SepM family pheromone-processing serine protease; This HMM describes a peptide pheromone-processing S16-type serine protease found broadly in Gram-positive bacteria, and named for the founding member from Streptococcus mutans (see BlastRule NBR014542). The Lon-like catalytic domain is located toward the C-terminus, and has a Ser-Lys active site dyad rather than the more common Ser-His-Asp triad found in large numbers of serine proteases. Members of this family also have a PDZ domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655907605   6 IKWTLI--IAAVVLLGLNFVSTPYYVQRPGKAESMAKMVQVTGAK-KVDGAYRLVYIYLGKANIYQYLWAKFdrNKYTTL 82
Cdd:NF041438   2 FKWWLLgiLALLLLLFALFFPLPYYIEMPGGAYDIRSVLTVNGKEdKEKGSYNFVAVSLSRATLAQLLYAWL--TPFTEI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655907605  83 VKENQVKMPEEDEqDYNLRQQNYMSSAQQSAAYVAYKAAGKAPKLTEAGVLVLGVMQGMPSSKVLKTGDLITGVDGQTIK 162
Cdd:NF041438  80 SSAEETTGGYSDA-DYMRINQFYMETSQNGAIYQALKLAGKKVSLDYKGVYVLDVSKDSTFKGVLNIADTVTGVNGKTFK 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655907605 163 TVQDMDRVIKMKKLGDTYRVTLMRGHRVRNVTVRSAPFPKqyvgaGRGwGIGIYQDNHVKVQVSPKVNFDIENIGGPSAG 242
Cdd:NF041438 159 SSKELIKYVSGLKLGSKVTVQYTSNGKKKSAKGKIIKLKN-----GKN-GIGIGLTDHTEVSSDDKVKFSTEGVGGPSAG 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655907605 243 LMMTLEVYDQLVPENLARGRDIAGTGTIGLNGQVGPIGGIAEKVVGASRSGADIFF-------------APAADHEYETA 309
Cdd:NF041438 233 LMFTLDIYDQLNKEDLRKGRKIAGTGTIEQDGSVGDIGGAGLKVVAAAKIGADIFFvpnnpvdkalkkaNPDAKTNYQEA 312

                        330       340
                 ....*....|....*....|....*...
gi 655907605 310 RKTAKDIHTRMKIVKVATFKEAIEYLEQ 337
Cdd:NF041438 313 KEAAKKLKTKMKIVPVKTVQEAIDYLKK 340

PDZ domain;

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 655907605  126 KLTEAGVLVLGVMQGMPSSKV-LKTGDLITGVDGQTIKTVQDMDRVIKMKKLGDTYRVTLMRGHRVRNVTV 195
Cdd:pfam13180   2 VDLEGGVVVVSVKSSGPAAKAgLKAGDVILSIDGRKINDLTDLESALYGHKPGDTVTLQVYRDGKLLTVEV 72

periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 655907605  131 GVLVLGVMQGMPSSKV-LKTGDLITGVDGQTIKTVQDMDRVIKMKKLGDTYRVTLMRGHRVRNVTVR 196
Cdd:TIGR02037 258 GALVAQVLPGSPAEKAgLKAGDVITSVNGKPISSFADLRRAIGTLKPGKKVTLGILRKGKEKTITVT 324

SepM family pheromone-processing serine protease; This HMM describes a peptide pheromone-processing S16-type serine protease found broadly in Gram-positive bacteria, and named for the founding member from Streptococcus mutans (see BlastRule NBR014542). The Lon-like catalytic domain is located toward the C-terminus, and has a Ser-Lys active site dyad rather than the more common Ser-His-Asp triad found in large numbers of serine proteases. Members of this family also have a PDZ domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655907605   6 IKWTLI--IAAVVLLGLNFVSTPYYVQRPGKAESMAKMVQVTGAK-KVDGAYRLVYIYLGKANIYQYLWAKFdrNKYTTL 82
Cdd:NF041438   2 FKWWLLgiLALLLLLFALFFPLPYYIEMPGGAYDIRSVLTVNGKEdKEKGSYNFVAVSLSRATLAQLLYAWL--TPFTEI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655907605  83 VKENQVKMPEEDEqDYNLRQQNYMSSAQQSAAYVAYKAAGKAPKLTEAGVLVLGVMQGMPSSKVLKTGDLITGVDGQTIK 162
Cdd:NF041438  80 SSAEETTGGYSDA-DYMRINQFYMETSQNGAIYQALKLAGKKVSLDYKGVYVLDVSKDSTFKGVLNIADTVTGVNGKTFK 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655907605 163 TVQDMDRVIKMKKLGDTYRVTLMRGHRVRNVTVRSAPFPKqyvgaGRGwGIGIYQDNHVKVQVSPKVNFDIENIGGPSAG 242
Cdd:NF041438 159 SSKELIKYVSGLKLGSKVTVQYTSNGKKKSAKGKIIKLKN-----GKN-GIGIGLTDHTEVSSDDKVKFSTEGVGGPSAG 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655907605 243 LMMTLEVYDQLVPENLARGRDIAGTGTIGLNGQVGPIGGIAEKVVGASRSGADIFF-------------APAADHEYETA 309
Cdd:NF041438 233 LMFTLDIYDQLNKEDLRKGRKIAGTGTIEQDGSVGDIGGAGLKVVAAAKIGADIFFvpnnpvdkalkkaNPDAKTNYQEA 312

