RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2880
(166 letters)
>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 = 262 bits (673), Expect = 2e-91
Identities = 77/166 (46%), Positives = 124/166 (74%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLI 60
M +L I+ +PD RL+ IA+P+ D ++++I +M ETMY A GIGLAA+QV++HK++++
Sbjct: 13 MAILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVV 72
Query: 61 LDISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMF 120
+D+S++ ++ +VFINP+ ++E Y EGCLS+PG + + R +++R+ AL+ +G F
Sbjct: 73 MDLSEDKSEPRVFINPEFEPLTEEMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPF 132
Query: 121 EIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
E +AEGLLA+C+QHE DHLNGK+F++YLS K++RI KK K ++
Sbjct: 133 EEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHRQ 178
>2w3t_A Peptide deformylase; protein biosynthesis, iron, nickel, hydrolase,
metal-binding; 1.69A {Escherichia coli} PDB: 2w3u_A
Length = 188
Score = 252 bits (647), Expect = 2e-87
Identities = 72/165 (43%), Positives = 122/165 (73%), Gaps = 1/165 (0%)
Query: 2 TLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL 61
++L +++ PD RL+K+A+P+ E + +++I+ +M ETMY GIGLAA+QVDIH++++++
Sbjct: 1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVI 60
Query: 62 DISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
D+S+N ++ V INP+++ S E EGCLS+P + R++++++ AL+ +GK FE
Sbjct: 61 DVSENRDERLVLINPELLEKSGE-TGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFE 119
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
+ A+GLLAIC+QHE+DHL GK+F++YLS K++RI +K K +
Sbjct: 120 LEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 164
>1xeo_A Peptide deformylase; cobalt deformylase, formate, hydrolase; 1.30A
{Escherichia coli} 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* 4al3_A
4al2_A 3k6l_A* 1dff_A 1def_A ...
Length = 168
Score = 251 bits (645), Expect = 2e-87
Identities = 72/164 (43%), Positives = 122/164 (74%), Gaps = 1/164 (0%)
Query: 2 TLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL 61
++L +++ PD RL+K+A+P+ E + +++I+ +M ETMY GIGLAA+QVDIH++++++
Sbjct: 1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVI 60
Query: 62 DISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
D+S+N ++ V INP+++ S E EGCLS+P + R++++++ AL+ +GK FE
Sbjct: 61 DVSENRDERLVLINPELLEKSGE-TGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFE 119
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIK 165
+ A+GLLAIC+QHE+DHL GK+F++YLS K++RI +K K +
Sbjct: 120 LEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDR 163
>3qu1_A Peptide deformylase 2; structural genomics, center for structural
genomics of infec diseases, csgid, metal binding; 1.80A
{Vibrio cholerae}
Length = 171
Score = 249 bits (638), Expect = 3e-86
Identities = 65/167 (38%), Positives = 106/167 (63%), Gaps = 3/167 (1%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHA-MGIGLAASQVDIHKQLL 59
