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= 033765
(112 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3CPM|A Chain A, Plant Peptide Deformylase Pdf1b Crystal Structure
Length = 193
Score = 189 bits (481), Expect = 2e-49, Method: Compositional matrix adjust.
Identities = 85/108 (78%), Positives = 101/108 (93%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MFDVMYKTDGIGLSAPQVG+NVQLMVFNP GE GEG+EIVLVNP++ KYS+K++P++EGC
Sbjct: 48 MFDVMYKTDGIGLSAPQVGLNVQLMVFNPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGC 107
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHLQ 108
LSFPGI+A+V RP+SVKIDARDI G RFS+SLS LPAR+FQHE+DHL+
Sbjct: 108 LSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPARIFQHEYDHLE 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 = 189 bits (480), Expect = 3e-49, Method: Compositional matrix adjust.
Identities = 85/108 (78%), Positives = 101/108 (93%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MFDVMYKTDGIGLSAPQVG+NVQLMVFNP GE GEG+EIVLVNP++ KYS+K++P++EGC
Sbjct: 32 MFDVMYKTDGIGLSAPQVGLNVQLMVFNPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGC 91
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHLQ 108
LSFPGI+A+V RP+SVKIDARDI G RFS+SLS LPAR+FQHE+DHL+
Sbjct: 92 LSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPARIFQHEYDHLE 139
>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 = 186 bits (473), Expect = 2e-48, Method: Compositional matrix adjust.
Identities = 84/108 (77%), Positives = 100/108 (92%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MFDVMYKTD IGLSAPQVG+NVQLMVFNP GE GEG+EIVLVNP++ KYS+K++P++EGC
Sbjct: 32 MFDVMYKTDQIGLSAPQVGLNVQLMVFNPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGC 91
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHLQ 108
LSFPGI+A+V RP+SVKIDARDI G RFS+SLS LPAR+FQHE+DHL+
Sbjct: 92 LSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPARIFQHEYDHLE 139
>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 = 186 bits (472), Expect = 3e-48, Method: Compositional matrix adjust.
Identities = 84/108 (77%), Positives = 100/108 (92%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MFDVMYKTD IGLSAPQVG+NVQLMVFNP GE GEG+EIVLVNP++ KYS+K++P++EGC
Sbjct: 32 MFDVMYKTDMIGLSAPQVGLNVQLMVFNPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGC 91
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHLQ 108
LSFPGI+A+V RP+SVKIDARDI G RFS+SLS LPAR+FQHE+DHL+
Sbjct: 92 LSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPARIFQHEYDHLE 139
>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 = 104 bits (260), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 53/108 (49%), Positives = 71/108 (65%), Gaps = 1/108 (0%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGE-RGEGEEIVLVNPRVNKYSNKMIPYEEG 59
MFD+MY++ GIGLSAPQV I+ +++V+N + E R E E + +NP + + S + EG
Sbjct: 40 MFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEG 99
Query: 60 CLSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
CLSFPGI VERP V I DING + L + +R+FQHEFDHL
Sbjct: 100 CLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHL 147
>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 = 102 bits (253), Expect = 7e-23, Method: Compositional matrix adjust.
Identities = 49/107 (45%), Positives = 67/107 (62%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
M MY DGIGL+APQVGIN QL+V + E + +VL+NP++ + + + +EGC
Sbjct: 50 MLQTMYSADGIGLAAPQVGINKQLIVIDLELEDEQAPPLVLINPKIERTAGDLEQCQEGC 109
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LS PG++ DVERPE V++ +D NG + L AR QHE DHL
Sbjct: 110 LSIPGVYLDVERPEIVEVSYKDENGRPQRLVADGLLARCIQHEMDHL 156
>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 = 99.8 bits (247), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 51/107 (47%), Positives = 69/107 (64%), Gaps = 1/107 (0%)
Query: 2 FDVMYKTDGIGLSAPQVGINVQLMVFNPVGE-RGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
FD+ Y++ GIGLSAPQV I+ +++V+N + E R E E + +NP + + S + EGC
Sbjct: 35 FDIXYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGC 94
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LSFPGI VERP V I DING + L + +R+FQHEFDHL
Sbjct: 95 LSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHL 141
>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 = 92.4 bits (228), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 50/107 (46%), Positives = 68/107 (63%), Gaps = 2/107 (1%)
Query: 2 FDVMYKTDGIGLSAPQVGINVQLMVFNPVGE-RGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
FD+ Y++ GIGLSAPQV I+ +++V+N + E R E E + +NP + + S + EGC
Sbjct: 34 FDIXYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGC 93
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LSF GI VERP V I DING + L + +R+FQHEFDHL
Sbjct: 94 LSF-GIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHL 139
>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 = 85.5 bits (210), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 41/106 (38%), Positives = 65/106 (61%)
Query: 3 DVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGCLS 62
+ + +DGIGL+APQVGIN +++V + E + VNP++ S + + ++EGCLS
Sbjct: 36 EAXWASDGIGLAAPQVGINKRVIVVDETTEEHGKYAHLXVNPKITWKSEEKVLFDEGCLS 95
Query: 63 FPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHLQ 108
P + +V RP+S+K+ ++ +G L L ARV QHE DHL+
Sbjct: 96 VPDQNGEVLRPKSIKVTFQNKDGKYKKWKLDGLAARVVQHEIDHLE 141
>pdb|3QU1|A Chain A, Peptide Deformylase From Vibrio Cholerae
pdb|3QU1|B Chain B, Peptide Deformylase From Vibrio Cholerae
Length = 171
Score = 83.2 bits (204), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 49/108 (45%), Positives = 65/108 (60%), Gaps = 4/108 (3%)
Query: 1 MFDVMYKTD-GIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEG 59
+ D +Y TD GIGL+APQVG ++V + R + +VL+NP+V SNK + +EG
Sbjct: 37 LLDTLYATDNGIGLAAPQVGREEAIVVIDLSDNRDQ--PLVLINPKVVSGSNKEMG-QEG 93
Query: 60 CLSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
CLS P +ADVER SV ++A D G + SD A V QHE DHL
Sbjct: 94 CLSVPDYYADVERYTSVVVEALDREGKPLRIETSDFLAIVMQHEIDHL 141
>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 = 81.3 bits (199), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 42/107 (39%), Positives = 63/107 (58%), Gaps = 2/107 (1%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MF+ MY+ GIGL+A QV ++ +++V + ++ E V +NP + +M Y+EGC
Sbjct: 47 MFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPR--VFINPEFEPLTEEMDQYQEGC 104
