR_CMR\|SPO_3812		443	SPO_3812 "carboxyl-terminal pr	0.598	0.636	0.364	5.7e-36
TIGR_CMR\|DET_0364		377	DET_0364 "carboxyl-terminal pr	0.647	0.809	0.299	1.6e-31
TIGR_CMR\|BA_5414		469	BA_5414 "carboxyl-terminal pro	0.628	0.631	0.297	6.9e-31

TAIR\|locus:2170443 AT5G46390 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1484 (527.5 bits), Expect = 4.1e-152, P = 4.1e-152
 Identities = 279/379 (73%), Positives = 334/379 (88%)

Query:    92 EPRQVVAKTNEGIVEEAWQIVNDSFLDTGRHRWTPQNWQRKREDILSSSIQTRSKAHGII 151
             EP+ V   TNEGIVEEAW+IVN +FLDT  H WTP+ WQ++++DIL+S I++RSKAH +I
Sbjct:   113 EPQLV---TNEGIVEEAWEIVNGAFLDTRSHSWTPETWQKQKDDILASPIKSRSKAHEVI 169

Query:   152 KRMLASLGDPYTRFLSPAEFSKMARYDMSGIGINLREVPDANGVVTLKVLGLILDGPAHS 211
             K MLASLGD YTRFLSP EFS+M++YD++GIGINLREV D  G V LKVLGL+LD  A  
Sbjct:   170 KNMLASLGDQYTRFLSPDEFSRMSKYDITGIGINLREVSDGGGNVKLKVLGLVLDSAADI 229

Query:   212 AGVRQGDEVLAVNGVDVRGKSAFEVSSLLQGPSETFVTIEVKHGNCGPIESIQVQRQLVA 271
             AGV+QGDE+LAVNG+DV GKS+FEVSSLLQGPS+TFV ++VKHG CGP++S+++QRQ+ A
Sbjct:   230 AGVKQGDEILAVNGMDVSGKSSFEVSSLLQGPSKTFVVLKVKHGKCGPVKSLKIQRQVNA 289

Query:   272 RTPVFYRLEHLDNGTTSVGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNLGGL 331
             +TPV YRLE +DNGT SVGY+RLKEFNALARKDLV AMKRL D GASYF++DLRDNLGGL
Sbjct:   290 QTPVSYRLEKVDNGTVSVGYIRLKEFNALARKDLVIAMKRLLDKGASYFVMDLRDNLGGL 349

Query:   332 VQAGIEIAKLFLNEGETITYTVGRDPQYQKTIVADNSPLVTAPVIVLVNNRTASASEIVA 391
             VQAGIE AKLFL+EG+T+ YT GRDP+ QKT+V+D  PL+TAP+IV+VNNRTASASEIVA
Sbjct:   350 VQAGIETAKLFLDEGDTVIYTAGRDPEAQKTVVSDKKPLITAPLIVMVNNRTASASEIVA 409

Query:   392 SALHDNCRAVLVGEKTFGKGLIQSVYELHDGSGVVVTIGKYVTPNHMDINGNGIEPDYRN 451
             SALHDNC+AVLVGE+T+GKGLIQSVYEL DGSGVVVTIGKYVTPNHMDING GIEPD+RN
Sbjct:   410 SALHDNCKAVLVGERTYGKGLIQSVYELRDGSGVVVTIGKYVTPNHMDINGGGIEPDFRN 469

Query:   452 LPAWNDVTKHLSQCTMHPQ 470
             LPAW++V + LS+C++  Q
Sbjct:   470 LPAWDEVKERLSKCSILQQ 488

GO:0005576 "extracellular region" evidence=ISM

GO:0006508 "proteolysis" evidence=IEA

GO:0008236 "serine-type peptidase activity" evidence=IEA

GO:0035556 "intracellular signal transduction" evidence=ISS

GO:0009543 "chloroplast thylakoid lumen" evidence=IDA

GO:0031977 "thylakoid lumen" evidence=IDA

GO:0016556 "mRNA modification" evidence=RCA

UNIPROTKB\|P73458 prc "Carboxyl-terminal protease" [Synechocystis sp. PCC 6803 substr. Kazusa (taxid:1111708)]	Back alignment and assigned GO terms

UNIPROTKB\|P75023 ctpB "Carboxyl-terminal protease" [Synechocystis sp. PCC 6803 substr. Kazusa (taxid:1111708)]	Back alignment and assigned GO terms

TAIR\|locus:2129411 AT4G17740 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TIGR_CMR\|CHY_0170 CHY_0170 "carboxyl-terminal protease" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]	Back alignment and assigned GO terms

TIGR_CMR\|GSU_1772 GSU_1772 "carboxy-terminal processing protease" [Geobacter sulfurreducens PCA (taxid:243231)]	Back alignment and assigned GO terms

TIGR_CMR\|GSU_0969 GSU_0969 "carboxy-terminal processing protease" [Geobacter sulfurreducens PCA (taxid:243231)]	Back alignment and assigned GO terms

TIGR_CMR\|SPO_3812 SPO_3812 "carboxyl-terminal protease family protein" [Ruegeria pomeroyi DSS-3 (taxid:246200)]	Back alignment and assigned GO terms

TIGR_CMR\|DET_0364 DET_0364 "carboxyl-terminal protease" [Dehalococcoides ethenogenes 195 (taxid:243164)]	Back alignment and assigned GO terms

TIGR_CMR\|BA_5414 BA_5414 "carboxyl-terminal protease" [Bacillus anthracis str. Ames (taxid:198094)]	Back alignment and assigned GO terms

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

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.4.21	0.766
3rd Layer	3.4.21.102	0.824

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	Alignment Graph	Length	Definition	E-value
Query		471
PLN00049		389	PLN00049, PLN00049, carboxyl-terminal processing p	7e-92
TIGR00225		334	TIGR00225, prc, C-terminal peptidase (prc)	1e-84
COG0793		406	COG0793, Prc, Periplasmic protease [Cell envelope	6e-77
cd07560		211	cd07560, Peptidase_S41_CPP, C-terminal processing	1e-70
smart00245		192	smart00245, TSPc, tail specific protease	2e-65
pfam03572		166	pfam03572, Peptidase_S41, Peptidase family S41	2e-60
cd06567		224	cd06567, Peptidase_S41, C-terminal processing pept	3e-57
TIGR03900		973	TIGR03900, prc_long_Delta, putative carboxyl-termi	7e-47
cd07563		250	cd07563, Peptidase_S41_IRBP, Interphotoreceptor re	2e-25
cd07561		256	cd07561, Peptidase_S41_CPP_like, C-terminal proces	2e-21
PRK11186		667	PRK11186, PRK11186, carboxy-terminal protease; Pro	2e-18
cd00988		85	cd00988, PDZ_CTP_protease, PDZ domain of C-termina	1e-17
cd07562		266	cd07562, Peptidase_S41_TRI, Tricorn protease; seri	2e-17
smart00228		85	smart00228, PDZ, Domain present in PSD-95, Dlg, an	3e-11
cd00992		82	cd00992, PDZ_signaling, PDZ domain found in a vari	2e-10
cd00136		70	cd00136, PDZ, PDZ domain, also called DHR (Dlg hom	6e-10
pfam00595		80	pfam00595, PDZ, PDZ domain (Also known as DHR or G	5e-06
pfam13180		81	pfam13180, PDZ_2, PDZ domain	4e-05
cd06567		224	cd06567, Peptidase_S41, C-terminal processing pept	5e-05
cd00987		90	cd00987, PDZ_serine_protease, PDZ domain of tryspi	5e-05
cd00990		80	cd00990, PDZ_glycyl_aminopeptidase, PDZ domain ass	7e-04
cd07021		178	cd07021, Clp_protease_NfeD_like, Nodulation format	7e-04
cd00989		79	cd00989, PDZ_metalloprotease, PDZ domain of bacter	0.003

>gnl\|CDD\|177681 PLN00049, PLN00049, carboxyl-terminal processing protease; Provisional	Back alignment and domain information

 Score =  283 bits (727), Expect = 7e-92
 Identities = 146/362 (40%), Positives = 210/362 (58%), Gaps = 26/362 (7%)

Query: 107 EAWQIVNDSFLDTGRHRWTPQNWQRKREDIL-SSSIQTRSKAHGIIKRMLASLGDPYTRF 165
           EAW+ V+ +++D     +  Q+W R RE+ L +  + TR + +  I++MLA+L DP+TRF
Sbjct: 11  EAWRTVDRAYVDKT---FNGQSWFRYRENALKNEPMNTREETYAAIRKMLATLDDPFTRF 67

Query: 166 LSPAEFSKMAR---YDMSGIGINLREVPDANGVVT-LKVLGLILDGPAHSAGVRQGDEVL 221
           L P +F  +       ++G+G+ +     ++G    L V+     GPA  AG+R GD +L
Sbjct: 68  LEPEKFKSLRSGTKGAVTGVGLEVGYPTGSDGPPAGLVVVAPAPGGPAARAGIRPGDVIL 127

Query: 222 AVNGVDVRGKSAFEVSSLLQGPSETFVTIEVKHGNCGPIESIQVQRQLVARTPVFYRL-- 279
           A++G    G S +E +  LQGP  + V + ++ G       + + R+ V+  PV  RL  
Sbjct: 128 AIDGTSTEGLSLYEAADRLQGPEGSSVELTLRRG--PETRLVTLTREKVSLNPVKSRLCE 185

Query: 280 -EHLDNGTTSVGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNLGGLVQAGIEI 338
                 G+  +GY++L  FN  A   +  A++ L+  G   F+LDLRDN GGL  AGIEI
Sbjct: 186 VPGPGAGSPKIGYIKLTTFNQNASSAVKEAIETLRANGVDAFVLDLRDNSGGLFPAGIEI 245

Query: 339 AKLFLNEGETITYTVG----RDPQYQKTIVADNSPLV--TAPVIVLVNNRTASASEIVAS 392
           AKL+L++G  I Y       RD  Y     AD S  +  + P+ VLVN  TASASEI+A 
Sbjct: 246 AKLWLDKG-VIVYIADSRGVRD-IYD----ADGSSAIATSEPLAVLVNKGTASASEILAG 299

Query: 393 ALHDNCRAVLVGEKTFGKGLIQSVYELHDGSGVVVTIGKYVTPNHMDINGNGIEPDYRNL 452
           AL DN RAV++GE TFGKGLIQSV+EL DGSG+ VT+ +Y TP   DI+  GI PD+  L
Sbjct: 300 ALKDNKRAVVLGEPTFGKGLIQSVFELSDGSGLAVTVARYQTPAGTDIDKVGITPDHP-L 358

Query: 453 PA 454
           P 
Sbjct: 359 PE 360

Length = 389

>gnl\|CDD\|232883 TIGR00225, prc, C-terminal peptidase (prc)	Back alignment and domain information

>gnl\|CDD\|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer membrane]	Back alignment and domain information

>gnl\|CDD\|143476 cd07560, Peptidase_S41_CPP, C-terminal processing peptidase; serine protease family S41	Back alignment and domain information

>gnl\|CDD\|214582 smart00245, TSPc, tail specific protease	Back alignment and domain information

>gnl\|CDD\|217620 pfam03572, Peptidase_S41, Peptidase family S41	Back alignment and domain information

>gnl\|CDD\|143475 cd06567, Peptidase_S41, C-terminal processing peptidase family S41	Back alignment and domain information

>gnl\|CDD\|234386 TIGR03900, prc_long_Delta, putative carboxyl-terminal-processing protease, deltaproteobacterial	Back alignment and domain information

>gnl\|CDD\|143479 cd07563, Peptidase_S41_IRBP, Interphotoreceptor retinoid-binding protein; serine protease family S41	Back alignment and domain information

>gnl\|CDD\|143477 cd07561, Peptidase_S41_CPP_like, C-terminal processing peptidase-like; serine protease family S41	Back alignment and domain information

>gnl\|CDD\|236873 PRK11186, PRK11186, carboxy-terminal protease; Provisional	Back alignment and domain information

>gnl\|CDD\|238488 cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts	Back alignment and domain information

>gnl\|CDD\|143478 cd07562, Peptidase_S41_TRI, Tricorn protease; serine protease family S41	Back alignment and domain information

>gnl\|CDD\|214570 smart00228, PDZ, Domain present in PSD-95, Dlg, and ZO-1/2	Back alignment and domain information

>gnl\|CDD\|238492 cd00992, PDZ_signaling, PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements	Back alignment and domain information

>gnl\|CDD\|238080 cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif)	Back alignment and domain information

>gnl\|CDD\|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF)	Back alignment and domain information

>gnl\|CDD\|221961 pfam13180, PDZ_2, PDZ domain	Back alignment and domain information

>gnl\|CDD\|143475 cd06567, Peptidase_S41, C-terminal processing peptidase family S41	Back alignment and domain information

>gnl\|CDD\|238487 cd00987, PDZ_serine_protease, PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis	Back alignment and domain information

>gnl\|CDD\|238490 cd00990, PDZ_glycyl_aminopeptidase, PDZ domain associated with archaeal and bacterial M61 glycyl-aminopeptidases	Back alignment and domain information

>gnl\|CDD\|132932 cd07021, Clp_protease_NfeD_like, Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease	Back alignment and domain information

>gnl\|CDD\|238489 cd00989, PDZ_metalloprotease, PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		471
PLN00049		389	carboxyl-terminal processing protease; Provisional	100.0
COG0793		406	Prc Periplasmic protease [Cell envelope biogenesis	100.0
PRK11186		667	carboxy-terminal protease; Provisional	100.0
TIGR00225		334	prc C-terminal peptidase (prc). A C-terminal pepti	100.0
cd06567		224	Peptidase_S41 C-terminal processing peptidase fami	100.0
cd07562		266	Peptidase_S41_TRI Tricorn protease; serine proteas	100.0
cd07563		250	Peptidase_S41_IRBP Interphotoreceptor retinoid-bin	100.0
smart00245		192	TSPc tail specific protease. tail specific proteas	100.0
cd07560		211	Peptidase_S41_CPP C-terminal processing peptidase;	100.0
cd07561		256	Peptidase_S41_CPP_like C-terminal processing pepti	100.0
PF03572		169	Peptidase_S41: Peptidase family S41; InterPro: IPR	99.97
COG3480		342	SdrC Predicted secreted protein containing a PDZ d	99.35
PF14684		70	Tricorn_C1: Tricorn protease C1 domain; PDB: 1N6F_	99.28
PF13180		82	PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_	99.28
cd00988		85	PDZ_CTP_protease PDZ domain of C-terminal processi	99.13
cd00136		70	PDZ PDZ domain, also called DHR (Dlg homologous re	98.92
PF00595		81	PDZ: PDZ domain (Also known as DHR or GLGF) Coordi	98.91
cd00991		79	PDZ_archaeal_metalloprotease PDZ domain of archaea	98.77
cd00990		80	PDZ_glycyl_aminopeptidase PDZ domain associated wi	98.71
cd00989		79	PDZ_metalloprotease PDZ domain of bacterial and pl	98.71
cd00986		79	PDZ_LON_protease PDZ domain of ATP-dependent LON s	98.63
PF14685		88	Tricorn_PDZ: Tricorn protease PDZ domain; PDB: 1N6	98.62
cd00992		82	PDZ_signaling PDZ domain found in a variety of Eum	98.59
smart00228		85	PDZ Domain present in PSD-95, Dlg, and ZO-1/2. Als	98.55
cd00987		90	PDZ_serine_protease PDZ domain of tryspin-like ser	98.43
COG3975		558	Predicted protease with the C-terminal PDZ domain	98.35
TIGR01713		259	typeII_sec_gspC general secretion pathway protein	98.23
PRK10779		449	zinc metallopeptidase RseP; Provisional	98.17
PRK10139		455	serine endoprotease; Provisional	98.16
PRK10942		473	serine endoprotease; Provisional	98.16
TIGR00054		420	RIP metalloprotease RseP. A model that detects fra	98.14
PRK10898		353	serine endoprotease; Provisional	98.14
TIGR02038		351	protease_degS periplasmic serine pepetdase DegS. T	98.11
PRK10779		449	zinc metallopeptidase RseP; Provisional	98.09
TIGR02037		428	degP_htrA_DO periplasmic serine protease, Do/DeqQ	98.09
KOG3209		984	consensus WW domain-containing protein [General fu	98.02
PF04495		138	GRASP55_65: GRASP55/65 PDZ-like domain ; InterPro:	97.94
TIGR02860		402	spore_IV_B stage IV sporulation protein B. SpoIVB,	97.91
TIGR02037		428	degP_htrA_DO periplasmic serine protease, Do/DeqQ	97.81
PRK10942		473	serine endoprotease; Provisional	97.8
KOG3550		207	consensus Receptor targeting protein Lin-7 [Extrac	97.79
PRK10139		455	serine endoprotease; Provisional	97.78
TIGR03279		433	cyano_FeS_chp putative FeS-containing Cyanobacteri	97.74
KOG3209		984	consensus WW domain-containing protein [General fu	97.52
TIGR00054		420	RIP metalloprotease RseP. A model that detects fra	97.51
KOG3553		124	consensus Tax interaction protein TIP1 [Cell wall/	97.49
COG0265		347	DegQ Trypsin-like serine proteases, typically peri	97.39
KOG3129		231	consensus 26S proteasome regulatory complex, subun	97.16
KOG3605		829	consensus Beta amyloid precursor-binding protein [	97.14
KOG3580		1027	consensus Tight junction proteins [Signal transduc	97.04
KOG3552		1298	consensus FERM domain protein FRM-8 [General funct	96.68
KOG3549		505	consensus Syntrophins (type gamma) [Extracellular	96.61
KOG3532		1051	consensus Predicted protein kinase [General functi	96.4
KOG3551		506	consensus Syntrophins (type beta) [Extracellular s	96.37
KOG3542		1283	consensus cAMP-regulated guanine nucleotide exchan	96.36
KOG3651		429	consensus Protein kinase C, alpha binding protein	96.29
KOG1892		1629	consensus Actin filament-binding protein Afadin [C	96.27
PRK09681		276	putative type II secretion protein GspC; Provision	96.21
KOG3580		1027	consensus Tight junction proteins [Signal transduc	96.05
KOG1421		955	consensus Predicted signaling-associated protein (	95.94
cd07021		178	Clp_protease_NfeD_like Nodulation formation effici	95.3
KOG0609		542	consensus Calcium/calmodulin-dependent serine prot	95.09
KOG3571		626	consensus Dishevelled 3 and related proteins [Gene	95.08
COG3031		275	PulC Type II secretory pathway, component PulC [In	94.85
KOG1320		473	consensus Serine protease [Posttranslational modif	94.26
KOG3606		358	consensus Cell polarity protein PAR6 [Signal trans	94.02
KOG3938		334	consensus RGS-GAIP interacting protein GIPC, conta	93.0
KOG0606		1205	consensus Microtubule-associated serine/threonine	92.4
cd07020		187	Clp_protease_NfeD_1 Nodulation formation efficienc	90.79
PF12812		78	PDZ_1: PDZ-like domain	90.24
KOG3605		829	consensus Beta amyloid precursor-binding protein [	90.23
KOG3834		462	consensus Golgi reassembly stacking protein GRASP6	89.88
KOG3834		462	consensus Golgi reassembly stacking protein GRASP6	88.98
COG0750		375	Predicted membrane-associated Zn-dependent proteas	88.48
cd07015		172	Clp_protease_NfeD Nodulation formation efficiency	86.47
COG1030		436	NfeD Membrane-bound serine protease (ClpP class) [	86.13
KOG1738		638	consensus Membrane-associated guanylate kinase-int	84.36
cd00394		161	Clp_protease_like Caseinolytic protease (ClpP) is	83.0

>PLN00049 carboxyl-terminal processing protease; Provisional	Back alignment and domain information

Probab=100.00  E-value=1.5e-62  Score=506.31  Aligned_cols=360  Identities=39%  Similarity=0.650  Sum_probs=303.9

Q ss_pred             chHHHHHHHHHHHHhhcccCCCCCCChhhHHHHHHHHhhc-cccChHHHHHHHHHHHHhcCCCceeecChHHhhhhh---
Q 012084          100 TNEGIVEEAWQIVNDSFLDTGRHRWTPQNWQRKREDILSS-SIQTRSKAHGIIKRMLASLGDPYTRFLSPAEFSKMA---  175 (471)
Q Consensus       100 ~~~~~f~~vw~~v~~~y~d~~~~~~~~~dW~~~~e~~~~~-~~~~~~~~~~~i~~ml~~L~D~Ht~~l~~~~~~~~~---  175 (471)
                      ++.++|+++|+.++++|||+.   |+++||++++++|++. .+.++.+++.++++|+++|+|+|++|++++++..+.   
T Consensus         4 ~~~~~f~e~w~~v~~~~~d~~---~~g~dW~~~~e~y~~~~~~~~~~~~~~~i~~ml~~L~D~hs~y~~~~~~~~~~~~~   80 (389)
T PLN00049          4 EENLLFLEAWRTVDRAYVDKT---FNGQSWFRYRENALKNEPMNTREETYAAIRKMLATLDDPFTRFLEPEKFKSLRSGT   80 (389)
T ss_pred             cHHHHHHHHHHHHHHHHcCcc---ccccCHHHHHHHHhhccCCCcHHHHHHHHHHHHhhCCCCcccCcCHHHHHHHHHhc
Confidence            688999999999999999986   8999999999999864 467888999999999999999999999998876432   


Q ss_pred             cccceeeeEEEEEeeCCCC-ceEEEEEEEcCCCchhhcCCCCCCEEEEECCEEcCCCCHHHHHHhhCCCCCcEEEEEEEc
Q 012084          176 RYDMSGIGINLREVPDANG-VVTLKVLGLILDGPAHSAGVRQGDEVLAVNGVDVRGKSAFEVSSLLQGPSETFVTIEVKH  254 (471)
Q Consensus       176 ~~~~~giG~~~~~~~d~~g-~~~~~V~~v~~~spA~~aGl~~GD~Il~InG~~v~~~~~~~~~~ll~g~~g~~v~l~v~r  254 (471)
                      ++.+.|||+.+......++ ..+++|..|.++|||+++||++||+|++|||+++.+++..++..+++|..|+.|.|+|.|
T Consensus        81 ~~~~~GiG~~~~~~~~~~~~~~g~~V~~V~~~SPA~~aGl~~GD~Iv~InG~~v~~~~~~~~~~~l~g~~g~~v~ltv~r  160 (389)
T PLN00049         81 KGAVTGVGLEVGYPTGSDGPPAGLVVVAPAPGGPAARAGIRPGDVILAIDGTSTEGLSLYEAADRLQGPEGSSVELTLRR  160 (389)
T ss_pred             cCCceEEEEEEEEccCCCCccCcEEEEEeCCCChHHHcCCCCCCEEEEECCEECCCCCHHHHHHHHhcCCCCEEEEEEEE
Confidence            5678899999876322111 126889999999999999999999999999999998877778888899999999999998


Q ss_pred             CCCCCeeEEEEeeeeeeeccceeeeee---ccCCCCeEEEEEeCchhhhHHHHHHHHHHHHHhcCCcEEEEeccCCCCcc
Q 012084          255 GNCGPIESIQVQRQLVARTPVFYRLEH---LDNGTTSVGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNLGGL  331 (471)
Q Consensus       255 ~~~~~~~~v~l~r~~~~~~~v~~~~~~---~~~~~~~igYi~i~sF~~~~~~~l~~~l~~l~~~~~~~LIIDLR~N~GG~  331 (471)
                      ++  ...++++.|..+..+++.++...   .+.++++||||+|++|...+.+++.+++++++++++++||||||+|+||.
T Consensus       161 ~g--~~~~~~l~r~~v~~~~v~~~~~~~~~~~~~~~~IgYi~i~~F~~~~~~~~~~~l~~l~~~~~~glIlDLR~N~GG~  238 (389)
T PLN00049        161 GP--ETRLVTLTREKVSLNPVKSRLCEVPGPGAGSPKIGYIKLTTFNQNASSAVKEAIETLRANGVDAFVLDLRDNSGGL  238 (389)
T ss_pred             CC--EEEEEEEEeeeEeccceeeEEEeeccccCCCCCEEEEEeccccchhHHHHHHHHHHHHHCCCCEEEEEcCCCCCCC
Confidence            65  46778888888777777665432   13345689999999999888899999999999999999999999999999


