BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy14392
(164 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3G5K|A Chain A, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
pdb|3G5K|B Chain B, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
pdb|3G5K|C Chain C, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
pdb|3G5K|D Chain D, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
pdb|3G5P|A Chain A, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
pdb|3G5P|B Chain B, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
pdb|3G5P|C Chain C, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
pdb|3G5P|D Chain D, Structure And Activity Of Human Mitochondrial Peptide
Deformylase, A Novel Cancer Target
Length = 183
Score = 118 bits (296), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 63/148 (42%), Positives = 90/148 (60%), Gaps = 6/148 (4%)
Query: 7 QMKNVMKRFDLFGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKF---EMQAFPHMVWIN 63
++ VM+R GLSAPQ+G+P + ++A PE E ++ +M+ FP V++N
Sbjct: 38 RLVQVMRRRRCVGLSAPQLGVPRQ--VLALELPEALCRECPPRQRALRQMEPFPLRVFVN 95
Query: 64 PEMKILDYKDKVTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQH 123
P +++LD + VT EGC S+ A VPR++ VQ++GLD G+ W A GWAARIIQH
Sbjct: 96 PSLRVLDSR-LVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQH 154
Query: 124 EMDHLDGLLFTDSMLPKSLECVCWQDIN 151
EMDHL G LF D M ++ V W +N
Sbjct: 155 EMDHLQGCLFIDKMDSRTFTNVYWMKVN 182
>pdb|1ZXZ|A Chain A, X-Ray Structure Of Peptide Deformylase From Arabidopsis
Thaliana (Atpdf1a); Crystals Grown In Peg-5000 Mme As
Precipitant
pdb|1ZXZ|B Chain B, X-Ray Structure Of Peptide Deformylase From Arabidopsis
Thaliana (Atpdf1a); Crystals Grown In Peg-5000 Mme As
Precipitant
pdb|1ZY0|A Chain A, X-Ray Structure Of Peptide Deformylase From Arabidopsis
Thaliana (Atpdf1a); Crystals Grown In Peg-6000
pdb|1ZY0|B Chain B, X-Ray Structure Of Peptide Deformylase From Arabidopsis
Thaliana (Atpdf1a); Crystals Grown In Peg-6000
pdb|1ZY1|A Chain A, X-Ray Structure Of Peptide Deformylase From Arabidopsis
Thaliana (Atpdf1a) In Complex With Met-Ala-Ser
pdb|1ZY1|B Chain B, X-Ray Structure Of Peptide Deformylase From Arabidopsis
Thaliana (Atpdf1a) In Complex With Met-Ala-Ser
Length = 197
Score = 104 bits (259), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 65/159 (40%), Positives = 87/159 (54%), Gaps = 6/159 (3%)
Query: 4 IILQMKNVMKRFDLFGLSAPQVGLPLRLFIVAFPDPEESFS---EGDIKKFEMQAFPHMV 60
II M VM+ GL+APQ+G+PLR I+ D +E S + +I E + F MV
Sbjct: 34 IIDDMIKVMRLAPGVGLAAPQIGVPLR--IIVLEDTKEYISYAPKEEILAQERRHFDLMV 91
Query: 61 WINPEMKILDYKDKVTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARI 120
+NP +K K K EGC S+ +A V RY +V +TG D GK A GW ARI
Sbjct: 92 MVNPVLKERSNK-KALFFEGCLSVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARI 150
Query: 121 IQHEMDHLDGLLFTDSMLPKSLECVCWQDINLQNGLLEL 159
+QHE DHLDG L+ D M+P++ V D+ L G +L
Sbjct: 151 LQHECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKL 189
>pdb|3M6R|A Chain A, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) G41m Mutant In Complex With
Actinonin
pdb|3M6R|B Chain B, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) G41m Mutant In Complex With
Actinonin
pdb|3M6R|C Chain C, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) G41m Mutant In Complex With
Actinonin
pdb|3M6R|D Chain D, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) G41m Mutant In Complex With
Actinonin
pdb|3PN6|A Chain A, Crystal Structure Of Arabidopsis Thaliana Petide
Deformylase 1b (Atpdf1b) G41m Mutant
pdb|3PN6|B Chain B, Crystal Structure Of Arabidopsis Thaliana Petide
Deformylase 1b (Atpdf1b) G41m Mutant
Length = 193
Score = 79.7 bits (195), Expect = 7e-16, Method: Compositional matrix adjust.
Identities = 53/146 (36%), Positives = 78/146 (53%), Gaps = 16/146 (10%)
Query: 1 MKIIILQMKNVMKRFDLFGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMV 60
+K ++ M +VM + D+ GLSAPQVGL ++L + +P EG +V
Sbjct: 25 LKNLVDAMFDVMYKTDMIGLSAPQVGLNVQLMVF---NPAGEPGEGK----------EIV 71
Query: 61 WINPEMKILDYKDKVTAL-EGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAAR 119
+NP KI Y DK+ EGC S + A+V R + V++ D TG+ S + AR
Sbjct: 72 LVNP--KIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPAR 129
Query: 120 IIQHEMDHLDGLLFTDSMLPKSLECV 145
I QHE DHL+G+LF D M + L+ +
Sbjct: 130 IFQHEYDHLEGVLFFDRMTDQVLDSI 155
>pdb|4DR9|A Chain A, Crystal Structure Of A Peptide Deformylase From
Synechococcus Elongatus In Complex With Actinonin
pdb|4DR9|B Chain B, Crystal Structure Of A Peptide Deformylase From
Synechococcus Elongatus In Complex With Actinonin
pdb|4DR9|C Chain C, Crystal Structure Of A Peptide Deformylase From
Synechococcus Elongatus In Complex With Actinonin
pdb|4DR9|D Chain D, Crystal Structure Of A Peptide Deformylase From
Synechococcus Elongatus In Complex With Actinonin
Length = 192
Score = 78.6 bits (192), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 47/137 (34%), Positives = 70/137 (51%), Gaps = 14/137 (10%)
Query: 1 MKIIILQMKNVMKRFDLFGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMV 60
++ I QM M D GL+APQVG+ +L ++ + E + P +V
Sbjct: 43 LRQTIRQMLQTMYSADGIGLAAPQVGINKQLIVIDL-------------ELEDEQAPPLV 89
Query: 61 WINPEMKILDYKDKVTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARI 120
INP+++ D EGC S+ + V R V+++ DE G+P A+G AR
Sbjct: 90 LINPKIE-RTAGDLEQCQEGCLSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARC 148
Query: 121 IQHEMDHLDGLLFTDSM 137
IQHEMDHL+G+LF D +
Sbjct: 149 IQHEMDHLNGVLFVDRV 165
>pdb|3M6Q|A Chain A, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) G41q Mutant In Complex With
Actinonin
pdb|3PN5|A Chain A, Crystal Structure Of Arabidopsis Thaliana Petide
Deformylase 1b (Atpdf1b) G41q Mutant
Length = 193
Score = 77.8 bits (190), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 53/146 (36%), Positives = 77/146 (52%), Gaps = 16/146 (10%)
Query: 1 MKIIILQMKNVMKRFDLFGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMV 60
+K ++ M +VM + D GLSAPQVGL ++L + +P EG +V
Sbjct: 25 LKNLVDAMFDVMYKTDQIGLSAPQVGLNVQLMVF---NPAGEPGEGK----------EIV 71
Query: 61 WINPEMKILDYKDKVTAL-EGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAAR 119
+NP KI Y DK+ EGC S + A+V R + V++ D TG+ S + AR
Sbjct: 72 LVNP--KIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPAR 129
Query: 120 IIQHEMDHLDGLLFTDSMLPKSLECV 145
I QHE DHL+G+LF D M + L+ +
Sbjct: 130 IFQHEYDHLEGVLFFDRMTDQVLDSI 155
>pdb|3M6O|A Chain A, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b)
pdb|3M6O|B Chain B, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b)