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LS PG + +V+RP+ V+I A D +G F L A QHE DHL
Sbjct: 105 LSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHL 151
>pdb|1LRY|A Chain A, Crystal Structure Of P. Aeruginosa Peptide Deformylase
Complexed With Antibiotic Actinonin
Length = 167
Score = 80.9 bits (198), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 42/107 (39%), Positives = 62/107 (57%), Gaps = 2/107 (1%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MF+ MY+ GIGL+A QV ++ +++V + ++ E V +NP + M Y+EGC
Sbjct: 34 MFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPR--VFINPEFEPLTEDMDQYQEGC 91
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LS PG + +V+RP+ V+I A D +G F L A QHE DHL
Sbjct: 92 LSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHL 138
>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 = 80.9 bits (198), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 42/107 (39%), Positives = 62/107 (57%), Gaps = 2/107 (1%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MF+ MY+ GIGL+A QV ++ +++V + ++ E V +NP + M Y+EGC
Sbjct: 35 MFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPR--VFINPEFEPLTEDMDQYQEGC 92
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LS PG + +V+RP+ V+I A D +G F L A QHE DHL
Sbjct: 93 LSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHL 139
>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 = 79.7 bits (195), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 43/113 (38%), Positives = 64/113 (56%), Gaps = 5/113 (4%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVF-NPVGERGEGE----EIVLVNPRVNKYSNKMIP 55
MFD M +G+GL+APQ+GI Q++V + ER G E +++NP + +
Sbjct: 37 MFDTMRHAEGVGLAAPQIGILKQIVVVGSEDNERYPGTPDVPERIILNPVITPLTKDTSG 96
Query: 56 YEEGCLSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHLQ 108
+ EGCLS PG+ VERP +++ D G +F ++ A V+QHE DHLQ
Sbjct: 97 FWEGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDETIDGYKAIVYQHECDHLQ 149
>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 = 77.4 bits (189), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 42/107 (39%), Positives = 61/107 (57%), Gaps = 5/107 (4%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
M + MY DG+GL+APQVGI+ + V + G G + ++NP + + + EEG
Sbjct: 45 MIETMYHYDGVGLAAPQVGISQRFFVMDV----GNGP-VAVINPEILEIDPETEVAEEGX 99
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LSFP I ++ER + +K+ ++ G L ARVFQHEFDHL
Sbjct: 100 LSFPEIFVEIERSKRIKVKYQNTRGEYVEEELEGYAARVFQHEFDHL 146
>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 = 77.4 bits (189), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 42/113 (37%), Positives = 63/113 (55%), Gaps = 5/113 (4%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVF-NPVGERGEGE----EIVLVNPRVNKYSNKMIP 55
MF M +G+GL+APQ+GI Q++V + ER G E +++NP + +
Sbjct: 37 MFTTMRHAEGVGLAAPQIGILKQIVVVGSEDNERYPGTPDVPERIILNPVITPLTKDTSG 96
Query: 56 YEEGCLSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHLQ 108
+ EGCLS PG+ VERP +++ D G +F ++ A V+QHE DHLQ
Sbjct: 97 FWEGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDETIDGYKAIVYQHECDHLQ 149
>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 = 77.4 bits (189), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 43/109 (39%), Positives = 66/109 (60%), Gaps = 6/109 (5%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRV-NKYSNKMIPYEEG 59
M + M DG+GL+APQVG+++Q+ V + + G+ I L+NP + K ++ P EG
Sbjct: 35 MHETMLIADGVGLAAPQVGVSLQVAVVDVDDDTGK---IELINPSILEKRGEQVGP--EG 89
Query: 60 CLSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHLQ 108
CLSFPG++ +VER + +K+ A++ G F + AR QHE DHL
Sbjct: 90 CLSFPGLYGEVERADYIKVRAQNRRGKVFLLEAEGFLARAIQHEIDHLH 138
>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 = 76.3 bits (186), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 46/107 (42%), Positives = 61/107 (57%), Gaps = 3/107 (2%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MF+ MY +GIGL+A QV I+ +++V + R E +VL+NP + + S + EEGC
Sbjct: 34 MFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDE--RLVLINPELLEKSGET-GIEEGC 90
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LS P A V R E VKI A D +G F + L A QHE DHL
Sbjct: 91 LSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHL 137
>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 = 76.3 bits (186), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 46/107 (42%), Positives = 61/107 (57%), Gaps = 3/107 (2%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MF+ MY +GIGL+A QV I+ +++V + R E +VL+NP + + S + EEGC
Sbjct: 34 MFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDE--RLVLINPELLEKSGET-GIEEGC 90
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LS P A V R E VKI A D +G F + L A QHE DHL
Sbjct: 91 LSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHL 137
>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 = 76.3 bits (186), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 46/107 (42%), Positives = 61/107 (57%), Gaps = 3/107 (2%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MF+ MY +GIGL+A QV I+ +++V + R E +VL+NP + + S + EEGC
Sbjct: 35 MFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDE--RLVLINPELLEKSGET-GIEEGC 91
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LS P A V R E VKI A D +G F + L A QHE DHL
Sbjct: 92 LSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHL 138
>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 = 76.3 bits (186), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 46/107 (42%), Positives = 61/107 (57%), Gaps = 3/107 (2%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MF+ MY +GIGL+A QV I+ +++V + R E +VL+NP + + S + EEGC
Sbjct: 34 MFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDE--RLVLINPELLEKSGET-GIEEGC 90
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LS P A V R E VKI A D +G F + L A QHE DHL
Sbjct: 91 LSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHL 137
>pdb|4AZ4|A Chain A, E.Coli Deformylase With Co(Ii) And Hydrosulfide
Length = 186
Score = 75.9 bits (185), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 46/107 (42%), Positives = 61/107 (57%), Gaps = 3/107 (2%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MF+ MY +GIGL+A QV I+ +++V + R E +VL+NP + + S + EEGC
Sbjct: 34 MFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDE--RLVLINPELLEKSGET-GIEEGC 90
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LS P A V R E VKI A D +G F + L A QHE DHL
