Citrus Sinensis ID: 033051

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------13
Protein Sequence
MVFFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQVYNVSYCQASSAQMLNLIHCVDLSSLNCL
Secondary Structure (PSIPRED)
ccccccccccccccccHHHHHHHHHHHHcccccEEEEcccccccEEEEcccccccccccEEEEEccccccHHHHHHcHHcccccEEEEccccccccEEEEEEEcccccccEEEEHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccHHHHHHHHHHHHcccccEEEEEEcccccEEEEEcccccccccccEEEEEccccccHHHHHHHHHHHccccEEEEcccccccEEEEEEEEEccccccEEEEEEEEccccccccc
Coil and Loop (DISEMBL)
mvffsppslsifqgglvkAGLDVAQIWLDGDETLVNAvdreghtlpinmvdghaithdPLVVLVNEGSASASEILAGALHDNGRAILVghktfgkgkIQVYNVSYCQASSAQMLNLIHcvdlsslncl
Flexible Loop (DISEMBL)
mvffsppslSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQVYNVSYCQASSAQMLNLIHCVDLSSLNCL
Low Complexity Region (SEG)
MVFFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQVYNVSYCQASSAQMLNLIHCVDLSSLNCL
Disordered region (IsUnstruct)
********LSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQVYNVSYCQASSAQMLNLIHCVDLSS****
Disordered Region (DISOPRED)
****SPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAV****************ITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQVYNVSYCQASSAQMLNLIHCVDLSSLNC*
Disordered Region (DISEMBL)
MVFFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQVYNVSYCQASSAQMLNLIHCVDLSSLNCL
Disordered Region (DISPRO)
*VFFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQVYNVSYCQASSAQMLNLIHCVDLSSL***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVFFSPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQVYNVSYCQASSAQMLNLIHCVDLSSLNCL
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	128	2.2.26 [Sep-21-2011]
P42784	414	Carboxyl-terminal-process	yes	no	0.656	0.202	0.604	3e-21
Q55669	427	Carboxyl-terminal-process	N/A	no	0.656	0.196	0.604	3e-20
O04073	464	C-terminal processing pep	N/A	no	0.648	0.178	0.511	1e-13
Q44879	434	Carboxy-terminal-processi	yes	no	0.710	0.209	0.362	9e-11
P23865	682	Tail-specific protease OS	N/A	no	0.531	0.099	0.485	2e-10
P43669	682	Tail-specific protease OS	yes	no	0.531	0.099	0.485	7e-10
Q4L6D0	496	Probable CtpA-like serine	yes	no	0.664	0.171	0.420	3e-09
Q49XN1	491	Probable CtpA-like serine	yes	no	0.656	0.171	0.404	8e-09
Q8NWR2	496	Probable CtpA-like serine	yes	no	0.664	0.171	0.409	5e-08
Q6G9E1	496	Probable CtpA-like serine	yes	no	0.664	0.171	0.409	5e-08

>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 =  100 bits (249), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 52/86 (60%), Positives = 67/86 (77%), Gaps = 2/86 (2%)

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  ILAGALHDNGRAILVGHKTFGKGKIQ 99
           ILAGAL DNGRA+LVG KTFGKG IQ
Sbjct: 314 ILAGALQDNGRAMLVGEKTFGKGLIQ 339

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 = 97.1 bits (240), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 52/86 (60%), Positives = 65/86 (75%), Gaps = 2/86 (2%)

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  ILAGALHDNGRAILVGHKTFGKGKIQ 99
           ILAGAL DN RA LVG KTFGKG IQ
Sbjct: 317 ILAGALQDNQRATLVGEKTFGKGLIQ 342

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 = 74.7 bits (182), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 45/88 (51%), Positives = 61/88 (69%), Gaps = 5/88 (5%)

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  SEILAGALHDNGRAILVGHKTFGKGKIQ 99
           SE+LAGAL D+ R ++ G +TFGKG IQ
Sbjct: 374 SEVLAGALKDSKRGLIAGERTFGKGLIQ 401

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 = 65.5 bits (158), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 33/91 (36%), Positives = 53/91 (58%)

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

Query: 69  ASASEILAGALHDNGRAILVGHKTFGKGKIQ 99
           ASASEI+AGAL D+ RA ++G ++FGKG +Q
Sbjct: 293 ASASEIVAGALQDHRRATIIGTQSFGKGSVQ 323

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|P23865|PRC_ECOLI Tail-specific protease OS=Escherichia coli (strain K12) GN=prc PE=1 SV=2

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 33/68 (48%), Positives = 40/68 (58%)

Query: 34  LVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTF 93
           +V   D  G     +  DG      PLVVLV+  SASASEI A A+ D GRA++VG  TF
Sbjct: 416 IVQVRDNNGKVREDSDTDGQVFYKGPLVVLVDRFSASASEIFAAAMQDYGRALVVGEPTF 475

Query: 94  GKGKIQVY 101
           GKG +Q Y
Sbjct: 476 GKGTVQQY 483

Involved in the cleavage of a C-terminal peptide of 11 residues from the precursor form of penicillin-binding protein 3 (PBP3). May be involved in protection of the bacterium from thermal and osmotic stresses.

Escherichia coli (strain K12) (taxid: 83333)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 1

EC: .

EC: 1

EC: 0

EC: 2

>sp|P43669|PRC_SALTY Tail-specific protease OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=prc PE=3 SV=2

 Score = 62.8 bits (151), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 33/68 (48%), Positives = 40/68 (58%)

Query: 34  LVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTF 93
           +V   D  G     +  DG      PLVVLV+  SASASEI A A+ D GRA++VG  TF
Sbjct: 416 IVQVRDNNGKVREDSDTDGVVYYKGPLVVLVDRFSASASEIFAAAMQDYGRALIVGEPTF 475

Query: 94  GKGKIQVY 101
           GKG +Q Y
Sbjct: 476 GKGTVQQY 483

Involved in the cleavage of a C-terminal peptide of 11 residues from the precursor form of penicillin-binding protein 3 (PBP3). May be involved in protection of the bacterium from thermal and osmotic stresses.

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (taxid: 99287)

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 = 60.5 bits (145), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 37/88 (42%), Positives = 54/88 (61%), Gaps = 3/88 (3%)

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

Query: 72  SEILAGALHDNGRAILVGHKTFGKGKIQ 99
           SE+  GA+ D+ +A + G KTFGKG +Q
Sbjct: 331 SEVFTGAMRDHKKAKVYGSKTFGKGIVQ 358

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 = 58.9 bits (141), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 36/89 (40%), Positives = 54/89 (60%), Gaps = 5/89 (5%)

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

Query: 71  ASEILAGALHDNGRAILVGHKTFGKGKIQ 99
           ASE+  GA+ D  +A + G KTFGKG +Q
Sbjct: 325 ASEVFTGAMKDYNKAKVYGSKTFGKGIVQ 353

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

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 = 56.6 bits (135), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 36/88 (40%), Positives = 52/88 (59%), Gaps = 3/88 (3%)

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

Query: 72  SEILAGALHDNGRAILVGHKTFGKGKIQ 99
           SE+  GAL D  +A + G KTFGKG +Q
Sbjct: 331 SEVFTGALKDYNKAKVYGSKTFGKGVVQ 358

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 = 56.6 bits (135), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 36/88 (40%), Positives = 52/88 (59%), Gaps = 3/88 (3%)

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

Query: 72  SEILAGALHDNGRAILVGHKTFGKGKIQ 99
           SE+  GAL D  +A + G KTFGKG +Q
Sbjct: 331 SEVFTGALKDYNKAKVYGSKTFGKGVVQ 358

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	128
413953829	491	hypothetical protein ZEAMMB73_760342 [Ze	0.703	0.183	0.877	2e-40
224087066	192	predicted protein [Populus trichocarpa]	0.671	0.447	0.941	9e-40
255571580	414	protease, putative [Ricinus communis] gi	0.671	0.207	0.930	1e-39
226493045	520	carboxyl-terminal-processing protease [Z	0.671	0.165	0.895	6e-39
223948537	509	unknown [Zea mays]	0.671	0.168	0.895	6e-39
413953827	520	carboxyl-terminal-processing protease is	0.671	0.165	0.895	7e-39
356534629	508	PREDICTED: carboxyl-terminal-processing	0.671	0.169	0.906	9e-39
359481833	520	PREDICTED: carboxyl-terminal-processing	0.671	0.165	0.918	1e-38
297739701	431	unnamed protein product [Vitis vinifera]	0.671	0.199	0.918	2e-38
242092926	522	hypothetical protein SORBIDRAFT_10g01216	0.671	0.164	0.883	2e-38

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

 Score =  170 bits (430), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 79/90 (87%), Positives = 86/90 (95%)

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

Query: 70  SASEILAGALHDNGRAILVGHKTFGKGKIQ 99
           SASEILAGALHDNGRAILVGH+TFGKGKIQ
Sbjct: 380 SASEILAGALHDNGRAILVGHRTFGKGKIQ 409

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  167 bits (424), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 81/86 (94%), Positives = 84/86 (97%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQ 99
           ILAGALHDNGRAILVGHKTFGKGKIQ
Sbjct: 85  ILAGALHDNGRAILVGHKTFGKGKIQ 110

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  167 bits (423), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 80/86 (93%), Positives = 84/86 (97%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQ 99
           ILAGALHDNGRAILVGHKTFGKGKIQ
Sbjct: 307 ILAGALHDNGRAILVGHKTFGKGKIQ 332

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  165 bits (417), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 77/86 (89%), Positives = 83/86 (96%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQ 99
           ILAGALHDNGRAILVGH+TFGKGKIQ
Sbjct: 413 ILAGALHDNGRAILVGHRTFGKGKIQ 438

