254780297

254780297

peptide deformylase

GeneID in NCBI database:8209279Locus tag:CLIBASIA_00910
Protein GI in NCBI database:254780297Protein Accession:YP_003064710.1
Gene range:-(187187, 187699)Protein Length:170aa
Gene description:peptide deformylase
COG prediction:[J] N-formylmethionyl-tRNA deformylase
KEGG prediction:def; peptide deformylase (EC:3.5.1.88); K01462 [EC:3.5.1.88]
SEED prediction:Peptide deformylase (EC 3.5.1.88)
Pathway involved in KEGG:not defined
Subsystem involved in SEED:Translation termination factors bacterial;
Bacterial RNA-metabolizing Zn-dependent hydrolases;
Conserved gene cluster associated with Met-tRNA formyltransferase
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOP1 TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170
MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQLRD
ccccccEEcccHHHcccccccccccHHHHHHHHHHHHHHHHccccEEEcccccccEEEEEEEccccccccccEEEEEEEEEEcccccEEccccccccccccEEEccccEEEEEEEcccccEEEEEEccHHHHHHHHHHHHHccEEEEEEccHHHHHHHHHHHHHHHHHcc
cccHHHcccccHHHHcEcEccccccHHHHHHHHHHHHHHHHHcccEEEHHHHcccEcEEEEcccccccccccEEEEEEEEEEccccEEEEEEEEccEEEEEEEEEEEcEEEEEEEcccccEEEEEEEHHHHHHHHHHHHHHccccHHHHccHHHHHHHHHHHHHHHccHc
mvkkplvifpdpilrrvsrpieKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLqdhahrknpmvfinpkiitfsddfsvyqegclsipdyradvkRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQLRD
mvkkplvifpdpilrrvsrpiekiNSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQLRD
MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQLRD
MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKM*KL*****
MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQLRD
*VKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQ***
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQLRD
MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQLRD
MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQLRD

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target170 peptide deformylase [Candidatus Liberibacter asiaticus
315122858165 peptide deformylase [Candidatus Liberibacter solanacear 1 2e-63
325291800170 polypeptide deformylase peptide deformylase [Agrobacter 1 5e-57
190890084171 peptide deformylase [Rhizobium etli CIAT 652] Length = 1 9e-57
86356069171 peptide deformylase [Rhizobium etli CFN 42] Length = 17 1 9e-57
327191106171 peptide deformylase protein [Rhizobium etli CNPAF512] L 1 1e-56
241202826171 peptide deformylase [Rhizobium leguminosarum bv. trifol 1 2e-56
218460831171 peptide deformylase [Rhizobium etli Kim 5] Length = 171 1 3e-56
116250199171 peptide deformylase [Rhizobium leguminosarum bv. viciae 1 3e-56
218672914171 peptide deformylase [Rhizobium etli GR56] Length = 171 1 3e-56
218513698171 peptide deformylase [Rhizobium etli 8C-3] Length = 171 1 3e-56
>gi|315122858|ref|YP_004063347.1| peptide deformylase [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 165 Back     alignment and organism information
 Score =  245 bits (625), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 117/167 (70%), Positives = 146/167 (87%), Gaps = 4/167 (2%)

Query: 1   MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVV 60
           M KK L+ FPDP+LRRVSR +E I+SDI++LI++M EVMYS+DGIGLAAVQIG+LYR+VV
Sbjct: 1   MKKKSLIFFPDPVLRRVSRSVETIDSDIIHLIEDMFEVMYSSDGIGLAAVQIGILYRVVV 60

Query: 61  IDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQ 120
           IDL    + K+P+VFINP I++ S+D SV  EGCLSIP++RADVKR++F+TV+Y+D NAQ
Sbjct: 61  IDL----NTKSPLVFINPTIVSSSNDCSVRAEGCLSIPNHRADVKRASFVTVKYLDSNAQ 116

Query: 121 HQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQ 167
            QIIYADGLLATCLQHE+DHLNGILFIDH+SRLKRDMI  K+ KL++
Sbjct: 117 PQIIYADGLLATCLQHEIDHLNGILFIDHISRLKRDMIINKILKLIR 163


