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