Citrus Sinensis ID: 030210

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-
Protein Sequence
MVFFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDMLSSPKESLLKNKSSVSSLEADSCIMVAEHELDVQESRGTAS
Secondary Structure (PSIPRED)
ccccccccccccccccHHHHHHHHHHHHcccccEEEEccccccEEEEEcccccccccccEEEEEccccccHHHHHHHHHHccccEEEEccccccccEEEEEEEcccccEEEEEEEEEEcccccccccccccccEEEcccccccHHHHHHccccccccccccHHHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccHHHHHHHHHHHHHHccccEEEEEEccccccEEEEcccccccccccEEEEEccccccHHHHHHHHHHHccccEEEEcccccccEEEEEEEcccccEEEEEEEEEEcccccEHHHHcccccEEcccccccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
mvffsppslsifqgglvkAGLDVAQIWLDGDETLVNAvdreghtlpinmvdghaithdPLVVLVNEGSASASEILAGALHDNGRAILVghktfgkgkiqsvtelhdgSALFVTVAKYlspalhdidhvgitpdvqcttdmlsspkesllknkssvssleadsciMVAEHELdvqesrgtas
Flexible Loop (DISEMBL)
mvffsppslSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDMLSSPKESLLKNKSSVSSLEADSCIMVAEHeldvqesrgtas
Low Complexity Region (SEG)
MVFFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDMLSSPkesllknkssvsslEADSCIMVAEHELDVQESRGTAS
Disordered region (IsUnstruct)
********LSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTT*******************************************
Disordered Region (DISOPRED)
***FSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVD**************AITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTD******************************************
Disordered Region (DISEMBL)
MVFFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDMLSSPK*************EADSCIMVAEHEL**********
Disordered Region (DISPRO)
*VFFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDMLSSPKESLLKNKSSVSSLEADSCIMVAEHELDV********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVFFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDMLSSPKESLLKNKSSVSSLEADSCIMVAEHELDVQESRGTAS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	181	2.2.26 [Sep-21-2011]
P42784	414	Carboxyl-terminal-process	yes	no	0.651	0.285	0.591	2e-32
Q55669	427	Carboxyl-terminal-process	N/A	no	0.651	0.276	0.591	2e-31
O04073	464	C-terminal processing pep	N/A	no	0.740	0.288	0.474	8e-26
Q44879	434	Carboxy-terminal-processi	yes	no	0.696	0.290	0.365	1e-17
Q4L6D0	496	Probable CtpA-like serine	yes	no	0.712	0.260	0.401	1e-17
Q49XN1	491	Probable CtpA-like serine	yes	no	0.668	0.246	0.412	3e-17
Q6GGY8	496	Probable CtpA-like serine	yes	no	0.712	0.260	0.409	4e-16
Q5HG01	496	Probable CtpA-like serine	yes	no	0.712	0.260	0.409	4e-16
Q8NWR2	496	Probable CtpA-like serine	yes	no	0.712	0.260	0.409	5e-16
Q6G9E1	496	Probable CtpA-like serine	yes	no	0.712	0.260	0.409	5e-16

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

 Score =  138 bits (348), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 71/120 (59%), Positives = 92/120 (76%), Gaps = 2/120 (1%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGL++AG+++A++WLD  ET+V  V+R+G     + V G  +T  PLVVLVN+ +ASASE
Sbjct: 256 GGLLQAGIEIARLWLD-QETIVYTVNRQGIFESYSAV-GQPLTDAPLVVLVNQATASASE 313

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           ILAGAL DNGRA+LVG KTFGKG IQS+ EL DG+ + VTVAKY +P  HDI+ +GI PD
Sbjct: 314 ILAGALQDNGRAMLVGEKTFGKGLIQSLFELPDGAGMAVTVAKYETPLHHDINKLGIMPD 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

 Score =  135 bits (339), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 71/120 (59%), Positives = 89/120 (74%), Gaps = 2/120 (1%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGL++AG+D+A++WL  + T+V  V+R+G T      +G A T  PLVVLVN+G+ASASE
Sbjct: 259 GGLLQAGIDIARLWLP-ESTIVYTVNRQG-TQESFTANGEAATDRPLVVLVNQGTASASE 316

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           ILAGAL DN RA LVG KTFGKG IQS+ EL DG+ + VTVAKY +P  HDI  +GI PD
Sbjct: 317 ILAGALQDNQRATLVGEKTFGKGLIQSLFELSDGAGIAVTVAKYETPQHHDIHKLGIMPD 376

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.

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

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 1

EC: 0

EC: 2

>sp|O04073|CTPA_SCEOB C-terminal processing peptidase, chloroplastic OS=Scenedesmus obliquus GN=ctpA PE=1 SV=1

 Score =  116 bits (290), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 66/139 (47%), Positives = 96/139 (69%), Gaps = 5/139 (3%)

Query: 14  GGLVKAGLDVAQIWLD-GDETLVNAVDREGHTLPINMVDGHAI-THDPLVVLVNEGSASA 71
           GGL  AG++VA++ +D GD  L+   D +G    I   DG++I +  PLVVLVN G+ASA
Sbjct: 317 GGLFPAGVNVARMLVDRGDLVLI--ADSQG-IRDIYSADGNSIDSATPLVVLVNRGTASA 373

Query: 72  SEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGIT 131
           SE+LAGAL D+ R ++ G +TFGKG IQ+V +L DGS + VTVA+Y +PA  DI+ +G++
Sbjct: 374 SEVLAGALKDSKRGLIAGERTFGKGLIQTVVDLSDGSGVAVTVARYQTPAGVDINKIGVS 433

Query: 132 PDVQCTTDMLSSPKESLLK 150
           PDVQ   ++L +  E + +
Sbjct: 434 PDVQLDPEVLPTDLEGVCR 452

Protease involved in the C-terminal processing of the chloroplastic D1 protein of photosystem II. This proteolytic processing is necessary to allow the light-driven assembly of the tetranuclear manganese cluster, which is responsible for photosynthetic water oxidation.

Scenedesmus obliquus (taxid: 3088)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 1

EC: 0

EC: 2

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

 Score = 89.4 bits (220), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 46/126 (36%), Positives = 74/126 (58%)

Query: 9   LSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGS 68
           L +  GGL+   + V   +L+  E +     ++   +  +   G      P++VL+N GS
Sbjct: 233 LRLNPGGLLDQAISVTDAFLNKGEIVSTRGRKQNDVMRFDAKLGDLTDEKPIIVLINGGS 292

Query: 69  ASASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHV 128
           ASASEI+AGAL D+ RA ++G ++FGKG +Q++  L +  AL +T A Y +P+   I  +
Sbjct: 293 ASASEIVAGALQDHRRATIIGTQSFGKGSVQTIIPLGENGALRLTTALYYTPSGTSIQGI 352

Query: 129 GITPDV 134
           GITPD+
Sbjct: 353 GITPDI 358

Involved in protection of the bacterium from thermal and osmotic stresses.

Bartonella bacilliformis (strain ATCC 35685 / KC583) (taxid: 360095)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 1

EC: 0

EC: 2

>sp|Q4L6D0|CTPAL_STAHJ Probable CtpA-like serine protease OS=Staphylococcus haemolyticus (strain JCSC1435) GN=SH1486 PE=3 SV=2

 Score = 89.0 bits (219), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 53/132 (40%), Positives = 76/132 (57%), Gaps = 3/132 (2%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMV-DGHAITHDPLV-VLVNEGSASA 71
           GGL+   + +A I++D D+T+V  +++   T  I    D      D  V +LVNEGSASA
Sbjct: 272 GGLLDEAVKMANIFIDKDQTVV-KLEKGDDTESIKTSNDASNEAKDMKVSILVNEGSASA 330

Query: 72  SEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGIT 131
           SE+  GA+ D+ +A + G KTFGKG +Q+  E  DGS L  T  K+L+P  H+I   GI 
Sbjct: 331 SEVFTGAMRDHKKAKVYGSKTFGKGIVQTTREFKDGSLLKYTQMKWLTPDGHNIHGKGIQ 390

Query: 132 PDVQCTTDMLSS 143
           PD +  +    S
Sbjct: 391 PDTKIASPQYQS 402

Staphylococcus haemolyticus (strain JCSC1435) (taxid: 279808)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

>sp|Q49XN1|CTPAL_STAS1 Probable CtpA-like serine protease OS=Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229) GN=SSP1319 PE=3 SV=1

 Score = 88.2 bits (217), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 52/126 (41%), Positives = 74/126 (58%), Gaps = 5/126 (3%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPI---NMVDGHAITHDPLVVLVNEGSAS 70
           GGL+   + +A I++D +ET+V  +++  H   I   N     A   D + +LVN+GSAS
Sbjct: 267 GGLLDEAVKMANIFIDKNETVV-QLEKGKHKEAIKASNDASKEAKDMD-VSILVNKGSAS 324

Query: 71  ASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGI 130
           ASE+  GA+ D  +A + G KTFGKG +Q+  E  DGS L  T  K+L+P  H I   GI
Sbjct: 325 ASEVFTGAMKDYNKAKVYGSKTFGKGIVQTTREFEDGSLLKFTNMKWLTPKSHYIHGKGI 384

Query: 131 TPDVQC 136
           TPD + 
Sbjct: 385 TPDKKI 390

Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229) (taxid: 342451)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

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

 Score = 84.3 bits (207), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 54/132 (40%), Positives = 73/132 (55%), Gaps = 3/132 (2%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMV-DGHAITHD-PLVVLVNEGSASA 71
           GGL+   + +A I++D  +T+V  +++   T  I    D      D  + +LVNEGSASA
Sbjct: 272 GGLLDEAVKMANIFIDKGKTVV-KLEKGKDTEAIQTSNDALKEAKDMDISILVNEGSASA 330

Query: 72  SEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGIT 131
           SE+  GAL D  +A + G KTFGKG +Q+  E  DGS L  T  K+L+P  H I   GI 
Sbjct: 331 SEVFTGALKDYNKAKVYGSKTFGKGVVQTTREFKDGSLLKYTEMKWLTPDGHYIHGKGIK 390

Query: 132 PDVQCTTDMLSS 143
           PDV   T    S
Sbjct: 391 PDVTIDTPKYQS 402

Staphylococcus aureus (strain MRSA252) (taxid: 282458)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

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

 Score = 84.3 bits (207), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 54/132 (40%), Positives = 73/132 (55%), Gaps = 3/132 (2%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMV-DGHAITHD-PLVVLVNEGSASA 71
           GGL+   + +A I++D  +T+V  +++   T  I    D      D  + +LVNEGSASA
Sbjct: 272 GGLLDEAVKMANIFIDKGKTVV-KLEKGKDTEAIQTSNDALKEAKDMDISILVNEGSASA 330

Query: 72  SEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGIT 131
           SE+  GAL D  +A + G KTFGKG +Q+  E  DGS L  T  K+L+P  H I   GI 
Sbjct: 331 SEVFTGALKDYNKAKVYGSKTFGKGVVQTTREFKDGSLLKYTEMKWLTPDGHYIHGKGIK 390

Query: 132 PDVQCTTDMLSS 143
           PDV   T    S
Sbjct: 391 PDVTIDTPKYQS 402

Staphylococcus aureus (strain COL) (taxid: 93062)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

>sp|Q8NWR2|CTPAL_STAAW Probable CtpA-like serine protease OS=Staphylococcus aureus (strain MW2) GN=MW1310 PE=3 SV=1

 Score = 84.0 bits (206), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 54/132 (40%), Positives = 73/132 (55%), Gaps = 3/132 (2%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMV-DGHAITHD-PLVVLVNEGSASA 71
           GGL+   + +A I++D  +T+V  +++   T  I    D      D  + +LVNEGSASA
Sbjct: 272 GGLLDEAVKMANIFIDKGKTVV-KLEKGKDTEAIQTSNDALKEAKDMDISILVNEGSASA 330

Query: 72  SEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGIT 131
           SE+  GAL D  +A + G KTFGKG +Q+  E  DGS L  T  K+L+P  H I   GI 
Sbjct: 331 SEVFTGALKDYNKAKVYGSKTFGKGVVQTTREFKDGSLLKYTEMKWLTPDGHYIHGKGIK 390

Query: 132 PDVQCTTDMLSS 143
           PDV   T    S
Sbjct: 391 PDVTIDTPKYQS 402

Staphylococcus aureus (strain MW2) (taxid: 196620)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

>sp|Q6G9E1|CTPAL_STAAS Probable CtpA-like serine protease OS=Staphylococcus aureus (strain MSSA476) GN=SAS1363 PE=3 SV=1

 Score = 84.0 bits (206), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 54/132 (40%), Positives = 73/132 (55%), Gaps = 3/132 (2%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMV-DGHAITHD-PLVVLVNEGSASA 71
           GGL+   + +A I++D  +T+V  +++   T  I    D      D  + +LVNEGSASA
Sbjct: 272 GGLLDEAVKMANIFIDKGKTVV-KLEKGKDTEAIQTSNDALKEAKDMDISILVNEGSASA 330

Query: 72  SEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGIT 131
           SE+  GAL D  +A + G KTFGKG +Q+  E  DGS L  T  K+L+P  H I   GI 
Sbjct: 331 SEVFTGALKDYNKAKVYGSKTFGKGVVQTTREFKDGSLLKYTEMKWLTPDGHYIHGKGIK 390

Query: 132 PDVQCTTDMLSS 143
           PDV   T    S
Sbjct: 391 PDVTIDTPKYQS 402

Staphylococcus aureus (strain MSSA476) (taxid: 282459)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: -

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	181
255571580	414	protease, putative [Ricinus communis] gi	0.928	0.405	0.904	4e-84
359481833	520	PREDICTED: carboxyl-terminal-processing	0.928	0.323	0.916	1e-83
297739701	431	unnamed protein product [Vitis vinifera]	0.928	0.389	0.916	1e-83
224087066	192	predicted protein [Populus trichocarpa]	0.928	0.875	0.904	6e-83
449453838	511	PREDICTED: carboxyl-terminal-processing	0.928	0.328	0.845	1e-78
356534629	508	PREDICTED: carboxyl-terminal-processing	0.928	0.330	0.858	3e-78
413953829	491	hypothetical protein ZEAMMB73_760342 [Ze	0.950	0.350	0.767	2e-74
223948537	509	unknown [Zea mays]	0.928	0.330	0.773	6e-73
226493045	520	carboxyl-terminal-processing protease [Z	0.928	0.323	0.773	6e-73
413953827	520	carboxyl-terminal-processing protease is	0.928	0.323	0.773	8e-73

>gi|255571580|ref|XP_002526736.1| protease, putative [Ricinus communis] gi|223533925|gb|EEF35650.1| protease, putative [Ricinus communis]

 Score =  315 bits (808), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 152/168 (90%), Positives = 162/168 (96%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGLVKAGLDVAQIWLDGDETLVN +DREG+ LPINMV+GHAITHDPLVVL+NEGSASASE
Sbjct: 247 GGLVKAGLDVAQIWLDGDETLVNTIDREGNMLPINMVNGHAITHDPLVVLINEGSASASE 306

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDID VGI PD
Sbjct: 307 ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDQVGIMPD 366

Query: 134 VQCTTDMLSSPKESLLKNKSSVSSLEADSCIMVAEHELDVQESRGTAS 181
           VQCT DMLSSP++SLLKNKSS S+LEADSCIM+AEHELD+QES+GTAS
Sbjct: 367 VQCTADMLSSPRDSLLKNKSSASTLEADSCIMIAEHELDIQESKGTAS 414

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359481833|ref|XP_002277512.2| PREDICTED: carboxyl-terminal-processing protease-like [Vitis vinifera]