M +L I+ PD RL+ ++ +T+ +++ +I ++ +T+Y GIGLAA QV + ++
Sbjct: 4 MAVLEILTAPDPRLRVQSKQVTDVA-SVQTLIDDLLDTLYATDNGIGLAAPQVGREEAIV 62
Query: 60 ILDISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKM 119
++D+S N +Q V INPK++ S K++ EGCLS+P + ++R + V AL+ EGK
Sbjct: 63 VIDLSDNRDQPLVLINPKVVSGS-NKEMGQEGCLSVPDYYADVERYTSVVVEALDREGKP 121
Query: 120 FEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
I LAI +QHEIDHL+G +FI+YLS K++ +KK K++K
Sbjct: 122 LRIETSDFLAIVMQHEIDHLSGNLFIDYLSPLKQQMAMKKVKKHVKN 168
>3pn3_A Peptide deformylase 1B, chloroplastic; PDF, N-terminal excision
pathway, N induced-FIT, hydrolase-hydrolase inhibitor
complex; HET: PN3; 1.30A {Arabidopsis thaliana} PDB:
3m6p_A* 3o3j_A* 3pn2_A 3m6o_A* 3pn4_A* 3pn5_A 3m6q_A
3pn6_A 3m6r_A 3cpm_A
Length = 193
Score = 249 bits (639), Expect = 4e-86
Identities = 57/165 (34%), Positives = 93/165 (56%), Gaps = 2/165 (1%)
Query: 4 LPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDI 63
+ I+ YPD L+ + I FD NLK ++ M + MY GIGL+A QV ++ QL++ +
Sbjct: 1 MEIVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDGIGLSAPQVGLNVQLMVFNP 60
Query: 64 SK--NNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFE 121
+ + V +NPKI YS + ++EGCLS PGI+ ++ R + +++ A +I G+ F
Sbjct: 61 AGEPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFS 120
Query: 122 IIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
I L A QHE DHL G +F + +++ + I ++ KK
Sbjct: 121 ISLSRLPARIFQHEYDHLEGVLFFDRMTDQVLDSIREELEALEKK 165
>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 = 248 bits (637), Expect = 5e-86
Identities = 68/166 (40%), Positives = 95/166 (57%), Gaps = 3/166 (1%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLI 60
+ I + D L+K A+P+T+FD NLKK I M ETMYH G+GLAA QV I ++ +
Sbjct: 11 HHMYRIRVFGDPVLRKRAKPVTKFDENLKKTIERMIETMYHYDGVGLAAPQVGISQRFFV 70
Query: 61 LDISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMF 120
+D+ INP+I+ E ++ EGCLS P IF +I+RSKRI+V N G+
Sbjct: 71 MDVGNG---PVAVINPEILEIDPETEVAEEGCLSFPEIFVEIERSKRIKVKYQNTRGEYV 127
Query: 121 EIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
E EG A QHE DHLNG + I+ +S K+ + KK + +
Sbjct: 128 EEELEGYAARVFQHEFDHLNGVLIIDRISPAKRLLLRKKLMDIART 173
>3u04_A Peptide deformylase 1; ssgcid, actinonin, ehrlichia chaffeensi
structural genomics; HET: BB2; 1.70A {Ehrlichia
chaffeensis} PDB: 3oca_A
Length = 190
Score = 248 bits (636), Expect = 1e-85
Identities = 72/185 (38%), Positives = 109/185 (58%), Gaps = 19/185 (10%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLI 60
M++L I+ PD RL +E + + D +++K++ +M ETM+ G+GLAA QV +HK++L+
Sbjct: 3 MSVLSIVTVPDKRLSLCSEEVEKVDQSIRKLVDDMFETMHANQGLGLAAVQVGVHKRILV 62
Query: 61 LDISKNNNQLQ-------------------VFINPKIIWYSKEKQIYNEGCLSLPGIFNK 101
+++ + + INPKI+ S+EK EGCLS+PG F+
Sbjct: 63 MNVPEEFEDSEDIENVEDKIEGYELYGGPYCIINPKIVDISQEKVKLKEGCLSVPGYFDY 122
Query: 102 IKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFL 161
I R +RI V L+ G I A+G LA CLQHEIDHLNG +F++YLS FK++ I+K
Sbjct: 123 IVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHEIDHLNGTVFLKYLSKFKRDFAIEKVK 182
Query: 162 KNIKK 166
K +
Sbjct: 183 KKERT 187
>1rl4_A Formylmethionine deformylase; crystal engineering, drug design,
malaria, PDF, peptide DEFO plasmodium, hydrolase; HET:
BRR BL5; 2.18A {Plasmodium falciparum} SCOP: d.167.1.1
PDB: 1rqc_A 1jym_A
Length = 188
Score = 247 bits (632), Expect = 4e-85
Identities = 58/169 (34%), Positives = 96/169 (56%), Gaps = 3/169 (1%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLI 60
+ I+ YPD L++ +E +T FD NLK+++ M + MY + GIGL+A QV+I K++++
Sbjct: 6 KDEIKIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIV 65
Query: 61 LDISKNNN---QLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEG 117
+ ++FINP I+ S K EGCLS PGI K++R + + +I G
Sbjct: 66 WNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDING 125
Query: 118 KMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
I +G+ + QHE DHLNG +FI+ ++ K+++ K + I+
Sbjct: 126 YKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRD 174
>1ws0_A Peptide deformylase 1; alpha + beta topology, hydrolase; 1.70A
{Bacillus cereus} PDB: 1ws1_A*
Length = 156
Score = 242 bits (620), Expect = 1e-83
Identities = 61/158 (38%), Positives = 98/158 (62%), Gaps = 2/158 (1%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLI 60
M +L II +P+ L+ E + FD L K++ +M ETM A G+GLAA QV + Q+ +
Sbjct: 1 MAVLEIIKHPNEVLETPCERVINFDKKLVKLLKDMHETMLIADGVGLAAPQVGVSLQVAV 60
Query: 61 LDISKNNNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMF 120
+D+ + ++ INP I+ E Q+ EGCLS PG++ +++R+ I+V A N GK+F
Sbjct: 61 VDVDDDTGKI-ELINPSILEKRGE-QVGPEGCLSFPGLYGEVERADYIKVRAQNRRGKVF 118
Query: 121 EIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIK 158
+ AEG LA +QHEIDHL+G +F ++ + +E ++
Sbjct: 119 LLEAEGFLARAIQHEIDHLHGVLFTSKVTRYYEENELE 156
>2ew5_A Peptide deformylase; inhibitor, hydrolase; HET: Y12; 2.20A
{Helicobacter pylori} PDB: 2ew6_A* 2ew7_A
Length = 181
Score = 239 bits (613), Expect = 2e-82
Identities = 60/169 (35%), Positives = 101/169 (59%), Gaps = 6/169 (3%)
Query: 3 LLPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILD 62
LL II+YP L+ I++ + FD L + + +M ETM + GIGLAA QV + ++LI++
Sbjct: 2 LLEIIHYPSKILRTISKEVVSFDAKLHQQLDDMYETMIASEGIGLAAIQVGLPLRMLIIN 61
Query: 63 ISKNN-----NQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEG 117
+ + + INPK I +Y EGCLS+PG + +++R +++++ N
Sbjct: 62 LPQEDGVQHKEDCLEIINPKFIETG-GSMMYKEGCLSVPGFYEEVERFEKVKIEYQNRFA 120
Query: 118 KMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
++ + A LLA+ +QHEIDHLNG +F++ LS K+++ K+ + KK
Sbjct: 121 EVKVLEASELLAVAIQHEIDHLNGVLFVDKLSILKRKKFEKELKELQKK 169
>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 = 235 bits (603), Expect = 9e-81
Identities = 56/175 (32%), Positives = 96/175 (54%), Gaps = 10/175 (5%)
Query: 2 TLLPIIYYPDIRLKKIAEPITEFDI---NLKKIIFNMTETMYHAMGIGLAASQVDIHKQL 58
++ I+ D L+KI+EP+TE +I KK+I +M +TM HA G+GLAA Q+ I KQ+
Sbjct: 1 SVRKILRMGDPILRKISEPVTEDEIQTKEFKKLIRDMFDTMRHAEGVGLAAPQIGILKQI 60
Query: 59 LILDISKNNNQ-------LQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVH 111
+++ N ++ +NP I +K+ + EGCLS+PG+ ++R +IR+
Sbjct: 61 VVVGSEDNERYPGTPDVPERIILNPVITPLTKDTSGFWEGCLSVPGMRGYVERPNQIRMQ 120
Query: 112 ALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
++ +G F+ +G AI QHE DHL G ++++ L + K + +
Sbjct: 121 WMDEKGNQFDETIDGYKAIVYQHECDHLQGILYVDRLKDTKLFGFNETLDSSHNV 175
>3e3u_A Peptide deformylase; metallo-enzyme, hydrolase, iron,
metal-binding, protein biosynthesis; HET: NVC; 1.56A
{Mycobacterium tuberculosis}
Length = 197
Score = 235 bits (602), Expect = 2e-80
Identities = 50/177 (28%), Positives = 79/177 (44%), Gaps = 14/177 (7%)
Query: 1 MTLLPIIYYPDIRLKKIAEPIT-----EFDINLKKIIFNMTETMYHAMGIGLAASQVDIH 55
M ++PI D L P+T +L ++I M +TM A G+GLAA+Q+
Sbjct: 1 MAVVPIRIVGDPVLHTATTPVTVAADGSLPADLAQLIATMYDTMDAANGVGLAANQIGCS 60
Query: 56 KQLLILDISKNN----NQLQVFINPKI-----IWYSKEKQIYNEGCLSLPGIFNKIKRSK 106
+L + D + + + V INP + + +EGCLS+PG R+K
Sbjct: 61 LRLFVYDCAADRAMTARRRGVVINPVLETSEIPETMPDPDTDDEGCLSVPGESFPTGRAK 120
Query: 107 RIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKN 163
RV L+ +G I GL A LQHE HL+G ++++ L + +
Sbjct: 121 WARVTGLDADGSPVSIEGTGLFARMLQHETGHLDGFLYLDRLIGRYARNAKRAVKSH 177
>3dld_A Peptide deformylase; bacterial blight, XOO1075, xanthomonas oryzae
PV. oryzae KACC10331, hydrolase; 2.60A {Xanthomonas
oryzae PV}
Length = 171
Score = 230 bits (588), Expect = 1e-78
Identities = 52/170 (30%), Positives = 78/170 (45%), Gaps = 8/170 (4%)
Query: 3 LLPIIYYPDIRLKKIAEPITEF-DINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLIL 61
+ II D RL ++A +T L ++ +M ETM A G+GLAA Q+ + QL++
Sbjct: 2 IRDIIRMGDKRLLRVAPQVTNLGSAELHALVSDMFETMGAAHGVGLAAPQIAVDLQLMVF 61
Query: 62 DISKNNNQ-------LQVFINPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALN 114
+ L N +I S E + EGCLS+PG+ I R + IR
Sbjct: 62 GFEASERYPEAPAVPLTALANAQIEPLSDEMENGWEGCLSIPGLRAVIPRYRYIRYRGFA 121
Query: 115 IEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNI 164
+G E AEG A +QHE DHL G+++ + NF ++
Sbjct: 122 PDGSPIEREAEGFHARVVQHEYDHLVGRLYPSRIENFDTFGFDDVLSYDL 171
>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 = 230 bits (588), Expect = 3e-78
Identities = 56/177 (31%), Positives = 94/177 (53%), Gaps = 16/177 (9%)
Query: 4 LPIIYYPDIRLKKIAEPITEFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDI 63
PI Y D L++ A P+ +F +K++ +M ETM+ A G+GLAA Q+ + ++L +
Sbjct: 3 YPIRLYGDPVLRRKARPVEDFS-GIKRLAEDMLETMFEAKGVGLAAPQIGLSQRLFVAVE 61
Query: 64 SKN-------------NNQLQVFINPKIIWYSKEKQIYNEGCLSLPGIFN-KIKRSKRIR 109
+ ++ V NP I + + EGCLSLPG+++ ++ R++RIR
Sbjct: 62 YADEPEGEEERPLRELVRRVYVVANPVITY-REGLVEGTEGCLSLPGLYSEEVPRAERIR 120
Query: 110 VHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLKNIKK 166
V + EG+ + EG +A QHEIDHL+G +F E L K+E ++ + +
Sbjct: 121 VEYQDEEGRGRVLELEGYMARVFQHEIDHLDGILFFERLPKPKREAFLEANRAELVR 177
>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 = 229 bits (586), Expect = 5e-78
Identities = 50/185 (27%), Positives = 88/185 (47%), Gaps = 20/185 (10%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDI---NLKKIIFNMTETMYHAMGIGLAASQVDIHKQ 57
M L I+ D L + A + +I ++KII +M + M A G+GLAA Q+ + +
Sbjct: 1 MDLPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPGVGLAAPQIGVPLR 60
Query: 58 LLILDISKNNNQ----------------LQVFINPKIIWYSKEKQIYNEGCLSLPGIFNK 101
+++L+ +K L V +NP + S +K ++ EGCLS+ G
Sbjct: 61 IIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCLSVDGFRAA 120
Query: 102 IKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFL 161
++R + V + +GK E+ A G A LQHE DHL+G ++++ + R +
Sbjct: 121 VERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTF-RTVDNLD 179
Query: 162 KNIKK 166
+ +
Sbjct: 180 LPLAE 184
>3g5k_A Peptide deformylase, mitochondrial; actinonin, hydrolase, iron,
metal-bindi mitochondrion, protein biosynthesis, transit
peptide; HET: BB2; 1.70A {Homo sapiens} PDB: 3g5p_A
Length = 183
Score = 223 bits (571), Expect = 8e-76
Identities = 39/175 (22%), Positives = 79/175 (45%), Gaps = 19/175 (10%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDI---NLKKIIFNMTETMYHAMGIGLAASQVDIHKQ 57
M+ + D L+ +A P+ + L+++ + + M +GL+A Q+ + +Q
Sbjct: 2 MSFSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQ 61
Query: 58 LLILDISKNNNQ----------------LQVFINPKIIWYSKEKQIYNEGCLSLPGIFNK 101
+L L++ + + L+VF+NP + + EGC S+ G
Sbjct: 62 VLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLAC 121
Query: 102 IKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERI 156
+ R + +++ L+ G+ A G A +QHE+DHL G +FI+ + + +
Sbjct: 122 VPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNV 176
>2okl_A Peptide deformylase 2; hydrolase; HET: BB2 CIT; 1.70A {Bacillus
cereus} PDB: 1lqy_A*
Length = 185
Score = 209 bits (534), Expect = 3e-70
Identities = 50/180 (27%), Positives = 82/180 (45%), Gaps = 18/180 (10%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEF-------------DINLKKIIFNMTETMYHAMGIGL 47
+T+ +I D L+ +AE ++ + + M E GIGL
Sbjct: 3 LTMKDVIREGDPILRNVAEEVSLPASEEDTTTLKEMIEFVINSQDPEMAEKYSLRPGIGL 62
Query: 48 AASQVDIHKQLLILDISKNNNQLQ--VFINPKIIWYSKEKQIY--NEGCLSLPGIFN-KI 102
AA Q+ + K+++ + ++ + L NPKII +S E+ EGCLS+ +
Sbjct: 63 AAPQIGVSKKMIAVHVTDADGTLYSHALFNPKIISHSVERTYLQGGEGCLSVDREVPGYV 122
Query: 103 KRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFLK 162
R RI V A +I G+ ++ +GL AI QHEIDHLNG +F ++++
Sbjct: 123 PRYTRITVKATSINGEEVKLRLKGLPAIVFQHEIDHLNGVMFYDHINKENPFAAPDDSKP 182
>3l87_A Peptide deformylase; hydrolase, iron, metal-binding, PR
biosynthesis; 2.00A {Streptococcus mutans}
Length = 238
Score = 203 bits (519), Expect = 3e-67
Identities = 45/192 (23%), Positives = 82/192 (42%), Gaps = 28/192 (14%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEF-DINLKKIIFNM------------TETMYHAMGIGL 47
+ + II L+ +A+ +T + + + M E M G+GL
Sbjct: 48 IDMNDIIREGHPTLRAVAQDVTFPLNEDDIILGEKMLQFLKNSQDPVTAEKMELRGGVGL 107
Query: 48 AASQVDIHKQLLILDISKNNN-----------QLQVFINPKIIWYSKEKQIY--NEGCLS 94
AA Q+DI K+++ + I + +V NP+II +S + EGCLS
Sbjct: 108 AAPQLDISKRIIAVLIPNPEDKDGNPPKEAYALKEVMYNPRIIAHSVQDAALADGEGCLS 167
Query: 95 LPGIFN-KIKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKK 153
+ + + R R+ + + ++ +G +I +QHEIDH NG +F + ++
Sbjct: 168 VDRVVEGYVIRHSRVTIEYYDKNSDKKKLKLKGYQSIVVQHEIDHTNGIMFFDRINEKNP 227
Query: 154 ERIIKKFLKNIK 165
I + L I+
Sbjct: 228 FEIKEG-LLLIE 238
>3svj_P Peptide deformylase 3; alpha-beta, metal binding protein, HYDR
hydrolase inhibitor complex; HET: 4LI; 1.55A
{Streptococcus pneumoniae} PDB: 3str_P* 3sw8_P* 1lm6_A
2aia_A* 2ai7_A* 2aie_P* 2os3_A*
Length = 203
Score = 199 bits (509), Expect = 3e-66
Identities = 46/188 (24%), Positives = 83/188 (44%), Gaps = 26/188 (13%)
Query: 1 MTLLPIIYYPDIRLKKIAEPITEFDINLKKII-------------FNMTETMYHAMGIGL 47
+ + II + L+ +AE +T + + I+ M E M G+GL
Sbjct: 14 IDMNDIIREGNPTLRTVAEEVTFPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLRGGVGL 73
Query: 48 AASQVDIHKQLLILDISKNN----------NQLQVFINPKIIWYSKEKQI--YNEGCLSL 95
AA Q+DI K+++ + + + + NPKI+ +S + EGCLS+
Sbjct: 74 AAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAALGEGEGCLSV 133
Query: 96 P-GIFNKIKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKE 154
+ + R R+ V + +G+ I +G +I +QHEIDH+NG +F + ++
Sbjct: 134 DRNVPGYVVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFYDRINEKDPF 193
Query: 155 RIIKKFLK 162
+ L
Sbjct: 194 AVKDGLLI 201
>2os0_A Peptide deformylase; PDF, hydrolase; 1.30A {Enterococcus faecalis}
PDB: 2os1_A* 3g6n_A 3cmd_A
Length = 188
Score = 199 bits (508), Expect = 3e-66
Identities = 43/184 (23%), Positives = 85/184 (46%), Gaps = 22/184 (11%)
Query: 1 MTLLPIIYYPDIRLKKIAEPIT-EFDINLKKIIFNMTET------------MYHAMGIGL 47
+T+ II + L+ +AE + +++ +M + +GL
Sbjct: 2 ITMKDIIREGNPTLRAVAEEVPVPITEEDRQLGEDMLTFLKNSQDPVKAEELQLRGDVGL 61
Query: 48 AASQVDIHKQLLILDISKNNNQ------LQVFINPKIIWYSKEKQI--YNEGCLSLP-GI 98
AA Q+DI K+++ + + N+ + V NPKI+ +S + EGCLS+ +
Sbjct: 62 AAPQLDISKRIIAVHVPSNDPENETPSLSTVMYNPKILSHSVQDVCLGEGEGCLSVDRDV 121
Query: 99 FNKIKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIK 158
+ R +I V ++ G+ ++ + AI +QHEIDH+NG +F ++++ + +
Sbjct: 122 PGYVVRHNKITVSYFDMAGEKHKVRLKNYEAIVVQHEIDHINGIMFYDHINKENPFALKE 181
Query: 159 KFLK 162
L
Sbjct: 182 GVLV 185
>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 = 199 bits (507), Expect = 5e-66
Identities = 47/181 (25%), Positives = 86/181 (47%), Gaps = 19/181 (10%)
Query: 1 MTLLPIIYYPDIRLKKIAEPIT-EFDINLKKIIFNMTETMYHAM------------GIGL 47
+T+ II L++ A + K+ + M E + ++ G+GL
Sbjct: 13 LTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGL 72