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|325291800|ref|YP_004277664.1| polypeptide deformylase peptide deformylase [Agrobacterium sp. H13-3] Length = 170 Back     alignment and organism information
>gi|190890084|ref|YP_001976626.1| peptide deformylase [Rhizobium etli CIAT 652] Length = 171 Back     alignment and organism information
>gi|86356069|ref|YP_467961.1| peptide deformylase [Rhizobium etli CFN 42] Length = 171 Back     alignment and organism information
>gi|327191106|gb|EGE58154.1| peptide deformylase protein [Rhizobium etli CNPAF512] Length = 171 Back     alignment and organism information
>gi|241202826|ref|YP_002973922.1| peptide deformylase [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 171 Back     alignment and organism information
>gi|218460831|ref|ZP_03500922.1| peptide deformylase [Rhizobium etli Kim 5] Length = 171 Back     alignment and organism information
>gi|116250199|ref|YP_766037.1| peptide deformylase [Rhizobium leguminosarum bv. viciae 3841] Length = 171 Back     alignment and organism information
>gi|218672914|ref|ZP_03522583.1| peptide deformylase [Rhizobium etli GR56] Length = 171 Back     alignment and organism information
>gi|218513698|ref|ZP_03510538.1| peptide deformylase [Rhizobium etli 8C-3] Length = 171 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target170 peptide deformylase [Candidatus Liberibacter asiaticus
PRK00150165 PRK00150, def, peptide deformylase; Reviewed 3e-60
COG0242168 COG0242, Def, N-formylmethionyl-tRNA deformylase [Trans 1e-53
PRK12846165 PRK12846, PRK12846, peptide deformylase; Reviewed 1e-51
cd00487141 cd00487, Pep_deformylase, Polypeptide or peptide deform 2e-46
TIGR00079161 TIGR00079, pept_deformyl, peptide deformylase 4e-45
PRK14597166 PRK14597, PRK14597, peptide deformylase; Provisional 7e-38
PRK14598187 PRK14598, PRK14598, peptide deformylase; Provisional 8e-37
PRK14596199 PRK14596, PRK14596, peptide deformylase; Provisional 4e-31
KOG3137267 KOG3137, KOG3137, KOG3137, Peptide deformylase [Transla 4e-28
PRK14595162 PRK14595, PRK14595, peptide deformylase; Provisional 4e-16
pfam01327155 pfam01327, Pep_deformylase, Polypeptide deformylase 4e-54
PRK09218136 PRK09218, PRK09218, peptide deformylase; Validated 7e-14
>gnl|CDD|178903 PRK00150, def, peptide deformylase; Reviewed Back     alignment and domain information
>gnl|CDD|30591 COG0242, Def, N-formylmethionyl-tRNA deformylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|183788 PRK12846, PRK12846, peptide deformylase; Reviewed Back     alignment and domain information
>gnl|CDD|29602 cd00487, Pep_deformylase, Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes Back     alignment and domain information
>gnl|CDD|161696 TIGR00079, pept_deformyl, peptide deformylase Back     alignment and domain information
>gnl|CDD|173061 PRK14597, PRK14597, peptide deformylase; Provisional Back     alignment and domain information
>gnl|CDD|173062 PRK14598, PRK14598, peptide deformylase; Provisional Back     alignment and domain information
>gnl|CDD|184758 PRK14596, PRK14596, peptide deformylase; Provisional Back     alignment and domain information
>gnl|CDD|38347 KOG3137, KOG3137, KOG3137, Peptide deformylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|184757 PRK14595, PRK14595, peptide deformylase; Provisional Back     alignment and domain information
>gnl|CDD|144794 pfam01327, Pep_deformylase, Polypeptide deformylase Back     alignment and domain information
>gnl|CDD|181704 PRK09218, PRK09218, peptide deformylase; Validated Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 170 peptide deformylase [Candidatus Liberibacter asiaticus
PRK12846168 peptide deformylase; Reviewed 100.0
PRK00150163 def peptide deformylase; Reviewed 100.0
COG0242168 Def N-formylmethionyl-tRNA deformylase [Translation, ri 100.0
TIGR00079188 pept_deformyl peptide deformylase; InterPro: IPR000181 100.0
pfam01327155 Pep_deformylase Polypeptide deformylase. 100.0
cd00487141 Pep_deformylase Polypeptide or peptide deformylase; a f 100.0
PRK09218136 peptide deformylase; Validated 100.0
KOG3137267 consensus 100.0
COG4740176 Predicted metalloprotease [General function prediction 96.01
>PRK12846 peptide deformylase; Reviewed Back     alignment and domain information
>PRK00150 def peptide deformylase; Reviewed Back     alignment and domain information
>COG0242 Def N-formylmethionyl-tRNA deformylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>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 Back     alignment and domain information
>pfam01327 Pep_deformylase Polypeptide deformylase Back     alignment and domain information
>cd00487 Pep_deformylase Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes Back     alignment and domain information
>PRK09218 peptide deformylase; Validated Back     alignment and domain information
>KOG3137 consensus Back     alignment and domain information
>COG4740 Predicted metalloprotease [General function prediction only] Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target170 peptide deformylase [Candidatus Liberibacter asiaticus
1n5n_A180 Crystal Structure Of Peptide Deformylase From Pseud 2e-37
1lry_A167 Crystal Structure Of P. Aeruginosa Peptide Deformyl 1e-36
1ix1_A171 Crystal Structure Of P.Aeruginosa Peptide Deformyla 1e-36
3fwx_A169 The Crystal Structure Of The Peptide Deformylase Fr 2e-31
1lme_A176 Crystal Structure Of Peptide Deformylase From Therm 8e-31
3k6l_A169 The Structure Of E.Coli Peptide Deformylase (Pdf) I 9e-31
2w3t_A188 Chloro Complex Of The Ni-Form Of E.Coli Deformylase 9e-31
1icj_A168 Pdf Protein Is Crystallized As Ni2+ Containing Form 8e-30
1dff_A164 Peptide Deformylase Length = 164 3e-29
3oca_A209 Crystal Structure Of Peptide Deformylase From Ehrli 7e-29
3qu1_A171 Peptide Deformylase From Vibrio Cholerae Length = 1 1e-28
3cpm_A193 Plant Peptide Deformylase Pdf1b Crystal Structure L 2e-27
3m6o_A193 Crystal Structure Of Arabidopsis Thaliana Peptide D 6e-27
1v3y_A192 The Crystal Structure Of Peptide Deformylase From T 8e-27
1y6h_A177 Crystal Structure Of Lipdf Length = 177 9e-27
3m6q_A193 Crystal Structure Of Arabidopsis Thaliana Peptide D 1e-26
1szz_A177 Crystal Structure Of Peptide Deformylase From Lepto 2e-26
3m6r_A193 Crystal Structure Of Arabidopsis Thaliana Peptide D 3e-26
2ew5_A181 Structure Of Helicobacter Pylori Peptide Deformylas 4e-26
2def_A147 Peptide Deformylase Catalytic Core (Residues 1-147) 1e-24
1rl4_A188 Plasmodium Falciparum Peptide Deformylase Complex W 2e-24
1def_A147 Peptide Deformylase Catalytic Core (Residues 1-147) 2e-24
1rqc_A185 Crystals Of Peptide Deformylase From Plasmodium Fal 2e-23
1ws0_A156 Structure Analysis Of Peptide Deformylase From Baci 3e-23
3dld_A171 Crystal Structure Of Peptide Deformylase, Xoo1075, 3e-22
1jym_A183 Crystals Of Peptide Deformylase From Plasmodium Fal 2e-21
1lqy_A184 Crystal Structure Of Bacillus Stearothermophilus Pe 4e-21
1zxz_A197 X-Ray Structure Of Peptide Deformylase From Arabido 3e-20
3e3u_A197 Crystal Structure Of Mycobacterium Tuberculosis Pep 4e-20
2okl_A185 Crystal Structure Of Peptide Deformylase 2 With Act 1e-19
2os1_A188 Structures Of Actinonin Bound Peptide Deformylases 1e-17
2os0_A188 Structures Of Actinonin Bound Peptide Deformylases 2e-17
3g5k_A183 Structure And Activity Of Human Mitochondrial Pepti 4e-17
1lqw_A183 Crystal Structure Of S.Aureus Peptide Deformylase L 3e-16
1lm4_A194 Structure Of Peptide Deformylase From Staphylococcu 5e-16
1q1y_A191 Crystal Structures Of Peptide Deformylase From Stap 7e-16
3cmd_A196 Crystal Structure Of Peptide Deformylase From Vre-E 3e-15
3g6n_A191 Crystal Structure Of An Efpdf Complex With Met-Ala- 4e-15
1lmh_A184 Crystal Structure Of S. Aureus Peptide Deformylase 1e-14
2os3_A205 Structures Of Actinonin Bound Peptide Deformylases 1e-13
2ai7_A203 S.Pneumoniae Polypeptide Deformylase Complexed With 7e-13
2aie_P203 S.Pneumoniae Polypeptide Deformylase Complexed With 8e-13
1lm6_A215 Crystal Structure Of Peptide Deformylase From Strep 9e-13
3l87_A238 The Crystal Structure Of Smu.143c From Streptococcu 8e-12
>gi|33357406|pdb|1N5N|A Chain A, Crystal Structure Of Peptide Deformylase From Pseudomonas Aeruginosa Length = 180 Back     alignment and structure
 Score =  158 bits (399), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 73/169 (43%), Positives = 106/169 (62%), Gaps = 2/169 (1%)

Query: 1   MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVV 60
           M    ++ FPDP LR +++P+E ++  +  LID+M E MY   GIGLAA Q+ V  R+VV
Sbjct: 13  MAILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVV 72

Query: 61  IDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQ 120
           +DL +      P VFINP+    +++   YQEGCLS+P +  +V R   + ++ +D +  
Sbjct: 73  MDLSEDKSE--PRVFINPEFEPLTEEMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGN 130

Query: 121 HQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQLR 169
                A+GLLA C+QHE DHLNG LF+D+LS LKRD I KK+ K  + +
Sbjct: 131 PFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHRQQ 179