pdb|3M6P|A Chain A, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) In Complex With Actinonin
pdb|3M6P|B Chain B, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) In Complex With Actinonin
pdb|3O3J|A Chain A, Crystal Structure Of Arabidopsis Thaliana Peptide
Deformylase 1b (Atpdf1b) In Complex With Inhibitor 6b
pdb|3PN2|A Chain A, Crystal Structure Of Arabidopsis Thaliana Petide
Deformylase 1b (Atpdf1b) (Crystallized In Peg-550-Mme)
pdb|3PN3|A Chain A, Crystal Structure Of Arabidopsis Thaliana Petide
Deformylase 1b (Atpdf1b) In Complex With Inhibitor 21
pdb|3PN3|B Chain B, Crystal Structure Of Arabidopsis Thaliana Petide
Deformylase 1b (Atpdf1b) In Complex With Inhibitor 21
pdb|3PN4|A Chain A, Crystal Structure Of Arabidopsis Thaliana Petide
Deformylase 1b (Atpdf1b) In Complex With Actinonin
(Crystallized In Peg-550-Mme)
Length = 193
Score = 77.4 bits (189), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 53/146 (36%), Positives = 77/146 (52%), Gaps = 16/146 (10%)
Query: 1 MKIIILQMKNVMKRFDLFGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMV 60
+K ++ M +VM + D GLSAPQVGL ++L + +P EG +V
Sbjct: 25 LKNLVDAMFDVMYKTDGIGLSAPQVGLNVQLMVF---NPAGEPGEGK----------EIV 71
Query: 61 WINPEMKILDYKDKVTAL-EGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAAR 119
+NP KI Y DK+ EGC S + A+V R + V++ D TG+ S + AR
Sbjct: 72 LVNP--KIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPAR 129
Query: 120 IIQHEMDHLDGLLFTDSMLPKSLECV 145
I QHE DHL+G+LF D M + L+ +
Sbjct: 130 IFQHEYDHLEGVLFFDRMTDQVLDSI 155
>pdb|3CPM|A Chain A, Plant Peptide Deformylase Pdf1b Crystal Structure
Length = 193
Score = 77.4 bits (189), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 53/146 (36%), Positives = 77/146 (52%), Gaps = 16/146 (10%)
Query: 1 MKIIILQMKNVMKRFDLFGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMV 60
+K ++ M +VM + D GLSAPQVGL ++L + +P EG +V
Sbjct: 41 LKNLVDAMFDVMYKTDGIGLSAPQVGLNVQLMVF---NPAGEPGEGK----------EIV 87
Query: 61 WINPEMKILDYKDKVTAL-EGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAAR 119
+NP KI Y DK+ EGC S + A+V R + V++ D TG+ S + AR
Sbjct: 88 LVNP--KIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPAR 145
Query: 120 IIQHEMDHLDGLLFTDSMLPKSLECV 145
I QHE DHL+G+LF D M + L+ +
Sbjct: 146 IFQHEYDHLEGVLFFDRMTDQVLDSI 171
>pdb|1V3Y|A Chain A, The Crystal Structure Of Peptide Deformylase From Thermus
Thermophilus Hb8
pdb|1V3Y|B Chain B, The Crystal Structure Of Peptide Deformylase From Thermus
Thermophilus Hb8
Length = 192
Score = 73.9 bits (180), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 47/125 (37%), Positives = 72/125 (57%), Gaps = 10/125 (8%)
Query: 19 GLSAPQVGLPLRLFI-VAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDK-VT 76
GL+APQ+GL RLF+ V + D E E +++ + + V NP ++ Y++ V
Sbjct: 44 GLAAPQIGLSQRLFVAVEYADEPEGEEERPLRELVRRVY---VVANP---VITYREGLVE 97
Query: 77 ALEGCASLKSLQAK-VPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EG SL L ++ VPR ++++ DE G+ EG+ AR+ QHE+DHLDG+LF +
Sbjct: 98 GTEGXLSLPGLYSEEVPRAERIRVEYQDEEGRGRVLELEGYMARVFQHEIDHLDGILFFE 157
Query: 136 SMLPK 140
LPK
Sbjct: 158 R-LPK 161
>pdb|3UWA|A Chain A, Crystal Structure Of A Probable Peptide Deformylase From
Synechococcus Phage S-Ssm7
pdb|3UWB|A Chain A, Crystal Structure Of A Probable Peptide Deformylase From
Strucynechococcus Phage S-Ssm7 In Complex With Actinonin
Length = 154
Score = 72.8 bits (177), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 40/120 (33%), Positives = 64/120 (53%), Gaps = 14/120 (11%)
Query: 16 DLFGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKV 75
D GL+APQVG+ R+ +V + +E K + P + W + E + D
Sbjct: 42 DGIGLAAPQVGINKRVIVV------DETTEEHGKYAHLXVNPKITWKSEEKVLFD----- 90
Query: 76 TALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EGC S+ +V R + +++T ++ GK W +G AAR++QHE+DHL+G+LF D
Sbjct: 91 ---EGCLSVPDQNGEVLRPKSIKVTFQNKDGKYKKWKLDGLAARVVQHEIDHLEGILFVD 147
>pdb|4AZ4|A Chain A, E.Coli Deformylase With Co(Ii) And Hydrosulfide
Length = 186
Score = 72.0 bits (175), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 46/122 (37%), Positives = 62/122 (50%), Gaps = 17/122 (13%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+A QV + R+ ++ D E+ E +V INPE+ L+ +
Sbjct: 44 IGLAATQVDIHQRIIVI---DVSENRDE------------RLVLINPEL--LEKSGETGI 86
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTDSM 137
EGC S+ +A VPR KV++ LD GKP A+G A IQHEMDHL G LF D +
Sbjct: 87 EEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAIXIQHEMDHLVGKLFMDYL 146
Query: 138 LP 139
P
Sbjct: 147 SP 148
>pdb|3K6L|A Chain A, The Structure Of E.Coli Peptide Deformylase (Pdf) In
Complex With Peptidomimetic Ligand Bb2827
pdb|3K6L|B Chain B, The Structure Of E.Coli Peptide Deformylase (Pdf) In
Complex With Peptidomimetic Ligand Bb2827
pdb|3K6L|C Chain C, The Structure Of E.Coli Peptide Deformylase (Pdf) In
Complex With Peptidomimetic Ligand Bb2827
Length = 169
Score = 71.6 bits (174), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 46/122 (37%), Positives = 62/122 (50%), Gaps = 17/122 (13%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+A QV + R+ ++ D E+ E +V INPE+ L+ +
Sbjct: 45 IGLAATQVDIHQRIIVI---DVSENRDE------------RLVLINPEL--LEKSGETGI 87
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTDSM 137
EGC S+ +A VPR KV++ LD GKP A+G A IQHEMDHL G LF D +
Sbjct: 88 EEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYL 147
Query: 138 LP 139
P
Sbjct: 148 SP 149
>pdb|1DFF|A Chain A, Peptide Deformylase
Length = 164
Score = 71.6 bits (174), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 46/122 (37%), Positives = 62/122 (50%), Gaps = 17/122 (13%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+A QV + R+ ++ D E+ E +V INPE+ L+ +
Sbjct: 44 IGLAATQVDIHQRIIVI---DVSENRDE------------RLVLINPEL--LEKSGETGI 86
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTDSM 137
EGC S+ +A VPR KV++ LD GKP A+G A IQHEMDHL G LF D +
Sbjct: 87 EEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYL 146
Query: 138 LP 139
P
Sbjct: 147 SP 148
>pdb|1ICJ|A Chain A, Pdf Protein Is Crystallized As Ni2+ Containing Form,
Cocrystallized With Inhibitor Polyethylene Glycol (Peg)
pdb|1ICJ|B Chain B, Pdf Protein Is Crystallized As Ni2+ Containing Form,
Cocrystallized With Inhibitor Polyethylene Glycol (Peg)
pdb|1ICJ|C Chain C, Pdf Protein Is Crystallized As Ni2+ Containing Form,
Cocrystallized With Inhibitor Polyethylene Glycol (Peg)
pdb|1BS4|A Chain A, Peptide Deformylase As Zn2+ Containing Form (Native) In
Complex With Inhibitor Polyethylene Glycol
pdb|1BS4|B Chain B, Peptide Deformylase As Zn2+ Containing Form (Native) In
Complex With Inhibitor Polyethylene Glycol
