RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780297|ref|YP_003064710.1| peptide deformylase [Candidatus Liberibacter asiaticus str. psy62] (170 letters) >3oca_A Peptide deformylase; ssgcid, structur genomics, seattle structural genomics center for infectious hydrolase; 2.40A {Ehrlichia chaffeensis} Length = 209 Score = 190 bits (485), Expect = 9e-50 Identities = 69/182 (37%), Positives = 100/182 (54%), Gaps = 17/182 (9%) Query: 1 MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVV 60 M +V PD L S +EK++ I L+D+M E M++ G+GLAAVQ+GV R++V Sbjct: 22 MSVLSIVTVPDKRLSLCSEEVEKVDQSIRKLVDDMFETMHANQGLGLAAVQVGVHKRILV 81 Query: 61 IDLQD-----------------HAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRAD 103 +++ + + P INPKI+ S + +EGCLS+P Y Sbjct: 82 MNVPEEFEDSEDIENVEDKIEGYELYGGPYCIINPKIVDISQEKVKLKEGCLSVPGYFDY 141 Query: 104 VKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMS 163 + R I V+Y+D N II A G LA CLQHE+DHLNG +F+ +LS+ KRD +K+ Sbjct: 142 IVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHEIDHLNGTVFLKYLSKFKRDFAIEKVK 201 Query: 164 KL 165 K Sbjct: 202 KK 203 >1n5n_A Peptide deformylase; metalloenzyme, drug design, deformylation, hydrolase; 1.80A {Pseudomonas aeruginosa} SCOP: d.167.1.1 PDB: 1s17_A* 1ix1_A* 1lry_A* Length = 180 Score = 188 bits (480), Expect = 4e-49 Identities = 73/165 (44%), Positives = 105/165 (63%), Gaps = 2/165 (1%) Query: 1 MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVV 60 M ++ FPDP LR +++P+E ++ + LID+M E MY GIGLAA Q+ V R+VV Sbjct: 13 MAILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVV 72 Query: 61 IDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQ 120 +DL + + P VFINP+ +++ YQEGCLS+P + +V R + ++ +D + Sbjct: 73 MDLSED--KSEPRVFINPEFEPLTEEMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGN 130 Query: 121 HQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKL 165 A+GLLA C+QHE DHLNG LF+D+LS LKRD I KK+ K Sbjct: 131 PFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQ 175 >1lme_A PDF, peptide deformylase; thermophIle, metalloenzyme, deformylation, structural genomics, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: d.167.1.1 Length = 176 Score = 177 bits (450), Expect = 1e-45 Identities = 58/161 (36%), Positives = 96/161 (59%), Gaps = 5/161 (3%) Query: 5 PLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQ 64 + +F DP+LR+ ++P+ K + ++ I+ M+E MY DG+GLAA Q+G+ R V+D+ Sbjct: 15 RIRVFGDPVLRKRAKPVTKFDENLKKTIERMIETMYHYDGVGLAAPQVGISQRFFVMDVG 74 Query: 65 DHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQII 124 + P+ INP+I+ + V +EGCLS P+ +++RS I V+Y + ++ Sbjct: 75 NG-----PVAVINPEILEIDPETEVAEEGCLSFPEIFVEIERSKRIKVKYQNTRGEYVEE 129 Query: 125 YADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKL 165 +G A QHE DHLNG+L ID +S KR ++ KK+ + Sbjct: 130 ELEGYAARVFQHEFDHLNGVLIIDRISPAKRLLLRKKLMDI 170 >2w3t_A Peptide deformylase; protein biosynthesis, iron, nickel, hydrolase, metal-binding; 1.69A {Escherichia coli} PDB: 2w3u_A Length = 188 Score = 175 bits (445), Expect = 4e-45 Identities = 69/166 (41%), Positives = 114/166 (68%), Gaps = 3/166 (1%) Query: 4 KPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDL 63 ++ PD LR+V++P+E++N++I ++D+M E MY+ +GIGLAA Q+ + R++VID+ Sbjct: 3 LQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDV 62 Query: 64 QDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQI 123 ++ R +V INP+++ + +EGCLSIP+ RA V R+ + +R +D + + Sbjct: 63 SEN--RDERLVLINPELLE-KSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFE 119 Query: 124 IYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQLR 169 + ADGLLA C+QHE+DHL G LF+D+LS LK+ I +K+ KL +L+ Sbjct: 120 LEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRLK 165 >3e3u_A Peptide deformylase; metallo-enzyme, hydrolase, iron, metal-binding, protein biosynthesis; HET: NVC; 1.56A {Mycobacterium tuberculosis} Length = 197 Score = 173 bits (440), Expect = 2e-44 Identities = 50/176 (28%), Positives = 72/176 (40%), Gaps = 12/176 (6%) Query: 1 MVKKPLVIFPDPILRRVSRPIE-----KINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVL 55 M P+ I DP+L + P+ + +D+ LI M + M + +G+GLAA QIG Sbjct: 1 MAVVPIRIVGDPVLHTATTPVTVAADGSLPADLAQLIATMYDTMDAANGVGLAANQIGCS 60 Query: 56 YRLVVIDLQD-------HAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSA 108 RL V D V +I D EGCLS+P R+ Sbjct: 61 LRLFVYDCAADRAMTARRRGVVINPVLETSEIPETMPDPDTDDEGCLSVPGESFPTGRAK 120 Query: 109 FITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSK 164 + V +D + I GL A LQHE HL+G L++D L + + Sbjct: 121 WARVTGLDADGSPVSIEGTGLFARMLQHETGHLDGFLYLDRLIGRYARNAKRAVKS 176 >3dld_A Peptide deformylase; bacterial blight, XOO1075, xanthomonas oryzae PV. oryzae KACC10331, hydrolase; 2.60A {Xanthomonas oryzae PV} Length = 171 Score = 166 bits (421), Expect = 3e-42 Identities = 48/170 (28%), Positives = 73/170 (42%), Gaps = 7/170 (4%) Query: 1 MVKKPLVIFPDPILRRVSRPIEKINSD-IMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLV 59 M++ ++ D L RV+ + + S + L+ +M E M + G+GLAA QI V +L+ Sbjct: 1 MIR-DIIRMGDKRLLRVAPQVTNLGSAELHALVSDMFETMGAAHGVGLAAPQIAVDLQLM 59 Query: 60 VIDLQDHAHRKN-----PMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRY 114 V + N +I SD+ EGCLSIP RA + R +I R Sbjct: 60 VFGFEASERYPEAPAVPLTALANAQIEPLSDEMENGWEGCLSIPGLRAVIPRYRYIRYRG 119 Query: 115 MDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSK 164 + A+G A +QHE DHL G L+ + +S Sbjct: 120 FAPDGSPIEREAEGFHARVVQHEYDHLVGRLYPSRIENFDTFGFDDVLSY 169 >1v3y_A Peptide deformylase; protein synthesis, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.81A {Thermus thermophilus} SCOP: d.167.1.1 Length = 192 Score = 152 bits (386), Expect = 3e-38 Identities = 58/175 (33%), Positives = 92/175 (52%), Gaps = 13/175 (7%) Query: 1 MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVV 60 MV P+ ++ DP+LRR +RP+E + I L ++MLE M+ G+GLAA QIG+ RL V Sbjct: 1 MVY-PIRLYGDPVLRRKARPVEDFS-GIKRLAEDMLETMFEAKGVGLAAPQIGLSQRLFV 58 Query: 61 I----------DLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPD-YRADVKRSAF 109 + + + + +IT+ + EGCLS+P Y +V R+ Sbjct: 59 AVEYADEPEGEEERPLRELVRRVYVVANPVITYREGLVEGTEGCLSLPGLYSEEVPRAER 118 Query: 110 ITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSK 164 I V Y D + +++ +G +A QHE+DHL+GILF + L + KR+ + Sbjct: 119 IRVEYQDEEGRGRVLELEGYMARVFQHEIDHLDGILFFERLPKPKREAFLEANRA 173 >1zxz_A PDF, peptide deformylase, mitochondrial; PDF1A, eukaryote, higher plant, zinc ION, hydrolase; 2.80A {Arabidopsis thaliana} PDB: 1zy0_A 1zy1_A Length = 197 Score = 142 bits (358), Expect = 4e-35 Identities = 54/184 (29%), Positives = 87/184 (47%), Gaps = 17/184 (9%) Query: 1 MVKKPLVIFPDPILRRVSRPIEKI---NSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYR 57 M +V DP+L +R ++ + I +ID+M++VM G+GLAA QIGV R Sbjct: 1 MDLPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPGVGLAAPQIGVPLR 60 Query: 58 LVVIDLQDHAHRKNP--------------MVFINPKIITFSDDFSVYQEGCLSIPDYRAD 103 ++V++ P MV +NP + S+ +++ EGCLS+ +RA Sbjct: 61 IIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCLSVDGFRAA 120 Query: 104 VKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMS 163 V+R + V D + + A G A LQHE DHL+G L++D + + Sbjct: 121 VERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTFRTVDNLDL 180 Query: 164 KLVQ 167 L + Sbjct: 181 PLAE 184 >1y6h_A Peptide deformylase; open and close conformation, PDF, hydrolase; 2.20A {Leptospira interrogans} SCOP: d.167.1.1 PDB: 1sv2_A* 1vey_A* 1vev_A 1vez_A 1szz_A* Length = 177 Score = 141 bits (356), Expect = 9e-35 Identities = 57/175 (32%), Positives = 87/175 (49%), Gaps = 8/175 (4%) Query: 4 KPLVIFPDPILRRVSRPI---EKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVV 60 + ++ DPILR++S P+ E + LI +M + M +G+GLAA QIG+L ++VV Sbjct: 3 RKILRMGDPILRKISEPVTEDEIQTKEFKKLIRDMFDTMRHAEGVGLAAPQIGILKQIVV 62 Query: 61 IDLQD-----HAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYM 115 + +D + +NP I + D S + EGCLS+P R V+R I +++M Sbjct: 63 VGSEDNERYPGTPDVPERIILNPVITPLTKDTSGFWEGCLSVPGMRGYVERPNQIRMQWM 122 Query: 116 DCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQLRD 170 D DG A QHE DHL GIL++D L K + + + D Sbjct: 123 DEKGNQFDETIDGYKAIVYQHECDHLQGILYVDRLKDTKLFGFNETLDSSHNVLD 177 >3cpm_A Peptide deformylase, chloroplast; alpha beta, hydrolase, iron, metal-binding, plastid, protein biosynthesis, transit peptide; 2.40A {Arabidopsis thaliana} Length = 193 Score = 140 bits (354), Expect = 1e-34 Identities = 59/167 (35%), Positives = 90/167 (53%) Query: 1 MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVV 60 +V +PDPILR ++ I+ + ++ NL+D M +VMY TDGIGL+A Q+G+ +L+V Sbjct: 14 ETPLKIVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDGIGLSAPQVGLNVQLMV 73 Query: 61 IDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQ 120 + +V +NPKI +SD + EGCLS P A+V R + + D + Sbjct: 74 FNPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGE 133 Query: 121 HQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQ 167 I L A QHE DHL G+LF D ++ D I +++ L + Sbjct: 134 RFSISLSRLPARIFQHEYDHLEGVLFFDRMTDQVLDSIREELEALEK 180 >1rl4_A Formylmethionine deformylase; crystal engineering, drug design, malaria, PDF, peptide deformylase, hydrolase; HET: BRR BL5; 2.18A {Plasmodium falciparum 3D7} SCOP: d.167.1.1 PDB: 1rqc_A 1jym_A Length = 188 Score = 136 bits (343), Expect = 2e-33 Identities = 47/164 (28%), Positives = 86/164 (52%), Gaps = 1/164 (0%) Query: 5 PLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQ 64 +V +PDPILRR S + + ++ ++ M ++MY + GIGL+A Q+ + R++V + Sbjct: 10 KIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNAL 69 Query: 65 DHAHRKNPMVFINPKIITFSDDFSV-YQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQI 123 ++ I + EGCLS P V+R + +++ Y D N + Sbjct: 70 YEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHL 129 Query: 124 IYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQ 167 G+ + QHE DHLNG LFID ++++ + + K+++L++ Sbjct: 130 KILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIR 173 >2ew5_A Peptide deformylase; inhibitor, hydrolase; HET: Y12; 2.20A {Helicobacter pylori} PDB: 2ew6_A* 2ew7_A Length = 181 Score = 134 bits (337), Expect = 1e-32 Identities = 59/164 (35%), Positives = 104/164 (63%), Gaps = 4/164 (2%) Query: 5 PLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDL- 63 ++ +P ILR +S+ + ++ + +D+M E M +++GIGLAA+Q+G+ R+++I+L Sbjct: 4 EIIHYPSKILRTISKEVVSFDAKLHQQLDDMYETMIASEGIGLAAIQVGLPLRMLIINLP 63 Query: 64 --QDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQH 121 H+++ + INPK I +Y+EGCLS+P + +V+R + + Y + A+ Sbjct: 64 QEDGVQHKEDCLEIINPKFIETGGSM-MYKEGCLSVPGFYEEVERFEKVKIEYQNRFAEV 122 Query: 122 QIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKL 165 +++ A LLA +QHE+DHLNG+LF+D LS LKR K++ +L Sbjct: 123 KVLEASELLAVAIQHEIDHLNGVLFVDKLSILKRKKFEKELKEL 166 >1lm4_A Peptide deformylase PDF1; metalloenzyme, hydrolase; 1.45A {Staphylococcus aureus} SCOP: d.167.1.1 PDB: 1lqw_A 2ai9_A 1lmh_A 1q1y_A* Length = 194 Score = 133 bits (336), Expect = 2e-32 Identities = 46/172 (26%), Positives = 80/172 (46%), Gaps = 17/172 (9%) Query: 1 MVKKPLVIFPDPILRRVSRPIEK-INSDIMNLIDNMLEVMYST------------DGIGL 47 + K ++ P LR+ + +E + + + M E + ++ G+GL Sbjct: 13 LTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGL 72 Query: 48 AAVQIGVLYRLVVIDL-QDHAHRKNPMVFINPKIITFSDDFSVY--QEGCLSIPDYRAD- 103 AA QI + R++ + + D + + + +NPKI++ S + EGCLS+ D A Sbjct: 73 AAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGL 132 Query: 104 VKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKR 155 V R IT++ D + G A QHE+DHLNG++F DH+ + Sbjct: 133 VHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHP 184 >3g5k_A Peptide deformylase, mitochondrial; actinonin, hydrolase, iron, metal- binding, mitochondrion, protein biosynthesis, transit peptide; HET: BB2; 1.70A {Homo sapiens} PDB: 3g5p_A Length = 183 Score = 129 bits (326), Expect = 2e-31 Identities = 49/179 (27%), Positives = 84/179 (46%), Gaps = 18/179 (10%) Query: 1 MVKKPLVIFPDPILRRVSRPIEKI---NSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYR 57 M + DP+LR V+ P+E+ ++ L +++VM +GL+A Q+GV + Sbjct: 2 MSFSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQ 61 Query: 58 LVVIDLQDHAHRKNPM--------------VFINPKIITFSDDFSVYQEGCLSIPDYRAD 103 ++ ++L + R+ P VF+NP + + EGC S+ + A Sbjct: 62 VLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLAC 121 Query: 104 VKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLS-RLKRDMITKK 161 V R + + +D N + + A G A +QHE+DHL G LFID + R ++ K Sbjct: 122 VPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMK 180 >1xeo_A Peptide deformylase; cobalt deformylase, formate, hydrolase; 1.30A {Escherichia coli BL21} SCOP: d.167.1.1 PDB: 1bs5_A 1bs6_A 1bs7_A 1bs8_A 1bsj_A* 1bsk_A* 1bsz_A* 1g27_A* 1bs4_A* 1icj_A* 1lru_A* 1xem_A 1xen_A 1g2a_A 2ai8_A* 3k6l_A* 1dff_A 1def_A 2kmn_A* 2def_A ... Length = 168 Score = 129 bits (325), Expect = 3e-31 Identities = 64/166 (38%), Positives = 110/166 (66%), Gaps = 3/166 (1%) Query: 4 KPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDL 63 ++ PD LR+V++P+E++N++I ++D+M E MY+ +GIGLAA Q+ + R++VID+ Sbjct: 3 LQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDV 62 Query: 64 QDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQI 123 ++ ++ + + + + +EGCLSIP+ RA V R+ + +R +D + + Sbjct: 63 SEN---RDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFE 119 Query: 124 IYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSKLVQLR 169 + ADGLLA C+QHE+DHL G LF+D+LS LK+ I +K+ KL +L+ Sbjct: 120 LEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRLK 165 >1ws0_A Peptide deformylase 1; alpha + beta topology, hydrolase; 1.70A {Bacillus cereus} PDB: 1ws1_A* Length = 156 Score = 119 bits (299), Expect = 3e-28 Identities = 44/156 (28%), Positives = 77/156 (49%), Gaps = 4/156 (2%) Query: 1 MVKKPLVIFPDPILRRVSRPIEKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVV 60 M ++ P+ +L + + ++ L+ +M E M DG+GLAA Q+GV ++ V Sbjct: 1 MAVLEIIKHPNEVLETPCERVINFDKKLVKLLKDMHETMLIADGVGLAAPQVGVSLQVAV 60 Query: 61 IDLQDHAHRKNPMVFINPKIITFSDDFSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQ 120 + + + I V EGCLS P +V+R+ +I VR + + Sbjct: 61 V----DVDDDTGKIELINPSILEKRGEQVGPEGCLSFPGLYGEVERADYIKVRAQNRRGK 116 Query: 121 HQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRD 156 ++ A+G LA +QHE+DHL+G+LF ++R + Sbjct: 117 VFLLEAEGFLARAIQHEIDHLHGVLFTSKVTRYYEE 152 >2okl_A Peptide deformylase 2; hydrolase; HET: BB2 CIT; 1.70A {Bacillus cereus atcc 14579} PDB: 1lqy_A* Length = 185 Score = 116 bits (290), Expect = 3e-27 Identities = 55/181 (30%), Positives = 81/181 (44%), Gaps = 16/181 (8%) Query: 1 MVKKPLVIFPDPILRRVSRPIEKINSD-------------IMNLIDNMLEVMYSTDGIGL 47 + K ++ DPILR V+ + S+ I + M E GIGL Sbjct: 3 LTMKDVIREGDPILRNVAEEVSLPASEEDTTTLKEMIEFVINSQDPEMAEKYSLRPGIGL 62 Query: 48 AAVQIGVLYRLVVIDLQDHAHRKNPMVFINPKIITFSDDFSVYQ--EGCLSIP-DYRADV 104 AA QIGV +++ + + D NPKII+ S + + Q EGCLS+ + V Sbjct: 63 AAPQIGVSKKMIAVHVTDADGTLYSHALFNPKIISHSVERTYLQGGEGCLSVDREVPGYV 122 Query: 105 KRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITKKMSK 164 R ITV+ N + + GL A QHE+DHLNG++F DH+++ Sbjct: 123 PRYTRITVKATSINGEEVKLRLKGLPAIVFQHEIDHLNGVMFYDHINKENPFAAPDDSKP 182 Query: 165 L 165 L Sbjct: 183 L 183 >2os0_A Peptide deformylase; PDF, hydrolase; 1.30A {Enterococcus faecalis} PDB: 2os1_A* 3g6n_A 3cmd_A Length = 188 Score = 113 bits (284), Expect = 2e-26 Identities = 47/182 (25%), Positives = 82/182 (45%), Gaps = 20/182 (10%) Query: 1 MVKKPLVIFPDPILRRVSRPIE-KINSDIMNLIDNMLEVMYSTD------------GIGL 47 + K ++ +P LR V+ + I + L ++ML + ++ +GL Sbjct: 2 ITMKDIIREGNPTLRAVAEEVPVPITEEDRQLGEDMLTFLKNSQDPVKAEELQLRGDVGL 61 Query: 48 AAVQIGVLYRLVVIDLQDHAHRKN----PMVFINPKIITFS--DDFSVYQEGCLSIP-DY 100 AA Q+ + R++ + + + V NPKI++ S D EGCLS+ D Sbjct: 62 AAPQLDISKRIIAVHVPSNDPENETPSLSTVMYNPKILSHSVQDVCLGEGEGCLSVDRDV 121 Query: 101 RADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRDMITK 160 V R ITV Y D + + A +QHE+DH+NGI+F DH+++ + + Sbjct: 122 PGYVVRHNKITVSYFDMAGEKHKVRLKNYEAIVVQHEIDHINGIMFYDHINKENPFALKE 181 Query: 161 KM 162 + Sbjct: 182 GV 183 >2aia_A Peptide deformylase; hydrolase; HET: SB8; 1.70A {Streptococcus pneumoniae} PDB: 2ai7_A* 2aie_P* 1lm6_A 2os3_A* Length = 203 Score = 112 bits (281), Expect = 3e-26 Identities = 46/189 (24%), Positives = 80/189 (42%), Gaps = 24/189 (12%) Query: 1 MVKKPLVIFPDPILRRVSRPIEKINSDIMNLID-------------NMLEVMYSTDGIGL 47 + ++ +P LR V+ + SD ++ M E M G+GL Sbjct: 14 IDMCDIIREGNPSLRTVAEEVTFPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLRGGVGL 73 Query: 48 AAVQIGVLYRLVVIDLQD--------HAHRKNPMVFINPKIITFSDDFSVY--QEGCLSI 97 AA Q+ + R++ + + + + NPKI++ S + EGCLS+ Sbjct: 74 AAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAALGEGEGCLSV 133 Query: 98 P-DYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHELDHLNGILFIDHLSRLKRD 156 + V R A +TV Y D + + I G + +QHE+DH+NGI+F D ++ Sbjct: 134 DRNVPGYVVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFYDRINEKDPF 193 Query: 157 MITKKMSKL 165 + + L Sbjct: 194 AVKDGLLIL 202 >1ug3_A EIF4GI, eukaryotic protein synthesis initiation factor 4G; heat repeat, translation; 2.24A {Homo sapiens} SCOP: a.118.1.14 a.118.1.14 Length = 339 Score = 28.3 bits (63), Expect = 0.90 Identities = 18/140 (12%), Positives = 41/140 (29%), Gaps = 6/140 (4%) Query: 32 IDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRKNPMV-----FINPKIITFSDD 86 +++M E + + ++ + V L+ A + M + ++ + Sbjct: 24 LNDMKEAVQCVQELASPSLLFIFVRHGVESTLERSAIAREHMGQLLHQLLCAGHLSTAQY 83 Query: 87 FSVYQEGCLSIPDYRADVKRSAFITVRYMDCNAQHQIIYADGLLATCLQHEL-DHLNGIL 145 + E D D+ + Q + L + L Sbjct: 84 YQGLYEILELAEDMEIDIPHVWLYLAELVTPILQEGGVPMGELFREITKPLRPLGKAASL 143 Query: 146 FIDHLSRLKRDMITKKMSKL 165 ++ L L + M KK+ L Sbjct: 144 LLEILGLLCKSMGPKKVGTL 163 >1hsj_A Fusion protein consisting of staphylococcus accessary regulator protein R and maltose...; novel fold for DNA binding; HET: GLC; 2.30A {Escherichia coli} SCOP: a.4.5.28 c.94.1.1 Length = 487 Score = 26.4 bits (57), Expect = 3.2 Identities = 9/71 (12%), Positives = 30/71 (42%), Gaps = 12/71 (16%) Query: 22 EKINSDIMNLIDNMLEVMYSTDGIGLAAVQIGVLYRLVVIDLQDHAHRK-NPMVFINPKI 80 ++ M+ I+++ +++ +T Q+ +R D + + + +N + Sbjct: 366 TNAAAEFMSKINDINDLVNATF-------QVKKFFR----DTKKKFNLNYEEIYILNHIL 414 Query: 81 ITFSDDFSVYQ 91 + S++ S + Sbjct: 415 RSESNEISSKE 425 >3m3m_A Glutathione S-transferase; PSI-II, structural genomics, protein structure initiative; HET: GTT; 1.75A {Pseudomonas fluorescens} Length = 210 Score = 25.4 bits (55), Expect = 6.6 Identities = 11/59 (18%), Positives = 21/59 (35%), Gaps = 2/59 (3%) Query: 47 LAAVQIGVLYRLVVIDLQDHAHRKNPMVFINP--KIITFSDDFSVYQEGCLSIPDYRAD 103 L +G+ Y +D+ + + NP KI + +I ++ AD Sbjct: 20 LMLNLLGLPYEWQAVDILGGDTQTEAFLAKNPNGKIPVLELEDGTCLWESNAILNFLAD 78 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.327 0.143 0.418 Gapped Lambda K H 0.267 0.0565 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,490,836 Number of extensions: 66798 Number of successful extensions: 317 Number of sequences better than 10.0: 1 Number of HSP's gapped: 283 Number of HSP's successfully gapped: 27 Length of query: 170 Length of database: 5,693,230 Length adjustment: 86 Effective length of query: 84 Effective length of database: 3,608,246 Effective search space: 303092664 Effective search space used: 303092664 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 53 (24.6 bits)