 Score =  314 bits (804), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 154/168 (91%), Positives = 161/168 (95%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGLVK GLDVAQIWLDGDETLVN +DR+G+ LPINMVDGHAIT DPLVVLVNEGSASASE
Sbjct: 353 GGLVKVGLDVAQIWLDGDETLVNTIDRDGNMLPINMVDGHAITRDPLVVLVNEGSASASE 412

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDID VGITPD
Sbjct: 413 ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDQVGITPD 472

Query: 134 VQCTTDMLSSPKESLLKNKSSVSSLEADSCIMVAEHELDVQESRGTAS 181
           VQC+T+MLSSPKESLLK+KSS SSLEADSCIMVAEHELDVQES+GT S
Sbjct: 473 VQCSTEMLSSPKESLLKDKSSASSLEADSCIMVAEHELDVQESKGTPS 520

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297739701|emb|CBI29883.3| unnamed protein product [Vitis vinifera]

 Score =  313 bits (803), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 154/168 (91%), Positives = 161/168 (95%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGLVK GLDVAQIWLDGDETLVN +DR+G+ LPINMVDGHAIT DPLVVLVNEGSASASE
Sbjct: 264 GGLVKVGLDVAQIWLDGDETLVNTIDRDGNMLPINMVDGHAITRDPLVVLVNEGSASASE 323

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDID VGITPD
Sbjct: 324 ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDQVGITPD 383

Query: 134 VQCTTDMLSSPKESLLKNKSSVSSLEADSCIMVAEHELDVQESRGTAS 181
           VQC+T+MLSSPKESLLK+KSS SSLEADSCIMVAEHELDVQES+GT S
Sbjct: 384 VQCSTEMLSSPKESLLKDKSSASSLEADSCIMVAEHELDVQESKGTPS 431

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224087066|ref|XP_002308051.1| predicted protein [Populus trichocarpa] gi|222854027|gb|EEE91574.1| predicted protein [Populus trichocarpa]

 Score =  311 bits (798), Expect = 6e-83,   Method: Compositional matrix adjust.
 Identities = 152/168 (90%), Positives = 161/168 (95%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGLVKAGLDVAQIWLDGDETLVN +DR+G+ LPINMVDGHAITHDPLVVLVNEGSASASE
Sbjct: 25  GGLVKAGLDVAQIWLDGDETLVNTIDRDGNMLPINMVDGHAITHDPLVVLVNEGSASASE 84

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDID VGI PD
Sbjct: 85  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDQVGIMPD 144

Query: 134 VQCTTDMLSSPKESLLKNKSSVSSLEADSCIMVAEHELDVQESRGTAS 181
           VQCTTDML+SP++SLLKN+SS SSLE DSCI+VAEHELD+QES GTAS
Sbjct: 145 VQCTTDMLNSPRDSLLKNESSTSSLEGDSCILVAEHELDIQESGGTAS 192

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449453838|ref|XP_004144663.1| PREDICTED: carboxyl-terminal-processing protease-like [Cucumis sativus] gi|449480092|ref|XP_004155797.1| PREDICTED: carboxyl-terminal-processing protease-like [Cucumis sativus]

 Score =  297 bits (760), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 142/168 (84%), Positives = 155/168 (92%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGLVKAGL+VAQIWLDGDETLVN +DR+G+  PINM+DGHAITHDPLVVLVNEGSASASE
Sbjct: 344 GGLVKAGLEVAQIWLDGDETLVNTIDRDGNMSPINMIDGHAITHDPLVVLVNEGSASASE 403

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           ILAGALHDNGRA LVGHKTFGKGKIQSVTELHDGSALF+TVAKYLSPA H+ID VGI PD
Sbjct: 404 ILAGALHDNGRATLVGHKTFGKGKIQSVTELHDGSALFITVAKYLSPARHEIDQVGIVPD 463

Query: 134 VQCTTDMLSSPKESLLKNKSSVSSLEADSCIMVAEHELDVQESRGTAS 181
           +QCT D L+SPKE L KNKSS S LEADSCIM+AEHELD+Q+S+GTAS
Sbjct: 464 IQCTADALNSPKEILGKNKSSASPLEADSCIMIAEHELDIQQSKGTAS 511

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356534629|ref|XP_003535855.1| PREDICTED: carboxyl-terminal-processing protease-like [Glycine max]

 Score =  296 bits (758), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 146/170 (85%), Positives = 161/170 (94%), Gaps = 2/170 (1%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGLVKAGLDVAQ+WLDG+ETLVN +DR+G+ LPINMVDGHAITHDPLVV+VNEGSASASE
Sbjct: 339 GGLVKAGLDVAQMWLDGNETLVNTIDRDGNMLPINMVDGHAITHDPLVVIVNEGSASASE 398

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           ILAGALHDNGRAILVGHKTFGKGKIQSVT+LHDGSALFVTVAKYLSPALHDID VGITPD
Sbjct: 399 ILAGALHDNGRAILVGHKTFGKGKIQSVTQLHDGSALFVTVAKYLSPALHDIDQVGITPD 458

Query: 134 VQCTTDMLSSPKE--SLLKNKSSVSSLEADSCIMVAEHELDVQESRGTAS 181
           VQCTT+ML+S K+  +  K+K+SVSSLEADSCIMVAEHELD++ES GTAS
Sbjct: 459 VQCTTEMLNSTKDISNSTKDKASVSSLEADSCIMVAEHELDLEESMGTAS 508

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413953829|gb|AFW86478.1| hypothetical protein ZEAMMB73_760342 [Zea mays]

 Score =  283 bits (724), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 132/172 (76%), Positives = 154/172 (89%)

Query: 10  SIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSA 69
           S +QGGLVKAGLDVAQIWLDGDETLVN +DREG+ LPINM+ GH++THDPLVVLVNEGSA
Sbjct: 320 SFYQGGLVKAGLDVAQIWLDGDETLVNTIDREGNVLPINMIQGHSLTHDPLVVLVNEGSA 379

Query: 70  SASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVG 129
           SASEILAGALHDNGRAILVGH+TFGKGKIQSVTEL DGSALF+TVAKYLSPALH+ID VG
Sbjct: 380 SASEILAGALHDNGRAILVGHRTFGKGKIQSVTELDDGSALFITVAKYLSPALHEIDQVG 439

Query: 130 ITPDVQCTTDMLSSPKESLLKNKSSVSSLEADSCIMVAEHELDVQESRGTAS 181
           I PD+QC+ D+LS P+   L+  S+ ++LE DSCIMVAE  L++Q+S+G+AS
Sbjct: 440 IQPDIQCSPDILSLPRAPSLRENSNATNLEMDSCIMVAEQALEIQQSKGSAS 491

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|223948537|gb|ACN28352.1| unknown [Zea mays]

 Score =  278 bits (711), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 130/168 (77%), Positives = 151/168 (89%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGLVKAGLDVAQIWLDGDETLVN +DREG+ LPINM+ GH++THDPLVVLVNEGSASASE
Sbjct: 342 GGLVKAGLDVAQIWLDGDETLVNTIDREGNVLPINMIQGHSLTHDPLVVLVNEGSASASE 401

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           ILAGALHDNGRAILVGH+TFGKGKIQSVTEL DGSALF+TVAKYLSPALH+ID VGI PD
Sbjct: 402 ILAGALHDNGRAILVGHRTFGKGKIQSVTELDDGSALFITVAKYLSPALHEIDQVGIQPD 461

Query: 134 VQCTTDMLSSPKESLLKNKSSVSSLEADSCIMVAEHELDVQESRGTAS 181
           +QC+ D+LS P+   L+  S+ ++LE DSCIMVAE  L++Q+S+G+AS
Sbjct: 462 IQCSPDILSLPRAPSLRENSNATNLEMDSCIMVAEQALEIQQSKGSAS 509

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226493045|ref|NP_001148747.1| carboxyl-terminal-processing protease [Zea mays] gi|195621830|gb|ACG32745.1| carboxyl-terminal-processing protease precursor [Zea mays]

 Score =  278 bits (711), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 130/168 (77%), Positives = 151/168 (89%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGLVKAGLDVAQIWLDGDETLVN +DREG+ LPINM+ GH++THDPLVVLVNEGSASASE
Sbjct: 353 GGLVKAGLDVAQIWLDGDETLVNTIDREGNVLPINMIQGHSLTHDPLVVLVNEGSASASE 412

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           ILAGALHDNGRAILVGH+TFGKGKIQSVTEL DGSALF+TVAKYLSPALH+ID VGI PD
Sbjct: 413 ILAGALHDNGRAILVGHRTFGKGKIQSVTELDDGSALFITVAKYLSPALHEIDQVGIQPD 472

Query: 134 VQCTTDMLSSPKESLLKNKSSVSSLEADSCIMVAEHELDVQESRGTAS 181
           +QC+ D+LS P+   L+  S+ ++LE DSCIMVAE  L++Q+S+G+AS
Sbjct: 473 IQCSPDILSLPRAPSLRENSNATNLEMDSCIMVAEQALEIQQSKGSAS 520

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413953827|gb|AFW86476.1| carboxyl-terminal-processing protease isoform 1 [Zea mays] gi|413953828|gb|AFW86477.1| carboxyl-terminal-processing protease isoform 2 [Zea mays]

 Score =  278 bits (710), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 130/168 (77%), Positives = 151/168 (89%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGLVKAGLDVAQIWLDGDETLVN +DREG+ LPINM+ GH++THDPLVVLVNEGSASASE
Sbjct: 353 GGLVKAGLDVAQIWLDGDETLVNTIDREGNVLPINMIQGHSLTHDPLVVLVNEGSASASE 412

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           ILAGALHDNGRAILVGH+TFGKGKIQSVTEL DGSALF+TVAKYLSPALH+ID VGI PD
Sbjct: 413 ILAGALHDNGRAILVGHRTFGKGKIQSVTELDDGSALFITVAKYLSPALHEIDQVGIQPD 472

Query: 134 VQCTTDMLSSPKESLLKNKSSVSSLEADSCIMVAEHELDVQESRGTAS 181
           +QC+ D+LS P+   L+  S+ ++LE DSCIMVAE  L++Q+S+G+AS
Sbjct: 473 IQCSPDILSLPRAPSLRENSNATNLEMDSCIMVAEQALEIQQSKGSAS 520

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	181
UNIPROTKB|P73458	423	prc "Carboxyl-terminal proteas	0.662	0.283	0.532	2.2e-27
TAIR|locus:2129411	515	AT4G17740 [Arabidopsis thalian	0.651	0.229	0.565	5e-26
UNIPROTKB|P75023	462	ctpB "Carboxyl-terminal protea	0.657	0.257	0.512	5.7e-26
TAIR|locus:2170443	489	AT5G46390 [Arabidopsis thalian	0.662	0.245	0.475	5.1e-24
TIGR_CMR|CHY_0170	377	CHY_0170 "carboxyl-terminal pr	0.657	0.315	0.479	2.4e-20
TIGR_CMR|SPO_3812	443	SPO_3812 "carboxyl-terminal pr	0.662	0.270	0.418	9.4e-18
TIGR_CMR|GSU_1772	443	GSU_1772 "carboxy-terminal pro	0.662	0.270	0.401	4.3e-17
TIGR_CMR|CBU_1538	456	CBU_1538 "carboxyl-terminal pr	0.723	0.287	0.391	6e-17
TIGR_CMR|GSU_0969	450	GSU_0969 "carboxy-terminal pro	0.668	0.268	0.416	7.4e-17
TIGR_CMR|SO_0047	402	SO_0047 "carboxyl-terminal pro	0.668	0.300	0.371	3.1e-16

UNIPROTKB|P73458 prc "Carboxyl-terminal protease" [Synechocystis sp. PCC 6803 substr. Kazusa (taxid:1111708)]

 Score = 307 (113.1 bits), Expect = 2.2e-27, P = 2.2e-27
 Identities = 65/122 (53%), Positives = 89/122 (72%)

Query:    14 GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
             GGL+ + +D+A+IWLD +  +V+ VDR G  +     +   +++ PLVVLV+ GSASASE
Sbjct:   261 GGLLYSSVDIARIWLD-EGGIVSTVDRRGE-VEQQSANKRQLSNRPLVVLVDGGSASASE 318

Query:    74 ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
             I++GAL DN RA++VG KTFGKG +QSV EL DGS + VT+AKYL+P   DI+  GI PD
Sbjct:   319 IVSGALQDNQRAVIVGTKTFGKGLVQSVRELGDGSGMAVTIAKYLTPNGRDINKHGIDPD 378

Query:   134 VQ 135
             V+
Sbjct:   379 VE 380

GO:0030288 "outer membrane-bounded periplasmic space" evidence=IDA

TAIR|locus:2129411 AT4G17740 [Arabidopsis thaliana (taxid:3702)]

 Score = 299 (110.3 bits), Expect = 5.0e-26, P = 5.0e-26
 Identities = 69/122 (56%), Positives = 84/122 (68%)

Query:    14 GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDG-HAI-THDPLVVLVNEGSASA 71
             GG    G+++A+ WLD    +V   D  G    I   DG +AI T +PL VLVN+G+ASA
Sbjct:   361 GGSFPEGIEIAKFWLDKG-VIVYICDSRG-VRDIYDTDGSNAIATSEPLAVLVNKGTASA 418

Query:    72 SEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGIT 131
             SEILAGAL DN RA++ G  T+GKGKIQSV EL DGS L VTVA+Y +PA  DID VG+T
Sbjct:   419 SEILAGALKDNKRALVYGEPTYGKGKIQSVFELSDGSGLAVTVARYETPAHTDIDKVGVT 478

Query:   132 PD 133
             PD
Sbjct:   479 PD 480

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:0005739 "mitochondrion" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0006655 "phosphatidylglycerol biosynthetic process" evidence=RCA

UNIPROTKB|P75023 ctpB "Carboxyl-terminal protease" [Synechocystis sp. PCC 6803 substr. Kazusa (taxid:1111708)]

 Score = 296 (109.3 bits), Expect = 5.7e-26, P = 5.7e-26
 Identities = 62/121 (51%), Positives = 86/121 (71%)

Query:    14 GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
             GGL+ + +D+A++WL+  E +V+ +DR G     +  +G ++T  PLVVLVNE SASASE
Sbjct:   285 GGLLLSSIDIARLWLNRGE-IVSTIDRRGGDRHFS-ANGRSLTDLPLVVLVNERSASASE 342

Query:    74 ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
             ILAGAL + GRA +VG  T+GKG +QSV  L DGS L VT+A+Y  P+  DI+  GI+PD
Sbjct:   343 ILAGALKEQGRATVVGTATYGKGTVQSVNTLSDGSGLAVTIARYYPPSGTDINRKGISPD 402

Query:   134 V 134
             +
Sbjct:   403 I 403

GO:0030288 "outer membrane-bounded periplasmic space" evidence=IDA

TAIR|locus:2170443 AT5G46390 [Arabidopsis thaliana (taxid:3702)]

 Score = 280 (103.6 bits), Expect = 5.1e-24, P = 5.1e-24
 Identities = 57/120 (47%), Positives = 82/120 (68%)

Query:    14 GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
             GGLV+AG++ A+++LD  +T++    R+       + D   +   PL+V+VN  +ASASE
Sbjct:   347 GGLVQAGIETAKLFLDEGDTVIYTAGRDPEAQKTVVSDKKPLITAPLIVMVNNRTASASE 406

Query:    74 ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
             I+A ALHDN +A+LVG +T+GKG IQSV EL DGS + VT+ KY++P   DI+  GI PD
Sbjct:   407 IVASALHDNCKAVLVGERTYGKGLIQSVYELRDGSGVVVTIGKYVTPNHMDINGGGIEPD 466

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

TIGR_CMR|CHY_0170 CHY_0170 "carboxyl-terminal protease" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 242 (90.2 bits), Expect = 2.4e-20, P = 2.4e-20
 Identities = 58/121 (47%), Positives = 78/121 (64%)

