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= 046989
(146 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|X Chain X, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 411
Score = 29.3 bits (64), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 16/32 (50%)
Query: 66 AEHFRNSQFVESILDVYRELPPVSGPSLTHQT 97
A+ N F E I DVYR LPP + L T
Sbjct: 189 ADEMLNKGFKEQIYDVYRYLPPATQVVLISAT 220
>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|B Chain B, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0S|A Chain A, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 410
Score = 29.3 bits (64), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 16/32 (50%)
Query: 66 AEHFRNSQFVESILDVYRELPPVSGPSLTHQT 97
A+ N F E I DVYR LPP + L T
Sbjct: 188 ADEMLNKGFKEQIYDVYRYLPPATQVVLISAT 219
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 29.3 bits (64), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 16/32 (50%)
Query: 66 AEHFRNSQFVESILDVYRELPPVSGPSLTHQT 97
A+ N F E I DVYR LPP + L T
Sbjct: 152 ADEMLNKGFKEQIYDVYRYLPPATQVVLISAT 183
>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|I Chain I, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|3EX7|C Chain C, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|H Chain H, The Crystal Structure Of Ejc In Its Transition State
Length = 413
Score = 29.3 bits (64), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 16/32 (50%)
Query: 66 AEHFRNSQFVESILDVYRELPPVSGPSLTHQT 97
A+ N F E I DVYR LPP + L T
Sbjct: 189 ADEMLNKGFKEQIYDVYRYLPPATQVVLISAT 220
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 29.3 bits (64), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 16/32 (50%)
Query: 66 AEHFRNSQFVESILDVYRELPPVSGPSLTHQT 97
A+ N F E I DVYR LPP + L T
Sbjct: 152 ADEMLNKGFKEQIYDVYRYLPPATQVVLISAT 183
>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|B Chain B, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|C Chain C, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|D Chain D, Crystal Structure Of Human Apo-Eif4aiii
Length = 391
Score = 29.3 bits (64), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 16/32 (50%)
Query: 66 AEHFRNSQFVESILDVYRELPPVSGPSLTHQT 97
A+ N F E I DVYR LPP + L T
Sbjct: 167 ADEMLNKGFKEQIYDVYRYLPPATQVVLISAT 198
>pdb|3O75|A Chain A, Crystal Structure Of Cra Transcriptional Dual Regulator
From Pseudomonas Putida In Complex With Fructose
1-Phosphate'
pdb|3O75|B Chain B, Crystal Structure Of Cra Transcriptional Dual Regulator
From Pseudomonas Putida In Complex With Fructose
1-Phosphate'
Length = 272
Score = 29.3 bits (64), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 71 NSQFVESIL----DVYRELPPVSGPSLTHQTRFDPARVCSPILED 111
++ FV S L D YREL P + R DPA CS I +D
Sbjct: 60 DALFVASCLPPEDDSYRELQDKGLPVIAIDRRLDPAHFCSVISDD 104
>pdb|3O74|A Chain A, Crystal Structure Of Cra Transcriptional Dual Regulator
From Pseudomonas Putida
pdb|3O74|B Chain B, Crystal Structure Of Cra Transcriptional Dual Regulator
From Pseudomonas Putida
Length = 272
Score = 29.3 bits (64), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 71 NSQFVESIL----DVYRELPPVSGPSLTHQTRFDPARVCSPILED 111
++ FV S L D YREL P + R DPA CS I +D
Sbjct: 60 DALFVASCLPPEDDSYRELQDKGLPVIAIDRRLDPAHFCSVISDD 104
>pdb|1LHP|A Chain A, Crystal Structure Of Pyridoxal Kinase From Sheep Brain
pdb|1LHP|B Chain B, Crystal Structure Of Pyridoxal Kinase From Sheep Brain
pdb|1LHR|A Chain A, Crystal Structure Of Pyridoxal Kinase Complexed With Atp
pdb|1LHR|B Chain B, Crystal Structure Of Pyridoxal Kinase Complexed With Atp
pdb|1RFT|A Chain A, Crystal Structure Of Pyridoxal Kinase Complexed With Amp-
Pcp And Pyridoxamine
pdb|1RFU|A Chain A, Crystal Structure Of Pyridoxal Kinase Complexed With Adp
And Plp
pdb|1RFU|B Chain B, Crystal Structure Of Pyridoxal Kinase Complexed With Adp
And Plp
pdb|1RFU|C Chain C, Crystal Structure Of Pyridoxal Kinase Complexed With Adp
And Plp
pdb|1RFU|D Chain D, Crystal Structure Of Pyridoxal Kinase Complexed With Adp
And Plp
pdb|1RFU|E Chain E, Crystal Structure Of Pyridoxal Kinase Complexed With Adp
And Plp
pdb|1RFU|F Chain F, Crystal Structure Of Pyridoxal Kinase Complexed With Adp
And Plp
pdb|1RFU|G Chain G, Crystal Structure Of Pyridoxal Kinase Complexed With Adp
And Plp
pdb|1RFU|H Chain H, Crystal Structure Of Pyridoxal Kinase Complexed With Adp
And Plp
pdb|1RFV|A Chain A, Crystal Structure Of Pyridoxal Kinase Complexed With Adp
pdb|1RFV|B Chain B, Crystal Structure Of Pyridoxal Kinase Complexed With Adp
pdb|1YGJ|A Chain A, Crystal Structure Of Pyridoxal Kinase In Complex With
Roscovitine And Derivatives
pdb|1YGK|A Chain A, Crystal Structure Of Pyridoxal Kinase In Complex With
Roscovitine And Derivatives
pdb|1YHJ|A Chain A, Crystal Structure Of Pyridoxal Kinase In Complex With
Roscovitine And Derivatives
Length = 312
Score = 27.7 bits (60), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 10/61 (16%)
Query: 56 FNHSNK-PISYAEHFRNSQFVESILDVYRELPPVSGPSLTHQTRFDPARVCSPILEDGRN 114
NH N+ + R+ F+ ++D+ +EL P L + VC P++ D RN
Sbjct: 71 LNHVNQYDYVLTGYTRDKSFLAMVVDIVQELKQ-QNPRLVY--------VCDPVMGDQRN 121
Query: 115 G 115
G
Sbjct: 122 G 122
>pdb|1NM8|A Chain A, Structure Of Human Carnitine Acetyltransferase: Molecular
Basis For Fatty Acyl Transfer
pdb|1S5O|A Chain A, Structural And Mutational Characterization Of L-Carnitine
Binding To Human Carnitine Acetyltransferase
Length = 616
Score = 26.6 bits (57), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 47 GVKEEMRGNFNHSNKPISYAEHFRNSQFVESILDVY 82
G K++ NF+ + KP ++ N QF E LDVY
Sbjct: 163 GPKQDTVSNFSKTKKPPTHITVVHNYQFFE--LDVY 196
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 0.137 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,614,424
Number of Sequences: 62578
Number of extensions: 182205
Number of successful extensions: 393
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 385
Number of HSP's gapped (non-prelim): 13
length of query: 146
length of database: 14,973,337
effective HSP length: 90
effective length of query: 56
effective length of database: 9,341,317
effective search space: 523113752
effective search space used: 523113752
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: 46 (22.3 bits)