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= 018647
(352 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3FOZ|A Chain A, Structure Of E. Coli Isopentenyl-Trna Transferase In
Complex With E. Coli Trna(Phe)
pdb|3FOZ|B Chain B, Structure Of E. Coli Isopentenyl-Trna Transferase In
Complex With E. Coli Trna(Phe)
pdb|2ZXU|A Chain A, Crystal Structure Of Trna Modification Enzyme Miaa In The
Complex With Trna(Phe) And Dmaspp
pdb|2ZXU|B Chain B, Crystal Structure Of Trna Modification Enzyme Miaa In The
Complex With Trna(Phe) And Dmaspp
Length = 316
Score = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 72/265 (27%), Positives = 112/265 (42%), Gaps = 44/265 (16%)
Query: 10 YSVGKFFEDARHATKDVLKKGRVPIVTGGTGLYLRWFIYGKPDVPKASPEIIAEVNSELA 69
YS F DA D+ GR+P++ GGT LY + + G +P A PE+ A + + A
Sbjct: 79 YSAADFRRDALAEMADITAAGRIPLLVGGTMLYFKALLEGLSPLPSADPEVRARIEQQAA 138
Query: 70 DLQRDGDWYAAVEFVVKAGDPKARS-LAANDWYRLRRSLEIIKSTGSPPSAFQIPYDSFR 128
+ + ++ ++ DP A + + ND RL R+LE+ F I +
Sbjct: 139 E-----QGWESLHRQLQEVDPVAAARIHPNDPQRLSRALEV----------FFISGKTLT 183
Query: 129 EHSDSSETDHSYERNSSAGASDTNPKDLDYDFMCFFLSSHRLDLYRSIDLRCEDMLPGSD 188
E + +S Y+ + A A + R L++ I+ R ML +
Sbjct: 184 ELTQTSGDALPYQVHQFAIA-----------------PASRELLHQRIEQRFHQML--AS 224
Query: 189 GILSEAAWLLDEGLLPNSNSATRAIGYRQAMEYLLRCRQQGGTSSTGEFYAFLAEFQKAS 248
G +E L G L + R +GYRQ YL +G S Y + A+
Sbjct: 225 GFEAEVRALFARGDLHTDLPSIRCVGYRQMWSYL-----EGEISYDEMVYRGVC----AT 275
Query: 249 RNFAKRQLTWFRNERIYHWLNAARP 273
R AKRQ+TW R HWL++ +P
Sbjct: 276 RQLAKRQITWLRGWEGVHWLDSEKP 300
>pdb|2ZM5|A Chain A, Crystal Structure Of Trna Modification Enzyme Miaa In The
Complex With Trna(Phe)
pdb|2ZM5|B Chain B, Crystal Structure Of Trna Modification Enzyme Miaa In The
Complex With Trna(Phe)
Length = 316
Score = 78.2 bits (191), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 69/266 (25%), Positives = 110/266 (41%), Gaps = 46/266 (17%)
Query: 10 YSVGKFFEDARHATKDVLKKGRVPIVTGGTGLYLRWFIYGKPDVPKASPEIIAEVNSELA 69
YS F DA D+ GR+P++ GGT LY + + G +P A PE+ A + + A
Sbjct: 79 YSAADFRRDALAEXADITAAGRIPLLVGGTXLYFKALLEGLSPLPSADPEVRARIEQQAA 138
Query: 70 DLQRDGDWYAAVEFVVKAGDPKARS-LAANDWYRLRRSLEIIKSTGSPPSAFQIPYDSFR 128
+ + ++ ++ DP A + + ND RL R+LE+ +G +
Sbjct: 139 E-----QGWESLHRQLQEVDPVAAARIHPNDPQRLSRALEVFFISGKTLTEL-------- 185
Query: 129 EHSDSSETDHSYERNSSAGASDTNPKDLDYDFMCFFLS-SHRLDLYRSIDLRCEDMLPGS 187
+ T+ L Y F ++ + R L++ I+ R L +
Sbjct: 186 --------------------TQTSGDALPYQVHQFAIAPASRELLHQRIEQRFHQXL--A 223
Query: 188 DGILSEAAWLLDEGLLPNSNSATRAIGYRQAMEYLLRCRQQGGTSSTGEFYAFLAEFQKA 247
G +E L G L + R +GYRQ YL +G S Y + A
Sbjct: 224 SGFEAEVRALFARGDLHTDLPSIRCVGYRQXWSYL-----EGEISYDEXVYRGVC----A 274
Query: 248 SRNFAKRQLTWFRNERIYHWLNAARP 273
+R AKRQ+TW R HWL++ +P
Sbjct: 275 TRQLAKRQITWLRGWEGVHWLDSEKP 300
>pdb|2QGN|A Chain A, Crystal Structure Of Trna Isopentenylpyrophosphate
Transferase (Bh2366) From Bacillus Halodurans, Northeast
Structural Genomics Consortium Target Bhr41.