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 =  165 bits (417), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 77/86 (89%), Positives = 83/86 (96%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQ 99
           ILAGALHDNGRAILVGH+TFGKGKIQ
Sbjct: 402 ILAGALHDNGRAILVGHRTFGKGKIQ 427

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 =  165 bits (417), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 77/86 (89%), Positives = 83/86 (96%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQ 99
           ILAGALHDNGRAILVGH+TFGKGKIQ
Sbjct: 413 ILAGALHDNGRAILVGHRTFGKGKIQ 438

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  164 bits (416), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 78/86 (90%), Positives = 84/86 (97%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQ 99
           ILAGALHDNGRAILVGHKTFGKGKIQ
Sbjct: 399 ILAGALHDNGRAILVGHKTFGKGKIQ 424

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  164 bits (415), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 79/86 (91%), Positives = 82/86 (95%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQ 99
           ILAGALHDNGRAILVGHKTFGKGKIQ
Sbjct: 413 ILAGALHDNGRAILVGHKTFGKGKIQ 438

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 =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 79/86 (91%), Positives = 82/86 (95%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQ 99
           ILAGALHDNGRAILVGHKTFGKGKIQ
Sbjct: 324 ILAGALHDNGRAILVGHKTFGKGKIQ 349

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242092926|ref|XP_002436953.1| hypothetical protein SORBIDRAFT_10g012160 [Sorghum bicolor] gi|241915176|gb|EER88320.1| hypothetical protein SORBIDRAFT_10g012160 [Sorghum bicolor]

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 76/86 (88%), Positives = 83/86 (96%)

Query: 14  GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
           GGLVKAGLDVAQIWLDGDETLVN +DR+G+ LPINM+ GH++THDPLVVLVNEGSASASE
Sbjct: 355 GGLVKAGLDVAQIWLDGDETLVNTIDRDGNVLPINMIQGHSLTHDPLVVLVNEGSASASE 414

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQ 99
           ILAGALHDNGRAILVGH+TFGKGKIQ
Sbjct: 415 ILAGALHDNGRAILVGHRTFGKGKIQ 440

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

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	128
UNIPROTKB|P75023	462	ctpB "Carboxyl-terminal protea	0.679	0.188	0.505	2.2e-16
UNIPROTKB|P73458	423	prc "Carboxyl-terminal proteas	0.656	0.198	0.511	2.8e-16
TAIR|locus:2170443	489	AT5G46390 [Arabidopsis thalian	0.703	0.184	0.450	5.1e-15
TAIR|locus:2129411	515	AT4G17740 [Arabidopsis thalian	0.695	0.172	0.510	1.5e-14
TIGR_CMR|CBU_1538	456	CBU_1538 "carboxyl-terminal pr	0.671	0.188	0.440	1.3e-11
TIGR_CMR|SPO_3812	443	SPO_3812 "carboxyl-terminal pr	0.664	0.191	0.459	3.4e-11
TIGR_CMR|CHY_0170	377	CHY_0170 "carboxyl-terminal pr	0.656	0.222	0.476	3.9e-11
TIGR_CMR|DET_0364	377	DET_0364 "carboxyl-terminal pr	0.703	0.238	0.402	8.4e-11
UNIPROTKB|P23865	682	prc [Escherichia coli K-12 (ta	0.679	0.127	0.397	6.4e-10
TIGR_CMR|GSU_0969	450	GSU_0969 "carboxy-terminal pro	0.671	0.191	0.422	1.1e-09

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

 Score = 210 (79.0 bits), Expect = 2.2e-16, P = 2.2e-16
 Identities = 45/89 (50%), Positives = 63/89 (70%)

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

Query:    74 ILAGALHDNGRAILVGHKTFGKGKIQVYN 102
             ILAGAL + GRA +VG  T+GKG +Q  N
Sbjct:   343 ILAGALKEQGRATVVGTATYGKGTVQSVN 371

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

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

 Score = 208 (78.3 bits), Expect = 2.8e-16, P = 2.8e-16
 Identities = 44/86 (51%), Positives = 63/86 (73%)

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

Query:    74 ILAGALHDNGRAILVGHKTFGKGKIQ 99
             I++GAL DN RA++VG KTFGKG +Q
Sbjct:   319 IVSGALQDNQRAVIVGTKTFGKGLVQ 344

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

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

 Score = 198 (74.8 bits), Expect = 5.1e-15, P = 5.1e-15
 Identities = 41/91 (45%), Positives = 62/91 (68%)

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

Query:    74 ILAGALHDNGRAILVGHKTFGKGKIQ-VYNV 103
             I+A ALHDN +A+LVG +T+GKG IQ VY +
Sbjct:   407 IVASALHDNCKAVLVGERTYGKGLIQSVYEL 437

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

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

 Score = 194 (73.4 bits), Expect = 1.5e-14, P = 1.5e-14
 Identities = 48/94 (51%), Positives = 62/94 (65%)

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 SEILAGALHDNGRAILVGHKTFGKGKIQ-VYNVS 104
             SEILAGAL DN RA++ G  T+GKGKIQ V+ +S
Sbjct:   419 SEILAGALKDNKRALVYGEPTYGKGKIQSVFELS 452

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

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

 Score = 166 (63.5 bits), Expect = 1.3e-11, P = 1.3e-11
 Identities = 41/93 (44%), Positives = 54/93 (58%)

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 GSASASEILAGALHDNGRAILVGHKTFGKGKIQ 99
             GSASASEI+AGAL D  RAI++G  +FGKG +Q
Sbjct:   314 GSASASEIVAGALQDYKRAIIMGTPSFGKGSVQ 346

GO:0006508 "proteolysis" evidence=ISS

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

 Score = 162 (62.1 bits), Expect = 3.4e-11, P = 3.4e-11
 Identities = 40/87 (45%), Positives = 53/87 (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 EILAGALHDNGRAILVGHKTFGKGKIQ 99
             EI+AGAL D+ RAI+VG K+FGKG +Q
Sbjct:   302 EIVAGALQDHRRAIVVGTKSFGKGSVQ 328

GO:0006508 "proteolysis" evidence=ISS

GO:0008233 "peptidase activity" evidence=ISS

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

 Score = 160 (61.4 bits), Expect = 3.9e-11, P = 3.9e-11
 Identities = 41/86 (47%), Positives = 55/86 (63%)

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

Query:    74 ILAGALHDNGRAILVGHKTFGKGKIQ 99
             I+AGAL D G A+LVG KTFGKG +Q
Sbjct:   291 IVAGALKDWGVAVLVGEKTFGKGVVQ 316

GO:0006508 "proteolysis" evidence=ISS

TIGR_CMR|DET_0364 DET_0364 "carboxyl-terminal protease" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 157 (60.3 bits), Expect = 8.4e-11, P = 8.4e-11
 Identities = 37/92 (40%), Positives = 56/92 (60%)

Query:    14 GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
             GGLV + ++V   ++     L   VD EG++   ++V     T  P+VVLV++ SAS SE
Sbjct:   237 GGLVSSVINVTSRFVSSGVVLTT-VDNEGNSSEYSVVPKTVTTSLPMVVLVDQYSASGSE 295

Query:    74 ILAGALHDNGRAILVGHKTFGKGKI-QVYNVS 104
              L+GAL D GRA + G  T+GKG + + +NV+
Sbjct:   296 ALSGALQDYGRATIAGKTTYGKGSVNRTFNVT 327

GO:0006464 "cellular protein modification process" evidence=ISS

GO:0006508 "proteolysis" evidence=ISS

UNIPROTKB|P23865 prc [Escherichia coli K-12 (taxid:83333)]

 Score = 153 (58.9 bits), Expect = 6.4e-10, P = 6.4e-10
 Identities = 35/88 (39%), Positives = 49/88 (55%)

Query:    14 GGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASE 73
             GG +   + ++ +++     +V   D  G     +  DG      PLVVLV+  SASASE
Sbjct:   397 GGALTEAVSLSGLFIPAGP-IVQVRDNNGKVREDSDTDGQVFYKGPLVVLVDRFSASASE 455

Query:    74 ILAGALHDNGRAILVGHKTFGKGKIQVY 101
             I A A+ D GRA++VG  TFGKG +Q Y
Sbjct:   456 IFAAAMQDYGRALVVGEPTFGKGTVQQY 483

GO:0030163 "protein catabolic process" evidence=IDA

GO:0006508 "proteolysis" evidence=IEA;IDA

GO:0004175 "endopeptidase activity" evidence=IDA

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

GO:0005886 "plasma membrane" evidence=IEA

GO:0016020 "membrane" evidence=IEA

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

GO:0042493 "response to drug" evidence=EXP

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

 Score = 148 (57.2 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 38/90 (42%), Positives = 53/90 (58%)

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

Query:    70 SASEILAGALHDNGRAILVGHKTFGKGKIQ 99
             SASEI+AGAL D+GRA+++G  +FGKG +Q
Sbjct:   302 SASEIVAGALQDHGRAVIMGTTSFGKGSVQ 331

