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= psy17229
(131 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/34 (50%), Positives = 24/34 (70%)
Query: 24 IDDILQRNKVPIIVGGTNYYIESLLWTILLDNKT 57
I DI +R KVPII GGT YI+SLL+ ++++
Sbjct: 89 IKDITRRGKVPIIAGGTGLYIQSLLYNYAFEDES 122
>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 = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 22/25 (88%)
Query: 24 IDDILQRNKVPIIVGGTNYYIESLL 48
I+DI +R K+PI+VGGT+YY+++L
Sbjct: 84 IEDIHRRGKIPIVVGGTHYYLQTLF 108
>pdb|3A8T|A Chain A, Plant Adenylate Isopentenyltransferase In Complex With Atp
Length = 339
Score = 33.1 bits (74), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 26/44 (59%)
Query: 24 IDDILQRNKVPIIVGGTNYYIESLLWTILLDNKTNINEQGEFTL 67
+ +I R K+P++VGG+N +I +LL + + E+G ++
Sbjct: 123 VSEITGRRKLPVLVGGSNSFIHALLVDRFDSSGPGVFEEGSHSV 166
>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 = 29.6 bits (65), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 10/27 (37%), Positives = 19/27 (70%)
Query: 22 SQIDDILQRNKVPIIVGGTNYYIESLL 48
+++ DI ++P++VGGT Y ++LL
Sbjct: 90 AEMADITAAGRIPLLVGGTMLYFKALL 116
>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 = 28.9 bits (63), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 22 SQIDDILQRNKVPIIVGGTNYYIESLL 48
++ DI ++P++VGGT Y ++LL
Sbjct: 90 AEXADITAAGRIPLLVGGTXLYFKALL 116
>pdb|1KMI|Z Chain Z, Crystal Structure Of An E.Coli Chemotaxis Protein, Chez
Length = 214
Score = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 8 PHLDTATGGVVCRASQIDDIL 28
P +DT+ GVV Q+DD+L
Sbjct: 189 PQVDTSKAGVVASQDQVDDLL 209
>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 = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 30 RNKVPIIVGGTNYYIESLL 48
R ++P++VGGT Y ++LL
Sbjct: 93 RGRIPLLVGGTMLYYKALL 111
>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 = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 18/25 (72%)
Query: 24 IDDILQRNKVPIIVGGTNYYIESLL 48
I +I +R ++P +VGGT Y+ +++
Sbjct: 85 ITEIHERGRLPFLVGGTGLYVNAVI 109
>pdb|3IJE|A Chain A, Crystal Structure Of The Complete Integrin Alhavbeta3
Ectodomain Plus An Alpha/beta Transmembrane Fragment
Length = 967
Score = 26.9 bits (58), Expect = 3.0, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 10/44 (22%)
Query: 17 VVCRASQIDDILQRNKVPIIVGGTNYYIESLLWTILLDNKTNIN 60
+VC+ ++D R K I+ Y++SLLWT NK N N
Sbjct: 882 IVCQVGRLD----RGKSAIL------YVKSLLWTETFMNKENQN 915
>pdb|4G1E|A Chain A, Crystal Structure Of Integrin Alpha V Beta 3 With
Coil-Coiled Tag
Length = 998
Score = 26.9 bits (58), Expect = 3.2, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 10/44 (22%)
Query: 17 VVCRASQIDDILQRNKVPIIVGGTNYYIESLLWTILLDNKTNIN 60
+VC+ ++D R K I+ Y++SLLWT NK N N
Sbjct: 882 IVCQVGRLD----RGKSAIL------YVKSLLWTETFMNKENQN 915
>pdb|4G1M|A Chain A, Re-Refinement Of Alpha V Beta 3 Structure
Length = 959
Score = 26.9 bits (58), Expect = 3.3, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 10/44 (22%)
Query: 17 VVCRASQIDDILQRNKVPIIVGGTNYYIESLLWTILLDNKTNIN 60
+VC+ ++D R K I+ Y++SLLWT NK N N
Sbjct: 882 IVCQVGRLD----RGKSAIL------YVKSLLWTETFMNKENQN 915
>pdb|1JV2|A Chain A, Crystal Structure Of The Extracellular Segment Of Integrin
Alphavbeta3
pdb|1L5G|A Chain A, Crystal Structure Of The Extracellular Segment Of Integrin
Avb3 In Complex With An Arg-Gly-Asp Ligand
pdb|1M1X|A Chain A, Crystal Structure Of The Extracellular Segment Of Integrin
Alpha Vbeta3 Bound To Mn2+
pdb|1U8C|A Chain A, A Novel Adaptation Of The Integrin Psi Domain Revealed
From Its Crystal Structure
Length = 957
Score = 26.9 bits (58), Expect = 3.3, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 10/44 (22%)
Query: 17 VVCRASQIDDILQRNKVPIIVGGTNYYIESLLWTILLDNKTNIN 60
+VC+ ++D R K I+ Y++SLLWT NK N N
Sbjct: 882 IVCQVGRLD----RGKSAIL------YVKSLLWTETFMNKENQN 915
>pdb|3H7N|A Chain A, Structure Of Nup120
pdb|3H7N|B Chain B, Structure Of Nup120
pdb|3H7N|C Chain C, Structure Of Nup120
pdb|3H7N|D Chain D, Structure Of Nup120
Length = 729
Score = 25.8 bits (55), Expect = 7.9, Method: Composition-based stats.
Identities = 20/49 (40%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 20 RASQIDDILQRNKVPIIVGGTNYYIESLLWTILLDNKTNINEQGEFTLY 68
RA QI L NK+ + Y+ +L TIL D KT NE TLY
Sbjct: 422 RAQQI---LSENKIIMAHNEDEEYLANL-ETILRDVKTAFNEASSITLY 466
>pdb|3F7F|A Chain A, Structure Of Nup120
pdb|3F7F|B Chain B, Structure Of Nup120
pdb|3F7F|C Chain C, Structure Of Nup120
pdb|3F7F|D Chain D, Structure Of Nup120
Length = 729
Score = 25.8 bits (55), Expect = 7.9, Method: Composition-based stats.
Identities = 20/49 (40%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 20 RASQIDDILQRNKVPIIVGGTNYYIESLLWTILLDNKTNINEQGEFTLY 68
RA QI L NK+ + Y+ +L TIL D KT NE TLY
Sbjct: 422 RAQQI---LSENKIIMAHNEDEEYLANLE-TILRDVKTAFNEASSITLY 466
>pdb|1TMO|A Chain A, Trimethylamine N-Oxide Reductase From Shewanella Massilia
Length = 829
Score = 25.4 bits (54), Expect = 9.8, Method: Composition-based stats.
Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 33 VPIIVGGTNYYIESLLWTILLDNKTNINEQGEFTLYDIDKMRNLEHG 79
+P ++G T Y + W ++L++ I L+ D +NL+ G
Sbjct: 188 LPYVLGSTEVYAQGTSWPLILEHSDTI------VLWSNDPYKNLQVG 228
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
0.318 0.140 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,783,712
Number of Sequences: 62578
Number of extensions: 133625
Number of successful extensions: 315
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 306
Number of HSP's gapped (non-prelim): 18
length of query: 131
length of database: 14,973,337
effective HSP length: 88
effective length of query: 43
effective length of database: 9,466,473
effective search space: 407058339
effective search space used: 407058339
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)