Q ss_pred             HHHHHHHHhhcccCCceEEEEeccCcccceeEecCCC--CCCCCCEEEEECCCCCChHHHHHHHHhcCCCeEEEccCCCC
Q 012084          332 VQAGIEIAKLFLNEGETITYTVGRDPQYQKTIVADNS--PLVTAPVIVLVNNRTASASEIVASALHDNCRAVLVGEKTFG  409 (471)
Q Consensus       332 ~~~~~~la~~f~~~~~~~~~~~~r~~~~~~~~~~~~~--~~~~~pi~VLvd~~TaSaaE~fa~~lk~~~~a~vVGe~T~G  409 (471)
                      +..+..++++|++++. +.+...+.+.. ..+.....  ..+.+|++||||+.||||||+|+.+||+++++++||++|+|
T Consensus       239 ~~~a~~ia~~f~~~~~-~~~~~~~~~~~-~~~~~~~~~~~~~~~PvvVLvn~~TaSasEi~a~alk~~~~~~vvG~~T~G  316 (389)
T PLN00049        239 FPAGIEIAKLWLDKGV-IVYIADSRGVR-DIYDADGSSAIATSEPLAVLVNKGTASASEILAGALKDNKRAVVLGEPTFG  316 (389)
T ss_pred             HHHHHHHHHHhcCCCc-EEEEecCCCce-eEEecCCCccccCCCCEEEEECCCCccHHHHHHHHHhhCCCeEEEecCCcC
Confidence            9999999999999886 44443333221 12222222  24679999999999999999999999999999999999999


Q ss_pred             CceeceEEECCCCCEEEEEEEEEEcCCCCcccCCcccCcEEcCCChHHHHHHHhhcc
Q 012084          410 KGLIQSVYELHDGSGVVVTIGKYVTPNHMDINGNGIEPDYRNLPAWNDVTKHLSQCT  466 (471)
Q Consensus       410 ~g~~~~~~~L~~g~~l~~t~~~~~~~~g~~~e~~GV~PDi~v~~t~~d~~~~l~~~~  466 (471)
                      ++..|..+.|+||+.+++|+++|++|+|..+|+.||+||+.|...+....+.+-.|-
T Consensus       317 kg~~q~~~~L~dG~~l~lt~~~~~~p~G~~ie~~Gi~PDi~v~~~~~~~~~~~~~~~  373 (389)
T PLN00049        317 KGLIQSVFELSDGSGLAVTVARYQTPAGTDIDKVGITPDHPLPESLPKDEEAFCGCL  373 (389)
T ss_pred             CcccceeEEeCCCCEEEEEEEEEECCCCCCcCCCCcCCCeECCCCCCcchHHHHHHh
Confidence            999999999999999999999999999999999999999999866655555554443

>COG0793 Prc Periplasmic protease [Cell envelope biogenesis, outer membrane]	Back alignment and domain information

>PRK11186 carboxy-terminal protease; Provisional	Back alignment and domain information

>TIGR00225 prc C-terminal peptidase (prc)	Back alignment and domain information

>cd06567 Peptidase_S41 C-terminal processing peptidase family S41	Back alignment and domain information

>cd07562 Peptidase_S41_TRI Tricorn protease; serine protease family S41	Back alignment and domain information

>cd07563 Peptidase_S41_IRBP Interphotoreceptor retinoid-binding protein; serine protease family S41	Back alignment and domain information

>smart00245 TSPc tail specific protease	Back alignment and domain information

>cd07560 Peptidase_S41_CPP C-terminal processing peptidase; serine protease family S41	Back alignment and domain information

>cd07561 Peptidase_S41_CPP_like C-terminal processing peptidase-like; serine protease family S41	Back alignment and domain information

>PF03572 Peptidase_S41: Peptidase family S41; InterPro: IPR005151 This group of putative serine peptidases belong to the MEROPS peptidase family S41 (C-terminal processing peptidase family, clan SM)	Back alignment and domain information

>COG3480 SdrC Predicted secreted protein containing a PDZ domain [Signal transduction mechanisms]	Back alignment and domain information

>PF14684 Tricorn_C1: Tricorn protease C1 domain; PDB: 1N6F_D 1N6D_C 1N6E_C 1K32_A	Back alignment and domain information

>PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C	Back alignment and domain information

>cd00988 PDZ_CTP_protease PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts	Back alignment and domain information

>cd00136 PDZ PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif)	Back alignment and domain information

>PF00595 PDZ: PDZ domain (Also known as DHR or GLGF) Coordinates are not yet available; InterPro: IPR001478 PDZ domains are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates [, ]	Back alignment and domain information

>cd00991 PDZ_archaeal_metalloprotease PDZ domain of archaeal zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms	Back alignment and domain information

>cd00990 PDZ_glycyl_aminopeptidase PDZ domain associated with archaeal and bacterial M61 glycyl-aminopeptidases	Back alignment and domain information

>cd00989 PDZ_metalloprotease PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms	Back alignment and domain information

>cd00986 PDZ_LON_protease PDZ domain of ATP-dependent LON serine proteases	Back alignment and domain information

>PF14685 Tricorn_PDZ: Tricorn protease PDZ domain; PDB: 1N6F_D 1N6D_C 1N6E_C 1K32_A	Back alignment and domain information

>cd00992 PDZ_signaling PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements	Back alignment and domain information

>smart00228 PDZ Domain present in PSD-95, Dlg, and ZO-1/2	Back alignment and domain information

>cd00987 PDZ_serine_protease PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis	Back alignment and domain information

>COG3975 Predicted protease with the C-terminal PDZ domain [General function prediction only]	Back alignment and domain information

>TIGR01713 typeII_sec_gspC general secretion pathway protein C	Back alignment and domain information

>PRK10779 zinc metallopeptidase RseP; Provisional	Back alignment and domain information

>PRK10139 serine endoprotease; Provisional	Back alignment and domain information

>PRK10942 serine endoprotease; Provisional	Back alignment and domain information

>TIGR00054 RIP metalloprotease RseP	Back alignment and domain information

>PRK10898 serine endoprotease; Provisional	Back alignment and domain information

>TIGR02038 protease_degS periplasmic serine pepetdase DegS	Back alignment and domain information

>PRK10779 zinc metallopeptidase RseP; Provisional	Back alignment and domain information

>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family	Back alignment and domain information

>KOG3209 consensus WW domain-containing protein [General function prediction only]	Back alignment and domain information

>PF04495 GRASP55_65: GRASP55/65 PDZ-like domain ; InterPro: IPR007583 GRASP55 (Golgi reassembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous	Back alignment and domain information

>TIGR02860 spore_IV_B stage IV sporulation protein B	Back alignment and domain information

>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family	Back alignment and domain information

>PRK10942 serine endoprotease; Provisional	Back alignment and domain information

>KOG3550 consensus Receptor targeting protein Lin-7 [Extracellular structures]	Back alignment and domain information

>PRK10139 serine endoprotease; Provisional	Back alignment and domain information

>TIGR03279 cyano_FeS_chp putative FeS-containing Cyanobacterial-specific oxidoreductase	Back alignment and domain information

>KOG3209 consensus WW domain-containing protein [General function prediction only]	Back alignment and domain information

>TIGR00054 RIP metalloprotease RseP	Back alignment and domain information

>KOG3553 consensus Tax interaction protein TIP1 [Cell wall/membrane/envelope biogenesis]	Back alignment and domain information

>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG3129 consensus 26S proteasome regulatory complex, subunit PSMD9 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG3605 consensus Beta amyloid precursor-binding protein [General function prediction only]	Back alignment and domain information

>KOG3580 consensus Tight junction proteins [Signal transduction mechanisms]	Back alignment and domain information

>KOG3552 consensus FERM domain protein FRM-8 [General function prediction only]	Back alignment and domain information

>KOG3549 consensus Syntrophins (type gamma) [Extracellular structures]	Back alignment and domain information

>KOG3532 consensus Predicted protein kinase [General function prediction only]	Back alignment and domain information

>KOG3551 consensus Syntrophins (type beta) [Extracellular structures]	Back alignment and domain information

>KOG3542 consensus cAMP-regulated guanine nucleotide exchange factor [Signal transduction mechanisms]	Back alignment and domain information

>KOG3651 consensus Protein kinase C, alpha binding protein [Signal transduction mechanisms]	Back alignment and domain information

>KOG1892 consensus Actin filament-binding protein Afadin [Cytoskeleton]	Back alignment and domain information

>PRK09681 putative type II secretion protein GspC; Provisional	Back alignment and domain information

>KOG3580 consensus Tight junction proteins [Signal transduction mechanisms]	Back alignment and domain information

>KOG1421 consensus Predicted signaling-associated protein (contains a PDZ domain) [General function prediction only]	Back alignment and domain information

>cd07021 Clp_protease_NfeD_like Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease	Back alignment and domain information

>KOG0609 consensus Calcium/calmodulin-dependent serine protein kinase/membrane-associated guanylate kinase [Signal transduction mechanisms]	Back alignment and domain information

>KOG3571 consensus Dishevelled 3 and related proteins [General function prediction only]	Back alignment and domain information

>COG3031 PulC Type II secretory pathway, component PulC [Intracellular trafficking and secretion]	Back alignment and domain information

>KOG1320 consensus Serine protease [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG3606 consensus Cell polarity protein PAR6 [Signal transduction mechanisms]	Back alignment and domain information

>KOG3938 consensus RGS-GAIP interacting protein GIPC, contains PDZ domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG0606 consensus Microtubule-associated serine/threonine kinase and related proteins [Signal transduction mechanisms; General function prediction only]	Back alignment and domain information

>cd07020 Clp_protease_NfeD_1 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease	Back alignment and domain information

>PF12812 PDZ_1: PDZ-like domain	Back alignment and domain information

>KOG3605 consensus Beta amyloid precursor-binding protein [General function prediction only]	Back alignment and domain information

>KOG3834 consensus Golgi reassembly stacking protein GRASP65, contains PDZ domain [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG3834 consensus Golgi reassembly stacking protein GRASP65, contains PDZ domain [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]	Back alignment and domain information

>cd07015 Clp_protease_NfeD Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease	Back alignment and domain information

>COG1030 NfeD Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1738 consensus Membrane-associated guanylate kinase-interacting protein/connector enhancer of KSR-like [Nucleotide transport and metabolism]	Back alignment and domain information

>cd00394 Clp_protease_like Caseinolytic protease (ClpP) is an ATP-dependent protease	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		471
1fc7_A		388	Photosystem Ii D1 C-Terminal Processing Protease Le		2e-52
1fc6_A		388	Photosystem Ii D1 C-Terminal Processing Protease Le		1e-51
3k50_A		403	Crystal Structure Of Putative S41 Protease (Yp_2116		3e-08
2he2_A		102	Crystal Structure Of The 3rd Pdz Domain Of Human Di		3e-04

>pdb|1FC7|A Chain A, Photosystem Ii D1 C-Terminal Processing Protease Length = 388

Back alignment and structure

Iteration: 1

Score = 202 bits (515), Expect = 2e-52, Method: Compositional matrix adjust. Identities = 128/361 (35%), Positives = 198/361 (54%), Gaps = 21/361 (5%) Query: 107 EAWQIVNDSFLDTGRHRWTPQNWQRKREDILSSS-IQTRSKAHGIIKRMLASLGDPYTRF 165 EAW+ V+ +++D + Q+W + RE L + R++ + I+++LA L DP+TRF Sbjct: 11 EAWRAVDRAYVD---KSFNGQSWFKLRETYLKKEPMDRRAQTYDAIRKLLAVLDDPFTRF 67 Query: 166 LSPAEFSKMARYDMSGI-GINLREVPDANGVVTLKVLGLILDGPAHSAGVRQGDEVLAVN 224 L P+ + + R + G+ L D + VL GPA AG R GD ++ V+ Sbjct: 68 LEPSRLAALRRGTAGSVTGVGLEITYDGGSGKDVVVLTPAPGGPAEKAGARAGDVIVTVD 127 Query: 225 GVDVRGKSAFEVSSLLQGPSETFVTIEVKHGNCGP--IESIQVQRQLVARTPVFY----- 277 G V+G S ++VS LLQG +++ V + V H P ++Q+ RQ V PV + Sbjct: 128 GTAVKGLSLYDVSDLLQGEADSQVEV-VLHAPGAPSNTRTLQLTRQKVTINPVTFTTCSN 186 Query: 278 ---RLEHLDNGTTSVGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNLGGLVQA 334 +GY+RL FN+ A L G + +LD+R+N GGL A Sbjct: 187 VAAAALPPGAAKQQLGYVRLATFNSNTTAAAQQAFTELSKQGVAGLVLDIRNNGGGLFPA 246 Query: 335 GIEIAKLFLNEGETITYTVGRDPQYQKTIV-ADNSPLVTA-PVIVLVNNRTASASEIVAS 392 G+ +A++ ++ G+ + D Q + I AD + + +A P++VLVN TASASE++A Sbjct: 247 GVNVARMLVDRGDLVLIA---DSQGIRDIYSADGNSIDSATPLVVLVNRGTASASEVLAG 303 Query: 393 ALHDNCRAVLVGEKTFGKGLIQSVYELHDGSGVVVTIGKYVTPNHMDINGNGIEPDYRNL 452 AL D+ R ++ GE+TFGKGLIQ+V +L DGSGV VT+ +Y TP +DIN G+ PD + Sbjct: 304 ALKDSKRGLIAGERTFGKGLIQTVVDLSDGSGVAVTVARYQTPAGVDINKIGVSPDVQLD 363 Query: 453 P 453 P Sbjct: 364 P 364

PyMOL of 1fc7

>pdb|1FC6|A Chain A, Photosystem Ii D1 C-Terminal Processing Protease Length = 388

Back alignment and structure

>pdb|3K50|A Chain A, Crystal Structure Of Putative S41 Protease (Yp_211611.1) From Bacteroides Fragilis Nctc 9343 At 2.00 A Resolution Length = 403

Back alignment and structure

>pdb|2HE2|A Chain A, Crystal Structure Of The 3rd Pdz Domain Of Human Discs Large Homologue 2, Dlg2 Length = 102

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		471
1fc6_A		388	Photosystem II D1 protease; D1 C-terminal processi	1e-107
3k50_A		403	Putative S41 protease; structural genomics, joint	5e-78
1j7x_A		302	IRBP, interphotoreceptor retinoid-binding protein;	7e-55
1k32_A		1045	Tricorn protease; protein degradation, substrate g	3e-53
3dor_A		583	Protein CT_858, CPAF; mature CPAF, dimer, transfer	3e-38
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-14
1w9e_A		166	Syntenin 1; cell adhesion, adhesion/complex, PDZ d	1e-13
2eei_A		106	PDZ domain-containing protein 1; regulatory factor	6e-11
2v90_A		96	PDZ domain-containing protein 3; membrane, protein	2e-10
2jxo_A		98	Ezrin-radixin-moesin-binding phosphoprotein 50; nh	3e-10
2vsp_A		91	PDZ domain-containing protein 1; membrane, cytopla	3e-10
3r68_A		95	Na(+)/H(+) exchange regulatory cofactor NHE-RF3; P	4e-10
1vae_A		111	Rhophilin 2, rhophilin, RHO GTPase binding protein	1e-09
2he4_A		90	Na(+)/H(+) exchange regulatory cofactor NHE-RF2; p	1e-09
1m5z_A		91	GRIP, AMPA receptor interacting protein; six beta-	2e-09
2d90_A		102	PDZ domain containing protein 1; structural genomi	2e-09
1g9o_A		91	NHE-RF; PDZ domain, complex, signaling protein; 1.	2e-09
3bpu_A		88	Membrane-associated guanylate kinase, WW and PDZ c	3e-09
2yuy_A		126	RHO GTPase activating protein 21; PDZ domain, stru	4e-09
2dls_A		93	PDZ-rhogef, RHO guanine nucleotide exchange factor	5e-09
2vsv_A		109	Rhophilin-2; scaffold protein, RHO GTPase binding,	9e-09
3ngh_A		106	PDZ domain-containing protein 1; adaptor protein,	1e-08
2edz_A		114	PDZ domain-containing protein 1; CFTR-associated p	1e-08
2kjd_A		128	Sodium/hydrogen exchange regulatory cofactor NHE-	1e-08
2ego_A		96	General receptor for phosphoinositides 1- associat	1e-08
2kv8_A		83	RGS12, regulator of G-protein signaling 12; PDZ do	2e-08
1y7n_A		90	Amyloid beta A4 precursor protein-binding family A	2e-08
1ujd_A		117	KIAA0559 protein; PDZ domain, structural genomics,	2e-08
3qe1_A		107	Sorting nexin-27, G protein-activated inward RECT	2e-08
3khf_A		99	Microtubule-associated serine/threonine-protein ki	2e-08
2f5y_A		91	Regulator of G-protein signalling 3 isoform 1; PDZ	3e-08
3o46_A		93	Maguk P55 subfamily member 7; PDZ domain, structur	3e-08
2krg_A		216	Na(+)/H(+) exchange regulatory cofactor NHE-RF1; a	4e-08
1va8_A		113	Maguk P55 subfamily member 5; PDZ domain, palmitoy	4e-08
1r6j_A		82	Syntenin 1; PDZ, membrane protein; 0.73A {Homo sap	5e-08
2eeh_A		100	PDZ domain-containing protein 7; structural genomi	5e-08
2z17_A		104	Pleckstrin homology SEC7 and coiled-coil domains-	5e-08
2eaq_A		90	LIM domain only protein 7; conserved hypothetical	5e-08
3tsv_A		124	Tight junction protein ZO-1; PDZ, scaffolding, JAM	6e-08
1uit_A		117	Human discs large 5 protein; PDZ domain, HDLG5, ma	6e-08
2qkv_A		96	Inactivation-NO-after-potential D protein; PDZ dom	7e-08
1tp5_A		119	Presynaptic density protein 95; PDZ-peptide ligand	1e-07
1p1d_A		196	PDZ45, glutamate receptor interacting protein; PDZ	1e-07
1p1d_A		196	PDZ45, glutamate receptor interacting protein; PDZ	6e-06
3i4w_A		104	Disks large homolog 4; alpha and beta protein, alt	1e-07
1wi2_A		104	Riken cDNA 2700099C19; structural genomics, riken	1e-07
2djt_A		104	Unnamed protein product; PDZ domain, structural ge	1e-07
2dkr_A		93	LIN-7 homolog B; LIN-7B, PDZ, structural genomics,	1e-07
1whd_A		100	RGS3, regulator of G-protein signaling 3; PDZ doma	1e-07
2i1n_A		102	Discs, large homolog 3; DLG3, PDZ, PDZ domain, sig	2e-07
1q3o_A		109	Shank1; PDZ, GKAP, peptide binding protein; 1.80A	2e-07
3k1r_A		192	Harmonin; protein-protein complex, alternative spl	2e-07
2kpk_A		129	Membrane-associated guanylate kinase, WW and PDZ c	2e-07
2la8_A		106	Inactivation-NO-after-potential D protein, KON-TI	2e-07
2d8i_A		114	T-cell lymphoma invasion and metastasis 1 variant;	2e-07
3l4f_D		132	SH3 and multiple ankyrin repeat domains protein 1;	2e-07
1um7_A		113	Synapse-associated protein 102; PDZ, discs large h	2e-07
2qt5_A		200	Glutamate receptor-interacting protein 1; PDZ-pept	3e-07
2qt5_A		200	Glutamate receptor-interacting protein 1; PDZ-pept	1e-06
2w4f_A		97	Protein LAP4; structural protein, phosphoprotein,	3e-07
2ejy_A		97	55 kDa erythrocyte membrane protein; GPC, maguk, P	4e-07
1n7e_A		97	AMPA receptor interacting protein GRIP; PDZ, prote	4e-07
1nf3_C		128	PAR-6B; semi-CRIB motif, switch I and II, PDZ doma	4e-07
2qg1_A		92	Multiple PDZ domain protein; MPDZ, MUPP1, structur	4e-07
1wif_A		126	RSGI RUH-020, riken cDNA 4930408O21; PDZ domain, s	4e-07
2vwr_A		95	Ligand of NUMB protein X 2; protein-binding, metal	5e-07
2xkx_A		721	Disks large homolog 4; structural protein, scaffol	6e-07
2xkx_A		721	Disks large homolog 4; structural protein, scaffol	1e-05
1v62_A		117	KIAA1719 protein; structural genomics, synaptic tr	6e-07
1x5n_A		114	Harmonin; PDZ domain, usher syndrome 1C protein, a	7e-07
2vz5_A		139	TAX1-binding protein 3; WNT signaling pathway, pro	7e-07
2d92_A		108	INAD-like protein; PDZ domain, inadl protein, hina	7e-07
3kzd_A		94	TIAM-1, T-lymphoma invasion and metastasis-inducin	8e-07
2eeg_A		94	PDZ and LIM domain protein 4; PDZ domain, structur	9e-07
1x5q_A		110	LAP4 protein; PDZ domain, scribble homolog protein	9e-07
3r0h_A		206	INAD, inactivation-NO-after-potential D protein; p	9e-07
3r0h_A		206	INAD, inactivation-NO-after-potential D protein; p	6e-05
3gsl_A		196	Disks large homolog 4; PDZ domain, tandem, PSD-95,	9e-07
3gsl_A		196	Disks large homolog 4; PDZ domain, tandem, PSD-95,	3e-06
1i16_A		130	Interleukin 16, LCF; cytokine, lymphocyte chemoatt	9e-07
1kwa_A		88	Hcask/LIN-2 protein; PDZ domain, neurexin, syndeca	1e-06
2ehr_A		117	INAD-like protein; PDZ domain, inadl protein, hina	1e-06
3hpk_A		125	Protein interacting with PRKCA 1; oxidized, PDZ do	1e-06
2dc2_A		103	GOPC, golgi associated PDZ and coiled-coil motif c	1e-06
2jik_A		101	Synaptojanin-2 binding protein; transmembrane, out	1e-06
1ujv_A		96	Membrane associated guanylate kinase inverted-2 (M	1e-06
2yt7_A		101	Amyloid beta A4 precursor protein-binding family A	1e-06
1uhp_A		107	Hypothetical protein KIAA1095; PDZ domain, semapho	2e-06
1v5l_A		103	PDZ and LIM domain 3; actinin alpha 2 associated L	2e-06
2i04_A		85	Membrane-associated guanylate kinase, WW and PDZ d	2e-06
1vb7_A		94	PDZ and LIM domain 2; PDZ domain PDZ-LIM protein,	2e-06
1uf1_A		128	KIAA1526 protein; PDZ domain, structural genomics,	2e-06
2fcf_A		103	Multiple PDZ domain protein; adaptor molecule, pro	2e-06
3cyy_A		92	Tight junction protein ZO-1; protein-ligand comple	3e-06
2eno_A		120	Synaptojanin-2-binding protein; mitochondrial oute	3e-06
2lob_A		112	Golgi-associated PDZ and coiled-coil motif-contai	3e-06
1qau_A		112	Neuronal nitric oxide synthase (residues 1-130); b	3e-06
1v5q_A		122	GRIP1 homolog, glutamate receptor interacting prot	4e-06
1rgw_A		85	ZAsp protein; PDZ, cypher, oracle, muscle, Z-DISK,	4e-06
2iwq_A		123	Multiple PDZ domain protein; SGC, MPDZ, MUPP1, MUP	4e-06
1uez_A		101	KIAA1526 protein; PDZ domain, structural genomics,	4e-06
2q3g_A		89	PDZ and LIM domain protein 7; structural genomics,	4e-06
1ueq_A		123	Membrane associated guanylate kinase inverted-2 (M	5e-06
1b8q_A		127	Protein (neuronal nitric oxide synthase); PDZ doma	5e-06
2uzc_A		88	Human pdlim5, PDZ and LIM domain 5; metal-binding,	5e-06
2q9v_A		90	Membrane-associated guanylate kinase, WW and PDZ c	5e-06
2jil_A		97	GRIP1 protein, glutamate receptor interacting prot	5e-06
2gzv_A		114	PRKCA-binding protein; protein kinase C, PDZ domai	6e-06
2pkt_A		91	PDZ and LIM domain protein 1; PDZ domain, structur	6e-06
3soe_A		113	Membrane-associated guanylate kinase, WW and PDZ c	7e-06
1qav_A		90	Alpha-1 syntrophin (residues 77-171); beta-finger,	7e-06
2pa1_A		87	PDZ and LIM domain protein 2; PDZ domain, structur	7e-06
2daz_A		124	INAD-like protein; PDZ domain, inadl protein, hina	8e-06
1wf7_A		103	Enigma homologue protein; PDZ domain, structural g	9e-06
1wfg_A		131	Regulating synaptic membrane exocytosis protein 2;	9e-06
2edv_A		96	FERM and PDZ domain-containing protein 1; cytoskel	9e-06
2fne_A		117	Multiple PDZ domain protein; structural protein, s	1e-05
1uep_A		103	Membrane associated guanylate kinase inverted-2 (M	1e-05
3suz_A		388	Amyloid beta A4 precursor protein-binding family 2	1e-05
3suz_A		388	Amyloid beta A4 precursor protein-binding family 2	4e-05
2rcz_A		81	Tight junction protein ZO-1; PDZ, domain-swapping,	1e-05
2awx_A		105	Synapse associated protein 97; membrane protein, s	1e-05
1wfv_A		103	Membrane associated guanylate kinase inverted-2; a	1e-05
1q7x_A		108	PDZ2B domain of PTP-BAS (HPTP1E); phosphatase, str	2e-05
2fe5_A		94	Presynaptic protein SAP102; PDZ domain, DLG3, huma	2e-05
2dlu_A		111	INAD-like protein; PDZ domain, inadl protein, hina	2e-05
2dm8_A		116	INAD-like protein; PDZ domain, inadl protein, hina	2e-05
3e17_A		88	Tight junction protein ZO-2; domain swapping, alte	2e-05
2r4h_A		112	Membrane-associated guanylate kinase, WW and PDZ c	2e-05
2e7k_A		91	Maguk P55 subfamily member 2; PDZ domain, MPP2 pro	3e-05
2byg_A		117	Channel associated protein of synapse-110; DLG2, P	3e-05
3gge_A		95	PDZ domain-containing protein GIPC2; structural ge	3e-05
2opg_A		98	Multiple PDZ domain protein; structural protein, s	3e-05
2h2b_A		107	Tight junction protein ZO-1; PDZ domain, phage der	3e-05
1wha_A		105	KIAA0147 protein, scribble; PDZ domain, cellular s	4e-05
1um1_A		110	KIAA1849 protein, RSGI RUH-007; PDZ domain, human	4e-05
3shw_A		468	Tight junction protein ZO-1; PDZ-SH3-GUK supramodu	4e-05
3tsz_A		391	Tight junction protein ZO-1; PDZ3-SH3-GUK, scaffol	4e-05
1ihj_A		98	INAD; intermolecular disulfide bond, PDZ domain, s	5e-05
2koj_A		111	Partitioning defective 3 homolog; PDZ domain, stru	5e-05
2jre_A		108	C60-1 PDZ domain peptide; de novo protein; NMR {Sy	5e-05
2kom_A		121	Partitioning defective 3 homolog; PAR-3B, PDZ doma	6e-05
2yub_A		118	LIMK-2, LIM domain kinase 2; PDZ domain, structura	8e-05
2dmz_A		129	INAD-like protein; PDZ domain, inadl protein, hina	1e-04
1uew_A		114	Membrane associated guanylate kinase inverted-2 (M	1e-04
3b76_A		118	E3 ubiquitin-protein ligase LNX; PDZ, bound ligand	1e-04
2iwo_A		120	Multiple PDZ domain protein; SGC, MPDZ, MUPP1, MUP	1e-04
1y8t_A		324	Hypothetical protein RV0983; serine protease, stru	1e-04
1d5g_A		96	Human phosphatase HPTP1E; protein-peptide complex,	1e-04
2csj_A		117	TJP2 protein; PDZ domain, structural genomics, NPP	1e-04
1v6b_A		118	Harmonin isoform A1; structural genomics, usher sy	1e-04
1ufx_A		103	KIAA1526 protein; PDZ domain, structural genomics,	2e-04
2cs5_A		119	Tyrosine-protein phosphatase, non-receptor type 4;	2e-04
2iwn_A		97	Multiple PDZ domain protein; SGC, MPDZ, MUPP1, MUP	3e-04
2pzd_A		113	Serine protease HTRA2; PDZ domain, apoptosis, mito	3e-04
1x6d_A		119	Interleukin-16; PDZ domain, lymphocyte chemoattrac	3e-04
1uju_A		111	Scribble; PDZ domain, cellular signaling, structur	3e-04
3axa_A		106	Afadin, nectin-3, protein AF-6; PDZ domain, fusion	3e-04
2edp_A		100	Fragment, shroom family member 4; APX/shroom famil	3e-04
3nfk_A		107	Tyrosine-protein phosphatase non-receptor type 4;	3e-04
1wi4_A		109	Synip, syntaxin binding protein 4; syntaxin4-inter	4e-04
4fgm_A		597	Aminopeptidase N family protein; structural genomi	4e-04
1wf8_A		107	Neurabin-I; PDZ domain, structural genomics, NPPSF	5e-04
2g5m_B		113	Neurabin-2; spinophilin, PDZ domain, CNS, synaptic	5e-04
1wh1_A		124	KIAA1095 protein; PDZ domain, structural genomics,	6e-04
1mfg_A		95	ERB-B2 interacting protein; PDZ domain, protein-pe	6e-04
3id1_A		95	Regulator of sigma E protease; hydrolase, cell inn	7e-04