pdb|3EXA|A Chain A, Crystal Structure Of The Full-Length Trna
Isopentenylpyrophosphate Transferase (Bh2366) From
Bacillus Halodurans, Northeast Structural Genomics
Consortium Target Bhr41.
pdb|3EXA|B Chain B, Crystal Structure Of The Full-Length Trna
Isopentenylpyrophosphate Transferase (Bh2366) From
Bacillus Halodurans, Northeast Structural Genomics
Consortium Target Bhr41.
pdb|3EXA|C Chain C, Crystal Structure Of The Full-Length Trna
Isopentenylpyrophosphate Transferase (Bh2366) From
Bacillus Halodurans, Northeast Structural Genomics
Consortium Target Bhr41.
pdb|3EXA|D Chain D, Crystal Structure Of The Full-Length Trna
Isopentenylpyrophosphate Transferase (Bh2366) From
Bacillus Halodurans, Northeast Structural Genomics
Consortium Target Bhr41
Length = 322
Score = 75.9 bits (185), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 74/273 (27%), Positives = 118/273 (43%), Gaps = 69/273 (25%)
Query: 10 YSVGKFFEDARHATKDVLKKGRVPIVTGGTGLYLRWFIYGKPDVPKASPEIIAEVNSELA 69
+SV F + A ++ ++GR+P + GGTGLY+ I+ L
Sbjct: 72 FSVADFQDLATPLITEIHERGRLPFLVGGTGLYVNAVIH----------------QFNLG 115
Query: 70 DLQRDGDWYAAVE-FVVKAG-----------DPKARS-LAANDWYRLRRSLEIIKSTGSP 116
D++ D D+ +E FV G DPKA + + N++ R+ R+LEIIK TG
Sbjct: 116 DIRADEDYRHELEAFVNSYGVQALHDKLSKIDPKAAAAIHPNNYRRVIRALEIIKLTGK- 174
Query: 117 PSAFQIPYDSFREHSDSSETDHSYERNSSAGASDTNPKDLDYDFMCFFLSSHRLDLYRSI 176
+ + + H E S Y+ + L+ R LY I
Sbjct: 175 --------------TVTEQARHEEETPSP------------YNLVXIGLTXERDVLYDRI 208
Query: 177 DLRCEDMLPGSDGILSEAAWLLDEGLLPNSNSATRAIGYRQAMEYLLRCRQQGGTSSTGE 236
+ R + + +G++ EA L D G+ + +AIGY++ +YL G + E
Sbjct: 209 NRRVDQXV--EEGLIDEAKKLYDRGI--RDCQSVQAIGYKEXYDYL------DGNVTLEE 258
Query: 237 FYAFLAEFQKASRNFAKRQLTWFRNERIYHWLN 269
L ++ SR +AKRQLTWFRN+ W +
Sbjct: 259 AIDTL---KRNSRRYAKRQLTWFRNKANVTWFD 288
>pdb|3D3Q|A Chain A, Crystal Structure Of Trna
Delta(2)-Isopentenylpyrophosphate Transferase (Se0981)
From Staphylococcus Epidermidis. Northeast Structural
Genomics Consortium Target Ser100
pdb|3D3Q|B Chain B, Crystal Structure Of Trna
Delta(2)-Isopentenylpyrophosphate Transferase (Se0981)
From Staphylococcus Epidermidis. Northeast Structural
Genomics Consortium Target Ser100
Length = 340
Score = 73.6 bits (179), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 65/275 (23%), Positives = 118/275 (42%), Gaps = 42/275 (15%)
Query: 10 YSVGKFFEDARHATKDVLKKGRVPIVTGGTGLYLRWFIYGKPDVPKASPEIIAEVNSELA 69
+S +F + A KD+ ++G+VPI+ GGTGLY++ +Y ++ E +
Sbjct: 76 FSAYEFKKRAEKYIKDITRRGKVPIIAGGTGLYIQSLLYNYAFEDESISEDKXKQVKLKL 135