GO:0006508 "proteolysis" 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

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: grail3.0024039601 hypothetical protein (192 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	128
cd07560	211	cd07560, Peptidase_S41_CPP, C-terminal processing	2e-32
COG0793	406	COG0793, Prc, Periplasmic protease [Cell envelope	5e-27
TIGR00225	334	TIGR00225, prc, C-terminal peptidase (prc)	1e-26
smart00245	192	smart00245, TSPc, tail specific protease	3e-25
cd06567	224	cd06567, Peptidase_S41, C-terminal processing pept	4e-25
pfam03572	166	pfam03572, Peptidase_S41, Peptidase family S41	1e-24
PLN00049	389	PLN00049, PLN00049, carboxyl-terminal processing p	3e-24
TIGR03900	973	TIGR03900, prc_long_Delta, putative carboxyl-termi	6e-18
PRK11186	667	PRK11186, PRK11186, carboxy-terminal protease; Pro	1e-15
cd07562	266	cd07562, Peptidase_S41_TRI, Tricorn protease; seri	3e-09
cd07561	256	cd07561, Peptidase_S41_CPP_like, C-terminal proces	8e-05
cd07563	250	cd07563, Peptidase_S41_IRBP, Interphotoreceptor re	8e-05

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

 Score =  112 bits (284), Expect = 2e-32
 Identities = 44/87 (50%), Positives = 56/87 (64%), Gaps = 2/87 (2%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQV 100
           I+AGAL DNGRA+LVG +TFGKG +Q 
Sbjct: 148 IVAGALQDNGRAVLVGERTFGKGSVQT 174

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

 Score =  102 bits (257), Expect = 5e-27
 Identities = 43/86 (50%), Positives = 52/86 (60%), Gaps = 1/86 (1%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQ 99
           I AGAL D GRA LVG  TFGKG +Q
Sbjct: 304 IFAGALQDYGRATLVGETTFGKGTVQ 329

Length = 406

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

 Score =  100 bits (251), Expect = 1e-26
 Identities = 42/89 (47%), Positives = 58/89 (65%), Gaps = 2/89 (2%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQVYN 102
           I AGAL DNGRA +VG KTFGKG +Q   
Sbjct: 251 IFAGALQDNGRATIVGEKTFGKGTVQQVR 279

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|214582 smart00245, TSPc, tail specific protease

 Score = 93.9 bits (234), Expect = 3e-25
 Identities = 42/102 (41%), Positives = 58/102 (56%), Gaps = 5/102 (4%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQ----VYNVSYCQASSA 111
           I AGAL D GRA +VG +TFGKG +Q    + + S  + + A
Sbjct: 129 IFAGALKDLGRATIVGERTFGKGLVQQTVPLGDGSGLKLTVA 170

tail specific protease. Length = 192

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

 Score = 94.3 bits (235), Expect = 4e-25
 Identities = 43/87 (49%), Positives = 56/87 (64%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQV 100
           I AGAL D GRA LVG +TFGKG +Q 
Sbjct: 161 IFAGALQDLGRATLVGERTFGKGSVQT 187

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|217620 pfam03572, Peptidase_S41, Peptidase family S41

 Score = 91.9 bits (229), Expect = 1e-24
 Identities = 45/89 (50%), Positives = 57/89 (64%), Gaps = 4/89 (4%)

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

Query: 71  ASEILAGALHDNGRAILVGHKTFGKGKIQ 99
           ASEI AGAL D GRA LVG +TFGKG +Q
Sbjct: 101 ASEIFAGALKDLGRATLVGERTFGKGLVQ 129

Length = 166

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

 Score = 94.8 bits (236), Expect = 3e-24
 Identities = 50/94 (53%), Positives = 64/94 (68%), Gaps = 5/94 (5%)

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  SEILAGALHDNGRAILVGHKTFGKGKIQ-VYNVS 104
           SEILAGAL DN RA+++G  TFGKG IQ V+ +S
Sbjct: 294 SEILAGALKDNKRAVVLGEPTFGKGLIQSVFELS 327

Length = 389

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

 Score = 78.3 bits (193), Expect = 6e-18
 Identities = 39/89 (43%), Positives = 56/89 (62%), Gaps = 4/89 (4%)

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

Query: 72  SEILAGALHDNGRAILVGHKTFGKGKIQV 100
           SEI+AGAL +  RA+++G +TFGKG +QV
Sbjct: 338 SEIVAGALKNLDRAVIIGRQTFGKGSVQV 366

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|236873 PRK11186, PRK11186, carboxy-terminal protease; Provisional

 Score = 71.5 bits (176), Expect = 1e-15
 Identities = 27/43 (62%), Positives = 33/43 (76%)

Query: 59  PLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQVY 101
           PLVVLV+  SASASEI A A+ D GRA++VG  TFGKG +Q +
Sbjct: 439 PLVVLVDRYSASASEIFAAAMQDYGRALIVGEPTFGKGTVQQH 481

Length = 667

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

 Score = 52.6 bits (127), Expect = 3e-09
 Identities = 19/36 (52%), Positives = 23/36 (63%)

Query: 59  PLVVLVNEGSASASEILAGALHDNGRAILVGHKTFG 94
           P+VVLVNEGSAS +EI A      G   +VG +T G
Sbjct: 165 PVVVLVNEGSASDAEIFAYGFRALGLGPVVGTRTAG 200

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

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 13/39 (33%), Positives = 24/39 (61%), Gaps = 4/39 (10%)

Query: 60  LVVLVNEGSASASEILAGAL--HDNGRAILVGHKTFGKG 96
           + VL +  +ASASE++  +L  + +   +L+G  T+GK 
Sbjct: 163 VYVLTSGSTASASELVINSLKPYMD--VVLIGETTYGKN 199

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

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

 Score = 40.4 bits (95), Expect = 8e-05
 Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 3/60 (5%)

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

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	128
COG0793	406	Prc Periplasmic protease [Cell envelope biogenesis	99.96
smart00245	192	TSPc tail specific protease. tail specific proteas	99.94
cd06567	224	Peptidase_S41 C-terminal processing peptidase fami	99.94
cd07560	211	Peptidase_S41_CPP C-terminal processing peptidase;	99.94
PLN00049	389	carboxyl-terminal processing protease; Provisional	99.94
TIGR00225	334	prc C-terminal peptidase (prc). A C-terminal pepti	99.93
PRK11186	667	carboxy-terminal protease; Provisional	99.93
cd07561	256	Peptidase_S41_CPP_like C-terminal processing pepti	99.93
cd07563	250	Peptidase_S41_IRBP Interphotoreceptor retinoid-bin	99.9
PF03572	169	Peptidase_S41: Peptidase family S41; InterPro: IPR	99.87
cd07562	266	Peptidase_S41_TRI Tricorn protease; serine proteas	99.84
cd07021	178	Clp_protease_NfeD_like Nodulation formation effici	85.39

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

Probab=99.96  E-value=2.5e-29  Score=208.13  Aligned_cols=109  Identities=41%  Similarity=0.578  Sum_probs=98.8

Q ss_pred             ceeeecCCCCCCHHHHHHHHhccccCCceeEEEEcCCCceeEEeccCCCccCCCcEEEEEcCCCCChHHHHHHHhhcCCC
Q 033051            5 SPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGR   84 (128)
Q Consensus         5 ~iiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pivVLvn~~TaSaaE~~a~alk~~~~   84 (128)
                      .|||||+|+||.+.+|..++++|++++ ++.+.++|+|+..++........+++|++||||+.|||||||||+|||+++|
T Consensus       236 lIlDLR~N~GG~L~~av~i~~~f~~~g-~iv~~~~r~g~~~~~~~~~~~~~~~~PlvvLvn~~SASAsEI~agalqd~~r  314 (406)
T COG0793         236 LILDLRNNPGGLLSQAVKLAGLFLPSG-PIVSTRGRNGKVNVYFSASGEALYDGPLVVLVNEGSASASEIFAGALQDYGR  314 (406)
T ss_pred             EEEEeCCCCCccHHHHHHHHHcccCCC-cEEEEecCCCceeeccccccccCCCCCEEEEECCCCccHHHHHHHHHHHcCC
Confidence            399999999999999999999999985 7899999999887776555555789999999999999999999999999999


Q ss_pred             eEEEcccCCCCceEEEEEEEccCCCcceeee
Q 033051           85 AILVGHKTFGKGKIQVYNVSYCQASSAQMLN  115 (128)
Q Consensus        85 a~vIG~~T~G~g~~q~~~~~l~dG~~~~~~~  115 (128)
                      |+|||++|||||++|+. .+|+||+..+++.
T Consensus       315 a~lVG~~TfGkg~vQ~~-~~L~dg~~lklT~  344 (406)
T COG0793         315 ATLVGETTFGKGTVQTL-RPLSDGSALKLTI  344 (406)
T ss_pred             cEEEecccccceEEEee-EEcCCCCeEEEEE
Confidence            99999999999999984 7899998877653

>smart00245 TSPc tail specific protease

Probab=99.94  E-value=4.1e-26  Score=171.48  Aligned_cols=108  Identities=42%  Similarity=0.576  Sum_probs=88.2

Q ss_pred             eeeecCCCCCCHHHHHHHHhccccCCceeEEEEcCC-CceeEEeccCCCccCCCcEEEEEcCCCCChHHHHHHHhhcCCC
Q 033051            6 PPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDRE-GHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGR   84 (128)
Q Consensus         6 iiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~-g~~~~~~~~~~~~~~~~pivVLvn~~TaSaaE~~a~alk~~~~   84 (128)
                      |||||+|+||.+..+..++++|++++. +.....++ ++...+.. .....+++|++||+|++|+||||+||++||++++
T Consensus        62 IiDLR~N~GG~~~~~~~~~~~f~~~~~-~~~~~~~~~~~~~~~~~-~~~~~~~~pv~vL~~~~TaSaaE~~a~~lk~~~~  139 (192)
T smart00245       62 ILDLRNNPGGLLSAAIDVSSLFLDKGV-IVYTIYRRTGELETYPA-NLGRKYSKPLVVLVNEGTASASEIFAGALKDLGR  139 (192)
T ss_pred             EEEecCCCCCCHHHHHHHHHHhcCCCc-EEEEEecCCCceEEEec-CCCcccCCCEEEEECCCCeeHHHHHHHHHhhCCC
Confidence            999999999999999999999999874 44555554 54433332 2334568999999999999999999999999999