>gi|22219294|pdb|1LRY|A Chain A, Crystal Structure Of P. Aeruginosa Peptide Deformylase Complexed With Antibiotic Actinonin Length = 167 Back     alignment and structure
>gi|34809567|pdb|1IX1|A Chain A, Crystal Structure Of P.Aeruginosa Peptide Deformylase Complexed With Antibiotic Actinonin Length = 171 Back     alignment and structure
>gi|225698067|pdb|3FWX|A Chain A, The Crystal Structure Of The Peptide Deformylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961 Length = 169 Back     alignment and structure
>gi|33357295|pdb|1LME|A Chain A, Crystal Structure Of Peptide Deformylase From Thermotoga Maritima Length = 176 Back     alignment and structure
gi|266618787|pdb|3K6L|A Chain A, The Structure Of E.Coli Peptide Deformylase (Pdf) In Complex With Peptidomimetic Ligand Bb2827 Length = 169 Back     alignment and structure
>gi|281306913|pdb|2W3T|A Chain A, Chloro Complex Of The Ni-Form Of E.Coli Deformylase Length = 188 Back     alignment and structure
>gi|4699740|pdb|1ICJ|A Chain A, Pdf Protein Is Crystallized As Ni2+ Containing Form, Cocrystallized With Inhibitor Polyethylene Glycol (Peg) Length = 168 Back     alignment and structure
>gi|157830814|pdb|1DFF|A Chain A, Peptide Deformylase Length = 164 Back     alignment and structure
>gi|306440704|pdb|3OCA|A Chain A, Crystal Structure Of Peptide Deformylase From Ehrlichia Chaffeensis Length = 209 Back     alignment and structure
>gi|325534093|pdb|3QU1|A Chain A, Peptide Deformylase From Vibrio Cholerae Length = 171 Back     alignment and structure
>gi|194368702|pdb|3CPM|A Chain A, Plant Peptide Deformylase Pdf1b Crystal Structure Length = 193 Back     alignment and structure
>gi|327200558|pdb|3M6O|A Chain A, Crystal Structure Of Arabidopsis Thaliana Peptide Deformylase 1b (Atpdf1b) Length = 193 Back     alignment and structure
>gi|58176979|pdb|1V3Y|A Chain A, The Crystal Structure Of Peptide Deformylase From Thermus Thermophilus Hb8 Length = 192 Back     alignment and structure
>gi|61679585|pdb|1Y6H|A Chain A, Crystal Structure Of Lipdf Length = 177 Back     alignment and structure
>gi|327200562|pdb|3M6Q|A Chain A, Crystal Structure Of Arabidopsis Thaliana Peptide Deformylase 1b (Atpdf1b) G41q Mutant In Complex With Actinonin Length = 193 Back     alignment and structure
>gi|75765204|pdb|1SZZ|A Chain A, Crystal Structure Of Peptide Deformylase From Leptospira Interrogans Complexed With Inhibitor Actinonin Length = 177 Back     alignment and structure
>gi|327200563|pdb|3M6R|A Chain A, Crystal Structure Of Arabidopsis Thaliana Peptide Deformylase 1b (Atpdf1b) G41m Mutant In Complex With Actinonin Length = 193 Back     alignment and structure
>gi|118137648|pdb|2EW5|A Chain A, Structure Of Helicobacter Pylori Peptide Deformylase In Complex With Inhibitor Length = 181 Back     alignment and structure
>gi|157834784|pdb|2DEF|A Chain A, Peptide Deformylase Catalytic Core (Residues 1-147), Nmr, 20 Structures Length = 147 Back     alignment and structure
>gi|40889670|pdb|1RL4|A Chain A, Plasmodium Falciparum Peptide Deformylase Complex With Inhibitor Length = 188 Back     alignment and structure
>gi|157830807|pdb|1DEF|A Chain A, Peptide Deformylase Catalytic Core (Residues 1-147), Nmr, 9 Structures Length = 147 Back     alignment and structure
>gi|42543585|pdb|1RQC|A Chain A, Crystals Of Peptide Deformylase From Plasmodium Falciparum With Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics Of The Active Site For Drug Design Length = 185 Back     alignment and structure
gi|78100858|pdb|1WS0|A Chain A, Structure Analysis Of Peptide Deformylase From Bacillus Cereus Length = 156 Back     alignment and structure
gi|242556373|pdb|3DLD|A Chain A, Crystal Structure Of Peptide Deformylase, Xoo1075, From Xanthomonas Oryzae Pv. Oryzae Kacc10331 Length = 171 Back     alignment and structure
>gi|20150600|pdb|1JYM|A Chain A, Crystals Of Peptide Deformylase From Plasmodium Falciparum With Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics Of The Active Site For Drug Design Length = 183 Back     alignment and structure
gi|22219287|pdb|1LQY|A Chain A, Crystal Structure Of Bacillus Stearothermophilus Peptide Deformylase Complexed With Antibiotic Actinonin Length = 184 Back     alignment and structure
>gi|78101135|pdb|1ZXZ|A Chain A, X-Ray Structure Of Peptide Deformylase From Arabidopsis Thaliana (Atpdf1a); Crystals Grown In Peg-5000 Mme As Precipitant Length = 197 Back     alignment and structure
gi|221046693|pdb|3E3U|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Peptide Deformylase In Complex With Inhibitor Length = 197 Back     alignment and structure
>gi|165760871|pdb|2OKL|A Chain A, Crystal Structure Of Peptide Deformylase 2 With Actinonin From Bacillus Cereus Length = 185 Back     alignment and structure
>gi|169404548|pdb|2OS1|A Chain A, Structures Of Actinonin Bound Peptide Deformylases From E. Faecalis And S. Pyogenes Length = 188 Back     alignment and structure
>gi|169404547|pdb|2OS0|A Chain A, Structures Of Actinonin Bound Peptide Deformylases From E. Faecalis And S. Pyogenes Length = 188 Back     alignment and structure
>gi|226438315|pdb|3G5K|A Chain A, Structure And Activity Of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target Length = 183 Back     alignment and structure
gi|22219285|pdb|1LQW|A Chain A, Crystal Structure Of S.Aureus Peptide Deformylase Length = 183 Back     alignment and structure
>gi|33357292|pdb|1LM4|A Chain A, Structure Of Peptide Deformylase From Staphylococcus Aureus At 1.45 A Length = 194 Back     alignment and structure
>gi|51247225|pdb|1Q1Y|A Chain A, Crystal Structures Of Peptide Deformylase From Staphylococcus Aureus Complexed With Actinonin Length = 191 Back     alignment and structure
>gi|220702375|pdb|3CMD|A Chain A, Crystal Structure Of Peptide Deformylase From Vre-E.Faecium Length = 196 Back     alignment and structure
>gi|224510906|pdb|3G6N|A Chain A, Crystal Structure Of An Efpdf Complex With Met-Ala-Ser Length = 191 Back     alignment and structure
>gi|21730762|pdb|1LMH|A Chain A, Crystal Structure Of S. Aureus Peptide Deformylase Length = 184 Back     alignment and structure
>gi|169404549|pdb|2OS3|A Chain A, Structures Of Actinonin Bound Peptide Deformylases From E. Faecalis And S. Pyogenes Length = 205 Back     alignment and structure
>gi|75766232|pdb|2AI7|A Chain A, S.Pneumoniae Polypeptide Deformylase Complexed With Sb- 485345 Length = 203 Back     alignment and structure
>gi|75766239|pdb|2AIE|P Chain P, S.Pneumoniae Polypeptide Deformylase Complexed With Sb- 505684 Length = 203 Back     alignment and structure
>gi|33357294|pdb|1LM6|A Chain A, Crystal Structure Of Peptide Deformylase From Streptococcus Pneumoniae Length = 215 Back     alignment and structure
>gi|316983220|pdb|3L87|A Chain A, The Crystal Structure Of Smu.143c From Streptococcus Mutans Ua159 Length = 238 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target170 peptide deformylase [Candidatus Liberibacter asiaticus
3oca_A209 Peptide deformylase; ssgcid, structur genomics, seattle 9e-50
1n5n_A180 Peptide deformylase; metalloenzyme, drug design, deform 4e-49
1lme_A176 PDF, peptide deformylase; thermophIle, metalloenzyme, d 1e-45
2w3t_A188 Peptide deformylase; protein biosynthesis, iron, nickel 4e-45
3e3u_A197 Peptide deformylase; metallo-enzyme, hydrolase, iron, m 2e-44
3dld_A171 Peptide deformylase; bacterial blight, XOO1075, xanthom 3e-42
1v3y_A192 Peptide deformylase; protein synthesis, riken structura 3e-38
1zxz_A197 PDF, peptide deformylase, mitochondrial; PDF1A, eukaryo 4e-35
1y6h_A177 Peptide deformylase; open and close conformation, PDF, 9e-35
3cpm_A193 Peptide deformylase, chloroplast; alpha beta, hydrolase 1e-34
1rl4_A188 Formylmethionine deformylase; crystal engineering, drug 2e-33
2ew5_A181 Peptide deformylase; inhibitor, hydrolase; HET: Y12; 2. 1e-32
1lm4_A194 Peptide deformylase PDF1; metalloenzyme, hydrolase; 1.4 2e-32
3g5k_A183 Peptide deformylase, mitochondrial; actinonin, hydrolas 2e-31
1xeo_A168 Peptide deformylase; cobalt deformylase, formate, hydro 3e-31
1ws0_A156 Peptide deformylase 1; alpha + beta topology, hydrolase 3e-28
2okl_A185 Peptide deformylase 2; hydrolase; HET: BB2 CIT; 1.70A { 3e-27
2os0_A188 Peptide deformylase; PDF, hydrolase; 1.30A {Enterococcu 2e-26
2aia_A203 Peptide deformylase; hydrolase; HET: SB8; 1.70A {Strept 3e-26
>3oca_A Peptide deformylase; ssgcid, structur genomics, seattle structural genomics center for infectious hydrolase; 2.40A {Ehrlichia chaffeensis} Length = 209 Back     alignment and structure
 Score =  190 bits (485), Expect = 9e-50
 Identities = 69/182 (37%), Positives = 100/182 (54%), Gaps = 17/182 (9%)

