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= psy2274
(244 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|OO Chain o, 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 = 188
Score = 116 bits (290), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 61/99 (61%), Positives = 81/99 (81%)
Query: 36 GVDICHKYDRRVRRTKPKSKDVYLELLVKLYRFLTRRTNSKFNKIILKRLFMSKINRPPM 95
GVDI H DR+VRR +PKS+D+YL LLVKLYRFL RRTNS FN+++LKRLFMS+ NRPP+
Sbjct: 2 GVDIRHNKDRKVRRKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRTNRPPL 61
Query: 96 AISKIVRFMKKPTREGRVAVIVGTIVDDPRMWTIPKLTI 134
++S+++R MK P RE + AV+VGT+ DD R+ +PKL +
Sbjct: 62 SLSRMIRKMKLPGRENKTAVVVGTVTDDVRILEVPKLKV 100
Score = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 20/27 (74%), Positives = 24/27 (88%)
Query: 168 LYRFLTRRTNSKFNKIILKRLFMSKIN 194
LYRFL RRTNS FN+++LKRLFMS+ N
Sbjct: 31 LYRFLARRTNSTFNQVVLKRLFMSRTN 57
>pdb|3IZR|R Chain R, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 188
Score = 111 bits (277), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 58/105 (55%), Positives = 76/105 (72%), Gaps = 4/105 (3%)
Query: 36 GVD-ICHKYDRRVRRTKPKSKDVYLELLVKLYRFLTRRTNSKFNKIILKRLFMSKINRPP 94
G+D + ++R +R PKS DVYL+LLVKLYRFL RRT SKFN +ILKRLFMSK NRPP
Sbjct: 2 GIDLVAGGRNKRTKRVAPKSDDVYLKLLVKLYRFLVRRTKSKFNAVILKRLFMSKTNRPP 61
Query: 95 MAISKIVRFMKKPTREGRVAVIVGTIVDDPRMWTIP--KLTIVRF 137
+++ ++ FMK E +AV+VGTI DD R+ +P K+T +RF
Sbjct: 62 LSMRRLSNFMKG-KEEKNIAVVVGTITDDMRIQEVPAMKVTALRF 105
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 22/27 (81%), Positives = 23/27 (85%)
Query: 168 LYRFLTRRTNSKFNKIILKRLFMSKIN 194
LYRFL RRT SKFN +ILKRLFMSK N
Sbjct: 32 LYRFLVRRTKSKFNAVILKRLFMSKTN 58
>pdb|3IZS|R Chain R, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|R Chain R, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|R Chain R, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|Q Chain Q, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|Q Chain Q, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|Q Chain Q, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 186
Score = 95.5 bits (236), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 51/101 (50%), Positives = 72/101 (71%), Gaps = 1/101 (0%)
Query: 36 GVDICHK-YDRRVRRTKPKSKDVYLELLVKLYRFLTRRTNSKFNKIILKRLFMSKINRPP 94
G+D K + R RT PKS +VYL+LLVKLY FL RRT++ FNK++LK LF+SKINRPP
Sbjct: 2 GIDHTSKQHKRSGHRTAPKSDNVYLKLLVKLYTFLARRTDAPFNKVVLKALFLSKINRPP 61
Query: 95 MAISKIVRFMKKPTREGRVAVIVGTIVDDPRMWTIPKLTIV 135
+++S+I R +K+ + V+VGT+ DD R++ PK T+
Sbjct: 62 VSVSRIARALKQEGAANKTVVVVGTVTDDARIFEFPKTTVA 102
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/27 (66%), Positives = 23/27 (85%)
Query: 168 LYRFLTRRTNSKFNKIILKRLFMSKIN 194
LY FL RRT++ FNK++LK LF+SKIN
Sbjct: 32 LYTFLARRTDAPFNKVVLKALFLSKIN 58
>pdb|4A17|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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 = 181
Score = 86.7 bits (213), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 49/120 (40%), Positives = 78/120 (65%), Gaps = 5/120 (4%)
Query: 36 GVDICHKYDRRVRRT---KPKSKDVYLELLVKLYRFLTRRTNSKFNKIILKRLFMSKINR 92
+D+ HK R V+R+ + KS +VY +LL+KLY+FL RRT+SKFN+ ILKRL S++N+
Sbjct: 2 AIDL-HKQGRVVKRSVVRQTKSTNVYHKLLIKLYKFLVRRTDSKFNQNILKRLSSSRLNK 60
