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= 039810
(113 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2OGH|A Chain A, Solution Structure Of Yeast Eif1
Length = 108
Score = 124 bits (310), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 56/103 (54%), Positives = 78/103 (75%), Gaps = 2/103 (1%)
Query: 11 AFDPFAEANAEDSGAGSKDYVHIRVQQRNGRKSLTTVQGLKKEFSYNKILKDLKKEFCCN 70
+FDPFA+ D + +Y+HIR+QQRNGRK+LTTVQG+ +E+ +ILK LKK+F CN
Sbjct: 8 SFDPFADTG--DDETATSNYIHIRIQQRNGRKTLTTVQGVPEEYDLKRILKVLKKDFACN 65
Query: 71 GTVVQDPELGQVIQLQGDQRKNVSTFLVQAGIVKKEFIKIHGF 113
G +V+DPE+G++IQLQGDQR V F++ ++K+ IKIHGF
Sbjct: 66 GNIVKDPEMGEIIQLQGDQRAKVCEFMISQLGLQKKNIKIHGF 108
>pdb|2IF1|A Chain A, Human Translation Initiation Factor Eif1, Nmr, 29
Structures
Length = 126
Score = 123 bits (309), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 60/105 (57%), Positives = 83/105 (79%), Gaps = 2/105 (1%)
Query: 11 AFDPFAEANAEDS--GAGSKDYVHIRVQQRNGRKSLTTVQGLKKEFSYNKILKDLKKEFC 68
+FDPFA+A+ D AG++DY+HIR+QQRNGRK+LTTVQG+ ++ K++K KK+F
Sbjct: 22 SFDPFADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFKKKFA 81
Query: 69 CNGTVVQDPELGQVIQLQGDQRKNVSTFLVQAGIVKKEFIKIHGF 113
CNGTV++ PE G+VIQLQGDQRKN+ FLV+ G+ K + +K+HGF
Sbjct: 82 CNGTVIEHPEYGEVIQLQGDQRKNICQFLVEIGLAKDDQLKVHGF 126
>pdb|2XZM|F Chain F, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 1
pdb|2XZN|F Chain F, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 2
Length = 101
Score = 86.3 bits (212), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 40/83 (48%), Positives = 54/83 (65%)
Query: 30 YVHIRVQQRNGRKSLTTVQGLKKEFSYNKILKDLKKEFCCNGTVVQDPELGQVIQLQGDQ 89
++HIRV+QR GRK TTV+G+ EF Y KI+K KK CN T+V++ E +VI+L GD
Sbjct: 18 HIHIRVEQRRGRKCFTTVEGIPPEFDYEKIMKYWKKWLSCNATIVEEDEGKKVIKLNGDH 77
Query: 90 RKNVSTFLVQAGIVKKEFIKIHG 112
R + FL + GI + I IHG
Sbjct: 78 RNQIQQFLSEEGIAAVDNITIHG 100
>pdb|3G5U|A Chain A, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
pdb|3G5U|B Chain B, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
Length = 1284
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 33/76 (43%), Gaps = 9/76 (11%)
Query: 41 RKSLTTVQGLKKEFSYNKILKDLKKEFCCNGTVVQ------DPELGQVIQLQGDQRK--N 92
R S+ +QGL E + L + C TVVQ DP G V L G + K N
Sbjct: 1043 RPSIPVLQGLSLEVKKGQTLALVGSSGCGKSTVVQLLERFYDPMAGSVF-LDGKEIKQLN 1101
Query: 93 VSTFLVQAGIVKKEFI 108
V Q GIV +E I
Sbjct: 1102 VQWLRAQLGIVSQEPI 1117
>pdb|3G60|A Chain A, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
pdb|3G60|B Chain B, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
pdb|3G61|A Chain A, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
pdb|3G61|B Chain B, Structure Of P-Glycoprotein Reveals A Molecular Basis For
Poly-Specific Drug Binding
Length = 1284
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 33/76 (43%), Gaps = 9/76 (11%)
Query: 41 RKSLTTVQGLKKEFSYNKILKDLKKEFCCNGTVVQ------DPELGQVIQLQGDQRK--N 92
R S+ +QGL E + L + C TVVQ DP G V L G + K N
Sbjct: 1043 RPSIPVLQGLSLEVKKGQTLALVGSSGCGKSTVVQLLERFYDPMAGSVF-LDGKEIKQLN 1101
Query: 93 VSTFLVQAGIVKKEFI 108
V Q GIV +E I
Sbjct: 1102 VQWLRAQLGIVSQEPI 1117
>pdb|1D1R|A Chain A, Nmr Solution Structure Of The Product Of The E. Coli Ycih
Gene
Length = 116
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 9/74 (12%)