Query: 1   MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVV 60
           M    +V  PD  L   S  +EK++  I  L+D+M E M++  G+GLAAVQ+GV  R++V
Sbjct: 22  MSVLSIVTVPDKRLSLCSEEVEKVDQSIRKLVDDMFETMHANQGLGLAAVQVGVHKRILV 81

Query: 61  IDLQD-----------------HAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRAD 103
           +++ +                 +     P   INPKI+  S +    +EGCLS+P Y   
Sbjct: 82  MNVPEEFEDSEDIENVEDKIEGYELYGGPYCIINPKIVDISQEKVKLKEGCLSVPGYFDY 141

Query: 104 VKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMS 163
           + R   I V+Y+D N    II A G LA CLQHE+DHLNG +F+ +LS+ KRD   +K+ 
Sbjct: 142 IVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHEIDHLNGTVFLKYLSKFKRDFAIEKVK 201

Query: 164 KL 165
           K 
Sbjct: 202 KK 203


>1n5n_A Peptide deformylase; metalloenzyme, drug design, deformylation, hydrolase; 1.80A {Pseudomonas aeruginosa} SCOP: d.167.1.1 PDB: 1s17_A* 1ix1_A* 1lry_A* Length = 180 Back     alignment and structure
>1lme_A PDF, peptide deformylase; thermophIle, metalloenzyme, deformylation, structural genomics, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: d.167.1.1 Length = 176 Back     alignment and structure
>2w3t_A Peptide deformylase; protein biosynthesis, iron, nickel, hydrolase, metal-binding; 1.69A {Escherichia coli} PDB: 2w3u_A Length = 188 Back     alignment and structure
>3e3u_A Peptide deformylase; metallo-enzyme, hydrolase, iron, metal-binding, protein biosynthesis; HET: NVC; 1.56A {Mycobacterium tuberculosis} Length = 197 Back     alignment and structure
>3dld_A Peptide deformylase; bacterial blight, XOO1075, xanthomonas oryzae PV. oryzae KACC10331, hydrolase; 2.60A {Xanthomonas oryzae PV} Length = 171 Back     alignment and structure
>1v3y_A Peptide deformylase; protein synthesis, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.81A {Thermus thermophilus} SCOP: d.167.1.1 Length = 192 Back     alignment and structure
>1zxz_A PDF, peptide deformylase, mitochondrial; PDF1A, eukaryote, higher plant, zinc ION, hydrolase; 2.80A {Arabidopsis thaliana} PDB: 1zy0_A 1zy1_A Length = 197 Back     alignment and structure
>1y6h_A Peptide deformylase; open and close conformation, PDF, hydrolase; 2.20A {Leptospira interrogans} SCOP: d.167.1.1 PDB: 1sv2_A* 1vey_A* 1vev_A 1vez_A 1szz_A* Length = 177 Back     alignment and structure
>3cpm_A Peptide deformylase, chloroplast; alpha beta, hydrolase, iron, metal-binding, plastid, protein biosynthesis, transit peptide; 2.40A {Arabidopsis thaliana} Length = 193 Back     alignment and structure
>1rl4_A Formylmethionine deformylase; crystal engineering, drug design, malaria, PDF, peptide deformylase, hydrolase; HET: BRR BL5; 2.18A {Plasmodium falciparum 3D7} SCOP: d.167.1.1 PDB: 1rqc_A 1jym_A Length = 188 Back     alignment and structure
>2ew5_A Peptide deformylase; inhibitor, hydrolase; HET: Y12; 2.20A {Helicobacter pylori} PDB: 2ew6_A* 2ew7_A Length = 181 Back     alignment and structure
>1lm4_A Peptide deformylase PDF1; metalloenzyme, hydrolase; 1.45A {Staphylococcus aureus} SCOP: d.167.1.1 PDB: 1lqw_A 2ai9_A 1lmh_A 1q1y_A* Length = 194 Back     alignment and structure
>3g5k_A Peptide deformylase, mitochondrial; actinonin, hydrolase, iron, metal- binding, mitochondrion, protein biosynthesis, transit peptide; HET: BB2; 1.70A {Homo sapiens} PDB: 3g5p_A Length = 183 Back     alignment and structure
>1xeo_A Peptide deformylase; cobalt deformylase, formate, hydrolase; 1.30A {Escherichia coli BL21} SCOP: d.167.1.1 PDB: 1bs5_A 1bs6_A 1bs7_A 1bs8_A 1bsj_A* 1bsk_A* 1bsz_A* 1g27_A* 1bs4_A* 1icj_A* 1lru_A* 1xem_A 1xen_A 1g2a_A 2ai8_A* 3k6l_A* 1dff_A 1def_A 2kmn_A* 2def_A ... Length = 168 Back     alignment and structure
>1ws0_A Peptide deformylase 1; alpha + beta topology, hydrolase; 1.70A {Bacillus cereus} PDB: 1ws1_A* Length = 156 Back     alignment and structure
>2okl_A Peptide deformylase 2; hydrolase; HET: BB2 CIT; 1.70A {Bacillus cereus atcc 14579} PDB: 1lqy_A* Length = 185 Back     alignment and structure
>2os0_A Peptide deformylase; PDF, hydrolase; 1.30A {Enterococcus faecalis} PDB: 2os1_A* 3g6n_A 3cmd_A Length = 188 Back     alignment and structure
>2aia_A Peptide deformylase; hydrolase; HET: SB8; 1.70A {Streptococcus pneumoniae} PDB: 2ai7_A* 2aie_P* 1lm6_A 2os3_A* Length = 203 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target170 peptide deformylase [Candidatus Liberibacter asiaticus
3oca_A209 Peptide deformylase; ssgcid, structur genomics, seattle 100.0
1n5n_A180 Peptide deformylase; metalloenzyme, drug design, deform 100.0
2w3t_A188 Peptide deformylase; protein biosynthesis, iron, nickel 100.0
3cpm_A193 Peptide deformylase, chloroplast; alpha beta, hydrolase 100.0
1lme_A176 PDF, peptide deformylase; thermophIle, metalloenzyme, d 100.0
2ew5_A181 Peptide deformylase; inhibitor, hydrolase; HET: Y12; 2. 100.0
1xeo_A168 Peptide deformylase; cobalt deformylase, formate, hydro 100.0
3e3u_A197 Peptide deformylase; metallo-enzyme, hydrolase, iron, m 100.0
1y6h_A177 Peptide deformylase; open and close conformation, PDF, 100.0
1rl4_A188 Formylmethionine deformylase; crystal engineering, drug 100.0
3g5k_A183 Peptide deformylase, mitochondrial; actinonin, hydrolas 100.0
1zxz_A197 PDF, peptide deformylase, mitochondrial; PDF1A, eukaryo 100.0
3dld_A171 Peptide deformylase; bacterial blight, XOO1075, xanthom 100.0
1v3y_A192 Peptide deformylase; protein synthesis, riken structura 100.0
1ws0_A156 Peptide deformylase 1; alpha + beta topology, hydrolase 100.0
2os0_A188 Peptide deformylase; PDF, hydrolase; 1.30A {Enterococcu 100.0
2okl_A185 Peptide deformylase 2; hydrolase; HET: BB2 CIT; 1.70A { 100.0
1lm4_A194 Peptide deformylase PDF1; metalloenzyme, hydrolase; 1.4 100.0
2aia_A203 Peptide deformylase; hydrolase; HET: SB8; 1.70A {Strept 100.0
>3oca_A Peptide deformylase; ssgcid, structur genomics, seattle structural genomics center for infectious hydrolase; 2.40A {Ehrlichia chaffeensis} Back     alignment and structure
Probab=100.00  E-value=0  Score=404.00  Aligned_cols=169  Identities=41%  Similarity=0.686  Sum_probs=160.0