pdb|1BS4|C Chain C, Peptide Deformylase As Zn2+ Containing Form (Native) In
Complex With Inhibitor Polyethylene Glycol
pdb|1BS5|A Chain A, Peptide Deformylase As Zn2+ Containing Form
pdb|1BS5|B Chain B, Peptide Deformylase As Zn2+ Containing Form
pdb|1BS5|C Chain C, Peptide Deformylase As Zn2+ Containing Form
pdb|1BS6|A Chain A, Peptide Deformylase As Ni2+ Containing Form In Complex
With Tripeptide Met-Ala-Ser
pdb|1BS6|B Chain B, Peptide Deformylase As Ni2+ Containing Form In Complex
With Tripeptide Met-Ala-Ser
pdb|1BS6|C Chain C, Peptide Deformylase As Ni2+ Containing Form In Complex
With Tripeptide Met-Ala-Ser
pdb|1BS7|A Chain A, Peptide Deformylase As Ni2+ Containing Form
pdb|1BS7|B Chain B, Peptide Deformylase As Ni2+ Containing Form
pdb|1BS7|C Chain C, Peptide Deformylase As Ni2+ Containing Form
pdb|1BS8|A Chain A, Peptide Deformylase As Zn2+ Containing Form In Complex
With Tripeptide Met-Ala-Ser
pdb|1BS8|B Chain B, Peptide Deformylase As Zn2+ Containing Form In Complex
With Tripeptide Met-Ala-Ser
pdb|1BS8|C Chain C, Peptide Deformylase As Zn2+ Containing Form In Complex
With Tripeptide Met-Ala-Ser
pdb|1BSZ|A Chain A, Peptide Deformylase As Fe2+ Containing Form (Native) In
Complex With Inhibitor Polyethylene Glycol
pdb|1BSZ|B Chain B, Peptide Deformylase As Fe2+ Containing Form (Native) In
Complex With Inhibitor Polyethylene Glycol
pdb|1BSZ|C Chain C, Peptide Deformylase As Fe2+ Containing Form (Native) In
Complex With Inhibitor Polyethylene Glycol
pdb|1BSJ|A Chain A, Cobalt Deformylase Inhibitor Complex From E.Coli
pdb|1BSK|A Chain A, Zinc Deformylase Inhibitor Complex From E.Coli
pdb|1G27|A Chain A, Crystal Structure Of E.Coli Polypeptide Deformylase
Complexed With The Inhibitor Bb-3497
pdb|1G27|B Chain B, Crystal Structure Of E.Coli Polypeptide Deformylase
Complexed With The Inhibitor Bb-3497
pdb|1G27|C Chain C, Crystal Structure Of E.Coli Polypeptide Deformylase
Complexed With The Inhibitor Bb-3497
pdb|1G2A|A Chain A, The Crystal Structure Of E.Coli Peptide Deformylase
Complexed With Actinonin
pdb|1G2A|B Chain B, The Crystal Structure Of E.Coli Peptide Deformylase
Complexed With Actinonin
pdb|1G2A|C Chain C, The Crystal Structure Of E.Coli Peptide Deformylase
Complexed With Actinonin
pdb|1LRU|A Chain A, Crystal Structure Of E.Coli Peptide Deformylase Complexed
With Antibiotic Actinonin
pdb|1LRU|B Chain B, Crystal Structure Of E.Coli Peptide Deformylase Complexed
With Antibiotic Actinonin
pdb|1LRU|C Chain C, Crystal Structure Of E.Coli Peptide Deformylase Complexed
With Antibiotic Actinonin
pdb|1XEM|A Chain A, High Resolution Crystal Structure Of Escherichia Coli
Zinc- Peptide Deformylase Bound To Formate
pdb|1XEN|A Chain A, High Resolution Crystal Structure Of Escherichia Coli
Iron- Peptide Deformylase Bound To Formate
pdb|1XEO|A Chain A, High Resolution Crystals Structure Of Cobalt- Peptide
Deformylase Bound To Formate
pdb|2AI8|A Chain A, E.Coli Polypeptide Deformylase Complexed With Sb-485343
pdb|2AI8|B Chain B, E.Coli Polypeptide Deformylase Complexed With Sb-485343
pdb|2AI8|C Chain C, E.Coli Polypeptide Deformylase Complexed With Sb-485343
Length = 168
Score = 71.6 bits (174), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 46/122 (37%), Positives = 62/122 (50%), Gaps = 17/122 (13%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+A QV + R+ ++ D E+ E +V INPE+ L+ +
Sbjct: 44 IGLAATQVDIHQRIIVI---DVSENRDE------------RLVLINPEL--LEKSGETGI 86
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTDSM 137
EGC S+ +A VPR KV++ LD GKP A+G A IQHEMDHL G LF D +
Sbjct: 87 EEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYL 146
Query: 138 LP 139
P
Sbjct: 147 SP 148
>pdb|4AL2|A Chain A, Peptide Deformylase (Ni-Form) With Hydrosulfide
pdb|4AL2|B Chain B, Peptide Deformylase (Ni-Form) With Hydrosulfide
pdb|4AL2|C Chain C, Peptide Deformylase (Ni-Form) With Hydrosulfide
Length = 186
Score = 71.6 bits (174), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 46/122 (37%), Positives = 62/122 (50%), Gaps = 17/122 (13%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+A QV + R+ ++ D E+ E +V INPE+ L+ +
Sbjct: 44 IGLAATQVDIHQRIIVI---DVSENRDE------------RLVLINPEL--LEKSGETGI 86
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTDSM 137
EGC S+ +A VPR KV++ LD GKP A+G A IQHEMDHL G LF D +
Sbjct: 87 EEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYL 146
Query: 138 LP 139
P
Sbjct: 147 SP 148
>pdb|3DLD|A Chain A, Crystal Structure Of Peptide Deformylase, Xoo1075, From
Xanthomonas Oryzae Pv. Oryzae Kacc10331
Length = 171
Score = 71.6 bits (174), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 42/133 (31%), Positives = 64/133 (48%), Gaps = 9/133 (6%)
Query: 1 MKIIILQMKNVMKRFDLFGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMV 60
+ ++ M M GL+APQ+ + L+L + F E + E A P
Sbjct: 28 LHALVSDMFETMGAAHGVGLAAPQIAVDLQLMVFGF--------EASERYPEAPAVPLTA 79
Query: 61 WINPEMKILDYKDKVTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARI 120
N +++ L + EGC S+ L+A +PRYR ++ G G P AEG+ AR+
Sbjct: 80 LANAQIEPLS-DEMENGWEGCLSIPGLRAVIPRYRYIRYRGFAPDGSPIEREAEGFHARV 138
Query: 121 IQHEMDHLDGLLF 133
+QHE DHL G L+
Sbjct: 139 VQHEYDHLVGRLY 151
>pdb|2W3T|A Chain A, Chloro Complex Of The Ni-Form Of E.Coli Deformylase
pdb|2W3U|A Chain A, Formate Complex Of The Ni-Form Of E.Coli Deformylase
Length = 188
Score = 71.6 bits (174), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 46/122 (37%), Positives = 62/122 (50%), Gaps = 17/122 (13%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+A QV + R+ ++ D E+ E +V INPE+ L+ +
Sbjct: 44 IGLAATQVDIHQRIIVI---DVSENRDE------------RLVLINPEL--LEKSGETGI 86
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTDSM 137
EGC S+ +A VPR KV++ LD GKP A+G A IQHEMDHL G LF D +
Sbjct: 87 EEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYL 146
Query: 138 LP 139
P
Sbjct: 147 SP 148
>pdb|1DEF|A Chain A, Peptide Deformylase Catalytic Core (Residues 1-147), Nmr,
9 Structures
pdb|2KMN|A Chain A, Solution Structure Of Peptide Deformylase Complexed With
Actinonin
Length = 147
Score = 69.7 bits (169), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 45/118 (38%), Positives = 60/118 (50%), Gaps = 17/118 (14%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+A QV + R+ ++ D E+ E +V INPE+ L+ +
Sbjct: 44 IGLAATQVDIHQRIIVI---DVSENRDE------------RLVLINPEL--LEKSGETGI 86
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EGC S+ +A VPR KV++ LD GKP A+G A IQHEMDHL G LF D
Sbjct: 87 EEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMD 144