>1fc6_A Photosystem II D1 protease; D1 C-terminal processing protease, serine protease, serine- lysine catalytic DYAD, PDZ domain, photosynthesis; 1.80A {Scenedesmus obliquus} SCOP: b.36.1.3 c.14.1.2 PDB: 1fc9_A 1fc7_A 1fcf_A Length = 388	Back alignment and structure

 Score =  322 bits (827), Expect = e-107
 Identities = 123/362 (33%), Positives = 195/362 (53%), Gaps = 25/362 (6%)

Query: 104 IVEEAWQIVNDSFLDTGRHRWTPQNWQRKREDILSSS-IQTRSKAHGIIKRMLASLGDPY 162
           +  EAW+ V+ +++D     +  Q+W + RE  L    +  R++ +  I++MLA L DP+
Sbjct: 8   LFLEAWRAVDRAYVDK---SFNGQSWFKLRETYLKKEPMDRRAQTYDAIRKMLAVLDDPF 64

Query: 163 TRFLSPAEFSKMARYDMS----GIGINLREVPDANGVVT-LKVLGLILDGPAHSAGVRQG 217
           TRFL P+  + + R   +    G+G+   E+    G    + VL     GPA  AG R G
Sbjct: 65  TRFLEPSRLAAL-RRGTAGSVTGVGL---EITYDGGSGKDVVVLTPAPGGPAEKAGARAG 120

Query: 218 DEVLAVNGVDVRGKSAFEVSSLLQGPSETFVTIEVKH-GNCGPIESIQVQRQLVARTPVF 276
           D ++ V+G  V+G S ++VS LLQG +++ V + +   G      ++Q+ RQ V   PV 
Sbjct: 121 DVIVTVDGTAVKGMSLYDVSDLLQGEADSQVEVVLHAPGAPSNTRTLQLTRQKVTINPVT 180

Query: 277 YRL--------EHLDNGTTSVGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNL 328
           +                   +GY+RL  FN+        A   L   G +  +LD+R+N 
Sbjct: 181 FTTCSNVAAAALPPGAAKQQLGYVRLATFNSNTTAAAQQAFTELSKQGVAGLVLDIRNNG 240

Query: 329 GGLVQAGIEIAKLFLNEGETITYTVGRDPQYQKTIVADNSPLVT-APVIVLVNNRTASAS 387
           GGL  AG+ +A++ ++ G+ +          +    AD + + +  P++VLVN  TASAS
Sbjct: 241 GGLFPAGVNVARMLVDRGD-LVLIADSQGI-RDIYSADGNSIDSATPLVVLVNRGTASAS 298

Query: 388 EIVASALHDNCRAVLVGEKTFGKGLIQSVYELHDGSGVVVTIGKYVTPNHMDINGNGIEP 447
           E++A AL D+ R ++ GE+TFGKGLIQ+V +L DGSGV VT+ +Y TP  +DIN  G+ P
Sbjct: 299 EVLAGALKDSKRGLIAGERTFGKGLIQTVVDLSDGSGVAVTVARYQTPAGVDINKIGVSP 358

Query: 448 DY 449
           D 
Sbjct: 359 DV 360

PyMOL of 1fc6

>3k50_A Putative S41 protease; structural genomics, joint center for structural genomics, JCSG, protein structure initiative; 2.00A {Bacteroides fragilis nctc 9343} Length = 403	Back alignment and structure

>1j7x_A IRBP, interphotoreceptor retinoid-binding protein; beta BETA alpha spiral, transport protein; 1.80A {Xenopus laevis} SCOP: c.14.1.2 Length = 302	Back alignment and structure

>1k32_A Tricorn protease; protein degradation, substrate gating, serine protease, beta propeller, proteasome, hydrolase; 2.00A {Thermoplasma acidophilum} SCOP: b.36.1.3 b.68.7.1 b.69.9.1 c.14.1.2 PDB: 1n6e_A 1n6d_A 1n6f_A* Length = 1045	Back alignment and structure

>3dor_A Protein CT_858, CPAF; mature CPAF, dimer, transferase; 2.20A {Chlamydia trachomatis} PDB: 3dpm_A* 3dpn_A 3dja_A Length = 583	Back alignment and structure

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

>1w9e_A Syntenin 1; cell adhesion, adhesion/complex, PDZ domain, scaffolding protein signaling protein; 1.56A {Homo sapiens} SCOP: b.36.1.1 b.36.1.1 PDB: 1n99_A 1v1t_A 1obz_A 1w9o_A 1w9q_A 1ybo_A Length = 166	Back alignment and structure

>2eei_A PDZ domain-containing protein 1; regulatory factor, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 106	Back alignment and structure

>2v90_A PDZ domain-containing protein 3; membrane, protein-binding; 2.00A {Homo sapiens} Length = 96	Back alignment and structure

>2jxo_A Ezrin-radixin-moesin-binding phosphoprotein 50; nherf-1, PDZ domain, PDZ2, acetylation, cell projection, membrane, polymorphism; NMR {Homo sapiens} Length = 98	Back alignment and structure

>2vsp_A PDZ domain-containing protein 1; membrane, cytoplasm, phosphoprotein, transport protein, CAsp; 2.60A {Homo sapiens} PDB: 2eej_A Length = 91	Back alignment and structure

>3r68_A Na(+)/H(+) exchange regulatory cofactor NHE-RF3; PDZ domain, adaptor protein, SR-BI, signaling protein; 1.30A {Mus musculus} PDB: 3r69_A* Length = 95	Back alignment and structure

>1vae_A Rhophilin 2, rhophilin, RHO GTPase binding protein 2; PDZ domain, intracellular signaling cascade, signal transduction; NMR {Mus musculus} SCOP: b.36.1.1 Length = 111	Back alignment and structure

>2he4_A Na(+)/H(+) exchange regulatory cofactor NHE-RF2; phosphorylation, structural genomics, structural genomics consortium, SGC, unknown function; 1.45A {Homo sapiens} PDB: 2ozf_A Length = 90	Back alignment and structure

>1m5z_A GRIP, AMPA receptor interacting protein; six beta-strands and two alpha-helices, protein binding; NMR {Rattus norvegicus} SCOP: b.36.1.1 Length = 91	Back alignment and structure

>2d90_A PDZ domain containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 102	Back alignment and structure

>1g9o_A NHE-RF; PDZ domain, complex, signaling protein; 1.50A {Homo sapiens} SCOP: b.36.1.1 PDB: 1i92_A 1gq4_A 1gq5_A 2ocs_A Length = 91	Back alignment and structure

>3bpu_A Membrane-associated guanylate kinase, WW and PDZ containing protein 1; structural genomi consortium, SGC, ATP-binding, cell junction; 1.60A {Homo sapiens} Length = 88	Back alignment and structure

>2yuy_A RHO GTPase activating protein 21; PDZ domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 126	Back alignment and structure

>2dls_A PDZ-rhogef, RHO guanine nucleotide exchange factor 11; PDZ domain, arhgef11, KIAA0380, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2omj_A 2os6_A Length = 93	Back alignment and structure

>2vsv_A Rhophilin-2; scaffold protein, RHO GTPase binding, protein-binding, RHOB, nitration, cytoplasm, PDZ domain, CAsp8; 1.82A {Homo sapiens} Length = 109	Back alignment and structure

>3ngh_A PDZ domain-containing protein 1; adaptor protein, SR-BI, signaling protein; 1.80A {Mus musculus} Length = 106	Back alignment and structure

>2edz_A PDZ domain-containing protein 1; CFTR-associated protein of 70 kDa, Na/PI cotransporter C- terminal-associated protein, NAPI-CAP1; NMR {Mus musculus} Length = 114	Back alignment and structure

>2kjd_A Sodium/hydrogen exchange regulatory cofactor NHE- RF1; PDZ domain, protein, acetylation, cell projection, disease mutation, membrane; NMR {Homo sapiens} Length = 128	Back alignment and structure

>2ego_A General receptor for phosphoinositides 1- associated scaffold protein; PDZ domain, ligand-free, protein binding; 1.80A {Rattus norvegicus} PDB: 2egn_A 2egk_A 2pnt_A Length = 96	Back alignment and structure

>2kv8_A RGS12, regulator of G-protein signaling 12; PDZ domain, signaling protein; NMR {Homo sapiens} Length = 83	Back alignment and structure

>1y7n_A Amyloid beta A4 precursor protein-binding family A member 1; copper chaperone for superoxide dismutase, neuronal adaptor, protein transport; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 90	Back alignment and structure

>1ujd_A KIAA0559 protein; PDZ domain, structural genomics, human cDNA, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 117	Back alignment and structure

>3khf_A Microtubule-associated serine/threonine-protein kinase 3; MAST3, microtubule associated serine/threonine kinase 3, PDZ domain, structural genomics; 1.20A {Homo sapiens} PDB: 2w7r_A 2kqf_A 2kyl_A 3ps4_A Length = 99	Back alignment and structure

>2f5y_A Regulator of G-protein signalling 3 isoform 1; PDZ domain, RGS-3, human, structural genomics, structural GE consortium, SGC, signaling protein; 2.39A {Homo sapiens} SCOP: b.36.1.1 Length = 91	Back alignment and structure

>3o46_A Maguk P55 subfamily member 7; PDZ domain, structural genomics consortium, SGC, protein BIN; 1.30A {Homo sapiens} Length = 93	Back alignment and structure

>2krg_A Na(+)/H(+) exchange regulatory cofactor NHE-RF1; acetylation, cell projection, disease mutation, membrane, phosphoprotein, polymorphism; NMR {Homo sapiens} Length = 216	Back alignment and structure

>1va8_A Maguk P55 subfamily member 5; PDZ domain, palmitoylated 5, PALS1 protein, structural genomics, riken structural genomics/proteomics initiative; NMR {Mus musculus} SCOP: b.36.1.1 Length = 113	Back alignment and structure

>1r6j_A Syntenin 1; PDZ, membrane protein; 0.73A {Homo sapiens} SCOP: b.36.1.1 PDB: 1nte_A 1obx_A 1oby_A Length = 82	Back alignment and structure

>2eeh_A PDZ domain-containing protein 7; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 100	Back alignment and structure

>2z17_A Pleckstrin homology SEC7 and coiled-coil domains- binding protein; PDZ domain, cytoplasm, membrane, polymorphism, protein binding; 2.70A {Homo sapiens} Length = 104	Back alignment and structure

>2eaq_A LIM domain only protein 7; conserved hypothetical protein, structural genomics, NPPSFA; 1.46A {Homo sapiens} Length = 90	Back alignment and structure

>3tsv_A Tight junction protein ZO-1; PDZ, scaffolding, JAM, cell adhesion; 1.99A {Homo sapiens} PDB: 3shu_A Length = 124	Back alignment and structure

>1uit_A Human discs large 5 protein; PDZ domain, HDLG5, maguk family, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 117	Back alignment and structure

>2qkv_A Inactivation-NO-after-potential D protein; PDZ domain, scaffolding protein, membrane, sensory transduction, vision; 1.55A {Drosophila melanogaster} PDB: 2qkt_A 2qku_A Length = 96	Back alignment and structure

>1tp5_A Presynaptic density protein 95; PDZ-peptide ligand complex, peptide binding protein; 1.54A {Rattus norvegicus} SCOP: b.36.1.1 PDB: 1tp3_A 1tq3_A 1be9_A 1bfe_A Length = 119	Back alignment and structure

>1p1d_A PDZ45, glutamate receptor interacting protein; PDZ domain, tandem repeats, scaffold protein, protein binding; NMR {Rattus norvegicus} SCOP: b.36.1.1 b.36.1.1 PDB: 1p1e_A 1x5r_A Length = 196	Back alignment and structure

>1p1d_A PDZ45, glutamate receptor interacting protein; PDZ domain, tandem repeats, scaffold protein, protein binding; NMR {Rattus norvegicus} SCOP: b.36.1.1 b.36.1.1 PDB: 1p1e_A 1x5r_A Length = 196	Back alignment and structure

>3i4w_A Disks large homolog 4; alpha and beta protein, alternative splicing, cell junction, cell membrane, lipoprotein, membrane, palmitate, phosphoprotein; 1.35A {Homo sapiens} PDB: 3k82_A* 3jxt_A* 2he2_A 1pdr_A 2i0i_A Length = 104	Back alignment and structure

>1wi2_A Riken cDNA 2700099C19; structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: b.36.1.1 Length = 104	Back alignment and structure

>2djt_A Unnamed protein product; PDZ domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 104	Back alignment and structure

>2dkr_A LIN-7 homolog B; LIN-7B, PDZ, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 93	Back alignment and structure

>1whd_A RGS3, regulator of G-protein signaling 3; PDZ domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, signaling protein; NMR {Mus musculus} SCOP: b.36.1.1 Length = 100	Back alignment and structure

>2i1n_A Discs, large homolog 3; DLG3, PDZ, PDZ domain, signal transduction, structural genom structural genomics consortium, SGC, signaling protein; 1.85A {Homo sapiens} PDB: 2wl7_A 3rl7_B 1rgr_A* 1kef_A 1zok_A 1iu0_A 1iu2_A Length = 102	Back alignment and structure

>1q3o_A Shank1; PDZ, GKAP, peptide binding protein; 1.80A {Rattus norvegicus} SCOP: b.36.1.1 PDB: 1q3p_A 3qjm_A 3qjn_A 3o5n_A* Length = 109	Back alignment and structure

>3k1r_A Harmonin; protein-protein complex, alternative splicing, coiled coil, deafness, hearing, non-syndromic deafness, polymorphism; 2.30A {Homo sapiens} PDB: 2kbq_A 2kbr_A Length = 192	Back alignment and structure

>2kpk_A Membrane-associated guanylate kinase, WW and PDZ containing protein 1; PDZ domain, ATP-binding, cell junction, cell membrane; NMR {Homo sapiens} PDB: 2kpl_A Length = 129	Back alignment and structure

>2la8_A Inactivation-NO-after-potential D protein, KON-TI peptide; peptide binding protein; NMR {Drosophila melanogaster} Length = 106	Back alignment and structure

>2d8i_A T-cell lymphoma invasion and metastasis 1 variant; PDZ domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114	Back alignment and structure

>3l4f_D SH3 and multiple ankyrin repeat domains protein 1; coiled-coil, PDZ, guanine-nucleotide releasing factor, phosphoprotein, SH3 domain; 2.80A {Rattus norvegicus} Length = 132	Back alignment and structure

>1um7_A Synapse-associated protein 102; PDZ, discs large homolog 3, DLG3-human presynaptic protein, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 113	Back alignment and structure

>2qt5_A Glutamate receptor-interacting protein 1; PDZ-peptide complex, PDZ tandem, alternative splicing, cell junction, cytoplasm; 2.30A {Rattus norvegicus} Length = 200	Back alignment and structure

>2qt5_A Glutamate receptor-interacting protein 1; PDZ-peptide complex, PDZ tandem, alternative splicing, cell junction, cytoplasm; 2.30A {Rattus norvegicus} Length = 200	Back alignment and structure

>2w4f_A Protein LAP4; structural protein, phosphoprotein, UBL conjugation, leucine-rich repeat, alternative splicing, cytoplasm, circletail, coiled coil; 1.30A {Homo sapiens} Length = 97	Back alignment and structure

>2ejy_A 55 kDa erythrocyte membrane protein; GPC, maguk, PDZ, membrane protein; NMR {Homo sapiens} PDB: 2ev8_A Length = 97	Back alignment and structure

>1n7e_A AMPA receptor interacting protein GRIP; PDZ, protein binding; 1.50A {Rattus norvegicus} SCOP: b.36.1.1 PDB: 1n7f_A Length = 97	Back alignment and structure

>1nf3_C PAR-6B; semi-CRIB motif, switch I and II, PDZ domain, GTPase binding domain, signaling protein; HET: GNP; 2.10A {Mus musculus} SCOP: b.36.1.1 PDB: 2lc6_A 1ry4_A 1x8s_A 2lc7_A 1rzx_A Length = 128	Back alignment and structure

>2qg1_A Multiple PDZ domain protein; MPDZ, MUPP1, structural genomics, structural genomics consortium, SGC, signaling protein; 1.40A {Homo sapiens} Length = 92	Back alignment and structure

>1wif_A RSGI RUH-020, riken cDNA 4930408O21; PDZ domain, structural genomics, mouse cDNA, riken structural genomics/proteomics initiative; NMR {Mus musculus} SCOP: b.36.1.1 Length = 126	Back alignment and structure

>2vwr_A Ligand of NUMB protein X 2; protein-binding, metal-binding, zinc, LNX2_human, zinc-finger, polymorphism, ring finger protein 1; 1.3A {Homo sapiens} Length = 95	Back alignment and structure

>2xkx_A Disks large homolog 4; structural protein, scaffold protein, membrane associated GU kinase; 22.9A {Rattus norvegicus} Length = 721	Back alignment and structure

>2xkx_A Disks large homolog 4; structural protein, scaffold protein, membrane associated GU kinase; 22.9A {Rattus norvegicus} Length = 721	Back alignment and structure

>1v62_A KIAA1719 protein; structural genomics, synaptic transmission, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 117	Back alignment and structure

>1x5n_A Harmonin; PDZ domain, usher syndrome 1C protein, autoimmune enteropathy-related antigen AIE-75 ,antigen NY-CO-38/NY-CO- 37, PDZ-73 protein; NMR {Homo sapiens} SCOP: b.36.1.1 PDB: 2kbs_A Length = 114	Back alignment and structure

>2vz5_A TAX1-binding protein 3; WNT signaling pathway, protein binding, nucleus, cytoplasm, PDZ domain; 1.74A {Homo sapiens} PDB: 3dj1_A 3diw_A 2l4s_A 2l4t_A 3gj9_A 2kg2_A 3dj3_A Length = 139	Back alignment and structure

>2d92_A INAD-like protein; PDZ domain, inadl protein, hinadl, PALS1- associated tight junction protein, protein associated to tight junctions, PATJ; NMR {Homo sapiens} Length = 108	Back alignment and structure

>3kzd_A TIAM-1, T-lymphoma invasion and metastasis-inducing prote; PDZ, cell junction, cell adhesion, signaling protein, nucleotide exchange factor; 1.30A {Homo sapiens} PDB: 3kze_A Length = 94	Back alignment and structure

>2eeg_A PDZ and LIM domain protein 4; PDZ domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 94	Back alignment and structure

>1x5q_A LAP4 protein; PDZ domain, scribble homolog protein, hscrib, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 110	Back alignment and structure

>3r0h_A INAD, inactivation-NO-after-potential D protein; protein-protein complex, PDZ domain, peptide binding protein; 2.60A {Drosophila melanogaster} Length = 206	Back alignment and structure

>3r0h_A INAD, inactivation-NO-after-potential D protein; protein-protein complex, PDZ domain, peptide binding protein; 2.60A {Drosophila melanogaster} Length = 206	Back alignment and structure

>3gsl_A Disks large homolog 4; PDZ domain, tandem, PSD-95, DLG4, SAP-90, GLUR6, cell juncti membrane, lipoprotein, membrane, palmitate, phosphoprotein; 2.05A {Rattus norvegicus} PDB: 3zrt_A 2ka9_A Length = 196	Back alignment and structure

>3gsl_A Disks large homolog 4; PDZ domain, tandem, PSD-95, DLG4, SAP-90, GLUR6, cell juncti membrane, lipoprotein, membrane, palmitate, phosphoprotein; 2.05A {Rattus norvegicus} PDB: 3zrt_A 2ka9_A Length = 196	Back alignment and structure

>1i16_A Interleukin 16, LCF; cytokine, lymphocyte chemoattractant factor, PDZ domain; NMR {Homo sapiens} SCOP: b.36.1.2 Length = 130	Back alignment and structure

>1kwa_A Hcask/LIN-2 protein; PDZ domain, neurexin, syndecan, receptor clustering, kinase; 1.93A {Homo sapiens} SCOP: b.36.1.1 Length = 88	Back alignment and structure

>2ehr_A INAD-like protein; PDZ domain, inadl protein, hinadl, PALS1- associated tight junction protein, protein associated to tight junctions, PATJ; NMR {Homo sapiens} Length = 117	Back alignment and structure

>3hpk_A Protein interacting with PRKCA 1; oxidized, PDZ domain, kinase, protein binding; 2.20A {Rattus norvegicus} PDB: 3hpm_A Length = 125	Back alignment and structure