Sbjct: 91 LSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAIXIQHEMDHL 137
>pdb|2DEF|A Chain A, Peptide Deformylase Catalytic Core (Residues 1-147), Nmr,
20 Structures
Length = 147
Score = 75.9 bits (185), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 46/107 (42%), Positives = 61/107 (57%), Gaps = 3/107 (2%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MF+ MY +GIGL+A QV I+ +++V + R E +VL+NP + + S + EEGC
Sbjct: 34 MFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDE--RLVLINPELLEKSGET-GIEEGC 90
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LS P A V R E VKI A D +G F + L A QHE DHL
Sbjct: 91 LSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHL 137
>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 = 75.9 bits (185), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 46/107 (42%), Positives = 61/107 (57%), Gaps = 3/107 (2%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MF+ MY +GIGL+A QV I+ +++V + R E +VL+NP + + S + EEGC
Sbjct: 34 MFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDE--RLVLINPELLEKSGET-GIEEGC 90
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LS P A V R E VKI A D +G F + L A QHE DHL
Sbjct: 91 LSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHL 137
>pdb|1DFF|A Chain A, Peptide Deformylase
Length = 164
Score = 75.9 bits (185), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 46/107 (42%), Positives = 61/107 (57%), Gaps = 3/107 (2%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MF+ MY +GIGL+A QV I+ +++V + R E +VL+NP + + S + EEGC
Sbjct: 34 MFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDE--RLVLINPELLEKSGET-GIEEGC 90
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LS P A V R E VKI A D +G F + L A QHE DHL
Sbjct: 91 LSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHL 137
>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 = 73.6 bits (179), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 44/121 (36%), Positives = 61/121 (50%), Gaps = 14/121 (11%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGE--------------RGEGEEIVLVNPRV 46
M VM G+GL+APQ+G+ ++++V E R + +V+VNP +
Sbjct: 38 MIKVMRLAPGVGLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVL 97
Query: 47 NKYSNKMIPYEEGCLSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDH 106
+ SNK + EGCLS G A VER V + D G R V+ S AR+ QHE DH
Sbjct: 98 KERSNKKALFFEGCLSVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDH 157
Query: 107 L 107
L
Sbjct: 158 L 158
>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 = 72.0 bits (175), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 40/110 (36%), Positives = 67/110 (60%), Gaps = 4/110 (3%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERG---EGEEIVLVNPRVNKYSNKMIPYE 57
M++ M ++GIGL+A QVG+ +++++ N E G + + + ++NP+ + M+ Y+
Sbjct: 34 MYETMIASEGIGLAAIQVGLPLRMLIINLPQEDGVQHKEDCLEIINPKFIETGGSMM-YK 92
Query: 58 EGCLSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
EGCLS PG + +VER E VKI+ ++ + S+L A QHE DHL
Sbjct: 93 EGCLSVPGFYEEVERFEKVKIEYQNRFAEVKVLEASELLAVAIQHEIDHL 142
>pdb|3U04|A Chain A, Crystal Structure Of Peptide Deformylase From Ehrlichia
Chaffeensis In Complex With Actinonin
Length = 190
Score = 71.6 bits (174), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 39/124 (31%), Positives = 63/124 (50%), Gaps = 17/124 (13%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFN------------PVGERGEGEEI-----VLVN 43
MF+ M+ G+GL+A QVG++ +++V N V ++ EG E+ ++N
Sbjct: 37 MFETMHANQGLGLAAVQVGVHKRILVMNVPEEFEDSEDIENVEDKIEGYELYGGPYCIIN 96
Query: 44 PRVNKYSNKMIPYEEGCLSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHE 103
P++ S + + +EGCLS PG + RP+ + + D NG + AR QHE
Sbjct: 97 PKIVDISQEKVKLKEGCLSVPGYFDYIVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHE 156
Query: 104 FDHL 107
DHL
Sbjct: 157 IDHL 160
>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 = 71.6 bits (174), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 39/124 (31%), Positives = 63/124 (50%), Gaps = 17/124 (13%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFN------------PVGERGEGEEI-----VLVN 43
MF+ M+ G+GL+A QVG++ +++V N V ++ EG E+ ++N
Sbjct: 56 MFETMHANQGLGLAAVQVGVHKRILVMNVPEEFEDSEDIENVEDKIEGYELYGGPYCIIN 115
Query: 44 PRVNKYSNKMIPYEEGCLSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHE 103
P++ S + + +EGCLS PG + RP+ + + D NG + AR QHE
Sbjct: 116 PKIVDISQEKVKLKEGCLSVPGYFDYIVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHE 175
Query: 104 FDHL 107
DHL
Sbjct: 176 IDHL 179
>pdb|4AL3|A Chain A, Peptide Deformylase (Co-Form) With Mercaptoethanol
Length = 186
Score = 71.6 bits (174), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 45/107 (42%), Positives = 60/107 (56%), Gaps = 3/107 (2%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGC 60
MF+ MY +GIGL+A QV I+ +++V + R E +VL+NP + + S + EEG
Sbjct: 34 MFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDE--RLVLINPELLEKSGET-GIEEGX 90
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LS P A V R E VKI A D +G F + L A QHE DHL
Sbjct: 91 LSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHL 137
>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 = 71.2 bits (173), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 42/119 (35%), Positives = 65/119 (54%), Gaps = 13/119 (10%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEE-----------IVLVNPRVNKY 49
M + M++ G+GL+APQ+G++ +L V + EGEE V+ NP V Y
Sbjct: 33 MLETMFEAKGVGLAAPQIGLSQRLFVAVEYADEPEGEEERPLRELVRRVYVVANP-VITY 91
Query: 50 SNKMIPYEEGCLSFPGIHA-DVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
++ EG LS PG+++ +V R E ++++ +D G + L ARVFQHE DHL
Sbjct: 92 REGLVEGTEGXLSLPGLYSEEVPRAERIRVEYQDEEGRGRVLELEGYMARVFQHEIDHL 150
>pdb|3DLD|A Chain A, Crystal Structure Of Peptide Deformylase, Xoo1075, From
Xanthomonas Oryzae Pv. Oryzae Kacc10331
Length = 171
Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 40/112 (35%), Positives = 58/112 (51%), Gaps = 5/112 (4%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFN-PVGERGEGEEIV----LVNPRVNKYSNKMIP 55
MF+ M G+GL+APQ+ +++QLMVF ER V L N ++ S++M
Sbjct: 35 MFETMGAAHGVGLAAPQIAVDLQLMVFGFEASERYPEAPAVPLTALANAQIEPLSDEMEN 94
Query: 56 YEEGCLSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
EGCLS PG+ A + R ++ +G+ ARV QHE+DHL
Sbjct: 95 GWEGCLSIPGLRAVIPRYRYIRYRGFAPDGSPIEREAEGFHARVVQHEYDHL 146
>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 = 65.9 bits (159), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 42/107 (39%), Positives = 55/107 (51%), Gaps = 5/107 (4%)