Query: 70 DLQRDGDWYAAVEFVVKAGDPKARSLAANDWYRLRRSLEIIKSTGSPPSAFQIPYDSFRE 129
+ E++ A+ + N+ R+ R++E T S+ + F E
Sbjct: 136 KELEHLNNNKLHEYLASFDKESAKDIHPNNRKRVLRAIEYYLKTKKLLSSRK-KVQQFTE 194
Query: 130 HSDSSETDHSYERNSSAGASDTNPKDLDYDFMCFFLSSHRLDLYRSIDLRCEDMLPGSDG 189
+YD + + R LY I+ R + L G
Sbjct: 195 ---------------------------NYDTLLIGIEXSRETLYLRINKRVDIXL--GHG 225
Query: 190 ILSEAAWLLDEGLLPNSNSATRAIGYRQAMEYLLRCRQQGGTSSTGEFYAFLAEFQKASR 249
+ +E L+++G ++ + +AIGY++ + + +G S + + ++ SR
Sbjct: 226 LFNEVQHLVEQGF--EASQSXQAIGYKELVPVI-----KGNISXENA----VEKLKQHSR 274
Query: 250 NFAKRQLTWFRNERIYHWLNAAR-PLENVLNYIIT 283
+AKRQLTWF+N+ HWLN R L+ L+ I T
Sbjct: 275 QYAKRQLTWFKNKXNVHWLNKERXSLQXXLDEITT 309
>pdb|3CRM|A Chain A, Structure Of Trna Dimethylallyltransferase: Rna
Modification Through A Channel
pdb|3CRQ|A Chain A, Structure Of Trna Dimethylallyltransferase: Rna
Modification Through A Channel
pdb|3CRR|A Chain A, Structure Of Trna Dimethylallyltransferase: Rna
Modification Through A Channel
Length = 323
Score = 67.8 bits (164), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 78/278 (28%), Positives = 112/278 (40%), Gaps = 37/278 (13%)
Query: 10 YSVGKFFEDARHATKDVLKKGRVPIVTGGTGLYLRWFIYGKPDVPKASPEIIAEVNSELA 69
YS +F DA A +GR+P++ GGT LY + + G D+P A P EV + +
Sbjct: 74 YSAAEFRADALAAMAKATARGRIPLLVGGTMLYYKALLEGLADMPGADP----EVRAAIE 129
Query: 70 DLQRDGDWYAAVEFVVKAGDPKARSLAANDWYRLRRSLEIIKSTGSPPSAFQIPYDSFRE 129
+ W A + + A + ND RL R+LE+ + G + R
Sbjct: 130 AEAQAEGWEALHRQLAEVDPESAARIHPNDPQRLMRALEVYRLGG-------VSMSDLRR 182
Query: 130 HSDSSETDHSYERNSSAGASDTNPKDLDYDFMCFFLS-SHRLDLYRSIDLRCEDMLPGSD 188
+ + D AS N L Y ++ R L+ I R ML
Sbjct: 183 RQSAEKADFD--------ASGRN--QLPYTVAQLAIAPEQRQVLHARIAQRFRQML--EQ 230
Query: 189 GILSEAAWLLDEGLLPNSNSATRAIGYRQAMEYLLRCRQQGGTSSTGEFYAFLAEFQ-KA 247
G ++E L L + RA+GYRQ +YL G S YA + E A
Sbjct: 231 GFIAEVEALHARSDLHAGLPSIRAVGYRQVWDYL-----DGKLS-----YAEMTERGIIA 280
Query: 248 SRNFAKRQLTWFRNERIYHWLN--AARPLENVLNYIIT 283
+R AKRQ TW R+ HW++ A L L Y+ T
Sbjct: 281 TRQLAKRQFTWLRSWSHLHWMDSLAGDNLPRALRYLKT 318
>pdb|3EPH|A Chain A, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
pdb|3EPH|B Chain B, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
pdb|3EPJ|A Chain A, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
pdb|3EPJ|B Chain B, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
pdb|3EPK|A Chain A, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
pdb|3EPK|B Chain B, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
