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= 047565
(106 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|U Chain U, Localization Of The Large Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 164
Score = 163 bits (412), Expect = 3e-41, Method: Compositional matrix adjust.
Identities = 76/80 (95%), Positives = 80/80 (100%)
Query: 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGR 60
MPAGHGLRSRTRDLFARPFRKKGYIPL+TYLRTYK+G++VDVKVNGAVHKGMPHKFYHGR
Sbjct: 1 MPAGHGLRSRTRDLFARPFRKKGYIPLTTYLRTYKVGEHVDVKVNGAVHKGMPHKFYHGR 60
Query: 61 TGRVWNVTKRAIGVEINKQV 80
TGRVWNVTKRAIGVEINKQV
Sbjct: 61 TGRVWNVTKRAIGVEINKQV 80
>pdb|3IZS|U Chain U, Localization Of The Large Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|T Chain T, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The First 80s In The Asymmetric Unit.
pdb|3O5H|T Chain T, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|T Chain T, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|T Chain T, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|T Chain T, Cryo-Em Structure Of The 60s Ribosomal Subunit In
Complex With Arx1 And Rei1
Length = 160
Score = 108 bits (269), Expect = 9e-25, Method: Compositional matrix adjust.
Identities = 50/80 (62%), Positives = 61/80 (76%)
Query: 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGR 60
M HG RSRTR +F R FRK G + LSTYL+ YK+GD VD+K NG++ KGMPHKFY G+
Sbjct: 1 MGKSHGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKGMPHKFYQGK 60
Query: 61 TGRVWNVTKRAIGVEINKQV 80
TG V+NVTK ++GV INK V
Sbjct: 61 TGVVYNVTKSSVGVIINKMV 80
>pdb|1S1I|Q Chain Q, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex
From Yeast Obtained By Docking Atomic Models For Rna
And Protein Components Into A 11.7 A Cryo-Em Map. This
File, 1s1i, Contains 60s Subunit. The 40s Ribosomal
Subunit Is In File 1s1h
Length = 100
Score = 108 bits (269), Expect = 9e-25, Method: Compositional matrix adjust.
Identities = 50/80 (62%), Positives = 61/80 (76%)
Query: 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGR 60
M HG RSRTR +F R FRK G + LSTYL+ YK+GD VD+K NG++ KGMPHKFY G+
Sbjct: 1 MGKSHGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKGMPHKFYQGK 60
Query: 61 TGRVWNVTKRAIGVEINKQV 80
TG V+NVTK ++GV INK V
Sbjct: 61 TGVVYNVTKSSVGVIINKMV 80
>pdb|3JYW|Q Chain Q, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus
Ribosome At 8.9a Resolution
Length = 116
Score = 106 bits (265), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 49/76 (64%), Positives = 60/76 (78%)
Query: 5 HGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRV 64
HG RSRTR +F R FRK G + LSTYL+ YK+GD VD+K NG++ KGMPHKFY G+TG V
Sbjct: 4 HGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKGMPHKFYQGKTGVV 63
Query: 65 WNVTKRAIGVEINKQV 80
+NVTK ++GV INK V
Sbjct: 64 YNVTKSSVGVIINKMV 79
>pdb|2ZKR|QQ Chain q, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 160
Score = 103 bits (256), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 49/81 (60%), Positives = 61/81 (75%)
Query: 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGR 60
M G R TR +F+RPFRK G +PL+TY+R YK GD VD+K G V KGMPHK YHG+
Sbjct: 1 MTNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQKGMPHKCYHGK 60
Query: 61 TGRVWNVTKRAIGVEINKQVK 81
TGRV+NVT+ A+G+ +NKQVK
Sbjct: 61 TGRVYNVTQHAVGIIVNKQVK 81
>pdb|3ZF7|U Chain U, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 159
Score = 95.5 bits (236), Expect = 6e-21, Method: Compositional matrix adjust.
Identities = 47/81 (58%), Positives = 56/81 (69%)
Query: 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGR 60
M HG + TR LFA+ FRK G +ST L +K+GDYVDV + AV GMPHK+YHGR
Sbjct: 1 MVHSHGYKCGTRHLFAKKFRKHGVPSVSTILTNFKVGDYVDVVADAAVRAGMPHKYYHGR 60
Query: 61 TGRVWNVTKRAIGVEINKQVK 81
TG VWNVT R +GV INK V+
Sbjct: 61 TGIVWNVTPRGVGVIINKPVR 81
>pdb|4A17|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 157
Score = 91.3 bits (225), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 41/80 (51%), Positives = 61/80 (76%)
Query: 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGR 60
M +G R +TR FA+ ++ KG++ +S YL TYK+G+YVD+ V+G+ HKGMP+K YHGR
Sbjct: 1 MTHSYGYRRQTRKKFAKAYKTKGHVRISRYLTTYKVGEYVDIMVDGSQHKGMPYKLYHGR 60
Query: 61 TGRVWNVTKRAIGVEINKQV 80
TG+V+NV R+IGV +++ V
Sbjct: 61 TGKVFNVNPRSIGVIVHRIV 80
>pdb|3J21|R Chain R, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 97
Score = 52.4 bits (124), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 41/74 (55%)
Query: 4 GHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGR 63
H R +TR ++ R++G PL+ +L+ +++G V + + + HKGMP +HGRTG
Sbjct: 5 AHSFRRKTRKKLSKHPRRRGLPPLTRFLQEFEVGQRVHIVIEPSYHKGMPDPRFHGRTGT 64
Query: 64 VWNVTKRAIGVEIN 77
V A VEI
Sbjct: 65 VVGKRGEAYIVEIK 78
>pdb|3ICJ|A Chain A, Crystal Structure Of An Uncharacterized Metal-Dependent
Hydrolase From Pyrococcus Furiosus
Length = 534
Score = 26.2 bits (56), Expect = 4.9, Method: Composition-based stats.
Identities = 19/80 (23%), Positives = 32/80 (40%), Gaps = 13/80 (16%)
Query: 24 YIPLSTYLRTYKIGDYVDVKVNGAVHKGM-PHK------------FYHGRTGRVWNVTKR 70
+ + ++ IGD + +NG ++ P K Y G + + +
Sbjct: 21 FTKVKNFMGVKHIGDCMKALINGTIYTSFSPVKKVSGLVISNERVLYAGDSSTALRIAEL 80
Query: 71 AIGVEINKQVKFFMPFLFDS 90
A G I+ + KF MP FDS
Sbjct: 81 AGGEIIDLKGKFVMPAFFDS 100
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
0.329 0.146 0.470
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,386,447
Number of Sequences: 62578
Number of extensions: 130408
Number of successful extensions: 314
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 306
Number of HSP's gapped (non-prelim): 10
length of query: 106
length of database: 14,973,337
effective HSP length: 71
effective length of query: 35
effective length of database: 10,530,299
effective search space: 368560465
effective search space used: 368560465
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 bits)