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= 041958
(126 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2J5C|A Chain A, Rational Conversion Of Substrate And Product Specificity
In A Monoterpene Synthase. Structural Insights Into The
Molecular Basis Of Rapid Evolution.
pdb|2J5C|B Chain B, Rational Conversion Of Substrate And Product Specificity
In A Monoterpene Synthase. Structural Insights Into The
Molecular Basis Of Rapid Evolution
Length = 569
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/44 (45%), Positives = 27/44 (61%), Gaps = 2/44 (4%)
Query: 33 ASKEELARVDASKSIDCYRHEINWHLEEEVARDHINDLVRQTWK 76
S +E+ R D KS+ CY +E N EE AR+H+ L+ QTWK
Sbjct: 471 TSLDEVERGDVPKSVQCYMNEKN--ASEEEAREHVRSLIDQTWK 512
>pdb|1N1B|A Chain A, Crystal Structure Of (+)-bornyl Diphosphate Synthase From
Sage
pdb|1N1B|B Chain B, Crystal Structure Of (+)-bornyl Diphosphate Synthase From
Sage
pdb|1N1Z|A Chain A, (+)-Bornyl Diphosphate Synthase: Complex With Mg And
Pyrophosphate
pdb|1N1Z|B Chain B, (+)-Bornyl Diphosphate Synthase: Complex With Mg And
Pyrophosphate
pdb|1N20|A Chain A, (+)-bornyl Diphosphate Synthase: Complex With Mg And
3-aza- 2,3-dihydrogeranyl Diphosphate
pdb|1N20|B Chain B, (+)-bornyl Diphosphate Synthase: Complex With Mg And
3-aza- 2,3-dihydrogeranyl Diphosphate
pdb|1N21|A Chain A, (+)-Bornyl Diphosphate Synthase: Cocrystal With Mg And 3-
Aza-2,3-Dihydrogeranyl Diphosphate
pdb|1N22|A Chain A, (+)-Bornyl Diphosphate Synthase: Complex With Mg,
Pyrophosphate, And (4r)-7-Aza-7,8-Dihydrolimonene
pdb|1N22|B Chain B, (+)-Bornyl Diphosphate Synthase: Complex With Mg,
Pyrophosphate, And (4r)-7-Aza-7,8-Dihydrolimonene
pdb|1N23|A Chain A, (+)-Bornyl Diphosphate Synthase: Complex With Mg,
Pyrophosphate, And (1r,4s)-2-Azabornane
pdb|1N23|B Chain B, (+)-Bornyl Diphosphate Synthase: Complex With Mg,
Pyrophosphate, And (1r,4s)-2-Azabornane
pdb|1N24|A Chain A, (+)-Bornyl Diphosphate Synthase: Complex With Mg And
Product
pdb|1N24|B Chain B, (+)-Bornyl Diphosphate Synthase: Complex With Mg And
Product
Length = 549
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 29/95 (30%), Positives = 43/95 (45%), Gaps = 24/95 (25%)
Query: 37 ELARVDASKSIDCYRHEINWHLEEEVARDHINDLVRQTWKKI-------LPYLK------ 83
ELAR D K+I CY E N EE A +H+ L+R+ WK + P+
Sbjct: 455 ELARGDVPKTIQCYMKETN--ASEEEAVEHVKFLIREAWKDMNTAIAAGYPFPDGMVAGA 512
Query: 84 ------LQLNFVESYDYGVQNQETMD---TLLFQP 109
Q ++ +GVQ+ +T + LLF+P
Sbjct: 513 ANIGRVAQFIYLHGDGFGVQHSKTYEHIAGLLFEP 547
>pdb|2ONG|A Chain A, Crystal Structure Of Of Limonene Synthase With 2-
Fluorogeranyl Diphosphate (Fgpp).
pdb|2ONG|B Chain B, Crystal Structure Of Of Limonene Synthase With 2-
Fluorogeranyl Diphosphate (Fgpp).