Q ss_pred             CCCCCHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEHHHCCCCCEEEEECCCCCCC-----------
Q ss_conf             987736457693105212137878889999999999865004764213022014400037731643233-----------
Q gi|254780297|r    1 MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHR-----------   69 (170)
Q Consensus         1 M~~~~Iv~~~dp~L~~~~~~v~~~~~~~~~li~dm~~tm~~~~GvGLAA~QIG~~~ri~vv~~~~~~~~-----------   69 (170)
                      |++++|++||||+||++|+||+.+|+++++|++||++||++++||||||||||+++|+||++.+++...           
T Consensus        22 M~vl~Iv~~pdp~Lr~~a~~V~~~d~~l~~li~dM~~Tm~~~~GvGLAApQIG~~~rifvi~~~~~~~~~~~~~~~~~~~  101 (209)
T 3oca_A           22 MSVLSIVTVPDKRLSLCSEEVEKVDQSIRKLVDDMFETMHANQGLGLAAVQVGVHKRILVMNVPEEFEDSEDIENVEDKI  101 (209)
T ss_dssp             -CCCCCCCTTCGGGGSCCBCCSCCCHHHHHHHHHHHHHHHHHTCSEEEGGGGTCCBSEEEEEECC--------CCSSCCC
T ss_pred             CEEEECCCCCCHHHHCCCEECCCCCHHHHHHHHHHHHHHHHCCCCEEEHHHCCCCCCEEEEECCCCCCCCCCCCCCCCCC
T ss_conf             26412432799799485726896898999999999999987899554266639763489997774223321111211112


Q ss_pred             ------CCCCEECCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHCCHHEEEEECCCCCEEEEEEECCEEEEEEEEHHHHCC
Q ss_conf             ------48210016442010000011100000122321012110000024632358557999729764643270013197
Q gi|254780297|r   70 ------KNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNG  143 (170)
Q Consensus        70 ------~~~~~~iNP~I~~~s~e~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G  143 (170)
                            ..+.+||||+|++.|+++..++|||||+||+++.|+||.+|+|+|+|++|+.++.+++||+|||||||+|||+|
T Consensus       102 ~~~~~~~~~~vlINP~I~~~s~e~~~~~EGCLS~Pg~~~~V~R~~~I~v~y~d~~G~~~~~~~~G~~Ar~~QHEiDHL~G  181 (209)
T 3oca_A          102 EGYELYGGPYCIINPKIVDISQEKVKLKEGCLSVPGYFDYIVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHEIDHLNG  181 (209)
T ss_dssp             TTCBSSEEEEEEEEEEEEEECSCEEEEEECCTTSTTCCEEEEEESCEEEEEECTTSCEEEEEECHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCEEEECCEEEECCCCEEEEEECCCCCCCCCCCCCCHHEEEEEEEEECCCEEEEEEEEHHHHHHHHHHHHHCC
T ss_conf             22114678469986737862765788641444448876666362239999998059199999976454688687684388


Q ss_pred             EEEEEECCHHHHHHHHHHHHHHHHHC
Q ss_conf             68536478899999999999998504
Q gi|254780297|r  144 ILFIDHLSRLKRDMITKKMSKLVQLR  169 (170)
Q Consensus       144 ~lf~drls~~kr~~~~~k~~k~~k~k  169 (170)
                      +||+||+|+++|.++.+|++|+.|..
T Consensus       182 iLf~Drls~~kr~~~~~k~~k~~k~~  207 (209)
T 3oca_A          182 TVFLKYLSKFKRDFAIEKVKKKERTD  207 (209)
T ss_dssp             CCGGGGSCHHHHHHHHHHHHHHTSCC
T ss_pred             CCHHHHCCHHHHHHHHHHHHHHHHHC
T ss_conf             93468489989999999999987422



>1n5n_A Peptide deformylase; metalloenzyme, drug design, deformylation, hydrolase; 1.80A {Pseudomonas aeruginosa} SCOP: d.167.1.1 PDB: 1s17_A* 1ix1_A* 1lry_A* Back     alignment and structure
>2w3t_A Peptide deformylase; protein biosynthesis, iron, nickel, hydrolase, metal-binding; 1.69A {Escherichia coli} PDB: 2w3u_A Back     alignment and structure
>3cpm_A Peptide deformylase, chloroplast; alpha beta, hydrolase, iron, metal-binding, plastid, protein biosynthesis, transit peptide; 2.40A {Arabidopsis thaliana} Back     alignment and structure
>1lme_A PDF, peptide deformylase; thermophIle, metalloenzyme, deformylation, structural genomics, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: d.167.1.1 Back     alignment and structure
>2ew5_A Peptide deformylase; inhibitor, hydrolase; HET: Y12; 2.20A {Helicobacter pylori} PDB: 2ew6_A* 2ew7_A Back     alignment and structure
>1xeo_A Peptide deformylase; cobalt deformylase, formate, hydrolase; 1.30A {Escherichia coli BL21} SCOP: d.167.1.1 PDB: 1bs5_A 1bs6_A 1bs7_A 1bs8_A 1bsj_A* 1bsk_A* 1bsz_A* 1g27_A* 1bs4_A* 1icj_A* 1lru_A* 1xem_A 1xen_A 1g2a_A 2ai8_A* 3k6l_A* 1dff_A 1def_A 2kmn_A* 2def_A ... Back     alignment and structure
>3e3u_A Peptide deformylase; metallo-enzyme, hydrolase, iron, metal-binding, protein biosynthesis; HET: NVC; 1.56A {Mycobacterium tuberculosis} Back     alignment and structure
>1y6h_A Peptide deformylase; open and close conformation, PDF, hydrolase; 2.20A {Leptospira interrogans} SCOP: d.167.1.1 PDB: 1sv2_A* 1vey_A* 1vev_A 1vez_A 1szz_A* Back     alignment and structure
>1rl4_A Formylmethionine deformylase; crystal engineering, drug design, malaria, PDF, peptide deformylase, hydrolase; HET: BRR BL5; 2.18A {Plasmodium falciparum 3D7} SCOP: d.167.1.1 PDB: 1rqc_A 1jym_A Back     alignment and structure
>3g5k_A Peptide deformylase, mitochondrial; actinonin, hydrolase, iron, metal- binding, mitochondrion, protein biosynthesis, transit peptide; HET: BB2; 1.70A {Homo sapiens} PDB: 3g5p_A Back     alignment and structure
>1zxz_A PDF, peptide deformylase, mitochondrial; PDF1A, eukaryote, higher plant, zinc ION, hydrolase; 2.80A {Arabidopsis thaliana} PDB: 1zy0_A 1zy1_A Back     alignment and structure
>3dld_A Peptide deformylase; bacterial blight, XOO1075, xanthomonas oryzae PV. oryzae KACC10331, hydrolase; 2.60A {Xanthomonas oryzae PV} Back     alignment and structure
>1v3y_A Peptide deformylase; protein synthesis, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.81A {Thermus thermophilus} SCOP: d.167.1.1 Back     alignment and structure
>1ws0_A Peptide deformylase 1; alpha + beta topology, hydrolase; 1.70A {Bacillus cereus} PDB: 1ws1_A* Back     alignment and structure
>2os0_A Peptide deformylase; PDF, hydrolase; 1.30A {Enterococcus faecalis} PDB: 2os1_A* 3g6n_A 3cmd_A Back     alignment and structure
>2okl_A Peptide deformylase 2; hydrolase; HET: BB2 CIT; 1.70A {Bacillus cereus atcc 14579} PDB: 1lqy_A* Back     alignment and structure
>1lm4_A Peptide deformylase PDF1; metalloenzyme, hydrolase; 1.45A {Staphylococcus aureus} SCOP: d.167.1.1 PDB: 1lqw_A 2ai9_A 1lmh_A 1q1y_A* Back     alignment and structure
>2aia_A Peptide deformylase; hydrolase; HET: SB8; 1.70A {Streptococcus pneumoniae} PDB: 2ai7_A* 2aie_P* 1lm6_A 2os3_A* Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 170 peptide deformylase [Candidatus Liberibacter asiaticus
d1v3ya_182 d.167.1.1 (A:) Peptide deformylase {Thermus thermophilu 3e-36
d1y6ha_177 d.167.1.1 (A:) Peptide deformylase {Leptospira interrog 1e-35
d1ix1a_169 d.167.1.1 (A:) Peptide deformylase {Pseudomonas aerugin 4e-34
d1xeoa1164 d.167.1.1 (A:1-164) Peptide deformylase {Escherichia co 2e-32
d1lmea_154 d.167.1.1 (A:) Peptide deformylase {Thermotoga maritima 4e-32
d1rl4a_165 d.167.1.1 (A:) Peptide deformylase {Malaria parasite (P 9e-30
d1lqya_184 d.167.1.1 (A:) Peptide deformylase {Bacillus stearother 2e-27
d1lm6a_202 d.167.1.1 (A:) Peptide deformylase {Streptococcus pneum 7e-26
d1lm4a_194 d.167.1.1 (A:) Peptide deformylase {Staphylococcus aure 2e-25
>d1v3ya_ d.167.1.1 (A:) Peptide deformylase {Thermus thermophilus [TaxId: 274]} Length = 182 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Peptide deformylase
superfamily: Peptide deformylase
family: Peptide deformylase
domain: Peptide deformylase
species: Thermus thermophilus [TaxId: 274]
 Score =  144 bits (365), Expect = 3e-36
 Identities = 58/175 (33%), Positives = 90/175 (51%), Gaps = 13/175 (7%)