Query:    14 GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
             GG +KA +++A I++   +T+V  VD           +   +   P+VVLVN GSASASE
Sbjct:   233 GGELKAAVEIADIFVPRGKTIVY-VDYRNQPDEEEKAEVPELGI-PVVVLVNGGSASASE 290

Query:    74 ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
             I+AGAL D G A+LVG KTFGKG +QS+  L   + L +TVA+YL+P  HDI+  GI PD
Sbjct:   291 IVAGALKDWGVAVLVGEKTFGKGVVQSIFRLPGNAGLKLTVARYLTPKKHDINKKGIMPD 350

Query:   134 V 134
             V
Sbjct:   351 V 351

GO:0006508 "proteolysis" evidence=ISS

TIGR_CMR|SPO_3812 SPO_3812 "carboxyl-terminal protease family protein" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 222 (83.2 bits), Expect = 9.4e-18, P = 9.4e-18
 Identities = 51/122 (41%), Positives = 74/122 (60%)

Query:    14 GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLP-INMVDGHAITHDPLVVLVNEGSASAS 72
             GGL+   + V+  +LD  E +V+   R        N   G      P+VVL+N GSASAS
Sbjct:   243 GGLLTQAIKVSDAFLDSGE-IVSTRGRNPEDGERFNATLGDLAQGKPVVVLINGGSASAS 301

Query:    73 EILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITP 132
             EI+AGAL D+ RAI+VG K+FGKG +Q+V  L    A+ +T A+Y +P+   I  +G++P
Sbjct:   302 EIVAGALQDHRRAIVVGTKSFGKGSVQTVMPLRGDGAMRLTTARYYTPSGRSIQALGVSP 361

Query:   133 DV 134
             D+
Sbjct:   362 DI 363

GO:0006508 "proteolysis" evidence=ISS

GO:0008233 "peptidase activity" evidence=ISS

TIGR_CMR|GSU_1772 GSU_1772 "carboxy-terminal processing protease" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 216 (81.1 bits), Expect = 4.3e-17, P = 4.3e-17
 Identities = 49/122 (40%), Positives = 75/122 (61%)

Query:    14 GGLVKAGLDVAQIWLDGDETLVNAVDREGHT-LPINMVDGHAITHDPLVVLVNEGSASAS 72
             GGL+   + VA  +++ D  +V    RE  + +           + P+VVL+N GSASAS
Sbjct:   244 GGLLDQAVKVADHFVE-DGLIVYTEGREKESRMQFTARKSGTEPNYPMVVLINSGSASAS 302

Query:    73 EILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITP 132
             EI+AGAL D+ RA+++G ++FGKG +Q++  L D S L +T A+Y +P+   I   GITP
Sbjct:   303 EIVAGALQDHKRAVVMGTQSFGKGSVQTIIPLSDESGLRLTTARYFTPSGRSIQAKGITP 362

Query:   133 DV 134
             D+
Sbjct:   363 DI 364

GO:0006508 "proteolysis" evidence=ISS

TIGR_CMR|CBU_1538 CBU_1538 "carboxyl-terminal protease family protein" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 215 (80.7 bits), Expect = 6.0e-17, P = 6.0e-17
 Identities = 54/138 (39%), Positives = 76/138 (55%)

Query:    14 GGLVKAGLDVAQIWLDG------DETLVNAVDR-EGHTLPINMVDGHAITHDPLVVLVNE 66
             GGL+     VA  +LD       ++ +V    R  G  + I    G  I H P+VVL+N 
Sbjct:   254 GGLLDVSAQVADSFLDASKMHRYNDLIVYTKGRVPGADIQIKATPGDLIPHTPMVVLING 313

Query:    67 GSASASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDID 126
             GSASASEI+AGAL D  RAI++G  +FGKG +Q+V  +    A+ +T A Y +PA  +I 
Sbjct:   314 GSASASEIVAGALQDYKRAIIMGTPSFGKGSVQTVLPIGKEDAIKLTTALYYTPAGREIQ 373

Query:   127 HVGITPDVQCTTDMLSSP 144
               GI P+V      ++ P
Sbjct:   374 AKGIIPNVAVPEFSITPP 391

GO:0006508 "proteolysis" evidence=ISS

TIGR_CMR|GSU_0969 GSU_0969 "carboxy-terminal processing protease" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 214 (80.4 bits), Expect = 7.4e-17, P = 7.4e-17
 Identities = 52/125 (41%), Positives = 73/125 (58%)

Query:    14 GGLVKAGLDVAQIWLDG--DETLVNAVDREGHTLP--INMVDGHAITHDPLVVLVNEGSA 69
             GGL+ A + VA  ++    D  L+   +   H      +   G      PLVVL+N GSA
Sbjct:   242 GGLLDAAVAVAGRFVGERLDNGLIVYTEGREHFAKRSYSATIGEKEPRYPLVVLINGGSA 301

Query:    70 SASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVG 129
             SASEI+AGAL D+GRA+++G  +FGKG +Q+V  L DG+ L +T A+Y +P    I   G
Sbjct:   302 SASEIVAGALQDHGRAVIMGTTSFGKGSVQTVVPLKDGAGLKLTTARYYTPKGRSIQARG 361

Query:   130 ITPDV 134
             I PD+
Sbjct:   362 IEPDI 366

GO:0006508 "proteolysis" evidence=ISS

TIGR_CMR|SO_0047 SO_0047 "carboxyl-terminal protease, putative" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 207 (77.9 bits), Expect = 3.1e-16, P = 3.1e-16
 Identities = 49/132 (37%), Positives = 82/132 (62%)

Query:    14 GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHA-----ITHDPLVVLVNEGS 68
             GGL+   +++A ++L         V   G     N  D +A     + + P++VL+N+GS
Sbjct:   238 GGLLDQAINIADLFLAKGRI----VSTSGRFFDANS-DYYASPQTMLANVPMLVLINKGS 292

Query:    69 ASASEILAGALHDNGRAILVGHKTFGKGKIQSVTE-LHDGSALFVTVAKYLSPALHDIDH 127
             ASASE+LA AL +NGRA L+G  +FGKG +QS+   L++G+A+ +T+A+Y +P   +I  
Sbjct:   293 ASASEVLAAALQENGRAKLLGETSFGKGTVQSLIPILNNGNAVKLTIAQYNTPKGENIHD 352

Query:   128 VGITPDVQCTTD 139
             +GI PD++  ++
Sbjct:   353 IGIKPDIKVVSE 364

GO:0006508 "proteolysis" evidence=ISS

GO:0008233 "peptidase activity" evidence=ISS

---

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	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00025542001	SubName- Full=Chromosome chr8 scaffold_34, whole genome shotgun sequence; (243 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00025543001	SubName- Full=Chromosome chr8 scaffold_34, whole genome shotgun sequence; (293 aa)		•	•						0.511

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	181
cd07560	211	cd07560, Peptidase_S41_CPP, C-terminal processing	3e-52
cd06567	224	cd06567, Peptidase_S41, C-terminal processing pept	4e-41
PLN00049	389	PLN00049, PLN00049, carboxyl-terminal processing p	5e-41
smart00245	192	smart00245, TSPc, tail specific protease	8e-41
COG0793	406	COG0793, Prc, Periplasmic protease [Cell envelope	1e-40
TIGR00225	334	TIGR00225, prc, C-terminal peptidase (prc)	7e-40
pfam03572	166	pfam03572, Peptidase_S41, Peptidase family S41	3e-39
TIGR03900	973	TIGR03900, prc_long_Delta, putative carboxyl-termi	4e-25
cd07562	266	cd07562, Peptidase_S41_TRI, Tricorn protease; seri	1e-14
PRK11186	667	PRK11186, PRK11186, carboxy-terminal protease; Pro	2e-14
cd07563	250	cd07563, Peptidase_S41_IRBP, Interphotoreceptor re	2e-09
cd07561	256	cd07561, Peptidase_S41_CPP_like, C-terminal proces	7e-05

>gnl|CDD|143476 cd07560, Peptidase_S41_CPP, C-terminal processing peptidase; serine protease family S41

 Score =  165 bits (421), Expect = 3e-52
 Identities = 61/122 (50%), Positives = 79/122 (64%), Gaps = 2/122 (1%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGL+   +++A ++L G   +V+   R G        DG      PLVVLVN GSASASE
Sbjct: 90  GGLLDEAVEIADLFLPG-GPIVSTKGRNGKREAYASDDGGL-YDGPLVVLVNGGSASASE 147

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           I+AGAL DNGRA+LVG +TFGKG +Q+V  L DGSAL +T AKY +P+   I   GI PD
Sbjct: 148 IVAGALQDNGRAVLVGERTFGKGSVQTVFPLSDGSALKLTTAKYYTPSGRSIQKKGIEPD 207

Query: 134 VQ 135
           ++
Sbjct: 208 IE 209

The C-terminal processing peptidase (CPP, EC 3.4.21.102) also known as tail-specific protease (tsp), the photosystem II D1 C-terminal processing protease (D1P), and other related S41 protease family members are present in this CD. CPP is synthesized as a precursor form with a carboxyl-terminal extension. It specifically recognizes a C-terminal tripeptide, Xaa-Yaa-Zaa, in which Xaa is preferably Ala or Leu, Yaa is preferably Ala or Tyr and Zaa is preferably Ala, but then cleaves at a variable distance from the C-terminus. The C-terminal carboxylate group is essential, and proteins where this group is amidated are not substrates. This family of proteases contains the PDZ domain that promotes protein-protein interactions and is important for substrate recognition. The active site consists of a serine/lysine catalytic dyad. The bacterial CCP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. In E. coli, it is involved in the cleavage of a C-terminal peptide of 11 residues from the precursor form of penicillin-binding protein 3 (PBP3). In the plant chloroplast, the enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II, allowing the light-driven assembly of the tetranuclear manganese cluster, which is responsible for photosynthetic water oxidation. Length = 211

>gnl|CDD|143475 cd06567, Peptidase_S41, C-terminal processing peptidase family S41

 Score =  137 bits (348), Expect = 4e-41
 Identities = 59/122 (48%), Positives = 80/122 (65%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGL+ A +++A ++L   + +V    R G+        G ++   PLVVLVNEGSASASE
Sbjct: 101 GGLLSAAVELASLFLPKGKIVVTTRRRGGNETEYVAPGGGSLYDGPLVVLVNEGSASASE 160

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           I AGAL D GRA LVG +TFGKG +Q+V  L DGSAL +T AKY +P+   I+  G+ PD
Sbjct: 161 IFAGALQDLGRATLVGERTFGKGSVQTVFPLLDGSALKLTTAKYYTPSGRSIEGKGVEPD 220

Query: 134 VQ 135
           ++
Sbjct: 221 IE 222

Peptidase family S41 (C-terminal processing peptidase or CTPase family) contains very different subfamilies; it includes photosystem II D1 C-terminal processing protease (CTPase), interphotoreceptor retinoid-binding protein IRBP and tricorn protease (TRI). CTPase and TRI both contain the PDZ domain while IRBP, although being very similar to the tail-specific protease domain, lacks the PDZ insertion domain and hydrolytic activity. These serine proteases have distinctly different active sites: in CTPase, the active site consists of a serine/lysine catalytic dyad while in tricorn core protease, it is a tetrad (serine, histidine, serine, glutamate). CPases with different substrate specificities in different species include processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein; and others such as tricorn protease (TRI) act as a carboxypeptidase, involved in the degradation of proteasomal products. CTPase homolog IRBP, secreted by photoreceptors into the interphotoreceptor matrix, having arisen in the early evolution of the vertebrate eye, promotes the release of all-trans retinol from photoreceptors and facilitates its delivery to the retinal pigment epithelium. Length = 224

>gnl|CDD|177681 PLN00049, PLN00049, carboxyl-terminal processing protease; Provisional

 Score =  141 bits (358), Expect = 5e-41
 Identities = 72/122 (59%), Positives = 86/122 (70%), Gaps = 4/122 (3%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDG-HAI-THDPLVVLVNEGSASA 71
           GGL  AG+++A++WLD    +V   D  G    I   DG  AI T +PL VLVN+G+ASA
Sbjct: 236 GGLFPAGIEIAKLWLDKG-VIVYIADSRG-VRDIYDADGSSAIATSEPLAVLVNKGTASA 293

Query: 72  SEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGIT 131
           SEILAGAL DN RA+++G  TFGKG IQSV EL DGS L VTVA+Y +PA  DID VGIT
Sbjct: 294 SEILAGALKDNKRAVVLGEPTFGKGLIQSVFELSDGSGLAVTVARYQTPAGTDIDKVGIT 353

Query: 132 PD 133
           PD
Sbjct: 354 PD 355

Length = 389

>gnl|CDD|214582 smart00245, TSPc, tail specific protease

 Score =  135 bits (343), Expect = 8e-41
 Identities = 56/123 (45%), Positives = 74/123 (60%), Gaps = 1/123 (0%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGL+ A +DV+ ++LD    +     R G        +       PLVVLVN+G+ASASE
Sbjct: 70  GGLLSAAIDVSSLFLDKGVIVYTVYRRTGELWTYP-ANLGRKYSKPLVVLVNKGTASASE 128

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           I AGAL D GRA +VG +TFGKG +Q    L DGS L +TVAKY +P+   I+  G+ PD
Sbjct: 129 IFAGALKDLGRATIVGERTFGKGLVQQTVPLGDGSGLKLTVAKYYTPSGKSIEKKGVEPD 188

Query: 134 VQC 136
           +Q 
Sbjct: 189 IQV 191

tail specific protease. Length = 192

>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer membrane]

 Score =  141 bits (357), Expect = 1e-40
 Identities = 60/121 (49%), Positives = 77/121 (63%), Gaps = 1/121 (0%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGL+   + +A ++L     +V+   R G         G A+   PLVVLVNEGSASASE
Sbjct: 245 GGLLSQAVKLAGLFLP-SGPIVSTRGRNGKVNVYFSASGEALYDGPLVVLVNEGSASASE 303

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           I AGAL D GRA LVG  TFGKG +Q++  L DGSAL +T+AKY +P+   I+  GITPD
Sbjct: 304 IFAGALQDYGRATLVGETTFGKGTVQTLRPLSDGSALKLTIAKYYTPSGRSIEGKGITPD 363

Query: 134 V 134
           +
Sbjct: 364 I 364

Length = 406

>gnl|CDD|232883 TIGR00225, prc, C-terminal peptidase (prc)

 Score =  137 bits (347), Expect = 7e-40
 Identities = 62/149 (41%), Positives = 89/149 (59%), Gaps = 8/149 (5%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGL+++ +D++++++     +V   DR G +      +G    + PLVVLVN GSASASE
Sbjct: 193 GGLLQSAVDISRLFIT-KGPIVQTKDRNG-SKRHYKANGRQPYNLPLVVLVNRGSASASE 250

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           I AGAL DNGRA +VG KTFGKG +Q V  L+DGS + VT+AKY +P    I   GI PD
Sbjct: 251 IFAGALQDNGRATIVGEKTFGKGTVQQVRPLNDGSGIKVTIAKYYTPNGGSIHKKGIEPD 310

Query: 134 VQCTTDMLSSPKESL-LKNKSSVSSLEAD 161
           +      +  P +    + K  +++L  D
Sbjct: 311 IV-----IEQPDDPKEYEEKFELNALPWD 334

A C-terminal peptidase with different substrates in different species including processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in E.coli E.coli and H influenza have the most distal branch of the tree and their proteins have an N-terminal 200 amino acids that show no homology to other proteins in the database [Protein fate, Degradation of proteins, peptides, and glycopeptides, Protein fate, Protein modification and repair]. Length = 334