Q ss_pred             eEEEcccCCCCceEEEEEEEccCCCcceeeee
Q 033051           85 AILVGHKTFGKGKIQVYNVSYCQASSAQMLNL  116 (128)
Q Consensus        85 a~vIG~~T~G~g~~q~~~~~l~dG~~~~~~~~  116 (128)
                      +++||++|+|++..|. .++++||+..++...
T Consensus       140 a~viG~~T~G~~~~~~-~~~l~~g~~l~it~~  170 (192)
T smart00245      140 ALIVGERTFGKGLVQQ-TVPLGDGSGLKLTVA  170 (192)
T ss_pred             EEEEecCCcCCcceee-EEEeCCCCEEEEEEE
Confidence            9999999999987765 568999987665544

tail specific protease

>cd06567 Peptidase_S41 C-terminal processing peptidase family S41

Probab=99.94  E-value=6.1e-26  Score=172.67  Aligned_cols=109  Identities=41%  Similarity=0.588  Sum_probs=88.4

Q ss_pred             ceeeecCCCCCCHHHHHHHHhccccCCceeEEEEcCCCceeEEeccCCCccCCCcEEEEEcCCCCChHHHHHHHhhcCCC
Q 033051            5 SPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGR   84 (128)
Q Consensus         5 ~iiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pivVLvn~~TaSaaE~~a~alk~~~~   84 (128)
                      .|||||+|+||.+..+..++++|++++..+.....+++....+........+.+|++||||+.|+||||+||++||++++
T Consensus        92 lIiDLR~N~GG~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~vL~~~~taSaaE~~a~~lk~~~~  171 (224)
T cd06567          92 LILDLRNNPGGLLSAAVELASLFLPKGKIVVTTRRRGGNETEYVAPGGGSLYDGPLVVLVNEGSASASEIFAGALQDLGR  171 (224)
T ss_pred             EEEEcCCCCCccHHHHHHHHHHhcCCCcEEEEEecCCCceeEEecCCCCcccCCCEEEEECCCCccHHHHHHHHHHhCCC
Confidence            49999999999999999999999998765544443333223333344556789999999999999999999999999999


Q ss_pred             eEEEcccCCCCceEEEEEEEccCCCcceee
Q 033051           85 AILVGHKTFGKGKIQVYNVSYCQASSAQML  114 (128)
Q Consensus        85 a~vIG~~T~G~g~~q~~~~~l~dG~~~~~~  114 (128)
                      +++||++|+|++..|. ..++++|....+.
T Consensus       172 ~~vvG~~T~G~~~~~~-~~~l~~g~~~~~~  200 (224)
T cd06567         172 ATLVGERTFGKGSVQT-VFPLLDGSALKLT  200 (224)
T ss_pred             eEEEeeCCCCCCcceE-EEEcCCCCEEEEE
Confidence            9999999999988654 4677788766665

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

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

Probab=99.94  E-value=6.1e-26  Score=173.39  Aligned_cols=113  Identities=40%  Similarity=0.610  Sum_probs=93.3

Q ss_pred             ceeeecCCCCCCHHHHHHHHhccccCCceeEEEEcCCCceeEEeccCCCccCCCcEEEEEcCCCCChHHHHHHHhhcCCC
Q 033051            5 SPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGR   84 (128)
Q Consensus         5 ~iiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pivVLvn~~TaSaaE~~a~alk~~~~   84 (128)
                      .|||||+|+||.+..+..++++|++++ .+++++.|+|+...+.. +....+.+|++||||+.|+||||+||++||++++
T Consensus        81 lIlDLR~N~GG~~~~~~~i~~~f~~~~-~~~~~~~~~g~~~~~~~-~~~~~~~~pvvVLvn~~TaSaaE~~a~~lk~~~~  158 (211)
T cd07560          81 LILDLRNNPGGLLDEAVEIADLFLPGG-PIVSTKGRNGKREAYAS-DDGGLYDGPLVVLVNGGSASASEIVAGALQDNGR  158 (211)
T ss_pred             EEEEcCCCCCCCHHHHHHHHHHhcCCC-eEEEEEecCCceEEEec-CCCccCCCCEEEEeCCCcccHHHHHHHHHhhcCC
Confidence            399999999999999999999999964 67778888876654432 3334689999999999999999999999999999


Q ss_pred             eEEEcccCCCCceEEEEEEEccCCCcceeeeeeEEee
Q 033051           85 AILVGHKTFGKGKIQVYNVSYCQASSAQMLNLIHCVD  121 (128)
Q Consensus        85 a~vIG~~T~G~g~~q~~~~~l~dG~~~~~~~~~~~~~  121 (128)
                      +++||++|+|++..+. .++++||...++. ..++++
T Consensus       159 ~~vIG~~T~G~~~~~~-~~~L~~g~~l~i~-~~~~~~  193 (211)
T cd07560         159 AVLVGERTFGKGSVQT-VFPLSDGSALKLT-TAKYYT  193 (211)
T ss_pred             EEEEecCCCCCCeeeE-EEEcCCCCEEEEE-EEEEEC
Confidence            9999999999987654 5789998766554 334443

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

>PLN00049 carboxyl-terminal processing protease; Provisional

Probab=99.94  E-value=3.4e-26  Score=188.26  Aligned_cols=108  Identities=42%  Similarity=0.591  Sum_probs=90.0

Q ss_pred             ceeeecCCCCCCHHHHHHHHhccccCCceeEEEEcCCCceeEEeccCC-CccCCCcEEEEEcCCCCChHHHHHHHhhcCC
Q 033051            5 SPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDG-HAITHDPLVVLVNEGSASASEILAGALHDNG   83 (128)
Q Consensus         5 ~iiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~-~~~~~~pivVLvn~~TaSaaE~~a~alk~~~   83 (128)
                      .|||||+|+||.+.+|..++++|++++. +.+..++++....+..... ...+.+|++||+|+.||||||+||++||+++
T Consensus       227 lIlDLR~N~GG~~~~a~~ia~~f~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~PvvVLvn~~TaSasEi~a~alk~~~  305 (389)
T PLN00049        227 FVLDLRDNSGGLFPAGIEIAKLWLDKGV-IVYIADSRGVRDIYDADGSSAIATSEPLAVLVNKGTASASEILAGALKDNK  305 (389)
T ss_pred             EEEEcCCCCCCCHHHHHHHHHHhcCCCc-EEEEecCCCceeEEecCCCccccCCCCEEEEECCCCccHHHHHHHHHhhCC
Confidence            3999999999999999999999999875 5565566665444443322 2357899999999999999999999999999


Q ss_pred             CeEEEcccCCCCceEEEEEEEccCCCcceee
Q 033051           84 RAILVGHKTFGKGKIQVYNVSYCQASSAQML  114 (128)
Q Consensus        84 ~a~vIG~~T~G~g~~q~~~~~l~dG~~~~~~  114 (128)
                      ++++||++|+|||++|.. ++|+||+..++.
T Consensus       306 ~~~vvG~~T~Gkg~~q~~-~~L~dG~~l~lt  335 (389)
T PLN00049        306 RAVVLGEPTFGKGLIQSV-FELSDGSGLAVT  335 (389)
T ss_pred             CeEEEecCCcCCccccee-EEeCCCCEEEEE
Confidence            999999999999998874 699999876544

>TIGR00225 prc C-terminal peptidase (prc)

Probab=99.93  E-value=1.1e-25  Score=181.48  Aligned_cols=107  Identities=41%  Similarity=0.610  Sum_probs=91.9

Q ss_pred             ceeeecCCCCCCHHHHHHHHhccccCCceeEEEEcCCCceeEEeccCCCccCCCcEEEEEcCCCCChHHHHHHHhhcCCC
Q 033051            5 SPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGR   84 (128)
Q Consensus         5 ~iiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pivVLvn~~TaSaaE~~a~alk~~~~   84 (128)
                      .|||||+|+||.+.++..++++|++++ .+++.++++++...+. .+....+++|++||||+.||||||+||++||++++
T Consensus       184 lIiDLR~N~GG~~~~a~~~a~~f~~~~-~~~~~~~~~g~~~~~~-~~~~~~~~~pv~vLvn~~TaSaaE~~a~~l~~~~~  261 (334)
T TIGR00225       184 YILDLRGNPGGLLQSAVDISRLFITKG-PIVQTKDRNGSKRHYK-ANGRQPYNLPLVVLVNRGSASASEIFAGALQDNGR  261 (334)
T ss_pred             EEEEcCCCCCCCHHHHHHHHHHhcCCC-cEEEEEcCCCcceEEe-cCCCccCCCCEEEEECCCCCcHHHHHHHHHHhCCC
Confidence            399999999999999999999999987 5778888888765333 23445789999999999999999999999999999


Q ss_pred             eEEEcccCCCCceEEEEEEEccCCCcceee
Q 033051           85 AILVGHKTFGKGKIQVYNVSYCQASSAQML  114 (128)
Q Consensus        85 a~vIG~~T~G~g~~q~~~~~l~dG~~~~~~  114 (128)
                      +++||++|+|++..|. .++|+||+..++.
T Consensus       262 a~viG~~T~G~~~~~~-~~~l~~g~~l~~~  290 (334)
T TIGR00225       262 ATIVGEKTFGKGTVQQ-VRPLNDGSGIKVT  290 (334)
T ss_pred             eEEEeeCCccCceeee-EEEcCCCCEEEEE
Confidence            9999999999988765 4789999765544

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.