Query: 1   MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVV 60
           MV  P+ ++ DP+LRR +RP+E  +  I  L ++MLE M+   G+GLAA QIG+  RL V
Sbjct: 1   MVY-PIRLYGDPVLRRKARPVEDFS-GIKRLAEDMLETMFEAKGVGLAAPQIGLSQRLFV 58

Query: 61  IDLQDHAHR----------KNPMVFINPKIITFSDDFSVYQEGCLSIPD-YRADVKRSAF 109
                                 +  +   +IT+ +      EGCLS+P  Y  +V R+  
Sbjct: 59  AVEYADEPEGEEERPLRELVRRVYVVANPVITYREGLVEGTEGCLSLPGLYSEEVPRAER 118

Query: 110 ITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSK 164
           I V Y D   + +++  +G +A   QHE+DHL+GILF + L + KR+   +    
Sbjct: 119 IRVEYQDEEGRGRVLELEGYMARVFQHEIDHLDGILFFERLPKPKREAFLEANRA 173


>d1y6ha_ d.167.1.1 (A:) Peptide deformylase {Leptospira interrogans [TaxId: 173]} Length = 177 Back     information, alignment and structure
>d1ix1a_ d.167.1.1 (A:) Peptide deformylase {Pseudomonas aeruginosa [TaxId: 287]} Length = 169 Back     information, alignment and structure
>d1xeoa1 d.167.1.1 (A:1-164) Peptide deformylase {Escherichia coli [TaxId: 562]} Length = 164 Back     information, alignment and structure
>d1lmea_ d.167.1.1 (A:) Peptide deformylase {Thermotoga maritima [TaxId: 2336]} Length = 154 Back     information, alignment and structure
>d1rl4a_ d.167.1.1 (A:) Peptide deformylase {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]} Length = 165 Back     information, alignment and structure
>d1lqya_ d.167.1.1 (A:) Peptide deformylase {Bacillus stearothermophilus [TaxId: 1422]} Length = 184 Back     information, alignment and structure
>d1lm6a_ d.167.1.1 (A:) Peptide deformylase {Streptococcus pneumoniae [TaxId: 1313]} Length = 202 Back     information, alignment and structure
>d1lm4a_ d.167.1.1 (A:) Peptide deformylase {Staphylococcus aureus [TaxId: 1280]} Length = 194 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target170 peptide deformylase [Candidatus Liberibacter asiaticus
d1xeoa1164 Peptide deformylase {Escherichia coli [TaxId: 562]} 100.0
d1ix1a_169 Peptide deformylase {Pseudomonas aeruginosa [TaxId: 287 100.0
d1rl4a_165 Peptide deformylase {Malaria parasite (Plasmodium falci 100.0
d1y6ha_177 Peptide deformylase {Leptospira interrogans [TaxId: 173 100.0
d1v3ya_182 Peptide deformylase {Thermus thermophilus [TaxId: 274]} 100.0
d1lmea_154 Peptide deformylase {Thermotoga maritima [TaxId: 2336]} 100.0
d1lqya_184 Peptide deformylase {Bacillus stearothermophilus [TaxId 100.0
d1lm4a_194 Peptide deformylase {Staphylococcus aureus [TaxId: 1280 100.0
d1lm6a_202 Peptide deformylase {Streptococcus pneumoniae [TaxId: 1 100.0
>d1xeoa1 d.167.1.1 (A:1-164) Peptide deformylase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Peptide deformylase
superfamily: Peptide deformylase
family: Peptide deformylase
domain: Peptide deformylase
species: Escherichia coli [TaxId: 562]
Probab=100.00  E-value=0  Score=388.82  Aligned_cols=164  Identities=42%  Similarity=0.734  Sum_probs=155.6

Q ss_pred             CCCCHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEHHHCCCCCEEEEECCCCCCCCCCCEECCCCCC
Q ss_conf             87736457693105212137878889999999999865004764213022014400037731643233482100164420
Q gi|254780297|r    2 VKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKII   81 (170)
Q Consensus         2 ~~~~Iv~~~dp~L~~~~~~v~~~~~~~~~li~dm~~tm~~~~GvGLAA~QIG~~~ri~vv~~~~~~~~~~~~~~iNP~I~   81 (170)
                      ++++|++||||+||++|.||+.+|++++++++||++||++++|+||||||||+++|+||++..+..  +.+.+||||+|+
T Consensus         1 ~v~~I~~~~dp~Lr~~a~~v~~~~~~~~~li~dm~~tm~~~~GvGLAApQIG~~~rifvv~~~~~~--~~~~v~iNP~I~   78 (164)
T d1xeoa1           1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENR--DERLVLINPELL   78 (164)
T ss_dssp             CCCCCCCTTCGGGGCCCBCCSCCCHHHHHHHHHHHHHHHHTTCSEEEGGGGTCCBSEEEECCCTTS--CCCEEEEEEEEE
T ss_pred             CCCCHHCCCCHHHHCCCEECCCCCHHHHHHHHHHHHHHHHCCCCEEEEHHHCCCCCEEEEEEECCC--CCEEEECCCEEE
T ss_conf             955410379869968373589799899999999999764227610130220222045899740256--743884472776


Q ss_pred             CHHHHHHHHHHHCCCCCCCCHHHHHCCHHEEEEECCCCCEEEEEEECCEEEEEEEEHHHHCCEEEEEECCHHHHHHHHHH
Q ss_conf             10000011100000122321012110000024632358557999729764643270013197685364788999999999
Q gi|254780297|r   82 TFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKK  161 (170)
Q Consensus        82 ~~s~e~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~lf~drls~~kr~~~~~k  161 (170)
                      +.|++. .++|||||+||+++.|+||.+|+|+|+|.+|++++.+++||+|||+|||+|||+|+||+||+|+.+|.++.+|
T Consensus        79 ~~~~~~-~~~EgCLS~Pg~~~~V~R~~~I~v~y~d~~G~~~~~~~~g~~Ar~~QHEiDHL~Gilf~Dr~~~~~~~~~~kk  157 (164)
T d1xeoa1          79 EKSGET-GIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQK  157 (164)
T ss_dssp             EEECCB-CCEECCTTSTTCCEECCBCSEEEEEEECTTSCEEEEEECHHHHHHHHHHHHHHTTCCGGGGSCHHHHHHHHHH
T ss_pred             EECCEE-EECCCCCCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEEEEEEHHHHHHHHHCCEEHHHHCCHHHHHHHHHH
T ss_conf             312214-3048864212112445543278999986899899999954002148777898688923663699899999999


Q ss_pred             HHHHHHH
Q ss_conf             9999850
Q gi|254780297|r  162 MSKLVQL  168 (170)
Q Consensus       162 ~~k~~k~  168 (170)
                      ++|+.|.
T Consensus       158 ~~k~~rl  164 (164)
T d1xeoa1         158 VEKLDRL  164 (164)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHCC
T ss_conf             9986459