>gnl|CDD|217620 pfam03572, Peptidase_S41, Peptidase family S41

 Score =  131 bits (331), Expect = 3e-39
 Identities = 61/124 (49%), Positives = 80/124 (64%), Gaps = 4/124 (3%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINM---VDGHAITHDPLVVLVNEGSAS 70
           GGL+ A +++A ++L  D T+V+  DR G               +T  PLVVLVNEG+AS
Sbjct: 42  GGLLSAAVEIASLFLP-DGTIVSTRDRIGDRPSNTTTQSSGERYLTKGPLVVLVNEGTAS 100

Query: 71  ASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGI 130
           ASEI AGAL D GRA LVG +TFGKG +Q V  L DGS L +T+A+YL+P    I+  G+
Sbjct: 101 ASEIFAGALKDLGRATLVGERTFGKGLVQGVYPLPDGSGLKLTIARYLTPDGGSIEGKGV 160

Query: 131 TPDV 134
           TPD+
Sbjct: 161 TPDI 164

Length = 166

>gnl|CDD|234386 TIGR03900, prc_long_Delta, putative carboxyl-terminal-processing protease, deltaproteobacterial

 Score =  101 bits (252), Expect = 4e-25
 Identities = 53/126 (42%), Positives = 78/126 (61%), Gaps = 6/126 (4%)

Query: 14  GGLVKAGLDVAQIWLDGDE--TLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASA 71
           GGL++  ++V+ ++LD     + V A +R             A    P+VVLVNEGSASA
Sbjct: 280 GGLLEQAIEVSDLFLDQGTIVSTVGASERREEKKATGDTVVEAKV--PVVVLVNEGSASA 337

Query: 72  SEILAGALHDNGRAILVGHKTFGKGKIQSV--TELHDGSALFVTVAKYLSPALHDIDHVG 129
           SEI+AGAL +  RA+++G +TFGKG +Q +      D SAL +T+A+YL+P    I  VG
Sbjct: 338 SEIVAGALKNLDRAVIIGRQTFGKGSVQVLYDATPADRSALKLTIAQYLTPGDRSIQSVG 397

Query: 130 ITPDVQ 135
           +TPD++
Sbjct: 398 VTPDIE 403

This model describes a multidomain protein of about 1070 residues, restricted to the order Myxococcales in the Deltaproteobacteria. Members contain a PDZ domain (pfam00595), an S41 family peptidase domain (pfam03572), and an SH3 domain (pfam06347). A core region of this family, including PDZ and S41 regions, is described by TIGR00225, C-terminal processing peptidase, which recognizes the Prc protease. The species distribution of this family approximates that of largely Deltaproteobacterial C-terminal putative protein-sorting domain, TIGR03901, analogous to LPXTG and PEP-CTERM, but the co-occurrence may reflect shared restriction to the Myxococcales rather than a substrate/target relationship. Length = 973

>gnl|CDD|143478 cd07562, Peptidase_S41_TRI, Tricorn protease; serine protease family S41

 Score = 69.5 bits (171), Expect = 1e-14
 Identities = 29/77 (37%), Positives = 40/77 (51%)

Query: 59  PLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYL 118
           P+VVLVNEGSAS +EI A      G   +VG +T G   I     L DG +L V      
Sbjct: 165 PVVVLVNEGSASDAEIFAYGFRALGLGPVVGTRTAGGVIISGRYRLPDGGSLTVPEFGVY 224

Query: 119 SPALHDIDHVGITPDVQ 135
            P    +++ G+ PD++
Sbjct: 225 LPDGGPLENRGVAPDIE 241

The tricorn protease (TRI), a member of the S41 peptidase family and named for its tricorn-like shape, exists only in some archaea and eubacteria. It has been shown to act as a carboxypeptidase, involved in the degradation of proteasomal products to preferentially yield di- and tripeptides, with subsequent and final degradations to free amino acid residues by tricorn interacting factors, F1, F2 and F3. Tricorn is a hexameric D3-symmetric protease of 720kD, and can self-associate further into a giant icosahedral capsid structure containing twenty copies of the complex. Each tricorn peptidase monomer consists of five structural domains: a six-bladed beta-propeller and a seven-bladed beta-propeller that limit access to the active site, the two domains (C1 and C2) that carry the active site residues, and a PDZ-like domain (proposed to be important for substrate recognition) between the C1 and C2 domains. The active site tetrad residues are distributed between the C1 and C2 domains, with serine and histidine on C1 and serine and glutamate on C2. Length = 266

>gnl|CDD|236873 PRK11186, PRK11186, carboxy-terminal protease; Provisional

 Score = 69.9 bits (172), Expect = 2e-14
 Identities = 38/91 (41%), Positives = 53/91 (58%), Gaps = 20/91 (21%)

Query: 59  PLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQ---SVTELHD------GSA 109
           PLVVLV+  SASASEI A A+ D GRA++VG  TFGKG +Q   S+  ++D      GS 
Sbjct: 439 PLVVLVDRYSASASEIFAAAMQDYGRALIVGEPTFGKGTVQQHRSLNRIYDQMLRPLGSV 498

Query: 110 LFVTVAKYLSPALHDID-----HVGITPDVQ 135
            + T+ K+     + I+       G+TPD+ 
Sbjct: 499 QY-TIQKF-----YRINGGSTQRKGVTPDII 523

Length = 667

>gnl|CDD|143479 cd07563, Peptidase_S41_IRBP, Interphotoreceptor retinoid-binding protein; serine protease family S41

 Score = 55.0 bits (133), Expect = 2e-09
 Identities = 29/103 (28%), Positives = 44/103 (42%), Gaps = 4/103 (3%)

Query: 36  NAVDREGHTLPINMVDGHAITHD-PLVVLVNEGSASASEILAGALHDNGRAILVGHKTFG 94
                E  TLP+    G    +  P+ VL +  + SA+E  A AL    RA +VG  T G
Sbjct: 137 GNTTTELWTLPVVP--GGRYGYTKPVYVLTSPVTFSAAEEFAYALKQLKRATVVGETTAG 194

Query: 95  KGKIQSVTELHDGSALFVTVAKYLSPALHD-IDHVGITPDVQC 136
                    L +G  L V  ++ + P      + VG+ PD++ 
Sbjct: 195 GASPVLPFPLPNGLYLTVPTSRSVDPITGTNWEGVGVPPDIEV 237

Interphotoreceptor retinoid-binding protein (IRBP) is a homolog of the S41 protease, C-terminal processing peptidase (CTPase) family. It is thought to facilitate the compartmentalization of the visual cycle that requires poorly soluble and potentially toxic retinoids to cross the aqueous subretinal space between the photoreceptors and the retinal pigment epithelium (RPE). IRBP is secreted by photoreceptors into the interphotoreceptor matrix (IPM) where it is rapidly turned over by a combination of RPE and photoreceptor endocytosis. It is the most abundant soluble protein component of the IPM, consisting of homologous modules, each repeat structure arising through the duplication (as in teleost IRBP) or quadruplication (in tetrapods) of an ancient gene, arisen in the early evolution of the vertebrate eye. IRBP has been shown to promote the release of all-trans retinol from photoreceptors and facilitates its delivery to the RPE. Conversely, IRBP can promote the release of 11-cis-retinal from the RPE, prevent its isomerization in the subretinal space, and transfer it to photoreceptors. In vivo evidence implicates IRBP as a retinoid transporter in the visual cycle, suggesting a critical role for IRBP in cone function essential for human vision. IRBP is a dominant autoimmune antigen in the eye; IRBP proteolysis analysis has proven a useful biomarker for autoimmune uveitis (AU) disorders, a major cause of blindness. This family also includes a chlamydia-secreted protein, designated chlamydia protease-like activity factor (CPAF), known to degrade host proteins, enabling Chlamydia to evade host defenses and replicate. Length = 250

>gnl|CDD|143477 cd07561, Peptidase_S41_CPP_like, C-terminal processing peptidase-like; serine protease family S41

 Score = 41.5 bits (98), Expect = 7e-05
 Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 8/80 (10%)

Query: 60  LVVLVNEGSASASEILAGAL--HDNGRAILVGHKTFGK--GKIQSVTELHDGSALFVTVA 115
           + VL +  +ASASE++  +L  + +   +L+G  T+GK  G +    +     AL   V 
Sbjct: 163 VYVLTSGSTASASELVINSLKPYMD--VVLIGETTYGKNVGSLTFEDDRKHKWALQPVVF 220

Query: 116 KYLSPALHDID-HVGITPDV 134
           K ++ A    D   G+TPD+
Sbjct: 221 KVVN-ADGQGDYSNGLTPDI 239

Bacterial protease homologs of the S41 family related to C-terminal processing peptidase (CPP). CPP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. CPP is synthesized with an extension on its carboxyl-terminus and specifically recognizes a C-terminal tripeptide, but cleaves at variable distance from the C-terminus. The CPP active site consists of a serine/lysine catalytic dyad. Conservation of these residues is seen in the CPP-like proteins of this group. CPP proteins contain a PDZ domain that promotes protein-protein interactions and is important for substrate recognition however, most of CPP-like proteins only have an internal fragment or lack the PDZ domain. Length = 256

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	181
COG0793	406	Prc Periplasmic protease [Cell envelope biogenesis	100.0
cd07560	211	Peptidase_S41_CPP C-terminal processing peptidase;	100.0
smart00245	192	TSPc tail specific protease. tail specific proteas	100.0
cd06567	224	Peptidase_S41 C-terminal processing peptidase fami	100.0
TIGR00225	334	prc C-terminal peptidase (prc). A C-terminal pepti	100.0
cd07561	256	Peptidase_S41_CPP_like C-terminal processing pepti	100.0
PLN00049	389	carboxyl-terminal processing protease; Provisional	100.0
cd07562	266	Peptidase_S41_TRI Tricorn protease; serine proteas	100.0
cd07563	250	Peptidase_S41_IRBP Interphotoreceptor retinoid-bin	100.0
PRK11186	667	carboxy-terminal protease; Provisional	99.98
PF03572	169	Peptidase_S41: Peptidase family S41; InterPro: IPR	99.97
cd07021	178	Clp_protease_NfeD_like Nodulation formation effici	82.41

>COG0793 Prc Periplasmic protease [Cell envelope biogenesis, outer membrane]

Probab=100.00  E-value=2.7e-37  Score=267.70  Aligned_cols=163  Identities=40%  Similarity=0.533  Sum_probs=145.6

Q ss_pred             ceEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhc
Q 030210            2 VFFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHD   81 (181)
Q Consensus         2 ~~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~   81 (181)
                      +.-||||||+|+||.+.++..++++|++++ ++++++.|+|+..++....+...+++|++||||++||||+|+||.+||+
T Consensus       233 ~~GlIlDLR~N~GG~L~~av~i~~~f~~~g-~iv~~~~r~g~~~~~~~~~~~~~~~~PlvvLvn~~SASAsEI~agalqd  311 (406)
T COG0793         233 AKGLILDLRNNPGGLLSQAVKLAGLFLPSG-PIVSTRGRNGKVNVYFSASGEALYDGPLVVLVNEGSASASEIFAGALQD  311 (406)
T ss_pred             CcEEEEEeCCCCCccHHHHHHHHHcccCCC-cEEEEecCCCceeeccccccccCCCCCEEEEECCCCccHHHHHHHHHHH
Confidence            356999999999999999999999999984 8899999999887776555555789999999999999999999999999


Q ss_pred             CCCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEecCCCCCCchhhhhccccCCCCCCCC
Q 030210           82 NGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDMLSSPKESLLKNKSSVSSLEAD  161 (181)
Q Consensus        82 ~~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~~~~~~~~~~~~~~~~~~~~~D  161 (181)
                      +++++|||++|+|++++|+.++|++|+.+++++++||+|+|+++++.||.|||+|+..... +..         ...++|
T Consensus       312 ~~ra~lVG~~TfGkg~vQ~~~~L~dg~~lklT~a~yytp~G~~i~~~GI~PDI~v~~~~~~-~~e---------~~~~~~  381 (406)
T COG0793         312 YGRATLVGETTFGKGTVQTLRPLSDGSALKLTIAKYYTPSGRSIEGKGITPDIEVPQADDE-PGE---------YAAGRD  381 (406)
T ss_pred             cCCcEEEecccccceEEEeeEEcCCCCeEEEEEEEEECCCCccccccCcCCCEeccCCccc-chh---------hhcccc
Confidence            9999999999999999999999999999999999999999999999999999999987531 111         122789


Q ss_pred             HHHHHHHHHHhhhc
Q 030210          162 SCIMVAEHELDVQE  175 (181)
Q Consensus       162 ~~l~~Ai~~L~~~~  175 (181)
                      ++++.|++.+....
T Consensus       382 ~~~~~~~~~~~~~~  395 (406)
T COG0793         382 PQLEAALEALLKGL  395 (406)
T ss_pred             hHhhhhhhhhhhhh
Confidence            99999999887665

>cd07560 Peptidase_S41_CPP C-terminal processing peptidase; serine protease family S41

Probab=100.00  E-value=1.5e-34  Score=231.28  Aligned_cols=133  Identities=46%  Similarity=0.689  Sum_probs=121.1

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhcC
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDN   82 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~~   82 (181)
                      ..||||||+|+||++..+..++++|+++. .+++++.|+|+...+.. .....+.+|++||||+.|+||||+||++||++
T Consensus        79 ~~lIlDLR~N~GG~~~~~~~i~~~f~~~~-~~~~~~~~~g~~~~~~~-~~~~~~~~pvvVLvn~~TaSaaE~~a~~lk~~  156 (211)
T cd07560          79 KGLILDLRNNPGGLLDEAVEIADLFLPGG-PIVSTKGRNGKREAYAS-DDGGLYDGPLVVLVNGGSASASEIVAGALQDN  156 (211)
T ss_pred             ceEEEEcCCCCCCCHHHHHHHHHHhcCCC-eEEEEEecCCceEEEec-CCCccCCCCEEEEeCCCcccHHHHHHHHHhhc
Confidence            57999999999999999999999999965 67788888887654433 33457899999999999999999999999999


Q ss_pred             CCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEec
Q 030210           83 GRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCT  137 (181)
Q Consensus        83 ~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~  137 (181)
                      +++++||++|+|++..+..+.|++|+.+++++.++++++|+.+|+.||+|||+|+
T Consensus       157 ~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~G~~~e~~GV~PDi~V~  211 (211)
T cd07560         157 GRAVLVGERTFGKGSVQTVFPLSDGSALKLTTAKYYTPSGRSIQKKGIEPDIEVP  211 (211)
T ss_pred             CCEEEEecCCCCCCeeeEEEEcCCCCEEEEEEEEEECCCCCCccCCCcCCCEECC
Confidence            9999999999999999999999999999999999999999999999999999985

The C-terminal processing peptidase (CPP, EC 3.4.21.102) also known as tail-specific protease (tsp), the photosystem II D1 C-terminal processing protease (D1P), and other related S41 protease family members are present in this CD. CPP is synthesized as a precursor form with a carboxyl-terminal extension. It specifically recognizes a C-terminal tripeptide, Xaa-Yaa-Zaa, in which Xaa is preferably Ala or Leu, Yaa is preferably Ala or Tyr and Zaa is preferably Ala, but then cleaves at a variable distance from the C-terminus. The C-terminal carboxylate group is essential, and proteins where this group is amidated are not substrates. This family of proteases contains the PDZ domain that promotes protein-protein interactions and is important for substrate recognition. The active site consists of a serine/lysine catalytic dyad. The bacterial CCP-1 is believed to be important for the degradation of incorrectl

>smart00245 TSPc tail specific protease

Probab=100.00  E-value=2.3e-34  Score=226.92  Aligned_cols=133  Identities=44%  Similarity=0.628  Sum_probs=116.9