                        330       340
                 ....*....|....*....|....*...
gi 655907605 310 RKTAKDIHTRMKIVKVATFKEAIEYLEQ 337
Cdd:NF041438 313 KEAAKKLKTKMKIVPVKTVQEAIDYLKK 340

circularly permuted PDZ domain of Bacillus subtilis YlbL and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Bacillus subtilis YlbL and related domains. YlbL is an S16 protease which participates with another unrelated S41 protease (CtpA) in a dual protease mechanism that promotes DNA damage checkpoint recovery. Deletion of both proteases leads to accumulation of the cell division inhibitor YneA. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This YlbL family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655907605 131 GVLVLGVMQGMPSSKVLKTGDLITGVDGQTIKTVQDMDRVIKMKKLGDTYRVTLMRGHRVRNVTVRSAPFPKQYVGAGRG 210
Cdd:cd23080    1 GVYVLSVVENMPAKGILEAGDKITAIDGQNFQSSEKLIDYISSKKAGDKVKVKYERDEKEKEAELKLKQFPDEKNRIGIG 80

circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, HhoB, and HtrA and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the cyanobacterial Synechocystis sp. PCC 6803 putative serine proteases HhoA, HhoB and HtrA, and related domains. These three proteases are functionally overlapping, and are involved in a number of key physiological responses, ranging from protection against light and heat stresses to phototaxis. HhoA assembles into trimers, mediated by its protease domain and further into a hexamer by a novel interaction between the PDZ domains of opposing trimers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This HhoA-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 655907605 131 GVLVLGVMQGMPSSKV-LKTGDLITGVDGQTIKTVQDMDRVIKMKKLGDTYRVTLMRGHRVRNVTVRSAPF 200
Cdd:cd10838   34 GVLIMQVLPNSPAARAgLRRGDVIQAVDGQPVTTADDVQRIVEQAGVGEELELTVLRGDRRQTLAVKPGDL 104

permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping serine proteases and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Deg/HtrA-type serine proteases that participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins. Typically, these proteases have an N-terminal serine protease domain and at least one C-terminal PDZ domain that recognizes substrates, and in some cases activates the protease function. An exception is yeast Nma11p which has two protease domains and four PDZ domains; its N-terminal half is comprised of a protease domain, followed by two PDZ domains, and its C-terminal half has a similar domain arrangement. HtrA-type proteases include the human HtrA1-4 and MBTPS2, tricorn protease, DegS, DegP and C-terminal processing peptidase, cyanobacterial serine proteases Hhoa, HhoB, and HtrA, and yeast Nma11p. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-termini of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This Deg/HtrA family PDZ domain is a circularly permuted PDZ domain which places beta-strand A at the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 655907605 131 GVLVLGVMQGMPSSK-VLKTGDLITGVDGQTIKTVQDMDRVIKMKKLGDTYRVTLMRGHRVRNVTV 195
Cdd:cd06779   26 GVLVAEVIPGSPAAKaGLKEGDVILSVNGKPVTSFNDLRAALDTKKPGDSLNLTILRDGKTLTVTV 91

circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Arabidopsis thaliana DEGP1 (also known as protease Do-like 1, chloroplastic, protein DEGRADATION OF PERIPLASMIC PROTEINS 1, DEGP PROTEASE 1 and DEG1), and related domains. DEGP1 is a serine protease that is required at high temperature and may be involved in the degradation of damaged proteins. This family also includes Arabidopsis protease DEGP8/Do-like 8 (chloroplastic), a probable serine protease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This AtDEGP-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655907605 131 GVLVLGVMQGMPSSK--------------VLktGDLITGVDGQTIKTVQDMDRVIKMKKLGDTYRVTLMRGHRVRNVTVR 196
Cdd:cd00990   24 GVLVLDVPPGGPAAKaglrgtkrdefgriVL--GDVIVAVDGKPVKNESDLYRALDEYKVGDVVTLKVLRGGTKVDLKVT 101

Lon protease (S16) C-terminal proteolytic domain; The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655907605  238 GPSAGLMMTLEVYDQLVpeNLARGRDIAGTGTIGLNGQVGPIGGIAEKVVGASRSGADIFFAPAADheyetaRKTAKDI- 316
Cdd:pfam05362 109 GPSAGVTMATALVSALT--GIPVRKDVAMTGEITLRGRVLPIGGLKEKLLAAHRAGIKTVIIPKEN------EKDLEDIp 180