>PRK11186 carboxy-terminal protease; Provisional

Probab=99.93  E-value=4.1e-26  Score=198.16  Aligned_cols=96  Identities=36%  Similarity=0.509  Sum_probs=85.5

Q ss_pred             ceeeecCCCCCCHHHHHHHHhccccCCceeEEEEcCCCceeEEeccCCCccCCCcEEEEEcCCCCChHHHHHHHhhcCCC
Q 033051            5 SPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGR   84 (128)
Q Consensus         5 ~iiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pivVLvn~~TaSaaE~~a~alk~~~~   84 (128)
                      .|||||+|+||.+.+|..++++|++++ ++.+.++++|+...+...++...|++|++||||++||||||+||++||+++|
T Consensus       386 LIlDLR~NgGG~l~~a~~la~lFi~~g-~vv~~~~~~g~~~~~~~~~~~~~~~gPlvVLVN~~SASASEIfA~alqd~~r  464 (667)
T PRK11186        386 IIIDLRGNGGGALTEAVSLSGLFIPSG-PVVQVRDNNGRVRVDSDTDGVVYYKGPLVVLVDRYSASASEIFAAAMQDYGR  464 (667)
T ss_pred             EEEEcCCCCCCcHHHHHHHHHHHhcCC-ceEEEecCCCceeccccCCcccccCCCEEEEeCCCCccHHHHHHHHHHhcCC
Confidence            499999999999999999999999986 5678888888765544344556789999999999999999999999999999


Q ss_pred             eEEEcccCCCCceEEEE
Q 033051           85 AILVGHKTFGKGKIQVY  101 (128)
Q Consensus        85 a~vIG~~T~G~g~~q~~  101 (128)
                      ++|||++|+|||++|+.
T Consensus       465 a~vVG~~T~GKGtvQ~~  481 (667)
T PRK11186        465 ALIVGEPTFGKGTVQQH  481 (667)
T ss_pred             EEEEeccCCCccccccc
Confidence            99999999999999875

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

Probab=99.93  E-value=1.4e-25  Score=175.95  Aligned_cols=106  Identities=20%  Similarity=0.216  Sum_probs=83.3

Q ss_pred             ceeeecCCCCCCHHHHHHHHhcccc---CCceeEEEEcCCCc-----eeEEeccC---CCccCCCcEEEEEcCCCCChHH
Q 033051            5 SPPSLSIFQGGLVKAGLDVAQIWLD---GDETLVNAVDREGH-----TLPINMVD---GHAITHDPLVVLVNEGSASASE   73 (128)
Q Consensus         5 ~iiDLR~N~GG~~~~a~~l~~~f~~---~~~~~~~~~~r~g~-----~~~~~~~~---~~~~~~~pivVLvn~~TaSaaE   73 (128)
                      .|||||+|+||.+.+|..++++|++   .++++...+.+++.     ...+....   ......+|++||||+.||||||
T Consensus        97 LIlDLR~N~GG~~~~a~~las~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~VL~~~~TASAaE  176 (256)
T cd07561          97 LVLDLRYNGGGLVSSANLLASLLAPAVALGQVFATLEYNDKRSANNEDLLFSSKTLAGGNSLNLSKVYVLTSGSTASASE  176 (256)
T ss_pred             EEEEeCCCCCccHHHHHHHHHHhcCcccCCCeEEEEEecCCccCCCceeecccccccccCcCCcccEEEEECCCcccHHH
Confidence            3999999999999999999999998   35667777666652     12222211   2334568999999999999999


Q ss_pred             HHHHHhhcCCCeEEEcccCCCCceEEEEEEEcc--CCCcc
Q 033051           74 ILAGALHDNGRAILVGHKTFGKGKIQVYNVSYC--QASSA  111 (128)
Q Consensus        74 ~~a~alk~~~~a~vIG~~T~G~g~~q~~~~~l~--dG~~~  111 (128)
                      +||++||+++++++||++|+||+++|.. ++++  +|...
T Consensus       177 ~~a~~Lk~~~~a~vIGe~T~Gk~~~~~~-~~l~~~~g~~l  215 (256)
T cd07561         177 LVINSLKPYMDVVLIGETTYGKNVGSLT-FEDDRKHKWAL  215 (256)
T ss_pred             HHHHHhhccCCEEEEeCCCCCCCccceE-EEccCCCCeEE
Confidence            9999999999999999999999887753 5665  55433

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.

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

Probab=99.90  E-value=1.9e-23  Score=162.02  Aligned_cols=108  Identities=23%  Similarity=0.162  Sum_probs=83.3

Q ss_pred             ceeeecCCCCCCHHHHHHHHhccccCCceeE--EEEcCCCceeE-----EeccCCCccCCCcEEEEEcCCCCChHHHHHH
Q 033051            5 SPPSLSIFQGGLVKAGLDVAQIWLDGDETLV--NAVDREGHTLP-----INMVDGHAITHDPLVVLVNEGSASASEILAG   77 (128)
Q Consensus         5 ~iiDLR~N~GG~~~~a~~l~~~f~~~~~~~~--~~~~r~g~~~~-----~~~~~~~~~~~~pivVLvn~~TaSaaE~~a~   77 (128)
                      .|||||+|+||+...+..++++|+++++.+.  ....+++....     +..+.....+++|++||+|+.|+||||+|++
T Consensus        98 LIIDLR~N~GG~~~~~~~l~s~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~vL~~~~T~SaaE~~a~  177 (250)
T cd07563          98 LIIDLRYNGGGSDSLVAYLASYFTDEDKPVHLYTIYKRPGNTTTELWTLPVVPGGRYGYTKPVYVLTSPVTFSAAEEFAY  177 (250)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHcCCCCCcEEEEEEEECCCCCCcccceeeecCCCcccCCCCEEEEeCCCcCcHHHHHHH
Confidence            3999999999999999999999996443332  33344433221     2223344578999999999999999999999


Q ss_pred             HhhcCCCeEEEcccCCCCceEEEEEEEccCCCccee
Q 033051           78 ALHDNGRAILVGHKTFGKGKIQVYNVSYCQASSAQM  113 (128)
Q Consensus        78 alk~~~~a~vIG~~T~G~g~~q~~~~~l~dG~~~~~  113 (128)
                      +||+++++++||++|+|++..+ ..++|++|....+
T Consensus       178 ~lk~~~~~~viGe~T~G~~~~~-~~~~Lp~g~~~~~  212 (250)
T cd07563         178 ALKQLKRATVVGETTAGGASPV-LPFPLPNGLYLTV  212 (250)
T ss_pred             HHHhCCCcEEEeecCCCCCCCc-eEEEcCCCeEEEE
Confidence            9999999999999999997743 4578999654433

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

>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=99.87  E-value=6.1e-22  Score=143.36  Aligned_cols=107  Identities=29%  Similarity=0.299  Sum_probs=73.0

Q ss_pred             ceeeecCCCCCCHHHHHHHHhccccCCceeEEEEcCCCcee----EEeccCCCccCCCcEEEEEcCCCCChHHHHHHHhh
Q 033051            5 SPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTL----PINMVDGHAITHDPLVVLVNEGSASASEILAGALH   80 (128)
Q Consensus         5 ~iiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~----~~~~~~~~~~~~~pivVLvn~~TaSaaE~~a~alk   80 (128)
                      .|||||+|+||+...+..++++|.+++. ......+.+...    ..........+++|++||+|+.|+|+||.|+++||
T Consensus        35 lIIDlR~N~GG~~~~~~~l~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~vL~~~~t~Saae~fa~~lk  113 (169)
T PF03572_consen   35 LIIDLRGNGGGSDEYAIELLSYLIPKPI-IFYYRDRIGSNKKWVSTIKWSTPKNRFNGPVYVLTDENTASAAEIFASALK  113 (169)
T ss_dssp             EEEE-TTB--BSHHHHHHHHHCHSSSSE-EEEEEEEEEEETTCCHEEEECSSTT-SSSEEEEEE-TTBBTHHHHHHHHHH
T ss_pred             EEEEcccCCCcchHHHHHHHhcccCCCc-EEEEecccccccccccCCCCccccccCCCCEEEEeCCCCCChhHHHHHHHH
Confidence            4999999999999999999999999753 333222221111    01111114578999999999999999999999999


Q ss_pred             cCCCeEEEcccCCCCceEEEEEEEccCCCccee
Q 033051           81 DNGRAILVGHKTFGKGKIQVYNVSYCQASSAQM  113 (128)
Q Consensus        81 ~~~~a~vIG~~T~G~g~~q~~~~~l~dG~~~~~  113 (128)
                      +++++++|||+|+|++..+. ...+++|...++
T Consensus       114 ~~~~~~ivGe~T~G~~~~~~-~~~l~~g~~~~i  145 (169)
T PF03572_consen  114 DNKRATIVGEPTAGAGGGQT-GFSLPSGSILSI  145 (169)
T ss_dssp             HTTSEEEEES--SB-EEEEE-EEE-TTSEEEEE
T ss_pred             hcCCCeEEeecCCCCCEEee-EEEECCCcEEEe
Confidence            99999999999999876544 467777766653

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 ....