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCC-CceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhc
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDRE-GHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHD   81 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~-g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~   81 (181)
                      ..||||||+|+||.+..+..++++|++++. +.....+. ++...+.. .....+++|++||||+.|+||||+||++||+
T Consensus        59 ~~lIiDLR~N~GG~~~~~~~~~~~f~~~~~-~~~~~~~~~~~~~~~~~-~~~~~~~~pv~vL~~~~TaSaaE~~a~~lk~  136 (192)
T smart00245       59 EGLILDLRNNPGGLLSAAIDVSSLFLDKGV-IVYTIYRRTGELETYPA-NLGRKYSKPLVVLVNEGTASASEIFAGALKD  136 (192)
T ss_pred             cEEEEEecCCCCCCHHHHHHHHHHhcCCCc-EEEEEecCCCceEEEec-CCCcccCCCEEEEECCCCeeHHHHHHHHHhh
Confidence            579999999999999999999999999874 44444444 54433332 3334679999999999999999999999999


Q ss_pred             CCCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEec
Q 030210           82 NGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCT  137 (181)
Q Consensus        82 ~~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~  137 (181)
                      ++++++||++|+|++..+..+.|++|+.+++++.++++++|+++|+.||+|||+|+
T Consensus       137 ~~~a~viG~~T~G~~~~~~~~~l~~g~~l~it~~~~~~~~g~~~e~~Gv~PDi~v~  192 (192)
T smart00245      137 LGRALIVGERTFGKGLVQQTVPLGDGSGLKLTVAKYYTPSGKSIEKKGVEPDIQVP  192 (192)
T ss_pred             CCCEEEEecCCcCCcceeeEEEeCCCCEEEEEEEEEECCCCCEecCCCcCCCEECc
Confidence            99999999999999999999999999999999999999999999999999999985

tail specific protease

>cd06567 Peptidase_S41 C-terminal processing peptidase family S41

Probab=100.00  E-value=1.1e-33  Score=227.21  Aligned_cols=135  Identities=44%  Similarity=0.633  Sum_probs=118.2

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhcC
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDN   82 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~~   82 (181)
                      ..||||||+|+||++..+..++++|+++...+.....+.+....+........+.+|++||||+.|+||||+|+.+||++
T Consensus        90 ~~lIiDLR~N~GG~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~vL~~~~taSaaE~~a~~lk~~  169 (224)
T cd06567          90 KGLILDLRNNPGGLLSAAVELASLFLPKGKIVVTTRRRGGNETEYVAPGGGSLYDGPLVVLVNEGSASASEIFAGALQDL  169 (224)
T ss_pred             CEEEEEcCCCCCccHHHHHHHHHHhcCCCcEEEEEecCCCceeEEecCCCCcccCCCEEEEECCCCccHHHHHHHHHHhC
Confidence            57999999999999999999999999987554444433332233333455678999999999999999999999999999


Q ss_pred             CCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEec
Q 030210           83 GRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCT  137 (181)
Q Consensus        83 ~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~  137 (181)
                      +++++||++|+|+++.+..+.|++|+.+.+|+.++++|+|..+|+.||+|||+|+
T Consensus       170 ~~~~vvG~~T~G~~~~~~~~~l~~g~~~~~~~~~~~~~~g~~~~~~Gv~PDi~v~  224 (224)
T cd06567         170 GRATLVGERTFGKGSVQTVFPLLDGSALKLTTAKYYTPSGRSIEGKGVEPDIEVP  224 (224)
T ss_pred             CCeEEEeeCCCCCCcceEEEEcCCCCEEEEEEEEEECCCCCCccCCccCCCEECC
Confidence            9999999999999998899999999999999999999999999999999999874

Peptidase family S41 (C-terminal processing peptidase or CTPase family) contains very different subfamilies; it includes photosystem II D1 C-terminal processing protease (CTPase), interphotoreceptor retinoid-binding protein IRBP and tricorn protease (TRI). CTPase and TRI both contain the PDZ domain while IRBP, although being very similar to the tail-specific protease domain, lacks the PDZ insertion domain and hydrolytic activity. These serine proteases have distinctly different active sites: in CTPase, the active site consists of a serine/lysine catalytic dyad while in tricorn core protease, it is a tetrad (serine, histidine, serine, glutamate). CPases with different substrate specificities in different species include processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein; and others such as tricorn pr

>TIGR00225 prc C-terminal peptidase (prc)

Probab=100.00  E-value=3.7e-33  Score=236.87  Aligned_cols=137  Identities=43%  Similarity=0.622  Sum_probs=124.9

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhcC
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDN   82 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~~   82 (181)
                      ..||||||+|+||++..+..++++|++++ .++++++++|+...+. .++...+++|++||||+.||||||+||++||++
T Consensus       182 ~~lIiDLR~N~GG~~~~a~~~a~~f~~~~-~~~~~~~~~g~~~~~~-~~~~~~~~~pv~vLvn~~TaSaaE~~a~~l~~~  259 (334)
T TIGR00225       182 KGYILDLRGNPGGLLQSAVDISRLFITKG-PIVQTKDRNGSKRHYK-ANGRQPYNLPLVVLVNRGSASASEIFAGALQDN  259 (334)
T ss_pred             ceEEEEcCCCCCCCHHHHHHHHHHhcCCC-cEEEEEcCCCcceEEe-cCCCccCCCCEEEEECCCCCcHHHHHHHHHHhC
Confidence            46999999999999999999999999987 6778888888765443 344567899999999999999999999999999


Q ss_pred             CCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEecCCCC
Q 030210           83 GRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDML  141 (181)
Q Consensus        83 ~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~~  141 (181)
                      +++++||++|+|++..+..+.|++|+.+.+++.++++|+|+++|+.||+|||+|+.++.
T Consensus       260 ~~a~viG~~T~G~~~~~~~~~l~~g~~l~~~~~~~~~~~g~~~e~~Gv~PDi~v~~~~~  318 (334)
T TIGR00225       260 GRATIVGEKTFGKGTVQQVRPLNDGSGIKVTIAKYYTPNGGSIHKKGIEPDIVIEQPDD  318 (334)
T ss_pred             CCeEEEeeCCccCceeeeEEEcCCCCEEEEEEEEEECCCCCCccCcCcCCCEEecCccc
Confidence            99999999999999989999999999999999999999999999999999999997764

A C-terminal peptidase with different substrates in different species including processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in E.coli E.coli and H influenza have the most distal branch of the tree and their proteins have an N-terminal 200 amino acids that show no homology to other proteins in the database.

>cd07561 Peptidase_S41_CPP_like C-terminal processing peptidase-like; serine protease family S41

Probab=100.00  E-value=5.8e-33  Score=227.91  Aligned_cols=138  Identities=22%  Similarity=0.233  Sum_probs=118.7

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCC---CceeEEEEcCCCc-----eeEEEccC---CCccCCCcEEEEEcCCCccH
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDG---DETLVNAVDREGH-----TLPINMVD---GHAITHDPLVVLVNEGSASA   71 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~---~~~~~~~~~r~g~-----~~~~~~~~---~~~~~~~pv~VL~~~~TaSa   71 (181)
                      ..||||||+|+||.+..|..+|++|+++   +.++.++.++++.     ...+....   ......+||+||||+.||||
T Consensus        95 ~~LIlDLR~N~GG~~~~a~~las~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~VL~~~~TASA  174 (256)
T cd07561          95 TELVLDLRYNGGGLVSSANLLASLLAPAVALGQVFATLEYNDKRSANNEDLLFSSKTLAGGNSLNLSKVYVLTSGSTASA  174 (256)
T ss_pred             CeEEEEeCCCCCccHHHHHHHHHHhcCcccCCCeEEEEEecCCccCCCceeecccccccccCcCCcccEEEEECCCcccH
Confidence            5799999999999999999999999994   4456666666652     12232221   23456789999999999999


Q ss_pred             HHHHHHHHhcCCCeEEEcccCCCCceeceEEEcc--CCceEEEEEEEEECCCCCcccCCCcccceEecCCC
Q 030210           72 SEILAGALHDNGRAILVGHKTFGKGKIQSVTELH--DGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDM  140 (181)
Q Consensus        72 aE~fa~~l~~~~~~~vIG~~T~G~~~~~~~~~L~--~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~  140 (181)
                      ||+||.+||+++++++||++|+|++..+..+.++  +|+.++++++++++|+|+.+++.||+||++|+.+.
T Consensus       175 aE~~a~~Lk~~~~a~vIGe~T~Gk~~~~~~~~l~~~~g~~l~~t~~~~~~~~G~~~~~~Gi~PDi~v~~~~  245 (256)
T cd07561         175 SELVINSLKPYMDVVLIGETTYGKNVGSLTFEDDRKHKWALQPVVFKVVNADGQGDYSNGLTPDIEVNEDS  245 (256)
T ss_pred             HHHHHHHhhccCCEEEEeCCCCCCCccceEEEccCCCCeEEEEEEEEEECCCCCCccCCCcCCceEeCccc
Confidence            9999999999999999999999999999999998  89999999999999999999999999999998764

Bacterial protease homologs of the S41 family related to C-terminal processing peptidase (CPP). CPP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. CPP is synthesized with an extension on its carboxyl-terminus and specifically recognizes a C-terminal tripeptide, but cleaves at variable distance from the C-terminus. The CPP active site consists of a serine/lysine catalytic dyad. Conservation of these residues is seen in the CPP-like proteins of this group. CPP proteins contain a PDZ domain that promotes protein-protein interactions and is important for substrate recognition however, most of CPP-like proteins only have an internal fragment or lack the PDZ domain.

>PLN00049 carboxyl-terminal processing protease; Provisional

Probab=100.00  E-value=6.2e-33  Score=239.82  Aligned_cols=137  Identities=50%  Similarity=0.685  Sum_probs=120.2

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCC-CccCCCcEEEEEcCCCccHHHHHHHHHhc
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDG-HAITHDPLVVLVNEGSASASEILAGALHD   81 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~-~~~~~~pv~VL~~~~TaSaaE~fa~~l~~   81 (181)
                      ..||||||+|+||.+..+..++++|++++ .+++...+++....+..... ...+.+|++||||+.||||||+||.+||+
T Consensus       225 ~glIlDLR~N~GG~~~~a~~ia~~f~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~PvvVLvn~~TaSasEi~a~alk~  303 (389)
T PLN00049        225 DAFVLDLRDNSGGLFPAGIEIAKLWLDKG-VIVYIADSRGVRDIYDADGSSAIATSEPLAVLVNKGTASASEILAGALKD  303 (389)
T ss_pred             CEEEEEcCCCCCCCHHHHHHHHHHhcCCC-cEEEEecCCCceeEEecCCCccccCCCCEEEEECCCCccHHHHHHHHHhh
Confidence            46999999999999999999999999987 45565555665444443222 23578999999999999999999999999


Q ss_pred             CCCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEecCCC
Q 030210           82 NGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDM  140 (181)
Q Consensus        82 ~~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~  140 (181)
                      ++++++||++|+|+++.+..+.|+||+.+++++++|++|+|+++|+.||+||++|+...
T Consensus       304 ~~~~~vvG~~T~Gkg~~q~~~~L~dG~~l~lt~~~~~~p~G~~ie~~Gi~PDi~v~~~~  362 (389)
T PLN00049        304 NKRAVVLGEPTFGKGLIQSVFELSDGSGLAVTVARYQTPAGTDIDKVGITPDHPLPESL  362 (389)
T ss_pred             CCCeEEEecCCcCCcccceeEEeCCCCEEEEEEEEEECCCCCCcCCCCcCCCeECCCCC
Confidence            99999999999999999999999999999999999999999999999999999998654

>cd07562 Peptidase_S41_TRI Tricorn protease; serine protease family S41

Probab=100.00  E-value=8.1e-33  Score=228.04  Aligned_cols=150  Identities=25%  Similarity=0.235  Sum_probs=126.6

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCC-CceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhc
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDRE-GHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHD   81 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~-g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~   81 (181)
                      ..||||||+|+||++  +..++++|.+.  .+.+...|+ +....    .+...|++|++||||+.|+||||+|+.+||+
T Consensus       116 ~glIiDlR~N~GG~~--~~~l~~~~~~~--~~~~~~~r~~~~~~~----~p~~~~~~pv~vL~~~~t~SaaE~~a~~lk~  187 (266)
T cd07562         116 DGLIIDVRFNGGGNV--ADLLLDFLSRR--RYGYDIPRGGGKPVT----YPSGRWRGPVVVLVNEGSASDAEIFAYGFRA  187 (266)
T ss_pred             ceEEEEecCCCCCcH--HHHHHHHhCCC--ceEEEccCCCCCCCC----CcccccCCCEEEEECCCCCchHHHHHHHHHH
Confidence            469999999999994  44678888765  455666666 33221    1122389999999999999999999999999


Q ss_pred             CCCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEecCCCCCCchhhhhccccCCCCCCCC
Q 030210           82 NGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDMLSSPKESLLKNKSSVSSLEAD  161 (181)
Q Consensus        82 ~~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~~~~~~~~~~~~~~~~~~~~~D  161 (181)
                      ++++++||++|+|++..+..+.||+|+.+.++...+++++|+.+|+.||.|||+|+.++...            .. ++|
T Consensus       188 ~~~~~vvG~~T~G~~~~~~~~~L~~g~~~~~~~~~~~~~~g~~~e~~Gi~PDi~v~~~~~~~------------~~-g~D  254 (266)
T cd07562         188 LGLGPVVGTRTAGGVIISGRYRLPDGGSLTVPEFGVYLPDGGPLENRGVAPDIEVENTPEDV------------AA-GRD  254 (266)
T ss_pred             cCCeeEEeeccCCceeecCceecCCCCEEEeeceeEEcCCCCccccCCCCCCEEecCCHhHh------------hc-CCC
Confidence            99999999999999998888999999999999999999999999999999999999876542            12 899


Q ss_pred             HHHHHHHHHHhh
Q 030210          162 SCIMVAEHELDV  173 (181)
Q Consensus       162 ~~l~~Ai~~L~~  173 (181)
                      |+|++|+++|.+
T Consensus       255 ~~L~~Al~~l~~  266 (266)
T cd07562         255 PQLEAAIEELLK  266 (266)
T ss_pred             HHHHHHHHHHhC
Confidence            999999999863

The tricorn protease (TRI), a member of the S41 peptidase family and named for its tricorn-like shape, exists only in some archaea and eubacteria. It has been shown to act as a carboxypeptidase, involved in the degradation of proteasomal products to preferentially yield di- and tripeptides, with subsequent and final degradations to free amino acid residues by tricorn interacting factors, F1, F2 and F3. Tricorn is a hexameric D3-symmetric protease of 720kD, and can self-associate further into a giant icosahedral capsid structure containing twenty copies of the complex. Each tricorn peptidase monomer consists of five structural domains: a six-bladed beta-propeller and a seven-bladed beta-propeller that limit access to the active site, the two domains (C1 and C2) that carry the active site residues, and a PDZ-like domain (proposed to be important for substrate recognition) between the C1 and C2 domains. The active sit

>cd07563 Peptidase_S41_IRBP Interphotoreceptor retinoid-binding protein; serine protease family S41

Probab=100.00  E-value=2e-32  Score=223.66  Aligned_cols=138  Identities=25%  Similarity=0.230  Sum_probs=117.2

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCcee--EEEEcCCCceeE-----EEccCCCccCCCcEEEEEcCCCccHHHHH
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETL--VNAVDREGHTLP-----INMVDGHAITHDPLVVLVNEGSASASEIL   75 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~--~~~~~r~g~~~~-----~~~~~~~~~~~~pv~VL~~~~TaSaaE~f   75 (181)
                      ..||||||+|+||+...+..++++|+++...+  .....|++....     +..+.....+++||+||||+.|+||||+|
T Consensus        96 ~~LIIDLR~N~GG~~~~~~~l~s~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~vL~~~~T~SaaE~~  175 (250)
T cd07563          96 DALIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNTTTELWTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEF  175 (250)
T ss_pred             CeEEEEECCCCCCCHHHHHHHHHHcCCCCCcEEEEEEEECCCCCCcccceeeecCCCcccCCCCEEEEeCCCcCcHHHHH
Confidence            36999999999999999999999999644333  333444443221     22234456799999999999999999999


Q ss_pred             HHHHhcCCCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCC-CCcccCCCcccceEecCCC
Q 030210           76 AGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPA-LHDIDHVGITPDVQCTTDM  140 (181)
Q Consensus        76 a~~l~~~~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~-g~~~e~~Gv~PDi~v~~~~  140 (181)
                      +++||+++++++||++|+|++..+..+.||+|+.+.+++.++++++ |..+|+.||.|||.|+.++
T Consensus       176 a~~lk~~~~~~viGe~T~G~~~~~~~~~Lp~g~~~~~~~~~~~~~~~g~~~e~~Gv~PDi~v~~~~  241 (250)
T cd07563         176 AYALKQLKRATVVGETTAGGASPVLPFPLPNGLYLTVPTSRSVDPITGTNWEGVGVPPDIEVPATP  241 (250)
T ss_pred             HHHHHhCCCcEEEeecCCCCCCCceEEEcCCCeEEEEecceeEeCCCCCcccccCcCCCeeecCCC
Confidence            9999999999999999999999889999999999999999999998 9999999999999998753

Interphotoreceptor retinoid-binding protein (IRBP) is a homolog of the S41 protease, C-terminal processing peptidase (CTPase) family. It is thought to facilitate the compartmentalization of the visual cycle that requires poorly soluble and potentially toxic retinoids to cross the aqueous subretinal space between the photoreceptors and the retinal pigment epithelium (RPE). IRBP is secreted by photoreceptors into the interphotoreceptor matrix (IPM) where it is rapidly turned over by a combination of RPE and photoreceptor endocytosis. It is the most abundant soluble protein component of the IPM, consisting of homologous modules, each repeat structure arising through the duplication (as in teleost IRBP) or quadruplication (in tetrapods) of an ancient gene, arisen in the early evolution of the vertebrate eye. IRBP has been shown to promote the release of all-trans retinol from photoreceptors

>PRK11186 carboxy-terminal protease; Provisional

Probab=99.98  E-value=5e-32  Score=245.73  Aligned_cols=137  Identities=31%  Similarity=0.427  Sum_probs=121.7

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhcC
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDN   82 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~~   82 (181)
                      ..||||||+|+||.+..|..++++|++++ ++++.++++|+...+....+...|.+|++||||++||||||+||++||++
T Consensus       384 ~gLIlDLR~NgGG~l~~a~~la~lFi~~g-~vv~~~~~~g~~~~~~~~~~~~~~~gPlvVLVN~~SASASEIfA~alqd~  462 (667)
T PRK11186        384 SGIIIDLRGNGGGALTEAVSLSGLFIPSG-PVVQVRDNNGRVRVDSDTDGVVYYKGPLVVLVDRYSASASEIFAAAMQDY  462 (667)
T ss_pred             CEEEEEcCCCCCCcHHHHHHHHHHHhcCC-ceEEEecCCCceeccccCCcccccCCCEEEEeCCCCccHHHHHHHHHHhc
Confidence            57999999999999999999999999986 67788888887655444455568999999999999999999999999999


Q ss_pred             CCeEEEcccCCCCceeceEEEccC--------CceEEEEEEEEECCCCCcccCCCcccceEecCCC
Q 030210           83 GRAILVGHKTFGKGKIQSVTELHD--------GSALFVTVAKYLSPALHDIDHVGITPDVQCTTDM  140 (181)
Q Consensus        83 ~~~~vIG~~T~G~~~~~~~~~L~~--------g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~  140 (181)
                      +++++||++|+|+|++|..++|++        +..+++|+++|++|+|.++++.||+|||.|+...
T Consensus       463 ~ra~vVG~~T~GKGtvQ~~~~L~~~~~~~~~~~G~lk~Tiak~y~p~G~s~q~~GV~PDi~vp~~~  528 (667)
T PRK11186        463 GRALIVGEPTFGKGTVQQHRSLNRIYDQMLRPLGSVQYTIQKFYRINGGSTQRKGVTPDIIFPTGI  528 (667)
T ss_pred             CCEEEEeccCCCccccccccccccccccccCCCCeeEEEEeEEECCCCCcccCCCCCCCeEcCCCc
Confidence            999999999999999998777653        3469999999999999999999999999998643

>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)

Probab=99.97  E-value=4.2e-30  Score=196.84  Aligned_cols=133  Identities=30%  Similarity=0.379  Sum_probs=99.5

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCcee----EEEccCCCccCCCcEEEEEcCCCccHHHHHHHH
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTL----PINMVDGHAITHDPLVVLVNEGSASASEILAGA   78 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~----~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~   78 (181)
                      ..||||||+|+||+...+..++++|.++. ..+....+.+...    ..........+.+|++||||+.|+||||.|+.+
T Consensus        33 ~~lIIDlR~N~GG~~~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~vL~~~~t~Saae~fa~~  111 (169)
T PF03572_consen   33 DGLIIDLRGNGGGSDEYAIELLSYLIPKP-IIFYYRDRIGSNKKWVSTIKWSTPKNRFNGPVYVLTDENTASAAEIFASA  111 (169)
T ss_dssp             SEEEEE-TTB--BSHHHHHHHHHCHSSSS-EEEEEEEEEEEETTCCHEEEECSSTT-SSSEEEEEE-TTBBTHHHHHHHH
T ss_pred             CEEEEEcccCCCcchHHHHHHHhcccCCC-cEEEEecccccccccccCCCCccccccCCCCEEEEeCCCCCChhHHHHHH
Confidence            57999999999999999999999999975 3333222211111    000111156799999999999999999999999


Q ss_pred             HhcCCCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEe
Q 030210           79 LHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQC  136 (181)
Q Consensus        79 l~~~~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v  136 (181)
                      ||+++++++||++|+|.+..+..+.|++|+.++++...+++++|..+|+.||.|||+|
T Consensus       112 lk~~~~~~ivGe~T~G~~~~~~~~~l~~g~~~~i~~~~~~~~~g~~~~~~Gi~PDi~V  169 (169)
T PF03572_consen  112 LKDNKRATIVGEPTAGAGGGQTGFSLPSGSILSIPTSRYYNPDGQKIEGIGIEPDIEV  169 (169)
T ss_dssp             HHHTTSEEEEES--SB-EEEEEEEE-TTSEEEEEEEEEEEETTSBBTTTTS---SEE-
T ss_pred             HHhcCCCeEEeecCCCCCEEeeEEEECCCcEEEeEeEEEEeCCCCEEcCCcEEccEEC
Confidence            9999999999999999998888999999999999999999999999999999999987

The members of this group include: the tricorn protease of bacteria and archaea, C-terminal peptidases with different substrates specificities in different species including processing of D1 protein of the photosystem II reaction centre in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein; and some appear to be responsible for degrading oligopeptides, probably derived from the proteasome. ; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis; PDB: 1N6F_D 1N6D_C 1N6E_C 1K32_A 3K50_A 3DJA_B 3DPM_B 3DPN_A 3DOR_B 1J7X_A ....

>cd07021 Clp_protease_NfeD_like Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease

Probab=82.41  E-value=3.1  Score=32.33  Aligned_cols=25  Identities=32%  Similarity=0.384  Sum_probs=21.3

Q ss_pred             CCCcEEEEEcCCCccHHHHHHHHHh
Q 030210           56 THDPLVVLVNEGSASASEILAGALH   80 (181)
Q Consensus        56 ~~~pv~VL~~~~TaSaaE~fa~~l~   80 (181)
                      ..+|+++.+++..+|++-+++.+-.
T Consensus        57 ~~~pvva~V~g~AaSaG~~ia~a~d   81 (178)
T cd07021          57 SPIPTIAYVNDRAASAGALIALAAD   81 (178)
T ss_pred             CCCCEEEEECCchHHHHHHHHHhCC
Confidence            3479999999999999999988654

Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentiall

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	181
1fc7_A	388	Photosystem Ii D1 C-Terminal Processing Protease Le		2e-26
1fc6_A	388	Photosystem Ii D1 C-Terminal Processing Protease Le		4e-26

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

Iteration: 1
 Score =  114 bits (286), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 65/132 (49%), Positives = 93/132 (70%), Gaps = 5/132 (3%)
Query: 14  GGLVKAGLDVAQIWLD-GDETLVNAVDREGHTLPINMVDGHAI-THDPLVVLVNEGSASA 71
           GGL  AG++VA++ +D GD  L+   D +G    I   DG++I +  PLVVLVN G+ASA
Sbjct: 241 GGLFPAGVNVARMLVDRGDLVLI--ADSQG-IRDIYSADGNSIDSATPLVVLVNRGTASA 297
Query: 72  SEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGIT 131
           SE+LAGAL D+ R ++ G +TFGKG IQ+V +L DGS + VTVA+Y +PA  DI+ +G++
Sbjct: 298 SEVLAGALKDSKRGLIAGERTFGKGLIQTVVDLSDGSGVAVTVARYQTPAGVDINKIGVS 357
Query: 132 PDVQCTTDMLSS 143
           PDVQ   ++L +
Sbjct: 358 PDVQLDPEVLPT 369

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

Iteration: 1
 Score =  114 bits (284), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 65/132 (49%), Positives = 92/132 (69%), Gaps = 5/132 (3%)
Query: 14  GGLVKAGLDVAQIWLD-GDETLVNAVDREGHTLPINMVDGHAI-THDPLVVLVNEGSASA 71
           GGL  AG++VA+  +D GD  L+   D +G    I   DG++I +  PLVVLVN G+ASA
Sbjct: 241 GGLFPAGVNVARXLVDRGDLVLI--ADSQG-IRDIYSADGNSIDSATPLVVLVNRGTASA 297
Query: 72  SEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGIT 131
           SE+LAGAL D+ R ++ G +TFGKG IQ+V +L DGS + VTVA+Y +PA  DI+ +G++
Sbjct: 298 SEVLAGALKDSKRGLIAGERTFGKGLIQTVVDLSDGSGVAVTVARYQTPAGVDINKIGVS 357
Query: 132 PDVQCTTDMLSS 143
           PDVQ   ++L +
Sbjct: 358 PDVQLDPEVLPT 369

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	181
1fc6_A	388	Photosystem II D1 protease; D1 C-terminal processi	3e-59
3k50_A	403	Putative S41 protease; structural genomics, joint	3e-38
1j7x_A	302	IRBP, interphotoreceptor retinoid-binding protein;	6e-36
3dor_A	583	Protein CT_858, CPAF; mature CPAF, dimer, transfer	2e-30
1k32_A	1045	Tricorn protease; protein degradation, substrate g	3e-27

>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

 Score =  188 bits (480), Expect = 3e-59
 Identities = 62/141 (43%), Positives = 91/141 (64%), Gaps = 1/141 (0%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGL  AG++VA++ +D  + LV   D +G     +       +  PLVVLVN G+ASASE
Sbjct: 241 GGLFPAGVNVARMLVDRGD-LVLIADSQGIRDIYSADGNSIDSATPLVVLVNRGTASASE 299

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPD 133
           +LAGAL D+ R ++ G +TFGKG IQ+V +L DGS + VTVA+Y +PA  DI+ +G++PD
Sbjct: 300 VLAGALKDSKRGLIAGERTFGKGLIQTVVDLSDGSGVAVTVARYQTPAGVDINKIGVSPD 359

Query: 134 VQCTTDMLSSPKESLLKNKSS 154
           VQ   ++L +  E + +   S
Sbjct: 360 VQLDPEVLPTDLEGVCRVLGS 380

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

 Score =  134 bits (338), Expect = 3e-38
 Identities = 23/156 (14%), Positives = 48/156 (30%), Gaps = 19/156 (12%)

Query: 14  GGLVKAGLDVAQIWLDGDETL-----------VNAVDREGHTLPINMVDGHAITHDPLVV 62
           GG +     +  +    D+                 +++    P  +  G  +    + V
Sbjct: 236 GGSLDCAQLLCTMLAPADKMNQLLALLRYSDKRVEANQDLTFNPELIQSGANLNLSTVYV 295

Query: 63  LVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQ-SVTELHDGSALFVTVAKYLSPA 121
           L    +  A+E++   L+   + +L+G KT G+           D   L + V    +  
Sbjct: 296 LTTNATRGAAEMVINCLNPYMKVVLIGTKTAGEYVATKPFVHPTDRFILNLVVCNVYNAE 355

Query: 122 LHDIDHVGITPD--VQCTTDM-----LSSPKESLLK 150
                  G  P       + +       +  E+LL 
Sbjct: 356 EKSDYATGFKPTYEYNEDSYLSTYLPFGNTNETLLN 391

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

 Score =  125 bits (317), Expect = 6e-36
 Identities = 25/136 (18%), Positives = 49/136 (36%), Gaps = 12/136 (8%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREG---------HTLPINMVDGHAITHDPLVVLV 64
           GG   A   +   +LD + T ++               ++ P  +   +  +   + VL 
Sbjct: 152 GGSSTAVPLLLSYFLDPE-TKIHLFTLHNRQQNSTDEVYSHPKVLGKPYG-SKKGVYVLT 209

Query: 65  NEGSASASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGS-ALFVTVAKYLSPALH 123
           +  +A+A+E  A  +    RA ++G  T G      V    D   ++ V +  ++     
Sbjct: 210 SHQTATAAEEFAYLMQSLSRATIIGEITSGNLMHSKVFPFGDTQLSVTVPIINFIDSNGD 269

Query: 124 DIDHVGITPDVQCTTD 139
                G+ PD     D
Sbjct: 270 YWLGGGVVPDAIVLAD 285

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

 Score =  115 bits (288), Expect = 2e-30
 Identities = 28/125 (22%), Positives = 47/125 (37%), Gaps = 5/125 (4%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
             L   G  V   W  GD  L   +   G                P+ VL+NE   S ++
Sbjct: 413 EYLKSFGRQVLNCWSKGDIELSTPIPLFGFEKIHP--HPRVQYSKPICVLINEQDFSCAD 470

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGS---ALFVTVAKYLSPALHDIDHVGI 130
                L DN RA++VG +T G G      +  + +      +T +  +      I+++G+
Sbjct: 471 FFPVVLKDNDRALIVGTRTAGAGGFVFNVQFPNRTGIKTCSLTGSLAVREHGAFIENIGV 530

Query: 131 TPDVQ 135
            P + 
Sbjct: 531 EPHID 535

>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

 Score =  106 bits (265), Expect = 3e-27
 Identities = 28/124 (22%), Positives = 49/124 (39%), Gaps = 10/124 (8%)

Query: 14   GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
            GG V     + +  ++      N         P N V G       ++ + NE + S  +
Sbjct: 891  GGFVSQ--LIIEKLMNKRIGYDNPRRGTLSPYPTNSVRG------KIIAITNEYAGSDGD 942

Query: 74   ILAGALHDNGRAILVGHKTFGKG-KIQSVTELHDGSALFV-TVAKYLSPALHDIDHVGIT 131
            I + +    G   L+G +T+G    I     L DG+ L     A +   A   +++ G+ 
Sbjct: 943  IFSFSFKKLGLGKLIGTRTWGGVVGITPKRRLIDGTVLTQPEFAFWFRDAGFGVENYGVD 1002

Query: 132  PDVQ 135
            PDV+
Sbjct: 1003 PDVE 1006

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	181
1j7x_A	302	IRBP, interphotoreceptor retinoid-binding protein;	100.0
3k50_A	403	Putative S41 protease; structural genomics, joint	100.0
1fc6_A	388	Photosystem II D1 protease; D1 C-terminal processi	100.0
3dor_A	583	Protein CT_858, CPAF; mature CPAF, dimer, transfer	99.97
1k32_A	1045	Tricorn protease; protein degradation, substrate g	99.97

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

Probab=100.00  E-value=4e-35  Score=244.47  Aligned_cols=152  Identities=18%  Similarity=0.161  Sum_probs=129.2

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCc--eeEEEEcCCCce-eEEEccC---CC-ccCCCcEEEEEcCCCccHHHHH
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDE--TLVNAVDREGHT-LPINMVD---GH-AITHDPLVVLVNEGSASASEIL   75 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~--~~~~~~~r~g~~-~~~~~~~---~~-~~~~~pv~VL~~~~TaSaaE~f   75 (181)
                      ..||||||+|+||++..+..++++|++++.  .++++++|+++. ..++..+   +. ..+++|++||||++||||||+|
T Consensus       141 ~~LIiDLR~N~GG~~~~~~~l~~~f~~~~~~~~i~~~~~r~~~~~~~~~~~~~~~~~~~~~~~pvvVLvn~~TaSAsE~~  220 (302)
T 1j7x_A          141 ENLIIDLRYNVGGSSTAVPLLLSYFLDPETKIHLFTLHNRQQNSTDEVYSHPKVLGKPYGSKKGVYVLTSHQTATAAEEF  220 (302)
T ss_dssp             SEEEEECTTCCCBCSTTHHHHHHTTSCSSCCCEEEEEEETTTTCCEEEECCSCCSSCCCCSSSEEEEEECTTCCTHHHHH
T ss_pred             CeEEEEeCCCCCCChhHHHHHHHHhcCCCcceeeEEEEccCCCCceeecccccccCCccCCCCCEEEEeCCCcCcHHHHH
Confidence            479999999999999999999999998764  357777787763 3444322   11 2368999999999999999999


Q ss_pred             HHHHhcCCCeEEEcccCCCCceeceEEEccCC-ceEEEEEEEEECCCCCcccCCCcccceEecCCCCCCchhhhhccccC
Q 030210           76 AGALHDNGRAILVGHKTFGKGKIQSVTELHDG-SALFVTVAKYLSPALHDIDHVGITPDVQCTTDMLSSPKESLLKNKSS  154 (181)
Q Consensus        76 a~~l~~~~~~~vIG~~T~G~~~~~~~~~L~~g-~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~~~~~~~~~~~~~~~  154 (181)
                      +++||+++++++||++|+|++..+..++|++| +.+.++++++++|+|+.+++.||.|||+|+.                
T Consensus       221 a~alq~~~~a~vVG~~T~Gk~~~~~~~~L~~g~~~lt~p~~~~~~p~G~~~~~~Gi~PDi~v~~----------------  284 (302)
T 1j7x_A          221 AYLMQSLSRATIIGEITSGNLMHSKVFPFGDTQLSVTVPIINFIDSNGDYWLGGGVVPDAIVLA----------------  284 (302)
T ss_dssp             HHHHHHTTCCEEEESCCCCCCSCEEEEECTTSSEEEEEECEEEEETTSCBCCCSCCCCSEECCG----------------
T ss_pred             HHHHHhCCCEEEEcccCCCCCCCceEEEeCCCcEEEEEEEEEEECCCCCccCCcCcCCCeeeCH----------------
Confidence            99999999999999999999999999999997 5556666899999999999999999999852                


Q ss_pred             CCCCCCCHHHHHHHHHHhhhcc
Q 030210          155 VSSLEADSCIMVAEHELDVQES  176 (181)
Q Consensus       155 ~~~~~~D~~l~~Ai~~L~~~~~  176 (181)
                            |++|++|+++|+.+++
T Consensus       285 ------d~~L~~A~~~l~~~~~  300 (302)
T 1j7x_A          285 ------DEALDKAKEIIAFHPP  300 (302)
T ss_dssp             ------GGHHHHHHHHHHTCCC
T ss_pred             ------HHHHHHHHHHHHhhhc
Confidence                  7899999999987653

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

Probab=100.00  E-value=7.6e-35  Score=251.37  Aligned_cols=167  Identities=16%  Similarity=0.134  Sum_probs=135.6

Q ss_pred             ceEEEeecCCCCCCCHHHHHHHHhhccCCCce---eEEEE--cCCCceeE-EEcc-----CCCccCCCcEEEEEcCCCcc
Q 030210            2 VFFSPPSLSIFQGGLVKAGLDVAQIWLDGDET---LVNAV--DREGHTLP-INMV-----DGHAITHDPLVVLVNEGSAS   70 (181)
Q Consensus         2 ~~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~---~~~~~--~r~g~~~~-~~~~-----~~~~~~~~pv~VL~~~~TaS   70 (181)
                      +..||||||+|+||.+..|..++++|++++..   +++++  +|.+.... +...     .+...+.+|++||||+.|||
T Consensus       224 ~~~lIlDLR~N~GG~l~~a~~la~~f~~~g~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~vL~~~~taS  303 (403)
T 3k50_A          224 VNEFVLDLRYNTGGSLDCAQLLCTMLAPADKMNQLLALLRYSDKRVEANQDLTFNPELIQSGANLNLSTVYVLTTNATRG  303 (403)
T ss_dssp             CCEEEEECTTCCCBCHHHHHHHHHHHSCGGGTTSEEEEEECCTTCGGGCEEEECCGGGTTTSCCCCCSEEEEEECTTCCT
T ss_pred             CcEEEEEcCCCCCCCHHHHHHHHHHhcCCCccceeEEEEEEcCCCCcceeEEeccccccccccccCCCCEEEEECCCCcc
Confidence            35799999999999999999999999998643   66776  45554322 2221     12234568999999999999


Q ss_pred             HHHHHHHHHhcCCCeEEEcccCCCCceeceEEE-ccCCceEEEEEEEEECCCCCcccCCCcccceEecCCCCCCchhhhh
Q 030210           71 ASEILAGALHDNGRAILVGHKTFGKGKIQSVTE-LHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDMLSSPKESLL  149 (181)
Q Consensus        71 aaE~fa~~l~~~~~~~vIG~~T~G~~~~~~~~~-L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~~~~~~~~~~  149 (181)
                      |||+|+++||+++++++||++|+|+++.+..+. +++|+.++++++++++|+|..+++.||.|||+|+.++....     
T Consensus       304 a~E~~~~~l~~~~~~~~iG~~T~G~~~~~~~~~~~~~g~~l~~t~~~~~~~~G~~~~~~Gi~PDi~v~~~~~~~~-----  378 (403)
T 3k50_A          304 AAEMVINCLNPYMKVVLIGTKTAGEYVATKPFVHPTDRFILNLVVCNVYNAEEKSDYATGFKPTYEYNEDSYLST-----  378 (403)
T ss_dssp             HHHHHHHHHTTTSEEEEEESCCCCCCEEEEEEECSSSCEEEEEEEEEEECTTSCCCCTTCCCCSEECCGGGCGGG-----
T ss_pred             HHHHHHHHHhhCCCEEEEeecCCCCCeeeeEEEeCCCCcEEEEEEEEEECCCCCCccCCCcCceEEeCCCccccc-----
Confidence            999999999999999999999999998888886 78899999999999999999999999999999997642000     


Q ss_pred             ccccCCCCCCCCHHHHHHHHHHhhhcc
Q 030210          150 KNKSSVSSLEADSCIMVAEHELDVQES  176 (181)
Q Consensus       150 ~~~~~~~~~~~D~~l~~Ai~~L~~~~~  176 (181)
                        ...+. .++|+||++||++|..+++
T Consensus       379 --~~~~~-~~~D~~L~~Al~~l~~~~~  402 (403)
T 3k50_A          379 --YLPFG-NTNETLLNAALKIMSGITD  402 (403)
T ss_dssp             --CCCTT-CTTSHHHHHHHHHHHTSCC
T ss_pred             --ccccC-CCccHHHHHHHHHHHhccc
Confidence              01112 2799999999999988764

>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

Probab=100.00  E-value=3e-34  Score=246.40  Aligned_cols=137  Identities=43%  Similarity=0.620  Sum_probs=123.9

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhcC
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDN   82 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~~   82 (181)
                      ..||||||+|+||.+..+..++++|++++ .+++++.|+|....|........+.+|++||||++||||||+||.+||++
T Consensus       230 ~~lIlDLR~N~GG~~~~~~~~~~~f~~~~-~i~~~~~r~~~~~~~~~~~~~~~~~~pv~VLvn~~taSasEi~a~al~~~  308 (388)
T 1fc6_A          230 AGLVLDIRNNGGGLFPAGVNVARMLVDRG-DLVLIADSQGIRDIYSADGNSIDSATPLVVLVNRGTASASEVLAGALKDS  308 (388)
T ss_dssp             SEEEEECTTCCCBCHHHHHHHHHHHCSSS-EEEEEEETTEEEEEEECCSCCSCSSSCEEEEECTTCCTHHHHHHHHHHHT
T ss_pred             CeEEEEcCCCCCCCHHHHHHHHHHHcCCC-cEEEEecCCCceeEEecCCccccCCCCEEEEeCCCCccHHHHHHHHHhhC
Confidence            57999999999999999999999999986 57778888887666654322224899999999999999999999999999


Q ss_pred             CCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEecCCC
Q 030210           83 GRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDM  140 (181)
Q Consensus        83 ~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~  140 (181)
                      +++++||++|+|+++.+..++|++|+.++++++++++|+|+.+++.||.|||+|+.+.
T Consensus       309 ~~~~~vG~~T~Gkg~~~~~~~L~~g~~l~~t~~~~~~p~G~~~~~~Gi~PDi~v~~~~  366 (388)
T 1fc6_A          309 KRGLIAGERTFGKGLIQTVVDLSDGSGVAVTVARYQTPAGVDINKIGVSPDVQLDPEV  366 (388)
T ss_dssp             TSEEEEESCCCCCCEEEEEEECTTSCEEEEEEEEEECTTSCBCTTTCCCCSEECCTTS
T ss_pred             CCEEEEeecCCCCCeeeeEEEcCCCCEEEEEEEEEEcCCCCCccCCCcCCCEEeCCcc
Confidence            9999999999999999999999999999999999999999999999999999999874

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

Probab=99.97  E-value=1.1e-30  Score=231.59  Aligned_cols=160  Identities=19%  Similarity=0.160  Sum_probs=130.6

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEE----E----------------------------------------
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNA----V----------------------------------------   38 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~----~----------------------------------------   38 (181)
                      ..||||+|+|+||+......++++|.+++-.+-..    .                                        
T Consensus       332 ~~liid~~~n~gg~~~~~~~~~~~l~~~p~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~  411 (583)
T 3dor_A          332 EALIIDQTNNPGGSVLYLYALLSMLTDRPLELPKHRMILTQDEVVDALDWLTLLENVDTNVESRLALGDNMEGYTVDLQV  411 (583)
T ss_dssp             SEEEEECCSBCCBCHHHHHHHHHTTCSSCEECCEEEECCCHHHHHHHHHHHHHHTTCCSHHHHHHHHCSEETTEECCHHH
T ss_pred             CeEEEEecCCCCccHHHHHHHHHHHhcCCCCCcceeeEEecHHHHHHHHHHHHHHhhhhhhhhhhhccccccccCccHHH
Confidence            47999999999999999999999999974211111    0                                        


Q ss_pred             --------------cCCCcee---E-------EEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhcCCCeEEEcccCCC
Q 030210           39 --------------DREGHTL---P-------INMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFG   94 (181)
Q Consensus        39 --------------~r~g~~~---~-------~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~~~~~~vIG~~T~G   94 (181)
                                    ..+|...   +       ...+.+...|++|++||||+.||||||+||.+||+++++++||++|+|
T Consensus       412 ~~~l~~~~~~~l~~~~~G~~t~s~p~pl~g~~~i~p~~~~~~~gPvvVLVN~~SASASEifA~aLKd~~ra~lVGe~T~G  491 (583)
T 3dor_A          412 AEYLKSFGRQVLNCWSKGDIELSTPIPLFGFEKIHPHPRVQYSKPICVLINEQDFSCADFFPVVLKDNDRALIVGTRTAG  491 (583)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCSSCSCBCGGGCCEECCCSSCCCCSCEEEEECTTBCTHHHHHHHHHHHTTCEEEEESCCCC
T ss_pred             HHHHHHHHHHHHHHHhCCCceecCCcccccceeeccCCCccCCCCEEEEECCCCccHHHHHHHHHHhCCCEEEEeeCCCC
Confidence                          0011100   0       011334467999999999999999999999999999999999999999


Q ss_pred             CceeceEEEccCCceE---EEEEEEEECCCCCcccCCCcccceEecCCCCCCchhhhhccccCCCCCCCCHHHHHHHHHH
Q 030210           95 KGKIQSVTELHDGSAL---FVTVAKYLSPALHDIDHVGITPDVQCTTDMLSSPKESLLKNKSSVSSLEADSCIMVAEHEL  171 (181)
Q Consensus        95 ~~~~~~~~~L~~g~~l---~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~~~~~~~~~~~~~~~~~~~~~D~~l~~Ai~~L  171 (181)
                      +++.+..+.|++|+.+   +++++++++|+|+.+++.||.|||+|+.++...            .. ++|+|+++|++.|
T Consensus       492 kg~vq~~~~Lpdg~~l~~lklT~a~~~tp~G~~ie~~GV~PDI~V~~t~~dl------------~~-GrD~ql~~AV~~l  558 (583)
T 3dor_A          492 AGGFVFNVQFPNRTGIKTCSLTGSLAVREHGAFIENIGVEPHIDLPFTANDI------------RY-KGYSEYLDKVKKL  558 (583)
T ss_dssp             CCSCEEEECCCCSSCEEEEEEECEEEECTTSCBCTTTCCCCSEECCCCHHHH------------HT-TCCHHHHHHHHHH
T ss_pred             CCceeeEEEcCCCCeEEEEEeeeEEEECCCCCCcCCCCcCCcEEeCCCHHHH------------Hc-CCCHHHHHHHHHH
Confidence            9999999999999855   599999999999999999999999999876431            12 8999999999999


Q ss_pred             hhhc
Q 030210          172 DVQE  175 (181)
Q Consensus       172 ~~~~  175 (181)
                      .+++
T Consensus       559 Lk~L  562 (583)
T 3dor_A          559 VCQL  562 (583)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9887

>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*

Probab=99.97  E-value=7.8e-31  Score=246.58  Aligned_cols=153  Identities=20%  Similarity=0.250  Sum_probs=129.8

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhcC
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDN   82 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~~   82 (181)
                      ..||||||+|+||.+..+  ++++|..  .++++++.|+|+...+..    ..+.+|++||||++||||||+||.+||++
T Consensus       880 ~~liiDlR~N~GG~~~~~--~~~~~~~--~~~~~~~~~~~~~~~~~~----~~~~~~~~vL~~~~taSa~e~~~~~l~~~  951 (1045)
T 1k32_A          880 QGLIVDVRFNGGGFVSQL--IIEKLMN--KRIGYDNPRRGTLSPYPT----NSVRGKIIAITNEYAGSDGDIFSFSFKKL  951 (1045)
T ss_dssp             SEEEEECTTCCCBSCHHH--HHHHHTC--BCCEEEEESSSCCEEEST----TCBCSEEEEEECTTCCTHHHHHHHHHHHT
T ss_pred             CEEEEEcCcCCCCCHHHH--HHhhccC--CcEEEEecCCCceeeccc----cCCCCCEEEEECCCCccHHHHHHHHHhhc
Confidence            579999999999999875  4777743  367888888887665531    24789999999999999999999999999