>2dc2_A GOPC, golgi associated PDZ and coiled-coil motif containing isoform B; GOPC PDZ domain, structural protein; NMR {Homo sapiens} Length = 103	Back alignment and structure

>2jik_A Synaptojanin-2 binding protein; transmembrane, outer membrane, mitochondria distribution, PDZ, membrane, scaffold, mitochondrion, membrane protein; 1.35A {Homo sapiens} PDB: 2jin_A Length = 101	Back alignment and structure

>1ujv_A Membrane associated guanylate kinase inverted-2 (MAGI-2); atrophin-1 interacting protein 1, PDZ domain, structural genomics, KIAA0705 protein; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 96	Back alignment and structure

>2yt7_A Amyloid beta A4 precursor protein-binding family A member 3; neuron-specific X11L2 protein, neuronal MUNC18-1-interacting protein 3, MINT-3; NMR {Homo sapiens} Length = 101	Back alignment and structure

>1uhp_A Hypothetical protein KIAA1095; PDZ domain, semaphorin cytoplasmic domain associated protein, structural genomics; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 107	Back alignment and structure

>1v5l_A PDZ and LIM domain 3; actinin alpha 2 associated LIM protein; PDZ domain, cytoskeleton, actin binding, structural genomics; NMR {Mus musculus} SCOP: b.36.1.1 Length = 103	Back alignment and structure

>2i04_A Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1; PDZ, E6 binding, tumor suppressor, peptide binding protein; 2.15A {Mus musculus} Length = 85	Back alignment and structure

>1vb7_A PDZ and LIM domain 2; PDZ domain PDZ-LIM protein, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: b.36.1.1 Length = 94	Back alignment and structure

>1uf1_A KIAA1526 protein; PDZ domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 128	Back alignment and structure

>2fcf_A Multiple PDZ domain protein; adaptor molecule, protein linker, structural genomics, struc genomics consortium, SGC, structural protein; 1.76A {Homo sapiens} SCOP: b.36.1.1 Length = 103	Back alignment and structure

>3cyy_A Tight junction protein ZO-1; protein-ligand complex, cell junction, membrane, phosphoprot domain, tight junction, transmembrane; 2.40A {Homo sapiens} Length = 92	Back alignment and structure

>2eno_A Synaptojanin-2-binding protein; mitochondrial outer membrane protein 25, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 120	Back alignment and structure

>2lob_A Golgi-associated PDZ and coiled-coil motif-contai protein; structural protein-hydrolase complex, peptide binding protei; NMR {Homo sapiens} Length = 112	Back alignment and structure

>1qau_A Neuronal nitric oxide synthase (residues 1-130); beta-finger, oxidoreductase; 1.25A {Rattus norvegicus} SCOP: b.36.1.1 PDB: 1qav_B Length = 112	Back alignment and structure

>1v5q_A GRIP1 homolog, glutamate receptor interacting protein 1A-L homolog; PDZ domain, cellular signaling, structural genomics; NMR {Mus musculus} SCOP: b.36.1.1 Length = 122	Back alignment and structure

>1rgw_A ZAsp protein; PDZ, cypher, oracle, muscle, Z-DISK, sarcomere, structural protein; NMR {Homo sapiens} SCOP: b.36.1.1 PDB: 1wjl_A Length = 85	Back alignment and structure

>2iwq_A Multiple PDZ domain protein; SGC, MPDZ, MUPP1, MUPP- 1, membrane, HOST- interaction, structural genomics consortium, synaptosome, T junction; 1.80A {Homo sapiens} Length = 123	Back alignment and structure

>1uez_A KIAA1526 protein; PDZ domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 101	Back alignment and structure

>2q3g_A PDZ and LIM domain protein 7; structural genomics, structural genomics consortium, SGC; 1.11A {Homo sapiens} Length = 89	Back alignment and structure

>1ueq_A Membrane associated guanylate kinase inverted-2 (MAGI-2); atrophin-1 interacting protein 1, PDZ domain, structural genomics; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 123	Back alignment and structure

>1b8q_A Protein (neuronal nitric oxide synthase); PDZ domain, NNOS, nitric oxide synthase, oxidoreductase; NMR {Rattus norvegicus} SCOP: b.36.1.1 Length = 127	Back alignment and structure

>2uzc_A Human pdlim5, PDZ and LIM domain 5; metal-binding, enigma homolog, phosphorylation, signaling PR LIM domain, PDZ domain; 1.5A {Homo sapiens} Length = 88	Back alignment and structure

>2q9v_A Membrane-associated guanylate kinase, WW and PDZ containing protein 1; Cys Ser mutant, S genomics consortium, SGC, transferase; 2.00A {Homo sapiens} Length = 90	Back alignment and structure

>2jil_A GRIP1 protein, glutamate receptor interacting protein-1; endoplasmic reticulum, postsynaptic membrane, membrane, MEMB protein; 1.5A {Homo sapiens} Length = 97	Back alignment and structure

>2gzv_A PRKCA-binding protein; protein kinase C, PDZ domain, structural genomics, structura genomics consortium, SGC, signaling protein; 1.12A {Homo sapiens} PDB: 2pku_A Length = 114	Back alignment and structure

>2pkt_A PDZ and LIM domain protein 1; PDZ domain, structural genomics, structural genomics consort unknown function; HET: PG4; 1.50A {Homo sapiens} PDB: 2v1w_A* Length = 91	Back alignment and structure

>3soe_A Membrane-associated guanylate kinase, WW and PDZ containing protein 3; structural genomics consortium, SGC, PDZ domain, signaling P; 1.60A {Homo sapiens} Length = 113	Back alignment and structure

>1qav_A Alpha-1 syntrophin (residues 77-171); beta-finger, heterodimer, membrane protein-oxidoreductase CO; 1.90A {Mus musculus} SCOP: b.36.1.1 PDB: 1z86_A 2pdz_A 2vrf_A Length = 90	Back alignment and structure

>2pa1_A PDZ and LIM domain protein 2; PDZ domain, structural genomics, structural genomics consort metal binding protein; 1.70A {Homo sapiens} PDB: 3pdv_A Length = 87	Back alignment and structure

>2daz_A INAD-like protein; PDZ domain, inadl protein, hinadl, PALS1- associated tight junction protein, protein associated to tight junctions, PATJ; NMR {Homo sapiens} Length = 124	Back alignment and structure

>1wf7_A Enigma homologue protein; PDZ domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: b.36.1.1 Length = 103	Back alignment and structure

>1wfg_A Regulating synaptic membrane exocytosis protein 2; PDZ domain, RAB3-interacting molecule, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: b.36.1.1 PDB: 2css_A 1zub_A Length = 131	Back alignment and structure

>2edv_A FERM and PDZ domain-containing protein 1; cytoskeletal-associated protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96	Back alignment and structure

>2fne_A Multiple PDZ domain protein; structural protein, structural genomics, SGC, structural genomics consortium, unknown function; 1.83A {Homo sapiens} SCOP: b.36.1.1 Length = 117	Back alignment and structure

>1uep_A Membrane associated guanylate kinase inverted-2 (MAGI-2); atrophin-1 interacting protein 1, PDZ domain, structural genomics; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 103	Back alignment and structure

>3suz_A Amyloid beta A4 precursor protein-binding family 2; APP binding; 2.70A {Rattus norvegicus} PDB: 1u3b_A 1u39_A 1x45_A 1u37_A 1u38_A 2yt8_A Length = 388	Back alignment and structure

>3suz_A Amyloid beta A4 precursor protein-binding family 2; APP binding; 2.70A {Rattus norvegicus} PDB: 1u3b_A 1u39_A 1x45_A 1u37_A 1u38_A 2yt8_A Length = 388	Back alignment and structure

>2rcz_A Tight junction protein ZO-1; PDZ, domain-swapping, cell junction, membrane, phosphorylati domain, protein binding; 1.70A {Homo sapiens} PDB: 2jwe_A 2osg_A Length = 81	Back alignment and structure

>2awx_A Synapse associated protein 97; membrane protein, synaptic signaling, trafficking protein; HET: HIS; 1.80A {Rattus norvegicus} PDB: 2g2l_A 2awu_A 2aww_A 3rl8_A Length = 105	Back alignment and structure

>1wfv_A Membrane associated guanylate kinase inverted-2; atrophin-1 interacting protein 1, activin receptor interacting protein 1; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 103	Back alignment and structure

>1q7x_A PDZ2B domain of PTP-BAS (HPTP1E); phosphatase, structural proteomics in europe, spine, structural genomics, hydrolase; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 108	Back alignment and structure

>2fe5_A Presynaptic protein SAP102; PDZ domain, DLG3, human, structural genomics, structural GEN consortium, SGC, structural protein; HET: GOL; 1.10A {Homo sapiens} SCOP: b.36.1.1 PDB: 2x7z_A 2oqs_A 1qlc_A 2i0l_A Length = 94	Back alignment and structure

>2dlu_A INAD-like protein; PDZ domain, inadl protein, hinadl, PALS1- associated tight junction protein, protein associated to tight junctions, PATJ; NMR {Homo sapiens} Length = 111	Back alignment and structure

>2dm8_A INAD-like protein; PDZ domain, inadl protein, hinadl, PALS1- associated tight junction protein, protein associated to tight junctions, PATJ; NMR {Homo sapiens} Length = 116	Back alignment and structure

>3e17_A Tight junction protein ZO-2; domain swapping, alternative promoter usage, alternative splicing, cell junction, cell membrane, disease mutation; 1.75A {Homo sapiens} Length = 88	Back alignment and structure

>2r4h_A Membrane-associated guanylate kinase, WW and PDZ containing protein 1; transferase, STRU genomics, structural genomics consortium, SGC, ATP-binding; HET: HIS; 2.05A {Homo sapiens} Length = 112	Back alignment and structure

>2e7k_A Maguk P55 subfamily member 2; PDZ domain, MPP2 protein, discs large homolog 2, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 91	Back alignment and structure

>2byg_A Channel associated protein of synapse-110; DLG2, PDZ, PDZ domain, structural genomics, structural genom consortium, SGC, phosphorylation; 1.85A {Homo sapiens} SCOP: b.36.1.1 Length = 117	Back alignment and structure

>3gge_A PDZ domain-containing protein GIPC2; structural genomics, structural genomics consort protein binding; 2.60A {Homo sapiens} Length = 95	Back alignment and structure

>2opg_A Multiple PDZ domain protein; structural protein, structural genomics, structural genomics consortium, SGC; 1.50A {Homo sapiens} Length = 98	Back alignment and structure

>2h2b_A Tight junction protein ZO-1; PDZ domain, phage derived high affinity ligand, cell adhesio; 1.60A {Homo sapiens} PDB: 2h2c_A 2h3m_A 2rrm_A Length = 107	Back alignment and structure

>1wha_A KIAA0147 protein, scribble; PDZ domain, cellular signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 105	Back alignment and structure

>1um1_A KIAA1849 protein, RSGI RUH-007; PDZ domain, human cDNA, structural genomics, riken structural genomics/proteomics initiative, unknown function; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 110	Back alignment and structure

>3shw_A Tight junction protein ZO-1; PDZ-SH3-GUK supramodule, cell adhesion; 2.90A {Homo sapiens} Length = 468	Back alignment and structure

>3tsz_A Tight junction protein ZO-1; PDZ3-SH3-GUK, scaffolding, JAM, tight junction, cell adhesio; 2.50A {Homo sapiens} PDB: 3tsw_A 3lh5_A Length = 391	Back alignment and structure

>1ihj_A INAD; intermolecular disulfide bond, PDZ domain, signaling protein; 1.80A {Drosophila melanogaster} SCOP: b.36.1.1 Length = 98	Back alignment and structure

>2koj_A Partitioning defective 3 homolog; PDZ domain, structural genomics, alternative splicing, cell cycle, cell division, cell junction, coiled coil; NMR {Mus musculus} PDB: 2ogp_A Length = 111	Back alignment and structure

>2jre_A C60-1 PDZ domain peptide; de novo protein; NMR {Synthetic} Length = 108	Back alignment and structure

>2kom_A Partitioning defective 3 homolog; PAR-3B, PDZ domain, PSI, structural genomics, alternative splicing, cell cycle, cell division, cell junction; NMR {Homo sapiens} Length = 121	Back alignment and structure

>2yub_A LIMK-2, LIM domain kinase 2; PDZ domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118	Back alignment and structure

>2dmz_A INAD-like protein; PDZ domain, inadl protein, hinadl, PALS1- associated tight junction protein, protein associated to tight junctions, PATJ; NMR {Homo sapiens} Length = 129	Back alignment and structure

>1uew_A Membrane associated guanylate kinase inverted-2 (MAGI-2); atrophin-1 interacting protein 1, PDZ domain, structural genomics; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 114	Back alignment and structure

>3b76_A E3 ubiquitin-protein ligase LNX; PDZ, bound ligand, structural genomics, structural genomics consortium, SGC, metal-binding; 1.75A {Homo sapiens} Length = 118	Back alignment and structure

>2iwo_A Multiple PDZ domain protein; SGC, MPDZ, MUPP1, MUPP-1, HOST-virus interaction, structural genomics consortium, synaptosome, tight junction; 1.7A {Homo sapiens} PDB: 2iwp_A Length = 120	Back alignment and structure

>1y8t_A Hypothetical protein RV0983; serine protease, structural genomics, PSI, protein structure initiative; 2.00A {Mycobacterium tuberculosis} SCOP: b.36.1.4 b.47.1.1 PDB: 2z9i_A Length = 324	Back alignment and structure

>1d5g_A Human phosphatase HPTP1E; protein-peptide complex, hydrolase; NMR {Homo sapiens} SCOP: b.36.1.1 PDB: 3lnx_A 3lny_A 3pdz_A 1vj6_A 1gm1_A 1ozi_A Length = 96	Back alignment and structure

>2csj_A TJP2 protein; PDZ domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: b.36.1.1 Length = 117	Back alignment and structure

>1v6b_A Harmonin isoform A1; structural genomics, usher syndrome, USH1, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Mus musculus} SCOP: b.36.1.1 Length = 118	Back alignment and structure

>1ufx_A KIAA1526 protein; PDZ domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 103	Back alignment and structure

>2cs5_A Tyrosine-protein phosphatase, non-receptor type 4; PDZ domain, ptpase, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 119	Back alignment and structure

>2iwn_A Multiple PDZ domain protein; SGC, MPDZ, MUPP1, MUPP- 1, HOST-virus interaction, structural genomics consortium, synaptosome, tight junction; 1.35A {Homo sapiens} Length = 97	Back alignment and structure

>2pzd_A Serine protease HTRA2; PDZ domain, apoptosis, mitochondria, peptid module, hydrolase; 2.75A {Homo sapiens} SCOP: b.36.1.4 Length = 113	Back alignment and structure

>1x6d_A Interleukin-16; PDZ domain, lymphocyte chemoattractant factor (LCF), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: b.36.1.2 Length = 119	Back alignment and structure

>1uju_A Scribble; PDZ domain, cellular signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI, signaling protein; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 111	Back alignment and structure

>3axa_A Afadin, nectin-3, protein AF-6; PDZ domain, fusion protein, cell adhesion; 2.78A {Mus musculus} PDB: 1xz9_A 2exg_A* 1t2m_A 2ain_A Length = 106	Back alignment and structure

>2edp_A Fragment, shroom family member 4; APX/shroom family member, KIAA1202 protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100	Back alignment and structure

>3nfk_A Tyrosine-protein phosphatase non-receptor type 4; PDZ-PDZ-binding site complex, protein binding; 1.43A {Homo sapiens} PDB: 3nfl_A 2vph_A Length = 107	Back alignment and structure

>1wi4_A Synip, syntaxin binding protein 4; syntaxin4-interacting protein, STXBP4 protein, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: b.36.1.1 Length = 109	Back alignment and structure

>4fgm_A Aminopeptidase N family protein; structural genomics, PSI-biology, northeast structural genom consortium, NESG, peptidase_M61, PDZ; 2.39A {Idiomarina loihiensis L2TR} Length = 597	Back alignment and structure

>1wf8_A Neurabin-I; PDZ domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 107	Back alignment and structure

>2g5m_B Neurabin-2; spinophilin, PDZ domain, CNS, synaptic transmission, protein binding; NMR {Rattus norvegicus} Length = 113	Back alignment and structure

>1wh1_A KIAA1095 protein; PDZ domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.36.1.1 Length = 124	Back alignment and structure

>1mfg_A ERB-B2 interacting protein; PDZ domain, protein-peptide complex, erbin., signaling protein; 1.25A {Homo sapiens} SCOP: b.36.1.1 PDB: 1mfl_A Length = 95	Back alignment and structure