>cd07562 Peptidase_S41_TRI Tricorn protease; serine protease family S41

Probab=99.84  E-value=8.8e-21  Score=148.69  Aligned_cols=101  Identities=26%  Similarity=0.222  Sum_probs=78.8

Q ss_pred             ceeeecCCCCCCHHHHHHHHhccccCCceeEEEEcCC-CceeEEeccCCCccCCCcEEEEEcCCCCChHHHHHHHhhcCC
Q 033051            5 SPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDRE-GHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNG   83 (128)
Q Consensus         5 ~iiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~-g~~~~~~~~~~~~~~~~pivVLvn~~TaSaaE~~a~alk~~~   83 (128)
                      .|||||+|+||++.  ..++++|.+.  .+.+...|+ +.....   +. ..+++|++||+|+.|+||||+|+.+||+++
T Consensus       118 lIiDlR~N~GG~~~--~~l~~~~~~~--~~~~~~~r~~~~~~~~---p~-~~~~~pv~vL~~~~t~SaaE~~a~~lk~~~  189 (266)
T cd07562         118 LIIDVRFNGGGNVA--DLLLDFLSRR--RYGYDIPRGGGKPVTY---PS-GRWRGPVVVLVNEGSASDAEIFAYGFRALG  189 (266)
T ss_pred             EEEEecCCCCCcHH--HHHHHHhCCC--ceEEEccCCCCCCCCC---cc-cccCCCEEEEECCCCCchHHHHHHHHHHcC
Confidence            39999999999955  4678888764  456666666 332111   11 237899999999999999999999999999


Q ss_pred             CeEEEcccCCCCceEEEEEEEccCCCcceee
Q 033051           84 RAILVGHKTFGKGKIQVYNVSYCQASSAQML  114 (128)
Q Consensus        84 ~a~vIG~~T~G~g~~q~~~~~l~dG~~~~~~  114 (128)
                      ++++||++|+|++.. ...++|++|...++.
T Consensus       190 ~~~vvG~~T~G~~~~-~~~~~L~~g~~~~~~  219 (266)
T cd07562         190 LGPVVGTRTAGGVII-SGRYRLPDGGSLTVP  219 (266)
T ss_pred             CeeEEeeccCCceee-cCceecCCCCEEEee
Confidence            999999999999774 345788898766544

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

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

Probab=85.39  E-value=1.7  Score=32.45  Aligned_cols=25  Identities=32%  Similarity=0.384  Sum_probs=21.0

Q ss_pred             CCCcEEEEEcCCCCChHHHHHHHhh
Q 033051           56 THDPLVVLVNEGSASASEILAGALH   80 (128)
Q Consensus        56 ~~~pivVLvn~~TaSaaE~~a~alk   80 (128)
                      ..+|++..+++..+|++-+++.+-.
T Consensus        57 ~~~pvva~V~g~AaSaG~~ia~a~d   81 (178)
T cd07021          57 SPIPTIAYVNDRAASAGALIALAAD   81 (178)
T ss_pred             CCCCEEEEECCchHHHHHHHHHhCC
Confidence            3489999999999999999888654

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	128
1fc7_A	388	Photosystem Ii D1 C-Terminal Processing Protease Le		2e-14
1fc6_A	388	Photosystem Ii D1 C-Terminal Processing Protease Le		4e-14
3dor_A	583	Crystal Structure Of Mature Cpaf Length = 583		8e-04
3dja_A	579	Crystal Structure Of Cpaf Solved With Mad Length =		9e-04

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

Iteration: 1
 Score = 73.9 bits (180), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 45/88 (51%), Positives = 61/88 (69%), Gaps = 5/88 (5%)
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  SEILAGALHDNGRAILVGHKTFGKGKIQ 99
           SE+LAGAL D+ R ++ G +TFGKG IQ
Sbjct: 298 SEVLAGALKDSKRGLIAGERTFGKGLIQ 325

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

Iteration: 1
 Score = 72.8 bits (177), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 45/88 (51%), Positives = 60/88 (68%), Gaps = 5/88 (5%)
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  SEILAGALHDNGRAILVGHKTFGKGKIQ 99
           SE+LAGAL D+ R ++ G +TFGKG IQ
Sbjct: 298 SEVLAGALKDSKRGLIAGERTFGKGLIQ 325

>pdb|3DOR|A Chain A, Crystal Structure Of Mature Cpaf Length = 583

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 59  PLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQVYNVSYCQASSAQMLNL 116
           P+ VL+NE   S ++     L DN RA++VG +T G G   V+NV +   +  +  +L
Sbjct: 456 PICVLINEQDFSCADFFPVVLKDNDRALIVGTRTAGAGGF-VFNVQFPNRTGIKTCSL 512

>pdb|3DJA|A Chain A, Crystal Structure Of Cpaf Solved With Mad Length = 579

Iteration: 1
 Score = 38.9 bits (89), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 59  PLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQVYNVSY 105
           P+ VL+NE   S ++     L DN RA++VG +T G G   V+NV +
Sbjct: 458 PICVLINEQDFSCADFFPVVLKDNDRALIVGTRTAGAGGF-VFNVQF 503

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	128
1fc6_A	388	Photosystem II D1 protease; D1 C-terminal processi	3e-38
3k50_A	403	Putative S41 protease; structural genomics, joint	8e-26
1j7x_A	302	IRBP, interphotoreceptor retinoid-binding protein;	2e-23
3dor_A	583	Protein CT_858, CPAF; mature CPAF, dimer, transfer	4e-22
1k32_A	1045	Tricorn protease; protein degradation, substrate g	2e-17

>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 =  131 bits (332), Expect = 3e-38
 Identities = 40/86 (46%), Positives = 55/86 (63%), Gaps = 1/86 (1%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQ 99
           +LAGAL D+ R ++ G +TFGKG IQ
Sbjct: 300 VLAGALKDSKRGLIAGERTFGKGLIQ 325

>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 = 99.1 bits (247), Expect = 8e-26
 Identities = 15/97 (15%), Positives = 34/97 (35%), Gaps = 11/97 (11%)

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

Query: 63  LVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQ 99
           L    +  A+E++   L+   + +L+G KT G+    
Sbjct: 296 LTTNATRGAAEMVINCLNPYMKVVLIGTKTAGEYVAT 332

>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 = 90.9 bits (226), Expect = 2e-23
 Identities = 18/95 (18%), Positives = 36/95 (37%), Gaps = 11/95 (11%)

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

Query: 65  NEGSASASEILAGALHDNGRAILVGHKTFGKGKIQ 99
           +  +A+A+E  A  +    RA ++G  T G     
Sbjct: 210 SHQTATAAEEFAYLMQSLSRATIIGEITSGNLMHS 244

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

 Score = 89.5 bits (221), Expect = 4e-22
 Identities = 24/86 (27%), Positives = 32/86 (37%), Gaps = 2/86 (2%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKGKIQ 99
                L DN RA++VG +T G G   
Sbjct: 471 FFPVVLKDNDRALIVGTRTAGAGGFV 496

>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 = 76.0 bits (186), Expect = 2e-17
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 8/83 (9%)

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

Query: 74  ILAGALHDNGRAILVGHKTFGKG 96
           I + +    G   L+G +T+G  
Sbjct: 943 IFSFSFKKLGLGKLIGTRTWGGV 965

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	128
1fc6_A	388	Photosystem II D1 protease; D1 C-terminal processi	99.94
1j7x_A	302	IRBP, interphotoreceptor retinoid-binding protein;	99.93
3k50_A	403	Putative S41 protease; structural genomics, joint	99.91
1k32_A	1045	Tricorn protease; protein degradation, substrate g	99.84
3dor_A	583	Protein CT_858, CPAF; mature CPAF, dimer, transfer	99.79

>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=99.94  E-value=1.9e-26  Score=187.47  Aligned_cols=106  Identities=40%  Similarity=0.551  Sum_probs=91.2

Q ss_pred             eeeecCCCCCCHHHHHHHHhccccCCceeEEEEcCCCceeEEeccCCCccCCCcEEEEEcCCCCChHHHHHHHhhcCCCe
Q 033051            6 PPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGRA   85 (128)
Q Consensus         6 iiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pivVLvn~~TaSaaE~~a~alk~~~~a   85 (128)
                      |||||+|+||.+.++..++++|++++ .+.+.++|++....+........+++|++||||++||||||+||++||+++++
T Consensus       233 IlDLR~N~GG~~~~~~~~~~~f~~~~-~i~~~~~r~~~~~~~~~~~~~~~~~~pv~VLvn~~taSasEi~a~al~~~~~~  311 (388)
T 1fc6_A          233 VLDIRNNGGGLFPAGVNVARMLVDRG-DLVLIADSQGIRDIYSADGNSIDSATPLVVLVNRGTASASEVLAGALKDSKRG  311 (388)
T ss_dssp             EEECTTCCCBCHHHHHHHHHHHCSSS-EEEEEEETTEEEEEEECCSCCSCSSSCEEEEECTTCCTHHHHHHHHHHHTTSE
T ss_pred             EEEcCCCCCCCHHHHHHHHHHHcCCC-cEEEEecCCCceeEEecCCccccCCCCEEEEeCCCCccHHHHHHHHHhhCCCE
Confidence            89999999999999999999999987 56777888887665654332224789999999999999999999999999999


Q ss_pred             EEEcccCCCCceEEEEEEEccCCCccee
Q 033051           86 ILVGHKTFGKGKIQVYNVSYCQASSAQM  113 (128)
Q Consensus        86 ~vIG~~T~G~g~~q~~~~~l~dG~~~~~  113 (128)
                      ++||++|+|+|.+|.. ++|+||+...+
T Consensus       312 ~~vG~~T~Gkg~~~~~-~~L~~g~~l~~  338 (388)
T 1fc6_A          312 LIAGERTFGKGLIQTV-VDLSDGSGVAV  338 (388)
T ss_dssp             EEEESCCCCCCEEEEE-EECTTSCEEEE
T ss_pred             EEEeecCCCCCeeeeE-EEcCCCCEEEE
Confidence            9999999999998864 68999975543

