>gnl|CDD|132923 cd00394, Clp_protease_like, Caseinolytic protease (ClpP) is an ATP-dependent protease. Clp protease (caseinolytic protease; ClpP; endopeptidase Clp; Peptidase S14; ATP-dependent protease, ClpAP)-like enzymes are highly conserved serine proteases and belong to the ClpP/Crotonase superfamily. Included in this family are Clp proteases that are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. The functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP. Active site consists of the triad Ser, His and Asp, preferring hydrophobic or non-polar residues at P1 or P1' positions. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function. Another family included in this class of enzymes is the signal peptide peptidase A (SppA; S49) which is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Mutagenesis studies suggest that the catalytic center of SppA comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-terminal domain. Others, including sohB peptidase, protein C, protein 1510-N and archaeal signal peptide peptidase, do not contain the amino-terminal domain. The third family included in this hierarchy is nodulation formation efficiency D (NfeD) which is a membrane-bound Clp-class protease and only found in bacteria and archaea. Majority of the NfeD genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named stomatin operon partner protein (STOPP). 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 from Pyrococcus horikoshii has been shown to possess serine protease activity having a Ser-Lys catalytic dyad. Length = 161

 Score = 86.3 bits (214), Expect = 1e-17
 Identities = 58/190 (30%), Positives = 84/190 (44%), Gaps = 33/190 (17%)

Query: 41  IAIRGQIED-SQELIERIERISRDD-SATALIVSLSSPGGSAYAGEAIFRAIQKVKNRKP 98
           I I G IED S + +    R +  D S  A+++ +++PGG   AG  I  A+Q    RKP
Sbjct: 2   IFINGVIEDVSADQLAAQIRFAEADNSVKAIVLEVNTPGGRVDAGMNIVDALQAS--RKP 59

Query: 99  VITEVHEMAASAGYLISCASNIIVAAETSLVGSIGVLFQYPYVKPFLDKLGVSIKSVKSS 158
           VI  V   AASAGY I+ A+N IV A  + VGS G +  Y                    
Sbjct: 60  VIAYVGGQAASAGYYIATAANKIVMAPGTRVGSHGPIGGYGGNG---------------- 103

Query: 159 PMKAEPSPFSEVNPKAVQMMQDVVDSSYHWFVRLVSESRNIPYDKTLV-LSDGRIWTGAE 217
                       NP A +  Q ++      F+ LV+E+R    +K    +    + T  E
Sbjct: 104 ------------NPTAQEADQRIILYFIARFISLVAENRGQTTEKLEEDIEKDLVLTAQE 151

Query: 218 AKKVGLIDVV 227
           A + GL+D +
Sbjct: 152 ALEYGLVDAL 161