>pdb|2DEF|A Chain A, Peptide Deformylase Catalytic Core (Residues 1-147), Nmr,
20 Structures
Length = 147
Score = 69.7 bits (169), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 45/118 (38%), Positives = 60/118 (50%), Gaps = 17/118 (14%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+A QV + R+ ++ D E+ E +V INPE+ L+ +
Sbjct: 44 IGLAATQVDIHQRIIVI---DVSENRDE------------RLVLINPEL--LEKSGETGI 86
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EGC S+ +A VPR KV++ LD GKP A+G A IQHEMDHL G LF D
Sbjct: 87 EEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMD 144
>pdb|1Y6H|A Chain A, Crystal Structure Of Lipdf
pdb|1Y6H|B Chain B, Crystal Structure Of Lipdf
pdb|1SV2|A Chain A, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans (lipdf) At Ph7.5
pdb|1SV2|B Chain B, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans (lipdf) At Ph7.5
pdb|1VEV|A Chain A, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans (Lipdf) At Ph6.5
pdb|1VEV|B Chain B, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans (Lipdf) At Ph6.5
pdb|1VEY|A Chain A, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans (Lipdf) At Ph7.0
pdb|1VEY|B Chain B, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans (Lipdf) At Ph7.0
pdb|1VEZ|A Chain A, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans(lipdf) At Ph8.0
pdb|1VEZ|B Chain B, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans(lipdf) At Ph8.0
Length = 177
Score = 68.6 bits (166), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 41/136 (30%), Positives = 69/136 (50%), Gaps = 9/136 (6%)
Query: 2 KIIILQMKNVMKRFDLFGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVW 61
K +I M + M+ + GL+APQ+G+ ++ +V D E D+ P +
Sbjct: 31 KKLIRDMFDTMRHAEGVGLAAPQIGILKQIVVVGSEDNERYPGTPDV--------PERII 82
Query: 62 INPEMKILDYKDKVTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARII 121
+NP + L KD EGC S+ ++ V R ++++ +DE G T +G+ A +
Sbjct: 83 LNPVITPL-TKDTSGFWEGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDETIDGYKAIVY 141
Query: 122 QHEMDHLDGLLFTDSM 137
QHE DHL G+L+ D +
Sbjct: 142 QHECDHLQGILYVDRL 157
>pdb|1SZZ|A Chain A, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
pdb|1SZZ|B Chain B, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
pdb|1SZZ|C Chain C, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
pdb|1SZZ|D Chain D, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
pdb|1SZZ|E Chain E, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
pdb|1SZZ|F Chain F, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
pdb|1SZZ|G Chain G, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
pdb|1SZZ|H Chain H, Crystal Structure Of Peptide Deformylase From Leptospira
Interrogans Complexed With Inhibitor Actinonin
Length = 177
Score = 67.8 bits (164), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 41/136 (30%), Positives = 68/136 (50%), Gaps = 9/136 (6%)
Query: 2 KIIILQMKNVMKRFDLFGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVW 61
K +I M M+ + GL+APQ+G+ ++ +V D E D+ P +
Sbjct: 31 KKLIRDMFTTMRHAEGVGLAAPQIGILKQIVVVGSEDNERYPGTPDV--------PERII 82
Query: 62 INPEMKILDYKDKVTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARII 121
+NP + L KD EGC S+ ++ V R ++++ +DE G T +G+ A +
Sbjct: 83 LNPVITPL-TKDTSGFWEGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDETIDGYKAIVY 141
Query: 122 QHEMDHLDGLLFTDSM 137
QHE DHL G+L+ D +
Sbjct: 142 QHECDHLQGILYVDRL 157
>pdb|3U04|A Chain A, Crystal Structure Of Peptide Deformylase From Ehrlichia
Chaffeensis In Complex With Actinonin
Length = 190
Score = 67.4 bits (163), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 42/122 (34%), Positives = 67/122 (54%), Gaps = 9/122 (7%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFS-----EGDIKKFEMQAFPHMVWINPEMKILDY- 71
GL+A QVG+ R+ ++ P+ E E I+ +E+ P+ + INP KI+D
Sbjct: 47 LGLAAVQVGVHKRILVMNVPEEFEDSEDIENVEDKIEGYELYGGPYCI-INP--KIVDIS 103
Query: 72 KDKVTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGL 131
++KV EGC S+ + R +++ + LD G A+GW AR +QHE+DHL+G
Sbjct: 104 QEKVKLKEGCLSVPGYFDYIVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHEIDHLNGT 163
Query: 132 LF 133
+F
Sbjct: 164 VF 165
>pdb|3OCA|A Chain A, Crystal Structure Of Peptide Deformylase From Ehrlichia
Chaffeensis
pdb|3OCA|B Chain B, Crystal Structure Of Peptide Deformylase From Ehrlichia
Chaffeensis
Length = 209
Score = 67.4 bits (163), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 42/122 (34%), Positives = 67/122 (54%), Gaps = 9/122 (7%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFS-----EGDIKKFEMQAFPHMVWINPEMKILDY- 71
GL+A QVG+ R+ ++ P+ E E I+ +E+ P+ + INP KI+D
Sbjct: 66 LGLAAVQVGVHKRILVMNVPEEFEDSEDIENVEDKIEGYELYGGPYCI-INP--KIVDIS 122
Query: 72 KDKVTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGL 131
++KV EGC S+ + R +++ + LD G A+GW AR +QHE+DHL+G
Sbjct: 123 QEKVKLKEGCLSVPGYFDYIVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHEIDHLNGT 182
Query: 132 LF 133
+F
Sbjct: 183 VF 184
>pdb|4AL3|A Chain A, Peptide Deformylase (Co-Form) With Mercaptoethanol
Length = 186
Score = 67.4 bits (163), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 45/122 (36%), Positives = 61/122 (50%), Gaps = 17/122 (13%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+A QV + R+ ++ D E+ E +V INPE+ L+ +
Sbjct: 44 IGLAATQVDIHQRIIVI---DVSENRDE------------RLVLINPEL--LEKSGETGI 86
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTDSM 137
EG S+ +A VPR KV++ LD GKP A+G A IQHEMDHL G LF D +
Sbjct: 87 EEGXLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYL 146
Query: 138 LP 139
P
Sbjct: 147 SP 148
>pdb|1LME|A Chain A, Crystal Structure Of Peptide Deformylase From Thermotoga
Maritima
pdb|1LME|B Chain B, Crystal Structure Of Peptide Deformylase From Thermotoga
Maritima
Length = 176
Score = 65.5 bits (158), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 42/139 (30%), Positives = 69/139 (49%), Gaps = 19/139 (13%)
Query: 1 MKIIILQMKNVMKRFDLFGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMV 60
+K I +M M +D GL+APQVG+ R F++ G +
Sbjct: 38 LKKTIERMIETMYHYDGVGLAAPQVGISQRFFVM-------DVGNGPV-----------A 79
Query: 61 WINPEMKILDYKDKVTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARI 120
INPE+ +D + +V A EG S + ++ R +++++ + G+ EG+AAR+
Sbjct: 80 VINPEILEIDPETEV-AEEGXLSFPEIFVEIERSKRIKVKYQNTRGEYVEEELEGYAARV 138
Query: 121 IQHEMDHLDGLLFTDSMLP 139
QHE DHL+G+L D + P
Sbjct: 139 FQHEFDHLNGVLIIDRISP 157
>pdb|3QU1|A Chain A, Peptide Deformylase From Vibrio Cholerae
pdb|3QU1|B Chain B, Peptide Deformylase From Vibrio Cholerae
Length = 171