>3id1_A Regulator of sigma E protease; hydrolase, cell inner membrane, cell membrane, membrane, metal-binding, metalloprotease, transmembrane; 1.67A {Escherichia coli k-12} PDB: 2zpl_A Length = 95	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		471
1fc6_A		388	Photosystem II D1 protease; D1 C-terminal processi	100.0
1k32_A		1045	Tricorn protease; protein degradation, substrate g	100.0
3k50_A		403	Putative S41 protease; structural genomics, joint	100.0
3dor_A		583	Protein CT_858, CPAF; mature CPAF, dimer, transfer	100.0
1j7x_A		302	IRBP, interphotoreceptor retinoid-binding protein;	99.98
2kom_A		121	Partitioning defective 3 homolog; PAR-3B, PDZ doma	99.3
2koj_A		111	Partitioning defective 3 homolog; PDZ domain, stru	99.26
2r4h_A		112	Membrane-associated guanylate kinase, WW and PDZ c	99.24
2byg_A		117	Channel associated protein of synapse-110; DLG2, P	99.23
2edz_A		114	PDZ domain-containing protein 1; CFTR-associated p	99.2
2v90_A		96	PDZ domain-containing protein 3; membrane, protein	99.19
2jxo_A		98	Ezrin-radixin-moesin-binding phosphoprotein 50; nh	99.13
1qau_A		112	Neuronal nitric oxide synthase (residues 1-130); b	99.12
3l4f_D		132	SH3 and multiple ankyrin repeat domains protein 1;	99.12
2he4_A		90	Na(+)/H(+) exchange regulatory cofactor NHE-RF2; p	99.11
2iwq_A		123	Multiple PDZ domain protein; SGC, MPDZ, MUPP1, MUP	99.11
2dm8_A		116	INAD-like protein; PDZ domain, inadl protein, hina	99.11
2pkt_A		91	PDZ and LIM domain protein 1; PDZ domain, structur	99.09
1wg6_A		127	Hypothetical protein (riken cDNA 2810455B10); stru	99.09
1v6b_A		118	Harmonin isoform A1; structural genomics, usher sy	99.08
1g9o_A		91	NHE-RF; PDZ domain, complex, signaling protein; 1.	99.07
1r6j_A		82	Syntenin 1; PDZ, membrane protein; 0.73A {Homo sap	99.07
2uzc_A		88	Human pdlim5, PDZ and LIM domain 5; metal-binding,	99.06
4amh_A		106	Disks large homolog 1; permutation, protein foldin	99.05
1n7e_A		97	AMPA receptor interacting protein GRIP; PDZ, prote	99.05
2pa1_A		87	PDZ and LIM domain protein 2; PDZ domain, structur	99.05
2vz5_A		139	TAX1-binding protein 3; WNT signaling pathway, pro	99.04
3b76_A		118	E3 ubiquitin-protein ligase LNX; PDZ, bound ligand	99.04
3cbz_A		108	Dishevelled-2; PDZ domain, phage derived high affi	99.03
1wfv_A		103	Membrane associated guanylate kinase inverted-2; a	99.03
2vsp_A		91	PDZ domain-containing protein 1; membrane, cytopla	99.03
2dls_A		93	PDZ-rhogef, RHO guanine nucleotide exchange factor	99.02
2q3g_A		89	PDZ and LIM domain protein 7; structural genomics,	99.02
2w4f_A		97	Protein LAP4; structural protein, phosphoprotein,	99.01
1wi4_A		109	Synip, syntaxin binding protein 4; syntaxin4-inter	99.01
2fcf_A		103	Multiple PDZ domain protein; adaptor molecule, pro	99.01
2djt_A		104	Unnamed protein product; PDZ domain, structural ge	99.01
1kwa_A		88	Hcask/LIN-2 protein; PDZ domain, neurexin, syndeca	99.0
2iwo_A		120	Multiple PDZ domain protein; SGC, MPDZ, MUPP1, MUP	99.0
2db5_A		128	INAD-like protein; PDZ domain, hinadl, PALS1- asso	99.0
1ihj_A		98	INAD; intermolecular disulfide bond, PDZ domain, s	99.0
3khf_A		99	Microtubule-associated serine/threonine-protein ki	99.0
1x5q_A		110	LAP4 protein; PDZ domain, scribble homolog protein	99.0
3sfj_A		104	TAX1-binding protein 3; PDZ:peptide complex, signa	98.99
2i04_A		85	Membrane-associated guanylate kinase, WW and PDZ d	98.99
2jil_A		97	GRIP1 protein, glutamate receptor interacting prot	98.99
3suz_A		388	Amyloid beta A4 precursor protein-binding family 2	98.98
2eaq_A		90	LIM domain only protein 7; conserved hypothetical	98.97
3bpu_A		88	Membrane-associated guanylate kinase, WW and PDZ c	98.97
2vwr_A		95	Ligand of NUMB protein X 2; protein-binding, metal	98.96
1b8q_A		127	Protein (neuronal nitric oxide synthase); PDZ doma	98.95
2opg_A		98	Multiple PDZ domain protein; structural protein, s	98.95
1m5z_A		91	GRIP, AMPA receptor interacting protein; six beta-	98.95
2eeh_A		100	PDZ domain-containing protein 7; structural genomi	98.95
2dmz_A		129	INAD-like protein; PDZ domain, inadl protein, hina	98.95
1q3o_A		109	Shank1; PDZ, GKAP, peptide binding protein; 1.80A	98.94
2d90_A		102	PDZ domain containing protein 1; structural genomi	98.94
1wh1_A		124	KIAA1095 protein; PDZ domain, structural genomics,	98.94
3r0h_A		206	INAD, inactivation-NO-after-potential D protein; p	98.94
3kzd_A		94	TIAM-1, T-lymphoma invasion and metastasis-inducin	98.93
2qg1_A		92	Multiple PDZ domain protein; MPDZ, MUPP1, structur	98.93
3o46_A		93	Maguk P55 subfamily member 7; PDZ domain, structur	98.93
1uep_A		103	Membrane associated guanylate kinase inverted-2 (M	98.93
2d92_A		108	INAD-like protein; PDZ domain, inadl protein, hina	98.92
2jre_A		108	C60-1 PDZ domain peptide; de novo protein; NMR {Sy	98.92
2jik_A		101	Synaptojanin-2 binding protein; transmembrane, out	98.92
2f5y_A		91	Regulator of G-protein signalling 3 isoform 1; PDZ	98.92
2iwn_A		97	Multiple PDZ domain protein; SGC, MPDZ, MUPP1, MUP	98.92
1rgw_A		85	ZAsp protein; PDZ, cypher, oracle, muscle, Z-DISK,	98.92
1ujd_A		117	KIAA0559 protein; PDZ domain, structural genomics,	98.91
3r68_A		95	Na(+)/H(+) exchange regulatory cofactor NHE-RF3; P	98.91
1vb7_A		94	PDZ and LIM domain 2; PDZ domain PDZ-LIM protein,	98.91
1wi2_A		104	Riken cDNA 2700099C19; structural genomics, riken	98.91
2awx_A		105	Synapse associated protein 97; membrane protein, s	98.91
2ego_A		96	General receptor for phosphoinositides 1- associat	98.91
1ueq_A		123	Membrane associated guanylate kinase inverted-2 (M	98.9
2fe5_A		94	Presynaptic protein SAP102; PDZ domain, DLG3, huma	98.9
2i1n_A		102	Discs, large homolog 3; DLG3, PDZ, PDZ domain, sig	98.9
2vsv_A		109	Rhophilin-2; scaffold protein, RHO GTPase binding,	98.9
1wif_A		126	RSGI RUH-020, riken cDNA 4930408O21; PDZ domain, s	98.9
1i16_A		130	Interleukin 16, LCF; cytokine, lymphocyte chemoatt	98.9
4fgm_A		597	Aminopeptidase N family protein; structural genomi	98.9
2o2t_A		117	Multiple PDZ domain protein; structural protein, s	98.9
3ngh_A		106	PDZ domain-containing protein 1; adaptor protein,	98.9
2ejy_A		97	55 kDa erythrocyte membrane protein; GPC, maguk, P	98.9
2qkv_A		96	Inactivation-NO-after-potential D protein; PDZ dom	98.9
3axa_A		106	Afadin, nectin-3, protein AF-6; PDZ domain, fusion	98.9
3cyy_A		92	Tight junction protein ZO-1; protein-ligand comple	98.89
3id1_A		95	Regulator of sigma E protease; hydrolase, cell inn	98.89
2kjd_A		128	Sodium/hydrogen exchange regulatory cofactor NHE-	98.89
1wha_A		105	KIAA0147 protein, scribble; PDZ domain, cellular s	98.89
1wf7_A		103	Enigma homologue protein; PDZ domain, structural g	98.89
2yt7_A		101	Amyloid beta A4 precursor protein-binding family A	98.88
1d5g_A		96	Human phosphatase HPTP1E; protein-peptide complex,	98.88
1wfg_A		131	Regulating synaptic membrane exocytosis protein 2;	98.88
2fne_A		117	Multiple PDZ domain protein; structural protein, s	98.88
1uez_A		101	KIAA1526 protein; PDZ domain, structural genomics,	98.88
1qav_A		90	Alpha-1 syntrophin (residues 77-171); beta-finger,	98.88
1v5l_A		103	PDZ and LIM domain 3; actinin alpha 2 associated L	98.88
2eeg_A		94	PDZ and LIM domain protein 4; PDZ domain, structur	98.88
2q9v_A		90	Membrane-associated guanylate kinase, WW and PDZ c	98.87
3i4w_A		104	Disks large homolog 4; alpha and beta protein, alt	98.87
2yuy_A		126	RHO GTPase activating protein 21; PDZ domain, stru	98.87
2kpk_A		129	Membrane-associated guanylate kinase, WW and PDZ c	98.86
2rcz_A		81	Tight junction protein ZO-1; PDZ, domain-swapping,	98.86
1v62_A		117	KIAA1719 protein; structural genomics, synaptic tr	98.86
3qe1_A		107	Sorting nexin-27, G protein-activated inward RECT	98.86
1w9e_A		166	Syntenin 1; cell adhesion, adhesion/complex, PDZ d	98.86
1va8_A		113	Maguk P55 subfamily member 5; PDZ domain, palmitoy	98.85
1wf8_A		107	Neurabin-I; PDZ domain, structural genomics, NPPSF	98.85
1v5q_A		122	GRIP1 homolog, glutamate receptor interacting prot	98.85
3tsv_A		124	Tight junction protein ZO-1; PDZ, scaffolding, JAM	98.84
2g5m_B		113	Neurabin-2; spinophilin, PDZ domain, CNS, synaptic	98.84
2z17_A		104	Pleckstrin homology SEC7 and coiled-coil domains-	98.84
1y7n_A		90	Amyloid beta A4 precursor protein-binding family A	98.83
2h2b_A		107	Tight junction protein ZO-1; PDZ domain, phage der	98.83
1ujv_A		96	Membrane associated guanylate kinase inverted-2 (M	98.83
3qik_A		101	Phosphatidylinositol 3,4,5-trisphosphate-dependen	98.82
2dkr_A		93	LIN-7 homolog B; LIN-7B, PDZ, structural genomics,	98.82
2la8_A		106	Inactivation-NO-after-potential D protein, KON-TI	98.82
4e34_A		87	Golgi-associated PDZ and coiled-coil motif-contai	98.81
1um1_A		110	KIAA1849 protein, RSGI RUH-007; PDZ domain, human	98.81
3e17_A		88	Tight junction protein ZO-2; domain swapping, alte	98.81
2kv8_A		83	RGS12, regulator of G-protein signaling 12; PDZ do	98.81
2e7k_A		91	Maguk P55 subfamily member 2; PDZ domain, MPP2 pro	98.81
1x6d_A		119	Interleukin-16; PDZ domain, lymphocyte chemoattrac	98.81
3nfk_A		107	Tyrosine-protein phosphatase non-receptor type 4;	98.8
3i18_A		100	LMO2051 protein; alpha-beta protein, structural ge	98.8
2d8i_A		114	T-cell lymphoma invasion and metastasis 1 variant;	98.8
2dlu_A		111	INAD-like protein; PDZ domain, inadl protein, hina	98.79
2kjp_A		91	Uncharacterized protein YLBL; mixed alpha-beta pro	98.79
1uf1_A		128	KIAA1526 protein; PDZ domain, structural genomics,	98.78
1uew_A		114	Membrane associated guanylate kinase inverted-2 (M	98.78
1uit_A		117	Human discs large 5 protein; PDZ domain, HDLG5, ma	98.78
3hpk_A		125	Protein interacting with PRKCA 1; oxidized, PDZ do	98.78
3egg_C		170	Spinophilin; PP1, serine/threonine phosphatase, po	98.78
2i6v_A		87	General secretion pathway protein C; EPSC, GSPC, P	98.77
2dc2_A		103	GOPC, golgi associated PDZ and coiled-coil motif c	98.76
1nf3_C		128	PAR-6B; semi-CRIB motif, switch I and II, PDZ doma	98.76
1tp5_A		119	Presynaptic density protein 95; PDZ-peptide ligand	98.76
3k1r_A		192	Harmonin; protein-protein complex, alternative spl	98.75
1whd_A		100	RGS3, regulator of G-protein signaling 3; PDZ doma	98.75
3gge_A		95	PDZ domain-containing protein GIPC2; structural ge	98.75
2gzv_A		114	PRKCA-binding protein; protein kinase C, PDZ domai	98.75
1q7x_A		108	PDZ2B domain of PTP-BAS (HPTP1E); phosphatase, str	98.75
2cs5_A		119	Tyrosine-protein phosphatase, non-receptor type 4;	98.74
2eei_A		106	PDZ domain-containing protein 1; regulatory factor	98.74
1mfg_A		95	ERB-B2 interacting protein; PDZ domain, protein-pe	98.74
2l97_A		134	HTRA, putative serine protease; HTRA-PDZ, protein	98.74
2daz_A		124	INAD-like protein; PDZ domain, inadl protein, hina	98.72
1uhp_A		107	Hypothetical protein KIAA1095; PDZ domain, semapho	98.72
2edp_A		100	Fragment, shroom family member 4; APX/shroom famil	98.71
2lob_A		112	Golgi-associated PDZ and coiled-coil motif-contai	98.17
1uju_A		111	Scribble; PDZ domain, cellular signaling, structur	98.71
2zpm_A		91	Regulator of sigma E protease; metalloproteinase,	98.7
2i4s_A		105	General secretion pathway protein C; EPSC, GSPC, P	98.7
2eno_A		120	Synaptojanin-2-binding protein; mitochondrial oute	98.7
2yub_A		118	LIMK-2, LIM domain kinase 2; PDZ domain, structura	98.69
2kl1_A		94	YLBL protein; structure genomics, structural genom	98.69
3soe_A		113	Membrane-associated guanylate kinase, WW and PDZ c	98.68
1x5n_A		114	Harmonin; PDZ domain, usher syndrome 1C protein, a	98.68
1y8t_A		324	Hypothetical protein RV0983; serine protease, stru	98.67
2ehr_A		117	INAD-like protein; PDZ domain, inadl protein, hina	98.67
3gsl_A		196	Disks large homolog 4; PDZ domain, tandem, PSD-95,	98.67
3rle_A		209	Golgi reassembly-stacking protein 2; PDZ, tether,	98.66
2csj_A		117	TJP2 protein; PDZ domain, structural genomics, NPP	98.66
1n7t_A		103	99-MER peptide of densin-180-like protein; PDZ dom	98.66
2pzd_A		113	Serine protease HTRA2; PDZ domain, apoptosis, mito	98.65
1te0_A		318	Protease DEGS; two domains, serine protease, PDZ,	98.64
2qbw_A		195	PDZ-fibronectin fusion protein; fibronectin PDZ, u	98.64
1ufx_A		103	KIAA1526 protein; PDZ domain, structural genomics,	98.64
1p1d_A		196	PDZ45, glutamate receptor interacting protein; PDZ	98.63
2qt5_A		200	Glutamate receptor-interacting protein 1; PDZ-pept	98.61
2p3w_A		112	Probable serine protease HTRA3; PDZ domain, phage	98.6
1vae_A		111	Rhophilin 2, rhophilin, RHO GTPase binding protein	98.6
3tsz_A		391	Tight junction protein ZO-1; PDZ3-SH3-GUK, scaffol	98.57
1z87_A		263	Alpha-1-syntrophin; protein binding; NMR {Mus musc	98.55
1um7_A		113	Synapse-associated protein 102; PDZ, discs large h	98.55
2edv_A		96	FERM and PDZ domain-containing protein 1; cytoskel	98.53
3stj_A		345	Protease DEGQ; serine protease, PDZ domain, protea	98.51
3r0h_A		206	INAD, inactivation-NO-after-potential D protein; p	98.48
2krg_A		216	Na(+)/H(+) exchange regulatory cofactor NHE-RF1; a	98.48
2hga_A		125	Conserved protein MTH1368; GFT structural genomics	98.46
3rle_A		209	Golgi reassembly-stacking protein 2; PDZ, tether,	98.4
1p1d_A		196	PDZ45, glutamate receptor interacting protein; PDZ	98.39
3gsl_A		196	Disks large homolog 4; PDZ domain, tandem, PSD-95,	98.39
3qo6_A		348	Protease DO-like 1, chloroplastic; protease, HTRA,	98.39
3shw_A		468	Tight junction protein ZO-1; PDZ-SH3-GUK supramodu	98.39
3pv2_A		451	DEGQ; trypsin fold, PDZ domain, chaperone protease	98.37
2qt5_A		200	Glutamate receptor-interacting protein 1; PDZ-pept	98.32
2xkx_A		721	Disks large homolog 4; structural protein, scaffol	98.3
1lcy_A		325	HTRA2 serine protease; apoptosis, PDZ domain, casp	98.29
4a8c_A		436	Periplasmic PH-dependent serine endoprotease DEGQ;	98.23
3pv2_A		451	DEGQ; trypsin fold, PDZ domain, chaperone protease	98.06
3num_A		332	Serine protease HTRA1; DEGP, hydrolase; 2.75A {Hom	98.06
4a8c_A		436	Periplasmic PH-dependent serine endoprotease DEGQ;	98.03
1ky9_A		448	Protease DO, DEGP, HTRA; protein quality control,	97.95
2xkx_A		721	Disks large homolog 4; structural protein, scaffol	97.88
4fln_A		539	Protease DO-like 2, chloroplastic; protease, DEG,	97.7
1ky9_A		448	Protease DO, DEGP, HTRA; protein quality control,	97.55
1w9e_A		166	Syntenin 1; cell adhesion, adhesion/complex, PDZ d	97.44
3suz_A		388	Amyloid beta A4 precursor protein-binding family 2	97.26
4fln_A		539	Protease DO-like 2, chloroplastic; protease, DEG,	96.27
3viv_A		230	441AA long hypothetical NFED protein; protein-pept	90.36
1y7o_A		218	ATP-dependent CLP protease proteolytic subunit; hy	84.61

>1fc6_A Photosystem II D1 protease; D1 C-terminal processing protease, serine protease, serine- lysine catalytic DYAD, PDZ domain, photosynthesis; 1.80A {Scenedesmus obliquus} SCOP: b.36.1.3 c.14.1.2 PDB: 1fc9_A 1fc7_A 1fcf_A	Back alignment and structure

Probab=100.00  E-value=2.6e-61  Score=497.55  Aligned_cols=349  Identities=34%  Similarity=0.603  Sum_probs=302.9

Q ss_pred             cchHHHHHHHHHHHHhhcccCCCCCCChhhHHHHHHHHhh-ccccChHHHHHHHHHHHHhcCCCceeecChHHhhhhh--
Q 012084           99 KTNEGIVEEAWQIVNDSFLDTGRHRWTPQNWQRKREDILS-SSIQTRSKAHGIIKRMLASLGDPYTRFLSPAEFSKMA--  175 (471)
Q Consensus        99 ~~~~~~f~~vw~~v~~~y~d~~~~~~~~~dW~~~~e~~~~-~~~~~~~~~~~~i~~ml~~L~D~Ht~~l~~~~~~~~~--  175 (471)
                      ++++++|+++|+.++++|+++.   |++.||++++++|++ ...+++.+++.+|+.|+++|+|+|+.|+++++++.+.  
T Consensus         3 ~~~~~~f~~~w~~i~~~y~~~~---~~~~dW~~~~~~y~~~~~~~~~~~~~~~i~~ml~~L~D~hs~~~~~~~~~~~~~~   79 (388)
T 1fc6_A            3 TSEQLLFLEAWRAVDRAYVDKS---FNGQSWFKLRETYLKKEPMDRRAQTYDAIRKMLAVLDDPFTRFLEPSRLAALRRG   79 (388)
T ss_dssp             CHHHHHHHHHHHHHHHHCSCTT---GGGCCHHHHHHHHHHHSCCSSHHHHHHHHHHHHHTTCCTTCEEECHHHHHHHHHC
T ss_pred             ccHHHHHHHHHHHHHHHHhccc---ccCccHHHHHHHhhhccCCCCHHHHHHHHHHHHHhcCCCcceecCHHHHHHHHHh
Confidence            4688999999999999999875   889999999999987 5678899999999999999999999999999876543  


Q ss_pred             -cccceeeeEEEEEeeCCCCceEEEEEEEcCCCchhhcCCCCCCEEEEECCEEcCCCCHHHHHHhhCCCCCcEEEEEEEc
Q 012084          176 -RYDMSGIGINLREVPDANGVVTLKVLGLILDGPAHSAGVRQGDEVLAVNGVDVRGKSAFEVSSLLQGPSETFVTIEVKH  254 (471)
Q Consensus       176 -~~~~~giG~~~~~~~d~~g~~~~~V~~v~~~spA~~aGl~~GD~Il~InG~~v~~~~~~~~~~ll~g~~g~~v~l~v~r  254 (471)
                       .+.+.|+|+.+......+  .+++|..|.++|||++|||++||+|++|||+++.++...++..++++..|++|+|+|.|
T Consensus        80 ~~g~~~giG~~~~~~~~~~--~~~~V~~v~~~spA~~aGl~~GD~I~~Ing~~v~~~~~~~~~~~l~~~~g~~v~l~v~r  157 (388)
T 1fc6_A           80 TAGSVTGVGLEITYDGGSG--KDVVVLTPAPGGPAEKAGARAGDVIVTVDGTAVKGMSLYDVSDLLQGEADSQVEVVLHA  157 (388)
T ss_dssp             SSSSCBBCSEEEEECTTCS--SCEEEEEECTTSHHHHTTCCTTCEEEEETTEECTTCCHHHHHHHHCBSTTCEEEEEEEE
T ss_pred             hcCceEEEEEEEEEeecCC--CcEEEEEeCCCChHHHcCCCCCCEEEEECCEECCCCCHHHHHHHHhcCCCCEEEEEEEe
Confidence             467889999997630012  26899999999999999999999999999999999877888889999999999999999


Q ss_pred             CCCC-CeeEEEEeeeeeeeccceeeeee--------ccCCCCeEEEEEeCchhhhHHHHHHHHHHHHHhcCCcEEEEecc
Q 012084          255 GNCG-PIESIQVQRQLVARTPVFYRLEH--------LDNGTTSVGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLR  325 (471)
Q Consensus       255 ~~~~-~~~~v~l~r~~~~~~~v~~~~~~--------~~~~~~~igYi~i~sF~~~~~~~l~~~l~~l~~~~~~~LIIDLR  325 (471)
                      ++.. ..++++++|..+...++.+....        .+..+++||||+|++|...+.++|.+++.+|+++++++||||||
T Consensus       158 ~g~~~~~~~~~l~r~~i~~~~v~~~~~~~~~~~~~~~~~~~~~igYi~i~~F~~~~~~~~~~~l~~l~~~~~~~lIlDLR  237 (388)
T 1fc6_A          158 PGAPSNTRTLQLTRQKVTINPVTFTTCSNVAAAALPPGAAKQQLGYVRLATFNSNTTAAAQQAFTELSKQGVAGLVLDIR  237 (388)
T ss_dssp             TTEEEEEEEEEEECBCCCCCCEEEEEECSCCGGGSCTTCSSSCEEEEEECCBSTTHHHHHHHHHHHHHHTTCSEEEEECT
T ss_pred             CCCCcceEEEEEEEceeecCceeeeeeccccccccccccCCCCEEEEEeCccCcchHHHHHHHHHHHHhCCCCeEEEEcC
Confidence            7632 25778888887776677655421        23446799999999999888899999999999889999999999


Q ss_pred             CCCCccHHHHHHHHhhcccCCceEEEEeccCcccceeEecCCCC-CCCCCEEEEECCCCCChHHHHHHHHhcCCCeEEEc
Q 012084          326 DNLGGLVQAGIEIAKLFLNEGETITYTVGRDPQYQKTIVADNSP-LVTAPVIVLVNNRTASASEIVASALHDNCRAVLVG  404 (471)
Q Consensus       326 ~N~GG~~~~~~~la~~f~~~~~~~~~~~~r~~~~~~~~~~~~~~-~~~~pi~VLvd~~TaSaaE~fa~~lk~~~~a~vVG  404 (471)
                      +|+||++..+..++++|++++ .+.++..|.+... .+...... .+++|++||||++|+||||+|+++||+++++++||
T Consensus       238 ~N~GG~~~~~~~~~~~f~~~~-~i~~~~~r~~~~~-~~~~~~~~~~~~~pv~VLvn~~taSasEi~a~al~~~~~~~~vG  315 (388)
T 1fc6_A          238 NNGGGLFPAGVNVARMLVDRG-DLVLIADSQGIRD-IYSADGNSIDSATPLVVLVNRGTASASEVLAGALKDSKRGLIAG  315 (388)
T ss_dssp             TCCCBCHHHHHHHHHHHCSSS-EEEEEEETTEEEE-EEECCSCCSCSSSCEEEEECTTCCTHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCCCHHHHHHHHHHHcCCC-cEEEEecCCCcee-EEecCCccccCCCCEEEEeCCCCccHHHHHHHHHhhCCCEEEEe
Confidence            999999999999999999987 4666666765432 23333334 37899999999999999999999999999999999


Q ss_pred             cCCCCCceeceEEECCCCCEEEEEEEEEEcCCCCcccCCcccCcEEcCCC
Q 012084          405 EKTFGKGLIQSVYELHDGSGVVVTIGKYVTPNHMDINGNGIEPDYRNLPA  454 (471)
Q Consensus       405 e~T~G~g~~~~~~~L~~g~~l~~t~~~~~~~~g~~~e~~GV~PDi~v~~t  454 (471)
                      ++|+|++..+..+.|+||+.+++|++++++|+|+.+++.||.|||+|.++
T Consensus       316 ~~T~Gkg~~~~~~~L~~g~~l~~t~~~~~~p~G~~~~~~Gi~PDi~v~~~  365 (388)
T 1fc6_A          316 ERTFGKGLIQTVVDLSDGSGVAVTVARYQTPAGVDINKIGVSPDVQLDPE  365 (388)
T ss_dssp             SCCCCCCEEEEEEECTTSCEEEEEEEEEECTTSCBCTTTCCCCSEECCTT
T ss_pred             ecCCCCCeeeeEEEcCCCCEEEEEEEEEEcCCCCCccCCCcCCCEEeCCc
Confidence            99999999999999999999999999999999999999999999999876

PyMOL of 1fc6

>1k32_A Tricorn protease; protein degradation, substrate gating, serine protease, beta propeller, proteasome, hydrolase; 2.00A {Thermoplasma acidophilum} SCOP: b.36.1.3 b.68.7.1 b.69.9.1 c.14.1.2 PDB: 1n6e_A 1n6d_A 1n6f_A*	Back alignment and structure

>3k50_A Putative S41 protease; structural genomics, joint center for structural genomics, JCSG, protein structure initiative; 2.00A {Bacteroides fragilis nctc 9343}	Back alignment and structure

>3dor_A Protein CT_858, CPAF; mature CPAF, dimer, transferase; 2.20A {Chlamydia trachomatis} PDB: 3dpm_A* 3dpn_A 3dja_A	Back alignment and structure

>1j7x_A IRBP, interphotoreceptor retinoid-binding protein; beta BETA alpha spiral, transport protein; 1.80A {Xenopus laevis} SCOP: c.14.1.2	Back alignment and structure

>2kom_A Partitioning defective 3 homolog; PAR-3B, PDZ domain, PSI, structural genomics, alternative splicing, cell cycle, cell division, cell junction; NMR {Homo sapiens}	Back alignment and structure

>2koj_A Partitioning defective 3 homolog; PDZ domain, structural genomics, alternative splicing, cell cycle, cell division, cell junction, coiled coil; NMR {Mus musculus} PDB: 2ogp_A	Back alignment and structure

>2r4h_A Membrane-associated guanylate kinase, WW and PDZ containing protein 1; transferase, STRU genomics, structural genomics consortium, SGC, ATP-binding; HET: HIS; 2.05A {Homo sapiens}	Back alignment and structure

>2byg_A Channel associated protein of synapse-110; DLG2, PDZ, PDZ domain, structural genomics, structural genom consortium, SGC, phosphorylation; 1.85A {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>2edz_A PDZ domain-containing protein 1; CFTR-associated protein of 70 kDa, Na/PI cotransporter C- terminal-associated protein, NAPI-CAP1; NMR {Mus musculus}	Back alignment and structure

>2v90_A PDZ domain-containing protein 3; membrane, protein-binding; 2.00A {Homo sapiens}	Back alignment and structure

>2jxo_A Ezrin-radixin-moesin-binding phosphoprotein 50; nherf-1, PDZ domain, PDZ2, acetylation, cell projection, membrane, polymorphism; NMR {Homo sapiens}	Back alignment and structure

>1qau_A Neuronal nitric oxide synthase (residues 1-130); beta-finger, oxidoreductase; 1.25A {Rattus norvegicus} SCOP: b.36.1.1 PDB: 1qav_B	Back alignment and structure

>3l4f_D SH3 and multiple ankyrin repeat domains protein 1; coiled-coil, PDZ, guanine-nucleotide releasing factor, phosphoprotein, SH3 domain; 2.80A {Rattus norvegicus}	Back alignment and structure

>2he4_A Na(+)/H(+) exchange regulatory cofactor NHE-RF2; phosphorylation, structural genomics, structural genomics consortium, SGC, unknown function; 1.45A {Homo sapiens} PDB: 2ozf_A	Back alignment and structure

>2iwq_A Multiple PDZ domain protein; SGC, MPDZ, MUPP1, MUPP- 1, membrane, HOST- interaction, structural genomics consortium, synaptosome, T junction; 1.80A {Homo sapiens}	Back alignment and structure

>2dm8_A INAD-like protein; PDZ domain, inadl protein, hinadl, PALS1- associated tight junction protein, protein associated to tight junctions, PATJ; NMR {Homo sapiens}	Back alignment and structure

>2pkt_A PDZ and LIM domain protein 1; PDZ domain, structural genomics, structural genomics consort unknown function; HET: PG4; 1.50A {Homo sapiens} PDB: 2v1w_A*	Back alignment and structure

>1wg6_A Hypothetical protein (riken cDNA 2810455B10); structural genomics, PDZ domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: b.36.1.1 PDB: 2koh_A 2k1z_A 2k20_A	Back alignment and structure

>1v6b_A Harmonin isoform A1; structural genomics, usher syndrome, USH1, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Mus musculus} SCOP: b.36.1.1	Back alignment and structure

>1g9o_A NHE-RF; PDZ domain, complex, signaling protein; 1.50A {Homo sapiens} SCOP: b.36.1.1 PDB: 1i92_A 1gq4_A 1gq5_A 2ocs_A	Back alignment and structure

>1r6j_A Syntenin 1; PDZ, membrane protein; 0.73A {Homo sapiens} SCOP: b.36.1.1 PDB: 1nte_A 1obx_A 1oby_A	Back alignment and structure

>2uzc_A Human pdlim5, PDZ and LIM domain 5; metal-binding, enigma homolog, phosphorylation, signaling PR LIM domain, PDZ domain; 1.5A {Homo sapiens}	Back alignment and structure

>4amh_A Disks large homolog 1; permutation, protein folding, structural protein; 2.30A {Homo sapiens}	Back alignment and structure

>1n7e_A AMPA receptor interacting protein GRIP; PDZ, protein binding; 1.50A {Rattus norvegicus} SCOP: b.36.1.1 PDB: 1n7f_A	Back alignment and structure

>2pa1_A PDZ and LIM domain protein 2; PDZ domain, structural genomics, structural genomics consort metal binding protein; 1.70A {Homo sapiens} PDB: 3pdv_A	Back alignment and structure

>2vz5_A TAX1-binding protein 3; WNT signaling pathway, protein binding, nucleus, cytoplasm, PDZ domain; 1.74A {Homo sapiens} PDB: 3dj1_A 3diw_A 2l4s_A 2l4t_A 3gj9_A 2kg2_A 3dj3_A	Back alignment and structure

