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= psy5287
(65 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZ6|Y Chain Y, Localization Of The Small Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 65
Score = 77.8 bits (190), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 37/51 (72%), Positives = 44/51 (86%)
Query: 1 MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDI 51
MD QV LA V+K +GRTGS+GQ TQV+V+F+ DQNR I+RNVKGPVREGDI
Sbjct: 1 MDTQVKLAVVVKVMGRTGSRGQVTQVRVKFLDDQNRLIMRNVKGPVREGDI 51
>pdb|3IZB|Y Chain Y, Localization Of The Small Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O2Z|R Chain R, Yeast 80s Ribosome. This Entry Consists Of The 40s
Subunit Of The First 80s In The Asymmetric Unit.
pdb|3O30|R Chain R, Yeast 80s Ribosome. This Entry Consists Of The 40s
Subunit Of The Second 80s In The Asymmetric Unit.
pdb|3U5C|CC Chain c, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|CC Chain c, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 67
Score = 70.9 bits (172), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 36/53 (67%), Positives = 43/53 (81%), Gaps = 2/53 (3%)
Query: 1 MDKQ--VVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDI 51
MD + V LA+VIK LGRTGS+G TQV+VEF+ D +RTI+RNVKGPVRE DI
Sbjct: 1 MDNKTPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDI 53
>pdb|3ZEY|Z Chain Z, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 103
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/47 (55%), Positives = 35/47 (74%), Gaps = 5/47 (10%)
Query: 10 VIKTLGRTGSQGQCTQVKVEFIGDQ-----NRTIIRNVKGPVREGDI 51
+IK LGRTGS+G TQV+V + ++ NRTI+RNVKGP +EGD+
Sbjct: 43 IIKVLGRTGSRGNVTQVRVRLMAEEGSPEANRTIVRNVKGPCKEGDM 89
>pdb|1NY4|A Chain A, Solution Structure Of The 30s Ribosomal Protein S28e
From Pyrococcus Horikoshii. Northeast Structural
Genomics Consortium Target Jr19
Length = 82
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/46 (56%), Positives = 32/46 (69%), Gaps = 2/46 (4%)
Query: 8 ARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDI 51
A VI+ +GRTG+ G TQVKV + D+ R I RNV+GPVR GDI
Sbjct: 9 AEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDI 54
>pdb|3J20|X Chain X, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 71
Score = 46.2 bits (108), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/46 (56%), Positives = 32/46 (69%), Gaps = 2/46 (4%)
Query: 8 ARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDI 51
A VI+ +GRTG+ G TQVKV + D+ R I RNV+GPVR GDI
Sbjct: 9 AEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRIGDI 54
>pdb|1NE3|A Chain A, Solution Structure Of Ribosomal Protein S28e From
Methanobacterium Thermoautotrophicum. Ontario Centre
For Structural Proteomics Target Mth0256_1_68;
Northeast Structural Genomics Target Tt744
Length = 68
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/46 (50%), Positives = 29/46 (63%), Gaps = 2/46 (4%)
Query: 8 ARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDI 51
A VI+ L RTG G+ QVK + D+ R + RNV GP+REGDI
Sbjct: 7 AEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDI 52
>pdb|2XZM|1 Chain 1, 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|1 Chain 1, 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 = 68
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/46 (50%), Positives = 32/46 (69%), Gaps = 2/46 (4%)
Query: 8 ARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDI 51
AR++ LG+TGS+G TQV+V I ++ R +IRNVKG R GD+
Sbjct: 9 ARIMDVLGKTGSRGGITQVRVVLISGKEEGRQLIRNVKGACRVGDV 54
>pdb|2VT1|A Chain A, Crystal Structure Of The Cytoplasmic Domain Of Spa40,
The Specificity Switch For The Shigella Flexneri Type
Iii Secretion System
Length = 52
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 24/43 (55%)
Query: 1 MDKQVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVK 43
MDKQ + I+ G ++ + ++ +E + +Q ++ IRN K
Sbjct: 5 MDKQEIKREYIEQEGHFETKSRRRELHIEILSEQTKSDIRNSK 47
>pdb|1WUH|L Chain L, Three-Dimensional Structure Of The Ni-A State Of
[nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki
F
pdb|1WUI|L Chain L, Ultra-High Resolution Structure Of The Ni-A State Of
[nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki
F
Length = 534
Score = 25.4 bits (54), Expect = 8.9, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 10 VIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGD 50
+ TLGRT ++G T V E++G +++ K + +GD
Sbjct: 402 LFSTLGRTAARGIETAVIAEYVG----VMLQEYKDNIAKGD 438
>pdb|1WUJ|L Chain L, Three-Dimensional Structure Of The Ni-B State Of
[nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki
F
pdb|1WUK|L Chain L, High Resolution Structure Of The Oxidized State Of
[nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki
F
pdb|1WUL|L Chain L, High Resolution Structure Of The Reduced State Of
[nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki
F
Length = 534
Score = 25.4 bits (54), Expect = 8.9, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 10 VIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGD 50
+ TLGRT ++G T V E++G +++ K + +GD
Sbjct: 402 LFSTLGRTAARGIETAVIAEYVG----VMLQEYKDNIAKGD 438
>pdb|1UBH|L Chain L, Three-Dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBJ|L Chain L, Three-Dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBK|L Chain L, Three-dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBL|L Chain L, Three-Dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBM|L Chain L, Three-dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBO|L Chain L, Three-Dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBR|L Chain L, Three-Dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBT|L Chain L, Three-Dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
pdb|1UBU|L Chain L, Three-Dimensional Structure Of The Carbon Monoxide Complex
Of [nife]hydrogenase From Desulufovibrio Vulgaris
Miyazaki F
Length = 534
Score = 25.4 bits (54), Expect = 8.9, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 10 VIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGD 50
+ TLGRT ++G T V E++G +++ K + +GD
Sbjct: 402 LFSTLGRTAARGIETAVIAEYVG----VMLQEYKDNIAKGD 438
>pdb|1H2R|L Chain L, Three-Dimensional Structure Of Ni-Fe Hydrogenase From
Desulfivibrio Vulgaris Miyazaki F In The Reduced Form At
1.4 A Resolution
Length = 534
Score = 25.4 bits (54), Expect = 8.9, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 10 VIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGD 50
+ TLGRT ++G T V E++G +++ K + +GD
Sbjct: 402 LFSTLGRTAARGIETAVIAEYVG----VMLQEYKDNIAKGD 438
>pdb|1H2A|L Chain L, Single Crystals Of Hydrogenase From Desulfovibrio Vulgaris
Length = 567
Score = 25.4 bits (54), Expect = 8.9, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 10 VIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGD 50
+ TLGRT ++G T V E++G +++ K + +GD
Sbjct: 420 LFSTLGRTAARGIETAVIAEYVG----VMLQEYKDNIAKGD 456
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 0.139 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,255,085
Number of Sequences: 62578
Number of extensions: 28979
Number of successful extensions: 63
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: 50
Number of HSP's gapped (non-prelim): 13
length of query: 65
length of database: 14,973,337
effective HSP length: 36
effective length of query: 29
effective length of database: 12,720,529
effective search space: 368895341
effective search space used: 368895341
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)