Score = 64.7 bits (156), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 40/122 (32%), Positives = 56/122 (45%), Gaps = 17/122 (13%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+APQVG + ++ D + +V INP K++ +K
Sbjct: 48 IGLAAPQVGREEAIVVIDLSDNRDQ---------------PLVLINP--KVVSGSNKEMG 90
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTDSM 137
EGC S+ A V RY V + LD GKP + A ++QHE+DHL G LF D +
Sbjct: 91 QEGCLSVPDYYADVERYTSVVVEALDREGKPLRIETSDFLAIVMQHEIDHLSGNLFIDYL 150
Query: 138 LP 139
P
Sbjct: 151 SP 152
>pdb|3E3U|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Peptide
Deformylase In Complex With Inhibitor
Length = 197
Score = 63.2 bits (152), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 44/141 (31%), Positives = 63/141 (44%), Gaps = 15/141 (10%)
Query: 4 IILQMKNVMKRFDLFGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWIN 63
+I M + M + GL+A Q+G LRLF+ M A V IN
Sbjct: 36 LIATMYDTMDAANGVGLAANQIGCSLRLFVYDC-----------AADRAMTARRRGVVIN 84
Query: 64 PEMKILDYK----DKVTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAAR 119
P ++ + D T EGC S+ R + ++TGLD G P S G AR
Sbjct: 85 PVLETSEIPETMPDPDTDDEGCLSVPGESFPTGRAKWARVTGLDADGSPVSIEGTGLFAR 144
Query: 120 IIQHEMDHLDGLLFTDSMLPK 140
++QHE HLDG L+ D ++ +
Sbjct: 145 MLQHETGHLDGFLYLDRLIGR 165
>pdb|1IX1|A Chain A, Crystal Structure Of P.Aeruginosa Peptide Deformylase
Complexed With Antibiotic Actinonin
pdb|1IX1|B Chain B, Crystal Structure Of P.Aeruginosa Peptide Deformylase
Complexed With Antibiotic Actinonin
Length = 171
Score = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 44/120 (36%), Positives = 58/120 (48%), Gaps = 16/120 (13%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+A QV + R+ ++ D E SE V+INPE + L +D
Sbjct: 45 IGLAATQVNVHKRIVVM---DLSEDKSEP------------RVFINPEFEPL-TEDMDQY 88
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTDSM 137
EGC S+ V R +KV++ LD G P AEG A IQHE DHL+G LF D +
Sbjct: 89 QEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYL 148
>pdb|1LRY|A Chain A, Crystal Structure Of P. Aeruginosa Peptide Deformylase
Complexed With Antibiotic Actinonin
Length = 167
Score = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 44/120 (36%), Positives = 58/120 (48%), Gaps = 16/120 (13%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+A QV + R+ ++ D E SE V+INPE + L +D
Sbjct: 44 IGLAATQVNVHKRIVVM---DLSEDKSEP------------RVFINPEFEPL-TEDMDQY 87
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTDSM 137
EGC S+ V R +KV++ LD G P AEG A IQHE DHL+G LF D +
Sbjct: 88 QEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYL 147
>pdb|2EW5|A Chain A, Structure Of Helicobacter Pylori Peptide Deformylase In
Complex With Inhibitor
pdb|2EW6|A Chain A, Structure Of Helicobacter Pylori Peptide Deformylase In
Complex With Inhibitor
pdb|2EW7|A Chain A, Crystal Structure Of Helicobacter Pylori Peptide
Deformylase
Length = 181
Score = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 38/120 (31%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+A QVGLPLR+ I+ P + + D + INP K ++ +
Sbjct: 44 IGLAAIQVGLPLRMLIINLPQEDGVQHKEDC----------LEIINP--KFIETGGSMMY 91
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTDSM 137
EGC S+ +V R+ KV++ + + A A IQHE+DHL+G+LF D +
Sbjct: 92 KEGCLSVPGFYEEVERFEKVKIEYQNRFAEVKVLEASELLAVAIQHEIDHLNGVLFVDKL 151
>pdb|1N5N|A Chain A, Crystal Structure Of Peptide Deformylase From Pseudomonas
Aeruginosa
pdb|1N5N|B Chain B, Crystal Structure Of Peptide Deformylase From Pseudomonas
Aeruginosa
pdb|1S17|A Chain A, Identification Of Novel Potent Bicyclic Peptide
Deformylase Inhibitors
pdb|1S17|B Chain B, Identification Of Novel Potent Bicyclic Peptide
Deformylase Inhibitors
Length = 180
Score = 60.5 bits (145), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 43/120 (35%), Positives = 58/120 (48%), Gaps = 16/120 (13%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+A QV + R+ ++ D E SE V+INPE + L ++
Sbjct: 57 IGLAATQVNVHKRIVVM---DLSEDKSEP------------RVFINPEFEPL-TEEMDQY 100
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTDSM 137
EGC S+ V R +KV++ LD G P AEG A IQHE DHL+G LF D +
Sbjct: 101 QEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYL 160
>pdb|1WS0|A Chain A, Structure Analysis Of Peptide Deformylase From Bacillus
Cereus
pdb|1WS1|A Chain A, Structure Analysis Of Peptide Deformylase From Bacillus
Cereus
Length = 156
Score = 60.1 bits (144), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 44/130 (33%), Positives = 62/130 (47%), Gaps = 18/130 (13%)
Query: 8 MKNVMKRFDLFGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMK 67
M M D GL+APQVG+ L++ +V G I+ INP
Sbjct: 35 MHETMLIADGVGLAAPQVGVSLQVAVVDV-----DDDTGKIE-----------LINP--S 76
Query: 68 ILDYKDKVTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDH 127
IL+ + + EGC S L +V R +++ + GK AEG+ AR IQHE+DH
Sbjct: 77 ILEKRGEQVGPEGCLSFPGLYGEVERADYIKVRAQNRRGKVFLLEAEGFLARAIQHEIDH 136
Query: 128 LDGLLFTDSM 137
L G+LFT +
Sbjct: 137 LHGVLFTSKV 146
>pdb|1RL4|A Chain A, Plasmodium Falciparum Peptide Deformylase Complex With
Inhibitor
pdb|1RL4|B Chain B, Plasmodium Falciparum Peptide Deformylase Complex With
Inhibitor
Length = 188
Score = 59.7 bits (143), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 41/138 (29%), Positives = 66/138 (47%), Gaps = 15/138 (10%)
Query: 1 MKIIILQMKNVMKRFDLFGLSAPQVGLPLRLFI-VAFPDPEESFSEGDIKKFEMQAFPHM 59
+K ++ +M ++M GLSAPQV + R+ + A + + +E
Sbjct: 33 LKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENE-------------R 79
Query: 60 VWINPEMKILDYKDKVTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAAR 119
++INP + + K+ +EGC S ++ KV R V ++ D G +G +R
Sbjct: 80 IFINPSI-VEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSR 138
Query: 120 IIQHEMDHLDGLLFTDSM 137
I QHE DHL+G LF D M
Sbjct: 139 IFQHEFDHLNGTLFIDKM 156
>pdb|3FWX|A Chain A, The Crystal Structure Of The Peptide Deformylase From
Vibrio Cholerae O1 Biovar El Tor Str. N16961
pdb|3FWX|B Chain B, The Crystal Structure Of The Peptide Deformylase From
Vibrio Cholerae O1 Biovar El Tor Str. N16961
Length = 169
Score = 59.3 bits (142), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 40/122 (32%), Positives = 60/122 (49%), Gaps = 17/122 (13%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+A QV + R+ ++ DI + Q V INPE I++ + +
Sbjct: 45 IGLAATQVDIHQRIVVI------------DISETRDQP---XVLINPE--IIEKRGEDGI 87
Query: 78 LEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTDSM 137
EGC S+ +A VPR +V + LD G+ + A+ A +QHE+DHL G LF D +
Sbjct: 88 EEGCLSVPGARALVPRAAEVTVKALDRNGQEYQFDADDLLAICVQHELDHLAGKLFVDYL 147
Query: 138 LP 139
P
Sbjct: 148 SP 149
>pdb|2OS3|A Chain A, Structures Of Actinonin Bound Peptide Deformylases From E.