Query: 48 AASQVDIHKQLLILDISKNNN---QLQVFINPKIIWYSKEK--QIYNEGCLSLPGIFN-K 101
AA Q++I K+++ + I + + + +NPKI+ +S ++ EGCLS+
Sbjct: 73 AAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGL 132
Query: 102 IKRSKRIRVHALNIEGKMFEIIAEGLLAICLQHEIDHLNGKIFIEYLSNFKKERIIKKFL 161
+ R RI + A +IEG ++ +G AI QHEIDHLNG +F +++ + +
Sbjct: 133 VHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAV 192
Query: 162 K 162
+
Sbjct: 193 E 193
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 45.8 bits (108), Expect = 2e-06
Identities = 30/122 (24%), Positives = 41/122 (33%), Gaps = 49/122 (40%)
Query: 43 MGIGL-----AASQV----DIH-KQLL---ILDISKNNNQLQVFINPKIIWYSKEKQIYN 89
MG+ L AA V D H K ILDI N NP I+
Sbjct: 1631 MGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVIN--------NP------VNLTIHF 1676
Query: 90 EGCLSLPGIFNKIKRSKRIRVH--ALNIEG---------KMFEIIAEGLLAICLQHEIDH 138
G ++ KRIR + A+ E K+F+ I E + + E
Sbjct: 1677 GG-----------EKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGL 1725
Query: 139 LN 140
L+
Sbjct: 1726 LS 1727
Score = 29.6 bits (66), Expect = 0.61
Identities = 25/146 (17%), Positives = 42/146 (28%), Gaps = 68/146 (46%)
Query: 17 IAEPIT--EFDINLKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILDISKNNNQLQVF- 73
IAE + F ++++K I ++ IG+ + +
Sbjct: 283 IAETDSWESFFVSVRKAI----TVLFF---IGVR-CY-------------------EAYP 315
Query: 74 ---INPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHALNIEGKMFEIIAEGLLAI 130
+ P I+ S E NEG S P M I L
Sbjct: 316 NTSLPPSILEDSLEN---NEGVPS-P----------------------MLSI--SNLTQE 347
Query: 131 CLQHEIDHLNG------KIFIEYLSN 150
+Q ++ N ++ I L N
Sbjct: 348 QVQDYVNKTNSHLPAGKQVEI-SLVN 372
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 41.8 bits (97), Expect = 4e-05
Identities = 28/195 (14%), Positives = 59/195 (30%), Gaps = 47/195 (24%)
Query: 7 IYYPDIRLKKIAEPITEFDINL-KKIIFNMTETMYHAMGIGLAASQVDIHKQ-------- 57
I++ +++ E + E L +I N T H+ I L + +
Sbjct: 184 IFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPY 243
Query: 58 ---LLILDISKNNNQLQVF-INPKIIWYSKEKQIYNEGCLSLPGIFNKIKRSKRIRVHAL 113
LL+L +N F ++ KI+ ++ KQ+ + + + +
Sbjct: 244 ENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQV-----------TDFLSAATTTHISLD 292
Query: 114 NIEGKMFEIIAEGLLAICLQHEIDHL--------------------NGKIFIEYLSNF-- 151
+ + + LL L L +G + +
Sbjct: 293 HHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNC 352
Query: 152 -KKERIIKKFLKNIK 165
K II+ L ++
Sbjct: 353 DKLTTIIESSLNVLE 367
Score = 35.6 bits (81), Expect = 0.006
Identities = 33/197 (16%), Positives = 71/197 (36%), Gaps = 49/197 (24%)
Query: 9 YPDIRLKKIAEP-ITEFDIN-----LKKIIFNMTETMYHAMGIGLAASQVDIHKQLLILD 62
Y DI L + + FD K I+ E + H + A S L
Sbjct: 18 YKDI-LSVFEDAFVDNFDCKDVQDMPKSIL--SKEEIDHIIMSKDAVSGTLR---LFWTL 71
Query: 63 ISKNNNQLQVFIN-----------------------PKIIWYSKEKQIYNEGCLSLPGIF 99
+SK +Q F+ ++ + ++YN+ +