Query: 33 IRVQ-QRNGRKS--LTTVQGLK-KEFSYNKILKDLKKEFCCNGTVVQDPELGQVIQLQGD 88
+R+Q Q +GRK + + G+ + K+ +LKK+ C G V VI++QGD
Sbjct: 33 VRIQRQTSGRKGKGVCLITGVDLDDAELTKLAAELKKKCGCGGAVKD-----GVIEIQGD 87
Query: 89 QRKNVSTFLVQAGI 102
+R + + L G+
Sbjct: 88 KRDLLKSLLEAKGM 101
>pdb|1MHS|A Chain A, Model Of Neurospora Crassa Proton Atpase
pdb|1MHS|B Chain B, Model Of Neurospora Crassa Proton Atpase
Length = 920
Score = 26.2 bits (56), Expect = 5.5, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 2/68 (2%)
Query: 15 FAEANAEDSGAGSKDYVHIRVQQRNGRKSLTTVQGLKKEFSYNKILKDLKKEFCCNGTVV 74
F A AG +D+V V G L V G +EF I+ +LKK V+
Sbjct: 126 FVMEGAAVLAAGLEDWVDFGVI--CGLLLLNAVVGFVQEFQAGSIVDELKKTLALKAVVL 183
Query: 75 QDPELGQV 82
+D L ++
Sbjct: 184 RDGTLKEI 191
>pdb|2V2G|A Chain A, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Monoclinic Form
pdb|2V2G|B Chain B, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Monoclinic Form
pdb|2V2G|C Chain C, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Monoclinic Form
pdb|2V2G|D Chain D, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Monoclinic Form
pdb|2V32|A Chain A, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Monoclinic Form 2
pdb|2V32|B Chain B, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Monoclinic Form 2
pdb|2V32|C Chain C, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Monoclinic Form 2
pdb|2V32|D Chain D, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Monoclinic Form 2
pdb|2V41|A Chain A, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Orthorhombic Form
pdb|2V41|B Chain B, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Orthorhombic Form
pdb|2V41|C Chain C, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Orthorhombic Form
pdb|2V41|D Chain D, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Orthorhombic Form
pdb|2V41|E Chain E, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Orthorhombic Form
pdb|2V41|F Chain F, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Orthorhombic Form
pdb|2V41|G Chain G, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Orthorhombic Form
pdb|2V41|H Chain H, Crystal Structure Of The C45s Mutant Of The
Peroxiredoxin 6 Of Arenicola Marina. Orthorhombic Form
Length = 233
Score = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 72 TVVQDPELGQVIQLQGDQRK 91
T V ELG+VIQL+GD +K
Sbjct: 42 TPVSTTELGRVIQLEGDFKK 61
>pdb|3ZF7|V Chain V, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 130
Score = 25.4 bits (54), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 23/51 (45%)
Query: 4 FDTQIPSAFDPFAEANAEDSGAGSKDYVHIRVQQRNGRKSLTTVQGLKKEF 54
F I S F + + N + +G K +RV R S+TT +K++
Sbjct: 39 FSDDILSNFQQYFQDNVKLNGRKGKLTSKVRVNMRENTLSITTTMAYRKKY 89
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
0.317 0.135 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,309,501
Number of Sequences: 62578
Number of extensions: 119463
Number of successful extensions: 261
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 253
Number of HSP's gapped (non-prelim): 12
length of query: 113
length of database: 14,973,337
effective HSP length: 77
effective length of query: 36
effective length of database: 10,154,831
effective search space: 365573916
effective search space used: 365573916
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: 45 (21.9 bits)