pdb|2ONH|A Chain A, Crystal Structure Of Of Limonene Synthase With 2-
Fluorolinalyl Diphosphate(flpp)
pdb|2ONH|B Chain B, Crystal Structure Of Of Limonene Synthase With 2-
Fluorolinalyl Diphosphate(flpp)
Length = 543
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 33 ASKEELARVDASKSIDCYRHEINWHLEEEVARDHINDLVRQTWKKI 78
S EE++R D KS+ CY + N E AR H+ L+ + WKK+
Sbjct: 444 TSVEEVSRGDVPKSLQCYMSDYN--ASEAEARKHVKWLIAEVWKKM 487
>pdb|3N0F|A Chain A, Crystal Structure Of Isoprene Synthase From Grey Poplar
Leaves (Populus X Canescens)
pdb|3N0F|B Chain B, Crystal Structure Of Isoprene Synthase From Grey Poplar
Leaves (Populus X Canescens)
pdb|3N0G|A Chain A, Crystal Structure Of Isoprene Synthase From Grey Poplar
Leaves (Populus X Canescens) In Complex With Three Mg2+
Ions And Dimethylallyl-S-Thiolodiphosphate
pdb|3N0G|B Chain B, Crystal Structure Of Isoprene Synthase From Grey Poplar
Leaves (Populus X Canescens) In Complex With Three Mg2+
Ions And Dimethylallyl-S-Thiolodiphosphate
Length = 555
Score = 32.0 bits (71), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 33 ASKEELARVDASKSIDCYRHEINWHLEEEVARDHINDLVRQTWKKI 78
++ E+AR + + S+ CY + EE+A + + +L+ +TWKK+
Sbjct: 453 SASAEIARGETANSVSCYMRTKG--ISEELATESVMNLIDETWKKM 496
>pdb|2VE3|A Chain A, Retinoic Acid Bound Cyanobacterial Cyp120a1
pdb|2VE3|B Chain B, Retinoic Acid Bound Cyanobacterial Cyp120a1
pdb|2VE4|A Chain A, Substrate Free Cyanobacterial Cyp120a1
pdb|2VE4|B Chain B, Substrate Free Cyanobacterial Cyp120a1
Length = 444
Score = 27.3 bits (59), Expect = 2.3, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 79 LPYLKLQLNFVESYDYGVQNQETMDTLLFQPILEDKGMVFTSSTL 123
LP+L LNF+ D+G + Q+ +F+ L K ++F S L
Sbjct: 20 LPWLGETLNFLNDGDFGKKRQQQFGP-IFKTRLFGKNVIFISGAL 63
>pdb|3US8|A Chain A, Crystal Structure Of An Isocitrate Dehydrogenase From
Sinorhizobium Meliloti 1021
pdb|3US8|B Chain B, Crystal Structure Of An Isocitrate Dehydrogenase From
Sinorhizobium Meliloti 1021
Length = 427
Score = 26.9 bits (58), Expect = 3.0, Method: Composition-based stats.
Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 76 KKILPYLKLQLNFVESYDYGVQNQETMD 103
K I PYL L L E YD GV+N++ D
Sbjct: 52 KLIHPYLDLDL---EYYDLGVENRDATD 76
>pdb|3P83|D Chain D, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus.
pdb|3P83|E Chain E, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus.
pdb|3P83|F Chain F, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus
Length = 217
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 26/37 (70%)
Query: 57 HLEEEVARDHINDLVRQTWKKILPYLKLQLNFVESYD 93
+L+E +A IN+++++ + +I+ LK ++ +V+S D
Sbjct: 80 NLDERMAAKTINEILKECYAEIILRLKPEIAYVDSPD 116
>pdb|1I39|A Chain A, Rnase Hii From Archaeoglobus Fulgidus
pdb|1I3A|A Chain A, Rnase Hii From Archaeoglobus Fulgidus With Cobalt
Hexammine Chloride
Length = 225
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 26/37 (70%)
Query: 57 HLEEEVARDHINDLVRQTWKKILPYLKLQLNFVESYD 93
+L+E +A IN+++++ + +I+ LK ++ +V+S D
Sbjct: 88 NLDERMAAKTINEILKECYAEIILRLKPEIAYVDSPD 124
>pdb|3SAE|A Chain A, Structure Of A Three-Domain Sesquiterpene Synthase: A
Prospective Target For Advanced Biofuels Production
pdb|3SDQ|A Chain A, Structure Of A Three-Domain Sesquiterpene Synthase: A
Prospective Target For Advanced Biofuels Production
pdb|3SDR|A Chain A, Structure Of A Three-Domain Sesquiterpene Synthase: A
Prospective Target For Advanced Biofuels Production
pdb|3SDT|A Chain A, Structure Of A Three-Domain Sesquiterpene Synthase: A
Prospective Target For Advanced Biofuels Production
pdb|3SDU|A Chain A, Structure Of A Three-Domain Sesquiterpene Synthase: A
Prospective Target For Advanced Biofuels Production
pdb|3SDV|A Chain A, Structure Of A Three-Domain Sesquiterpene Synthase: A
Prospective Target For Advanced Biofuels Production
Length = 817
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 33/68 (48%), Gaps = 12/68 (17%)
Query: 20 GRTCLRSLNS--GELAS-----KEELARVDASKSIDCYRHEINWHLE--EEVARDHINDL 70
GR L LNS LA K E AR + + SI+CY + H E EE A DHI +
Sbjct: 697 GRRVLTELNSLISRLADDTKTYKAEKARGELASSIECYMKD---HPECTEEEALDHIYSI 753
Query: 71 VRQTWKKI 78
+ K++
Sbjct: 754 LEPAVKEL 761
>pdb|2CUN|A Chain A, Crystal Structure Of Phosphoglycerate Kinase From
Pyrococcus Horikoshii Ot3
pdb|2CUN|B Chain B, Crystal Structure Of Phosphoglycerate Kinase From
Pyrococcus Horikoshii Ot3
Length = 410
Score = 26.6 bits (57), Expect = 3.6, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 4 DLLDD-LELFIDTFERFGRTCLRSLNSGELASKEEL 38
+LLD +E D F R+ R ++ L SGE+A E L
Sbjct: 78 ELLDQHVEYIEDIFGRYAREKIKELKSGEVAILENL 113
>pdb|2ZU0|C Chain C, Crystal Structure Of Sufc-Sufd Complex Involved In The
Iron- Sulfur Cluster Biosynthesis
pdb|2ZU0|D Chain D, Crystal Structure Of Sufc-Sufd Complex Involved In The
Iron- Sulfur Cluster Biosynthesis
Length = 267
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 21/34 (61%), Gaps = 4/34 (11%)
Query: 81 YLKLQLNFVESYDYGVQNQETMDTLLFQPILEDK 114
+L+ LN V SY + QET+D FQ ++E+K
Sbjct: 117 FLQTALNAVRSY----RGQETLDRFDFQDLMEEK 146
>pdb|2D3W|A Chain A, Crystal Structure Of Escherichia Coli Sufc, An Atpase
Compenent Of The Suf Iron-Sulfur Cluster Assembly
Machinery
pdb|2D3W|B Chain B, Crystal Structure Of Escherichia Coli Sufc, An Atpase
Compenent Of The Suf Iron-Sulfur Cluster Assembly
Machinery
pdb|2D3W|C Chain C, Crystal Structure Of Escherichia Coli Sufc, An Atpase
Compenent Of The Suf Iron-Sulfur Cluster Assembly
Machinery
pdb|2D3W|D Chain D, Crystal Structure Of Escherichia Coli Sufc, An Atpase
Compenent Of The Suf Iron-Sulfur Cluster Assembly
Machinery
Length = 248
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 21/34 (61%), Gaps = 4/34 (11%)
Query: 81 YLKLQLNFVESYDYGVQNQETMDTLLFQPILEDK 114
+L+ LN V SY + QET+D FQ ++E+K
Sbjct: 98 FLQTALNAVRSY----RGQETLDRFDFQDLMEEK 127
>pdb|3G40|A Chain A, Crystal Structure Of The Cytoplasmic Domain Of A
Prokaryotic Cation Chloride Cotransporter
Length = 294
Score = 25.0 bits (53), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 2 SMDLLDDLELFIDTFERFGRTCLRSLNSGE 31
S+D DL+L E+ G +C+ +L+SGE
Sbjct: 251 SLDPNPDLDLARHLMEKAGSSCIFALDSGE 280
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
0.319 0.135 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,505,246
Number of Sequences: 62578
Number of extensions: 127548
Number of successful extensions: 316
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 300
Number of HSP's gapped (non-prelim): 24
length of query: 126
length of database: 14,973,337
effective HSP length: 87
effective length of query: 39
effective length of database: 9,529,051
effective search space: 371632989
effective search space used: 371632989
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)