Query: 2 FDVMYKTDGIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRV-NKYSNKMIPYEEGC 60
+ Y +GIGL+A QV I+ +++V + R + VL+NP + K I EEGC
Sbjct: 36 LETXYAEEGIGLAATQVDIHQRIVVIDISETRDQP--XVLINPEIIEKRGEDGI--EEGC 91
Query: 61 LSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
LS PG A V R V + A D NG + DL A QHE DHL
Sbjct: 92 LSVPGARALVPRAAEVTVKALDRNGQEYQFDADDLLAICVQHELDHL 138
>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 = 65.9 bits (159), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 39/102 (38%), Positives = 57/102 (55%), Gaps = 4/102 (3%)
Query: 10 GIGLSAPQVGINVQLM-VFNPVGERGEGEEIVLVNPRVNKYS--NKMIPYEEGCLSFP-G 65
G+GL+APQ+ I+ +++ V P G+ + +LVNP++ +S +P EGCLS
Sbjct: 58 GVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDN 117
Query: 66 IHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
+ V R + I A+DI G + L PA VFQHE DHL
Sbjct: 118 VAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHL 159
>pdb|1LMH|A Chain A, Crystal Structure Of S. Aureus Peptide Deformylase
Length = 184
Score = 64.3 bits (155), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 39/102 (38%), Positives = 55/102 (53%), Gaps = 4/102 (3%)
Query: 10 GIGLSAPQVGINVQ-LMVFNPVGERGEGEEIVLVNPRVNKYS--NKMIPYEEGCLSFP-G 65
G+GL+APQ+ I+ + + V P G+ + LVNP++ +S +P EGCLS
Sbjct: 58 GVGLAAPQINISKRXIAVLIPDDGSGKSYDYXLVNPKIVSHSVQEAYLPTGEGCLSVDDN 117
Query: 66 IHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
+ V R + I A+DI G + L PA VFQHE DHL
Sbjct: 118 VAGLVHRHNKITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHL 159
>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 = 63.5 bits (153), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 39/122 (31%), Positives = 59/122 (48%), Gaps = 14/122 (11%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFN---------PVGERGEGEE-----IVLVNPRV 46
+ VM + +GLSAPQ+G+ Q++ P +R + V VNP +
Sbjct: 39 LVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSL 98
Query: 47 NKYSNKMIPYEEGCLSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDH 106
++++ + EGC S G A V R ++V+I D NG + S AR+ QHE DH
Sbjct: 99 RVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDH 158
Query: 107 LQ 108
LQ
Sbjct: 159 LQ 160
>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 = 61.2 bits (147), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 38/102 (37%), Positives = 56/102 (54%), Gaps = 4/102 (3%)
Query: 10 GIGLSAPQVGINVQLM-VFNPVGERGEGEEIVLVNPRVNKYS--NKMIPYEEGCLSFP-G 65
G+GL+APQ+ I+ +++ V P G+ + +LVNP++ +S +P EG LS
Sbjct: 58 GVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGXLSVDDN 117
Query: 66 IHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
+ V R + I A+DI G + L PA VFQHE DHL
Sbjct: 118 VAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHL 159
>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 = 61.2 bits (147), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 38/102 (37%), Positives = 56/102 (54%), Gaps = 4/102 (3%)
Query: 10 GIGLSAPQVGINVQLM-VFNPVGERGEGEEIVLVNPRVNKYS--NKMIPYEEGCLSFP-G 65
G+GL+APQ+ I+ +++ V P G+ + +LVNP++ +S +P EG LS
Sbjct: 69 GVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGXLSVDDN 128
Query: 66 IHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
+ V R + I A+DI G + L PA VFQHE DHL
Sbjct: 129 VAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHL 170
>pdb|3E3U|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Peptide
Deformylase In Complex With Inhibitor
Length = 197
Score = 60.1 bits (144), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 36/118 (30%), Positives = 62/118 (52%), Gaps = 7/118 (5%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLMVFNPVGERG--EGEEIVLVNPRVNKYS-NKMIPY- 56
M+D M +G+GL+A Q+G +++L V++ +R V++NP + + +P
Sbjct: 40 MYDTMDAANGVGLAANQIGCSLRLFVYDCAADRAMTARRRGVVINPVLETSEIPETMPDP 99
Query: 57 ---EEGCLSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHLQVFV 111
+EGCLS PG R + ++ D +G+ S+ + L AR+ QHE HL F+
Sbjct: 100 DTDDEGCLSVPGESFPTGRAKWARVTGLDADGSPVSIEGTGLFARMLQHETGHLDGFL 157
>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 = 60.1 bits (144), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 38/104 (36%), Positives = 54/104 (51%), Gaps = 9/104 (8%)
Query: 10 GIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYE--EGCLSF---- 63
GIGL+APQ+G++ +++ + G L NP++ +S + + EGCLS
Sbjct: 59 GIGLAAPQIGVSKKMIAVHVTDADGTLYSHALFNPKIISHSVERTYLQGGEGCLSVDREV 118
Query: 64 PGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
PG V R + + A ING + L LPA VFQHE DHL
Sbjct: 119 PGY---VPRYTRITVKATSINGEEVKLRLKGLPAIVFQHEIDHL 159
>pdb|1LQY|A Chain A, Crystal Structure Of Bacillus Stearothermophilus Peptide
Deformylase Complexed With Antibiotic Actinonin
Length = 184
Score = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 35/104 (33%), Positives = 54/104 (51%), Gaps = 9/104 (8%)
Query: 10 GIGLSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKM--IPYEEGCLSF---- 63
GIGL+APQ+ ++ +++ + E G L NP++ +S + + EGCLS
Sbjct: 58 GIGLAAPQINVSKRMIAVHVTDENGTLYSYALFNPKIVSHSVQQCYLTTGEGCLSVDRDV 117
Query: 64 PGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
PG V R + + ++G ++ L LPA VFQHE DHL
Sbjct: 118 PGY---VLRYARITVTGTTLDGEEVTLRLKGLPAIVFQHEIDHL 158
>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 = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 34/108 (31%), Positives = 56/108 (51%), Gaps = 13/108 (12%)
Query: 10 GIGLSAPQVGINVQLM---VFNPVGER-GEGEEIVLVNPRVNKYS--NKMIPYEEGCLSF 63
G+GL+APQ+ I+ +++ V +P E G V+ NP++ +S + + EGCLS
Sbjct: 62 GVGLAAPQLDISKRIIAVHVPSPDPEADGPSLSTVMYNPKILSHSVQDACLGEGEGCLSV 121
Query: 64 ----PGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
PG V R + + D+NG + + L + + V QHE DH+
Sbjct: 122 DREVPGY---VVRHAKITVSYYDMNGEKHKIRLKNYESIVVQHEIDHI 166
>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 = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 34/108 (31%), Positives = 56/108 (51%), Gaps = 13/108 (12%)
Query: 10 GIGLSAPQVGINVQLM---VFNPVGER-GEGEEIVLVNPRVNKYS--NKMIPYEEGCLSF 63
G+GL+APQ+ I+ +++ V +P E G V+ NP++ +S + + EGCLS
Sbjct: 67 GVGLAAPQLDISKRIIAVHVPSPDPEADGPSLSTVMYNPKILSHSVQDACLGEGEGCLSV 126
Query: 64 ----PGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
PG V R + + D+NG + + L + + V QHE DH+
Sbjct: 127 DREVPGY---VVRHAKITVSYYDMNGEKHKIRLKNYESIVVQHEIDHI 171
>pdb|2OS3|A Chain A, Structures Of Actinonin Bound Peptide Deformylases From E.