>3b76_A E3 ubiquitin-protein ligase LNX; PDZ, bound ligand, structural genomics, structural genomics consortium, SGC, metal-binding; 1.75A {Homo sapiens}	Back alignment and structure

>3cbz_A Dishevelled-2; PDZ domain, phage derived high affinity ligand, cytoplasm, developmental protein, phosphoprotein, WNT signaling pathway; 1.38A {Homo sapiens} PDB: 3cby_A 3cc0_A 3cbx_A 2rey_A 2f0a_A 1l6o_A 3fy5_A 2kaw_A* 1mc7_A	Back alignment and structure

>1wfv_A Membrane associated guanylate kinase inverted-2; atrophin-1 interacting protein 1, activin receptor interacting protein 1; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>2vsp_A PDZ domain-containing protein 1; membrane, cytoplasm, phosphoprotein, transport protein, CAsp; 2.60A {Homo sapiens} PDB: 2eej_A	Back alignment and structure

>2dls_A PDZ-rhogef, RHO guanine nucleotide exchange factor 11; PDZ domain, arhgef11, KIAA0380, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2omj_A 2os6_A	Back alignment and structure

>2q3g_A PDZ and LIM domain protein 7; structural genomics, structural genomics consortium, SGC; 1.11A {Homo sapiens}	Back alignment and structure

>2w4f_A Protein LAP4; structural protein, phosphoprotein, UBL conjugation, leucine-rich repeat, alternative splicing, cytoplasm, circletail, coiled coil; 1.30A {Homo sapiens}	Back alignment and structure

>1wi4_A Synip, syntaxin binding protein 4; syntaxin4-interacting protein, STXBP4 protein, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: b.36.1.1	Back alignment and structure

>2fcf_A Multiple PDZ domain protein; adaptor molecule, protein linker, structural genomics, struc genomics consortium, SGC, structural protein; 1.76A {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>2djt_A Unnamed protein product; PDZ domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1kwa_A Hcask/LIN-2 protein; PDZ domain, neurexin, syndecan, receptor clustering, kinase; 1.93A {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>2iwo_A Multiple PDZ domain protein; SGC, MPDZ, MUPP1, MUPP-1, HOST-virus interaction, structural genomics consortium, synaptosome, tight junction; 1.7A {Homo sapiens} PDB: 2iwp_A	Back alignment and structure

>2db5_A INAD-like protein; PDZ domain, hinadl, PALS1- associated tight junction protein, protein associated to tight junctions, PATJ, structural genomics; NMR {Homo sapiens}	Back alignment and structure

>1ihj_A INAD; intermolecular disulfide bond, PDZ domain, signaling protein; 1.80A {Drosophila melanogaster} SCOP: b.36.1.1	Back alignment and structure

>3khf_A Microtubule-associated serine/threonine-protein kinase 3; MAST3, microtubule associated serine/threonine kinase 3, PDZ domain, structural genomics; 1.20A {Homo sapiens} PDB: 2w7r_A 2kqf_A 2kyl_A 3ps4_A	Back alignment and structure

>1x5q_A LAP4 protein; PDZ domain, scribble homolog protein, hscrib, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>3sfj_A TAX1-binding protein 3; PDZ:peptide complex, signaling protein-inhibitor complex; 1.24A {Homo sapiens} PDB: 3dj3_A	Back alignment and structure

>2i04_A Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1; PDZ, E6 binding, tumor suppressor, peptide binding protein; 2.15A {Mus musculus}	Back alignment and structure

>2jil_A GRIP1 protein, glutamate receptor interacting protein-1; endoplasmic reticulum, postsynaptic membrane, membrane, MEMB protein; 1.5A {Homo sapiens}	Back alignment and structure

>3suz_A Amyloid beta A4 precursor protein-binding family 2; APP binding; 2.70A {Rattus norvegicus} PDB: 1u3b_A 1u39_A 1x45_A 1u37_A 1u38_A 2yt8_A	Back alignment and structure

>2eaq_A LIM domain only protein 7; conserved hypothetical protein, structural genomics, NPPSFA; 1.46A {Homo sapiens}	Back alignment and structure

>3bpu_A Membrane-associated guanylate kinase, WW and PDZ containing protein 1; structural genomi consortium, SGC, ATP-binding, cell junction; 1.60A {Homo sapiens}	Back alignment and structure

>2vwr_A Ligand of NUMB protein X 2; protein-binding, metal-binding, zinc, LNX2_human, zinc-finger, polymorphism, ring finger protein 1; 1.3A {Homo sapiens}	Back alignment and structure

>1b8q_A Protein (neuronal nitric oxide synthase); PDZ domain, NNOS, nitric oxide synthase, oxidoreductase; NMR {Rattus norvegicus} SCOP: b.36.1.1	Back alignment and structure

>2opg_A Multiple PDZ domain protein; structural protein, structural genomics, structural genomics consortium, SGC; 1.50A {Homo sapiens}	Back alignment and structure

>1m5z_A GRIP, AMPA receptor interacting protein; six beta-strands and two alpha-helices, protein binding; NMR {Rattus norvegicus} SCOP: b.36.1.1	Back alignment and structure

>2eeh_A PDZ domain-containing protein 7; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2dmz_A INAD-like protein; PDZ domain, inadl protein, hinadl, PALS1- associated tight junction protein, protein associated to tight junctions, PATJ; NMR {Homo sapiens}	Back alignment and structure

>1q3o_A Shank1; PDZ, GKAP, peptide binding protein; 1.80A {Rattus norvegicus} SCOP: b.36.1.1 PDB: 1q3p_A 3qjm_A 3qjn_A 3o5n_A*	Back alignment and structure

>2d90_A PDZ domain containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}	Back alignment and structure

>1wh1_A KIAA1095 protein; PDZ domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>3r0h_A INAD, inactivation-NO-after-potential D protein; protein-protein complex, PDZ domain, peptide binding protein; 2.60A {Drosophila melanogaster}	Back alignment and structure

>3kzd_A TIAM-1, T-lymphoma invasion and metastasis-inducing prote; PDZ, cell junction, cell adhesion, signaling protein, nucleotide exchange factor; 1.30A {Homo sapiens} PDB: 3kze_A	Back alignment and structure

>2qg1_A Multiple PDZ domain protein; MPDZ, MUPP1, structural genomics, structural genomics consortium, SGC, signaling protein; 1.40A {Homo sapiens}	Back alignment and structure

>3o46_A Maguk P55 subfamily member 7; PDZ domain, structural genomics consortium, SGC, protein BIN; 1.30A {Homo sapiens} SCOP: b.36.1.0	Back alignment and structure

>1uep_A Membrane associated guanylate kinase inverted-2 (MAGI-2); atrophin-1 interacting protein 1, PDZ domain, structural genomics; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>2d92_A INAD-like protein; PDZ domain, inadl protein, hinadl, PALS1- associated tight junction protein, protein associated to tight junctions, PATJ; NMR {Homo sapiens}	Back alignment and structure

>2jre_A C60-1 PDZ domain peptide; de novo protein; NMR {Synthetic}	Back alignment and structure

>2jik_A Synaptojanin-2 binding protein; transmembrane, outer membrane, mitochondria distribution, PDZ, membrane, scaffold, mitochondrion, membrane protein; 1.35A {Homo sapiens} PDB: 2jin_A	Back alignment and structure

>2f5y_A Regulator of G-protein signalling 3 isoform 1; PDZ domain, RGS-3, human, structural genomics, structural GE consortium, SGC, signaling protein; 2.39A {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>2iwn_A Multiple PDZ domain protein; SGC, MPDZ, MUPP1, MUPP- 1, HOST-virus interaction, structural genomics consortium, synaptosome, tight junction; 1.35A {Homo sapiens}	Back alignment and structure

>1rgw_A ZAsp protein; PDZ, cypher, oracle, muscle, Z-DISK, sarcomere, structural protein; NMR {Homo sapiens} SCOP: b.36.1.1 PDB: 1wjl_A	Back alignment and structure

>1ujd_A KIAA0559 protein; PDZ domain, structural genomics, human cDNA, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>3r68_A Na(+)/H(+) exchange regulatory cofactor NHE-RF3; PDZ domain, adaptor protein, SR-BI, signaling protein; 1.30A {Mus musculus} SCOP: b.36.1.0 PDB: 3r69_A*	Back alignment and structure

>1vb7_A PDZ and LIM domain 2; PDZ domain PDZ-LIM protein, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: b.36.1.1	Back alignment and structure

>1wi2_A Riken cDNA 2700099C19; structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: b.36.1.1	Back alignment and structure

>2awx_A Synapse associated protein 97; membrane protein, synaptic signaling, trafficking protein; HET: HIS; 1.80A {Rattus norvegicus} PDB: 2g2l_A 2awu_A 2aww_A 3rl8_A	Back alignment and structure

>2ego_A General receptor for phosphoinositides 1- associated scaffold protein; PDZ domain, ligand-free, protein binding; 1.80A {Rattus norvegicus} PDB: 2egn_A 2egk_A 2pnt_A	Back alignment and structure

>1ueq_A Membrane associated guanylate kinase inverted-2 (MAGI-2); atrophin-1 interacting protein 1, PDZ domain, structural genomics; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>2fe5_A Presynaptic protein SAP102; PDZ domain, DLG3, human, structural genomics, structural GEN consortium, SGC, structural protein; HET: GOL; 1.10A {Homo sapiens} SCOP: b.36.1.1 PDB: 2x7z_A 2oqs_A 1qlc_A 2i0l_A	Back alignment and structure

>2i1n_A Discs, large homolog 3; DLG3, PDZ, PDZ domain, signal transduction, structural genom structural genomics consortium, SGC, signaling protein; 1.85A {Homo sapiens} PDB: 2wl7_A 3rl7_B 1rgr_A* 1kef_A 1zok_A 1iu0_A 1iu2_A	Back alignment and structure

>2vsv_A Rhophilin-2; scaffold protein, RHO GTPase binding, protein-binding, RHOB, nitration, cytoplasm, PDZ domain, CAsp8; 1.82A {Homo sapiens}	Back alignment and structure

>1wif_A RSGI RUH-020, riken cDNA 4930408O21; PDZ domain, structural genomics, mouse cDNA, riken structural genomics/proteomics initiative; NMR {Mus musculus} SCOP: b.36.1.1	Back alignment and structure

>1i16_A Interleukin 16, LCF; cytokine, lymphocyte chemoattractant factor, PDZ domain; NMR {Homo sapiens} SCOP: b.36.1.2	Back alignment and structure

>4fgm_A Aminopeptidase N family protein; structural genomics, PSI-biology, northeast structural genom consortium, NESG, peptidase_M61, PDZ; 2.39A {Idiomarina loihiensis L2TR}	Back alignment and structure

>2o2t_A Multiple PDZ domain protein; structural protein, structural genomics, structural genomics consortium, SGC; 2.70A {Homo sapiens}	Back alignment and structure

>3ngh_A PDZ domain-containing protein 1; adaptor protein, SR-BI, signaling protein; 1.80A {Mus musculus} SCOP: b.36.1.0	Back alignment and structure

>2ejy_A 55 kDa erythrocyte membrane protein; GPC, maguk, PDZ, membrane protein; NMR {Homo sapiens} PDB: 2ev8_A	Back alignment and structure

>2qkv_A Inactivation-NO-after-potential D protein; PDZ domain, scaffolding protein, membrane, sensory transduction, vision; 1.55A {Drosophila melanogaster} PDB: 2qkt_A 2qku_A	Back alignment and structure

>3axa_A Afadin, nectin-3, protein AF-6; PDZ domain, fusion protein, cell adhesion; 2.78A {Mus musculus} PDB: 1xz9_A 2exg_A* 1t2m_A 2ain_A	Back alignment and structure

>3cyy_A Tight junction protein ZO-1; protein-ligand complex, cell junction, membrane, phosphoprot domain, tight junction, transmembrane; 2.40A {Homo sapiens}	Back alignment and structure

>3id1_A Regulator of sigma E protease; hydrolase, cell inner membrane, cell membrane, membrane, metal-binding, metalloprotease, transmembrane; 1.67A {Escherichia coli k-12} PDB: 2zpl_A	Back alignment and structure

>2kjd_A Sodium/hydrogen exchange regulatory cofactor NHE- RF1; PDZ domain, protein, acetylation, cell projection, disease mutation, membrane; NMR {Homo sapiens}	Back alignment and structure

>1wha_A KIAA0147 protein, scribble; PDZ domain, cellular signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>1wf7_A Enigma homologue protein; PDZ domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: b.36.1.1	Back alignment and structure

>2yt7_A Amyloid beta A4 precursor protein-binding family A member 3; neuron-specific X11L2 protein, neuronal MUNC18-1-interacting protein 3, MINT-3; NMR {Homo sapiens}	Back alignment and structure

>1d5g_A Human phosphatase HPTP1E; protein-peptide complex, hydrolase; NMR {Homo sapiens} SCOP: b.36.1.1 PDB: 3lnx_A 3lny_A 3pdz_A 1vj6_A 1gm1_A 1ozi_A	Back alignment and structure

>1wfg_A Regulating synaptic membrane exocytosis protein 2; PDZ domain, RAB3-interacting molecule, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: b.36.1.1 PDB: 2css_A 1zub_A	Back alignment and structure

>2fne_A Multiple PDZ domain protein; structural protein, structural genomics, SGC, structural genomics consortium, unknown function; 1.83A {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>1uez_A KIAA1526 protein; PDZ domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>1qav_A Alpha-1 syntrophin (residues 77-171); beta-finger, heterodimer, membrane protein-oxidoreductase CO; 1.90A {Mus musculus} SCOP: b.36.1.1 PDB: 1z86_A 2pdz_A 2vrf_A	Back alignment and structure

>1v5l_A PDZ and LIM domain 3; actinin alpha 2 associated LIM protein; PDZ domain, cytoskeleton, actin binding, structural genomics; NMR {Mus musculus} SCOP: b.36.1.1	Back alignment and structure

>2eeg_A PDZ and LIM domain protein 4; PDZ domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2q9v_A Membrane-associated guanylate kinase, WW and PDZ containing protein 1; Cys Ser mutant, S genomics consortium, SGC, transferase; 2.00A {Homo sapiens}	Back alignment and structure

>3i4w_A Disks large homolog 4; alpha and beta protein, alternative splicing, cell junction, cell membrane, lipoprotein, membrane, palmitate, phosphoprotein; 1.35A {Homo sapiens} SCOP: b.36.1.1 PDB: 3k82_A* 3jxt_A* 2he2_A 1pdr_A 2i0i_A	Back alignment and structure

>2yuy_A RHO GTPase activating protein 21; PDZ domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2kpk_A Membrane-associated guanylate kinase, WW and PDZ containing protein 1; PDZ domain, ATP-binding, cell junction, cell membrane; NMR {Homo sapiens} PDB: 2kpl_A	Back alignment and structure

>2rcz_A Tight junction protein ZO-1; PDZ, domain-swapping, cell junction, membrane, phosphorylati domain, protein binding; 1.70A {Homo sapiens} PDB: 2jwe_A 2osg_A	Back alignment and structure

>1v62_A KIAA1719 protein; structural genomics, synaptic transmission, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>1w9e_A Syntenin 1; cell adhesion, adhesion/complex, PDZ domain, scaffolding protein signaling protein; 1.56A {Homo sapiens} SCOP: b.36.1.1 b.36.1.1 PDB: 1n99_A 1v1t_A 1obz_A 1w9o_A 1w9q_A 1ybo_A	Back alignment and structure

>1va8_A Maguk P55 subfamily member 5; PDZ domain, palmitoylated 5, PALS1 protein, structural genomics, riken structural genomics/proteomics initiative; NMR {Mus musculus} SCOP: b.36.1.1	Back alignment and structure

>1wf8_A Neurabin-I; PDZ domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>1v5q_A GRIP1 homolog, glutamate receptor interacting protein 1A-L homolog; PDZ domain, cellular signaling, structural genomics; NMR {Mus musculus} SCOP: b.36.1.1	Back alignment and structure

>3tsv_A Tight junction protein ZO-1; PDZ, scaffolding, JAM, cell adhesion; 1.99A {Homo sapiens} PDB: 3shu_A	Back alignment and structure

>2g5m_B Neurabin-2; spinophilin, PDZ domain, CNS, synaptic transmission, protein binding; NMR {Rattus norvegicus}	Back alignment and structure

>2z17_A Pleckstrin homology SEC7 and coiled-coil domains- binding protein; PDZ domain, cytoplasm, membrane, polymorphism, protein binding; 2.70A {Homo sapiens}	Back alignment and structure

>1y7n_A Amyloid beta A4 precursor protein-binding family A member 1; copper chaperone for superoxide dismutase, neuronal adaptor, protein transport; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>2h2b_A Tight junction protein ZO-1; PDZ domain, phage derived high affinity ligand, cell adhesio; 1.60A {Homo sapiens} PDB: 2h2c_A 2h3m_A 2rrm_A	Back alignment and structure

>1ujv_A Membrane associated guanylate kinase inverted-2 (MAGI-2); atrophin-1 interacting protein 1, PDZ domain, structural genomics, KIAA0705 protein; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>3qik_A Phosphatidylinositol 3,4,5-trisphosphate-dependen exchanger 1 protein; PDZ domain, structural genomics consortium, SGC, hydrolase R; 2.29A {Homo sapiens}	Back alignment and structure

>2dkr_A LIN-7 homolog B; LIN-7B, PDZ, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2la8_A Inactivation-NO-after-potential D protein, KON-TI peptide; peptide binding protein; NMR {Drosophila melanogaster}	Back alignment and structure

>4e34_A Golgi-associated PDZ and coiled-coil motif-contai protein; PDZ-peptide complex, protein transport-inhibitor complex; 1.40A {Homo sapiens} PDB: 4e35_A	Back alignment and structure

>1um1_A KIAA1849 protein, RSGI RUH-007; PDZ domain, human cDNA, structural genomics, riken structural genomics/proteomics initiative, unknown function; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>3e17_A Tight junction protein ZO-2; domain swapping, alternative promoter usage, alternative splicing, cell junction, cell membrane, disease mutation; 1.75A {Homo sapiens}	Back alignment and structure

>2kv8_A RGS12, regulator of G-protein signaling 12; PDZ domain, signaling protein; NMR {Homo sapiens}	Back alignment and structure

>2e7k_A Maguk P55 subfamily member 2; PDZ domain, MPP2 protein, discs large homolog 2, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1x6d_A Interleukin-16; PDZ domain, lymphocyte chemoattractant factor (LCF), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: b.36.1.2	Back alignment and structure

>3nfk_A Tyrosine-protein phosphatase non-receptor type 4; PDZ-PDZ-binding site complex, protein binding; 1.43A {Homo sapiens} SCOP: b.36.1.1 PDB: 3nfl_A 2vph_A	Back alignment and structure

>3i18_A LMO2051 protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; 1.70A {Listeria monocytogenes} PDB: 2kjk_A 3i1e_A	Back alignment and structure

>2d8i_A T-cell lymphoma invasion and metastasis 1 variant; PDZ domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2dlu_A INAD-like protein; PDZ domain, inadl protein, hinadl, PALS1- associated tight junction protein, protein associated to tight junctions, PATJ; NMR {Homo sapiens}	Back alignment and structure

>2kjp_A Uncharacterized protein YLBL; mixed alpha-beta protein, cell membrane, hydrolase, membrane, protease, serine protease, transmembrane; NMR {Bacillus subtilis}	Back alignment and structure

>1uf1_A KIAA1526 protein; PDZ domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>1uew_A Membrane associated guanylate kinase inverted-2 (MAGI-2); atrophin-1 interacting protein 1, PDZ domain, structural genomics; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>1uit_A Human discs large 5 protein; PDZ domain, HDLG5, maguk family, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>3hpk_A Protein interacting with PRKCA 1; oxidized, PDZ domain, kinase, protein binding; 2.20A {Rattus norvegicus} PDB: 3hpm_A	Back alignment and structure

>3egg_C Spinophilin; PP1, serine/threonine phosphatase, post synapti density, glutametergic receptors, carbohydrate metabolism, cycle, cell division; HET: MES; 1.85A {Rattus norvegicus} PDB: 3egh_C* 3hvq_C 2fn5_A	Back alignment and structure

>2i6v_A General secretion pathway protein C; EPSC, GSPC, PDZ domain, type 2 secretion system, protein transport, membrane protein; 1.63A {Vibrio cholerae} SCOP: b.36.1.5	Back alignment and structure

>2dc2_A GOPC, golgi associated PDZ and coiled-coil motif containing isoform B; GOPC PDZ domain, structural protein; NMR {Homo sapiens}	Back alignment and structure

>1nf3_C PAR-6B; semi-CRIB motif, switch I and II, PDZ domain, GTPase binding domain, signaling protein; HET: GNP; 2.10A {Mus musculus} SCOP: b.36.1.1 PDB: 2lc6_A 1ry4_A 1x8s_A 2lc7_A 1rzx_A	Back alignment and structure

>1tp5_A Presynaptic density protein 95; PDZ-peptide ligand complex, peptide binding protein; 1.54A {Rattus norvegicus} SCOP: b.36.1.1 PDB: 1tp3_A 1tq3_A 1be9_A 1bfe_A	Back alignment and structure

>3k1r_A Harmonin; protein-protein complex, alternative splicing, coiled coil, deafness, hearing, non-syndromic deafness, polymorphism; 2.30A {Homo sapiens} PDB: 2kbq_A 2kbr_A 2lsr_A	Back alignment and structure

>1whd_A RGS3, regulator of G-protein signaling 3; PDZ domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, signaling protein; NMR {Mus musculus} SCOP: b.36.1.1	Back alignment and structure

>3gge_A PDZ domain-containing protein GIPC2; structural genomics, structural genomics consort protein binding; 2.60A {Homo sapiens}	Back alignment and structure

>2gzv_A PRKCA-binding protein; protein kinase C, PDZ domain, structural genomics, structura genomics consortium, SGC, signaling protein; 1.12A {Homo sapiens} PDB: 2pku_A	Back alignment and structure

>1q7x_A PDZ2B domain of PTP-BAS (HPTP1E); phosphatase, structural proteomics in europe, spine, structural genomics, hydrolase; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>2cs5_A Tyrosine-protein phosphatase, non-receptor type 4; PDZ domain, ptpase, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>2eei_A PDZ domain-containing protein 1; regulatory factor, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1mfg_A ERB-B2 interacting protein; PDZ domain, protein-peptide complex, erbin., signaling protein; 1.25A {Homo sapiens} SCOP: b.36.1.1 PDB: 1mfl_A	Back alignment and structure

>2l97_A HTRA, putative serine protease; HTRA-PDZ, protein binding; NMR {Streptococcus pneumoniae}	Back alignment and structure

>2daz_A INAD-like protein; PDZ domain, inadl protein, hinadl, PALS1- associated tight junction protein, protein associated to tight junctions, PATJ; NMR {Homo sapiens}	Back alignment and structure

>1uhp_A Hypothetical protein KIAA1095; PDZ domain, semaphorin cytoplasmic domain associated protein, structural genomics; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>2edp_A Fragment, shroom family member 4; APX/shroom family member, KIAA1202 protein, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2lob_A Golgi-associated PDZ and coiled-coil motif-contai protein; structural protein-hydrolase complex, peptide binding protei; NMR {Homo sapiens}	Back alignment and structure

>1uju_A Scribble; PDZ domain, cellular signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI, signaling protein; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>2zpm_A Regulator of sigma E protease; metalloproteinase, membrane protein, PDZ domain, hydrolase, inner membrane, membrane, metal-binding; HET: MLY MSE; 0.98A {Escherichia coli} PDB: 3id2_A 3id3_A 3id4_A	Back alignment and structure

>2i4s_A General secretion pathway protein C; EPSC, GSPC, PDZ domain, type 2 secretion system, protein transport, membrane protein; 1.92A {Vibrio cholerae} SCOP: b.36.1.5	Back alignment and structure

>2eno_A Synaptojanin-2-binding protein; mitochondrial outer membrane protein 25, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2yub_A LIMK-2, LIM domain kinase 2; PDZ domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}	Back alignment and structure

>2kl1_A YLBL protein; structure genomics, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium; NMR {Geobacillus thermodenitrificans}	Back alignment and structure

>3soe_A Membrane-associated guanylate kinase, WW and PDZ containing protein 3; structural genomics consortium, SGC, PDZ domain, signaling P; 1.60A {Homo sapiens}	Back alignment and structure

>1x5n_A Harmonin; PDZ domain, usher syndrome 1C protein, autoimmune enteropathy-related antigen AIE-75 ,antigen NY-CO-38/NY-CO- 37, PDZ-73 protein; NMR {Homo sapiens} SCOP: b.36.1.1 PDB: 2kbs_A	Back alignment and structure

