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= psy7547
(138 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|EE Chain e, 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 = 192
Score = 55.8 bits (133), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 22/37 (59%), Positives = 31/37 (83%)
Query: 4 KRVLKVEKWFGTKKEIAAVRTVCSHISNMLKGVTKDF 40
K+ L+V+KW+G +KE+A VRT+CSH+ NM+KGVT F
Sbjct: 52 KKRLRVDKWWGNRKELATVRTICSHVQNMIKGVTLGF 88
>pdb|2CQL|A Chain A, Solution Structure Of The N-Terminal Domain Of Human
Ribosomal Protein L9
Length = 100
Score = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 21/34 (61%), Positives = 30/34 (88%)
Query: 4 KRVLKVEKWFGTKKEIAAVRTVCSHISNMLKGVT 37
K+ L+V+KW+G +KE+A VRT+CSH+ NM+KGVT
Sbjct: 59 KKRLRVDKWWGNRKELATVRTICSHVQNMIKGVT 92
>pdb|3IZR|F Chain F, Localization Of The Large Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 190
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 28/36 (77%)
Query: 5 RVLKVEKWFGTKKEIAAVRTVCSHISNMLKGVTKDF 40
R L+V+ WFGT++ +AA+RT SH+ N++ GVTK +
Sbjct: 52 RKLQVDAWFGTRRTMAAIRTAISHVQNLITGVTKGY 87
>pdb|3J21|F Chain F, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 184
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 21/29 (72%)
Query: 13 FGTKKEIAAVRTVCSHISNMLKGVTKDFT 41
F +K++A RT +HI NM+KGVT+ FT
Sbjct: 59 FPRRKDVAIARTFAAHIRNMIKGVTEGFT 87
>pdb|3JYW|H Chain H, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus
Ribosome At 8.9a Resolution
Length = 179
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/39 (46%), Positives = 27/39 (69%)
Query: 2 VNKRVLKVEKWFGTKKEIAAVRTVCSHISNMLKGVTKDF 40
VN +++KV G +K +AA+RTV S + NM+ GVTK +
Sbjct: 43 VNNQLIKVAVHNGGRKHVAALRTVKSLVDNMITGVTKGY 81
>pdb|1S1I|H Chain H, 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.
pdb|3IZS|F Chain F, Localization Of The Large Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|I Chain I, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The First 80s In The Asymmetric Unit.
pdb|3O5H|I Chain I, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|H Chain H, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|H Chain H, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|3J16|F Chain F, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
pdb|4B6A|H Chain H, Cryo-Em Structure Of The 60s Ribosomal Subunit In
Complex With Arx1 And Rei1
Length = 191
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/39 (46%), Positives = 27/39 (69%)
Query: 2 VNKRVLKVEKWFGTKKEIAAVRTVCSHISNMLKGVTKDF 40
VN +++KV G +K +AA+RTV S + NM+ GVTK +
Sbjct: 48 VNNQLIKVAVHNGGRKHVAALRTVKSLVDNMITGVTKGY 86
>pdb|4A17|E Chain E, 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|E Chain E, 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|E Chain E, 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|E Chain E, 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 = 188
Score = 34.7 bits (78), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 25/34 (73%)
Query: 7 LKVEKWFGTKKEIAAVRTVCSHISNMLKGVTKDF 40
+K++ W ++KE A ++++ S I NM++GVT+ +
Sbjct: 53 VKLQIWQASRKERAVLQSIASQIKNMIRGVTEGY 86
>pdb|3ZF7|YY Chain y, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 189
Score = 34.3 bits (77), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 11 KWFGTKKEIAAVRTVCSHISNMLKGVTKDF 40
+WFG K + + T SH+ NM+ GVTK F
Sbjct: 57 RWFGNKINNSTINTALSHVRNMITGVTKGF 86
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
0.322 0.132 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,132,825
Number of Sequences: 62578
Number of extensions: 147067
Number of successful extensions: 301
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 291
Number of HSP's gapped (non-prelim): 11
length of query: 138
length of database: 14,973,337
effective HSP length: 89
effective length of query: 49
effective length of database: 9,403,895
effective search space: 460790855
effective search space used: 460790855
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 46 (22.3 bits)