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= psy7554
(115 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 21/44 (47%), Positives = 32/44 (72%)
Query: 58 MVYKGLDVITNKVTPEEAEGIPHHLLDFLDPNTRFTVVDYRNRA 101
VY+G D+ T K+T EE +G+PHHL+D DP+ F+V D+++ A
Sbjct: 38 QVYRGXDIGTAKITAEEXDGVPHHLIDIKDPSESFSVADFQDLA 81
>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 = 52.4 bits (124), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 22/47 (46%), Positives = 32/47 (68%)
Query: 58 MVYKGLDVITNKVTPEEAEGIPHHLLDFLDPNTRFTVVDYRNRALKH 104
VY+G D+ T KVT EE EGIPH+ +D L P+ F+ +++ RA K+
Sbjct: 42 QVYQGXDIGTAKVTTEEXEGIPHYXIDILPPDASFSAYEFKKRAEKY 88
>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 = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 27/45 (60%)
Query: 58 MVYKGLDVITNKVTPEEAEGIPHHLLDFLDPNTRFTVVDYRNRAL 102
++YKG+D+ T K EE PH LLD DP+ ++ D+R AL
Sbjct: 45 LIYKGMDIGTAKPNAEELLAAPHRLLDIRDPSQAYSAADFRRDAL 89
>pdb|3A8T|A Chain A, Plant Adenylate Isopentenyltransferase In Complex With Atp
Length = 339
Score = 45.8 bits (107), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 22/48 (45%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 57 LMVYKGLDVITNKVTPEEAEGIPHHLLDFLDP-NTRFTVVDYRNRALK 103
+ VYKGLD+ TNK++ + G+PHHLL +DP T D+R+ A K
Sbjct: 74 MQVYKGLDITTNKISVPDRGGVPHHLLGEVDPARGELTPADFRSLAGK 121
>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 = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 26/45 (57%)
Query: 58 MVYKGLDVITNKVTPEEAEGIPHHLLDFLDPNTRFTVVDYRNRAL 102
++YKG D+ T K EE PH LLD DP+ ++ D+R AL
Sbjct: 45 LIYKGXDIGTAKPNAEELLAAPHRLLDIRDPSQAYSAADFRRDAL 89
>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: Composition-based stats.
Identities = 15/31 (48%), Positives = 23/31 (74%)
Query: 57 LMVYKGLDVITNKVTPEEAEGIPHHLLDFLD 87
+ VYK + +ITNK +E EGIPHH+++ +D
Sbjct: 36 MQVYKDIPIITNKHPLQEREGIPHHVMNHVD 66
>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 = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 58 MVYKGLDVITNKVTPEEAEGIPHHLLDFLDPNTRFTVVDYR 98
++Y+G+D+ T K + E PH L+D DP ++ ++R
Sbjct: 40 LIYRGMDIGTAKPSRELLARYPHRLIDIRDPAESYSAAEFR 80
>pdb|3UNG|C Chain C, Structure Of The Cmr2 Subunit Of The Crispr Rna
Silencing Complex
pdb|3UR3|C Chain C, Structure Of The Cmr2 Subunit Of The Crispr Rna
Silencing Complex
Length = 693
Score = 27.3 bits (59), Expect = 2.2, Method: Composition-based stats.
Identities = 10/27 (37%), Positives = 19/27 (70%)
Query: 47 DLFCRTYQVYLMVYKGLDVITNKVTPE 73
DL+ ++ + +++YK L+VI +K PE
Sbjct: 63 DLWASSHLLSMLMYKALEVIVDKFGPE 89
>pdb|4DOZ|A Chain A, Crystal Structure Of Pyrococcus Furiosus Cmr2 (Cas10)
Length = 686
Score = 27.3 bits (59), Expect = 2.2, Method: Composition-based stats.