>1y8t_A Hypothetical protein RV0983; serine protease, structural genomics, PSI, protein structure initiative; 2.00A {Mycobacterium tuberculosis} SCOP: b.36.1.4 b.47.1.1 PDB: 2z9i_A	Back alignment and structure

>2ehr_A INAD-like protein; PDZ domain, inadl protein, hinadl, PALS1- associated tight junction protein, protein associated to tight junctions, PATJ; NMR {Homo sapiens}	Back alignment and structure

>3gsl_A Disks large homolog 4; PDZ domain, tandem, PSD-95, DLG4, SAP-90, GLUR6, cell juncti membrane, lipoprotein, membrane, palmitate, phosphoprotein; 2.05A {Rattus norvegicus} PDB: 3zrt_A 2ka9_A	Back alignment and structure

>3rle_A Golgi reassembly-stacking protein 2; PDZ, tether, golgin, membrane protein; 1.65A {Homo sapiens} PDB: 4edj_A	Back alignment and structure

>2csj_A TJP2 protein; PDZ domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: b.36.1.1	Back alignment and structure

>1n7t_A 99-MER peptide of densin-180-like protein; PDZ domain, C-terminal peptide complex, high affnity ligand, signaling protein; NMR {Homo sapiens} SCOP: b.36.1.1 PDB: 2h3l_A	Back alignment and structure

>2pzd_A Serine protease HTRA2; PDZ domain, apoptosis, mitochondria, peptid module, hydrolase; 2.75A {Homo sapiens} SCOP: b.36.1.4	Back alignment and structure

>1te0_A Protease DEGS; two domains, serine protease, PDZ, alpha-beta protein, hydro; 2.20A {Escherichia coli} SCOP: b.36.1.4 b.47.1.1 PDB: 3gdv_A* 3gcn_A* 3gds_A* 3gdu_A* 3gco_A* 1sot_A 1soz_A 1vcw_A 2r3y_A	Back alignment and structure

>2qbw_A PDZ-fibronectin fusion protein; fibronectin PDZ, unknown function; 1.80A {Homo sapiens} PDB: 3ch8_A	Back alignment and structure

>1ufx_A KIAA1526 protein; PDZ domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>1p1d_A PDZ45, glutamate receptor interacting protein; PDZ domain, tandem repeats, scaffold protein, protein binding; NMR {Rattus norvegicus} SCOP: b.36.1.1 b.36.1.1 PDB: 1p1e_A 1x5r_A	Back alignment and structure

>2qt5_A Glutamate receptor-interacting protein 1; PDZ-peptide complex, PDZ tandem, alternative splicing, cell junction, cytoplasm; 2.30A {Rattus norvegicus}	Back alignment and structure

>2p3w_A Probable serine protease HTRA3; PDZ domain, phage derived high affinity ligand, protein BIND; 1.70A {Homo sapiens}	Back alignment and structure

>1vae_A Rhophilin 2, rhophilin, RHO GTPase binding protein 2; PDZ domain, intracellular signaling cascade, signal transduction; NMR {Mus musculus} SCOP: b.36.1.1	Back alignment and structure

>3tsz_A Tight junction protein ZO-1; PDZ3-SH3-GUK, scaffolding, JAM, tight junction, cell adhesio; 2.50A {Homo sapiens} PDB: 3tsw_A 3lh5_A	Back alignment and structure

>1z87_A Alpha-1-syntrophin; protein binding; NMR {Mus musculus}	Back alignment and structure

>1um7_A Synapse-associated protein 102; PDZ, discs large homolog 3, DLG3-human presynaptic protein, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: b.36.1.1	Back alignment and structure

>2edv_A FERM and PDZ domain-containing protein 1; cytoskeletal-associated protein, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3stj_A Protease DEGQ; serine protease, PDZ domain, protease, chaperone, DEGP, DEGQ hydrolase; 2.60A {Escherichia coli}	Back alignment and structure

>3r0h_A INAD, inactivation-NO-after-potential D protein; protein-protein complex, PDZ domain, peptide binding protein; 2.60A {Drosophila melanogaster}	Back alignment and structure

>2krg_A Na(+)/H(+) exchange regulatory cofactor NHE-RF1; acetylation, cell projection, disease mutation, membrane, phosphoprotein, polymorphism; NMR {Homo sapiens}	Back alignment and structure

>2hga_A Conserved protein MTH1368; GFT structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: b.36.1.6	Back alignment and structure

>3rle_A Golgi reassembly-stacking protein 2; PDZ, tether, golgin, membrane protein; 1.65A {Homo sapiens} PDB: 4edj_A	Back alignment and structure

>1p1d_A PDZ45, glutamate receptor interacting protein; PDZ domain, tandem repeats, scaffold protein, protein binding; NMR {Rattus norvegicus} SCOP: b.36.1.1 b.36.1.1 PDB: 1p1e_A 1x5r_A	Back alignment and structure

>3gsl_A Disks large homolog 4; PDZ domain, tandem, PSD-95, DLG4, SAP-90, GLUR6, cell juncti membrane, lipoprotein, membrane, palmitate, phosphoprotein; 2.05A {Rattus norvegicus} PDB: 3zrt_A 2ka9_A	Back alignment and structure

>3qo6_A Protease DO-like 1, chloroplastic; protease, HTRA, PH-sensor, hydrolase, photosynthesis; 2.50A {Arabidopsis thaliana}	Back alignment and structure

>3shw_A Tight junction protein ZO-1; PDZ-SH3-GUK supramodule, cell adhesion; 2.90A {Homo sapiens}	Back alignment and structure

>3pv2_A DEGQ; trypsin fold, PDZ domain, chaperone protease, hydrolase; 2.15A {Legionella fallonii} PDB: 3pv3_A 3pv5_A 3pv4_A	Back alignment and structure

>2qt5_A Glutamate receptor-interacting protein 1; PDZ-peptide complex, PDZ tandem, alternative splicing, cell junction, cytoplasm; 2.30A {Rattus norvegicus}	Back alignment and structure

>2xkx_A Disks large homolog 4; structural protein, scaffold protein, membrane associated GU kinase; 22.9A {Rattus norvegicus}	Back alignment and structure

>1lcy_A HTRA2 serine protease; apoptosis, PDZ domain, caspase activation, binding, hydrolase; 2.00A {Homo sapiens} SCOP: b.36.1.4 b.47.1.1	Back alignment and structure

>4a8c_A Periplasmic PH-dependent serine endoprotease DEGQ; chaperone, hydrolase; 7.50A {Escherichia coli} PDB: 4a8a_A 4a8b_A 4a9g_A	Back alignment and structure

>3pv2_A DEGQ; trypsin fold, PDZ domain, chaperone protease, hydrolase; 2.15A {Legionella fallonii} PDB: 3pv3_A 3pv5_A 3pv4_A	Back alignment and structure

>3num_A Serine protease HTRA1; DEGP, hydrolase; 2.75A {Homo sapiens} PDB: 3nzi_A 2ytw_A 2joa_A	Back alignment and structure

>4a8c_A Periplasmic PH-dependent serine endoprotease DEGQ; chaperone, hydrolase; 7.50A {Escherichia coli} PDB: 4a8a_A 4a8b_A 4a9g_A	Back alignment and structure

>1ky9_A Protease DO, DEGP, HTRA; protein quality control, serine protease, trypsin, chaperone, PDZ, ATP-independent, temperature-regulated, periplasm; 2.80A {Escherichia coli} SCOP: b.36.1.4 b.47.1.1 PDB: 3ou0_A 4a8d_A 3otp_A 3mh7_A 3mh4_A 3mh5_A* 3mh6_A* 3cs0_A 2zle_A	Back alignment and structure

>2xkx_A Disks large homolog 4; structural protein, scaffold protein, membrane associated GU kinase; 22.9A {Rattus norvegicus}	Back alignment and structure

>4fln_A Protease DO-like 2, chloroplastic; protease, DEG, PDZ, hydrolase; 2.80A {Arabidopsis thaliana}	Back alignment and structure

>1ky9_A Protease DO, DEGP, HTRA; protein quality control, serine protease, trypsin, chaperone, PDZ, ATP-independent, temperature-regulated, periplasm; 2.80A {Escherichia coli} SCOP: b.36.1.4 b.47.1.1 PDB: 3ou0_A 4a8d_A 3otp_A 3mh7_A 3mh4_A 3mh5_A* 3mh6_A* 3cs0_A 2zle_A	Back alignment and structure

>1w9e_A Syntenin 1; cell adhesion, adhesion/complex, PDZ domain, scaffolding protein signaling protein; 1.56A {Homo sapiens} SCOP: b.36.1.1 b.36.1.1 PDB: 1n99_A 1v1t_A 1obz_A 1w9o_A 1w9q_A 1ybo_A	Back alignment and structure

>3suz_A Amyloid beta A4 precursor protein-binding family 2; APP binding; 2.70A {Rattus norvegicus} PDB: 1u3b_A 1u39_A 1x45_A 1u37_A 1u38_A 2yt8_A	Back alignment and structure

>4fln_A Protease DO-like 2, chloroplastic; protease, DEG, PDZ, hydrolase; 2.80A {Arabidopsis thaliana}	Back alignment and structure

>3viv_A 441AA long hypothetical NFED protein; protein-peptide complex, alpha / beta motif, protease, membr protein stomatin, hydrolase-protein binding complex; 2.25A {Pyrococcus horikoshii} PDB: 3bpp_A 2deo_A	Back alignment and structure

>1y7o_A ATP-dependent CLP protease proteolytic subunit; hydrolase; 2.51A {Streptococcus pneumoniae} SCOP: c.14.1.1	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		471
d1fc6a4		294	c.14.1.2 (A:78-156,A:249-463) Photosystem II D1 C-	7e-45
d1j7xa_		302	c.14.1.2 (A:) Interphotoreceptor retinoid-binding	9e-33
d1k32a4		291	c.14.1.2 (A:680-762,A:854-1061) Tricorn protease {	3e-26
d1k32a4		291	c.14.1.2 (A:680-762,A:854-1061) Tricorn protease {	3e-11
d1fc6a3		92	b.36.1.3 (A:157-248) Photosystem II D1 C-terminal	2e-11
d1g9oa_		91	b.36.1.1 (A:) Na+/H+ exchanger regulatory factor,	1e-10
d2f5ya1		77	b.36.1.1 (A:19-95) Regulator of G-protein signalin	4e-10
d1ujda_		117	b.36.1.1 (A:) Hypothetical protein KIAA0559 {Human	1e-09
d1w9ea1		85	b.36.1.1 (A:110-194) Syntenin 1 {Human (Homo sapie	3e-09
d1m5za_		91	b.36.1.1 (A:) Glutamate receptor interacting prote	6e-09
d1ueqa_		123	b.36.1.1 (A:) Membrane associated guanylate kinase	1e-08
d2csja1		104	b.36.1.1 (A:8-111) Tight junction protein ZO-2, Tj	2e-08
d1x5qa1		97	b.36.1.1 (A:8-104) Scribble (KIAA0147) {Human (Hom	2e-08
d1x45a1		85	b.36.1.1 (A:8-92) Amyloid beta A4 precursor protei	3e-08
d1wi4a1		96	b.36.1.1 (A:8-103) Syntaxin binding protein 4 {Mou	5e-08
d1q3oa_		104	b.36.1.1 (A:) Shank1, PDZ domain {Rat (Rattus norv	5e-08
d1n7ea_		95	b.36.1.1 (A:) Glutamate receptor-interacting prote	5e-08
d1vb7a_		94	b.36.1.1 (A:) PDZ-LIM protein mystique {Mouse (Mus	7e-08
d1x5na1		101	b.36.1.1 (A:8-108) Harmonin {Human (Homo sapiens)	7e-08
d1uita_		117	b.36.1.1 (A:) Discs large 5 protein KIAA0583 {Huma	8e-08
d1kwaa_		88	b.36.1.1 (A:) Cask/Lin-2 {Human (Homo sapiens) [Ta	1e-07
d1rgwa_		85	b.36.1.1 (A:) Zasp (Cypher, Oracle 1) {Human (Homo	2e-07
d1x5ra1		99	b.36.1.1 (A:8-106) Glutamate receptor interacting	2e-07
d2z9ia1		88	b.36.1.4 (A:227-314) Protease PepD {Mycobacterium	2e-07
d1uepa_		103	b.36.1.1 (A:) Membrane associated guanylate kinase	3e-07
d1y7na1		79	b.36.1.1 (A:12-90) Amyloid beta A4 precursor prote	3e-07
d1qava_		90	b.36.1.1 (A:) Syntrophin {Mouse (Mus musculus) [Ta	4e-07
d1ueza_		101	b.36.1.1 (A:) KIAA1526 protein {Human (Homo sapien	4e-07
d2fcfa1		96	b.36.1.1 (A:1148-1243) Multiple PDZ domain protein	5e-07
d1p1da2		99	b.36.1.1 (A:115-213) Glutamate receptor interactin	7e-07
d1wi2a_		104	b.36.1.1 (A:) PDZ domain containing protein 11, Pd	8e-07
d1ufxa_		103	b.36.1.1 (A:) KIAA1526 protein {Human (Homo sapien	8e-07
d1wifa_		126	b.36.1.1 (A:) hypothetical PDZ domain containing p	9e-07
d1uf1a_		128	b.36.1.1 (A:) KIAA1526 protein {Human (Homo sapien	2e-06
d1wg6a_		127	b.36.1.1 (A:) Partitioning-defective 3-like protei	2e-06
d2fnea1		88	b.36.1.1 (A:1955-2042) Multiple PDZ domain protein	2e-06
d2fe5a1		92	b.36.1.1 (A:223-314) Synapse-associated protein 10	5e-06
d2cs5a1		106	b.36.1.1 (A:8-113) Tyrosine-protein phosphatase no	7e-06
d1i16a_		130	b.36.1.2 (A:) Interleukin 16 {Human (Homo sapiens)	1e-05
d1vaea_		111	b.36.1.1 (A:) Rhophilin-2 {Mouse (Mus musculus) [T	1e-05
d1wh1a_		124	b.36.1.1 (A:) Hypothetical protein KIAA1095 {Human	1e-05
d1wf7a_		103	b.36.1.1 (A:) Enigma homolog ENH {Mouse (Mus muscu	1e-05
d1wf8a1		94	b.36.1.1 (A:8-101) Neurabin-i {Human (Homo sapiens	2e-05
d1v5la_		103	b.36.1.1 (A:) Alpha-actinin-2 associated LIM prote	2e-05
d1ihja_		94	b.36.1.1 (A:) Inad {Fruit fly (Drosophila melanoga	3e-05
d1v6ba_		118	b.36.1.1 (A:) Harmonin {Mouse (Mus musculus) [TaxI	5e-05
d1v5qa_		122	b.36.1.1 (A:) Glutamate receptor interacting prote	5e-05
d2cssa1		108	b.36.1.1 (A:8-115) Regulating synaptic membrane ex	5e-05
d1rzxa_		98	b.36.1.1 (A:) GTPase-binding domain of the cell po	9e-05
d1ky9b2		88	b.36.1.4 (B:359-446) Protease Do (DegP, HtrA), C-t	1e-04
d2f0aa1		92	b.36.1.1 (A:251-342) Segment polarity protein dish	1e-04
d1r6ja_		82	b.36.1.1 (A:) Syntenin 1 {Human (Homo sapiens) [Ta	3e-04
d2i6va1		87	b.36.1.5 (A:219-305) General secretion pathway pro	0.004
d1k32a1		91	b.36.1.3 (A:763-853) Tricorn protease {Archaeon Th	0.004

>d1fc6a4 c.14.1.2 (A:78-156,A:249-463) Photosystem II D1 C-terminal processing protease {Algae (Scenedesmus obliquus) [TaxId: 3088]} Length = 294	Back information, alignment and structure


class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Tail specific protease, catalytic domain
domain: Photosystem II D1 C-terminal processing protease
species: Algae (Scenedesmus obliquus) [TaxId: 3088]

 Score =  156 bits (396), Expect = 7e-45
 Identities = 96/350 (27%), Positives = 155/350 (44%), Gaps = 87/350 (24%)

Query: 101 NEGIVEEAWQIVNDSFLDTGRHRWTPQNWQRKREDILS-SSIQTRSKAHGIIKRMLASLG 159
            + +  EAW+ V+ +++D     +  Q+W + RE  L    +  R++ +  I++MLA L 
Sbjct: 4   EQLLFLEAWRAVDRAYVD---KSFNGQSWFKLRETYLKKEPMDRRAQTYDAIRKMLAVLD 60

Query: 160 DPYTRFLSPAEFSKMARYDMSGIGINLREVPDANGVVTLKVLGLILDGPAHSAGVRQGDE 219
           DP+TRFL P+  + +                                        R+G +
Sbjct: 61  DPFTRFLEPSRLAAL----------------------------------------RRGTK 80

Query: 220 VLAVNGVDVRGKSAFEVSSLLQGPSETFVTIEVKHGNCGPIESIQVQRQLVARTPVFYRL 279
           V  +N V     S    ++L  G ++            G +                 RL
Sbjct: 81  V-TINPVTFTTCSNVAAAALPPGAAK---------QQLGYV-----------------RL 113

Query: 280 EHLDNGTTSVGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNLGGLVQAGIEIA 339
              ++ TT+       E +      LV               LD+R+N GGL  AG+ +A
Sbjct: 114 ATFNSNTTAAAQQAFTELSKQGVAGLV---------------LDIRNNGGGLFPAGVNVA 158

Query: 340 KLFLNEGETITYTVGRDPQYQKTIVADNSPLVTAPVIVLVNNRTASASEIVASALHDNCR 399
           ++ ++ G+ +     +  +   +    NS     P++VLVN  TASASE++A AL D+ R
Sbjct: 159 RMLVDRGDLVLIADSQGIRDIYSAD-GNSIDSATPLVVLVNRGTASASEVLAGALKDSKR 217

Query: 400 AVLVGEKTFGKGLIQSVYELHDGSGVVVTIGKYVTPNHMDINGNGIEPDY 449
            ++ GE+TFGKGLIQ+V +L DGSGV VT+ +Y TP  +DIN  G+ PD 
Sbjct: 218 GLIAGERTFGKGLIQTVVDLSDGSGVAVTVARYQTPAGVDINKIGVSPDV 267

PyMOL of d1fc6a4

>d1j7xa_ c.14.1.2 (A:) Interphotoreceptor retinoid-binding protein IRBP {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 302	Back information, alignment and structure

>d1k32a4 c.14.1.2 (A:680-762,A:854-1061) Tricorn protease {Archaeon Thermoplasma acidophilum [TaxId: 2303]} Length = 291	Back information, alignment and structure

>d1k32a4 c.14.1.2 (A:680-762,A:854-1061) Tricorn protease {Archaeon Thermoplasma acidophilum [TaxId: 2303]} Length = 291	Back information, alignment and structure

>d1fc6a3 b.36.1.3 (A:157-248) Photosystem II D1 C-terminal processing protease {Algae (Scenedesmus obliquus) [TaxId: 3088]} Length = 92	Back information, alignment and structure

>d1g9oa_ b.36.1.1 (A:) Na+/H+ exchanger regulatory factor, NHERF {Human (Homo sapiens) [TaxId: 9606]} Length = 91	Back information, alignment and structure

>d2f5ya1 b.36.1.1 (A:19-95) Regulator of G-protein signaling 3, RGS3 {Human (Homo sapiens) [TaxId: 9606]} Length = 77	Back information, alignment and structure

>d1ujda_ b.36.1.1 (A:) Hypothetical protein KIAA0559 {Human (Homo sapiens) [TaxId: 9606]} Length = 117	Back information, alignment and structure

>d1w9ea1 b.36.1.1 (A:110-194) Syntenin 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 85	Back information, alignment and structure

>d1m5za_ b.36.1.1 (A:) Glutamate receptor interacting protein {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 91	Back information, alignment and structure

>d1ueqa_ b.36.1.1 (A:) Membrane associated guanylate kinase inverted-2 (MAGI-2, KIAA0705) {Human (Homo sapiens) [TaxId: 9606]} Length = 123	Back information, alignment and structure

>d2csja1 b.36.1.1 (A:8-111) Tight junction protein ZO-2, Tjp2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104	Back information, alignment and structure

>d1x5qa1 b.36.1.1 (A:8-104) Scribble (KIAA0147) {Human (Homo sapiens) [TaxId: 9606]} Length = 97	Back information, alignment and structure

>d1x45a1 b.36.1.1 (A:8-92) Amyloid beta A4 precursor protein-binding family A member 1 (APBA1, X11) {Human (Homo sapiens) [TaxId: 9606]} Length = 85	Back information, alignment and structure

>d1wi4a1 b.36.1.1 (A:8-103) Syntaxin binding protein 4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 96	Back information, alignment and structure

>d1q3oa_ b.36.1.1 (A:) Shank1, PDZ domain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 104	Back information, alignment and structure

>d1n7ea_ b.36.1.1 (A:) Glutamate receptor-interacting protein 1, GRIP1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 95	Back information, alignment and structure

>d1vb7a_ b.36.1.1 (A:) PDZ-LIM protein mystique {Mouse (Mus musculus) [TaxId: 10090]} Length = 94	Back information, alignment and structure

>d1x5na1 b.36.1.1 (A:8-108) Harmonin {Human (Homo sapiens) [TaxId: 9606]} Length = 101	Back information, alignment and structure

>d1uita_ b.36.1.1 (A:) Discs large 5 protein KIAA0583 {Human (Homo sapiens) [TaxId: 9606]} Length = 117	Back information, alignment and structure

>d1kwaa_ b.36.1.1 (A:) Cask/Lin-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88	Back information, alignment and structure

>d1rgwa_ b.36.1.1 (A:) Zasp (Cypher, Oracle 1) {Human (Homo sapiens) [TaxId: 9606]} Length = 85	Back information, alignment and structure

>d1x5ra1 b.36.1.1 (A:8-106) Glutamate receptor interacting protein 2, GRIP2 (KIAA1719) {Human (Homo sapiens) [TaxId: 9606]} Length = 99	Back information, alignment and structure

>d2z9ia1 b.36.1.4 (A:227-314) Protease PepD {Mycobacterium tuberculosis [TaxId: 1773]} Length = 88	Back information, alignment and structure

>d1uepa_ b.36.1.1 (A:) Membrane associated guanylate kinase inverted-2 (MAGI-2, KIAA0705) {Human (Homo sapiens) [TaxId: 9606]} Length = 103	Back information, alignment and structure

>d1y7na1 b.36.1.1 (A:12-90) Amyloid beta A4 precursor protein-binding family A member 1 (APBA1, X11) {Human (Homo sapiens) [TaxId: 9606]} Length = 79	Back information, alignment and structure

>d1qava_ b.36.1.1 (A:) Syntrophin {Mouse (Mus musculus) [TaxId: 10090]} Length = 90	Back information, alignment and structure

>d1ueza_ b.36.1.1 (A:) KIAA1526 protein {Human (Homo sapiens) [TaxId: 9606]} Length = 101	Back information, alignment and structure

>d2fcfa1 b.36.1.1 (A:1148-1243) Multiple PDZ domain protein {Human (Homo sapiens) [TaxId: 9606]} Length = 96	Back information, alignment and structure

>d1p1da2 b.36.1.1 (A:115-213) Glutamate receptor interacting protein {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 99	Back information, alignment and structure

>d1wi2a_ b.36.1.1 (A:) PDZ domain containing protein 11, Pdzk11 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104	Back information, alignment and structure

>d1ufxa_ b.36.1.1 (A:) KIAA1526 protein {Human (Homo sapiens) [TaxId: 9606]} Length = 103	Back information, alignment and structure

>d1wifa_ b.36.1.1 (A:) hypothetical PDZ domain containing protein Uqcrc2 (4930408O21Rik) {Mouse (Mus musculus) [TaxId: 10090]} Length = 126	Back information, alignment and structure

>d1uf1a_ b.36.1.1 (A:) KIAA1526 protein {Human (Homo sapiens) [TaxId: 9606]} Length = 128	Back information, alignment and structure

>d1wg6a_ b.36.1.1 (A:) Partitioning-defective 3-like protein, PAR3-L (RIKEN cDNA 2810455b10) {Mouse (Mus musculus) [TaxId: 10090]} Length = 127	Back information, alignment and structure

>d2fnea1 b.36.1.1 (A:1955-2042) Multiple PDZ domain protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88	Back information, alignment and structure

>d2fe5a1 b.36.1.1 (A:223-314) Synapse-associated protein 102 {Human (Homo sapiens) [TaxId: 9606]} Length = 92	Back information, alignment and structure

>d2cs5a1 b.36.1.1 (A:8-113) Tyrosine-protein phosphatase non-receptor type 4, PTPN4 {Human (Homo sapiens) [TaxId: 9606]} Length = 106	Back information, alignment and structure