pdb|3EPL|A Chain A, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
pdb|3EPL|B Chain B, Crystallographic Snapshots Of Eukaryotic
Dimethylallyltransferase Acting On Trna: Insight Into
Trna Recognition And Reaction Mechanism
Length = 409
Score = 61.6 bits (148), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 62/259 (23%), Positives = 107/259 (41%), Gaps = 47/259 (18%)
Query: 9 YYSVGKFFEDARHATKDVLKKGRVPIVTGGTGLYLRWFIYGKPDVPKASPEIIAEVNSEL 68
YYS +F + +A +D+ ++G++PIV GGT YL+ + D + ++ +
Sbjct: 71 YYS-HRFETECMNAIEDIHRRGKIPIVVGGTHYYLQTLFNKRVDTKSSE----RKLTRKQ 125
Query: 69 ADLQRDGDWYAAVEFVVKAGDPKARSLAANDWYRLRRSLEIIKSTGSPPSAFQIPYDSFR 128
D+ D +VK A ND+ R++R LEI TG PS ++F
Sbjct: 126 LDILESTDPDVIYNTLVKCDPDIATKYHPNDYRRVQRMLEIYYKTGKKPS------ETFN 179
Query: 129 EHSDSSETDHSYERNSSAGASDTNPKDLDYDFMCFFLSSHRLDLYRSIDLRCEDMLPGSD 188
E + L +D + +L S L++ +D R +DML
Sbjct: 180 EQKIT----------------------LKFDTLFLWLYSKPEPLFQRLDDRVDDML--ER 215
Query: 189 GILSEAAWLLD----EGLLPNS--NSATRAIGYRQAMEYLLRCRQQGGT-SSTGEFYAFL 241
G L E L + P N + IG+++ + +L G T +T + +
Sbjct: 216 GALQEIKQLYEYYSQNKFTPEQCENGVWQVIGFKEFLPWLT-----GKTDDNTVKLEDCI 270
Query: 242 AEFQKASRNFAKRQLTWFR 260
+ +R +AKRQ+ W +
Sbjct: 271 ERMKTRTRQYAKRQVKWIK 289
>pdb|3NA8|A Chain A, Crystal Structure Of A Putative Dihydrodipicolinate
Synthetase From Pseudomonas Aeruginosa
pdb|3NA8|B Chain B, Crystal Structure Of A Putative Dihydrodipicolinate
Synthetase From Pseudomonas Aeruginosa
pdb|3NA8|C Chain C, Crystal Structure Of A Putative Dihydrodipicolinate
Synthetase From Pseudomonas Aeruginosa
pdb|3NA8|D Chain D, Crystal Structure Of A Putative Dihydrodipicolinate
Synthetase From Pseudomonas Aeruginosa
Length = 315
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 10/75 (13%)
Query: 26 VLKKGRVPIVTGGTGLYLRWFIYGKPDVPKASPEIIAEVNSELADLQRDGDWYAA----- 80
+L +GRVP G L L F+ G A+P +I +N +L DGD A
Sbjct: 199 LLGEGRVPFYNGXNPLALEAFVAGAKGWCSAAPNLIPTLNGQLYQAVLDGDLEKARALFY 258
Query: 81 -----VEFVVKAGDP 90
++F+++ G P
Sbjct: 259 RQLPLLDFILRRGLP 273
>pdb|1XUU|A Chain A, Crystal Structure Of Sialic Acid Synthase (Neub) In
Complex With Mn2+ And Malate From Neisseria Meningitidis
pdb|1XUZ|A Chain A, Crystal Structure Analysis Of Sialic Acid Synthase
(Neub)from Neisseria Meningitidis, Bound To Mn2+,
Phosphoenolpyruvate, And N- Acetyl Mannosaminitol
pdb|2ZDR|A Chain A, Crystal Structure Of Sialic Acid Synthase (Neub) From
Neisseria Meningitidis In Complex With Mg2+ And (4s)-2-
Methyl-2,4-Pentanediol
pdb|3CM4|A Chain A, Crystal Structure Of Metal-Free Sialic Acid Synthase