>d1ix1a_ d.167.1.1 (A:) Peptide deformylase {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1rl4a_ d.167.1.1 (A:) Peptide deformylase {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]} Back     information, alignment and structure
>d1y6ha_ d.167.1.1 (A:) Peptide deformylase {Leptospira interrogans [TaxId: 173]} Back     information, alignment and structure
>d1v3ya_ d.167.1.1 (A:) Peptide deformylase {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1lmea_ d.167.1.1 (A:) Peptide deformylase {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1lqya_ d.167.1.1 (A:) Peptide deformylase {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1lm4a_ d.167.1.1 (A:) Peptide deformylase {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d1lm6a_ d.167.1.1 (A:) Peptide deformylase {Streptococcus pneumoniae [TaxId: 1313]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 170 peptide deformylase [Candidatus Liberibacter asiat
3dld_A_171 (A:) Peptide deformylase; bacterial blight, XOO107 9e-46
1rl4_A_188 (A:) Formylmethionine deformylase; crystal enginee 3e-45
3cpm_A_1-172172 (A:1-172) Peptide deformylase, chloroplast; alpha 5e-45
1y6h_A_177 (A:) Peptide deformylase; open and close conformat 6e-45
1zxz_A_197 (A:) PDF, peptide deformylase, mitochondrial; PDF1 3e-44
1ws0_A_156 (A:) Peptide deformylase 1; alpha + beta topology, 5e-44
1lme_A_176 (A:) PDF, peptide deformylase; thermophIle, metall 1e-43
3g5k_A_183 (A:) Peptide deformylase, mitochondrial; actinonin 7e-43
1n5n_A_1-157157 (A:1-157) Peptide deformylase; metalloenzyme, drug 6e-42
2ew5_A_1-148148 (A:1-148) Peptide deformylase; inhibitor, hydrolas 4e-41
3e3u_A_22-180159 (A:22-180) Peptide deformylase; metallo-enzyme, hy 9e-41
2okl_A_185 (A:) Peptide deformylase 2; hydrolase; HET: BB2 CI 4e-40
2aia_A_203 (A:) Peptide deformylase; hydrolase; HET: SB8; 1.7 6e-40
2w3t_A_1-143143 (A:1-143) Peptide deformylase; protein biosynthesi 1e-39
1xeo_A_1-143143 (A:1-143) Peptide deformylase; cobalt deformylase, 1e-39
1lm4_A_194 (A:) Peptide deformylase PDF1; metalloenzyme, hydr 7e-39
2os0_A_188 (A:) Peptide deformylase; PDF, hydrolase; 1.30A {E 1e-38
1v3y_A_1-156156 (A:1-156) Peptide deformylase; protein synthesis, 8e-36
>3dld_A (A:) Peptide deformylase; bacterial blight, XOO1075, xanthomonas oryzae PV. oryzae KACC10331, hydrolase; 2.60A {Xanthomonas oryzae PV}Length = 171 Back     alignment and structure
 Score =  177 bits (449), Expect = 9e-46
 Identities = 49/170 (28%), Positives = 74/170 (43%), Gaps = 7/170 (4%)

Query: 1   MVKKPLVIFPDPILRRVSRPIEKINSD-IMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLV 59
           M++  ++   D  L RV+  +  + S  +  L+ +M E M +  G+GLAA QI V  +L+
Sbjct: 1   MIR-DIIRMGDKRLLRVAPQVTNLGSAELHALVSDMFETMGAAHGVGLAAPQIAVDLQLM 59

Query: 60  VIDLQD-----HAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRY 114
           V   +       A         N +I   SD+     EGCLSIP  RA + R  +I  R 
Sbjct: 60  VFGFEASERYPEAPAVPLTALANAQIEPLSDEMENGWEGCLSIPGLRAVIPRYRYIRYRG 119

Query: 115 MDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSK 164
              +       A+G  A  +QHE DHL G L+   +           +S 
Sbjct: 120 FAPDGSPIEREAEGFHARVVQHEYDHLVGRLYPSRIENFDTFGFDDVLSY 169


>1rl4_A (A:) Formylmethionine deformylase; crystal engineering, drug design, malaria, PDF, peptide deformylase, hydrolase; HET: BRR BL5; 2.18A {Plasmodium falciparum 3D7}Length = 188 Back     alignment and structure
>3cpm_A (A:1-172) Peptide deformylase, chloroplast; alpha beta, hydrolase, iron, metal-binding, plastid, protein biosynthesis, transit peptide; 2.40A {Arabidopsis thaliana}Length = 172 Back     alignment and structure
>1y6h_A (A:) Peptide deformylase; open and close conformation, PDF, hydrolase; 2.20A {Leptospira interrogans}Length = 177 Back     alignment and structure
>1zxz_A (A:) PDF, peptide deformylase, mitochondrial; PDF1A, eukaryote, higher plant, zinc ION, hydrolase; 2.80A {Arabidopsis thaliana} PDB: 1zy0_A 1zy1_ALength = 197 Back     alignment and structure
>1ws0_A (A:) Peptide deformylase 1; alpha + beta topology, hydrolase; 1.70A {Bacillus cereus} PDB: 1ws1_A*Length = 156 Back     alignment and structure
>1lme_A (A:) PDF, peptide deformylase; thermophIle, metalloenzyme, deformylation, structural genomics, PSI, protein structure initiative; 2.20A {Thermotoga maritima}Length = 176 Back     alignment and structure
>3g5k_A (A:) Peptide deformylase, mitochondrial; actinonin, hydrolase, iron, metal- binding, mitochondrion, protein biosynthesis, transit peptide; HET: BB2; 1.70A {Homo sapiens} PDB: 3g5p_ALength = 183 Back     alignment and structure
>1n5n_A (A:1-157) Peptide deformylase; metalloenzyme, drug design, deformylation, hydrolase; 1.80A {Pseudomonas aeruginosa}Length = 157 Back     alignment and structure
>2ew5_A (A:1-148) Peptide deformylase; inhibitor, hydrolase; HET: Y12; 2.20A {Helicobacter pylori} PDB: 2ew6_A* 2ew7_ALength = 148 Back     alignment and structure
>3e3u_A (A:22-180) Peptide deformylase; metallo-enzyme, hydrolase, iron, metal-binding, protein biosynthesis; HET: NVC; 1.56A {Mycobacterium tuberculosis}Length = 159 Back     alignment and structure
>2okl_A (A:) Peptide deformylase 2; hydrolase; HET: BB2 CIT; 1.70A {Bacillus cereus atcc 14579} PDB: 1lqy_A*Length = 185 Back     alignment and structure
>2aia_A (A:) Peptide deformylase; hydrolase; HET: SB8; 1.70A {Streptococcus pneumoniae} PDB: 2ai7_A* 2aie_P* 1lm6_A 2os3_A*Length = 203 Back     alignment and structure
>2w3t_A (A:1-143) Peptide deformylase; protein biosynthesis, iron, nickel, hydrolase, metal-binding; 1.69A {Escherichia coli} PDB: 2w3u_ALength = 143 Back     alignment and structure
>1xeo_A (A:1-143) Peptide deformylase; cobalt deformylase, formate, hydrolase; 1.30A {Escherichia coli BL21}Length = 143 Back     alignment and structure
>1lm4_A (A:) Peptide deformylase PDF1; metalloenzyme, hydrolase; 1.45A {Staphylococcus aureus}Length = 194 Back     alignment and structure
>2os0_A (A:) Peptide deformylase; PDF, hydrolase; 1.30A {Enterococcus faecalis} PDB: 2os1_A* 3g6n_A 3cmd_ALength = 188 Back     alignment and structure
>1v3y_A (A:1-156) Peptide deformylase; protein synthesis, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.81A {Thermus thermophilus}Length = 156 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target170 peptide deformylase [Candidatus Liberibacter asiaticus
1rl4_A_188 Formylmethionine deformylase; crystal engineering, 100.0
1lme_A_176 PDF, peptide deformylase; thermophIle, metalloenzy 100.0
3cpm_A_1-172172 Peptide deformylase, chloroplast; alpha beta, hydr 100.0
1y6h_A_177 Peptide deformylase; open and close conformation, 100.0
1zxz_A_197 PDF, peptide deformylase, mitochondrial; PDF1A, eu 100.0
1ws0_A_156 Peptide deformylase 1; alpha + beta topology, hydr 100.0
3g5k_A_183 Peptide deformylase, mitochondrial; actinonin, hyd 100.0
3dld_A_171 Peptide deformylase; bacterial blight, XOO1075, xa 100.0
2okl_A_185 Peptide deformylase 2; hydrolase; HET: BB2 CIT; 1. 100.0
2os0_A_188 Peptide deformylase; PDF, hydrolase; 1.30A {Entero 100.0
2aia_A_203 Peptide deformylase; hydrolase; HET: SB8; 1.70A {S 100.0
1lm4_A_194 Peptide deformylase PDF1; metalloenzyme, hydrolase 100.0
1n5n_A_1-157157 Peptide deformylase; metalloenzyme, drug design, d 100.0
2ew5_A_1-148148 Peptide deformylase; inhibitor, hydrolase; HET: Y1 100.0
1xeo_A_1-143143 Peptide deformylase; cobalt deformylase, formate, 100.0
2w3t_A_1-143143 Peptide deformylase; protein biosynthesis, iron, n 100.0
3e3u_A_22-180159 Peptide deformylase; metallo-enzyme, hydrolase, ir 100.0
1v3y_A_1-156156 Peptide deformylase; protein synthesis, riken stru 100.0
>1rl4_A (A:) Formylmethionine deformylase; crystal engineering, drug design, malaria, PDF, peptide deformylase, hydrolase; HET: BRR BL5; 2.18A {Plasmodium falciparum 3D7} Back     alignment and structure
Probab=100.00  E-value=0  Score=386.13  Aligned_cols=169  Identities=31%  Similarity=0.600  Sum_probs=162.2