Query: 93 PPMAISKIVRFMKKPTREGRVAVIVGTIVDDPRMWTIPKLTIVRFMKKPTREGRVAVIVG 152
P+++S+IV+ + + +E +V V T+ +D R+ T+PKLT+ T R+ G
Sbjct: 61 FPLSLSRIVKNLNETNKE-QVIVSTSTVTNDERLLTVPKLTVCALKFTETARKRILAAGG 119
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 35/56 (62%), Gaps = 4/56 (7%)
Query: 168 LYRFLTRRTNSKFNKIILKRLFMSKIN----SISERELDVKPTNTLALLPVFPTVT 219
LY+FL RRT+SKFN+ ILKRL S++N S+S ++ TN ++ TVT
Sbjct: 33 LYKFLVRRTDSKFNQNILKRLSSSRLNKFPLSLSRIVKNLNETNKEQVIVSTSTVT 88
>pdb|3JYW|O Chain O, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 121
Score = 85.5 bits (210), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 43/82 (52%), Positives = 62/82 (75%)
Query: 54 SKDVYLELLVKLYRFLTRRTNSKFNKIILKRLFMSKINRPPMAISKIVRFMKKPTREGRV 113
S +VYL+LLVKLY FL RRT++ FNK++LK LF+SKINRPP+++S+I R +K+ +
Sbjct: 1 SDNVYLKLLVKLYTFLARRTDAPFNKVVLKALFLSKINRPPVSVSRIARALKQEGAANKT 60
Query: 114 AVIVGTIVDDPRMWTIPKLTIV 135
V+VGT+ DD R++ PK T+
Sbjct: 61 VVVVGTVTDDARIFEFPKTTVA 82
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/27 (66%), Positives = 23/27 (85%)
Query: 168 LYRFLTRRTNSKFNKIILKRLFMSKIN 194
LY FL RRT++ FNK++LK LF+SKIN
Sbjct: 12 LYTFLARRTDAPFNKVVLKALFLSKIN 38
>pdb|1S1I|O Chain O, 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 = 120
Score = 84.0 bits (206), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 42/80 (52%), Positives = 61/80 (76%)
Query: 56 DVYLELLVKLYRFLTRRTNSKFNKIILKRLFMSKINRPPMAISKIVRFMKKPTREGRVAV 115
+VYL+LLVKLY FL RRT++ FNK++LK LF+SKINRPP+++S+I R +K+ + V
Sbjct: 2 NVYLKLLVKLYTFLARRTDAPFNKVVLKALFLSKINRPPVSVSRIARALKQEGAANKTVV 61
Query: 116 IVGTIVDDPRMWTIPKLTIV 135
+VGT+ DD R++ PK T+
Sbjct: 62 VVGTVTDDARIFEFPKTTVA 81
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/27 (66%), Positives = 23/27 (85%)
Query: 168 LYRFLTRRTNSKFNKIILKRLFMSKIN 194
LY FL RRT++ FNK++LK LF+SKIN
Sbjct: 11 LYTFLARRTDAPFNKVVLKALFLSKIN 37
>pdb|3ZF7|I Chain I, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 193
Score = 80.9 bits (198), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 51/113 (45%), Positives = 75/113 (66%), Gaps = 9/113 (7%)
Query: 36 GVDICH-KYDRRVRRTKPKSKDVYLELLVKLYRFLTRRTNSKFNKIILKRLFMSKINRPP 94
GVD+ + +RV R S + Y++LL+KLY+FL +RTNS FNK+I KRL S+ NR P
Sbjct: 2 GVDLTGVQKKKRVVRHHTYSTNPYIKLLIKLYKFLGKRTNSPFNKLIHKRLLKSRNNRAP 61
Query: 95 MAISKIVRFMKKPT---REGR---VAVIVGTIVDDPRMWTIPKLTI--VRFMK 139
+++S+I M++ T ++G+ +AVIVG ++DD RM IP L I +RF K
Sbjct: 62 ISLSRIAVCMRRRTVWLKKGKKSPIAVIVGDVLDDVRMTRIPALRICALRFSK 114
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/29 (58%), Positives = 22/29 (75%)
Query: 166 LTLYRFLTRRTNSKFNKIILKRLFMSKIN 194
+ LY+FL +RTNS FNK+I KRL S+ N
Sbjct: 30 IKLYKFLGKRTNSPFNKLIHKRLLKSRNN 58
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
0.325 0.138 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,108,984
Number of Sequences: 62578
Number of extensions: 216756
Number of successful extensions: 599
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 575
Number of HSP's gapped (non-prelim): 25
length of query: 244
length of database: 14,973,337
effective HSP length: 96
effective length of query: 148
effective length of database: 8,965,849
effective search space: 1326945652
effective search space used: 1326945652
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 bits)