Faecalis And S. Pyogenes
Length = 205
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 34/111 (30%), Positives = 53/111 (47%), Gaps = 14/111 (12%)
Query: 10 GIGLSAPQVGINVQLMVF----------NPVGERGEGEEIVLVNPRVNKYS--NKMIPYE 57
G+GL+APQ+ ++ +++ NP E +E VL NP++ +S + +
Sbjct: 69 GVGLAAPQIDVSKRIIAVLVPNLPDKEGNPPKEAYSWQE-VLYNPKIVSHSVQDAALSDG 127
Query: 58 EGCLSFPGI-HADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
EGCLS + V R V +D D G + + L A V QHE DH+
Sbjct: 128 EGCLSVDRVVEGYVVRHARVTVDYYDKEGQQHRIKLKGYNAIVVQHEIDHI 178
>pdb|2OS1|A Chain A, Structures Of Actinonin Bound Peptide Deformylases From E.
Faecalis And S. Pyogenes
Length = 188
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 33/108 (30%), Positives = 53/108 (49%), Gaps = 13/108 (12%)
Query: 10 GIGLSAPQVGINVQLMVFNPVGERGEGE----EIVLVNPRVNKYS--NKMIPYEEGCLSF 63
G+GL+APQ+ I+ +++ + E E V+ NP++ +S + + EGCLS
Sbjct: 58 GVGLAAPQLDISKRIIAVHVPSNDPENETPSLSTVMYNPKILSHSVQDVCLGEGEGCLSV 117
Query: 64 ----PGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
PG V R + + D+ G + V L + A V QHE DH+
Sbjct: 118 DRDVPGY---VVRHNKITVSYFDMAGEKHKVRLKNYEAIVVQHEIDHI 162
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 38/121 (31%), Positives = 60/121 (49%), Gaps = 17/121 (14%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLM-VFNP-VGERGEGE------EIVLVNPRVNKYS-- 50
M + M G+GL+APQ+ I+ +++ V P + E GE E ++ NP++ +S
Sbjct: 61 MAEKMGLRGGVGLAAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQ 120
Query: 51 NKMIPYEEGCLSF----PGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDH 106
+ + EGCLS PG V R V +D D +G + + L + V QHE DH
Sbjct: 121 DAALGEGEGCLSVDRNVPGY---VVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDH 177
Query: 107 L 107
+
Sbjct: 178 I 178
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 38/121 (31%), Positives = 60/121 (49%), Gaps = 17/121 (14%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLM-VFNP-VGERGEGE------EIVLVNPRVNKYS-- 50
M + M G+GL+APQ+ I+ +++ V P + E GE E ++ NP++ +S
Sbjct: 61 MAEKMGLRGGVGLAAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQ 120
Query: 51 NKMIPYEEGCLSF----PGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDH 106
+ + EGCLS PG V R V +D D +G + + L + V QHE DH
Sbjct: 121 DAALGEGEGCLSVDRNVPGY---VVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDH 177
Query: 107 L 107
+
Sbjct: 178 I 178
>pdb|2AIE|P Chain P, S.Pneumoniae Polypeptide Deformylase Complexed With Sb-
505684
Length = 203
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 38/121 (31%), Positives = 60/121 (49%), Gaps = 17/121 (14%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLM-VFNP-VGERGEGE------EIVLVNPRVNKYS-- 50
M + M G+GL+APQ+ I+ +++ V P + E GE E ++ NP++ +S
Sbjct: 61 MAEKMGLRGGVGLAAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQ 120
Query: 51 NKMIPYEEGCLSF----PGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDH 106
+ + EGCLS PG V R V +D D +G + + L + V QHE DH
Sbjct: 121 DAALGEGEGCLSVDRNVPGY---VVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDH 177
Query: 107 L 107
+
Sbjct: 178 I 178
>pdb|2OS0|A Chain A, Structures Of Actinonin Bound Peptide Deformylases From E.