>d1i16a_ b.36.1.2 (A:) Interleukin 16 {Human (Homo sapiens) [TaxId: 9606]} Length = 130	Back information, alignment and structure

>d1vaea_ b.36.1.1 (A:) Rhophilin-2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111	Back information, alignment and structure

>d1wh1a_ b.36.1.1 (A:) Hypothetical protein KIAA1095 {Human (Homo sapiens) [TaxId: 9606]} Length = 124	Back information, alignment and structure

>d1wf7a_ b.36.1.1 (A:) Enigma homolog ENH {Mouse (Mus musculus) [TaxId: 10090]} Length = 103	Back information, alignment and structure

>d1wf8a1 b.36.1.1 (A:8-101) Neurabin-i {Human (Homo sapiens) [TaxId: 9606]} Length = 94	Back information, alignment and structure

>d1v5la_ b.36.1.1 (A:) Alpha-actinin-2 associated LIM protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 103	Back information, alignment and structure

>d1ihja_ b.36.1.1 (A:) Inad {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 94	Back information, alignment and structure

>d1v6ba_ b.36.1.1 (A:) Harmonin {Mouse (Mus musculus) [TaxId: 10090]} Length = 118	Back information, alignment and structure

>d1v5qa_ b.36.1.1 (A:) Glutamate receptor interacting protein {Mouse (Mus musculus) [TaxId: 10090]} Length = 122	Back information, alignment and structure

>d2cssa1 b.36.1.1 (A:8-115) Regulating synaptic membrane exocytosis protein 1, RIMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 108	Back information, alignment and structure

>d1rzxa_ b.36.1.1 (A:) GTPase-binding domain of the cell polarity protein par6 (Par-6B) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 98	Back information, alignment and structure

>d1ky9b2 b.36.1.4 (B:359-446) Protease Do (DegP, HtrA), C-terminal domains {Escherichia coli [TaxId: 562]} Length = 88	Back information, alignment and structure

>d2f0aa1 b.36.1.1 (A:251-342) Segment polarity protein dishevelled homolog Dvl-2 {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 92	Back information, alignment and structure

>d1r6ja_ b.36.1.1 (A:) Syntenin 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 82	Back information, alignment and structure

>d2i6va1 b.36.1.5 (A:219-305) General secretion pathway protein C, EpsC {Vibrio cholerae [TaxId: 666]} Length = 87	Back information, alignment and structure

>d1k32a1 b.36.1.3 (A:763-853) Tricorn protease {Archaeon Thermoplasma acidophilum [TaxId: 2303]} Length = 91	Back information, alignment and structure

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		471
d1fc6a4		294	Photosystem II D1 C-terminal processing protease {	100.0
d1k32a4		291	Tricorn protease {Archaeon Thermoplasma acidophilu	100.0
d1j7xa_		302	Interphotoreceptor retinoid-binding protein IRBP {	99.97
d1fc6a3		92	Photosystem II D1 C-terminal processing protease {	99.62
d1k32a1		91	Tricorn protease {Archaeon Thermoplasma acidophilu	99.3
d2z9ia1		88	Protease PepD {Mycobacterium tuberculosis [TaxId:	99.28
d1w9ea1		85	Syntenin 1 {Human (Homo sapiens) [TaxId: 9606]}	99.22
d1g9oa_		91	Na+/H+ exchanger regulatory factor, NHERF {Human (	99.1
d1m5za_		91	Glutamate receptor interacting protein {Rat (Rattu	99.09
d2f5ya1		77	Regulator of G-protein signaling 3, RGS3 {Human (H	99.08
d1rgwa_		85	Zasp (Cypher, Oracle 1) {Human (Homo sapiens) [Tax	99.05
d2fe5a1		92	Synapse-associated protein 102 {Human (Homo sapien	99.04
d1x5qa1		97	Scribble (KIAA0147) {Human (Homo sapiens) [TaxId:	99.02
d1qaua_		112	Neuronal nitric oxide synthase, NNOS {Rat (Rattus	99.0
d1p1da2		99	Glutamate receptor interacting protein {Rat (Rattu	98.99
d1t2ma1		92	Afadin {Human (Homo sapiens) [TaxId: 9606]}	98.99
d2fcfa1		96	Multiple PDZ domain protein {Human (Homo sapiens)	98.98
d1wifa_		126	hypothetical PDZ domain containing protein Uqcrc2	98.98
d1qava_		90	Syntrophin {Mouse (Mus musculus) [TaxId: 10090]}	98.95
d1ozia_		99	Phosphatase hPTP1e {Mouse (Mus musculus) [TaxId: 1	98.94
d1lcya1		100	Mitochondrial serine protease HtrA2 {Human (Homo s	98.93
d1vb7a_		94	PDZ-LIM protein mystique {Mouse (Mus musculus) [Ta	98.92
d1ihja_		94	Inad {Fruit fly (Drosophila melanogaster) [TaxId:	98.92
d1rgra_		93	Synaptic protein PSD-95 {Rat (Rattus norvegicus) [	98.92
d1wf8a1		94	Neurabin-i {Human (Homo sapiens) [TaxId: 9606]}	98.9
d1n7ea_		95	Glutamate receptor-interacting protein 1, GRIP1 {R	98.9
d2f0aa1		92	Segment polarity protein dishevelled homolog Dvl-2	98.89
d1ujda_		117	Hypothetical protein KIAA0559 {Human (Homo sapiens	98.89
d1tp5a1		102	Synaptic protein PSD-95 {Rat (Rattus norvegicus) [	98.88
d1ueqa_		123	Membrane associated guanylate kinase inverted-2 (M	98.88
d1r6ja_		82	Syntenin 1 {Human (Homo sapiens) [TaxId: 9606]}	98.88
d1wi4a1		96	Syntaxin binding protein 4 {Mouse (Mus musculus) [	98.88
d1q3oa_		104	Shank1, PDZ domain {Rat (Rattus norvegicus) [TaxId	98.87
d1x45a1		85	Amyloid beta A4 precursor protein-binding family A	98.87
d1vaea_		111	Rhophilin-2 {Mouse (Mus musculus) [TaxId: 10090]}	98.86
d2i6va1		87	General secretion pathway protein C, EpsC {Vibrio	98.85
d1uita_		117	Discs large 5 protein KIAA0583 {Human (Homo sapien	98.85
d1wi2a_		104	PDZ domain containing protein 11, Pdzk11 {Mouse (M	98.85
d1kwaa_		88	Cask/Lin-2 {Human (Homo sapiens) [TaxId: 9606]}	98.84
d1uepa_		103	Membrane associated guanylate kinase inverted-2 (M	98.84
d1y7na1		79	Amyloid beta A4 precursor protein-binding family A	98.84
d1ky9b2		88	Protease Do (DegP, HtrA), C-terminal domains {Esch	98.83
d1whaa_		105	Scribble (KIAA0147) {Human (Homo sapiens) [TaxId:	98.83
d1va8a1		100	Maguk p55 subfamily member 5 {Mouse (Mus musculus)	98.83
d1ueza_		101	KIAA1526 protein {Human (Homo sapiens) [TaxId: 960	98.8
d1wf7a_		103	Enigma homolog ENH {Mouse (Mus musculus) [TaxId: 1	98.8
d1sota1		99	Stress sensor protease DegS, C-terminal domain {Es	98.79
d1uf1a_		128	KIAA1526 protein {Human (Homo sapiens) [TaxId: 960	98.78
d1um1a_		110	Hypothetical protein KIAA1849 {Human (Homo sapiens	98.78
d2cssa1		108	Regulating synaptic membrane exocytosis protein 1,	98.78
d1uhpa_		107	Hypothetical protein KIAA1095 {Human (Homo sapiens	98.77
d2cs5a1		106	Tyrosine-protein phosphatase non-receptor type 4,	98.76
d1v5la_		103	Alpha-actinin-2 associated LIM protein {Mouse (Mus	98.75
d1x5na1		101	Harmonin {Human (Homo sapiens) [TaxId: 9606]}	98.75
d1i16a_		130	Interleukin 16 {Human (Homo sapiens) [TaxId: 9606]	98.74
d2fnea1		88	Multiple PDZ domain protein {Human (Homo sapiens)	98.73
d1ky9a1		94	Protease Do (DegP, HtrA), C-terminal domains {Esch	98.73
d1ujua_		111	Scribble (KIAA0147) {Human (Homo sapiens) [TaxId:	98.72
d1wg6a_		127	Partitioning-defective 3-like protein, PAR3-L (RIK	98.71
d1v62a_		117	Glutamate receptor interacting protein 2, GRIP2 (K	98.71
d2hgaa1		103	Uncharacterized protein MTH1368 {Methanobacterium	98.71
d1wfva_		103	Membrane associated guanylate kinase inverted-2 (M	98.7
d1rzxa_		98	GTPase-binding domain of the cell polarity protein	98.68
d1uewa_		114	Membrane associated guanylate kinase inverted-2 (M	98.68
d1x6da1		107	Interleukin 16 {Human (Homo sapiens) [TaxId: 9606]	98.67
d2csja1		104	Tight junction protein ZO-2, Tjp2 {Mouse (Mus musc	98.67
d1wh1a_		124	Hypothetical protein KIAA1095 {Human (Homo sapiens	98.64
d1v6ba_		118	Harmonin {Mouse (Mus musculus) [TaxId: 10090]}	98.58
d2h3la1		103	Erbin {Human (Homo sapiens) [TaxId: 9606]}	98.56
d1ufxa_		103	KIAA1526 protein {Human (Homo sapiens) [TaxId: 960	98.53
d1x5ra1		99	Glutamate receptor interacting protein 2, GRIP2 (K	98.52
d1v5qa_		122	Glutamate receptor interacting protein {Mouse (Mus	98.45
d1ujva_		96	Membrane associated guanylate kinase inverted-2 (M	98.42

>d1fc6a4 c.14.1.2 (A:78-156,A:249-463) Photosystem II D1 C-terminal processing protease {Algae (Scenedesmus obliquus) [TaxId: 3088]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Tail specific protease, catalytic domain
domain: Photosystem II D1 C-terminal processing protease
species: Algae (Scenedesmus obliquus) [TaxId: 3088]

Probab=100.00  E-value=1.4e-48  Score=385.45  Aligned_cols=283  Identities=35%  Similarity=0.574  Sum_probs=224.0

Q ss_pred             chHHHHHHHHHHHHhhcccCCCCCCChhhHHHHHHHHhhc-cccChHHHHHHHHHHHHhcCCCceeecChHHhhhhhccc
Q 012084          100 TNEGIVEEAWQIVNDSFLDTGRHRWTPQNWQRKREDILSS-SIQTRSKAHGIIKRMLASLGDPYTRFLSPAEFSKMARYD  178 (471)
Q Consensus       100 ~~~~~f~~vw~~v~~~y~d~~~~~~~~~dW~~~~e~~~~~-~~~~~~~~~~~i~~ml~~L~D~Ht~~l~~~~~~~~~~~~  178 (471)
                      +++++|+++|+.++++|+|+.   |+++||++++++|++. .+.++.+++.+|++|+++|+|+|++|++++++..+.++.
T Consensus         3 ~~~~if~e~W~~~~~~y~~~~---~~gvDW~a~~~~y~~~~~~~~~~e~~~~i~~ml~~L~D~Ht~~~~~~~~~~~~~g~   79 (294)
T d1fc6a4           3 SEQLLFLEAWRAVDRAYVDKS---FNGQSWFKLRETYLKKEPMDRRAQTYDAIRKMLAVLDDPFTRFLEPSRLAALRRGT   79 (294)
T ss_dssp             HHHHHHHHHHHHHHHHCSCTT---GGGCCHHHHHHHHHHHSCCSSHHHHHHHHHHHHHTTCCTTCEEECHHHHHHHHHCS
T ss_pred             cHHHHHHHHHHHhhccccCCC---CCccCHHHHHHHHhccccCCCHHHHHHHHHHHHHHhCCCceEEeChHHhhhhccCc
Confidence            566799999999999999976   8999999999999865 357888999999999999999999999999876654321


Q ss_pred             ceeeeEEEEEeeCCCCceEEEEEEEcCCCchhhcCCCCCCEEEEECCEEcCCCCHHHHHHhhCCCCCcEEEEEEEcCCCC
Q 012084          179 MSGIGINLREVPDANGVVTLKVLGLILDGPAHSAGVRQGDEVLAVNGVDVRGKSAFEVSSLLQGPSETFVTIEVKHGNCG  258 (471)
Q Consensus       179 ~~giG~~~~~~~d~~g~~~~~V~~v~~~spA~~aGl~~GD~Il~InG~~v~~~~~~~~~~ll~g~~g~~v~l~v~r~~~~  258 (471)
                      ...+                                                               ..+..+....   
T Consensus        80 ~~~~---------------------------------------------------------------~~~~~~~~~~---   93 (294)
T d1fc6a4          80 KVTI---------------------------------------------------------------NPVTFTTCSN---   93 (294)
T ss_dssp             CCCC---------------------------------------------------------------CCEEEEEECS---
T ss_pred             eEEe---------------------------------------------------------------cccCCCcccc---
Confidence            0000                                                               0000000000   


Q ss_pred             CeeEEEEeeeeeeeccceeeeeeccCCCCeEEEEEeCchhhhHHHHHHHHHHHHHhcCCcEEEEeccCCCCccHHHHHHH
Q 012084          259 PIESIQVQRQLVARTPVFYRLEHLDNGTTSVGYMRLKEFNALARKDLVTAMKRLQDMGASYFILDLRDNLGGLVQAGIEI  338 (471)
Q Consensus       259 ~~~~v~l~r~~~~~~~v~~~~~~~~~~~~~igYi~i~sF~~~~~~~l~~~l~~l~~~~~~~LIIDLR~N~GG~~~~~~~l  338 (471)
                                 +....+.     ....+++||||+|++|+..+.+++++++++++++++++||||||+|+||++..+..+
T Consensus        94 -----------~~~~~~~-----~~~~~~~IGYi~i~~F~~~~~~~~~~~l~~l~~~~~~~lIiDLR~N~GG~~~~a~~~  157 (294)
T d1fc6a4          94 -----------VAAAALP-----PGAAKQQLGYVRLATFNSNTTAAAQQAFTELSKQGVAGLVLDIRNNGGGLFPAGVNV  157 (294)
T ss_dssp             -----------CCGGGSC-----TTCSSSCEEEEEECCBSTTHHHHHHHHHHHHHHTTCSEEEEECTTCCCBCHHHHHHH
T ss_pred             -----------ccccccc-----CCCCCCcEEEEEEcccCchhHHHHHHHHHHHHHCCCcEEEEEeecCcccchhhhHHH
Confidence                       0000000     012357999999999998888999999999999899999999999999999999999


Q ss_pred             HhhcccCCceEEEEeccCcccceeEecCCCCCCCCCEEEEECCCCCChHHHHHHHHhcCCCeEEEccCCCCCceeceEEE
Q 012084          339 AKLFLNEGETITYTVGRDPQYQKTIVADNSPLVTAPVIVLVNNRTASASEIVASALHDNCRAVLVGEKTFGKGLIQSVYE  418 (471)
Q Consensus       339 a~~f~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~pi~VLvd~~TaSaaE~fa~~lk~~~~a~vVGe~T~G~g~~~~~~~  418 (471)
                      +++|++++..+.+. .+...............+.+|++||||+.|+||||+||++||+++++++||++|+|++..+..+.
T Consensus       158 ~~~f~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~~a~~lk~~~~a~vvG~~T~G~g~~~~~~~  236 (294)
T d1fc6a4         158 ARMLVDRGDLVLIA-DSQGIRDIYSADGNSIDSATPLVVLVNRGTASASEVLAGALKDSKRGLIAGERTFGKGLIQTVVD  236 (294)
T ss_dssp             HHHHCSSSEEEEEE-ETTEEEEEEECCSCCSCSSSCEEEEECTTCCTHHHHHHHHHHHTTSEEEEESCCCCCCEEEEEEE
T ss_pred             HHhhcccccceEEE-EeccccceeccccccccccceEEEEecCCccchHHHHHHHhhhcCeEEEEeeeccCcceeeEEEE
Confidence            99999988655443 33332222223344556789999999999999999999999999999999999999999999999


Q ss_pred             CCCCCEEEEEEEEEEcCCCCcccCCcccCcEEcCCC-----hHHHHHHHhhccCC
Q 012084          419 LHDGSGVVVTIGKYVTPNHMDINGNGIEPDYRNLPA-----WNDVTKHLSQCTMH  468 (471)
Q Consensus       419 L~~g~~l~~t~~~~~~~~g~~~e~~GV~PDi~v~~t-----~~d~~~~l~~~~~~  468 (471)
                      |+||+.+++|+.++++|+|+.+|+.||+|||+|.++     .+...+.|..-..|
T Consensus       237 L~dG~~l~~t~~~~~~p~G~~~e~~Gv~PDi~v~~~~~~~d~~~~~~~l~~~~~p  291 (294)
T d1fc6a4         237 LSDGSGVAVTVARYQTPAGVDINKIGVSPDVQLDPEVLPTDLEGVCRVLGSDAAP  291 (294)
T ss_dssp             CTTSCEEEEEEEEEECTTSCBCTTTCCCCSEECCTTSSCSSHHHHHHHHHSTTCC
T ss_pred             eCCCCEEEEEeEEEECCCCCEeeCcccCCCeEECCccCchhhhccccccCCCCCC
Confidence            999999999999999999999999999999998644     44555556544444

PyMOL of d1fc6a4

>d1k32a4 c.14.1.2 (A:680-762,A:854-1061) Tricorn protease {Archaeon Thermoplasma acidophilum [TaxId: 2303]}	Back information, alignment and structure

>d1j7xa_ c.14.1.2 (A:) Interphotoreceptor retinoid-binding protein IRBP {African clawed frog (Xenopus laevis) [TaxId: 8355]}	Back information, alignment and structure

>d1fc6a3 b.36.1.3 (A:157-248) Photosystem II D1 C-terminal processing protease {Algae (Scenedesmus obliquus) [TaxId: 3088]}	Back information, alignment and structure

>d1k32a1 b.36.1.3 (A:763-853) Tricorn protease {Archaeon Thermoplasma acidophilum [TaxId: 2303]}	Back information, alignment and structure

>d2z9ia1 b.36.1.4 (A:227-314) Protease PepD {Mycobacterium tuberculosis [TaxId: 1773]}	Back information, alignment and structure

>d1w9ea1 b.36.1.1 (A:110-194) Syntenin 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1g9oa_ b.36.1.1 (A:) Na+/H+ exchanger regulatory factor, NHERF {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1m5za_ b.36.1.1 (A:) Glutamate receptor interacting protein {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d2f5ya1 b.36.1.1 (A:19-95) Regulator of G-protein signaling 3, RGS3 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1rgwa_ b.36.1.1 (A:) Zasp (Cypher, Oracle 1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2fe5a1 b.36.1.1 (A:223-314) Synapse-associated protein 102 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x5qa1 b.36.1.1 (A:8-104) Scribble (KIAA0147) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1qaua_ b.36.1.1 (A:) Neuronal nitric oxide synthase, NNOS {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1p1da2 b.36.1.1 (A:115-213) Glutamate receptor interacting protein {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1t2ma1 b.36.1.1 (A:2-93) Afadin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2fcfa1 b.36.1.1 (A:1148-1243) Multiple PDZ domain protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wifa_ b.36.1.1 (A:) hypothetical PDZ domain containing protein Uqcrc2 (4930408O21Rik) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1qava_ b.36.1.1 (A:) Syntrophin {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1ozia_ b.36.1.1 (A:) Phosphatase hPTP1e {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1lcya1 b.36.1.4 (A:226-325) Mitochondrial serine protease HtrA2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1vb7a_ b.36.1.1 (A:) PDZ-LIM protein mystique {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1ihja_ b.36.1.1 (A:) Inad {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1rgra_ b.36.1.1 (A:) Synaptic protein PSD-95 {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1wf8a1 b.36.1.1 (A:8-101) Neurabin-i {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1n7ea_ b.36.1.1 (A:) Glutamate receptor-interacting protein 1, GRIP1 {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d2f0aa1 b.36.1.1 (A:251-342) Segment polarity protein dishevelled homolog Dvl-2 {African clawed frog (Xenopus laevis) [TaxId: 8355]}	Back information, alignment and structure

>d1ujda_ b.36.1.1 (A:) Hypothetical protein KIAA0559 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1tp5a1 b.36.1.1 (A:302-403) Synaptic protein PSD-95 {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1ueqa_ b.36.1.1 (A:) Membrane associated guanylate kinase inverted-2 (MAGI-2, KIAA0705) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1r6ja_ b.36.1.1 (A:) Syntenin 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wi4a1 b.36.1.1 (A:8-103) Syntaxin binding protein 4 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1q3oa_ b.36.1.1 (A:) Shank1, PDZ domain {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1x45a1 b.36.1.1 (A:8-92) Amyloid beta A4 precursor protein-binding family A member 1 (APBA1, X11) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1vaea_ b.36.1.1 (A:) Rhophilin-2 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2i6va1 b.36.1.5 (A:219-305) General secretion pathway protein C, EpsC {Vibrio cholerae [TaxId: 666]}	Back information, alignment and structure

>d1uita_ b.36.1.1 (A:) Discs large 5 protein KIAA0583 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wi2a_ b.36.1.1 (A:) PDZ domain containing protein 11, Pdzk11 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1kwaa_ b.36.1.1 (A:) Cask/Lin-2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1uepa_ b.36.1.1 (A:) Membrane associated guanylate kinase inverted-2 (MAGI-2, KIAA0705) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1y7na1 b.36.1.1 (A:12-90) Amyloid beta A4 precursor protein-binding family A member 1 (APBA1, X11) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ky9b2 b.36.1.4 (B:359-446) Protease Do (DegP, HtrA), C-terminal domains {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1whaa_ b.36.1.1 (A:) Scribble (KIAA0147) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1va8a1 b.36.1.1 (A:8-107) Maguk p55 subfamily member 5 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1ueza_ b.36.1.1 (A:) KIAA1526 protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wf7a_ b.36.1.1 (A:) Enigma homolog ENH {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1sota1 b.36.1.4 (A:255-353) Stress sensor protease DegS, C-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1uf1a_ b.36.1.1 (A:) KIAA1526 protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1um1a_ b.36.1.1 (A:) Hypothetical protein KIAA1849 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cssa1 b.36.1.1 (A:8-115) Regulating synaptic membrane exocytosis protein 1, RIMS1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1uhpa_ b.36.1.1 (A:) Hypothetical protein KIAA1095 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cs5a1 b.36.1.1 (A:8-113) Tyrosine-protein phosphatase non-receptor type 4, PTPN4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1v5la_ b.36.1.1 (A:) Alpha-actinin-2 associated LIM protein {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x5na1 b.36.1.1 (A:8-108) Harmonin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1i16a_ b.36.1.2 (A:) Interleukin 16 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2fnea1 b.36.1.1 (A:1955-2042) Multiple PDZ domain protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ky9a1 b.36.1.4 (A:260-353) Protease Do (DegP, HtrA), C-terminal domains {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1ujua_ b.36.1.1 (A:) Scribble (KIAA0147) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wg6a_ b.36.1.1 (A:) Partitioning-defective 3-like protein, PAR3-L (RIKEN cDNA 2810455b10) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1v62a_ b.36.1.1 (A:) Glutamate receptor interacting protein 2, GRIP2 (KIAA1719) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2hgaa1 b.36.1.6 (A:23-125) Uncharacterized protein MTH1368 {Methanobacterium thermoautotrophicum [TaxId: 145262]}	Back information, alignment and structure

>d1wfva_ b.36.1.1 (A:) Membrane associated guanylate kinase inverted-2 (MAGI-2, KIAA0705) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1rzxa_ b.36.1.1 (A:) GTPase-binding domain of the cell polarity protein par6 (Par-6B) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1uewa_ b.36.1.1 (A:) Membrane associated guanylate kinase inverted-2 (MAGI-2, KIAA0705) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x6da1 b.36.1.2 (A:8-114) Interleukin 16 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2csja1 b.36.1.1 (A:8-111) Tight junction protein ZO-2, Tjp2 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1wh1a_ b.36.1.1 (A:) Hypothetical protein KIAA1095 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1v6ba_ b.36.1.1 (A:) Harmonin {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2h3la1 b.36.1.1 (A:1310-1412) Erbin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ufxa_ b.36.1.1 (A:) KIAA1526 protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x5ra1 b.36.1.1 (A:8-106) Glutamate receptor interacting protein 2, GRIP2 (KIAA1719) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1v5qa_ b.36.1.1 (A:) Glutamate receptor interacting protein {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1ujva_ b.36.1.1 (A:) Membrane associated guanylate kinase inverted-2 (MAGI-2, KIAA0705) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure