HHsearch alignment for GI: 254780749 and conserved domain: TIGR00077

>TIGR00077 lspA signal peptidase II; InterPro: IPR001872 Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised . More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin and archaean preflagellin have been described , . Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of aspartic peptidases belong to the MEROPS peptidase family A8 (signal peptidase II family, clan AC). The catalytic residues have not been identified, but three conserved aspartates can be identified from sequence alignments. The type example is the Escherichia coli lipoprotein signal peptidase or SPase II (). This enzyme recognises a conserved sequence and cuts in front of a cysteine residue to which a glyceride-fatty acid lipid is attached. SPase II is an integral membrane protein that is anchored in the membrane. Bacterial cell walls contain large amounts of murein lipoprotein, a small protein that is both N-terminally bound to lipid and attached to membrane peptidoglycan (murein) through the epsilon-amino group of its C-terminal lysine residue . Secretion of this lipoprotein is facilitated by the action of lipoprotein signal peptidase (also known as leader peptidase II), located in the inner membrane , . The enzyme is inhibited by globomycin and also by pepstatin, suggesting that it is an aspartic peptidase . ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis, 0016020 membrane.
Probab=100.00  E-value=1.3e-32  Score=185.36  Aligned_cols=101  Identities=25%  Similarity=0.420  Sum_probs=95.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH--CCCCEEEEEECCCC----CHHHH
Q ss_conf             5200299999999999999999996555022899999999998879999989763--12757766236815----40899
Q gi|254780749|r    3 SNVSPTILVSIRILIIAFIFFIWKKNPKTKSIFDIGYILITTGALGNVVDHCLYG--YVIDYIMIHTQTWS----FAVFN   76 (108)
Q Consensus         3 s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~li~gGaiGNliDR~~~G--~VvDfi~~~~~~~~----~pvFN   76 (108)
T Consensus        77 ~GW~~~fl~~l~~~i~~~l~vF~~~~~~~~k~~~~a~gli~gGa~GN~~DRl~~gs~~VvDf~~f~~~~~~Gldrfp~FN  156 (183)
T TIGR00077        77 GGWQVYFLKGLALAISLGLVVFLLRYKELQKITNIAYGLILGGAVGNVIDRLVRGSDGVVDFLDFYLGNYHGLDRFPIFN  156 (183)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEEEECCCCCCHHH
T ss_conf             50689999999999999999998530677889889999999988988887301689934889999874230522042445


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             999999999999999999400043211
Q gi|254780749|r   77 LADLFISIGTCIIIYDDIILQHRQKGK  103 (108)
Q Consensus        77 vAD~~I~iG~~lli~~~~~~~~~~k~~  103 (108)
T Consensus       157 ~AD~~I~~G~~~Lll~~f~~~~k~~~~  183 (183)
T TIGR00077       157 LADVSICVGVILLLLKFFFPKRKKKKD  183 (183)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             888999998999999987454210279