Faecalis And S. Pyogenes
Length = 188
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 32/107 (29%), Positives = 52/107 (48%), Gaps = 13/107 (12%)
Query: 11 IGLSAPQVGINVQLMVFNPVGERGEGE----EIVLVNPRVNKYS--NKMIPYEEGCLSF- 63
+GL+APQ+ I+ +++ + E E V+ NP++ +S + + EGCLS
Sbjct: 59 VGLAAPQLDISKRIIAVHVPSNDPENETPSLSTVMYNPKILSHSVQDVCLGEGEGCLSVD 118
Query: 64 ---PGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDHL 107
PG V R + + D+ G + V L + A V QHE DH+
Sbjct: 119 RDVPGY---VVRHNKITVSYFDMAGEKHKVRLKNYEAIVVQHEIDHI 162
>pdb|3SVJ|P Chain P, Strep Peptide Deformylase With A Time Dependent
Thiazolidine Amide
Length = 203
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 37/121 (30%), Positives = 59/121 (48%), Gaps = 17/121 (14%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLM-VFNP-VGERGEGE------EIVLVNPRVNKYS-- 50
M + M G+GL+APQ+ I+ +++ V P + E GE E ++ NP++ +S
Sbjct: 61 MAEKMGLRGGVGLAAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQ 120
Query: 51 NKMIPYEEGCLSF----PGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDH 106
+ + EG LS PG V R V +D D +G + + L + V QHE DH
Sbjct: 121 DAALGEGEGXLSVDRNVPGY---VVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDH 177
Query: 107 L 107
+
Sbjct: 178 I 178
>pdb|1LM6|A Chain A, Crystal Structure Of Peptide Deformylase From
Streptococcus Pneumoniae
Length = 215
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 37/121 (30%), Positives = 59/121 (48%), Gaps = 17/121 (14%)
Query: 1 MFDVMYKTDGIGLSAPQVGINVQLM-VFNP-VGERGEGE------EIVLVNPRVNKYS-- 50
M + M G+GL+APQ+ I+ +++ V P + E GE E ++ NP++ +S
Sbjct: 73 MAEKMGLRGGVGLAAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQ 132
Query: 51 NKMIPYEEGCLSF----PGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDH 106
+ + EG LS PG V R V +D D +G + + L + V QHE DH
Sbjct: 133 DAALGEGEGXLSVDRNVPGY---VVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDH 189
Query: 107 L 107
+
Sbjct: 190 I 190
>pdb|3L87|A Chain A, The Crystal Structure Of Smu.143c From Streptococcus
Mutans Ua159
Length = 238
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 52/109 (47%), Gaps = 12/109 (11%)
Query: 10 GIGLSAPQVGIN---VQLMVFNPVGERGE------GEEIVLVNPRVNKYS--NKMIPYEE 58
G+GL+APQ+ I+ + +++ NP + G + V+ NPR+ +S + + E
Sbjct: 104 GVGLAAPQLDISKRIIAVLIPNPEDKDGNPPKEAYALKEVMYNPRIIAHSVQDAALADGE 163
Query: 59 GCLSFPGI-HADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFDH 106
G LS + V R V I+ D N + + L + V QHE DH
Sbjct: 164 GXLSVDRVVEGYVIRHSRVTIEYYDKNSDKKKLKLKGYQSIVVQHEIDH 212
>pdb|2Q80|A Chain A, Crystal Structure Of Human Geranylgeranyl Pyrophosphate
Synthase Bound To Ggpp
pdb|2Q80|B Chain B, Crystal Structure Of Human Geranylgeranyl Pyrophosphate
Synthase Bound To Ggpp
pdb|2Q80|C Chain C, Crystal Structure Of Human Geranylgeranyl Pyrophosphate
Synthase Bound To Ggpp
pdb|2Q80|D Chain D, Crystal Structure Of Human Geranylgeranyl Pyrophosphate
Synthase Bound To Ggpp
pdb|2Q80|E Chain E, Crystal Structure Of Human Geranylgeranyl Pyrophosphate
Synthase Bound To Ggpp
pdb|2Q80|F Chain F, Crystal Structure Of Human Geranylgeranyl Pyrophosphate
Synthase Bound To Ggpp
Length = 301
Score = 29.6 bits (65), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 58 EGCLSFPGIHADVERPESVKI 78
EG SFP IHA RPES ++
Sbjct: 211 EGKFSFPTIHAIWSRPESTQV 231
>pdb|3S4C|A Chain A, Lactose Phosphorylase In Complex With Sulfate
pdb|3S4D|A Chain A, Lactose Phosphorylase In A Ternary Complex With Cellobiose
And Sulfate
Length = 822
Score = 28.9 bits (63), Expect = 0.70, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 26/49 (53%)
Query: 13 LSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGCL 61
++ + G+ V+ + F PVGE E +++ + N + S + + E CL
Sbjct: 106 ITGERNGVRVETLFFVPVGENAEVQKVTVTNTSDSYKSLTLFSFVEFCL 154
>pdb|3RRS|A Chain A, Crystal Structure Analysis Of Cellobiose Phosphorylase
From Cellulomonas Uda
pdb|3RRS|B Chain B, Crystal Structure Analysis Of Cellobiose Phosphorylase
From Cellulomonas Uda
pdb|3RSY|A Chain A, Cellobiose Phosphorylase From Cellulomonas Uda In Complex
With Sulfate And Glycerol
pdb|3RSY|B Chain B, Cellobiose Phosphorylase From Cellulomonas Uda In Complex
With Sulfate And Glycerol
pdb|3S4A|A Chain A, Cellobiose Phosphorylase From Cellulomonas Uda In Complex
With Cellobiose
pdb|3S4A|B Chain B, Cellobiose Phosphorylase From Cellulomonas Uda In Complex
With Cellobiose
pdb|3S4B|A Chain A, Cellobiose Phosphorylase From Cellulomonas Uda In Complex
With Glucose
pdb|3S4B|B Chain B, Cellobiose Phosphorylase From Cellulomonas Uda In Complex
With Glucose
Length = 822
Score = 28.9 bits (63), Expect = 0.70, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 26/49 (53%)
Query: 13 LSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGCL 61
++ + G+ V+ + F PVGE E +++ + N + S + + E CL
Sbjct: 106 ITGERNGVRVETLFFVPVGENAEVQKVTVTNTSDSYKSLTLFSFVEFCL 154
>pdb|2R47|A Chain A, Crystal Structure Of Mth_862 Protein Of Unknown Function
From Methanothermobacter Thermautotrophicus
pdb|2R47|B Chain B, Crystal Structure Of Mth_862 Protein Of Unknown Function
From Methanothermobacter Thermautotrophicus
pdb|2R47|C Chain C, Crystal Structure Of Mth_862 Protein Of Unknown Function
From Methanothermobacter Thermautotrophicus
pdb|2R47|D Chain D, Crystal Structure Of Mth_862 Protein Of Unknown Function
From Methanothermobacter Thermautotrophicus
pdb|2R47|E Chain E, Crystal Structure Of Mth_862 Protein Of Unknown Function
From Methanothermobacter Thermautotrophicus
Length = 157
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 23/46 (50%)
Query: 59 GCLSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEF 104
G LS PGI +D+E + + DA + G + D+ AR +E
Sbjct: 92 GGLSMPGIGSDIEDVKKLVEDALEEGGELMGLCYMDMFARAGWYEL 137
>pdb|3ISS|A Chain A, Crystal Structure Of Enolpyruvyl-Udp-Glcnac Synthase
(Mura):udp-N- Acetylmuramic Acid:phosphite From
Escherichia Coli
pdb|3ISS|B Chain B, Crystal Structure Of Enolpyruvyl-Udp-Glcnac Synthase
(Mura):udp-N- Acetylmuramic Acid:phosphite From
Escherichia Coli
pdb|3ISS|C Chain C, Crystal Structure Of Enolpyruvyl-Udp-Glcnac Synthase
(Mura):udp-N- Acetylmuramic Acid:phosphite From
Escherichia Coli
pdb|3ISS|D Chain D, Crystal Structure Of Enolpyruvyl-Udp-Glcnac Synthase
(Mura):udp-N- Acetylmuramic Acid:phosphite From
Escherichia Coli
pdb|3ISS|E Chain E, Crystal Structure Of Enolpyruvyl-Udp-Glcnac Synthase
(Mura):udp-N- Acetylmuramic Acid:phosphite From
Escherichia Coli
pdb|3ISS|F Chain F, Crystal Structure Of Enolpyruvyl-Udp-Glcnac Synthase
(Mura):udp-N- Acetylmuramic Acid:phosphite From
Escherichia Coli
pdb|3ISS|G Chain G, Crystal Structure Of Enolpyruvyl-Udp-Glcnac Synthase
(Mura):udp-N- Acetylmuramic Acid:phosphite From
Escherichia Coli
pdb|3ISS|H Chain H, Crystal Structure Of Enolpyruvyl-Udp-Glcnac Synthase
(Mura):udp-N- Acetylmuramic Acid:phosphite From
Escherichia Coli
pdb|3ISS|I Chain I, Crystal Structure Of Enolpyruvyl-Udp-Glcnac Synthase
(Mura):udp-N- Acetylmuramic Acid:phosphite From
Escherichia Coli
pdb|3ISS|J Chain J, Crystal Structure Of Enolpyruvyl-Udp-Glcnac Synthase
(Mura):udp-N- Acetylmuramic Acid:phosphite From
Escherichia Coli
pdb|3ISS|K Chain K, Crystal Structure Of Enolpyruvyl-Udp-Glcnac Synthase
(Mura):udp-N- Acetylmuramic Acid:phosphite From
Escherichia Coli
pdb|3ISS|L Chain L, Crystal Structure Of Enolpyruvyl-Udp-Glcnac Synthase
(Mura):udp-N- Acetylmuramic Acid:phosphite From
Escherichia Coli
Length = 418
Score = 26.9 bits (58), Expect = 2.8, Method: Composition-based stats.
Identities = 12/17 (70%), Positives = 13/17 (76%)
Query: 68 ADVERPESVKIDARDIN 84
A VER SV IDARD+N
Sbjct: 62 AKVERDGSVHIDARDVN 78
>pdb|3KQJ|A Chain A, Mura Binary Complex With Udp-N-Acetylglucosamine
pdb|3KR6|A Chain A, Mura Dead-End Complex With Fosfomycin
Length = 419
Score = 26.9 bits (58), Expect = 2.8, Method: Composition-based stats.
Identities = 12/17 (70%), Positives = 13/17 (76%)
Query: 68 ADVERPESVKIDARDIN 84
A VER SV IDARD+N
Sbjct: 62 AKVERXGSVHIDARDVN 78
>pdb|3SWD|A Chain A, E. Coli Mura In Complex With Udp-N-Acetylmuramic Acid
And Covalent Adduct Of Pep With Cys115
pdb|3SWD|B Chain B, E. Coli Mura In Complex With Udp-N-Acetylmuramic Acid
And Covalent Adduct Of Pep With Cys115
pdb|3SWD|C Chain C, E. Coli Mura In Complex With Udp-N-Acetylmuramic Acid
And Covalent Adduct Of Pep With Cys115
pdb|3SWD|D Chain D, E. Coli Mura In Complex With Udp-N-Acetylmuramic Acid
And Covalent Adduct Of Pep With Cys115
pdb|3SWD|E Chain E, E. Coli Mura In Complex With Udp-N-Acetylmuramic Acid
And Covalent Adduct Of Pep With Cys115
pdb|3SWD|F Chain F, E. Coli Mura In Complex With Udp-N-Acetylmuramic Acid
And Covalent Adduct Of Pep With Cys115
pdb|3SWD|G Chain G, E. Coli Mura In Complex With Udp-N-Acetylmuramic Acid
And Covalent Adduct Of Pep With Cys115
pdb|3SWD|H Chain H, E. Coli Mura In Complex With Udp-N-Acetylmuramic Acid
And Covalent Adduct Of Pep With Cys115
pdb|3SWD|I Chain I, E. Coli Mura In Complex With Udp-N-Acetylmuramic Acid
And Covalent Adduct Of Pep With Cys115
pdb|3SWD|J Chain J, E. Coli Mura In Complex With Udp-N-Acetylmuramic Acid
And Covalent Adduct Of Pep With Cys115
pdb|3SWD|K Chain K, E. Coli Mura In Complex With Udp-N-Acetylmuramic Acid
And Covalent Adduct Of Pep With Cys115
pdb|3SWD|L Chain L, E. Coli Mura In Complex With Udp-N-Acetylmuramic Acid
And Covalent Adduct Of Pep With Cys115
Length = 418
Score = 26.9 bits (58), Expect = 2.9, Method: Composition-based stats.
Identities = 12/17 (70%), Positives = 13/17 (76%)
Query: 68 ADVERPESVKIDARDIN 84
A VER SV IDARD+N
Sbjct: 62 AKVERXGSVHIDARDVN 78
>pdb|2Z2C|A Chain A, Mura Inhibited By Unag-Cnicin Adduct
pdb|2Z2C|B Chain B, Mura Inhibited By Unag-Cnicin Adduct
pdb|2Z2C|C Chain C, Mura Inhibited By Unag-Cnicin Adduct
pdb|2Z2C|D Chain D, Mura Inhibited By Unag-Cnicin Adduct
Length = 423
Score = 26.9 bits (58), Expect = 2.9, Method: Composition-based stats.
Identities = 12/17 (70%), Positives = 13/17 (76%)
Query: 68 ADVERPESVKIDARDIN 84
A VER SV IDARD+N
Sbjct: 62 AKVERXGSVHIDARDVN 78
>pdb|4B1B|A Chain A, Crystal Structure Of Plasmodium Falciparum Oxidised
Thioredoxin Reductase At 2.9 Angstrom
pdb|4B1B|B Chain B, Crystal Structure Of Plasmodium Falciparum Oxidised
Thioredoxin Reductase At 2.9 Angstrom
Length = 542
Score = 26.9 bits (58), Expect = 3.1, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 26 VFNPVGERGE--GEEIVLVNPRVNKYSNKMIPYEEGCLSFPGIHADVERPESV 76
V +G +G+ G + +N VNK +NK+I C + P I A + E+V
Sbjct: 311 VLYAIGRKGDIDGLNLESLNMNVNKSNNKIIADHLSCTNIPSIFAVGDVAENV 363
>pdb|1UAE|A Chain A, Structure Of Udp-N-Acetylglucosamine Enolpyruvyl
Transferase
Length = 419
Score = 26.6 bits (57), Expect = 3.3, Method: Composition-based stats.
Identities = 12/17 (70%), Positives = 13/17 (76%)
Query: 68 ADVERPESVKIDARDIN 84
A VER SV IDARD+N
Sbjct: 62 AKVERNGSVHIDARDVN 78
>pdb|1A2N|A Chain A, Structure Of The C115a Mutant Of Mura Complexed With The
Fluorinated Analog Of The Reaction Tetrahedral
Intermediate
Length = 419
Score = 26.6 bits (57), Expect = 3.3, Method: Composition-based stats.
Identities = 12/17 (70%), Positives = 13/17 (76%)
Query: 68 ADVERPESVKIDARDIN 84
A VER SV IDARD+N
Sbjct: 62 AKVERNGSVHIDARDVN 78
>pdb|3AFJ|A Chain A, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase Triple Mutant
pdb|3AFJ|B Chain B, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase Triple Mutant
Length = 842
Score = 26.6 bits (57), Expect = 3.7, Method: Composition-based stats.
Identities = 11/49 (22%), Positives = 25/49 (51%)
Query: 13 LSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGCL 61
++ + G+ V+ + F P+GE E +++ + N + + + E CL
Sbjct: 126 ITGERNGLKVETLFFVPLGENAEVQKVTVTNTSDAPKTATLFSFVEFCL 174
>pdb|3ACT|A Chain A, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase Histidine Mutant
pdb|3ACT|B Chain B, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase Histidine Mutant
Length = 842
Score = 26.6 bits (57), Expect = 3.7, Method: Composition-based stats.
Identities = 11/49 (22%), Positives = 25/49 (51%)
Query: 13 LSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGCL 61
++ + G+ V+ + F P+GE E +++ + N + + + E CL
Sbjct: 126 ITGERNGLKVETLFFVPLGENAEVQKVTVTNTSDAPKTATLFSFVEFCL 174
>pdb|2CQS|A Chain A, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase Crystallized From Ammonium Sulfate
pdb|2CQS|B Chain B, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase Crystallized From Ammonium Sulfate
pdb|2CQT|A Chain A, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase Crystallized From SodiumPOTASSIUM
PHOSPHATE
pdb|2CQT|B Chain B, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase Crystallized From SodiumPOTASSIUM
PHOSPHATE
pdb|3QFY|A Chain A, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase Complexed With Sulfate And Isofagomine
pdb|3QFY|B Chain B, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase Complexed With Sulfate And Isofagomine
pdb|3QFZ|A Chain A, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase Complexed With Sulfate And
1-Deoxynojirimycin
pdb|3QFZ|B Chain B, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase Complexed With Sulfate And
1-Deoxynojirimycin
pdb|3QG0|A Chain A, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase Complexed With Phosphate And
1-Deoxynojirimycin
pdb|3QG0|B Chain B, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase Complexed With Phosphate And
1-Deoxynojirimycin
Length = 842
Score = 26.6 bits (57), Expect = 3.7, Method: Composition-based stats.
Identities = 11/49 (22%), Positives = 25/49 (51%)
Query: 13 LSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGCL 61
++ + G+ V+ + F P+GE E +++ + N + + + E CL
Sbjct: 126 ITGERNGLKVETLFFVPLGENAEVQKVTVTNTSDAPKTATLFSFVEFCL 174
>pdb|3U1N|A Chain A, Structure Of The Catalytic Core Of Human Samhd1
pdb|3U1N|B Chain B, Structure Of The Catalytic Core Of Human Samhd1
pdb|3U1N|C Chain C, Structure Of The Catalytic Core Of Human Samhd1
pdb|3U1N|D Chain D, Structure Of The Catalytic Core Of Human Samhd1
Length = 528
Score = 26.6 bits (57), Expect = 3.9, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 47 NKYSNKM-IPYEEGCLSFPGIHADVERPESVKIDARDINGARFSVSLSDLPARVFQHEFD 105
N++ + + + Y GCL +HA E+ ++I RD+ + + DL F H FD
Sbjct: 65 NRFEHSLGVGYLAGCL----VHALGEKQPELQISERDVLCVQIAGLCHDLGHGPFSHXFD 120
>pdb|3ACS|A Chain A, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase W488f Mutant
pdb|3ACS|B Chain B, Crystal Structure Of Cellvibrio Gilvus Cellobiose
Phosphorylase W488f Mutant
Length = 842
Score = 26.6 bits (57), Expect = 3.9, Method: Composition-based stats.
Identities = 11/49 (22%), Positives = 25/49 (51%)
Query: 13 LSAPQVGINVQLMVFNPVGERGEGEEIVLVNPRVNKYSNKMIPYEEGCL 61
++ + G+ V+ + F P+GE E +++ + N + + + E CL
Sbjct: 126 ITGERNGLKVETLFFVPLGENAEVQKVTVTNTSDAPKTATLFSFVEFCL 174
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
0.321 0.141 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,457,176
Number of Sequences: 62578
Number of extensions: 132526
Number of successful extensions: 348
Number of sequences better than 100.0: 71
Number of HSP's better than 100.0 without gapping: 67
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 234
Number of HSP's gapped (non-prelim): 71
length of query: 112
length of database: 14,973,337
effective HSP length: 76
effective length of query: 36
effective length of database: 10,217,409
effective search space: 367826724
effective search space used: 367826724
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)