Q ss_pred             CCeEEEcccCCCCceec--eEEEccCCceEEEE-EEEEECCCCCcccCCCcccceEecCCCCCCchhhhhccccCCCCCC
Q 030210           83 GRAILVGHKTFGKGKIQ--SVTELHDGSALFVT-VAKYLSPALHDIDHVGITPDVQCTTDMLSSPKESLLKNKSSVSSLE  159 (181)
Q Consensus        83 ~~~~vIG~~T~G~~~~~--~~~~L~~g~~l~i~-~~~~~~~~g~~~e~~Gv~PDi~v~~~~~~~~~~~~~~~~~~~~~~~  159 (181)
                      +++++||++|+| +..+  ..++|++|+.++++ ++++++|+|..+++.||.|||+|+.++..      +      .. +
T Consensus       952 ~~~~~vG~~t~G-g~~~~~~~~~l~~~~~~~~~~~~~~~~~~g~~~~~~Gi~Pdi~v~~~~~~------~------~~-~ 1017 (1045)
T 1k32_A          952 GLGKLIGTRTWG-GVVGITPKRRLIDGTVLTQPEFAFWFRDAGFGVENYGVDPDVEIEYAPHD------Y------LS-G 1017 (1045)
T ss_dssp             TSEEEEESCCCC-CCEECCCCCBCTTSCEECCCCEEEEETTTBTTTTTTCCCCSEECCCCHHH------H------HT-T
T ss_pred             CCEEEEccCCCC-CccccCceEEcCCCCeEEEeeEEEEECCCCCccCCCCccCCEEeCCChHH------h------cc-C
Confidence            999999999999 5554  56899999999998 89999999999999999999999976532      1      12 7


Q ss_pred             CCHHHHHHHHHHhhhccc
Q 030210          160 ADSCIMVAEHELDVQESR  177 (181)
Q Consensus       160 ~D~~l~~Ai~~L~~~~~~  177 (181)
                      +|++|++|+++|.+++++
T Consensus      1018 ~d~~l~~a~~~l~~~~~~ 1035 (1045)
T 1k32_A         1018 KDPQIDYAIDALIEELRN 1035 (1045)
T ss_dssp             CCHHHHHHHHHHHHHTTC
T ss_pred             ccHHHHHHHHHHHHHHHh
Confidence            999999999999988743

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	181
d1fc6a4	294	c.14.1.2 (A:78-156,A:249-463) Photosystem II D1 C-	3e-25
d1j7xa_	302	c.14.1.2 (A:) Interphotoreceptor retinoid-binding	2e-22
d1k32a4	291	c.14.1.2 (A:680-762,A:854-1061) Tricorn protease {	4e-17

>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

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 = 96.7 bits (240), Expect = 3e-25
 Identities = 58/138 (42%), Positives = 89/138 (64%), Gaps = 1/138 (0%)

Query: 13  QGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASAS 72
            GGL  AG++VA++ +D  + ++ A  +       +       +  PLVVLVN G+ASAS
Sbjct: 147 GGGLFPAGVNVARMLVDRGDLVLIADSQGIRD-IYSADGNSIDSATPLVVLVNRGTASAS 205

Query: 73  EILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITP 132
           E+LAGAL D+ R ++ G +TFGKG IQ+V +L DGS + VTVA+Y +PA  DI+ +G++P
Sbjct: 206 EVLAGALKDSKRGLIAGERTFGKGLIQTVVDLSDGSGVAVTVARYQTPAGVDINKIGVSP 265

Query: 133 DVQCTTDMLSSPKESLLK 150
           DVQ   ++L +  E + +
Sbjct: 266 DVQLDPEVLPTDLEGVCR 283

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

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Tail specific protease, catalytic domain
domain: Interphotoreceptor retinoid-binding protein IRBP
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

 Score = 89.3 bits (221), Expect = 2e-22
 Identities = 25/135 (18%), Positives = 46/135 (34%), Gaps = 10/135 (7%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPIN--------MVDGHAITHDPLVVLVN 65
           GG   A   +   +LD  ET ++                    ++     +   + VL +
Sbjct: 152 GGSSTAVPLLLSYFLDP-ETKIHLFTLHNRQQNSTDEVYSHPKVLGKPYGSKKGVYVLTS 210

Query: 66  EGSASASEILAGALHDNGRAILVGHKTFGKGKIQSVTELHDGS-ALFVTVAKYLSPALHD 124
             +A+A+E  A  +    RA ++G  T G      V    D   ++ V +  ++      
Sbjct: 211 HQTATAAEEFAYLMQSLSRATIIGEITSGNLMHSKVFPFGDTQLSVTVPIINFIDSNGDY 270

Query: 125 IDHVGITPDVQCTTD 139
               G+ PD     D
Sbjct: 271 WLGGGVVPDAIVLAD 285

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

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Tail specific protease, catalytic domain
domain: Tricorn protease
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

 Score = 74.8 bits (183), Expect = 4e-17
 Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 2/79 (2%)

Query: 59  PLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKG-KIQSVTELHDGSALF-VTVAK 116
            ++ + NE + S  +I + +    G   L+G +T+G    I     L DG+ L     A 
Sbjct: 184 KIIAITNEYAGSDGDIFSFSFKKLGLGKLIGTRTWGGVVGITPKRRLIDGTVLTQPEFAF 243

Query: 117 YLSPALHDIDHVGITPDVQ 135
           +   A   +++ G+ PDV+
Sbjct: 244 WFRDAGFGVENYGVDPDVE 262

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	181
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 {	100.0

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

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=3.9e-36  Score=247.88  Aligned_cols=138  Identities=43%  Similarity=0.632  Sum_probs=123.4

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhcC
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDN   82 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~~   82 (181)
                      ..||||||+|+||++..|..++++|++++. ...+..+++....+....+...+.+|++||||+.|+||||+||++||++
T Consensus       137 ~~lIiDLR~N~GG~~~~a~~~~~~f~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~~a~~lk~~  215 (294)
T d1fc6a4         137 AGLVLDIRNNGGGLFPAGVNVARMLVDRGD-LVLIADSQGIRDIYSADGNSIDSATPLVVLVNRGTASASEVLAGALKDS  215 (294)
T ss_dssp             SEEEEECTTCCCBCHHHHHHHHHHHCSSSE-EEEEEETTEEEEEEECCSCCSCSSSCEEEEECTTCCTHHHHHHHHHHHT
T ss_pred             cEEEEEeecCcccchhhhHHHHHhhccccc-ceEEEEeccccceeccccccccccceEEEEecCCccchHHHHHHHhhhc
Confidence            569999999999999999999999999874 4455555555555555556678999999999999999999999999999


Q ss_pred             CCeEEEcccCCCCceeceEEEccCCceEEEEEEEEECCCCCcccCCCcccceEecCCCC
Q 030210           83 GRAILVGHKTFGKGKIQSVTELHDGSALFVTVAKYLSPALHDIDHVGITPDVQCTTDML  141 (181)
Q Consensus        83 ~~~~vIG~~T~G~~~~~~~~~L~~g~~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~~  141 (181)
                      +++++||++|+|+++.+..++|+||+.++++++++++|+|+++|+.||+|||+|+++..
T Consensus       216 ~~a~vvG~~T~G~g~~~~~~~L~dG~~l~~t~~~~~~p~G~~~e~~Gv~PDi~v~~~~~  274 (294)
T d1fc6a4         216 KRGLIAGERTFGKGLIQTVVDLSDGSGVAVTVARYQTPAGVDINKIGVSPDVQLDPEVL  274 (294)
T ss_dssp             TSEEEEESCCCCCCEEEEEEECTTSCEEEEEEEEEECTTSCBCTTTCCCCSEECCTTSS
T ss_pred             CeEEEEeeeccCcceeeEEEEeCCCCEEEEEeEEEECCCCCEeeCcccCCCeEECCccC
Confidence            99999999999999999999999999999999999999999999999999999986643

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

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Tail specific protease, catalytic domain
domain: Tricorn protease
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=100.00  E-value=1.8e-34  Score=237.40  Aligned_cols=153  Identities=20%  Similarity=0.196  Sum_probs=125.3

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCceeEEEEcCCCceeEEEccCCCccCCCcEEEEEcCCCccHHHHHHHHHhcC
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDN   82 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~fa~~l~~~   82 (181)
                      ..||||||+|+||++..+  ++.+|.++  .+.+...+.+...+.    ....|++|++||||+.|+||||+||++||++
T Consensus       136 ~~lIiDLR~N~GG~l~~~--i~~~~~~~--~~~~~~~~~~~~~~~----~~~~~~~pv~vLv~~~T~SaaE~~a~~lk~~  207 (291)
T d1k32a4         136 QGLIVDVRFNGGGFVSQL--IIEKLMNK--RIGYDNPRRGTLSPY----PTNSVRGKIIAITNEYAGSDGDIFSFSFKKL  207 (291)
T ss_dssp             SEEEEECTTCCCBSCHHH--HHHHHTCB--CCEEEEESSSCCEEE----STTCBCSEEEEEECTTCCTHHHHHHHHHHHT
T ss_pred             ceEEEecccCcchhHHHH--HHHHhccC--CeEEEecCcCccccC----CccccCCCEEEEECCCCCccchHHHHHHHhc
Confidence            469999999999998764  57777665  445555555544332    3457999999999999999999999999999


Q ss_pred             CCeEEEcccCCCCceec-eEEEccCCceEEE-EEEEEECCCCCcccCCCcccceEecCCCCCCchhhhhccccCCCCCCC
Q 030210           83 GRAILVGHKTFGKGKIQ-SVTELHDGSALFV-TVAKYLSPALHDIDHVGITPDVQCTTDMLSSPKESLLKNKSSVSSLEA  160 (181)
Q Consensus        83 ~~~~vIG~~T~G~~~~~-~~~~L~~g~~l~i-~~~~~~~~~g~~~e~~Gv~PDi~v~~~~~~~~~~~~~~~~~~~~~~~~  160 (181)
                      +++++||++|+|++... ..+.|++|+.+.+ +.+.+++++|..+|+.||+|||+|+.++...            .. ++
T Consensus       208 ~~~~vvG~~T~G~~~~~~~~~~l~~g~~~~~~~~~~~~~~~g~~~e~~Gv~PDi~V~~t~~~~------------~~-g~  274 (291)
T d1k32a4         208 GLGKLIGTRTWGGVVGITPKRRLIDGTVLTQPEFAFWFRDAGFGVENYGVDPDVEIEYAPHDY------------LS-GK  274 (291)
T ss_dssp             TSEEEEESCCCCCCEECCCCCBCTTSCEECCCCEEEEETTTBTTTTTTCCCCSEECCCCHHHH------------HT-TC
T ss_pred             CCeEEeeecCCCCCcceeeeEecCCCCeEEEEEEEEEECCCCcEeeCcCeecCEEECCCHHHH------------hc-Cc
Confidence            99999999999986554 4578999998876 4667888999999999999999999876532            12 79


Q ss_pred             CHHHHHHHHHHhhhcc
Q 030210          161 DSCIMVAEHELDVQES  176 (181)
Q Consensus       161 D~~l~~Ai~~L~~~~~  176 (181)
                      ||+|++||++|+++++
T Consensus       275 D~~Le~Ai~~l~~~ik  290 (291)
T d1k32a4         275 DPQIDYAIDALIEELR  290 (291)
T ss_dssp             CHHHHHHHHHHHHHTT
T ss_pred             cHHHHHHHHHHHHHhc
Confidence            9999999999999876

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

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Tail specific protease, catalytic domain
domain: Interphotoreceptor retinoid-binding protein IRBP
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=100.00  E-value=1.3e-32  Score=227.49  Aligned_cols=151  Identities=18%  Similarity=0.154  Sum_probs=126.5

Q ss_pred             eEEEeecCCCCCCCHHHHHHHHhhccCCCce--eEEEEcCCCceeE-EEc-c---CCCccCCCcEEEEEcCCCccHHHHH
Q 030210            3 FFSPPSLSIFQGGLVKAGLDVAQIWLDGDET--LVNAVDREGHTLP-INM-V---DGHAITHDPLVVLVNEGSASASEIL   75 (181)
Q Consensus         3 ~~lIiDLR~N~GG~~~~a~~l~~~f~~~~~~--~~~~~~r~g~~~~-~~~-~---~~~~~~~~pv~VL~~~~TaSaaE~f   75 (181)
                      ..||||||+|+||++..+..++++|++++..  +...++|.+.... .+. +   .....+++|++||||+.|+||||.|
T Consensus       141 ~~LIiDLR~N~GG~~~~~~~i~s~f~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~g~~~~~~kpv~VLt~~~T~SaaE~f  220 (302)
T d1j7xa_         141 ENLIIDLRYNVGGSSTAVPLLLSYFLDPETKIHLFTLHNRQQNSTDEVYSHPKVLGKPYGSKKGVYVLTSHQTATAAEEF  220 (302)
T ss_dssp             SEEEEECTTCCCBCSTTHHHHHHTTSCSSCCCEEEEEEETTTTCCEEEECCSCCSSCCCCSSSEEEEEECTTCCTHHHHH
T ss_pred             ceEEEEcCcCCCCCHHHHHHHHHHhcCCCceEEEEEEccCccccceEEeccccccCCCcccCCCEEEEECCCCCCchhhh
Confidence            4699999999999999999999999997643  3344556554322 221 1   1234578999999999999999999


Q ss_pred             HHHHhcCCCeEEEcccCCCCceeceEEEccCCc-eEEEEEEEEECCCCCcccCCCcccceEecCCCCCCchhhhhccccC
Q 030210           76 AGALHDNGRAILVGHKTFGKGKIQSVTELHDGS-ALFVTVAKYLSPALHDIDHVGITPDVQCTTDMLSSPKESLLKNKSS  154 (181)
Q Consensus        76 a~~l~~~~~~~vIG~~T~G~~~~~~~~~L~~g~-~l~i~~~~~~~~~g~~~e~~Gv~PDi~v~~~~~~~~~~~~~~~~~~  154 (181)
                      |++||+++++++||++|+|++..+..+.++++. .+.+++.++++++|+.||+.||.||+.|+.                
T Consensus       221 a~~lk~~~ra~vVGe~T~G~~~~~~~~~l~~~~~~l~vp~~~~~~~~G~~~eg~GV~PDv~V~~----------------  284 (302)
T d1j7xa_         221 AYLMQSLSRATIIGEITSGNLMHSKVFPFGDTQLSVTVPIINFIDSNGDYWLGGGVVPDAIVLA----------------  284 (302)
T ss_dssp             HHHHHHTTCCEEEESCCCCCCSCEEEEECTTSSEEEEEECEEEEETTSCBCCCSCCCCSEECCG----------------
T ss_pred             hhccccCCeEEEEEEeccCCCccceEEEeCCCCEEEEEeEEEEEcCCCCEeeCcCcCCCEeeCc----------------
Confidence            999999999999999999999888999998864 789999999999999999999999999852                


Q ss_pred             CCCCCCCHHHHHHHHHHhhhc
Q 030210          155 VSSLEADSCIMVAEHELDVQE  175 (181)
Q Consensus       155 ~~~~~~D~~l~~Ai~~L~~~~  175 (181)
                            |..|++|+++|+...
T Consensus       285 ------e~aL~~A~~ll~~~~  299 (302)
T d1j7xa_         285 ------DEALDKAKEIIAFHP  299 (302)
T ss_dssp             ------GGHHHHHHHHHHTCC
T ss_pred             ------hHHHHHHHHHHhcCc
Confidence                  567999999997653