Q ss_pred             CCCCCHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEHHHCCCCCEEEEECCCCCC-CCCCCEECCCC
Q ss_conf             98773645769310521213787888999999999986500476421302201440003773164323-34821001644
Q gi|254780297|r    1 MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAH-RKNPMVFINPK   79 (170)
Q Consensus         1 M~~~~Iv~~~dp~L~~~~~~v~~~~~~~~~li~dm~~tm~~~~GvGLAA~QIG~~~ri~vv~~~~~~~-~~~~~~~iNP~   79 (170)
                      |++++|++||||+||++|.||+.++++++++++||++||++++|+||||||||+++|+|+|++++... ...+.+||||+
T Consensus         6 m~~~~I~~~~d~~Lr~~a~~V~~~~~~~~~li~dM~~tm~~~~gvGLAApQIG~~~ri~vi~~~~~~~~~~~~~v~INP~   85 (188)
T 1rl4_A            6 KDEIKIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPS   85 (188)
T ss_dssp             ----CCCCTTCGGGGSCCBCCCCCSHHHHHHHHHHHHHHHHTTCSEEEGGGGTCCBSEEEEC-----------CEEEEEE
T ss_pred             CCCCCEEECCCHHHHCCCEECCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCHHHEEECCCCCCCCCCEEEEEECCC
T ss_conf             88862766899799742711898998999999999999855366553234425132203533563322220147862144


Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCHHHHHCCHHEEEEECCCCCEEEEEEECCEEEEEEEEHHHHCCEEEEEECCHHHHHHHH
Q ss_conf             20100000111000001223210121100000246323585579997297646432700131976853647889999999
Q gi|254780297|r   80 IITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMIT  159 (170)
Q Consensus        80 I~~~s~e~~~~~EGCLS~Pg~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~lf~drls~~kr~~~~  159 (170)
                      |++.|+++..+||||||+||+++.|+||.+|+|+|+|++|++++.+++||+|||||||+|||+|+||+||+++.++..+.
T Consensus        86 I~~~s~e~~~~~EgClS~p~~~~~V~R~~~I~v~~~d~~G~~~~~~~~g~~Ar~~QHEiDHL~G~l~~Drl~~~~~~~~~  165 (188)
T 1rl4_A           86 IVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVR  165 (188)
T ss_dssp             EEEECSCEEEEEECCTTSTTCCEEEEEESCEEEEEECTTSCEEEEEECHHHHHHHHHHHHHHTTCCGGGGBCHHHHHHHH
T ss_pred             CCCCCCEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCEEEEEECEEEEEEEHHHHHCCEEEHHHCCHHHHHHHH
T ss_conf             33332057765125455798653322344545555322221122689502224325054876888404517999999999


Q ss_pred             HHHHHHHHHC
Q ss_conf             9999998504
Q gi|254780297|r  160 KKMSKLVQLR  169 (170)
Q Consensus       160 ~k~~k~~k~k  169 (170)
                      ++++++.+.+
T Consensus       166 ~~~~~~~~~~  175 (188)
T 1rl4_A          166 PKLNELIRDY  175 (188)
T ss_dssp             HHHHHHHHC-
T ss_pred             HHHHHHHHHH
T ss_conf             9999999988



>1lme_A (A:) PDF, peptide deformylase; thermophIle, metalloenzyme, deformylation, structural genomics, PSI, protein structure initiative; 2.20A {Thermotoga maritima} Back     alignment and structure
>3cpm_A (A:1-172) Peptide deformylase, chloroplast; alpha beta, hydrolase, iron, metal-binding, plastid, protein biosynthesis, transit peptide; 2.40A {Arabidopsis thaliana} Back     alignment and structure
>1y6h_A (A:) Peptide deformylase; open and close conformation, PDF, hydrolase; 2.20A {Leptospira interrogans} Back     alignment and structure
>1zxz_A (A:) PDF, peptide deformylase, mitochondrial; PDF1A, eukaryote, higher plant, zinc ION, hydrolase; 2.80A {Arabidopsis thaliana} PDB: 1zy0_A 1zy1_A Back     alignment and structure
>1ws0_A (A:) Peptide deformylase 1; alpha + beta topology, hydrolase; 1.70A {Bacillus cereus} PDB: 1ws1_A* Back     alignment and structure
>3g5k_A (A:) Peptide deformylase, mitochondrial; actinonin, hydrolase, iron, metal- binding, mitochondrion, protein biosynthesis, transit peptide; HET: BB2; 1.70A {Homo sapiens} PDB: 3g5p_A Back     alignment and structure
>3dld_A (A:) Peptide deformylase; bacterial blight, XOO1075, xanthomonas oryzae PV. oryzae KACC10331, hydrolase; 2.60A {Xanthomonas oryzae PV} Back     alignment and structure
>2okl_A (A:) Peptide deformylase 2; hydrolase; HET: BB2 CIT; 1.70A {Bacillus cereus atcc 14579} PDB: 1lqy_A* Back     alignment and structure
>2os0_A (A:) Peptide deformylase; PDF, hydrolase; 1.30A {Enterococcus faecalis} PDB: 2os1_A* 3g6n_A 3cmd_A Back     alignment and structure
>2aia_A (A:) Peptide deformylase; hydrolase; HET: SB8; 1.70A {Streptococcus pneumoniae} PDB: 2ai7_A* 2aie_P* 1lm6_A 2os3_A* Back     alignment and structure
>1lm4_A (A:) Peptide deformylase PDF1; metalloenzyme, hydrolase; 1.45A {Staphylococcus aureus} Back     alignment and structure
>1n5n_A (A:1-157) Peptide deformylase; metalloenzyme, drug design, deformylation, hydrolase; 1.80A {Pseudomonas aeruginosa} Back     alignment and structure
>2ew5_A (A:1-148) Peptide deformylase; inhibitor, hydrolase; HET: Y12; 2.20A {Helicobacter pylori} PDB: 2ew6_A* 2ew7_A Back     alignment and structure
>1xeo_A (A:1-143) Peptide deformylase; cobalt deformylase, formate, hydrolase; 1.30A {Escherichia coli BL21} Back     alignment and structure
>2w3t_A (A:1-143) Peptide deformylase; protein biosynthesis, iron, nickel, hydrolase, metal-binding; 1.69A {Escherichia coli} PDB: 2w3u_A Back     alignment and structure
>3e3u_A (A:22-180) Peptide deformylase; metallo-enzyme, hydrolase, iron, metal-binding, protein biosynthesis; HET: NVC; 1.56A {Mycobacterium tuberculosis} Back     alignment and structure
>1v3y_A (A:1-156) Peptide deformylase; protein synthesis, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.81A {Thermus thermophilus} Back     alignment and structure