Faecalis And S. Pyogenes
Length = 205
Score = 56.2 bits (134), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 41/130 (31%), Positives = 73/130 (56%), Gaps = 14/130 (10%)
Query: 18 FGLSAPQVGLPLRLFIVAFPD-PEESFSEGDIKKFEMQAFP-HMVWINPEMKILDYKDKV 75
GL+APQ+ + R+ V P+ P++ EG+ K +A+ V NP KI+ + +
Sbjct: 70 VGLAAPQIDVSKRIIAVLVPNLPDK---EGNPPK---EAYSWQEVLYNP--KIVSHSVQD 121
Query: 76 TAL---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGL 131
AL EGC S+ + ++ V R+ +V + D+ G+ +G+ A ++QHE+DH++G+
Sbjct: 122 AALSDGEGCLSVDRVVEGYVVRHARVTVDYYDKEGQQHRIKLKGYNAIVVQHEIDHINGV 181
Query: 132 LFTDSMLPKS 141
LF D + K+
Sbjct: 182 LFYDRINAKN 191
>pdb|2AI7|A Chain A, S.Pneumoniae Polypeptide Deformylase Complexed With Sb-
485345
pdb|2AIA|A Chain A, S.Pneumoniae Pdf Complexed With Sb-543668
Length = 203
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 36/126 (28%), Positives = 70/126 (55%), Gaps = 11/126 (8%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQ+ + R+ V P+ E E + ++++A + NP KI+ + + AL
Sbjct: 72 GLAAPQLDISKRIIAVLVPNIVEE-GETPQEAYDLEA----IMYNP--KIVSHSVQDAAL 124
Query: 79 ---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFT 134
EGC S+ +++ V R+ +V + D+ G+ +G+ + ++QHE+DH++G++F
Sbjct: 125 GEGEGCLSVDRNVPGYVVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFY 184
Query: 135 DSMLPK 140
D + K
Sbjct: 185 DRINEK 190
>pdb|1LQW|A Chain A, Crystal Structure Of S.Aureus Peptide Deformylase
pdb|1LQW|B Chain B, Crystal Structure Of S.Aureus Peptide Deformylase
pdb|2AI9|A Chain A, S.Aureus Polypeptide Deformylase
pdb|2AI9|B Chain B, S.Aureus Polypeptide Deformylase
Length = 183
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 39/138 (28%), Positives = 69/138 (50%), Gaps = 21/138 (15%)
Query: 7 QMKNVMKRFDL---FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWIN 63
Q + + KR+ L GL+APQ+ + R+ V PD +G K ++ + +N
Sbjct: 45 QDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPD------DGSGKSYDY------MLVN 92
Query: 64 PEMKILDYKDKVTAL---EGCASLK-SLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAAR 119
P KI+ + + L EGC S+ ++ V R+ ++ + D G +G+ A
Sbjct: 93 P--KIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAI 150
Query: 120 IIQHEMDHLDGLLFTDSM 137
+ QHE+DHL+G++F D +
Sbjct: 151 VFQHEIDHLNGVMFYDHI 168
>pdb|2AIE|P Chain P, S.Pneumoniae Polypeptide Deformylase Complexed With Sb-
505684
Length = 203
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 36/126 (28%), Positives = 70/126 (55%), Gaps = 11/126 (8%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQ+ + R+ V P+ E E + ++++A + NP KI+ + + AL
Sbjct: 72 GLAAPQLDISKRIIAVLVPNIVEE-GETPQEAYDLEA----IMYNP--KIVSHSVQDAAL 124
Query: 79 ---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFT 134
EGC S+ +++ V R+ +V + D+ G+ +G+ + ++QHE+DH++G++F
Sbjct: 125 GEGEGCLSVDRNVPGYVVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFY 184
Query: 135 DSMLPK 140
D + K
Sbjct: 185 DRINEK 190
>pdb|3STR|P Chain P, Strep Peptide Deformylase With A Time Dependent
Thiazolidine Hydroxamic Acid
pdb|3SW8|P Chain P, Strep Peptide Deformylase With A Time Dependent
Dichlorobenzamide- Reverse Hydroxamic Acid
pdb|4EOX|P Chain P, X-Ray Structure Of Polypeptide Deformylase Bound To A
Acylprolinamide Inhibitor
Length = 203
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 36/126 (28%), Positives = 70/126 (55%), Gaps = 11/126 (8%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQ+ + R+ V P+ E E + ++++A + NP KI+ + + AL
Sbjct: 72 GLAAPQLDISKRIIAVLVPNIVEE-GETPQEAYDLEA----IMYNP--KIVSHSVQDAAL 124
Query: 79 ---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFT 134
EGC S+ +++ V R+ +V + D+ G+ +G+ + ++QHE+DH++G++F
Sbjct: 125 GEGEGCLSVDRNVPGYVVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFY 184
Query: 135 DSMLPK 140
D + K
Sbjct: 185 DRINEK 190
>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
pdb|1RQC|B Chain B, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|C Chain C, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|D Chain D, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|E Chain E, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|F Chain F, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|G Chain G, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|H Chain H, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|I Chain I, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|J Chain J, 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
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 41/132 (31%), Positives = 61/132 (46%), Gaps = 21/132 (15%)
Query: 11 VMKRFDL------FGLSAPQVGLPLRLFI-VAFPDPEESFSEGDIKKFEMQAFPHMVWIN 63
V K FD+ GLSAPQV + R+ + A + + +E ++IN
Sbjct: 31 VRKXFDIXYESKGIGLSAPQVNISKRIIVWNALYEKRKEENE-------------RIFIN 77
Query: 64 PEMKILDYKDKVTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQH 123
P + + K+ +EGC S ++ KV R V ++ D G +G +RI QH
Sbjct: 78 PSI-VEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQH 136
Query: 124 EMDHLDGLLFTD 135
E DHL+G LF D
Sbjct: 137 EFDHLNGTLFID 148
>pdb|2OKL|A Chain A, Crystal Structure Of Peptide Deformylase 2 With Actinonin
From Bacillus Cereus
pdb|2OKL|B Chain B, Crystal Structure Of Peptide Deformylase 2 With Actinonin
From Bacillus Cereus
Length = 185
Score = 53.9 bits (128), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 35/124 (28%), Positives = 62/124 (50%), Gaps = 19/124 (15%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+APQ+G+ ++ V D + + + H ++ NP KI+ + + T
Sbjct: 60 IGLAAPQIGVSKKMIAVHVTDADGTL------------YSHALF-NP--KIISHSVERTY 104
Query: 78 L---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLF 133
L EGC S+ + + VPRY ++ + G+ +G A + QHE+DHL+G++F
Sbjct: 105 LQGGEGCLSVDREVPGYVPRYTRITVKATSINGEEVKLRLKGLPAIVFQHEIDHLNGVMF 164
Query: 134 TDSM 137
D +
Sbjct: 165 YDHI 168
>pdb|1LMH|A Chain A, Crystal Structure Of S. Aureus Peptide Deformylase
Length = 184
Score = 53.5 bits (127), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 40/138 (28%), Positives = 66/138 (47%), Gaps = 21/138 (15%)
Query: 7 QMKNVMKRFDL---FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWIN 63
Q + + KR+ L GL+APQ+ + R V PD +G K ++ +N
Sbjct: 45 QDEEIAKRYGLRSGVGLAAPQINISKRXIAVLIPD------DGSGKSYDYX------LVN 92
Query: 64 PEMKILDYKDKVTAL---EGCASLK-SLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAAR 119
P KI+ + + L EGC S+ ++ V R+ K+ + D G +G+ A
Sbjct: 93 P--KIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNKITIKAKDIEGNDIQLRLKGYPAI 150
Query: 120 IIQHEMDHLDGLLFTDSM 137
+ QHE+DHL+G+ F D +
Sbjct: 151 VFQHEIDHLNGVXFYDHI 168
>pdb|3L87|A Chain A, The Crystal Structure Of Smu.143c From Streptococcus
Mutans Ua159
Length = 238
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 35/126 (27%), Positives = 67/126 (53%), Gaps = 6/126 (4%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+APQ+ + R+ V P+PE+ +G+ K E A +++ NP + +D A
Sbjct: 105 VGLAAPQLDISKRIIAVLIPNPEDK--DGNPPK-EAYALKEVMY-NPRIIAHSVQDAALA 160
Query: 78 -LEGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFTD 135
EG S+ + ++ V R+ +V + D+ +G+ + ++QHE+DH +G++F D
Sbjct: 161 DGEGXLSVDRVVEGYVIRHSRVTIEYYDKNSDKKKLKLKGYQSIVVQHEIDHTNGIMFFD 220
Query: 136 SMLPKS 141
+ K+
Sbjct: 221 RINEKN 226
>pdb|2OS1|A Chain A, Structures Of Actinonin Bound Peptide Deformylases From E.