                          90       100
                  ....*....|....*....|..
gi 655907605  317 -HTR--MKIVKVATFKEAIEYL 335
Cdd:pfam05362 181 eNVRegLEIIPVEHVDEVLKHA 202

periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 655907605  131 GVLVLGVMQGMPSSKV-LKTGDLITGVDGQTIKTVQDMDRVIKMKKLGDTYRVTLMRGHRVRNVTVR 196
Cdd:TIGR02037 258 GALVAQVLPGSPAEKAgLKAGDVITSVNGKPISSFADLRRAIGTLKPGKKVTLGILRKGKEKTITVT 324

circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine endoprotease DegP and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Escherichia coli DegP (also known as heat shock protein DegP and Protease Do) and related domains. DegP belongs to the HtrA family of housekeeping proteases. It acts as a protease, degrading transiently denatured and unfolded or misfolded proteins which accumulate in the periplasm following heat shock or other stress conditions, and as a molecular chaperone at low temperatures. DegP has two PDZ domains in addition to the protease domain; its PDZ1 domain is responsible for identifying the distinct substrate sequences that affect degradation (degron) of the substrate sequence, and its PDZ2 domain is responsible for combining with other DegP monomers to form a stable oligomer structure. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This DegP family PDZ domain 1 is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 655907605 130 AGVLVLGVMQGMPSSKV-LKTGDLITGVDGQTIKTVQDMDRVIKMKKLGDTYRVTLMRGHRVRNVTV 195
Cdd:cd10839   25 KGALVAQVLPDSPAAKAgLKAGDVILSLNGKPITSSADLRNRVATTKPGTKVELKILRDGKEKTLTV 91

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP), Bacillus subtilis YlbL protease, and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), Bacillus subtilis YlbL, and related domains, including archaeal and chloroplast PDZ domains. RseP participates in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmaE) protein RseA. YlbL is an S16 protease which participates with another unrelated S41 protease (CtpA) in a dual protease mechanism that promotes DNA damage checkpoint recovery. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP-YlbL family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655907605 132 VLVLGVMQGMPSSKVLKTGDLITGVDGQTIKTVQDMDRVIKMKKLGDTYRVTLMRGHRVRNVTVRSAPFPKqyvGAGRGw 211
Cdd:cd10824    1 VVVLSVKPNSPAAKALHAGDLITEIDGQPTKSWQTFIDYIHDKKVGESVKITYKHGNKNEEASLKLTAIPK---EKGTP- 76

                 ....
gi 655907605 212 GIGI 215
Cdd:cd10824   77 GIGI 80

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with its associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655907605 136 GVMQGMPSSKV-LKTGDLITGVDGQTIKTVQDMDRVIKMKKlGDTYRVTLMRGHRVRNVTVRSAPFPKQYVGAGRgwgIG 214
Cdd:cd23081    5 EVVANSPAAEAgLKPGDRILKIDGQKVRTWEDIVRIVRENP-GKPLTLKIERDGKILTVTVTPELVEVEGKGVGR---IG 80

                 ...
gi 655907605 215 IYQ 217
Cdd:cd23081   81 VQP 83

Peptidase family M50;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 655907605  132 VLVLGVMQGMPSSKV-LKTGDLITGVDGQTIKTVQDMDRVIKMKKlGDTYRVTLMRGHRVRNVTVRSAPFPKQYVgagrg 210
Cdd:pfam02163  95 PVIGGVAPGSPAAKAgLKPGDVILSINGKKITSWQDLVEALAKSP-GKPITLTVERGGQTLTVTITPKSSEESKF----- 168

                  ....*..
gi 655907605  211 wgIGIYQ 217
Cdd:pfam02163 169 --IGIGP 173

C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, protein turnover, chaperones];

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 655907605 131 GVLVLGVMQGMPSSKV-LKTGDLITGVDGQTIKTVQDMDRVIKMK-KLGDTYRVTLMRG--HRVRNVTVRSAPFPKQYV 205
Cdd:COG0793   72 KVVVVSVIPGSPAEKAgIKPGDIILAIDGKSVAGLTLDDAVKLLRgKAGTKVTLTIKRPgeGEPITVTLTRAEIKLPSV 150

circularly permuted PDZ domain 1 of Magnetospirillum magneticum magnetosome formation protease MamE and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Magnetospirillum magneticum MamE (also known as magnetochrome MamE and magnetosome serine protease MamE), and related domains. MamE is a serine protease required to produce magnetite crystals in the magnetotactic bacterium M. magneticum. It is involved in localization of some proteins (at least MamA, MamC, MamF, MamI and MamJ) to the magnetosome, and likely cleaves at least itself, MamO and MamP. MamE-PDZ1 may bind MamB. Its autoproteolysis is stimulated by exogenous substrates or peptides that bind to its PDZ domains. Peptide binding to either the first or the second PDZ domain of MamE can activate proteolysis; activation through PDZ2 is much weaker. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This MamE-like PDZ domain 1 is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 655907605 131 GVLVLGVMQGMPSSKV-LKTGDLITGVDGQTIKTVQDMDRVIKMKKLGDTYRVTLMRGHRVRNVTV 195
Cdd:cd23087   26 GVFVSGVTPNTPAAAAgLRPGDVILKVDGRPVHQPEEVSAIMAEMPNGRSVRLGVLRDGDVRNMSL 91