(Neub) From Neisseria Meningitidis In Complex With
Malate
Length = 349
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 78 YAAVEFVVKAGDPKARSLAANDWYRLRRSLEIIKSTGSP------PSAFQIPYDSFR 128
Y ++ V G P S N +++S+EII+ G P + + PY+ R
Sbjct: 138 YPLIKLVASFGKPIILSTGMNSIESIKKSVEIIREAGVPYALLHCTNIYPTPYEDVR 194
>pdb|2WQP|A Chain A, Crystal Structure Of Sialic Acid Synthase Neub-Inhibitor
Complex
Length = 349
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 78 YAAVEFVVKAGDPKARSLAANDWYRLRRSLEIIKSTGSP------PSAFQIPYDSFR 128
Y ++ V G P S N +++S+EII+ G P + + PY+ R
Sbjct: 138 YPLIKLVASFGKPIILSTGXNSIESIKKSVEIIREAGVPYALLHCTNIYPTPYEDVR 194
>pdb|1UM9|A Chain A, Branched-chain 2-oxo Acid Dehydrogenase (e1) From Thermus
Thermophilus Hb8 In Apo-form
pdb|1UM9|C Chain C, Branched-chain 2-oxo Acid Dehydrogenase (e1) From Thermus
Thermophilus Hb8 In Apo-form
pdb|1UMB|A Chain A, Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus
Thermophilus Hb8 In Holo-Form
pdb|1UMB|C Chain C, Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus
Thermophilus Hb8 In Holo-Form
pdb|1UMC|A Chain A, Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus
Thermophilus Hb8 With 4-Methylpentanoate
pdb|1UMC|C Chain C, Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus
Thermophilus Hb8 With 4-Methylpentanoate
pdb|1UMD|A Chain A, Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus
Thermophilus Hb8 With 4-Methyl-2-Oxopentanoate As An
Intermediate
pdb|1UMD|C Chain C, Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus
Thermophilus Hb8 With 4-Methyl-2-Oxopentanoate As An
Intermediate
Length = 367
Score = 28.5 bits (62), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 8/55 (14%)
Query: 74 DGDWYAAVEFVVKAGDPKARSLAANDWYRLRRSLEIIKSTGSP-----PSAFQIP 123
+GDWYA + F G P A +A N++Y + S++ T SP AF IP
Sbjct: 180 EGDWYAGINFAAVQGAP-AVFIAENNFYAI--SVDYRHQTHSPTIADKAHAFGIP 231
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
0.320 0.135 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,830,889
Number of Sequences: 62578
Number of extensions: 439810
Number of successful extensions: 961
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 938
Number of HSP's gapped (non-prelim): 15
length of query: 352
length of database: 14,973,337
effective HSP length: 100
effective length of query: 252
effective length of database: 8,715,537
effective search space: 2196315324
effective search space used: 2196315324
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: 52 (24.6 bits)