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

Probab=99.93  E-value=2.4e-25  Score=175.97  Aligned_cols=103  Identities=18%  Similarity=0.141  Sum_probs=85.6

Q ss_pred             ceeeecCCCCCCHHHHHHHHhccccCCc--eeEEEEcCCCce-eEEeccCC----CccCCCcEEEEEcCCCCChHHHHHH
Q 033051            5 SPPSLSIFQGGLVKAGLDVAQIWLDGDE--TLVNAVDREGHT-LPINMVDG----HAITHDPLVVLVNEGSASASEILAG   77 (128)
Q Consensus         5 ~iiDLR~N~GG~~~~a~~l~~~f~~~~~--~~~~~~~r~g~~-~~~~~~~~----~~~~~~pivVLvn~~TaSaaE~~a~   77 (128)
                      .|||||+|+||.+..+..++++|++++.  .+.+.++|+++. ..++..+.    ...+++|++||||++|+||||+||+
T Consensus       143 LIiDLR~N~GG~~~~~~~l~~~f~~~~~~~~i~~~~~r~~~~~~~~~~~~~~~~~~~~~~~pvvVLvn~~TaSAsE~~a~  222 (302)
T 1j7x_A          143 LIIDLRYNVGGSSTAVPLLLSYFLDPETKIHLFTLHNRQQNSTDEVYSHPKVLGKPYGSKKGVYVLTSHQTATAAEEFAY  222 (302)
T ss_dssp             EEEECTTCCCBCSTTHHHHHHTTSCSSCCCEEEEEEETTTTCCEEEECCSCCSSCCCCSSSEEEEEECTTCCTHHHHHHH
T ss_pred             EEEEeCCCCCCChhHHHHHHHHhcCCCcceeeEEEEccCCCCceeecccccccCCccCCCCCEEEEeCCCcCcHHHHHHH
Confidence            3999999999999999999999998764  356777787763 33443221    1236799999999999999999999


Q ss_pred             HhhcCCCeEEEcccCCCCceEEEEEEEccCC
Q 033051           78 ALHDNGRAILVGHKTFGKGKIQVYNVSYCQA  108 (128)
Q Consensus        78 alk~~~~a~vIG~~T~G~g~~q~~~~~l~dG  108 (128)
                      +||+++++++||++|+|++.+|.. ++++||
T Consensus       223 alq~~~~a~vVG~~T~Gk~~~~~~-~~L~~g  252 (302)
T 1j7x_A          223 LMQSLSRATIIGEITSGNLMHSKV-FPFGDT  252 (302)
T ss_dssp             HHHHTTCCEEEESCCCCCCSCEEE-EECTTS
T ss_pred             HHHhCCCEEEEcccCCCCCCCceE-EEeCCC
Confidence            999999999999999999988764 789988

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

Probab=99.91  E-value=2.2e-24  Score=177.21  Aligned_cols=108  Identities=17%  Similarity=0.167  Sum_probs=84.2

Q ss_pred             ceeeecCCCCCCHHHHHHHHhccccCCce---eEEEE--cCCCceeE-EeccC-----CCccCCCcEEEEEcCCCCChHH
Q 033051            5 SPPSLSIFQGGLVKAGLDVAQIWLDGDET---LVNAV--DREGHTLP-INMVD-----GHAITHDPLVVLVNEGSASASE   73 (128)
Q Consensus         5 ~iiDLR~N~GG~~~~a~~l~~~f~~~~~~---~~~~~--~r~g~~~~-~~~~~-----~~~~~~~pivVLvn~~TaSaaE   73 (128)
                      .|||||+|+||.+.+|..++++|++++..   +.+.+  +|++.... +...+     +.....+|++||+|+.||||||
T Consensus       227 lIlDLR~N~GG~l~~a~~la~~f~~~g~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~vL~~~~taSa~E  306 (403)
T 3k50_A          227 FVLDLRYNTGGSLDCAQLLCTMLAPADKMNQLLALLRYSDKRVEANQDLTFNPELIQSGANLNLSTVYVLTTNATRGAAE  306 (403)
T ss_dssp             EEEECTTCCCBCHHHHHHHHHHHSCGGGTTSEEEEEECCTTCGGGCEEEECCGGGTTTSCCCCCSEEEEEECTTCCTHHH
T ss_pred             EEEEcCCCCCCCHHHHHHHHHHhcCCCccceeEEEEEEcCCCCcceeEEeccccccccccccCCCCEEEEECCCCccHHH
Confidence            49999999999999999999999998643   66766  45554322 22211     1233457999999999999999


Q ss_pred             HHHHHhhcCCCeEEEcccCCCCceEEEEEEEccCCCcce
Q 033051           74 ILAGALHDNGRAILVGHKTFGKGKIQVYNVSYCQASSAQ  112 (128)
Q Consensus        74 ~~a~alk~~~~a~vIG~~T~G~g~~q~~~~~l~dG~~~~  112 (128)
                      +|+++||+++++++||++|+|++.+|....++.+|...+
T Consensus       307 ~~~~~l~~~~~~~~iG~~T~G~~~~~~~~~~~~~g~~l~  345 (403)
T 3k50_A          307 MVINCLNPYMKVVLIGTKTAGEYVATKPFVHPTDRFILN  345 (403)
T ss_dssp             HHHHHHTTTSEEEEEESCCCCCCEEEEEEECSSSCEEEE
T ss_pred             HHHHHHhhCCCEEEEeecCCCCCeeeeEEEeCCCCcEEE
Confidence            999999999999999999999998876543456665443

>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=99.84  E-value=4.8e-21  Score=168.81  Aligned_cols=100  Identities=16%  Similarity=0.254  Sum_probs=82.5

Q ss_pred             ceeeecCCCCCCHHHHHHHHhccccCCceeEEEEcCCCceeEEeccCCCccCCCcEEEEEcCCCCChHHHHHHHhhcCCC
Q 033051            5 SPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGR   84 (128)
Q Consensus         5 ~iiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pivVLvn~~TaSaaE~~a~alk~~~~   84 (128)
                      .|||||+|+||.+.++.  +++|. + +++.+.++|+++...+..    ..+++|++||||++||||||+||++||++++
T Consensus       882 liiDlR~N~GG~~~~~~--~~~~~-~-~~~~~~~~~~~~~~~~~~----~~~~~~~~vL~~~~taSa~e~~~~~l~~~~~  953 (1045)
T 1k32_A          882 LIVDVRFNGGGFVSQLI--IEKLM-N-KRIGYDNPRRGTLSPYPT----NSVRGKIIAITNEYAGSDGDIFSFSFKKLGL  953 (1045)
T ss_dssp             EEEECTTCCCBSCHHHH--HHHHT-C-BCCEEEEESSSCCEEEST----TCBCSEEEEEECTTCCTHHHHHHHHHHHTTS
T ss_pred             EEEEcCcCCCCCHHHHH--Hhhcc-C-CcEEEEecCCCceeeccc----cCCCCCEEEEECCCCccHHHHHHHHHhhcCC
Confidence            49999999999998754  77764 3 467888899987665531    2478999999999999999999999999999


Q ss_pred             eEEEcccCCCCceEEE-EEEEccCCCccee
Q 033051           85 AILVGHKTFGKGKIQV-YNVSYCQASSAQM  113 (128)
Q Consensus        85 a~vIG~~T~G~g~~q~-~~~~l~dG~~~~~  113 (128)
                      ++|||++|+| |.+|. ..++|+||+...+
T Consensus       954 ~~~vG~~t~G-g~~~~~~~~~l~~~~~~~~  982 (1045)
T 1k32_A          954 GKLIGTRTWG-GVVGITPKRRLIDGTVLTQ  982 (1045)
T ss_dssp             EEEEESCCCC-CCEECCCCCBCTTSCEECC
T ss_pred             EEEEccCCCC-CccccCceEEcCCCCeEEE
Confidence            9999999999 77763 3468999987643

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

Probab=99.79  E-value=2.2e-19  Score=152.79  Aligned_cols=60  Identities=28%  Similarity=0.470  Sum_probs=53.9

Q ss_pred             CCccCCCcEEEEEcCCCCChHHHHHHHhhcCCCeEEEcccCCCCceEEEEEEEccCCCcce
Q 033051           52 GHAITHDPLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQVYNVSYCQASSAQ  112 (128)
Q Consensus        52 ~~~~~~~pivVLvn~~TaSaaE~~a~alk~~~~a~vIG~~T~G~g~~q~~~~~l~dG~~~~  112 (128)
                      +...+++|++||||+.||||||+||++||++++|++||++|+|+|.+|.. .+|+||+...
T Consensus       449 ~~~~~~gPvvVLVN~~SASASEifA~aLKd~~ra~lVGe~T~Gkg~vq~~-~~Lpdg~~l~  508 (583)
T 3dor_A          449 PRVQYSKPICVLINEQDFSCADFFPVVLKDNDRALIVGTRTAGAGGFVFN-VQFPNRTGIK  508 (583)
T ss_dssp             SSCCCCSCEEEEECTTBCTHHHHHHHHHHHTTCEEEEESCCCCCCSCEEE-ECCCCSSCEE
T ss_pred             CCccCCCCEEEEECCCCccHHHHHHHHHHhCCCEEEEeeCCCCCCceeeE-EEcCCCCeEE
Confidence            34578999999999999999999999999999999999999999988764 6899987654

---

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	128
d1j7xa_	302	c.14.1.2 (A:) Interphotoreceptor retinoid-binding	2e-10
d1fc6a4	294	c.14.1.2 (A:78-156,A:249-463) Photosystem II D1 C-	9e-09
d1k32a4	291	c.14.1.2 (A:680-762,A:854-1061) Tricorn protease {	7e-08