Identities = 10/27 (37%), Positives = 19/27 (70%)
Query: 47 DLFCRTYQVYLMVYKGLDVITNKVTPE 73
DL+ ++ + +++YK L+VI +K PE
Sbjct: 48 DLWASSHLLSMLMYKALEVIVDKFGPE 74
>pdb|1NNT|A Chain A, Structural Evidence For A Ph-Sensitive Di-Lysine Trigger
In The Hen Ovotransferrin N-Lobe: Implications For
Transferrin Iron Release
Length = 328
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 32/84 (38%), Gaps = 5/84 (5%)
Query: 24 SYLSCLPDSVCPHAHQVDLTDGPDLFCRTYQVYLMVYKGLDVITNKVTPEEAEGIPHHLL 83
+YL C+ A + L G + ++ L YK + E ++ +
Sbjct: 37 TYLDCIKAIANNEADAISLDGG-----QAFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAV 91
Query: 84 DFLDPNTRFTVVDYRNRALKHTGL 107
+ T FTV D + + HTGL
Sbjct: 92 AVVKKGTEFTVNDLQGKTSCHTGL 115
>pdb|4HKJ|D Chain D, Structure Of Cowpox Cpxv203 In Complex With Mhci (H-2kb)
pdb|4HKJ|H Chain H, Structure Of Cowpox Cpxv203 In Complex With Mhci (H-2kb)
pdb|4HKJ|L Chain L, Structure Of Cowpox Cpxv203 In Complex With Mhci (H-2kb)
pdb|4HKJ|P Chain P, Structure Of Cowpox Cpxv203 In Complex With Mhci (H-2kb)
Length = 206
Score = 25.8 bits (55), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 11/42 (26%), Positives = 18/42 (42%)
Query: 73 EEAEGIPHHLLDFLDPNTRFTVVDYRNRALKHTGLKVDLTTE 114
+EA G+ H L +++ N V Y + H G+ E
Sbjct: 112 QEASGLDFHTLKYVESNYLHITVKYDTSCINHLGVNYSFXNE 153
>pdb|1NFT|A Chain A, Ovotransferrin, N-Terminal Lobe, Iron Loaded Open Form
pdb|1TFA|A Chain A, Ovotransferrin, N-Terminal Lobe, Apo Form
Length = 329
Score = 25.8 bits (55), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 32/84 (38%), Gaps = 5/84 (5%)
Query: 24 SYLSCLPDSVCPHAHQVDLTDGPDLFCRTYQVYLMVYKGLDVITNKVTPEEAEGIPHHLL 83
+YL C+ A + L G + ++ L YK + E ++ +
Sbjct: 38 TYLDCIKAIANNEADAISLDGG-----QVFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAV 92
Query: 84 DFLDPNTRFTVVDYRNRALKHTGL 107
+ T FTV D + + HTGL
Sbjct: 93 AVVKKGTEFTVNDLQGKTSCHTGL 116
>pdb|1KH7|A Chain A, E. Coli Alkaline Phosphatase Mutant (D153gd330n)
pdb|1KH7|B Chain B, E. Coli Alkaline Phosphatase Mutant (D153gd330n)
Length = 449
Score = 25.4 bits (54), Expect = 7.4, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 30/71 (42%), Gaps = 2/71 (2%)
Query: 7 THYQVNLLTGTPDQVYLSYLSCLPDSVCPHAHQVDLTDGPDLFCRTYQVYLMVYKGLDVI 66
THY +N TG PD V S S S + L G D+ + + L + K +
Sbjct: 85 THYALNKKTGKPDYVTDSAASATAWSTGVKTYNGAL--GVDIHEKDHPTILEMAKAAGLA 142
Query: 67 TNKVTPEEAEG 77
T V+ E +G
Sbjct: 143 TGNVSTAELQG 153
>pdb|1AJD|A Chain A, Three-Dimensional Structure Of The D153g Mutant Of E. Coli
Alkaline Phosphatase: A Mutant With Weaker Magnesium
Binding And Increased Catalytic Activity
pdb|1AJD|B Chain B, Three-Dimensional Structure Of The D153g Mutant Of E. Coli
Alkaline Phosphatase: A Mutant With Weaker Magnesium
Binding And Increased Catalytic Activity
pdb|1AJC|A Chain A, Three-Dimensional Structure Of The D153g Mutant Of E. Coli