Faecalis And S. Pyogenes
Length = 188
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 36/126 (28%), Positives = 64/126 (50%), Gaps = 19/126 (15%)
Query: 18 FGLSAPQVGLPLRLFIVAFP--DPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKV 75
GL+APQ+ + R+ V P DPE E + +++ NP KIL + +
Sbjct: 59 VGLAAPQLDISKRIIAVHVPSNDPEN----------ETPSLSTVMY-NP--KILSHSVQD 105
Query: 76 TAL---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGL 131
L EGC S+ + + V R+ K+ ++ D G+ + + A ++QHE+DH++G+
Sbjct: 106 VCLGEGEGCLSVDRDVPGYVVRHNKITVSYFDMAGEKHKVRLKNYEAIVVQHEIDHINGI 165
Query: 132 LFTDSM 137
+F D +
Sbjct: 166 MFYDHI 171
>pdb|2OS0|A Chain A, Structures Of Actinonin Bound Peptide Deformylases From E.
Faecalis And S. Pyogenes
Length = 188
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 36/126 (28%), Positives = 64/126 (50%), Gaps = 19/126 (15%)
Query: 18 FGLSAPQVGLPLRLFIVAFP--DPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKV 75
GL+APQ+ + R+ V P DPE E + +++ NP KIL + +
Sbjct: 59 VGLAAPQLDISKRIIAVHVPSNDPEN----------ETPSLSTVMY-NP--KILSHSVQD 105
Query: 76 TAL---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGL 131
L EGC S+ + + V R+ K+ ++ D G+ + + A ++QHE+DH++G+
Sbjct: 106 VCLGEGEGCLSVDRDVPGYVVRHNKITVSYFDMAGEKHKVRLKNYEAIVVQHEIDHINGI 165
Query: 132 LFTDSM 137
+F D +
Sbjct: 166 MFYDHI 171
>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
pdb|1JYM|B Chain B, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|C Chain C, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|D Chain D, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|E Chain E, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|F Chain F, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|G Chain G, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|H Chain H, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|I Chain I, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1JYM|J Chain J, 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
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 41/132 (31%), Positives = 61/132 (46%), Gaps = 22/132 (16%)
Query: 11 VMKRFDL------FGLSAPQVGLPLRLFI-VAFPDPEESFSEGDIKKFEMQAFPHMVWIN 63
V K FD+ GLSAPQV + R+ + A + + +E ++IN
Sbjct: 30 VRKXFDIXYESKGIGLSAPQVNISKRIIVWNALYEKRKEENE-------------RIFIN 76
Query: 64 PEMKILDYKDKVTALEGCASLKSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQH 123
P + + K+ +EGC S ++ KV R V ++ D G +G +RI QH
Sbjct: 77 PSI-VEQSLVKLKLIEGCLSF-GIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQH 134
Query: 124 EMDHLDGLLFTD 135
E DHL+G LF D
Sbjct: 135 EFDHLNGTLFID 146
>pdb|1LQY|A Chain A, Crystal Structure Of Bacillus Stearothermophilus Peptide
Deformylase Complexed With Antibiotic Actinonin
Length = 184
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 36/126 (28%), Positives = 62/126 (49%), Gaps = 19/126 (15%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDK--- 74
GL+APQ+ + R+ V D G + + + NP KI+ + +
Sbjct: 59 IGLAAPQINVSKRMIAVHVTD-----ENGTLYSYAL--------FNP--KIVSHSVQQCY 103
Query: 75 VTALEGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLF 133
+T EGC S+ + + V RY ++ +TG G+ + +G A + QHE+DHL+G++F
Sbjct: 104 LTTGEGCLSVDRDVPGYVLRYARITVTGTTLDGEEVTLRLKGLPAIVFQHEIDHLNGIMF 163
Query: 134 TDSMLP 139
D + P
Sbjct: 164 YDRINP 169
>pdb|3G6N|A Chain A, Crystal Structure Of An Efpdf Complex With Met-Ala-Ser
pdb|3G6N|B Chain B, Crystal Structure Of An Efpdf Complex With Met-Ala-Ser
Length = 191
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 35/124 (28%), Positives = 61/124 (49%), Gaps = 15/124 (12%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+APQ+ + R+ V P P+ E D V NP KIL + +
Sbjct: 63 VGLAAPQLDISKRIIAVHVPSPD---PEADGPSLST------VMYNP--KILSHSVQDAC 111
Query: 78 L---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLF 133
L EGC S+ + + V R+ K+ ++ D G+ + + + ++QHE+DH++G++F
Sbjct: 112 LGEGEGCLSVDREVPGYVVRHAKITVSYYDMNGEKHKIRLKNYESIVVQHEIDHINGVMF 171
Query: 134 TDSM 137
D +
Sbjct: 172 YDHI 175
>pdb|3CMD|A Chain A, Crystal Structure Of Peptide Deformylase From
Vre-E.Faecium
pdb|3CMD|B Chain B, Crystal Structure Of Peptide Deformylase From
Vre-E.Faecium
Length = 196
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 35/124 (28%), Positives = 61/124 (49%), Gaps = 15/124 (12%)
Query: 18 FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTA 77
GL+APQ+ + R+ V P P+ E D V NP KIL + +
Sbjct: 68 VGLAAPQLDISKRIIAVHVPSPD---PEADGPSLST------VMYNP--KILSHSVQDAC 116
Query: 78 L---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLF 133
L EGC S+ + + V R+ K+ ++ D G+ + + + ++QHE+DH++G++F
Sbjct: 117 LGEGEGCLSVDREVPGYVVRHAKITVSYYDMNGEKHKIRLKNYESIVVQHEIDHINGVMF 176
Query: 134 TDSM 137
D +
Sbjct: 177 YDHI 180
>pdb|1Q1Y|A Chain A, Crystal Structures Of Peptide Deformylase From
Staphylococcus Aureus Complexed With Actinonin
pdb|3U7K|A Chain A, Crystal Structures Of The Staphylococcus Aureus Peptide
Deformylase In Complex With Two Classes Of New
Inhibitors
pdb|3U7L|A Chain A, Crystal Structures Of The Staphylococcus Aureus Peptide
Deformylase In Complex With Two Classes Of New
Inhibitors
pdb|3U7M|A Chain A, Crystal Structures Of The Staphylococcus Aureus Peptide
Deformylase In Complex With Two Classes Of New
Inhibitors
pdb|3U7N|A Chain A, Crystal Structures Of The Staphylococcus Aureus Peptide
Deformylase In Complex With Two Classes Of New
Inhibitors
Length = 191
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 38/138 (27%), Positives = 68/138 (49%), Gaps = 21/138 (15%)
Query: 7 QMKNVMKRFDL---FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWIN 63
Q + + KR+ L GL+APQ+ + R+ V PD +G K ++ + +N
Sbjct: 45 QDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPD------DGSGKSYDY------MLVN 92
Query: 64 PEMKILDYKDKVTAL---EGCASLK-SLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAAR 119
P KI+ + + L EG S+ ++ V R+ ++ + D G +G+ A
Sbjct: 93 P--KIVSHSVQEAYLPTGEGXLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAI 150
Query: 120 IIQHEMDHLDGLLFTDSM 137
+ QHE+DHL+G++F D +
Sbjct: 151 VFQHEIDHLNGVMFYDHI 168
>pdb|3SVJ|P Chain P, Strep Peptide Deformylase With A Time Dependent
Thiazolidine Amide
Length = 203
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 35/126 (27%), Positives = 69/126 (54%), Gaps = 11/126 (8%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQ+ + R+ V P+ E E + ++++A + NP KI+ + + AL
Sbjct: 72 GLAAPQLDISKRIIAVLVPNIVEE-GETPQEAYDLEA----IMYNP--KIVSHSVQDAAL 124