Sbjct: 72 LSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV 131
Query: 100 NKIKRSKRIRVHALNIEGKMFEIIAEGL-------LAI--CLQHEI-DHLNGKIFIEYLS 149
++++ ++R L + ++ +G+ +A+ CL +++ ++ KIF +L
Sbjct: 132 SRLQPYLKLRQALLELRPAKN-VLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF--WL- 187
Query: 150 NFKKERIIKKFLKNIKK 166
N K + L+ ++K
Sbjct: 188 NLKNCNSPETVLEMLQK 204
Score = 28.3 bits (62), Expect = 1.4
Identities = 5/33 (15%), Positives = 11/33 (33%), Gaps = 3/33 (9%)
Query: 135 EIDHLNGKIFIEYLSNFKKE---RIIKKFLKNI 164
E + I + F + ++ K+I
Sbjct: 13 EHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSI 45
>1eye_A DHPS 1, dihydropteroate synthase I; alpha-beta barrel, transferase;
HET: PMM; 1.70A {Mycobacterium tuberculosis H37RV} SCOP:
c.1.21.1
Length = 280
Score = 26.7 bits (60), Expect = 3.8
Identities = 6/25 (24%), Positives = 10/25 (40%)
Query: 110 VHALNIEGKMFEIIAEGLLAICLQH 134
V + M ++AE + L H
Sbjct: 107 VSGGRADPAMGPLLAEADVPWVLMH 131
>2vef_A Dihydropteroate synthase; antibiotic resistance, transferase,
folate biosynthesis; 1.8A {Streptococcus pneumoniae}
PDB: 2veg_A*
Length = 314
Score = 26.1 bits (58), Expect = 7.1
Identities = 5/25 (20%), Positives = 11/25 (44%)
Query: 110 VHALNIEGKMFEIIAEGLLAICLQH 134
+ L + KM ++AE + +
Sbjct: 112 ITGLMGDEKMPHVVAEARAQVVIMF 136
>1tx2_A DHPS, dihydropteroate synthase; folate biosynthesis, pterine, MA
transferase; HET: 680; 1.83A {Bacillus anthracis} SCOP:
c.1.21.1 PDB: 1tww_A* 1twz_A* 1tx0_A* 1tws_A* 3h21_A*
3h22_A* 3h23_A* 3h24_A* 3h26_A* 3h2a_A* 3h2c_A* 3h2e_A*
3h2f_A* 3h2m_A* 3h2n_A* 3h2o_A* 3tya_A* 3tyb_A* 3tyc_A*
3tyd_A* ...
Length = 297
Score = 25.6 bits (57), Expect = 8.6
Identities = 7/25 (28%), Positives = 11/25 (44%)
Query: 110 VHALNIEGKMFEIIAEGLLAICLQH 134
+ E K+ E+ A + I L H
Sbjct: 142 IWGAKAEPKIAEVAAHYDVPIILMH 166
>3lb2_A Dehaloperoxidase A; globin, oxidoreductase; HET: HEM; 1.06A
{Amphitrite ornata} PDB: 1ewa_A* 1ew6_A* 2qfk_A* 3kun_A*
3lb1_A* 3dr9_A* 3lb3_A* 3lb4_A* 3mou_A* 3ord_A* 3mym_A*
3k3u_A* 3o7n_A* 3kuo_A* 2qfn_A* 3myn_A* 3oj1_A* 3ok5_A*
3ixf_A*
Length = 137
Score = 25.0 bits (54), Expect = 9.2
Identities = 5/58 (8%), Positives = 13/58 (22%), Gaps = 5/58 (8%)
Query: 100 NKIKRSKRIRVHALNIEGKMFEIIA-----EGLLAICLQHEIDHLNGKIFIEYLSNFK 152
++K + H + M E+ L + + +
Sbjct: 44 QELKSMAKFGDHTEKVFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKLF 101
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.325 0.143 0.410
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,622,863
Number of extensions: 151783
Number of successful extensions: 551
Number of sequences better than 10.0: 1
Number of HSP's gapped: 499
Number of HSP's successfully gapped: 35
Length of query: 166
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 79
Effective length of database: 4,272,666
Effective search space: 337540614
Effective search space used: 337540614
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)