Alkaline Phosphatase: A Mutant With Weaker Magnesium
Binding And Increased Catalytic Activity
pdb|1AJC|B Chain B, Three-Dimensional Structure Of The D153g Mutant Of E. Coli
Alkaline Phosphatase: A Mutant With Weaker Magnesium
Binding And Increased Catalytic Activity
pdb|1AJB|A Chain A, Three-Dimensional Structure Of The D153g Mutant Of E. Coli
Alkaline Phosphatase: A Mutant With Weaker Magnesium
Binding And Increased Catalytic Activity
pdb|1AJB|B Chain B, Three-Dimensional Structure Of The D153g Mutant Of E. Coli
Alkaline Phosphatase: A Mutant With Weaker Magnesium
Binding And Increased Catalytic Activity
pdb|1AJA|A Chain A, Three-Dimensional Structure Of The D153g Mutant Of E. Coli
Alkaline Phosphatase: A Mutant With Weaker Magnesium
Binding And Increased Catalytic Activity
pdb|1AJA|B Chain B, Three-Dimensional Structure Of The D153g Mutant Of E. Coli
Alkaline Phosphatase: A Mutant With Weaker Magnesium
Binding And Increased Catalytic Activity
Length = 449
Score = 25.4 bits (54), Expect = 8.0, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 30/71 (42%), Gaps = 2/71 (2%)
Query: 7 THYQVNLLTGTPDQVYLSYLSCLPDSVCPHAHQVDLTDGPDLFCRTYQVYLMVYKGLDVI 66
THY +N TG PD V S S S + L G D+ + + L + K +
Sbjct: 85 THYALNKKTGKPDYVTDSAASATAWSTGVKTYNGAL--GVDIHEKDHPTILEMAKAAGLA 142
Query: 67 TNKVTPEEAEG 77
T V+ E +G
Sbjct: 143 TGNVSTAELQG 153
>pdb|1CRN|A Chain A, Water Structure Of A Hydrophobic Protein At Atomic
Resolution. Pentagon Rings Of Water Molecules In
Crystals Of Crambin
Length = 46
Score = 25.4 bits (54), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 7 THYQVNLLTGTPDQVYLSYLSC--LPDSVCP 35
+++ V L GTP+ + +Y C +P + CP
Sbjct: 11 SNFNVCRLPGTPEAICATYTGCIIIPGATCP 41
>pdb|1IEJ|A Chain A, Ovotransferrin, N-Terminal Lobe, Holo Form, At 1.65 A
Resolution
Length = 332
Score = 25.0 bits (53), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 32/84 (38%), Gaps = 5/84 (5%)
Query: 24 SYLSCLPDSVCPHAHQVDLTDGPDLFCRTYQVYLMVYKGLDVITNKVTPEEAEGIPHHLL 83
+YL C+ A + L G + ++ L YK + E ++ +
Sbjct: 41 TYLDCIKAIANNEADAITLDGG-----QVFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAV 95
Query: 84 DFLDPNTRFTVVDYRNRALKHTGL 107
+ T FTV D + + HTGL
Sbjct: 96 AVVKKGTEFTVNDLQGKTSCHTGL 119
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
0.321 0.138 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,910,801
Number of Sequences: 62578
Number of extensions: 157435
Number of successful extensions: 386
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 376
Number of HSP's gapped (non-prelim): 19
length of query: 115
length of database: 14,973,337
effective HSP length: 78
effective length of query: 37
effective length of database: 10,092,253
effective search space: 373413361
effective search space used: 373413361
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)