Query: 79 ---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFT 134
EG S+ +++ V R+ +V + D+ G+ +G+ + ++QHE+DH++G++F
Sbjct: 125 GEGEGXLSVDRNVPGYVVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFY 184
Query: 135 DSMLPK 140
D + K
Sbjct: 185 DRINEK 190
>pdb|1LM4|A Chain A, Structure Of Peptide Deformylase From Staphylococcus
Aureus At 1.45 A
pdb|1LM4|B Chain B, Structure Of Peptide Deformylase From Staphylococcus
Aureus At 1.45 A
Length = 194
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 38/138 (27%), Positives = 68/138 (49%), Gaps = 21/138 (15%)
Query: 7 QMKNVMKRFDL---FGLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWIN 63
Q + + KR+ L GL+APQ+ + R+ V PD +G K ++ + +N
Sbjct: 56 QDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPD------DGSGKSYDY------MLVN 103
Query: 64 PEMKILDYKDKVTAL---EGCASLK-SLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAAR 119
P KI+ + + L EG S+ ++ V R+ ++ + D G +G+ A
Sbjct: 104 P--KIVSHSVQEAYLPTGEGXLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAI 161
Query: 120 IIQHEMDHLDGLLFTDSM 137
+ QHE+DHL+G++F D +
Sbjct: 162 VFQHEIDHLNGVMFYDHI 179
>pdb|1LM6|A Chain A, Crystal Structure Of Peptide Deformylase From
Streptococcus Pneumoniae
Length = 215
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 35/126 (27%), Positives = 69/126 (54%), Gaps = 11/126 (8%)
Query: 19 GLSAPQVGLPLRLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDYKDKVTAL 78
GL+APQ+ + R+ V P+ E E + ++++A + NP KI+ + + AL
Sbjct: 84 GLAAPQLDISKRIIAVLVPNIVEE-GETPQEAYDLEA----IMYNP--KIVSHSVQDAAL 136
Query: 79 ---EGCASL-KSLQAKVPRYRKVQLTGLDETGKPDSWTAEGWAARIIQHEMDHLDGLLFT 134
EG S+ +++ V R+ +V + D+ G+ +G+ + ++QHE+DH++G++F
Sbjct: 137 GEGEGXLSVDRNVPGYVVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFY 196
Query: 135 DSMLPK 140
D + K
Sbjct: 197 DRINEK 202
>pdb|1WE5|A Chain A, Crystal Structure Of Alpha-Xylosidase From Escherichia
Coli
pdb|1WE5|B Chain B, Crystal Structure Of Alpha-Xylosidase From Escherichia
Coli
pdb|1WE5|C Chain C, Crystal Structure Of Alpha-Xylosidase From Escherichia
Coli
pdb|1WE5|D Chain D, Crystal Structure Of Alpha-Xylosidase From Escherichia
Coli
pdb|1WE5|E Chain E, Crystal Structure Of Alpha-Xylosidase From Escherichia
Coli
pdb|1WE5|F Chain F, Crystal Structure Of Alpha-Xylosidase From Escherichia
Coli
Length = 772
Score = 28.5 bits (62), Expect = 1.6, Method: Composition-based stats.
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 5/31 (16%)
Query: 34 VAFPDPEESFSEGDIKKFEMQAFPHMVWINP 64
+ FPDPE G I++ + + VWINP
Sbjct: 323 LTFPDPE-----GXIRRLKAKGLKICVWINP 348
>pdb|2IMR|A Chain A, Crystal Structure Of Amidohydrolase Dr_0824 From
Deinococcus Radiodurans
Length = 420
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 3/62 (4%)
Query: 30 RLFIVAFPDPEESFSEGDIKKFEMQAFPHMVWINPEMKILDY--KDKVTALEGCASLKSL 87
R V P P + + D+ +E QA P+ WI PE+ I + A G +L L
Sbjct: 86 RAGAVIAPPPVNAHTHLDMSAYEFQALPYFQWI-PEVVIRGRHLRGVAAAQAGADTLTRL 144
Query: 88 QA 89
A
Sbjct: 145 GA 146
>pdb|3UX8|A Chain A, Crystal Structure Of Uvra
Length = 670
Score = 27.7 bits (60), Expect = 3.5, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 23/37 (62%), Gaps = 4/37 (10%)
Query: 83 SLKSLQAKVPRYRKVQLTGLDETGKP----DSWTAEG 115
+LK++ ++PR + V LTGL +GK D+ AEG
Sbjct: 33 NLKNIDVEIPRGKLVVLTGLSGSGKSSLAFDTIYAEG 69
>pdb|2R6F|A Chain A, Crystal Structure Of Bacillus Stearothermophilus Uvra
pdb|2R6F|B Chain B, Crystal Structure Of Bacillus Stearothermophilus Uvra
Length = 972
Score = 27.7 bits (60), Expect = 3.5, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 23/37 (62%), Gaps = 4/37 (10%)
Query: 83 SLKSLQAKVPRYRKVQLTGLDETGKP----DSWTAEG 115
+LK++ ++PR + V LTGL +GK D+ AEG
Sbjct: 33 NLKNIDVEIPRGKLVVLTGLSGSGKSSLAFDTIYAEG 69
>pdb|3UWX|A Chain A, Crystal Structure Of Uvra-Uvrb Complex
Length = 972
Score = 27.3 bits (59), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 23/37 (62%), Gaps = 4/37 (10%)
Query: 83 SLKSLQAKVPRYRKVQLTGLDETGKP----DSWTAEG 115
+LK++ ++PR + V LTGL +GK D+ AEG
Sbjct: 33 NLKNIDVEIPRGKLVVLTGLSGSGKSSLAFDTIYAEG 69
>pdb|3IZ3|B Chain B, Cryoem Structure Of Cytoplasmic Polyhedrosis Virus
pdb|3IZ3|C Chain C, Cryoem Structure Of Cytoplasmic Polyhedrosis Virus
pdb|3J17|B Chain B, Structure Of A Transcribing Cypovirus By Cryo-Electron
Microscopy
pdb|3J17|C Chain C, Structure Of A Transcribing Cypovirus By Cryo-Electron
Microscopy
Length = 1333
Score = 27.3 bits (59), Expect = 4.3, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 99 LTGLDETGKPDSW---TAEGWAARIIQHEMDHLDGLLFTDSMLPKSLECVCWQDINLQNG 155
+G T KPD + + EG II+ + + +DGL D+ + + C C + Q+G
Sbjct: 720 FSGNHATFKPDQYVITSPEGSYKPIIERQGETVDGLTIIDTSIVWPILCQCTYPLVRQSG 779
>pdb|3CNF|A Chain A, 3.88 Angstrom Structure Of Cytoplasmic Polyhedrosis Virus
By Cryo-Electron Microscopy
pdb|3CNF|B Chain B, 3.88 Angstrom Structure Of Cytoplasmic Polyhedrosis Virus
By Cryo-Electron Microscopy
pdb|3IZX|B Chain B, 3.1 Angstrom Cryoem Structure Of Cytoplasmic Polyhedrosis
Virus
pdb|3IZX|C Chain C, 3.1 Angstrom Cryoem Structure Of Cytoplasmic Polyhedrosis
Virus
Length = 1333
Score = 27.3 bits (59), Expect = 4.3, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 99 LTGLDETGKPDSW---TAEGWAARIIQHEMDHLDGLLFTDSMLPKSLECVCWQDINLQNG 155
+G T KPD + + EG II+ + + +DGL D+ + + C C + Q+G
Sbjct: 720 FSGNHATFKPDQYVITSPEGSYKPIIERQGETVDGLTIIDTSIVWPILCQCTYPLVRQSG 779
>pdb|1HNR|A Chain A, H-Ns (Dna-Binding Domain)
pdb|1HNS|A Chain A, H-Ns (Dna-Binding Domain)
Length = 47
Score = 26.9 bits (58), Expect = 4.9, Method: Composition-based stats.
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 95 RKVQLTGLDETGKPDSWTAEGWAARIIQHEMD 126
R + + +DE G+ +WT +G +I+ MD
Sbjct: 3 RPAKYSYVDENGETKTWTGQGRTPAVIKKAMD 34
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.323 0.139 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,012,290
Number of Sequences: 62578
Number of extensions: 195568
Number of successful extensions: 424
Number of sequences better than 100.0: 62
Number of HSP's better than 100.0 without gapping: 58
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 327
Number of HSP's gapped (non-prelim): 65
length of query: 164
length of database: 14,973,337
effective HSP length: 91
effective length of query: 73
effective length of database: 9,278,739
effective search space: 677347947
effective search space used: 677347947
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)