HHsearch alignment for GI: 254780297 and conserved domain: TIGR00079

>TIGR00079 pept_deformyl peptide deformylase; InterPro: IPR000181 Peptide deformylase (PDF) is an essential metalloenzyme required for the removal of the formyl group at the N-terminus of nascent polypeptide chains in eubacteria 3.5.1.88 from EC. The enzyme acts as a monomer and binds a single zinc ion, catalysing the reaction:: N-formyl-L-methionine + H_2O = formate + methionyl peptide Catalytic efficiency strongly depends on the identity of the bound metal . The structure of these enzymes is known , . PDF, a member of the zinc metalloproteases family, comprises an active core domain of 147 residues and a C-terminal tail of 21 residue. The 3D fold of the catalytic core has been determined by X-ray crystallography and NMR. Overall, the structure contains a series of anti-parallel beta- strands that surround two perpendicular alpha-helices. The C-terminal helix contains the characteristic HEXXH motif of metalloenzymes, which is crucial for activity. The helical arrangement, and the way the histidine residues bind the zinc ion, is reminiscent of other metalloproteases, such as thermolysin or metzincins. However, the arrangement of secondary and tertiary structures of PDF, and the positioning of its third zinc ligand (a cysteine residue), are quite different. These discrepancies, together with notable biochemical differences, suggest that PDF constitutes a new class of zinc-metalloproteases. .; GO: 0005506 iron ion binding, 0042586 peptide deformylase activity, 0006412 translation.
Probab=100.00  E-value=0  Score=373.59  Aligned_cols=160  Identities=44%  Similarity=0.818  Sum_probs=152.7

Q ss_pred             CCHHHC-CCCCCCCCCCCCCCCCHHHH-HHHHHHHHHHHH----------CC-----CCCEEEHHHCCCCCEEEEECCCC
Q ss_conf             736457-69310521213787888999-999999986500----------47-----64213022014400037731643
Q gi|254780297|r    4 KPLVIF-PDPILRRVSRPIEKINSDIM-NLIDNMLEVMYS----------TD-----GIGLAAVQIGVLYRLVVIDLQDH   66 (170)
Q Consensus         4 ~~Iv~~-~dp~L~~~~~~v~~~~~~~~-~li~dm~~tm~~----------~~-----GvGLAA~QIG~~~ri~vv~~~~~   66 (170)
T Consensus         2 ~~vv~~Lp~~~Lr~~ak~v~~vd~~i~k~~~~dM~~~M~~~~~a~Y~G~A~~Y~~~PGiGLAApQvgi~kr~~~v~~~~~   81 (188)
T TIGR00079         2 LEVVHYLPDDVLREIAKPVEKVDDKIRKKQLDDMIETMYAYVDASYDGLAEEYKIIPGIGLAAPQVGILKRLIVVDLEDD   81 (188)
T ss_pred             CEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCC
T ss_conf             50676557722524555211588368899999999999986198758742365237744101010281101587753588


Q ss_pred             CC---CCCCCEECCCCCCCHHHHHHHHH--HHCCCCCCC-CHHHHHCCHHEEEEECCC-CCEEEEEEECCEEEEEEEEHH
Q ss_conf             23---34821001644201000001110--000012232-101211000002463235-855799972976464327001
Q gi|254780297|r   67 AH---RKNPMVFINPKIITFSDDFSVYQ--EGCLSIPDY-RADVKRSAFITVRYMDCN-AQHQIIYADGLLATCLQHELD  139 (170)
Q Consensus        67 ~~---~~~~~~~iNP~I~~~s~e~~~~~--EGCLS~Pg~-~~~V~R~~~I~v~~~d~~-G~~~~~~~~g~~Ar~~QHEiD  139 (170)
T Consensus        82 ~gvqh~~~~~~lINP~I~~~S~e~~~~~SGEGCLSvP~~~~~~V~R~~~v~i~~~d~~~gk~~~~~a~gllA~~iQHE~D  161 (188)
T TIGR00079        82 KGVQHKEKKLVLINPKIIETSEEKSGLESGEGCLSVPGVHYGDVPRAEKVKIRALDRDEGKEFTLEASGLLAICIQHEMD  161 (188)
T ss_pred             CCCCCCCCCEEEECCHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEHHHCCEEEEEECCCEEEEEEEEEE
T ss_conf             88311347457756044201576036765672006577521210433128888741322741588625883588764411


Q ss_pred             HHCCEEEEEECC-HHH-HHHHHHHHH
Q ss_conf             319768536478-899-999999999
Q gi|254780297|r  140 HLNGILFIDHLS-RLK-RDMITKKMS  163 (170)
Q Consensus       140 HL~G~lf~drls-~~k-r~~~~~k~~  163 (170)
T Consensus       162 HLnGvlF~d~~~~~l~l~~~~~~~~~  187 (188)
T TIGR00079       162 HLNGVLFVDRISEPLKLPEKLKKELK  187 (188)
T ss_pred             CCCCEEEEEECCCHHHHHHHHCCCCC
T ss_conf             25844676532663320132022124