>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 = 54.7 bits (131), Expect = 2e-10
 Identities = 18/94 (19%), Positives = 33/94 (35%), Gaps = 9/94 (9%)

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

Query: 66  EGSASASEILAGALHDNGRAILVGHKTFGKGKIQ 99
             +A+A+E  A  +    RA ++G  T G     
Sbjct: 211 HQTATAAEEFAYLMQSLSRATIIGEITSGNLMHS 244

>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 = 49.7 bits (118), Expect = 9e-09
 Identities = 37/87 (42%), Positives = 54/87 (62%), Gaps = 1/87 (1%)

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

Query: 73  EILAGALHDNGRAILVGHKTFGKGKIQ 99
           E+LAGAL D+ R ++ G +TFGKG IQ
Sbjct: 206 EVLAGALKDSKRGLIAGERTFGKGLIQ 232

>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 = 47.0 bits (111), Expect = 7e-08
 Identities = 9/56 (16%), Positives = 20/56 (35%)

Query: 59  PLVVLVNEGSASASEILAGALHDNGRAILVGHKTFGKGKIQVYNVSYCQASSAQML 114
            ++ + NE + S  +I + +    G   L+G +T+G              +     
Sbjct: 184 KIIAITNEYAGSDGDIFSFSFKKLGLGKLIGTRTWGGVVGITPKRRLIDGTVLTQP 239

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	128
d1fc6a4	294	Photosystem II D1 C-terminal processing protease {	99.95
d1j7xa_	302	Interphotoreceptor retinoid-binding protein IRBP {	99.88
d1k32a4	291	Tricorn protease {Archaeon Thermoplasma acidophilu	99.85

>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=99.95  E-value=2.9e-27  Score=184.76  Aligned_cols=109  Identities=39%  Similarity=0.524  Sum_probs=93.2

Q ss_pred             ceeeecCCCCCCHHHHHHHHhccccCCceeEEEEcCCCceeEEeccCCCccCCCcEEEEEcCCCCChHHHHHHHhhcCCC
Q 033051            5 SPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGR   84 (128)
Q Consensus         5 ~iiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pivVLvn~~TaSaaE~~a~alk~~~~   84 (128)
                      .|||||+|+||.+..|..++++|++++. ......+++....+........+.+|++||||+.|+||||+||++||++++
T Consensus       139 lIiDLR~N~GG~~~~a~~~~~~f~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~pv~VL~~~~TaSaaE~~a~~lk~~~~  217 (294)
T d1fc6a4         139 LVLDIRNNGGGLFPAGVNVARMLVDRGD-LVLIADSQGIRDIYSADGNSIDSATPLVVLVNRGTASASEVLAGALKDSKR  217 (294)
T ss_dssp             EEEECTTCCCBCHHHHHHHHHHHCSSSE-EEEEEETTEEEEEEECCSCCSCSSSCEEEEECTTCCTHHHHHHHHHHHTTS
T ss_pred             EEEEeecCcccchhhhHHHHHhhccccc-ceEEEEeccccceeccccccccccceEEEEecCCccchHHHHHHHhhhcCe
Confidence            3999999999999999999999999874 445556666555555555666788999999999999999999999999999


Q ss_pred             eEEEcccCCCCceEEEEEEEccCCCcceeee
Q 033051           85 AILVGHKTFGKGKIQVYNVSYCQASSAQMLN  115 (128)
Q Consensus        85 a~vIG~~T~G~g~~q~~~~~l~dG~~~~~~~  115 (128)
                      +++||++|+|+|..|. .++|+||+..++..
T Consensus       218 a~vvG~~T~G~g~~~~-~~~L~dG~~l~~t~  247 (294)
T d1fc6a4         218 GLIAGERTFGKGLIQT-VVDLSDGSGVAVTV  247 (294)
T ss_dssp             EEEEESCCCCCCEEEE-EEECTTSCEEEEEE
T ss_pred             EEEEeeeccCcceeeE-EEEeCCCCEEEEEe
Confidence            9999999999998876 46899998776654

>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=99.88  E-value=1e-22  Score=159.83  Aligned_cols=115  Identities=18%  Similarity=0.178  Sum_probs=85.9

Q ss_pred             eeeecCCCCCCHHHHHHHHhccccCCce--eEEEEcCCCceeE-Eec-c---CCCccCCCcEEEEEcCCCCChHHHHHHH
Q 033051            6 PPSLSIFQGGLVKAGLDVAQIWLDGDET--LVNAVDREGHTLP-INM-V---DGHAITHDPLVVLVNEGSASASEILAGA   78 (128)
Q Consensus         6 iiDLR~N~GG~~~~a~~l~~~f~~~~~~--~~~~~~r~g~~~~-~~~-~---~~~~~~~~pivVLvn~~TaSaaE~~a~a   78 (128)
                      |||||+|+||++..+..++++|++++..  +....+|.+.... .+. +   .....+++|++||||+.|+|+||.||++
T Consensus       144 IiDLR~N~GG~~~~~~~i~s~f~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~g~~~~~~kpv~VLt~~~T~SaaE~fa~~  223 (302)
T d1j7xa_         144 IIDLRYNVGGSSTAVPLLLSYFLDPETKIHLFTLHNRQQNSTDEVYSHPKVLGKPYGSKKGVYVLTSHQTATAAEEFAYL  223 (302)
T ss_dssp             EEECTTCCCBCSTTHHHHHHTTSCSSCCCEEEEEEETTTTCCEEEECCSCCSSCCCCSSSEEEEEECTTCCTHHHHHHHH
T ss_pred             EEEcCcCCCCCHHHHHHHHHHhcCCCceEEEEEEccCccccceEEeccccccCCCcccCCCEEEEECCCCCCchhhhhhc
Confidence            9999999999999999999999987643  2334455543322 222 1   1233568999999999999999999999


Q ss_pred             hhcCCCeEEEcccCCCCceEEEEEEEccCCCcceeeeeeEEee
Q 033051           79 LHDNGRAILVGHKTFGKGKIQVYNVSYCQASSAQMLNLIHCVD  121 (128)
Q Consensus        79 lk~~~~a~vIG~~T~G~g~~q~~~~~l~dG~~~~~~~~~~~~~  121 (128)
                      ||.++++++|||+|+|++..+. .+++.++...-.+-..+.++
T Consensus       224 lk~~~ra~vVGe~T~G~~~~~~-~~~l~~~~~~l~vp~~~~~~  265 (302)
T d1j7xa_         224 MQSLSRATIIGEITSGNLMHSK-VFPFGDTQLSVTVPIINFID  265 (302)
T ss_dssp             HHHTTCCEEEESCCCCCCSCEE-EEECTTSSEEEEEECEEEEE
T ss_pred             cccCCeEEEEEEeccCCCccce-EEEeCCCCEEEEEeEEEEEc
Confidence            9999999999999999876544 46888876433333333333

>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=99.85  E-value=7.1e-22  Score=153.47  Aligned_cols=102  Identities=15%  Similarity=0.166  Sum_probs=79.2

Q ss_pred             ceeeecCCCCCCHHHHHHHHhccccCCceeEEEEcCCCceeEEeccCCCccCCCcEEEEEcCCCCChHHHHHHHhhcCCC
Q 033051            5 SPPSLSIFQGGLVKAGLDVAQIWLDGDETLVNAVDREGHTLPINMVDGHAITHDPLVVLVNEGSASASEILAGALHDNGR   84 (128)
Q Consensus         5 ~iiDLR~N~GG~~~~a~~l~~~f~~~~~~~~~~~~r~g~~~~~~~~~~~~~~~~pivVLvn~~TaSaaE~~a~alk~~~~   84 (128)
                      .|||||+|+||.+.++  ++.+|.++  .+.+...+.+...+.    ....+++|++||||+.|+||||+||++||++++
T Consensus       138 lIiDLR~N~GG~l~~~--i~~~~~~~--~~~~~~~~~~~~~~~----~~~~~~~pv~vLv~~~T~SaaE~~a~~lk~~~~  209 (291)
T d1k32a4         138 LIVDVRFNGGGFVSQL--IIEKLMNK--RIGYDNPRRGTLSPY----PTNSVRGKIIAITNEYAGSDGDIFSFSFKKLGL  209 (291)
T ss_dssp             EEEECTTCCCBSCHHH--HHHHHTCB--CCEEEEESSSCCEEE----STTCBCSEEEEEECTTCCTHHHHHHHHHHHTTS
T ss_pred             EEEecccCcchhHHHH--HHHHhccC--CeEEEecCcCccccC----CccccCCCEEEEECCCCCccchHHHHHHHhcCC
Confidence            4999999999998764  56777654  455666666554333    234689999999999999999999999999999


Q ss_pred             eEEEcccCCCCceEEEEEEEccCCCcceee
Q 033051           85 AILVGHKTFGKGKIQVYNVSYCQASSAQML  114 (128)
Q Consensus        85 a~vIG~~T~G~g~~q~~~~~l~dG~~~~~~  114 (128)
                      +++||++|+|++........+++|....+.
T Consensus       210 ~~vvG~~T~G~~~~~~~~~~l~~g~~~~~~  239 (291)
T d1k32a4         210 GKLIGTRTWGGVVGITPKRRLIDGTVLTQP  239 (291)
T ss_dssp             EEEEESCCCCCCEECCCCCBCTTSCEECCC
T ss_pred             eEEeeecCCCCCcceeeeEecCCCCeEEEE
Confidence            999999999986554434567888766543